#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
FZD2	2535	hgsc.bcm.edu	37	17	42636477	42636477	+	Frame_Shift_Del	DEL	C	C	-			TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr17:42636477delC	ENST00000315323.3	+	1	1553	c.1421delC	c.(1420-1422)accfs	p.T474fs		NM_001466.3	NP_001457.1	Q14332	FZD2_HUMAN	frizzled class receptor 2	474					axonogenesis (GO:0007409)|brain development (GO:0007420)|canonical Wnt signaling pathway (GO:0060070)|cell-cell signaling (GO:0007267)|cochlea morphogenesis (GO:0090103)|epithelial cell differentiation (GO:0030855)|G-protein coupled receptor signaling pathway coupled to cGMP nucleotide second messenger (GO:0007199)|gonad development (GO:0008406)|hard palate development (GO:0060022)|inner ear receptor cell development (GO:0060119)|membranous septum morphogenesis (GO:0003149)|muscular septum morphogenesis (GO:0003150)|neuron differentiation (GO:0030182)|outflow tract morphogenesis (GO:0003151)|planar cell polarity pathway involved in neural tube closure (GO:0090179)|positive regulation of cGMP metabolic process (GO:0030825)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|positive regulation of transcription, DNA-templated (GO:0045893)|sensory perception of smell (GO:0007608)|vasculature development (GO:0001944)|Wnt signaling pathway, calcium modulating pathway (GO:0007223)	apical part of cell (GO:0045177)|clathrin-coated endocytic vesicle membrane (GO:0030669)|cytoplasm (GO:0005737)|focal adhesion (GO:0005925)|integral component of membrane (GO:0016021)|neuron projection membrane (GO:0032589)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|PDZ domain binding (GO:0030165)|Wnt-activated receptor activity (GO:0042813)|Wnt-protein binding (GO:0017147)			central_nervous_system(1)|endometrium(2)|kidney(3)|large_intestine(7)|lung(9)|ovary(3)|prostate(8)	33		Prostate(33;0.0181)		BRCA - Breast invasive adenocarcinoma(366;0.189)		GTGCCCGCCACCATCGTCATC	0.632																																					p.T474fs		Pindel,Atlas-Indel	.											.	FZD2	81	.	0			c.1420delA						PASS	.						73.0	59.0	64.0					17																	42636477		2203	4300	6503	SO:0001589	frameshift_variant	2535	exon1			.	L37882	CCDS11484.1	17q21.1	2014-01-29	2014-01-29			ENSG00000180340		"""GPCR / Class F : Frizzled receptors"""	4040	protein-coding gene	gene with protein product		600667	"""frizzled (Drosophila) homolog 2"", ""frizzled homolog 2 (Drosophila)"", ""frizzled 2, seven transmembrane spanning receptor"", ""frizzled family receptor 2"""			7558010, 9813155	Standard	NM_001466		Approved		uc002igx.2	Q14332		ENST00000315323.3:c.1421delC	17.37:g.42636477delC	ENSP00000323901:p.Thr474fs	96.0	0.0	.		90.0	19.0	0.211	NM_001466	Q0VG82	Frame_Shift_Del	DEL	ENST00000315323.3	37	CCDS11484.1																																																																																			.	.	none		0.632	FZD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000457806.1	NM_001466	
C20orf202	400831	hgsc.bcm.edu	37	20	1187535	1187536	+	Frame_Shift_Del	DEL	AG	AG	-	rs375391788|rs529757520		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	AG	AG	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr20:1187535_1187536delAG	ENST00000400633.1	+	2	221_222	c.158_159delAG	c.(157-159)cagfs	p.Q53fs		NM_001009612.2	NP_001009612.1	A1L168	CT202_HUMAN	chromosome 20 open reading frame 202	53										endometrium(1)	1						ATTCAAGATCAGAGTCTCCTGC	0.604																																					p.53_53del		Pindel,Atlas-Indel	.											.	C20orf202	12	.	0			c.157_158del						PASS	.			2,2824		1,0,1412						3.5	1.0			37	19,5057		3,13,2522	no	frameshift	C20orf202	NM_001009612.2		4,13,3934	A1A1,A1R,RR		0.3743,0.0708,0.2658				21,7881				SO:0001589	frameshift_variant	400831	exon2			.		CCDS46567.1	20p13	2009-09-10			ENSG00000215595	ENSG00000215595			37254	protein-coding gene	gene with protein product							Standard	NM_001009612		Approved		uc002wer.4	A1L168	OTTHUMG00000129375	ENST00000400633.1:c.158_159delAG	20.37:g.1187537_1187538delAG	ENSP00000383474:p.Gln53fs	135.0	0.0	.		107.0	37.0	0.346	NM_001009612		Frame_Shift_Del	DEL	ENST00000400633.1	37	CCDS46567.1																																																																																			.	.	none		0.604	C20orf202-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251531.1	NM_001009612	
PGGT1B	5229	hgsc.bcm.edu	37	5	114557642	114557643	+	Frame_Shift_Ins	INS	-	-	A			TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr5:114557642_114557643insA	ENST00000419445.1	-	7	741_742	c.721_722insT	c.(721-723)tcafs	p.S241fs	PGGT1B_ENST00000514178.1_5'UTR|PGGT1B_ENST00000379615.3_Intron	NM_005023.3	NP_005014.2	P53609	PGTB1_HUMAN	protein geranylgeranyltransferase type I, beta subunit	241					negative regulation of nitric-oxide synthase biosynthetic process (GO:0051771)|positive regulation of cell cycle (GO:0045787)|positive regulation of cell proliferation (GO:0008284)|protein geranylgeranylation (GO:0018344)|response to cytokine (GO:0034097)	CAAX-protein geranylgeranyltransferase complex (GO:0005953)	CAAX-protein geranylgeranyltransferase activity (GO:0004662)|protein geranylgeranyltransferase activity (GO:0004661)|zinc ion binding (GO:0008270)			breast(2)|endometrium(1)|large_intestine(2)|lung(1)	6		all_cancers(142;0.000523)|all_epithelial(76;6.45e-06)|Prostate(80;0.00955)|Ovarian(225;0.0443)|all_lung(232;0.132)|Breast(839;0.195)		Epithelial(69;2.95e-08)|OV - Ovarian serous cystadenocarcinoma(64;4.98e-08)|all cancers(49;3.1e-06)		TTCTTTTTCTGAAAAAACTTCT	0.351																																					p.S241fs		Pindel,Atlas-Indel	.											.	PGGT1B	26	.	0			c.722_723insT						PASS	.																																			SO:0001589	frameshift_variant	5229	exon7			.		CCDS4116.1	5q23.1	2008-02-05			ENSG00000164219	ENSG00000164219			8895	protein-coding gene	gene with protein product		602031				8106351	Standard	NM_005023		Approved	GGTI, BGGI	uc003kqw.4	P53609	OTTHUMG00000128893	ENST00000419445.1:c.722dupT	5.37:g.114557648_114557648dupA	ENSP00000404676:p.Ser241fs	475.0	0.0	.		423.0	73.0	0.173	NM_005023	Q5MJP9	Frame_Shift_Ins	INS	ENST00000419445.1	37	CCDS4116.1																																																																																			.	.	none		0.351	PGGT1B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250855.2	NM_005023	
SULT2B1	6820	hgsc.bcm.edu	37	19	49102605	49102610	+	In_Frame_Del	DEL	CCAGCC	CCAGCC	-	rs16989366|rs535907004		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	CCAGCC	CCAGCC	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr19:49102605_49102610delCCAGCC	ENST00000201586.2	+	7	1218_1223	c.1040_1045delCCAGCC	c.(1039-1047)tccagcccc>tcc	p.SP352del	SULT2B1_ENST00000323090.4_In_Frame_Del_p.SP337del	NM_177973.1	NP_814444.1	O00204	ST2B1_HUMAN	sulfotransferase family, cytosolic, 2B, member 1	352	Pro/Ser-rich.				3'-phosphoadenosine 5'-phosphosulfate metabolic process (GO:0050427)|small molecule metabolic process (GO:0044281)|steroid metabolic process (GO:0008202)|sulfate assimilation (GO:0000103)|xenobiotic metabolic process (GO:0006805)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|extracellular vesicular exosome (GO:0070062)|intracellular membrane-bounded organelle (GO:0043231)|nucleus (GO:0005634)	alcohol sulfotransferase activity (GO:0004027)|steroid sulfotransferase activity (GO:0050294)			central_nervous_system(1)|cervix(1)|endometrium(1)|kidney(2)|large_intestine(1)|lung(2)|skin(2)|urinary_tract(1)	11		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;0.000115)|all cancers(93;0.000147)|GBM - Glioblastoma multiforme(486;0.00707)|Epithelial(262;0.0178)		agacccaactccagccccagccccag	0.66																																					p.347_348del		Pindel,Atlas-Indel	.											.	SULT2B1	72	.	0			c.1039_1044del						PASS	.		,	1,4133		0,1,2066					,	-3.9	0.0		dbSNP_126	21	16,8050		0,16,4017	no	coding,coding	SULT2B1	NM_177973.1,NM_004605.2	,	0,17,6083	A1A1,A1R,RR		0.1984,0.0242,0.1393	,	,		17,12183				SO:0001651	inframe_deletion	6820	exon7			.	U92314	CCDS12723.1, CCDS12724.1	19q13.3	2008-02-05				ENSG00000088002		"""Sulfotransferases, cytosolic"""	11459	protein-coding gene	gene with protein product		604125				9799594	Standard	NM_177973		Approved	HSST2	uc002pjl.3	O00204		ENST00000201586.2:c.1040_1045delCCAGCC	19.37:g.49102611_49102616delCCAGCC	ENSP00000201586:p.Ser352_Pro353del	244.0	0.0	.		203.0	38.0	0.187	NM_177973	O00205|O75814	In_Frame_Del	DEL	ENST00000201586.2	37	CCDS12723.1																																																																																			.	.	none		0.660	SULT2B1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000466140.1	NM_004605	
ACAA1	30	hgsc.bcm.edu	37	3	38162039	38162042	+	IGR	DEL	GAGA	GAGA	-	rs140494598		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	GAGA	GAGA	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr3:38162039_38162042delGAGA	ENST00000333167.8	-	0	1785				DLEC1_ENST00000346219.3_Frame_Shift_Del_p.GE1602fs|DLEC1_ENST00000308059.6_Frame_Shift_Del_p.GE1602fs|DLEC1_ENST00000452631.2_Frame_Shift_Del_p.GE1605fs|ACAA1_ENST00000480865.1_5'Flank	NM_001607.3	NP_001598.1	P09110	THIK_HUMAN	acetyl-CoA acyltransferase 1						alpha-linolenic acid metabolic process (GO:0036109)|bile acid metabolic process (GO:0008206)|cellular lipid metabolic process (GO:0044255)|fatty acid beta-oxidation (GO:0006635)|fatty acid beta-oxidation using acyl-CoA oxidase (GO:0033540)|small molecule metabolic process (GO:0044281)|unsaturated fatty acid metabolic process (GO:0033559)|very long-chain fatty acid metabolic process (GO:0000038)	intracellular membrane-bounded organelle (GO:0043231)|membrane (GO:0016020)|peroxisomal matrix (GO:0005782)|peroxisome (GO:0005777)	acetyl-CoA C-acyltransferase activity (GO:0003988)|palmitoyl-CoA oxidase activity (GO:0016401)			endometrium(1)|large_intestine(4)|lung(2)|ovary(1)|prostate(1)	9				KIRC - Kidney renal clear cell carcinoma(284;0.0523)|Kidney(284;0.0657)		AGTGCGAGTGGAGAGAGAGAGATG	0.578																																					p.1602_1603del		Pindel,Atlas-Indel	.											.	DLEC1	278	.	0			c.4804_4807del						PASS	.																																			SO:0001628	intergenic_variant	9940	exon34			.	X14813	CCDS2673.1, CCDS46794.1	3p22.2	2012-05-16	2010-04-30		ENSG00000060971	ENSG00000060971	2.3.1.16		82	protein-coding gene	gene with protein product	"""peroxisomal 3-oxoacyl-Coenzyme A thiolase"""	604054	"""acetyl-Coenzyme A acyltransferase 1"""				Standard	NM_001607		Approved		uc003cht.3	P09110	OTTHUMG00000131087		3.37:g.38162047_38162050delGAGA		322.0	0.0	.		301.0	66.0	0.219	NM_007335	G5E935|Q96CA6	Frame_Shift_Del	DEL	ENST00000333167.8	37	CCDS2673.1																																																																																			.	.	alt		0.578	ACAA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000342980.1	NM_001607	
MEF2B	100271849	hgsc.bcm.edu	37	19	19257101	19257102	+	Intron	INS	-	-	G			TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr19:19257101_19257102insG	ENST00000602424.2	-	9	1496				MEF2B_ENST00000424583.2_Frame_Shift_Ins_p.A288fs|MEF2B_ENST00000410050.1_Frame_Shift_Ins_p.A295fs|MEF2B_ENST00000409224.1_Frame_Shift_Ins_p.A291fs|MEF2BNB-MEF2B_ENST00000602276.1_5'Flank|MEF2B_ENST00000162023.5_Frame_Shift_Ins_p.A288fs|MEF2BNB-MEF2B_ENST00000514819.3_Intron|MEF2BNB-MEF2B_ENST00000444486.3_Intron|MEF2B_ENST00000409447.2_Intron	NM_005919.3	NP_005910.1	Q02080	MEF2B_HUMAN	myocyte enhancer factor 2B						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)			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)			GAGGACACGGCGGGGGGCCCAT	0.703											OREG0025379	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.A288fs		Atlas-Indel	.											.	MEF2B	41	.	0			c.862_863insC						PASS	.																																			SO:0001627	intron_variant	100271849	exon8			.	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.769+261->C	19.37:g.19257107_19257107dupG		21.0	0.0	0	731	33.0	11.0	0.333333	NM_001145785	A0AV80|B4DVH7|B7ZVY1|G5E9M1	Frame_Shift_Ins	INS	ENST00000602424.2	37	CCDS12394.1																																																																																			.	.	none		0.703	MEF2B-202	KNOWN	basic|CCDS	protein_coding	protein_coding		NM_005919	
GGA3	23163	hgsc.bcm.edu	37	17	73234805	73234806	+	Frame_Shift_Ins	INS	-	-	TCTG			TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr17:73234805_73234806insTCTG	ENST00000245541.6	-	16	2204_2205	c.1988_1989insCAGA	c.(1987-1989)gaafs	p.E663fs	GGA3_ENST00000582486.1_Frame_Shift_Ins_p.E591fs|GGA3_ENST00000582717.1_Frame_Shift_Ins_p.E591fs|GGA3_ENST00000578348.1_Frame_Shift_Ins_p.E541fs|GGA3_ENST00000351904.7_Frame_Shift_Ins_p.E630fs|GGA3_ENST00000538886.1_Frame_Shift_Ins_p.E541fs	NM_138619.2	NP_619525.1	Q9NZ52	GGA3_HUMAN	golgi-associated, gamma adaptin ear containing, ARF binding protein 3	663	GAE. {ECO:0000255|PROSITE- ProRule:PRU00093}.				intracellular protein transport (GO:0006886)|vesicle-mediated transport (GO:0016192)	clathrin adaptor complex (GO:0030131)|endosome (GO:0005768)|trans-Golgi network (GO:0005802)	ADP-ribosylation factor binding (GO:0030306)			breast(2)|endometrium(3)|large_intestine(4)|liver(1)|lung(4)|ovary(2)|prostate(2)|skin(1)|urinary_tract(1)	20			all cancers(21;2.39e-06)|Epithelial(20;2.38e-05)			ATGGAGAGAGTTCTGTCCCAGA	0.535											OREG0024729	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.E663fs		Pindel,Atlas-Indel	.											GGA3,NS,carcinoma,0,1	GGA3	54	1	0			c.1989_1990insCAGA						PASS	.																																			SO:0001589	frameshift_variant	23163	exon16			.	AF190864	CCDS11716.1, CCDS11717.1, CCDS54164.1, CCDS58597.1	17q25	2010-02-12	2010-02-12			ENSG00000125447			17079	protein-coding gene	gene with protein product		606006				10747089, 10749927	Standard	NR_033345		Approved	KIAA0154	uc002jni.2	Q9NZ52		ENST00000245541.6:c.1985_1988dupCAGA	17.37:g.73234806_73234809dupTCTG	ENSP00000245541:p.Glu663fs	203.0	0.0	.	1143	205.0	45.0	0.220	NM_138619	B7Z7E2|B7Z7M9|J3KRN0|Q15017|Q6IS16|Q9UJY3	Frame_Shift_Ins	INS	ENST00000245541.6	37	CCDS11717.1																																																																																			.	.	none		0.535	GGA3-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000446645.1	NM_138619	
CACNA1A	773	hgsc.bcm.edu	37	19	13395957	13395959	+	In_Frame_Del	DEL	TCC	TCC	-			TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	TCC	TCC	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr19:13395957_13395959delTCC	ENST00000360228.5	-	21	3614_3616	c.3615_3617delGGA	c.(3613-3618)gaggaa>gaa	p.1205_1206EE>E	CACNA1A_ENST00000573710.2_In_Frame_Del_p.1206_1207EE>E	NM_000068.3|NM_001127222.1|NM_001174080.1|NM_023035.2	NP_000059.3|NP_001120694.1|NP_001167551.1|NP_075461.2	O00555	CAC1A_HUMAN	calcium channel, voltage-dependent, P/Q type, alpha 1A subunit	1206	Poly-Glu.				adult walking behavior (GO:0007628)|behavioral response to pain (GO:0048266)|calcium ion import (GO:0070509)|calcium ion-dependent exocytosis (GO:0017156)|calcium ion-dependent exocytosis of neurotransmitter (GO:0048791)|cell death (GO:0008219)|cell growth (GO:0016049)|cellular chloride ion homeostasis (GO:0030644)|cerebellar molecular layer development (GO:0021679)|cerebellar Purkinje cell differentiation (GO:0021702)|cerebellum maturation (GO:0021590)|dendrite morphogenesis (GO:0048813)|energy reserve metabolic process (GO:0006112)|gamma-aminobutyric acid secretion (GO:0014051)|gamma-aminobutyric acid signaling pathway (GO:0007214)|glucose metabolic process (GO:0006006)|hormone metabolic process (GO:0042445)|membrane depolarization (GO:0051899)|membrane depolarization during action potential (GO:0086010)|musculoskeletal movement, spinal reflex action (GO:0050883)|negative regulation of hormone biosynthetic process (GO:0032353)|negative regulation of neuron apoptotic process (GO:0043524)|neuromuscular process controlling balance (GO:0050885)|neuromuscular synaptic transmission (GO:0007274)|neurotransmitter metabolic process (GO:0042133)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|receptor clustering (GO:0043113)|regulation of acetylcholine secretion, neurotransmission (GO:0014056)|regulation of axonogenesis (GO:0050770)|regulation of calcium ion-dependent exocytosis (GO:0017158)|regulation of insulin secretion (GO:0050796)|rhythmic synaptic transmission (GO:0060024)|small molecule metabolic process (GO:0044281)|spinal cord motor neuron differentiation (GO:0021522)|sulfur amino acid metabolic process (GO:0000096)|synapse assembly (GO:0007416)|synaptic transmission (GO:0007268)|synaptic transmission, glutamatergic (GO:0035249)|transmission of nerve impulse (GO:0019226)|vestibular nucleus development (GO:0021750)	cell projection (GO:0042995)|cytoplasm (GO:0005737)|dendrite (GO:0030425)|integral component of membrane (GO:0016021)|neuronal cell body (GO:0043025)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|voltage-gated calcium channel complex (GO:0005891)	high voltage-gated calcium channel activity (GO:0008331)|metal ion binding (GO:0046872)|syntaxin binding (GO:0019905)|voltage-gated calcium channel activity (GO:0005245)			breast(2)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(3)|lung(25)|prostate(2)|urinary_tract(1)	42			OV - Ovarian serous cystadenocarcinoma(19;5.07e-21)		Bepridil(DB01244)|Loperamide(DB00836)|Pregabalin(DB00230)|Spironolactone(DB00421)|Verapamil(DB00661)	ACGGtcgtcttcctcctcctcct	0.552																																					p.1207_1207del		Pindel,Atlas-Indel	.											.	CACNA1A	715	.	0			c.3619_3621del						PASS	.		,,,,	3,3657		1,1,1828					,,,,	-3.5	0.6			103	12,7868		0,12,3928	no	coding,coding,coding,coding,coding	CACNA1A	NM_023035.2,NM_001174080.1,NM_001127222.1,NM_001127221.1,NM_000068.3	,,,,	1,13,5756	A1A1,A1R,RR		0.1523,0.082,0.13	,,,,	,,,,		15,11525				SO:0001651	inframe_deletion	773	exon21			.	U79666	CCDS45998.1, CCDS45999.1	19p13	2014-09-17			ENSG00000141837	ENSG00000141837		"""Calcium channel subunits"", ""Voltage-gated ion channels / Calcium channels"""	1388	protein-coding gene	gene with protein product		601011		CACNL1A4, SCA6, MHP1, MHP		8825650, 16382099, 23827678	Standard	NM_000068		Approved	Cav2.1, EA2, APCA, HPCA, FHM	uc010xne.2	O00555	OTTHUMG00000044590	ENST00000360228.5:c.3615_3617delGGA	19.37:g.13395966_13395968delTCC	ENSP00000353362:p.Glu1206del	170.0	0.0	.		172.0	45.0	0.262	NM_001127221	J3KP41|P78510|P78511|Q16290|Q92690|Q99790|Q99791|Q99792|Q99793|Q9NS88|Q9UDC4	In_Frame_Del	DEL	ENST00000360228.5	37	CCDS45998.1																																																																																			.	.	none		0.552	CACNA1A-001	KNOWN	non_canonical_U12|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000104062.2	NM_000068	
CCL27	10850	hgsc.bcm.edu	37	9	34661945	34661945	+	Frame_Shift_Del	DEL	C	C	-			TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr9:34661945delC	ENST00000259631.4	-	3	393	c.335delG	c.(334-336)ggcfs	p.G112fs	RP11-195F19.30_ENST00000564224.1_RNA|CCL27_ENST00000557161.1_5'UTR	NM_006664.2	NP_006655.1	Q9Y4X3	CCL27_HUMAN	chemokine (C-C motif) ligand 27	112					cell chemotaxis (GO:0060326)|cell-cell signaling (GO:0007267)|chemotaxis (GO:0006935)|immune response (GO:0006955)	extracellular region (GO:0005576)|extracellular space (GO:0005615)	chemokine activity (GO:0008009)			kidney(1)|large_intestine(3)|ovary(1)	5	all_epithelial(49;0.102)		STAD - Stomach adenocarcinoma(86;0.178)	GBM - Glioblastoma multiforme(74;0.173)		GGGGCTTCAGCCCATTTTCCT	0.448																																					p.G112fs		Pindel,Atlas-Indel	.											.	CCL27	6	.	0			c.336delC						PASS	.						88.0	97.0	94.0					9																	34661945		2203	4300	6503	SO:0001589	frameshift_variant	10850	exon3			.	AJ243542	CCDS6569.1	9p13	2014-05-16	2002-08-22	2002-08-23	ENSG00000213927	ENSG00000213927		"""Chemokine ligands"", ""Endogenous ligands"""	10626	protein-coding gene	gene with protein product	"""CC chemokine ILC"", ""IL-11 Ralpha-locus chemokine"", ""cutaneous T-cell attracting chemokine"""	604833	"""small inducible cytokine subfamily A (Cys-Cys), member 27"""	SCYA27		10556532, 10588729	Standard	NM_006664		Approved	ALP, ILC, CTACK, skinkine, ESkine, PESKY, CTAK	uc003zvm.1	Q9Y4X3	OTTHUMG00000019834	ENST00000259631.4:c.335delG	9.37:g.34661945delC	ENSP00000259631:p.Gly112fs	122.0	0.0	.		107.0	32.0	0.299	NM_006664		Frame_Shift_Del	DEL	ENST00000259631.4	37	CCDS6569.1																																																																																			.	.	none		0.448	CCL27-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052228.1	NM_006664	
C1orf141	400757	hgsc.bcm.edu	37	1	67558870	67558874	+	Frame_Shift_Del	DEL	TCATT	TCATT	-	rs200104842|rs373816272|rs577736835	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	TCATT	TCATT	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr1:67558870_67558874delTCATT	ENST00000371007.2	-	8	1126_1130	c.1017_1021delAATGA	c.(1015-1023)gaaatgagtfs	p.MS340fs	C1orf141_ENST00000544837.1_Frame_Shift_Del_p.MS340fs|C1orf141_ENST00000371006.1_Frame_Shift_Del_p.MS340fs	NM_001276351.1	NP_001263280.1	Q5JVX7	CA141_HUMAN	chromosome 1 open reading frame 141	340										NS(1)|breast(1)|endometrium(1)|large_intestine(5)|lung(8)|ovary(1)|skin(1)	18						GTTTGGGCACTCATTTCATGAATAA	0.361														19	0.00379393	0.0023	0.0072	5008	,	,		16889	0.0		0.0109	False		,,,				2504	0.0				p.340_341del		Atlas-Indel	.											.	C1orf141	58	.	0			c.1018_1022del						PASS	.			10,4244		0,10,2117						-2.1	0.0			110	69,8177		2,65,4056	no	frameshift	C1orf141	NM_001013674.1		2,75,6173	A1A1,A1R,RR		0.8368,0.2351,0.632				79,12421				SO:0001589	frameshift_variant	400757	exon8			.	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.1017_1021delAATGA	1.37:g.67558870_67558874delTCATT	ENSP00000360046:p.Met340fs	267.0	0.0	0		125.0	14.0	0.112	NM_001276351	Q0P5P5|Q5JVX5	Frame_Shift_Del	DEL	ENST00000371007.2	37	CCDS30745.1																																																																																			TCATT|0.994;-|0.006	0.006	strong		0.361	C1orf141-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000026096.2	NM_001013674	
EIF3A	8661	hgsc.bcm.edu	37	10	120819176	120819187	+	In_Frame_Del	DEL	AAGGAACCAAAG	AAGGAACCAAAG	-	rs374628063		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	AAGGAACCAAAG	AAGGAACCAAAG	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr10:120819176_120819187delAAGGAACCAAAG	ENST00000369144.3	-	10	1497_1508	c.1370_1381delCTTTGGTTCCTT	c.(1369-1383)tctttggttcctttt>ttt	p.SLVP457del	SNORA19_ENST00000410656.1_RNA|EIF3A_ENST00000541549.1_In_Frame_Del_p.SLVP423del|SNORA19_ENST00000384737.1_RNA	NM_003750.2	NP_003741.1	P56537	IF6_HUMAN	eukaryotic translation initiation factor 3, subunit A	0					mature ribosome assembly (GO:0042256)|ribosomal large subunit biogenesis (GO:0042273)|ribosomal subunit export from nucleus (GO:0000054)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|lamin filament (GO:0005638)|nucleus (GO:0005634)	ribosomal large subunit binding (GO:0043023)|ribosome binding (GO:0043022)|translation initiation factor activity (GO:0003743)	p.P460F(1)		endometrium(8)|kidney(4)|large_intestine(14)|lung(22)|prostate(1)|skin(4)|urinary_tract(3)	56		Lung NSC(174;0.094)|all_lung(145;0.123)		all cancers(201;0.0236)		GCATCAACAAAAGGAACCAAAGAAGTCAAACG	0.434																																					p.457_461del		Atlas-Indel	.											.	EIF3A	142	.	1	Substitution - Missense(1)	skin(1)	c.1371_1382del						PASS	.																																			SO:0001651	inframe_deletion	8661	exon10			.	U78311	CCDS7608.1	10q26.11	2007-08-03	2007-07-27	2007-07-27	ENSG00000107581	ENSG00000107581			3271	protein-coding gene	gene with protein product		602039	"""eukaryotic translation initiation factor 3, subunit 10 theta, 150/170kDa"""	EIF3, EIF3S10		9054404, 8590280	Standard	NM_003750		Approved	eIF3-theta, eIF3-p170, KIAA0139, eIF3a, TIF32	uc001ldu.3	Q14152	OTTHUMG00000019144	ENST00000369144.3:c.1370_1381delCTTTGGTTCCTT	10.37:g.120819176_120819187delAAGGAACCAAAG	ENSP00000358140:p.Ser457_Pro460del	215.0	0.0	0		176.0	25.0	0.142045	NM_003750	B7ZBG9|Q6IBN8|Q96TD5	In_Frame_Del	DEL	ENST00000369144.3	37	CCDS7608.1																																																																																			.	.	none		0.434	EIF3A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050634.1	NM_003750	
CHD8	57680	hgsc.bcm.edu	37	14	21862616	21862616	+	Frame_Shift_Del	DEL	A	A	-			TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr14:21862616delA	ENST00000557364.1	-	31	5682	c.5419delT	c.(5419-5421)tatfs	p.Y1807fs	SNORD9_ENST00000362566.1_RNA|CHD8_ENST00000555962.1_5'Flank|CHD8_ENST00000430710.3_Frame_Shift_Del_p.Y1528fs|CHD8_ENST00000399982.2_Frame_Shift_Del_p.Y1807fs|SNORD8_ENST00000363915.1_RNA			Q9HCK8	CHD8_HUMAN	chromodomain helicase DNA binding protein 8	1807					ATP catabolic process (GO:0006200)|ATP-dependent chromatin remodeling (GO:0043044)|canonical Wnt signaling pathway (GO:0060070)|DNA duplex unwinding (GO:0032508)|in utero embryonic development (GO:0001701)|negative regulation of fibroblast apoptotic process (GO:2000270)|negative regulation of transcription, DNA-templated (GO:0045892)|negative regulation of Wnt signaling pathway (GO:0030178)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription from RNA polymerase III promoter (GO:0045945)|positive regulation of transcription, DNA-templated (GO:0045893)|transcription, DNA-templated (GO:0006351)	MLL1 complex (GO:0071339)|nucleus (GO:0005634)|protein complex (GO:0043234)	ATP binding (GO:0005524)|beta-catenin binding (GO:0008013)|DNA binding (GO:0003677)|DNA helicase activity (GO:0003678)|DNA-dependent ATPase activity (GO:0008094)|histone binding (GO:0042393)|methylated histone binding (GO:0035064)|p53 binding (GO:0002039)			NS(2)|breast(1)|central_nervous_system(1)|cervix(4)|endometrium(8)|haematopoietic_and_lymphoid_tissue(2)|kidney(6)|large_intestine(8)|lung(33)|ovary(6)|prostate(7)|skin(3)|upper_aerodigestive_tract(2)|urinary_tract(2)	85	all_cancers(95;0.00121)		Epithelial(56;2.55e-06)|all cancers(55;1.73e-05)	GBM - Glioblastoma multiforme(265;0.00424)		ACCACTCGATAAAAATCAGTT	0.413																																					p.Y1807fs		Pindel,Atlas-Indel	.											.	CHD8	339	.	0			c.5420delA						PASS	.						53.0	52.0	52.0					14																	21862616		1958	4159	6117	SO:0001589	frameshift_variant	57680	exon30			.	AB046784	CCDS45081.1, CCDS53885.1	14q11.2	2008-02-05	2004-06-22	2004-06-23		ENSG00000100888			20153	protein-coding gene	gene with protein product		610528	"""helicase with SNF2 domain 1"""	HELSNF1		10997877	Standard	NM_020920		Approved	KIAA1564, DUPLIN	uc001war.2	Q9HCK8		ENST00000557364.1:c.5419delT	14.37:g.21862616delA	ENSP00000451601:p.Tyr1807fs	121.0	0.0	.		156.0	30.0	0.192	NM_001170629	Q4G0D8|Q68DQ0|Q6DKH9|Q6P440|Q6ZNL7|Q8N3Z9|Q8NCY4|Q8TBR9|Q96F26	Frame_Shift_Del	DEL	ENST00000557364.1	37	CCDS53885.1																																																																																			.	.	none		0.413	CHD8-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000410436.1	NM_020920	
OR2T8	343172	hgsc.bcm.edu	37	1	248084470	248084471	+	Frame_Shift_Ins	INS	-	-	G	rs140846339|rs149623571|rs547311711	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr1:248084470_248084471insG	ENST00000319968.4	+	1	151_152	c.151_152insG	c.(151-153)cacfs	p.H51fs		NM_001005522.1	NP_001005522.1	A6NH00	OR2T8_HUMAN	olfactory receptor, family 2, subfamily T, member 8	51						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)	p.H51D(1)		central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(6)|lung(20)|pancreas(1)|prostate(1)|upper_aerodigestive_tract(1)	34	all_cancers(71;0.000139)|all_epithelial(71;1.58e-05)|Breast(184;0.0117)|Ovarian(71;0.0377)|all_lung(81;0.127)|Lung NSC(105;0.136)	all_cancers(173;0.0211)	OV - Ovarian serous cystadenocarcinoma(106;0.0319)			TCACTGGGACCACCGGCTCCAC	0.535																																					p.H51fs		Atlas-Indel	.											OR2T8,rectum,carcinoma,0,2	OR2T8	67	2	1	Substitution - Missense(1)	large_intestine(1)	c.151_152insG						PASS	.																																			SO:0001589	frameshift_variant	343172	exon1			.		CCDS31100.1	1q44	2012-08-09		2004-03-10	ENSG00000177462	ENSG00000177462		"""GPCR / Class A : Olfactory receptors"""	15020	protein-coding gene	gene with protein product				OR2T8P			Standard	XM_005273117		Approved		uc010pzc.2	A6NH00	OTTHUMG00000040205	Exception_encountered	1.37:g.248084470_248084471insG	ENSP00000326225:p.His51fs	726.0	0.0	0		441.0	69.0	0.156463	NM_001005522		Frame_Shift_Ins	INS	ENST00000319968.4	37	CCDS31100.1																																																																																			.	.	none		0.535	OR2T8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000096862.1	NM_001005522	
SPAG16	79582	hgsc.bcm.edu	37	2	215013915	215013915	+	Frame_Shift_Del	DEL	T	T	-			TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr2:215013915delT	ENST00000331683.5	+	15	1740	c.1645delT	c.(1645-1647)tttfs	p.F549fs	SPAG16_ENST00000374309.3_Frame_Shift_Del_p.F455fs	NM_024532.4	NP_078808.3	Q8N0X2	SPG16_HUMAN	sperm associated antigen 16	549					cilium assembly (GO:0042384)|spermatogenesis (GO:0007283)	axoneme (GO:0005930)|microtubule cytoskeleton (GO:0015630)|motile cilium (GO:0031514)|nucleus (GO:0005634)				endometrium(4)|kidney(1)|large_intestine(15)|lung(27)|ovary(1)|prostate(3)|skin(2)|stomach(1)|upper_aerodigestive_tract(2)	56		Renal(323;0.00461)		UCEC - Uterine corpus endometrioid carcinoma (47;0.0525)|Epithelial(149;7.07e-07)|all cancers(144;7.96e-05)|Lung(261;0.00255)|LUSC - Lung squamous cell carcinoma(224;0.00599)		GCTGTGGGACTTTCGGAAGCT	0.368																																					p.D548fs		Pindel,Atlas-Indel	.											.	SPAG16	134	.	0			c.1644delC						PASS	.						166.0	165.0	165.0					2																	215013915		2203	4300	6503	SO:0001589	frameshift_variant	79582	exon15			.	AF310672	CCDS2396.1, CCDS46508.1	2q34	2013-05-21			ENSG00000144451	ENSG00000144451		"""WD repeat domain containing"""	23225	protein-coding gene	gene with protein product		612173				12391165, 11867345	Standard	NM_024532		Approved	PF20, FLJ22724, DKFZp666P1710, WDR29	uc002veq.4	Q8N0X2	OTTHUMG00000133015	ENST00000331683.5:c.1645delT	2.37:g.215013915delT	ENSP00000332592:p.Phe549fs	307.0	0.0	.		179.0	55.0	0.307	NM_024532	Q498B7|Q658W1|Q68DB3|Q6I9Z6|Q8N9C7|Q9H601	Frame_Shift_Del	DEL	ENST00000331683.5	37	CCDS2396.1																																																																																			.	.	none		0.368	SPAG16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256601.2	NM_024532	
ANKRD34C	390616	hgsc.bcm.edu	37	15	79586693	79586695	+	In_Frame_Del	DEL	GTG	GTG	-	rs536236949	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	GTG	GTG	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr15:79586693_79586695delGTG	ENST00000558647.2	+	1	1067_1069	c.1067_1069delGTG	c.(1066-1071)tgtggt>tgt	p.G357del	ANKRD34C_ENST00000421388.2_In_Frame_Del_p.G357del			P0C6C1	AN34C_HUMAN	ankyrin repeat domain 34C	357										endometrium(3)|kidney(1)|skin(1)	5						CAAGAGAAATGTGGTATGGGTCC	0.542														6	0.00119808	0.0	0.0029	5008	,	,		19452	0.0		0.004	False		,,,				2504	0.0				p.356_356del		Pindel,Atlas-Indel	.											.	ANKRD34C	29	.	0			c.1066_1068del						PASS	.			7,2311		2,3,1154						-3.8	0.0			34	15,4489		2,11,2239	no	coding	ANKRD34C	NM_001146341.1		4,14,3393	A1A1,A1R,RR		0.333,0.302,0.3225				22,6800				SO:0001651	inframe_deletion	390616	exon2			.		CCDS53965.1	15q25.1	2013-01-10			ENSG00000235711	ENSG00000235711		"""Ankyrin repeat domain containing"""	33888	protein-coding gene	gene with protein product							Standard	NM_001146341		Approved		uc002bet.3	P0C6C1		ENST00000558647.2:c.1067_1069delGTG	15.37:g.79586693_79586695delGTG	ENSP00000454921:p.Gly357del	57.0	0.0	.		39.0	22.0	0.564	NM_001146341	H3BNM1	In_Frame_Del	DEL	ENST00000558647.2	37	CCDS53965.1																																																																																			.	.	none		0.542	ANKRD34C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000416713.2	NM_001146341	
SF3A2	8175	hgsc.bcm.edu	37	19	2248152	2248153	+	In_Frame_Ins	INS	-	-	GGAGTCCACCCTCCAGCCCCC	rs59267791|rs539335935	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr19:2248152_2248153insGGAGTCCACCCTCCAGCCCCC	ENST00000221494.5	+	9	1420_1421	c.1002_1003insGGAGTCCACCCTCCAGCCCCC	c.(1003-1005)gga>GGAGTCCACCCTCCAGCCCCCgga	p.335_335G>GVHPPAPG	AMH_ENST00000221496.4_5'Flank|MIR4321_ENST00000592276.1_RNA	NM_007165.4	NP_009096.2	Q15428	SF3A2_HUMAN	splicing factor 3a, subunit 2, 66kDa	335	Pro-rich.				gene expression (GO:0010467)|mRNA 3'-splice site recognition (GO:0000389)|mRNA processing (GO:0006397)|mRNA splicing, via spliceosome (GO:0000398)|RNA splicing (GO:0008380)	catalytic step 2 spliceosome (GO:0071013)|nucleoplasm (GO:0005654)|small nuclear ribonucleoprotein complex (GO:0030532)|spliceosomal complex (GO:0005681)	poly(A) RNA binding (GO:0044822)|zinc ion binding (GO:0008270)			NS(1)|large_intestine(1)|lung(2)	4		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)		CCCCAGCTCCTGGAGTCCACCC	0.733																																					p.P334delinsPGVHPPAP		Pindel	.											SF3A2,colon,carcinoma,0,1	SF3A2	22	1	0			c.1002_1003insGGAGTCCACCCTCCAGCCCCC						PASS	.																																			SO:0001652	inframe_insertion	8175	exon9			.	L21990	CCDS12084.1	19p13.3	2012-10-02	2002-08-29		ENSG00000104897	ENSG00000104897			10766	protein-coding gene	gene with protein product		600796	"""splicing factor 3a, subunit 2, 66kD"""			8211113, 8541848	Standard	NM_007165		Approved	SF3a66, SAP62, PRPF11, Prp11	uc002lvg.3	Q15428	OTTHUMG00000180414	ENST00000221494.5:c.1003_1023dupGGAGTCCACCCTCCAGCCCCC	19.37:g.2248152_2248153insGGAGTCCACCCTCCAGCCCCC	ENSP00000221494:p.ValHisProProAlaProGly363dup	28.0	0.0	.		16.0	10.0	0.625	NM_007165	B2RBU1|D6W605|O75245	In_Frame_Ins	INS	ENST00000221494.5	37	CCDS12084.1																																																																																			.	.	none		0.733	SF3A2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000451268.3		
KIAA0754	643314	hgsc.bcm.edu	37	1	39879397	39879435	+	In_Frame_Del	DEL	GAGGAATCCGCCTCCGCAGCTGTTGCAGTGCCCACCCCC	GAGGAATCCGCCTCCGCAGCTGTTGCAGTGCCCACCCCC	-	rs371382486|rs55976345|rs541496808|rs199726261|rs548996855|rs112569629|rs201613510	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	GAGGAATCCGCCTCCGCAGCTGTTGCAGTGCCCACCCCC	GAGGAATCCGCCTCCGCAGCTGTTGCAGTGCCCACCCCC	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr1:39879397_39879435delGAGGAATCCGCCTCCGCAGCTGTTGCAGTGCCCACCCCC	ENST00000530275.1	+	1	3247_3285	c.3052_3090delGAGGAATCCGCCTCCGCAGCTGTTGCAGTGCCCACCCCC	c.(3052-3090)gaggaatccgcctccgcagctgttgcagtgcccacccccdel	p.EESASAAVAVPTP1018del	MACF1_ENST00000564288.1_Intron|MACF1_ENST00000539005.1_Intron|MACF1_ENST00000317713.7_Intron|MACF1_ENST00000545844.1_Intron|MACF1_ENST00000567887.1_Intron|MACF1_ENST00000361689.2_Intron|MACF1_ENST00000289893.4_Intron|MACF1_ENST00000372915.3_Intron	NM_015038.1	NP_055853.1	O94854	K0754_HUMAN	KIAA0754	1018	Ala-rich.									central_nervous_system(1)|large_intestine(6)|skin(1)	8	Lung NSC(20;5.57e-06)|Ovarian(52;0.00769)|Acute lymphoblastic leukemia(166;0.074)	Myeloproliferative disorder(586;0.0393)	OV - Ovarian serous cystadenocarcinoma(33;7.78e-19)|Epithelial(16;1.73e-17)|all cancers(16;2.49e-16)|LUSC - Lung squamous cell carcinoma(16;0.00146)|Lung(16;0.00204)			GCCCACCCCAGAGGAATCCGCCTCCGCAGCTGTTGCAGTGCCCACCCCCGAGGAATCTG	0.682																																					p.1153_1166del		Pindel	.											.	KIAA0754	93	.	0			c.3459_3497del						PASS	.		,,	832,2850		248,336,1257					,,	0.0	0.0			18	1888,6000		448,992,2504	no	intron,coding,intron	MACF1,KIAA0754	NM_033044.3,NM_015038.1,NM_012090.4	,,	696,1328,3761	A1A1,A1R,RR		23.9351,22.5964,23.5091	,,	,,		2720,8850				SO:0001651	inframe_deletion	643314	exon1			.			1p34.2	2009-07-09				ENSG00000255103			29111	protein-coding gene	gene with protein product						9872452	Standard	NM_015038		Approved		uc009vvt.1	O94854		ENST00000530275.1:c.3052_3090delGAGGAATCCGCCTCCGCAGCTGTTGCAGTGCCCACCCCC	1.37:g.39879397_39879435delGAGGAATCCGCCTCCGCAGCTGTTGCAGTGCCCACCCCC	ENSP00000431179:p.Glu1018_Pro1030del	197.0	0.0	.		65.0	19.0	0.292	NM_015038	E9PMC2|Q6ZSB2	In_Frame_Del	DEL	ENST00000530275.1	37																																																																																				.	.	none		0.682	KIAA0754-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000392100.1	NM_015038	
DST	667	hgsc.bcm.edu	37	6	56457044	56457044	+	Missense_Mutation	SNP	T	T	C	rs186813964	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr6:56457044T>C	ENST00000361203.3	-	45	12213	c.12206A>G	c.(12205-12207)aAa>aGa	p.K4069R	DST_ENST00000370788.2_Missense_Mutation_p.K1983R|DST_ENST00000370754.5_Missense_Mutation_p.K4249R|DST_ENST00000446842.2_Missense_Mutation_p.K3745R|DST_ENST00000244364.6_Missense_Mutation_p.K1657R|DST_ENST00000312431.6_Missense_Mutation_p.K4069R|DST_ENST00000370769.4_Missense_Mutation_p.K4071R|DST_ENST00000421834.2_Missense_Mutation_p.K1983R			Q03001	DYST_HUMAN	dystonin	4069					axonogenesis (GO:0007409)|cell adhesion (GO:0007155)|cell cycle arrest (GO:0007050)|cell motility (GO:0048870)|cytoplasmic microtubule organization (GO:0031122)|cytoskeleton organization (GO:0007010)|extracellular matrix organization (GO:0030198)|hemidesmosome assembly (GO:0031581)|integrin-mediated signaling pathway (GO:0007229)|intermediate filament cytoskeleton organization (GO:0045104)|maintenance of cell polarity (GO:0030011)|microtubule cytoskeleton organization (GO:0000226)|regulation of microtubule polymerization or depolymerization (GO:0031110)|response to wounding (GO:0009611)|retrograde axon cargo transport (GO:0008090)	actin cytoskeleton (GO:0015629)|axon (GO:0030424)|basal plasma membrane (GO:0009925)|basement membrane (GO:0005604)|cell leading edge (GO:0031252)|cell projection (GO:0042995)|cytoplasm (GO:0005737)|cytoplasmic membrane-bounded vesicle (GO:0016023)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|hemidesmosome (GO:0030056)|integral component of membrane (GO:0016021)|intermediate filament (GO:0005882)|intermediate filament cytoskeleton (GO:0045111)|microtubule cytoskeleton (GO:0015630)|microtubule plus-end (GO:0035371)|neurofilament cytoskeleton (GO:0060053)|nucleus (GO:0005634)|Z disc (GO:0030018)	calcium ion binding (GO:0005509)|integrin binding (GO:0005178)|microtubule plus-end binding (GO:0051010)|protein C-terminus binding (GO:0008022)|protein homodimerization activity (GO:0042803)			NS(1)|breast(5)|central_nervous_system(8)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(22)|lung(43)|ovary(7)|prostate(1)|skin(4)|upper_aerodigestive_tract(3)	105	Lung NSC(77;0.103)		LUSC - Lung squamous cell carcinoma(124;0.0485)|Lung(124;0.0956)			AGATAAGTGTTTGCTCGCTGT	0.428													T|||	12	0.00239617	0.0	0.0029	5008	,	,		16441	0.0		0.004	False		,,,				2504	0.0061				p.K1657R		Atlas-SNP	.											DST_ENST00000370769,NS,lymphoid_neoplasm,0,2	DST	1427	2	0			c.A4970G						PASS	.	T	ARG/LYS	2,3780		0,2,1889	81.0	80.0	81.0		4970	3.2	1.0	6		81	44,8184		0,44,4070	yes	missense	DST	NM_015548.4	26	0,46,5959	CC,CT,TT		0.5348,0.0529,0.383	benign	1657/5172	56457044	46,11964	1891	4114	6005	SO:0001583	missense	667	exon30			AAGTGTTTGCTCG	M22942, M69225	CCDS4959.1, CCDS47443.1, CCDS75474.1	6p12.1	2013-01-10	2004-06-25	2004-07-01	ENSG00000151914	ENSG00000151914		"""EF-hand domain containing"""	1090	protein-coding gene	gene with protein product		113810	"""bullous pemphigoid antigen 1, 230/240kDa"""	BPAG1		2461961, 2276744	Standard	NM_001144770		Approved	BP240, KIAA0728, FLJ21489, FLJ13425, FLJ32235, FLJ30627, CATX-15, BPA, MACF2	uc021zba.2	Q03001	OTTHUMG00000014913	ENST00000361203.3:c.12206A>G	6.37:g.56457044T>C	ENSP00000354508:p.Lys4069Arg	197.0	0.0	0		131.0	64.0	0.48855	NM_015548	B7Z3H1|O94833|Q12825|Q13266|Q13267|Q13775|Q5TBT0|Q5TBT2|Q5TF23|Q5TF24|Q8N1T8|Q8N8J3|Q8WXK8|Q8WXK9|Q96AK9|Q96DQ5|Q96J76|Q96QT5|Q9H555|Q9UGD7|Q9UGD8|Q9UN10	Missense_Mutation	SNP	ENST00000361203.3	37		4	0.0018315018315018315	0	0.0	2	0.0055248618784530384	0	0.0	2	0.002638522427440633	T	12.87	2.068920	0.36470	5.29E-4	0.005348	ENSG00000151914	ENST00000244364;ENST00000370754;ENST00000370769;ENST00000421834;ENST00000446842;ENST00000312431;ENST00000370788;ENST00000361203	T;T;T;T;T;T;T;T	0.51325	1.35;1.35;1.35;1.35;1.35;0.71;1.35;1.35	5.8	3.23	0.37069	.	0.226724	0.30177	N	0.010236	T	0.17492	0.0420	L	0.41710	1.295	0.24732	N	0.993083	B;B;B;B;B	0.15473	0.01;0.011;0.005;0.013;0.004	B;B;B;B;B	0.22880	0.013;0.042;0.011;0.028;0.012	T	0.08722	-1.0708	9	0.15952	T	0.53	.	10.2141	0.43158	0.0:0.1428:0.0:0.8572	.	1983;4071;4249;4069;1657	Q5TBT1;E7ERU2;E9PEB9;Q03001;Q03001-8	.;.;.;DYST_HUMAN;.	R	1657;4249;4071;1983;3745;4069;1983;4069	ENSP00000244364:K1657R;ENSP00000359790:K4249R;ENSP00000359805:K4071R;ENSP00000400883:K1983R;ENSP00000393645:K3745R;ENSP00000307959:K4069R;ENSP00000359824:K1983R;ENSP00000354508:K4069R	ENSP00000244364:K1657R	K	-	2	0	DST	56565003	1.000000	0.71417	1.000000	0.80357	0.950000	0.60333	1.130000	0.31393	0.376000	0.24707	0.528000	0.53228	AAA	T|0.998;C|0.002	0.002	strong		0.428	DST-004	NOVEL	not_organism_supported|basic|appris_candidate	protein_coding	protein_coding	OTTHUMT00000041021.3	NM_001723	
PCDHGA8	9708	hgsc.bcm.edu	37	5	140773812	140773812	+	Missense_Mutation	SNP	G	G	A	rs144796076	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr5:140773812G>A	ENST00000398604.2	+	1	1432	c.1432G>A	c.(1432-1434)Gac>Aac	p.D478N	PCDHGA2_ENST00000394576.2_Intron|PCDHGA3_ENST00000253812.6_Intron|PCDHGB1_ENST00000523390.1_Intron|PCDHGB2_ENST00000522605.1_Intron|PCDHGA6_ENST00000517434.1_Intron|PCDHGA1_ENST00000517417.1_Intron|PCDHGA5_ENST00000518069.1_Intron|PCDHGB4_ENST00000519479.1_Intron|PCDHGA4_ENST00000571252.1_Intron|PCDHGB3_ENST00000576222.1_Intron|PCDHGA7_ENST00000518325.1_Intron	NM_032088.1	NP_114477.1	Q9Y5G5	PCDG8_HUMAN	protocadherin gamma subfamily A, 8	478	Cadherin 5. {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)			endometrium(6)|kidney(6)|large_intestine(6)|lung(30)|ovary(1)|stomach(1)|upper_aerodigestive_tract(1)	51			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			GACTGCACACGACCCCGACAG	0.547													.|||	10	0.00199681	0.0	0.0029	5008	,	,		17412	0.0		0.007	False		,,,				2504	0.001				p.D478N		Atlas-SNP	.											.	PCDHGA8	146	.	0			c.G1432A						PASS	.	G	,ASN/ASP,,,,,,,,,,,ASN/ASP	4,4204		0,4,2100	51.0	55.0	53.0		,1432,,,,,,,,,,,1432	5.1	0.4	5	dbSNP_134	53	26,8436		0,26,4205	yes	intron,missense,intron,intron,intron,intron,intron,intron,intron,intron,intron,intron,missense	PCDHGB4,PCDHGA8,PCDHGB3,PCDHGB2,PCDHGB1,PCDHGA7,PCDHGA6,PCDHGA5,PCDHGA4,PCDHGA3,PCDHGA2,PCDHGA1	NM_003736.2,NM_014004.2,NM_018912.2,NM_018915.2,NM_018916.3,NM_018917.2,NM_018918.2,NM_018919.2,NM_018920.2,NM_018922.2,NM_018923.2,NM_018924.2,NM_032088.1	,23,,,,,,,,,,,23	0,30,6305	AA,AG,GG		0.3073,0.0951,0.2368	,,,,,,,,,,,,	,478/821,,,,,,,,,,,478/933	140773812	30,12640	2104	4231	6335	SO:0001583	missense	9708	exon1			GCACACGACCCCG	AF152515	CCDS47291.1, CCDS75338.1	5q31	2010-01-26			ENSG00000253767	ENSG00000253767		"""Cadherins / Protocadherins : Clustered"""	8706	other	protocadherin		606295				10380929	Standard	NM_014004		Approved	KIAA0327, PCDH-GAMMA-A8		Q9Y5G5	OTTHUMG00000164053	ENST00000398604.2:c.1432G>A	5.37:g.140773812G>A	ENSP00000381605:p.Asp478Asn	166.0	0.0	0		182.0	78.0	0.428571	NM_014004	A7MCZ4|O15039	Missense_Mutation	SNP	ENST00000398604.2	37	CCDS47291.1	7	0.003205128205128205	0	0.0	2	0.0055248618784530384	0	0.0	5	0.006596306068601583	.	16.62	3.173397	0.57584	9.51E-4	0.003073	ENSG00000253767	ENST00000398604	T	0.74526	-0.85	5.06	5.06	0.68205	Cadherin (4);Cadherin-like (1);	0.000000	0.32273	U	0.006322	D	0.91958	0.7453	H	0.99970	5.12	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;1.0	D	0.95745	0.8787	10	0.87932	D	0	.	18.0785	0.89435	0.0:0.0:1.0:0.0	.	478;478	Q9Y5G5;Q9Y5G5-2	PCDG8_HUMAN;.	N	478	ENSP00000381605:D478N	ENSP00000381605:D478N	D	+	1	0	PCDHGA8	140753996	1.000000	0.71417	0.373000	0.26003	0.201000	0.24016	9.595000	0.98260	2.366000	0.80165	0.655000	0.94253	GAC	G|0.996;A|0.004	0.004	strong		0.547	PCDHGA8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000376972.1	NM_032088	
GBE1	2632	hgsc.bcm.edu	37	3	81720086	81720086	+	Missense_Mutation	SNP	G	G	A			TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr3:81720086G>A	ENST00000429644.2	-	3	975	c.332C>T	c.(331-333)tCg>tTg	p.S111L	GBE1_ENST00000489715.1_Missense_Mutation_p.S70L|GBE1_ENST00000477426.1_5'UTR	NM_000158.3	NP_000149	Q04446	GLGB_HUMAN	glucan (1,4-alpha-), branching enzyme 1	111					carbohydrate metabolic process (GO:0005975)|generation of precursor metabolites and energy (GO:0006091)|glucose metabolic process (GO:0006006)|glycogen biosynthetic process (GO:0005978)|glycogen metabolic process (GO:0005977)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)	1,4-alpha-glucan branching enzyme activity (GO:0003844)|cation binding (GO:0043169)|hydrolase activity, hydrolyzing O-glycosyl compounds (GO:0004553)	p.S111L(1)		breast(1)|endometrium(5)|large_intestine(2)|lung(4)|ovary(3)|prostate(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	18		Lung NSC(201;0.0117)		UCEC - Uterine corpus endometrioid carcinoma (27;0.0654)|Epithelial(33;0.00305)|LUSC - Lung squamous cell carcinoma(29;0.00646)|BRCA - Breast invasive adenocarcinoma(55;0.00813)|Lung(72;0.0129)|KIRC - Kidney renal clear cell carcinoma(39;0.212)|Kidney(39;0.247)		GTATGGGTACGAAAATGGATT	0.338									Glycogen Storage Disease, type IV																												p.S111L		Atlas-SNP	.											GBE1_ENST00000429644,colon,carcinoma,0,1	GBE1	111	1	1	Substitution - Missense(1)	large_intestine(1)	c.C332T						PASS	.						64.0	60.0	61.0					3																	81720086		1816	4085	5901	SO:0001583	missense	2632	exon3	Familial Cancer Database	Andersen Disease, Brancher deficiency	GGGTACGAAAATG		CCDS54612.1	3p12.2	2013-09-20	2008-08-01		ENSG00000114480	ENSG00000114480	2.4.1.18		4180	protein-coding gene	gene with protein product	"""glycogen branching enzyme"", ""Andersen disease"", ""glycogen storage disease type IV"""	607839				8463281	Standard	NM_000158		Approved		uc021xav.1	Q04446	OTTHUMG00000158978	ENST00000429644.2:c.332C>T	3.37:g.81720086G>A	ENSP00000410833:p.Ser111Leu	95.0	0.0	0		104.0	35.0	0.336538	NM_000158	B3KWV3|Q96EN0	Missense_Mutation	SNP	ENST00000429644.2	37	CCDS54612.1	.	.	.	.	.	.	.	.	.	.	G	19.31	3.802766	0.70682	.	.	ENSG00000114480	ENST00000429644;ENST00000264326;ENST00000489715	T;T	0.18657	2.2;2.21	5.5	3.72	0.42706	Immunoglobulin E-set (1);Glycoside hydrolase, family 13, N-terminal (1);Immunoglobulin-like fold (1);	0.000000	0.85682	D	0.000000	T	0.30386	0.0763	L	0.57536	1.79	0.38321	D	0.943534	P;D	0.54207	0.888;0.965	B;P	0.51055	0.3;0.657	T	0.14309	-1.0477	10	0.66056	D	0.02	-3.5779	11.1977	0.48722	0.1509:0.0:0.8491:0.0	.	70;111	E9PGM4;Q04446	.;GLGB_HUMAN	L	111;162;70	ENSP00000410833:S111L;ENSP00000419638:S70L	ENSP00000264326:S162L	S	-	2	0	GBE1	81802776	1.000000	0.71417	0.699000	0.30290	0.813000	0.45954	5.642000	0.67888	0.694000	0.31654	0.650000	0.86243	TCG	.	.	none		0.338	GBE1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000352760.2		
SRCAP	10847	hgsc.bcm.edu	37	16	30732558	30732558	+	Missense_Mutation	SNP	C	C	A	rs149248373	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr16:30732558C>A	ENST00000262518.4	+	21	3687	c.3302C>A	c.(3301-3303)aCg>aAg	p.T1101K	SRCAP_ENST00000395059.2_Missense_Mutation_p.T1101K|SRCAP_ENST00000344771.4_Intron	NM_006662.2	NP_006653.2	Q6ZRS2	SRCAP_HUMAN	Snf2-related CREBBP activator protein	1101	Pro-rich.				histone acetylation (GO:0016573)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription, DNA-templated (GO:0006351)|viral process (GO:0016032)	Golgi apparatus (GO:0005794)|nucleus (GO:0005634)|protein complex (GO:0043234)	ATP binding (GO:0005524)|DNA binding (GO:0003677)|helicase activity (GO:0004386)|histone acetyltransferase activity (GO:0004402)|transcription coactivator activity (GO:0003713)			NS(1)|breast(3)|cervix(3)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(8)|large_intestine(22)|liver(3)|lung(62)|ovary(6)|pancreas(1)|prostate(4)|skin(5)|upper_aerodigestive_tract(3)|urinary_tract(5)	136			Colorectal(24;0.198)			CGGCCTCCCACGCCAACCTTG	0.602													C|||	9	0.00179712	0.0	0.0014	5008	,	,		17448	0.0		0.006	False		,,,				2504	0.002				p.T1101K		Atlas-SNP	.											.	SRCAP	298	.	0			c.C3302A						PASS	.	C	LYS/THR	5,4389	9.9+/-24.2	0,5,2192	109.0	118.0	115.0		3302	4.4	0.9	16	dbSNP_134	115	75,8525	44.0+/-102.2	0,75,4225	yes	missense	SRCAP	NM_006662.2	78	0,80,6417	AA,AC,CC		0.8721,0.1138,0.6157	possibly-damaging	1101/3231	30732558	80,12914	2197	4300	6497	SO:0001583	missense	10847	exon21			CTCCCACGCCAAC	AB002307	CCDS10689.2	16p11.2	2009-08-06			ENSG00000080603	ENSG00000080603			16974	protein-coding gene	gene with protein product	"""Swi2/Snf2-related ATPase homolog (S. cerevisiae)"", ""domino homolog 1 (Drosophila)"""	611421				10347196, 9205841	Standard	NM_006662		Approved	KIAA0309, EAF1, SWR1, DOMO1	uc002dze.1	Q6ZRS2	OTTHUMG00000132393	ENST00000262518.4:c.3302C>A	16.37:g.30732558C>A	ENSP00000262518:p.Thr1101Lys	124.0	0.0	0		127.0	60.0	0.472441	NM_006662	B0JZA6|O15026|Q7Z744|Q9Y5L9	Missense_Mutation	SNP	ENST00000262518.4	37	CCDS10689.2	4	0.0018315018315018315	0	0.0	0	0.0	0	0.0	4	0.005277044854881266	C	11.98	1.799401	0.31869	0.001138	0.008721	ENSG00000080603	ENST00000262518;ENST00000395059	D;D	0.91351	-2.83;-2.72	5.36	4.41	0.53225	.	.	.	.	.	T	0.75759	0.3893	N	0.14661	0.345	0.80722	D	1	P;P	0.38020	0.615;0.481	B;B	0.38954	0.286;0.149	T	0.74940	-0.3493	9	0.28530	T	0.3	-1.5386	7.321	0.26528	0.0:0.7419:0.17:0.0881	.	1101;1101	Q6ZRS2-2;Q6ZRS2	.;SRCAP_HUMAN	K	1101	ENSP00000262518:T1101K;ENSP00000378499:T1101K	ENSP00000262518:T1101K	T	+	2	0	SRCAP	30640059	0.102000	0.21896	0.924000	0.36721	0.955000	0.61496	1.191000	0.32138	1.499000	0.48617	0.557000	0.71058	ACG	C|0.996;A|0.004	0.004	strong		0.602	SRCAP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255523.1	NM_006662	
ELP2	55250	hgsc.bcm.edu	37	18	33709898	33709898	+	Start_Codon_SNP	SNP	T	T	A	rs370904237		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr18:33709898T>A	ENST00000358232.6	+	1	65	c.2T>A	c.(1-3)aTg>aAg	p.M1K	SLC39A6_ENST00000269187.5_5'Flank|ELP2_ENST00000423854.2_Start_Codon_SNP_p.M1K|SLC39A6_ENST00000590986.1_5'Flank|ELP2_ENST00000542824.1_Start_Codon_SNP_p.M1K|ELP2_ENST00000351393.6_Start_Codon_SNP_p.M1K|ELP2_ENST00000350494.6_Start_Codon_SNP_p.M1K|SLC39A6_ENST00000440549.2_5'Flank|ELP2_ENST00000442325.2_Start_Codon_SNP_p.M1K	NM_018255.2	NP_060725.1	Q6IA86	ELP2_HUMAN	elongator acetyltransferase complex subunit 2	1					chromatin organization (GO:0006325)|regulation of JAK-STAT cascade (GO:0046425)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription elongation from RNA polymerase II promoter (GO:0006368)	cytoplasm (GO:0005737)|DNA-directed RNA polymerase II, holoenzyme (GO:0016591)|Elongator holoenzyme complex (GO:0033588)|nucleolus (GO:0005730)|transcription elongation factor complex (GO:0008023)				NS(1)|breast(4)|kidney(2)|large_intestine(8)|lung(10)|ovary(1)|skin(2)|urinary_tract(2)	30						GTTGGCGACATGGTGGCACCC	0.607																																					p.M1K		Atlas-SNP	.											.	ELP2	70	.	0			c.T2A						PASS	.						75.0	68.0	71.0					18																	33709898		2203	4300	6503	SO:0001582	initiator_codon_variant	55250	exon1			GCGACATGGTGGC	AK001741	CCDS11918.1, CCDS56065.1, CCDS56066.1, CCDS56067.1, CCDS56068.1, CCDS56069.1	18q12.1	2013-01-10	2012-08-08	2007-04-20	ENSG00000134759	ENSG00000134759		"""Elongator acetyltransferase complex subunits"", ""WD repeat domain containing"""	18248	protein-coding gene	gene with protein product			"""signal transducer and activator of transcription 3 interacting protein 1"", ""elongation protein 2 homolog (S. cerevisiae)"""	STATIP1		11714725, 10954736	Standard	NM_001242875		Approved	FLJ10879, StIP	uc002kzk.2	Q6IA86	OTTHUMG00000132589	ENST00000358232.6:c.2T>A	18.37:g.33709898T>A	ENSP00000350967:p.Met1Lys	125.0	0.0	0		93.0	39.0	0.419355	NM_001242879	A8KAI6|B4DTG0|B4DXP0|E7EP23|E9PCX0|Q53GZ0|Q687Y8|Q8N5C2|Q96GV4|Q96PI7|Q9H9N0|Q9NV81	Missense_Mutation	SNP	ENST00000358232.6	37	CCDS11918.1	.	.	.	.	.	.	.	.	.	.	T	20.6	4.022524	0.75275	.	.	ENSG00000134759	ENST00000358232;ENST00000351393;ENST00000442325;ENST00000423854;ENST00000350494;ENST00000542824	T;T;T;T;T;T	0.60299	0.2;0.36;0.67;0.84;0.43;0.35	5.61	5.61	0.85477	.	0.038317	0.85682	D	0.000000	T	0.75228	0.3821	.	.	.	0.80722	D	1	D;D;D;D;D;D	0.89917	1.0;1.0;0.992;1.0;1.0;1.0	D;D;D;D;D;D	0.87578	0.996;0.996;0.972;0.997;0.998;0.996	T	0.78620	-0.2133	9	0.87932	D	0	-22.5353	12.1884	0.54254	0.0:0.0:0.0:1.0	.	1;1;1;1;1;1	B4DTG0;E7EP23;E9PCX0;Q6IA86-2;Q6IA86-3;Q6IA86	.;.;.;.;.;ELP2_HUMAN	K	1	ENSP00000350967:M1K;ENSP00000257191:M1K;ENSP00000414851:M1K;ENSP00000391202:M1K;ENSP00000316051:M1K;ENSP00000443800:M1K	ENSP00000316051:M1K	M	+	2	0	ELP2	31963896	1.000000	0.71417	0.998000	0.56505	0.466000	0.32739	3.835000	0.55805	2.136000	0.66102	0.477000	0.44152	ATG	.	.	alt		0.607	ELP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255800.2	NM_018255	Missense_Mutation
CEP41	95681	hgsc.bcm.edu	37	7	130051013	130051013	+	Missense_Mutation	SNP	A	A	G			TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr7:130051013A>G	ENST00000223208.5	-	5	497	c.227T>C	c.(226-228)cTc>cCc	p.L76P	CEP41_ENST00000541543.1_Missense_Mutation_p.L60P|CEP41_ENST00000343969.5_Missense_Mutation_p.L76P	NM_001257158.1|NM_018718.2	NP_001244087.1|NP_061188.1	Q9BYV8	CEP41_HUMAN	centrosomal protein 41kDa	76					cilium assembly (GO:0042384)|G2/M transition of mitotic cell cycle (GO:0000086)|mitotic cell cycle (GO:0000278)|protein polyglutamylation (GO:0018095)|protein transport (GO:0015031)	centriole (GO:0005814)|centrosome (GO:0005813)|ciliary basal body (GO:0036064)|cytosol (GO:0005829)|membrane (GO:0016020)|primary cilium (GO:0072372)											TTGATCAGAGAGGGAAGCAAC	0.403																																					p.L76P		Atlas-SNP	.											TSGA14,NS,carcinoma,+1,1	.	.	1	0			c.T227C						PASS	.						167.0	153.0	157.0					7																	130051013		2203	4300	6503	SO:0001583	missense	95681	exon5			TCAGAGAGGGAAG	AJ278890	CCDS5821.1, CCDS59078.1, CCDS59079.1, CCDS59080.1	7q32	2014-02-20	2011-10-04	2011-10-04	ENSG00000106477	ENSG00000106477			12370	protein-coding gene	gene with protein product		610523	"""testis specific, 14"""	TSGA14		14654843, 22246503	Standard	NM_018718		Approved	DKFZp762H1311, FLJ22445, JBTS15	uc003vpz.4	Q9BYV8	OTTHUMG00000157823	ENST00000223208.5:c.227T>C	7.37:g.130051013A>G	ENSP00000223208:p.Leu76Pro	128.0	0.0	0		71.0	54.0	0.760563	NM_018718	A4D1M0|B4DQ35|F5H0V6|Q7Z496|Q86TM1|Q8NFU8|Q9H6A3|Q9NPV3	Missense_Mutation	SNP	ENST00000223208.5	37	CCDS5821.1	.	.	.	.	.	.	.	.	.	.	A	22.9	4.350277	0.82132	.	.	ENSG00000106477	ENST00000223208;ENST00000541543;ENST00000343969;ENST00000492389;ENST00000472739;ENST00000477003;ENST00000475282;ENST00000469826	D;D;D;D;D;D;D;D	0.90620	-2.7;-2.33;-2.66;-2.35;-2.34;-2.36;-1.84;-1.5	5.93	5.93	0.95920	Rhodanese-like (1);	0.242522	0.36409	N	0.002614	D	0.94371	0.8190	M	0.67953	2.075	0.80722	D	1	D;D;D	0.76494	0.999;0.997;0.997	D;D;D	0.71656	0.974;0.916;0.909	D	0.94745	0.7922	10	0.72032	D	0.01	-10.3632	15.1976	0.73104	1.0:0.0:0.0:0.0	.	60;76;76	F5H0V6;Q9BYV8-2;Q9BYV8	.;.;CEP41_HUMAN	P	76;60;76;41;41;73;41;63	ENSP00000223208:L76P;ENSP00000445888:L60P;ENSP00000342738:L76P;ENSP00000419192:L41P;ENSP00000417593:L41P;ENSP00000420670:L73P;ENSP00000418363:L41P;ENSP00000418712:L63P	ENSP00000223208:L76P	L	-	2	0	TSGA14	129838249	1.000000	0.71417	1.000000	0.80357	0.989000	0.77384	5.635000	0.67841	2.273000	0.75805	0.482000	0.46254	CTC	.	.	none		0.403	CEP41-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000349702.2	NM_018718	
LRRC4B	94030	hgsc.bcm.edu	37	19	51051935	51051935	+	Missense_Mutation	SNP	G	G	A			TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr19:51051935G>A	ENST00000599957.1	-	2	358	c.161C>T	c.(160-162)gCc>gTc	p.A54V	LRRC4B_ENST00000389201.3_Missense_Mutation_p.A54V			Q9NT99	LRC4B_HUMAN	leucine rich repeat containing 4B	54	LRRNT.				positive regulation of synapse assembly (GO:0051965)	cell junction (GO:0030054)|cerebellar mossy fiber (GO:0044300)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|synapse (GO:0045202)				breast(1)|central_nervous_system(1)|endometrium(4)|large_intestine(6)|liver(1)|lung(11)|prostate(4)|skin(1)|urinary_tract(1)	30		all_neural(266;0.131)		OV - Ovarian serous cystadenocarcinoma(262;0.00284)|GBM - Glioblastoma multiforme(134;0.0188)		GCAGGAGGTGGCCGGCGGGGA	0.716																																					p.A54V		Atlas-SNP	.											.	LRRC4B	89	.	0			c.C161T						PASS	.						5.0	7.0	6.0					19																	51051935		1891	4047	5938	SO:0001583	missense	94030	exon2			GAGGTGGCCGGCG	BC032460	CCDS42595.1	19q13.33	2014-01-30	2004-06-14	2004-06-16	ENSG00000131409	ENSG00000131409		"""Immunoglobulin superfamily / I-set domain containing"", ""Endogenous ligands"""	25042	protein-coding gene	gene with protein product	"""netrin-G3 ligand"""		"""leucine-rich repeats and immunoglobulin-like domains 4"""	LRIG4		11441184	Standard	NM_001080457		Approved	DKFZp761A179, HSM	uc002pss.3	Q9NT99		ENST00000599957.1:c.161C>T	19.37:g.51051935G>A	ENSP00000471502:p.Ala54Val	38.0	0.0	0		33.0	19.0	0.575758	NM_001080457	Q3ZCQ4|Q58F20	Missense_Mutation	SNP	ENST00000599957.1	37	CCDS42595.1	.	.	.	.	.	.	.	.	.	.	G	18.91	3.724144	0.68959	.	.	ENSG00000131409	ENST00000389201;ENST00000535879	T	0.44083	0.93	3.66	2.57	0.30868	.	0.000000	0.56097	U	0.000023	T	0.35393	0.0930	M	0.68317	2.08	0.40088	D	0.976213	B	0.29432	0.244	B	0.18871	0.023	T	0.19224	-1.0312	10	0.33940	T	0.23	.	8.9339	0.35688	0.0:0.229:0.771:0.0	.	54	Q9NT99	LRC4B_HUMAN	V	54	ENSP00000373853:A54V	ENSP00000373853:A54V	A	-	2	0	LRRC4B	55743747	1.000000	0.71417	1.000000	0.80357	0.951000	0.60555	4.242000	0.58714	0.830000	0.34757	0.544000	0.68410	GCC	.	.	none		0.716	LRRC4B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000464907.1	NM_001080457	
DSG1	1828	hgsc.bcm.edu	37	18	28919763	28919763	+	Missense_Mutation	SNP	A	A	C			TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr18:28919763A>C	ENST00000257192.4	+	11	1674	c.1462A>C	c.(1462-1464)Aat>Cat	p.N488H		NM_001942.2	NP_001933.2	Q02413	DSG1_HUMAN	desmoglein 1	488	Cadherin 4. {ECO:0000255|PROSITE- ProRule:PRU00043}.				apoptotic process (GO:0006915)|calcium-dependent cell-cell adhesion (GO:0016339)|cell-cell junction assembly (GO:0007043)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|homophilic cell adhesion (GO:0007156)|maternal process involved in female pregnancy (GO:0060135)|protein stabilization (GO:0050821)|response to progesterone (GO:0032570)|single organismal cell-cell adhesion (GO:0016337)	apical plasma membrane (GO:0016324)|cytoplasmic side of plasma membrane (GO:0009898)|cytosol (GO:0005829)|desmosome (GO:0030057)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|lateral plasma membrane (GO:0016328)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|gamma-catenin binding (GO:0045295)|toxic substance binding (GO:0015643)			NS(2)|central_nervous_system(2)|endometrium(5)|kidney(7)|large_intestine(11)|lung(36)|ovary(3)|prostate(1)|skin(7)|stomach(1)|upper_aerodigestive_tract(1)	76			OV - Ovarian serous cystadenocarcinoma(10;0.00559)			AAGTTTTGGTAATGACGACAG	0.328																																					p.N488H		Atlas-SNP	.											DSG1,NS,carcinoma,-2,1	DSG1	176	1	0			c.A1462C						PASS	.						80.0	81.0	81.0					18																	28919763		2203	4300	6503	SO:0001583	missense	1828	exon11			TTTGGTAATGACG	X56654	CCDS11896.1	18q12.1	2014-05-13			ENSG00000134760	ENSG00000134760		"""Cadherins / Major cadherins"""	3048	protein-coding gene	gene with protein product		125670		DSG		1889810	Standard	NM_001942		Approved	CDHF4	uc002kwp.3	Q02413	OTTHUMG00000131983	ENST00000257192.4:c.1462A>C	18.37:g.28919763A>C	ENSP00000257192:p.Asn488His	166.0	0.0	0		138.0	52.0	0.376812	NM_001942	B7Z845	Missense_Mutation	SNP	ENST00000257192.4	37	CCDS11896.1	.	.	.	.	.	.	.	.	.	.	A	4.359	0.066056	0.08388	.	.	ENSG00000134760	ENST00000257192	T	0.58210	0.35	3.05	-5.83	0.02325	Cadherin (2);	3.162780	0.00531	N	0.000201	T	0.32675	0.0837	N	0.22421	0.69	0.09310	N	1	B	0.09022	0.002	B	0.08055	0.003	T	0.16689	-1.0394	10	0.72032	D	0.01	.	0.9696	0.01413	0.2735:0.1294:0.3832:0.2139	.	488	Q02413	DSG1_HUMAN	H	488	ENSP00000257192:N488H	ENSP00000257192:N488H	N	+	1	0	DSG1	27173761	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-0.215000	0.09279	-0.831000	0.04256	-0.574000	0.04147	AAT	.	.	none		0.328	DSG1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254947.1	NM_001942	
PRDM5	11107	hgsc.bcm.edu	37	4	121737704	121737704	+	Missense_Mutation	SNP	G	G	A	rs190835070		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr4:121737704G>A	ENST00000264808.3	-	7	1009	c.769C>T	c.(769-771)Cgg>Tgg	p.R257W	PRDM5_ENST00000515109.1_Missense_Mutation_p.R226W|PRDM5_ENST00000428209.2_Missense_Mutation_p.R226W	NM_018699.2	NP_061169.2	Q9NQX1	PRDM5_HUMAN	PR domain containing 5	257					histone deacetylation (GO:0016575)|histone H3-K9 methylation (GO:0051567)|mitotic cell cycle (GO:0000278)|negative regulation of transcription, DNA-templated (GO:0045892)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	metal ion binding (GO:0046872)|methyltransferase activity (GO:0008168)|repressing transcription factor binding (GO:0070491)|sequence-specific DNA binding (GO:0043565)|transcription regulatory region DNA binding (GO:0044212)|transcription regulatory region sequence-specific DNA binding (GO:0000976)			central_nervous_system(1)|endometrium(3)|kidney(2)|large_intestine(5)|lung(17)|pancreas(1)|prostate(1)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	34						GCATCCCCCCGGCAAGTCTCC	0.493													G|||	1	0.000199681	0.0	0.0	5008	,	,		18108	0.0		0.001	False		,,,				2504	0.0				p.R257W		Atlas-SNP	.											PRDM5,NS,carcinoma,+1,1	PRDM5	76	1	0			c.C769T						scavenged	.	G	TRP/ARG	0,4406		0,0,2203	55.0	51.0	52.0		769	4.2	0.9	4		52	2,8598	2.2+/-6.3	0,2,4298	no	missense	PRDM5	NM_018699.2	101	0,2,6501	AA,AG,GG		0.0233,0.0,0.0154	probably-damaging	257/631	121737704	2,13004	2203	4300	6503	SO:0001583	missense	11107	exon7			CCCCCCGGCAAGT	AF272897	CCDS3716.1, CCDS75187.1, CCDS75188.1	4q25-q26	2013-01-08			ENSG00000138738	ENSG00000138738		"""Zinc fingers, C2H2-type"""	9349	protein-coding gene	gene with protein product		614161					Standard	XM_005262706		Approved	PFM2	uc003idn.3	Q9NQX1	OTTHUMG00000132970	ENST00000264808.3:c.769C>T	4.37:g.121737704G>A	ENSP00000264808:p.Arg257Trp	99.0	1.0	0.010101		78.0	24.0	0.307692	NM_018699	Q0VAI9|Q0VAJ0|Q6NXQ7	Missense_Mutation	SNP	ENST00000264808.3	37	CCDS3716.1	1	4.578754578754579E-4	0	0.0	0	0.0	0	0.0	1	0.0013192612137203166	G	23.5	4.419624	0.83559	0.0	2.33E-4	ENSG00000138738	ENST00000264808;ENST00000515109;ENST00000428209	T;T;T	0.15372	2.43;2.43;2.43	6.07	4.24	0.50183	Zinc finger, C2H2 (1);Zinc finger, C2H2-type/integrase, DNA-binding (1);	0.270689	0.41396	D	0.000900	T	0.29321	0.0730	L	0.48362	1.52	0.80722	D	1	D;D;D	0.76494	0.978;0.999;0.978	B;P;B	0.56916	0.425;0.809;0.306	T	0.04635	-1.0937	10	0.87932	D	0	-1.8067	14.4681	0.67497	0.0:0.0:0.5912:0.4088	.	226;226;257	Q0VAI9;Q9NQX1-2;Q9NQX1	.;.;PRDM5_HUMAN	W	257;226;226	ENSP00000264808:R257W;ENSP00000422309:R226W;ENSP00000404832:R226W	ENSP00000264808:R257W	R	-	1	2	PRDM5	121957154	1.000000	0.71417	0.861000	0.33841	0.998000	0.95712	3.119000	0.50422	1.546000	0.49388	0.655000	0.94253	CGG	G|1.000;A|0.000	0.000	strong		0.493	PRDM5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256528.2		
PKHD1L1	93035	hgsc.bcm.edu	37	8	110447512	110447512	+	Missense_Mutation	SNP	G	G	C	rs142972518	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	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	209.0	0.0	0		251.0	97.0	0.386454	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	
NLRP10	338322	hgsc.bcm.edu	37	11	7981822	7981822	+	Missense_Mutation	SNP	A	A	G	rs143403695	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr11:7981822A>G	ENST00000328600.2	-	2	1498	c.1337T>C	c.(1336-1338)tTc>tCc	p.F446S		NM_176821.3	NP_789791.1	Q86W26	NAL10_HUMAN	NLR family, pyrin domain containing 10	446	NACHT. {ECO:0000255|PROSITE- ProRule:PRU00136}.				defense response to fungus (GO:0050832)|defense response to Gram-negative bacterium (GO:0050829)|dendritic cell migration (GO:0036336)|helper T cell enhancement of adaptive immune response (GO:0035397)|innate immune response (GO:0045087)|positive regulation of interleukin-6 secretion (GO:2000778)|positive regulation of interleukin-8 secretion (GO:2000484)|positive regulation of T-helper 1 type immune response (GO:0002827)|positive regulation of T-helper 17 type immune response (GO:2000318)	cytoplasm (GO:0005737)|extrinsic component of plasma membrane (GO:0019897)	ATP binding (GO:0005524)			breast(1)|endometrium(2)|kidney(2)|large_intestine(8)|liver(1)|lung(28)|ovary(2)|pancreas(1)|prostate(2)|skin(8)|upper_aerodigestive_tract(1)|urinary_tract(2)	58				Epithelial(150;1.47e-07)|BRCA - Breast invasive adenocarcinoma(625;0.189)		ACTACTCAGGAAAGCGGCAAG	0.488																																					p.F446S		Atlas-SNP	.											.	NLRP10	146	.	0			c.T1337C						PASS	.	A	SER/PHE	1,4401		0,1,2200	99.0	109.0	106.0		1337	3.7	0.2	11	dbSNP_134	106	1,8591		0,1,4295	yes	missense	NLRP10	NM_176821.3	155	0,2,6495	GG,GA,AA		0.0116,0.0227,0.0154	possibly-damaging	446/656	7981822	2,12992	2201	4296	6497	SO:0001583	missense	338322	exon2			CTCAGGAAAGCGG	AY154465	CCDS7784.1	11p15.4	2006-12-08	2006-12-08	2006-12-08		ENSG00000182261		"""Nucleotide-binding domain and leucine rich repeat containing"""	21464	protein-coding gene	gene with protein product	"""nucleotide-binding oligomerization domain, leucine rich repeat and pyrin domain containing 10"""	609662	"""NACHT, leucine rich repeat and PYD containing 10"""	NALP10		12563287	Standard	NM_176821		Approved	NOD8, PAN5, Pynod, CLR11.1	uc001mfv.1	Q86W26		ENST00000328600.2:c.1337T>C	11.37:g.7981822A>G	ENSP00000327763:p.Phe446Ser	63.0	0.0	0		53.0	34.0	0.641509	NM_176821	Q2M3C4|Q6JGT0	Missense_Mutation	SNP	ENST00000328600.2	37	CCDS7784.1	.	.	.	.	.	.	.	.	.	.	A	10.78	1.446070	0.25987	2.27E-4	1.16E-4	ENSG00000182261	ENST00000328600	D	0.87103	-2.21	4.86	3.73	0.42828	.	0.000000	0.42548	D	0.000691	D	0.92205	0.7528	M	0.83012	2.62	0.09310	N	1	D	0.76494	0.999	D	0.75484	0.986	D	0.84554	0.0646	10	0.87932	D	0	.	7.3185	0.26513	0.8987:0.0:0.1013:0.0	.	446	Q86W26	NAL10_HUMAN	S	446	ENSP00000327763:F446S	ENSP00000327763:F446S	F	-	2	0	NLRP10	7938398	0.997000	0.39634	0.178000	0.23040	0.011000	0.07611	6.425000	0.73370	0.828000	0.34709	0.533000	0.62120	TTC	A|0.999;G|0.001	0.001	strong		0.488	NLRP10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000385705.1	NM_176821	
HTR2A	3356	hgsc.bcm.edu	37	13	47469939	47469939	+	Missense_Mutation	SNP	C	C	T			TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr13:47469939C>T	ENST00000378688.4	-	1	234	c.103G>A	c.(103-105)Gga>Aga	p.G35R	HTR2A_ENST00000542664.1_Missense_Mutation_p.G35R|HTR2A_ENST00000543956.1_Intron			P28223	5HT2A_HUMAN	5-hydroxytryptamine (serotonin) receptor 2A, G protein-coupled	35					activation of phospholipase C activity (GO:0007202)|aging (GO:0007568)|artery smooth muscle contraction (GO:0014824)|behavioral response to cocaine (GO:0048148)|cell death (GO:0008219)|cellular calcium ion homeostasis (GO:0006874)|detection of mechanical stimulus involved in sensory perception of pain (GO:0050966)|detection of temperature stimulus involved in sensory perception of pain (GO:0050965)|memory (GO:0007613)|negative regulation of potassium ion transport (GO:0043267)|negative regulation of synaptic transmission, glutamatergic (GO:0051967)|phosphatidylinositol 3-kinase signaling (GO:0014065)|phospholipase C-activating serotonin receptor signaling pathway (GO:0007208)|positive regulation of cell proliferation (GO:0008284)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of glycolytic process (GO:0045821)|positive regulation of MAP kinase activity (GO:0043406)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|positive regulation of phosphatidylinositol biosynthetic process (GO:0010513)|positive regulation of vasoconstriction (GO:0045907)|protein localization to cytoskeleton (GO:0044380)|regulation of behavior (GO:0050795)|regulation of dopamine secretion (GO:0014059)|regulation of hormone secretion (GO:0046883)|release of sequestered calcium ion into cytosol (GO:0051209)|response to drug (GO:0042493)|serotonin receptor signaling pathway (GO:0007210)|sleep (GO:0030431)|synaptic transmission (GO:0007268)|temperature homeostasis (GO:0001659)|urinary bladder smooth muscle contraction (GO:0014832)	cell body fiber (GO:0070852)|cytoplasmic vesicle (GO:0031410)|cytosol (GO:0005829)|dendritic shaft (GO:0043198)|integral component of plasma membrane (GO:0005887)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)	1-(4-iodo-2,5-dimethoxyphenyl)propan-2-amine binding (GO:0071886)|drug binding (GO:0008144)|serotonin binding (GO:0051378)|serotonin receptor activity (GO:0004993)			breast(1)|central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(6)|liver(1)|lung(10)|ovary(4)|prostate(1)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	36		all_lung(13;7.2e-10)|Lung NSC(96;3.77e-07)|Breast(56;2.06e-05)|Prostate(109;0.00116)|Hepatocellular(98;0.0207)|Lung SC(185;0.0262)|Myeloproliferative disorder(33;0.0333)		GBM - Glioblastoma multiforme(144;4.67e-05)|COAD - Colon adenocarcinoma(199;0.224)	Acepromazine(DB01614)|Amisulpride(DB06288)|Amitriptyline(DB00321)|Amoxapine(DB00543)|Apomorphine(DB00714)|Aripiprazole(DB01238)|Asenapine(DB06216)|Bromocriptine(DB01200)|Cabergoline(DB00248)|Chlorpromazine(DB00477)|Chlorprothixene(DB01239)|Cinitapride(DB08810)|Cisapride(DB00604)|Clomipramine(DB01242)|Clozapine(DB00363)|Cyclobenzaprine(DB00924)|Cyproheptadine(DB00434)|Desipramine(DB01151)|Donepezil(DB00843)|Doxepin(DB01142)|Epinastine(DB00751)|Ergoloid mesylate(DB01049)|Ergotamine(DB00696)|Flupentixol(DB00875)|Fluspirilene(DB04842)|Haloperidol(DB00502)|Iloperidone(DB04946)|Imipramine(DB00458)|Ketamine(DB01221)|Lisuride(DB00589)|Loxapine(DB00408)|Lurasidone(DB08815)|Maprotiline(DB00934)|Mesoridazine(DB00933)|Methotrimeprazine(DB01403)|Methysergide(DB00247)|Mianserin(DB06148)|Minaprine(DB00805)|Mirtazapine(DB00370)|Molindone(DB01618)|Nefazodone(DB01149)|Nortriptyline(DB00540)|Olanzapine(DB00334)|Paliperidone(DB01267)|Paroxetine(DB00715)|Pergolide(DB01186)|Pipotiazine(DB01621)|Pramipexole(DB00413)|Promazine(DB00420)|Promethazine(DB01069)|Propiomazine(DB00777)|Quetiapine(DB01224)|Remoxipride(DB00409)|Risperidone(DB00734)|Ropinirole(DB00268)|Sertindole(DB06144)|Thioproperazine(DB01622)|Thioridazine(DB00679)|Thiothixene(DB01623)|Trazodone(DB00656)|Trimipramine(DB00726)|Yohimbine(DB01392)|Ziprasidone(DB00246)	TTAGCTTCTCCGGAGTTAAAG	0.428																																					p.G35R		Atlas-SNP	.											.	HTR2A	98	.	0			c.G103A						PASS	.						102.0	100.0	101.0					13																	47469939		2203	4300	6503	SO:0001583	missense	3356	exon2			CTTCTCCGGAGTT	X57830	CCDS9405.1, CCDS53867.1	13q14-q21	2012-08-08	2012-02-03		ENSG00000102468	ENSG00000102468		"""5-HT (serotonin) receptors"", ""GPCR / Class A : 5-HT (serotonin) receptors, GPCR only"""	5293	protein-coding gene	gene with protein product		182135	"""5-hydroxytryptamine (serotonin) receptor 2A"""	HTR2		8035173	Standard	NM_000621		Approved	5-HT2A	uc010acr.4	P28223	OTTHUMG00000016881	ENST00000378688.4:c.103G>A	13.37:g.47469939C>T	ENSP00000367959:p.Gly35Arg	84.0	0.0	0		81.0	42.0	0.518519	NM_000621	B2RAC5|B4DZ79|F5GWE8|Q5T8C0	Missense_Mutation	SNP	ENST00000378688.4	37	CCDS9405.1	.	.	.	.	.	.	.	.	.	.	C	1.837	-0.468315	0.04445	.	.	ENSG00000102468	ENST00000378688;ENST00000542664	T;T	0.54866	0.55;0.55	5.49	1.83	0.25207	.	0.180503	0.39407	N	0.001371	T	0.29588	0.0738	N	0.17082	0.46	0.23309	N	0.997934	B	0.15473	0.013	B	0.08055	0.003	T	0.18272	-1.0342	10	0.13853	T	0.58	.	8.1078	0.30896	0.0:0.6054:0.0:0.3946	.	35	P28223	5HT2A_HUMAN	R	35	ENSP00000367959:G35R;ENSP00000437737:G35R	ENSP00000367959:G35R	G	-	1	0	HTR2A	46367940	0.018000	0.18449	0.035000	0.18076	0.996000	0.88848	0.190000	0.17057	0.028000	0.15324	0.585000	0.79938	GGA	.	.	none		0.428	HTR2A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044835.3	NM_000621	
LY75	4065	hgsc.bcm.edu	37	2	160697271	160697271	+	Missense_Mutation	SNP	G	G	A	rs147904044	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr2:160697271G>A	ENST00000263636.4	-	25	3503	c.3476C>T	c.(3475-3477)tCt>tTt	p.S1159F	LY75-CD302_ENST00000504764.1_Missense_Mutation_p.S1159F|LY75_ENST00000553424.1_Missense_Mutation_p.S1159F|LY75-CD302_ENST00000505052.1_Missense_Mutation_p.S1159F|LY75_ENST00000554112.1_Missense_Mutation_p.S1159F	NM_002349.3	NP_002340.2	O60449	LY75_HUMAN	lymphocyte antigen 75	1159	C-type lectin 7. {ECO:0000255|PROSITE- ProRule:PRU00040}.				endocytosis (GO:0006897)|immune response (GO:0006955)|inflammatory response (GO:0006954)	extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)	carbohydrate binding (GO:0030246)|receptor activity (GO:0004872)			NS(2)|central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(9)|lung(22)|prostate(7)|skin(6)|stomach(3)|upper_aerodigestive_tract(3)|urinary_tract(1)	59				COAD - Colon adenocarcinoma(177;0.132)		CCATAAGGAAGAGTTGTGAAG	0.483													G|||	6	0.00119808	0.0	0.0043	5008	,	,		18429	0.0		0.003	False		,,,				2504	0.0				p.S1159F		Atlas-SNP	.											.	LY75	151	.	0			c.C3476T						PASS	.	G	PHE/SER,PHE/SER,PHE/SER	8,4398	14.3+/-33.2	0,8,2195	150.0	143.0	145.0		3476,3476,3476	3.5	0.0	2	dbSNP_134	145	45,8555	27.9+/-77.7	0,45,4255	yes	missense,missense,missense	LY75,LY75-CD302	NM_001198759.1,NM_001198760.1,NM_002349.3	155,155,155	0,53,6450	AA,AG,GG		0.5233,0.1816,0.4075	benign,benign,benign	1159/1874,1159/1818,1159/1723	160697271	53,12953	2203	4300	6503	SO:0001583	missense	4065	exon25			AAGGAAGAGTTGT	AF011333	CCDS2211.1	2q24	2011-08-30			ENSG00000054219	ENSG00000054219		"""CD molecules"", ""C-type lectin domain containing"""	6729	protein-coding gene	gene with protein product		604524				9553150	Standard	NM_002349		Approved	DEC-205, CLEC13B, CD205		O60449	OTTHUMG00000132025	ENST00000263636.4:c.3476C>T	2.37:g.160697271G>A	ENSP00000263636:p.Ser1159Phe	125.0	0.0	0		132.0	61.0	0.462121	NM_002349	O75913|Q53R46|Q53TF5|Q7Z575|Q7Z577	Missense_Mutation	SNP	ENST00000263636.4	37	CCDS2211.1	5	0.0022893772893772895	0	0.0	4	0.011049723756906077	0	0.0	1	0.0013192612137203166	G	8.582	0.882464	0.17467	0.001816	0.005233	ENSG00000054219;ENSG00000054219;ENSG00000054219;ENSG00000248672;ENSG00000248672	ENST00000554112;ENST00000553424;ENST00000263636;ENST00000504764;ENST00000505052	T;T;T;T;T	0.19250	2.16;2.16;2.16;2.16;2.16	5.35	3.48	0.39840	C-type lectin fold (1);C-type lectin-like (1);C-type lectin (3);	.	.	.	.	T	0.24392	0.0591	L	0.50919	1.6	0.18873	N	0.999983	P;P;D	0.57571	0.899;0.952;0.98	P;P;P	0.56700	0.509;0.642;0.804	T	0.05194	-1.0900	9	0.44086	T	0.13	-0.8422	10.0198	0.42035	0.0:0.1485:0.6974:0.1541	.	1159;1159;1159	O60449-3;O60449;O60449-2	.;LY75_HUMAN;.	F	1159	ENSP00000451511:S1159F;ENSP00000451446:S1159F;ENSP00000263636:S1159F;ENSP00000423463:S1159F;ENSP00000421035:S1159F	ENSP00000423463:S1159F	S	-	2	0	LY75;LY75-CD302	160405517	0.933000	0.31639	0.011000	0.14972	0.281000	0.26958	1.035000	0.30216	0.570000	0.29347	0.655000	0.94253	TCT	G|0.996;A|0.004	0.004	strong		0.483	LY75-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000255035.1		
RREB1	6239	hgsc.bcm.edu	37	6	7189437	7189437	+	Missense_Mutation	SNP	G	G	A	rs201588284		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr6:7189437G>A	ENST00000349384.6	+	6	621	c.307G>A	c.(307-309)Gga>Aga	p.G103R	RREB1_ENST00000379933.3_Missense_Mutation_p.G103R|RREB1_ENST00000379938.2_Missense_Mutation_p.G103R|Y_RNA_ENST00000364613.1_RNA|RREB1_ENST00000334984.6_Missense_Mutation_p.G103R	NM_001003698.3	NP_001003698.1	Q92766	RREB1_HUMAN	ras responsive element binding protein 1	103					multicellular organismal development (GO:0007275)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of transcription, DNA-templated (GO:0045893)|Ras protein signal transduction (GO:0007265)|regulation of transcription, DNA-templated (GO:0006355)|transcription from RNA polymerase II promoter (GO:0006366)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|nuclear body (GO:0016604)|nucleolus (GO:0005730)|nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(3)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(5)|lung(18)|ovary(5)|pancreas(2)|prostate(3)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	58	Ovarian(93;0.0398)	all_hematologic(90;0.0384)|Prostate(151;0.191)				CAGCATCTGCGGAAAGTCACT	0.557													G|||	1	0.000199681	0.0	0.0	5008	,	,		18775	0.001		0.0	False		,,,				2504	0.0				p.G103R		Atlas-SNP	.											RREB1_ENST00000379938,NS,carcinoma,-2,2	RREB1	242	2	0			c.G307A						PASS	.						67.0	53.0	57.0					6																	7189437		2203	4300	6503	SO:0001583	missense	6239	exon6			ATCTGCGGAAAGT	U26914	CCDS34335.1, CCDS34336.1, CCDS54963.1	6p25	2013-01-08			ENSG00000124782	ENSG00000124782		"""Zinc fingers, C2H2-type"""	10449	protein-coding gene	gene with protein product	"""hindsight homolog (drosophila)"""	602209				9367691, 18394891	Standard	NM_001003698		Approved	HNT	uc003mxb.3	Q92766	OTTHUMG00000014201	ENST00000349384.6:c.307G>A	6.37:g.7189437G>A	ENSP00000305560:p.Gly103Arg	40.0	0.0	0		59.0	31.0	0.525424	NM_001003700	A2RRF5|E2GM80|E2GM81|O75567|O75568|Q5VYB2|Q6BEP5|Q6BEP6|Q6BEP8|Q86SU2|Q9Y474	Missense_Mutation	SNP	ENST00000349384.6	37	CCDS34336.1	1	4.578754578754579E-4	0	0.0	0	0.0	1	0.0017482517482517483	0	0.0	G	32	5.181977	0.94885	.	.	ENSG00000124782	ENST00000379933;ENST00000491191;ENST00000379938;ENST00000471433;ENST00000349384;ENST00000334984;ENST00000483150	T;T;T;T;T;T;T	0.66460	3.19;-0.21;3.19;3.19;3.19;3.19;3.19	5.65	5.65	0.86999	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	0.000000	0.64402	D	0.000016	T	0.80177	0.4575	M	0.75447	2.3	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.97110	1.0;0.997;0.962	T	0.80759	-0.1239	10	0.62326	D	0.03	-55.3388	19.7284	0.96174	0.0:0.0:1.0:0.0	.	103;103;103	Q92766-3;Q92766;Q92766-2	.;RREB1_HUMAN;.	R	103	ENSP00000369265:G103R;ENSP00000420519:G103R;ENSP00000369270:G103R;ENSP00000420299:G103R;ENSP00000305560:G103R;ENSP00000335574:G103R;ENSP00000419511:G103R	ENSP00000335574:G103R	G	+	1	0	RREB1	7134436	1.000000	0.71417	1.000000	0.80357	0.989000	0.77384	7.304000	0.78882	2.668000	0.90789	0.591000	0.81541	GGA	G|0.999;A|0.001	0.001	strong		0.557	RREB1-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000352985.1		
ZNF622	90441	hgsc.bcm.edu	37	5	16465442	16465442	+	Silent	SNP	T	T	C			TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr5:16465442T>C	ENST00000308683.2	-	1	459	c.333A>G	c.(331-333)gaA>gaG	p.E111E		NM_033414.2	NP_219482.1	Q969S3	ZN622_HUMAN	zinc finger protein 622	111					intrinsic apoptotic signaling pathway in response to oxidative stress (GO:0008631)|positive regulation of apoptotic process (GO:0043065)|positive regulation of JNK cascade (GO:0046330)|positive regulation of kinase activity (GO:0033674)|positive regulation of MAPK cascade (GO:0043410)	cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|nucleolus (GO:0005730)	poly(A) RNA binding (GO:0044822)|zinc ion binding (GO:0008270)			endometrium(2)|kidney(1)|large_intestine(3)|lung(15)|ovary(1)|prostate(2)|urinary_tract(1)	25						CCAAGTTCTTTTCATTCATCA	0.562																																					p.E111E		Atlas-SNP	.											ZNF622,NS,carcinoma,-2,1	ZNF622	49	1	0			c.A333G						PASS	.						167.0	152.0	157.0					5																	16465442		2203	4300	6503	SO:0001819	synonymous_variant	90441	exon1			GTTCTTTTCATTC	AY046059	CCDS3886.1	5p15.1	2012-10-05			ENSG00000173545	ENSG00000173545			30958	protein-coding gene	gene with protein product		608694				11802789, 12645566	Standard	NM_033414		Approved	MGC2485, MGC17552, ZPR9	uc003jfq.3	Q969S3	OTTHUMG00000090567	ENST00000308683.2:c.333A>G	5.37:g.16465442T>C		147.0	0.0	0		143.0	66.0	0.461538	NM_033414		Silent	SNP	ENST00000308683.2	37	CCDS3886.1																																																																																			.	.	none		0.562	ZNF622-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207105.1	NM_033414	
SYNE1	23345	hgsc.bcm.edu	37	6	152712440	152712440	+	Missense_Mutation	SNP	G	G	T	rs117480635	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr6:152712440G>T	ENST00000367255.5	-	52	8577	c.7976C>A	c.(7975-7977)aCc>aAc	p.T2659N	SYNE1_ENST00000341594.5_Missense_Mutation_p.T2698N|SYNE1_ENST00000265368.4_Missense_Mutation_p.T2659N|SYNE1_ENST00000423061.1_Missense_Mutation_p.T2666N|SYNE1_ENST00000448038.1_Missense_Mutation_p.T2666N	NM_182961.3	NP_892006.3	Q8NF91	SYNE1_HUMAN	spectrin repeat containing, nuclear envelope 1	2659					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)		TTTCTCCAGGGTGTCTTTGCT	0.507										HNSCC(10;0.0054)			G|||	8	0.00159744	0.0	0.0	5008	,	,		15514	0.0		0.006	False		,,,				2504	0.002				p.T2666N		Atlas-SNP	.											.	SYNE1	3227	.	0			c.C7997A						PASS	.	G	ASN/THR,ASN/THR	4,4402	8.1+/-20.4	0,4,2199	109.0	104.0	106.0		7997,7976	5.0	0.0	6	dbSNP_132	106	30,8570	20.4+/-63.3	0,30,4270	yes	missense,missense	SYNE1	NM_033071.3,NM_182961.3	65,65	0,34,6469	TT,TG,GG		0.3488,0.0908,0.2614	possibly-damaging,possibly-damaging	2666/8750,2659/8798	152712440	34,12972	2203	4300	6503	SO:0001583	missense	23345	exon52			TCCAGGGTGTCTT	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.7976C>A	6.37:g.152712440G>T	ENSP00000356224:p.Thr2659Asn	104.0	0.0	0		117.0	55.0	0.470085	NM_033071	E7EQI5|O94890|Q5JV19|Q5JV22|Q8N9P7|Q8TCP1|Q8WWW6|Q8WWW7|Q8WXF6|Q96N17|Q9C0A7|Q9H525|Q9H526|Q9NS36|Q9NU50|Q9UJ06|Q9UJ07|Q9ULF8	Missense_Mutation	SNP	ENST00000367255.5	37	CCDS5236.2	4	0.0018315018315018315	0	0.0	0	0.0	0	0.0	4	0.005277044854881266	G	9.754	1.168155	0.21621	9.08E-4	0.003488	ENSG00000131018	ENST00000367255;ENST00000423061;ENST00000265368;ENST00000448038;ENST00000341594	T;T;T;T;T	0.54279	0.67;0.67;0.58;0.67;0.79	5.91	5.04	0.67666	.	0.341353	0.25419	N	0.030816	T	0.31638	0.0803	M	0.62723	1.935	0.24214	N	0.995468	P;B;B;P	0.39696	0.612;0.413;0.413;0.683	B;B;B;B	0.40602	0.203;0.179;0.179;0.334	T	0.19095	-1.0316	10	0.17832	T	0.49	.	11.5958	0.50972	0.1855:0.0:0.8145:0.0	.	2642;2659;2659;2666	B3W695;Q8NF91;E7EQI5;Q8NF91-4	.;SYNE1_HUMAN;.;.	N	2659;2666;2659;2666;2698	ENSP00000356224:T2659N;ENSP00000396024:T2666N;ENSP00000265368:T2659N;ENSP00000390975:T2666N;ENSP00000341887:T2698N	ENSP00000265368:T2659N	T	-	2	0	SYNE1	152754133	0.997000	0.39634	0.010000	0.14722	0.702000	0.40608	3.098000	0.50259	1.500000	0.48636	0.655000	0.94253	ACC	G|0.998;T|0.002	0.002	strong		0.507	SYNE1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000334755.2	NM_182961	
TMEM199	147007	hgsc.bcm.edu	37	17	26684707	26684707	+	Nonsense_Mutation	SNP	T	T	A			TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr17:26684707T>A	ENST00000292114.3	+	1	104	c.14T>A	c.(13-15)tTg>tAg	p.L5*	POLDIP2_ENST00000003607.4_5'Flank|TMEM199_ENST00000395404.3_5'Flank|CTB-96E2.3_ENST00000591482.1_RNA|TMEM199_ENST00000581386.1_3'UTR|POLDIP2_ENST00000540200.1_5'Flank|MIR4723_ENST00000585070.1_RNA|TMEM199_ENST00000509083.1_Nonsense_Mutation_p.L5*	NM_152464.1	NP_689677.1	Q8N511	TM199_HUMAN	transmembrane protein 199	5						integral component of membrane (GO:0016021)				endometrium(1)|kidney(2)|large_intestine(1)|lung(2)	6	all_lung(13;0.000354)|Lung NSC(42;0.00115)			UCEC - Uterine corpus endometrioid carcinoma (53;0.153)		GCGTCCTCTTTGCTTGCGGGC	0.692																																					p.L5X		Atlas-SNP	.											.	TMEM199	15	.	0			c.T14A						PASS	.						46.0	53.0	50.0					17																	26684707		2203	4299	6502	SO:0001587	stop_gained	147007	exon1			CCTCTTTGCTTGC	AY074907	CCDS11228.1	17q11.2	2007-12-17	2007-12-17	2007-12-17	ENSG00000244045	ENSG00000244045			18085	protein-coding gene	gene with protein product			"""chromosome 17 open reading frame 32"""	C17orf32			Standard	NM_152464		Approved	MGC45714	uc002hba.3	Q8N511	OTTHUMG00000132498	ENST00000292114.3:c.14T>A	17.37:g.26684707T>A	ENSP00000292114:p.Leu5*	49.0	0.0	0		41.0	16.0	0.390244	NM_152464		Nonsense_Mutation	SNP	ENST00000292114.3	37	CCDS11228.1	.	.	.	.	.	.	.	.	.	.	T	18.87	3.715363	0.68844	.	.	ENSG00000244045	ENST00000292114;ENST00000509083	.	.	.	4.87	3.78	0.43462	.	0.423693	0.22233	N	0.062791	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-1.4721	9.6131	0.39674	0.0:0.0:0.1765:0.8235	.	.	.	.	X	5	.	ENSP00000292114:L5X	L	+	2	0	TMEM199	23708834	0.068000	0.21057	0.001000	0.08648	0.003000	0.03518	2.583000	0.46094	0.861000	0.35504	-0.313000	0.08912	TTG	.	.	none		0.692	TMEM199-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255676.2	NM_152464	
CASP8	841	hgsc.bcm.edu	37	2	202137432	202137432	+	Silent	SNP	A	A	G			TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr2:202137432A>G	ENST00000432109.2	+	5	672	c.483A>G	c.(481-483)aaA>aaG	p.K161K	CASP8_ENST00000264275.5_Silent_p.K193K|CASP8_ENST00000358485.4_Silent_p.K220K|CASP8_ENST00000392259.2_Silent_p.K161K|CASP8_ENST00000392258.3_Silent_p.K161K|CASP8_ENST00000323492.7_Silent_p.K161K|CASP8_ENST00000392266.3_Silent_p.K161K|CASP8_ENST00000264274.9_Silent_p.K161K	NM_033355.3	NP_203519.1	Q14790	CASP8_HUMAN	caspase 8, apoptosis-related cysteine peptidase	161	DED 2. {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)|angiogenesis (GO:0001525)|apoptotic process (GO:0006915)|apoptotic signaling pathway (GO:0097190)|B cell activation (GO:0042113)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|cellular response to mechanical stimulus (GO:0071260)|cellular response to organic cyclic compound (GO:0071407)|execution phase of apoptosis (GO:0097194)|extrinsic apoptotic signaling pathway (GO:0097191)|extrinsic apoptotic signaling pathway via death domain receptors (GO:0008625)|heart development (GO:0007507)|hepatocyte apoptotic process (GO:0097284)|innate immune response (GO:0045087)|intrinsic apoptotic signaling pathway (GO:0097193)|macrophage differentiation (GO:0030225)|MyD88-independent toll-like receptor signaling pathway (GO:0002756)|natural killer cell activation (GO:0030101)|negative regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043124)|negative regulation of necroptotic process (GO:0060546)|neural tube formation (GO:0001841)|nucleotide-binding domain, leucine rich repeat containing receptor signaling pathway (GO:0035872)|nucleotide-binding oligomerization domain containing signaling pathway (GO:0070423)|positive regulation of extrinsic apoptotic signaling pathway (GO:2001238)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of macrophage differentiation (GO:0045651)|positive regulation of protein insertion into mitochondrial membrane involved in apoptotic signaling pathway (GO:1900740)|positive regulation of proteolysis (GO:0045862)|protein heterooligomerization (GO:0051291)|proteolysis (GO:0006508)|proteolysis involved in cellular protein catabolic process (GO:0051603)|regulation of extrinsic apoptotic signaling pathway in absence of ligand (GO:2001239)|regulation of thymocyte apoptotic process (GO:0070243)|response to antibiotic (GO:0046677)|response to cobalt ion (GO:0032025)|response to cold (GO:0009409)|response to estradiol (GO:0032355)|response to ethanol (GO:0045471)|response to lipopolysaccharide (GO:0032496)|response to tumor necrosis factor (GO:0034612)|syncytiotrophoblast cell differentiation involved in labyrinthine layer development (GO:0060715)|T cell activation (GO:0042110)|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)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|death-inducing signaling complex (GO:0031264)|membrane raft (GO:0045121)|microtubule organizing center (GO:0005815)|mitochondrial outer membrane (GO:0005741)|mitochondrion (GO:0005739)|neuron projection (GO:0043005)|Noc1p-Noc2p complex (GO:0030690)|nucleus (GO:0005634)|ripoptosome (GO:0097342)	cysteine-type endopeptidase activity (GO:0004197)|cysteine-type endopeptidase activity involved in apoptotic process (GO:0097153)|cysteine-type endopeptidase activity involved in apoptotic signaling pathway (GO:0097199)|cysteine-type peptidase activity (GO:0008234)|death effector domain binding (GO:0035877)|peptidase activity (GO:0008233)|scaffold protein binding (GO:0097110)|ubiquitin protein ligase binding (GO:0031625)			breast(5)|cervix(2)|endometrium(6)|large_intestine(11)|lung(10)|ovary(3)|prostate(1)|skin(2)|upper_aerodigestive_tract(9)|urinary_tract(3)	52						ACATCCTGAAAAGAGTCTGTG	0.438										HNSCC(4;0.00038)																											p.K220K	Melanoma(82;831 1348 20716 36952 40159)	Atlas-SNP	.											.	CASP8	272	.	0			c.A660G						PASS	.						154.0	157.0	156.0					2																	202137432		2203	4300	6503	SO:0001819	synonymous_variant	841	exon4			CCTGAAAAGAGTC	U60520	CCDS2342.1, CCDS2343.1, CCDS2345.1, CCDS42798.1, CCDS42799.1	2q33-q34	2014-09-17	2005-08-17		ENSG00000064012	ENSG00000064012		"""Caspases"""	1509	protein-coding gene	gene with protein product		601763	"""caspase 8, apoptosis-related cysteine protease"""			8681376, 8681377	Standard	NM_033355		Approved	MCH5, MACH, FLICE, Casp-8	uc002uxt.1	Q14790	OTTHUMG00000132821	ENST00000432109.2:c.483A>G	2.37:g.202137432A>G		139.0	0.0	0		107.0	71.0	0.663551	NM_001080125	O14676|Q14791|Q14792|Q14793|Q14794|Q14795|Q14796|Q15780|Q15806|Q53TT5|Q8TDI1|Q8TDI2|Q8TDI3|Q8TDI4|Q8TDI5|Q96T22|Q9C0K4|Q9UQ81	Silent	SNP	ENST00000432109.2	37	CCDS2342.1																																																																																			.	.	none		0.438	CASP8-014	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000336853.2	NM_001228	
LURAP1L	286343	hgsc.bcm.edu	37	9	12775855	12775855	+	Silent	SNP	T	T	C	rs572021640		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr9:12775855T>C	ENST00000319264.3	+	1	836	c.141T>C	c.(139-141)ggT>ggC	p.G47G	LURAP1L_ENST00000489107.1_3'UTR|RP11-3L8.3_ENST00000417638.1_RNA	NM_203403.1	NP_981948.1	Q8IV03	LUR1L_HUMAN	leucine rich adaptor protein 1-like	50	Gly-rich.		Missing.														GGGGGAgcggtggtggtggcg	0.677																																					p.G47G		Atlas-SNP	.											.	.	.	.	0			c.T141C						PASS	.						5.0	6.0	5.0					9																	12775855		2076	4056	6132	SO:0001819	synonymous_variant	286343	exon1			GAGCGGTGGTGGT	AK095824	CCDS6473.1	9p22.3	2012-02-01	2012-02-01	2012-02-01	ENSG00000153714	ENSG00000153714			31452	protein-coding gene	gene with protein product	"""similar to DNA segment, Chr 4, Brigham & Womens Genetics 0951 expressed"""		"""chromosome 9 open reading frame 150"""	C9orf150		12766061	Standard	NM_203403		Approved	MGC46502, FLJ38505, bA3L8.2	uc003zkw.3	Q8IV03	OTTHUMG00000019557	ENST00000319264.3:c.141T>C	9.37:g.12775855T>C		15.0	0.0	0		17.0	7.0	0.411765	NM_203403	Q5VZX7|Q8N923|Q8NCG2	Silent	SNP	ENST00000319264.3	37	CCDS6473.1																																																																																			.	.	none		0.677	LURAP1L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051730.1	NM_203403	
LAMA1	284217	hgsc.bcm.edu	37	18	7080048	7080048	+	Missense_Mutation	SNP	T	T	C			TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr18:7080048T>C	ENST00000389658.3	-	3	364	c.271A>G	c.(271-273)Aac>Gac	p.N91D	RP11-76K13.3_ENST00000581502.1_RNA	NM_005559.3	NP_005550.2	P25391	LAMA1_HUMAN	laminin, alpha 1	91	Laminin N-terminal. {ECO:0000255|PROSITE- ProRule:PRU00466}.				axon guidance (GO:0007411)|branching involved in salivary gland morphogenesis (GO:0060445)|cell adhesion (GO:0007155)|cell surface receptor signaling pathway (GO:0007166)|epithelial tube branching involved in lung morphogenesis (GO:0060441)|establishment of epithelial cell apical/basal polarity (GO:0045198)|extracellular matrix organization (GO:0030198)|morphogenesis of an epithelial sheet (GO:0002011)|regulation of cell adhesion (GO:0030155)|regulation of cell migration (GO:0030334)|regulation of embryonic development (GO:0045995)|retinal blood vessel morphogenesis (GO:0061304)	basement membrane (GO:0005604)|cell-cell junction (GO:0005911)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|laminin-1 complex (GO:0005606)|laminin-3 complex (GO:0005608)|proteinaceous extracellular matrix (GO:0005578)	extracellular matrix structural constituent (GO:0005201)|glycosphingolipid binding (GO:0043208)			NS(4)|breast(7)|central_nervous_system(3)|cervix(2)|endometrium(8)|haematopoietic_and_lymphoid_tissue(2)|kidney(12)|large_intestine(49)|liver(1)|lung(71)|ovary(9)|pancreas(3)|prostate(5)|skin(11)|stomach(7)|upper_aerodigestive_tract(8)|urinary_tract(3)	205		Colorectal(10;0.172)				TGCCACCAGTTATTGGTGCCA	0.418																																					p.N91D		Atlas-SNP	.											.	LAMA1	458	.	0			c.A271G						PASS	.						167.0	135.0	146.0					18																	7080048		2203	4300	6503	SO:0001583	missense	284217	exon3			ACCAGTTATTGGT	X58531	CCDS32787.1	18p11.3	2013-03-01			ENSG00000101680	ENSG00000101680		"""Laminins"""	6481	protein-coding gene	gene with protein product		150320		LAMA		2591971	Standard	NM_005559		Approved		uc002knm.3	P25391	OTTHUMG00000133478	ENST00000389658.3:c.271A>G	18.37:g.7080048T>C	ENSP00000374309:p.Asn91Asp	315.0	0.0	0		246.0	116.0	0.471545	NM_005559		Missense_Mutation	SNP	ENST00000389658.3	37	CCDS32787.1	.	.	.	.	.	.	.	.	.	.	T	16.50	3.140937	0.56936	.	.	ENSG00000101680	ENST00000389658	T	0.75821	-0.97	5.61	4.45	0.53987	Laminin, N-terminal (3);	0.245554	0.40908	D	0.000990	T	0.60495	0.2273	L	0.31526	0.94	0.29065	N	0.883622	B	0.19200	0.034	B	0.16289	0.015	T	0.57911	-0.7729	10	0.72032	D	0.01	.	7.2768	0.26290	0.0:0.0731:0.157:0.7699	.	91	P25391	LAMA1_HUMAN	D	91	ENSP00000374309:N91D	ENSP00000374309:N91D	N	-	1	0	LAMA1	7070048	1.000000	0.71417	0.999000	0.59377	0.998000	0.95712	2.279000	0.43435	0.964000	0.38108	0.533000	0.62120	AAC	.	.	none		0.418	LAMA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257369.1	NM_005559	
ALOX12B	242	hgsc.bcm.edu	37	17	7989492	7989492	+	Missense_Mutation	SNP	A	A	G	rs542947562		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr17:7989492A>G	ENST00000319144.4	-	2	454	c.194T>C	c.(193-195)aTc>aCc	p.I65T	MIR4314_ENST00000583321.1_RNA	NM_001139.2	NP_001130.1	O75342	LX12B_HUMAN	arachidonate 12-lipoxygenase, 12R type	65	PLAT. {ECO:0000255|PROSITE- ProRule:PRU00152}.				arachidonic acid metabolic process (GO:0019369)|ceramide biosynthetic process (GO:0046513)|establishment of skin barrier (GO:0061436)|hepoxilin biosynthetic process (GO:0051122)|linoleic acid metabolic process (GO:0043651)|lipoxygenase pathway (GO:0019372)|oxidation-reduction process (GO:0055114)|positive regulation of gene expression (GO:0010628)|positive regulation of MAPK cascade (GO:0043410)|positive regulation of mucus secretion (GO:0070257)|protein lipidation (GO:0006497)|small molecule metabolic process (GO:0044281)|sphingolipid metabolic process (GO:0006665)	cytosol (GO:0005829)	arachidonate 12-lipoxygenase activity (GO:0004052)|iron ion binding (GO:0005506)|linoleate 9S-lipoxygenase activity (GO:1990136)|oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen (GO:0016702)			endometrium(5)|kidney(1)|large_intestine(3)|lung(5)|prostate(1)|stomach(1)	16						GCGGATGATGATGAGCTCACC	0.612										Multiple Myeloma(8;0.094)			A|||	1	0.000199681	0.0	0.0	5008	,	,		19749	0.0		0.001	False		,,,				2504	0.0				p.I65T		Atlas-SNP	.											.	ALOX12B	61	.	0			c.T194C						PASS	.						111.0	90.0	97.0					17																	7989492		2203	4300	6503	SO:0001583	missense	242	exon2			ATGATGATGAGCT	AF038461	CCDS11129.1	17p13.1	2008-03-18			ENSG00000179477	ENSG00000179477	1.13.11.-	"""Arachidonate lipoxygenases"""	430	protein-coding gene	gene with protein product		603741				9618483	Standard	NM_001139		Approved	12R-LOX	uc002gjy.1	O75342	OTTHUMG00000108180	ENST00000319144.4:c.194T>C	17.37:g.7989492A>G	ENSP00000315167:p.Ile65Thr	275.0	0.0	0		266.0	130.0	0.488722	NM_001139		Missense_Mutation	SNP	ENST00000319144.4	37	CCDS11129.1	.	.	.	.	.	.	.	.	.	.	A	14.64	2.595105	0.46318	.	.	ENSG00000179477	ENST00000319144	T	0.63417	-0.04	4.58	3.48	0.39840	Lipoxygenase, LH2 (4);Lipase/lipooxygenase, PLAT/LH2 (1);	0.253600	0.39909	N	0.001228	T	0.46502	0.1396	N	0.21142	0.635	0.29604	N	0.847425	B	0.29955	0.263	B	0.29440	0.102	T	0.49504	-0.8933	10	0.62326	D	0.03	-23.0942	10.4946	0.44770	0.8365:0.1635:0.0:0.0	.	65	O75342	LX12B_HUMAN	T	65	ENSP00000315167:I65T	ENSP00000315167:I65T	I	-	2	0	ALOX12B	7930217	0.990000	0.36364	0.952000	0.39060	0.922000	0.55478	7.844000	0.86867	0.765000	0.33221	0.529000	0.55759	ATC	.	.	none		0.612	ALOX12B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000226984.3		
GTF2A1	2957	hgsc.bcm.edu	37	14	81686832	81686832	+	Splice_Site	SNP	C	C	G	rs201410281		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr14:81686832C>G	ENST00000553612.1	-	1	434		c.e1+1		GTF2A1_ENST00000434192.2_Intron	NM_001278940.1|NM_015859.3	NP_001265869.1|NP_056943.1	P52655	TF2AA_HUMAN	general transcription factor IIA, 1, 19/37kDa						gene expression (GO:0010467)|regulation of transcription, DNA-templated (GO:0006355)|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)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|transcription factor TFIIA complex (GO:0005672)	DNA binding (GO:0003677)|protein heterodimerization activity (GO:0046982)|TBP-class protein binding (GO:0017025)|transcription coactivator activity (GO:0003713)|transcription factor binding (GO:0008134)			breast(1)|endometrium(1)|kidney(2)|large_intestine(2)|lung(5)|upper_aerodigestive_tract(1)	12				BRCA - Breast invasive adenocarcinoma(234;0.0287)		CACGTCCTTACCACGGTGTTT	0.577																																					.		Atlas-SNP	.											.	GTF2A1	34	.	0			c.30+1G>C						PASS	.						39.0	40.0	40.0					14																	81686832		2202	4293	6495	SO:0001630	splice_region_variant	2957	exon2			TCCTTACCACGGT	X75383	CCDS9873.1, CCDS9874.1	14q31	2010-03-23	2002-08-29					"""General transcription factors"""	4646	protein-coding gene	gene with protein product		600520	"""glucose regulated protein, 58kD pseudogene"""			8224848	Standard	NM_015859		Approved	TFIIA	uc001xvf.2	P52655		ENST00000553612.1:c.30+1G>C	14.37:g.81686832C>G		32.0	0.0	0		74.0	21.0	0.283784	NM_015859	Q3KNQ9	Splice_Site	SNP	ENST00000553612.1	37	CCDS9873.1	.	.	.	.	.	.	.	.	.	.	C	16.74	3.205504	0.58234	.	.	ENSG00000165417	ENST00000553612	.	.	.	3.35	3.35	0.38373	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	13.2408	0.59995	0.0:1.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	-	.	.	GTF2A1	80756585	1.000000	0.71417	1.000000	0.80357	0.931000	0.56810	5.468000	0.66743	1.400000	0.46741	0.305000	0.20034	.	C|1.000;T|0.000	.	alt		0.577	GTF2A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000413309.1	NM_015859	Intron
TBC1D2	55357	hgsc.bcm.edu	37	9	100961704	100961704	+	Missense_Mutation	SNP	C	C	T	rs34769888	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr9:100961704C>T	ENST00000375066.5	-	13	2804	c.2713G>A	c.(2713-2715)Gag>Aag	p.E905K	TBC1D2_ENST00000375064.1_3'UTR|TBC1D2_ENST00000342112.5_Missense_Mutation_p.E698K|TBC1D2_ENST00000375063.1_Missense_Mutation_p.E456K	NM_018421.3	NP_060891.3	Q9BYX2	TBD2A_HUMAN	TBC1 domain family, member 2	916					positive regulation of Rab GTPase activity (GO:0032851)	cell junction (GO:0030054)|cytoplasmic vesicle (GO:0031410)	cadherin binding (GO:0045296)|Rab GTPase activator activity (GO:0005097)			breast(1)|endometrium(5)|kidney(2)|large_intestine(7)|ovary(3)|prostate(4)|skin(1)|upper_aerodigestive_tract(1)	24		Myeloproliferative disorder(762;0.0255)		OV - Ovarian serous cystadenocarcinoma(323;2.55e-37)		GCACAGCCCTCGGACACAGCT	0.682													C|||	20	0.00399361	0.0	0.0043	5008	,	,		15710	0.0		0.006	False		,,,				2504	0.0112				p.E916K		Atlas-SNP	.											.	TBC1D2	70	.	0			c.G2746A						PASS	.	C	LYS/GLU	11,4395	16.8+/-37.8	0,11,2192	62.0	64.0	63.0		2713	3.5	0.0	9	dbSNP_126	63	80,8518	45.8+/-104.6	1,78,4220	yes	missense	TBC1D2	NM_018421.3	56	1,89,6412	TT,TC,CC		0.9304,0.2497,0.6998	benign	905/918	100961704	91,12913	2203	4299	6502	SO:0001583	missense	55357	exon13			AGCCCTCGGACAC	AY026527	CCDS35080.1, CCDS59137.1, CCDS75865.1	9q22.32	2011-11-30			ENSG00000095383	ENSG00000095383			18026	protein-coding gene	gene with protein product	"""prostate antigen recognized and identified by SEREX"""	609871					Standard	NM_018421		Approved	PARIS1, TBC1D2A, Armus	uc011lvb.2	Q9BYX2	OTTHUMG00000020343	ENST00000375066.5:c.2713G>A	9.37:g.100961704C>T	ENSP00000364207:p.Glu905Lys	144.0	0.0	0		135.0	64.0	0.474074	NM_001267571	B3KWD1|B4DQ05|B9A6J7|Q59EU0|Q5TBQ5|Q6IPC7|Q7L1K8|Q8WYT1|Q9H6A2|Q9NSH4	Missense_Mutation	SNP	ENST00000375066.5	37	CCDS35080.1	7	0.003205128205128205	0	0.0	2	0.0055248618784530384	0	0.0	5	0.006596306068601583	C	16.15	3.041987	0.55003	0.002497	0.009304	ENSG00000095383	ENST00000375066;ENST00000342112;ENST00000375063	T;T;T	0.08896	3.04;3.5;3.11	5.34	3.5	0.40072	.	0.512441	0.20582	N	0.089520	T	0.04907	0.0132	L	0.57536	1.79	0.09310	N	0.999999	B;B	0.33919	0.306;0.432	B;B	0.22386	0.017;0.039	T	0.33317	-0.9873	10	0.13470	T	0.59	.	9.2808	0.37727	0.0:0.8294:0.0:0.1706	rs34769888	916;905	Q9BYX2;Q9BYX2-2	TBD2A_HUMAN;.	K	905;698;456	ENSP00000364207:E905K;ENSP00000341567:E698K;ENSP00000364203:E456K	ENSP00000341567:E698K	E	-	1	0	TBC1D2	100001525	0.612000	0.27000	0.033000	0.17914	0.033000	0.12548	1.029000	0.30140	0.641000	0.30601	0.511000	0.50034	GAG	C|0.994;T|0.006	0.006	strong		0.682	TBC1D2-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000053367.1	NM_018421	
VWA5B1	127731	hgsc.bcm.edu	37	1	20650001	20650001	+	Silent	SNP	C	C	T	rs146423282	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr1:20650001C>T	ENST00000375079.2	+	8	1315	c.1119C>T	c.(1117-1119)agC>agT	p.S373S	VWA5B1_ENST00000289825.4_Silent_p.S90S|VWA5B1_ENST00000375083.4_Silent_p.S373S|VWA5B1_ENST00000289815.8_Silent_p.S373S|RP4-745E8.2_ENST00000444923.1_RNA	NM_001039500.2	NP_001034589.2	Q5TIE3	VW5B1_HUMAN	von Willebrand factor A domain containing 5B1	373	VWFA. {ECO:0000255|PROSITE- ProRule:PRU00219}.					extracellular region (GO:0005576)				central_nervous_system(1)|endometrium(3)|kidney(1)|prostate(1)|skin(1)	7						GCAGCATGAGCGGGATCAGCA	0.602													C|||	9	0.00179712	0.0008	0.0	5008	,	,		17207	0.0		0.007	False		,,,				2504	0.001				p.S373S		Atlas-SNP	.											.	VWA5B1	44	.	0			c.C1119T						PASS	.	C		5,1379		0,5,687	53.0	47.0	49.0		1119	-0.9	1.0	1	dbSNP_134	49	23,3159		0,23,1568	no	coding-synonymous	VWA5B1	NM_001039500.2		0,28,2255	TT,TC,CC		0.7228,0.3613,0.6132		373/1216	20650001	28,4538	692	1591	2283	SO:0001819	synonymous_variant	127731	exon8			CATGAGCGGGATC	AK125833, AK057346		1p36.12	2014-02-12			ENSG00000158816	ENSG00000158816			26538	protein-coding gene	gene with protein product							Standard	NM_001039500		Approved	FLJ32784	uc009vps.2	Q5TIE3	OTTHUMG00000002835	ENST00000375079.2:c.1119C>T	1.37:g.20650001C>T		37.0	0.0	0		47.0	8.0	0.170213	NM_001039500	A4IF35|A4IF36|Q3ZCM4|Q6ZUB4|Q96M71	Silent	SNP	ENST00000375079.2	37																																																																																				C|0.995;T|0.005	0.005	strong		0.602	VWA5B1-001	NOVEL	not_organism_supported|basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000007945.4	XM_001722222	
PSG2	5670	hgsc.bcm.edu	37	19	43575982	43575982	+	Silent	SNP	C	C	T	rs150568950	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr19:43575982C>T	ENST00000406487.1	-	4	932	c.834G>A	c.(832-834)aaG>aaA	p.K278K		NM_031246.3	NP_112536.2	P11465	PSG2_HUMAN	pregnancy specific beta-1-glycoprotein 2	278	Ig-like C2-type 2.				cell migration (GO:0016477)|female pregnancy (GO:0007565)	extracellular region (GO:0005576)				central_nervous_system(1)|endometrium(5)|kidney(1)|large_intestine(5)|lung(24)|ovary(1)|pancreas(2)|prostate(6)|stomach(2)|urinary_tract(2)	49		Prostate(69;0.00682)				ATTGCTGAAACTTCCCATTAA	0.448													C|||	3	0.000599042	0.0008	0.0014	5008	,	,		20458	0.0		0.001	False		,,,				2504	0.0				p.K278K		Atlas-SNP	.											PSG2,NS,carcinoma,-1,1	PSG2	84	1	0			c.G834A						PASS	.	C		6,4398	825.3+/-416.5	0,6,2196	190.0	199.0	196.0		834	-1.7	0.0	19	dbSNP_134	196	32,8566	817.7+/-406.9	0,32,4267	no	coding-synonymous	PSG2	NM_031246.3		0,38,6463	TT,TC,CC		0.3722,0.1362,0.2923		278/336	43575982	38,12964	2202	4299	6501	SO:0001819	synonymous_variant	5670	exon4			CTGAAACTTCCCA		CCDS12616.1	19q13.1-q13.2	2013-01-29			ENSG00000242221	ENSG00000242221		"""Immunoglobulin superfamily / V-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	9519	protein-coding gene	gene with protein product	"""pregnancy-specific beta-1 glycoprotein"", ""pregnancy-specific beta-1-glycoprotein 7"", ""carcinoembryonic antigen SG8"""	176391		PSBG2		2377620	Standard	NM_031246		Approved	PSGGB, PSG1, CEA	uc002ovr.3	P11465	OTTHUMG00000151547	ENST00000406487.1:c.834G>A	19.37:g.43575982C>T		249.0	1.0	0.00401606		234.0	108.0	0.461538	NM_031246	Q8TCD9|Q9UEA4|Q9UQ78	Silent	SNP	ENST00000406487.1	37	CCDS12616.1																																																																																			C|0.998;T|0.002	0.002	strong		0.448	PSG2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000323083.1	NM_031246	
DOCK1	1793	hgsc.bcm.edu	37	10	129046371	129046371	+	Missense_Mutation	SNP	G	G	A			TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr10:129046371G>A	ENST00000280333.6	+	28	2993	c.2884G>A	c.(2884-2886)Gta>Ata	p.V962I	DOCK1_ENST00000484400.1_3'UTR	NM_001380.3	NP_001371.1	Q14185	DOCK1_HUMAN	dedicator of cytokinesis 1	962					apoptotic process (GO:0006915)|axon guidance (GO:0007411)|blood coagulation (GO:0007596)|cell migration (GO:0016477)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|hematopoietic progenitor cell differentiation (GO:0002244)|innate immune response (GO:0045087)|integrin-mediated signaling pathway (GO:0007229)|phagocytosis, engulfment (GO:0006911)|positive regulation of GTPase activity (GO:0043547)|signal transduction (GO:0007165)|small GTPase mediated signal transduction (GO:0007264)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|membrane (GO:0016020)|nucleus (GO:0005634)	GTPase activator activity (GO:0005096)|guanyl-nucleotide exchange factor activity (GO:0005085)			NS(2)|breast(1)|central_nervous_system(7)|endometrium(13)|haematopoietic_and_lymphoid_tissue(2)|kidney(7)|large_intestine(10)|lung(15)|ovary(4)|prostate(3)|stomach(2)|upper_aerodigestive_tract(5)|urinary_tract(1)	72		all_epithelial(44;2.3e-07)|all_lung(145;0.00466)|Lung NSC(174;0.00685)|Colorectal(57;0.0107)|Renal(717;0.0113)|Breast(234;0.0492)|all_neural(114;0.108)|all_hematologic(284;0.14)		BRCA - Breast invasive adenocarcinoma(275;0.0221)|Colorectal(40;0.115)		GACTGATGTGGTAGTAAGTGT	0.388																																					p.V962I		Atlas-SNP	.											.	DOCK1	188	.	0			c.G2884A						PASS	.						112.0	103.0	106.0					10																	129046371		1898	4109	6007	SO:0001583	missense	1793	exon28			GATGTGGTAGTAA	D50857	CCDS73222.1	10q26.13-q26.3	2009-10-28			ENSG00000150760	ENSG00000150760			2987	protein-coding gene	gene with protein product	"""DOwnstream of CrK"""	601403	"""dedicator of cyto-kinesis 1"""			8657152, 8661160	Standard	XM_006717681		Approved	DOCK180, ced5	uc001ljt.3	Q14185	OTTHUMG00000019249	ENST00000280333.6:c.2884G>A	10.37:g.129046371G>A	ENSP00000280333:p.Val962Ile	193.0	0.0	0		186.0	85.0	0.456989	NM_001380	A9Z1Z5	Missense_Mutation	SNP	ENST00000280333.6	37		.	.	.	.	.	.	.	.	.	.	G	11.06	1.528362	0.27299	.	.	ENSG00000150760	ENST00000280333	T	0.21734	1.99	5.37	5.37	0.77165	.	0.000000	0.85682	D	0.000000	T	0.11495	0.0280	N	0.10733	0.035	0.80722	D	1	B;B	0.24426	0.01;0.103	B;B	0.18871	0.015;0.023	T	0.11084	-1.0602	10	0.07030	T	0.85	.	19.1025	0.93279	0.0:0.0:1.0:0.0	.	962;962	B2RUU3;Q14185	.;DOCK1_HUMAN	I	962	ENSP00000280333:V962I	ENSP00000280333:V962I	V	+	1	0	DOCK1	128936361	1.000000	0.71417	0.997000	0.53966	0.630000	0.37929	6.639000	0.74314	2.491000	0.84063	0.563000	0.77884	GTA	.	.	none		0.388	DOCK1-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000050979.2	NM_001380	
PLXNA1	5361	hgsc.bcm.edu	37	3	126741041	126741041	+	Silent	SNP	C	C	T	rs150052583	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr3:126741041C>T	ENST00000393409.2	+	21	4152	c.4152C>T	c.(4150-4152)cgC>cgT	p.R1384R	PLXNA1_ENST00000251772.4_Silent_p.R1361R	NM_032242.3	NP_115618.3	Q9UIW2	PLXA1_HUMAN	plexin A1	1384					axon guidance (GO:0007411)|dichotomous subdivision of terminal units involved in salivary gland branching (GO:0060666)|multicellular organismal development (GO:0007275)|regulation of smooth muscle cell migration (GO:0014910)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|semaphorin receptor complex (GO:0002116)	receptor activity (GO:0004872)|semaphorin receptor activity (GO:0017154)			breast(3)|central_nervous_system(5)|endometrium(10)|kidney(5)|large_intestine(4)|lung(32)|ovary(2)|pancreas(1)|prostate(2)|skin(3)	67				GBM - Glioblastoma multiforme(114;0.155)		TCTCCATGCGCGACCGCGGGA	0.612													C|||	28	0.00559105	0.0038	0.0101	5008	,	,		22692	0.001		0.0129	False		,,,				2504	0.002				p.R1384R		Atlas-SNP	.											PLXNA1,colon,carcinoma,+2,1	PLXNA1	185	1	0			c.C4152T						PASS	.	C		11,4393	17.9+/-39.9	0,11,2191	62.0	54.0	56.0		4152	-5.4	0.9	3	dbSNP_134	56	93,8505	53.1+/-113.8	0,93,4206	no	coding-synonymous	PLXNA1	NM_032242.3		0,104,6397	TT,TC,CC		1.0816,0.2498,0.7999		1384/1897	126741041	104,12898	2202	4299	6501	SO:0001819	synonymous_variant	5361	exon21			CATGCGCGACCGC	X87832	CCDS33847.1, CCDS33847.2	3q21.2	2006-12-19				ENSG00000114554		"""Plexins"""	9099	protein-coding gene	gene with protein product		601055		PLXN1		8570614	Standard	NM_032242		Approved	NOV	uc003ejg.3	Q9UIW2		ENST00000393409.2:c.4152C>T	3.37:g.126741041C>T		206.0	0.0	0		150.0	67.0	0.446667	NM_032242		Silent	SNP	ENST00000393409.2	37	CCDS33847.2																																																																																			C|0.992;T|0.008	0.008	strong		0.612	PLXNA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000356451.1	NM_032242	
APOBEC3F	200316	hgsc.bcm.edu	37	22	39441478	39441478	+	Missense_Mutation	SNP	C	C	A	rs138934952	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr22:39441478C>A	ENST00000308521.5	+	4	854	c.497C>A	c.(496-498)cCa>cAa	p.P166Q	APOBEC3G_ENST00000452957.2_Intron	NM_145298.5	NP_660341.2	Q8IUX4	ABC3F_HUMAN	apolipoprotein B mRNA editing enzyme, catalytic polypeptide-like 3F	166					base conversion or substitution editing (GO:0016553)|cytidine deamination (GO:0009972)|defense response to virus (GO:0051607)|DNA cytosine deamination (GO:0070383)|DNA demethylation (GO:0080111)|innate immune response (GO:0045087)|negative regulation of single stranded viral RNA replication via double stranded DNA intermediate (GO:0045869)|negative regulation of transposition (GO:0010529)|negative regulation of viral genome replication (GO:0045071)|negative regulation of viral process (GO:0048525)|positive regulation of defense response to virus by host (GO:0002230)	apolipoprotein B mRNA editing enzyme complex (GO:0030895)|cytoplasm (GO:0005737)|cytoplasmic mRNA processing body (GO:0000932)|ribonucleoprotein complex (GO:0030529)	cytidine deaminase activity (GO:0004126)|poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)|zinc ion binding (GO:0008270)			breast(3)|endometrium(1)|kidney(1)|large_intestine(3)|lung(6)|skin(2)	16	Melanoma(58;0.04)					GAAGGTCAGCCATTCATGCCT	0.527													C|||	9	0.00179712	0.0	0.0	5008	,	,		22581	0.0		0.0089	False		,,,				2504	0.0				p.P166Q		Atlas-SNP	.											.	APOBEC3F	37	.	0			c.C497A						PASS	.	C	GLN/PRO	1,4405		0,1,2202	363.0	299.0	321.0		497	-1.4	0.0	22	dbSNP_134	321	13,8587		0,13,4287	no	missense	APOBEC3F	NM_145298.5	76	0,14,6489	AA,AC,CC		0.1512,0.0227,0.1076	benign	166/374	39441478	14,12992	2203	4300	6503	SO:0001583	missense	200316	exon4			GTCAGCCATTCAT	BC038808	CCDS33648.1, CCDS33649.1	22q13.1-q13.2	2008-05-15			ENSG00000128394	ENSG00000128394		"""Apolipoprotein B mRNA editing enzymes"""	17356	protein-coding gene	gene with protein product		608993				11863358, 17121840	Standard	NM_145298		Approved	ARP8, BK150C2.4.MRNA, KA6	uc003aww.3	Q8IUX4	OTTHUMG00000151080	ENST00000308521.5:c.497C>A	22.37:g.39441478C>A	ENSP00000309749:p.Pro166Gln	455.0	0.0	0		425.0	197.0	0.463529	NM_145298	B0QYD4|Q45F03|Q6ICH3|Q7Z2N2|Q7Z2N5	Missense_Mutation	SNP	ENST00000308521.5	37	CCDS33648.1	7	0.003205128205128205	0	0.0	0	0.0	0	0.0	7	0.009234828496042216	.	5.006	0.186780	0.09547	2.27E-4	0.001512	ENSG00000128394	ENST00000308521	T	0.63096	-0.02	2.27	-1.43	0.08884	APOBEC-like, C-terminal (1);Cytidine deaminase-like (1);	.	.	.	.	T	0.30386	0.0763	N	0.25825	0.765	0.09310	N	1	B	0.18741	0.03	B	0.17433	0.018	T	0.15292	-1.0442	9	0.20519	T	0.43	.	1.0452	0.01568	0.2303:0.3935:0.226:0.1502	.	166	Q8IUX4	ABC3F_HUMAN	Q	166	ENSP00000309749:P166Q	ENSP00000309749:P166Q	P	+	2	0	APOBEC3F	37771424	0.000000	0.05858	0.000000	0.03702	0.005000	0.04900	-0.825000	0.04433	-0.226000	0.09899	0.400000	0.26472	CCA	C|0.998;A|0.002	0.002	strong		0.527	APOBEC3F-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000321216.1	NM_145298	
PHPT1	29085	hgsc.bcm.edu	37	9	139744524	139744524	+	Silent	SNP	C	C	T	rs8666	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr9:139744524C>T	ENST00000247665.10	+	2	557	c.220C>T	c.(220-222)Ctg>Ttg	p.L74L	MAMDC4_ENST00000317446.2_5'Flank|MAMDC4_ENST00000445819.1_5'Flank|PHPT1_ENST00000371661.1_Silent_p.L74L|PHPT1_ENST00000492540.1_3'UTR|PHPT1_ENST00000545326.1_Silent_p.L74L	NM_014172.4	NP_054891.2	Q9NRX4	PHP14_HUMAN	phosphohistidine phosphatase 1	74					negative regulation of ATP citrate synthase activity (GO:2000984)|negative regulation of lyase activity (GO:0051350)|negative regulation of T cell receptor signaling pathway (GO:0050860)|peptidyl-histidine dephosphorylation (GO:0035971)|positive regulation of cell motility (GO:2000147)|positive regulation of insulin secretion involved in cellular response to glucose stimulus (GO:0035774)|protein dephosphorylation (GO:0006470)|regulation of actin cytoskeleton reorganization (GO:2000249)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)	calcium channel inhibitor activity (GO:0019855)|ion channel binding (GO:0044325)|phosphohistidine phosphatase activity (GO:0008969)|phosphoprotein phosphatase activity (GO:0004721)			NS(1)|large_intestine(1)|lung(1)	3	all_cancers(76;0.0763)|all_epithelial(76;0.198)	Myeloproliferative disorder(178;0.0821)		OV - Ovarian serous cystadenocarcinoma(145;1.52e-05)|Epithelial(140;0.000171)		CTGTGAGTGTCTGGGCGGCGG	0.662													C|||	214	0.0427316	0.0015	0.0202	5008	,	,		14400	0.0089		0.0318	False		,,,				2504	0.1605				p.L74L		Atlas-SNP	.											.	PHPT1	14	.	0			c.C220T						PASS	.	C	,	33,4373		0,33,2170	104.0	100.0	101.0		220,220	4.6	1.0	9	dbSNP_52	101	283,8317		5,273,4022	no	coding-synonymous,coding-synonymous	PHPT1	NM_001135861.1,NM_014172.4	,	5,306,6192	TT,TC,CC		3.2907,0.749,2.4296	,	74/125,74/126	139744524	316,12690	2203	4300	6503	SO:0001819	synonymous_variant	29085	exon2			GAGTGTCTGGGCG	AF131857	CCDS7009.1, CCDS48060.1	9q34.3	2008-02-05			ENSG00000054148	ENSG00000054148	3.1.3.-		30033	protein-coding gene	gene with protein product	"""phosphohistidine phosphatase 14kDa"", "" sex-regulated protein janus-a"""	610167				11042152, 8619474	Standard	NM_014172		Approved	PHP14, HSPC141, CGI-202, DKFZp564M173, bA216L13.10	uc004cjq.4	Q9NRX4	OTTHUMG00000020950	ENST00000247665.10:c.220C>T	9.37:g.139744524C>T		167.0	0.0	0		176.0	82.0	0.465909	NM_001135861	B1AMX0|B1AMX1|Q9H0Y3	Silent	SNP	ENST00000247665.10	37	CCDS7009.1																																																																																			C|0.972;T|0.028	0.028	strong		0.662	PHPT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055150.1	NM_014172	
IPO9	55705	hgsc.bcm.edu	37	1	201798367	201798367	+	Silent	SNP	C	C	T	rs537589191		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr1:201798367C>T	ENST00000361565.4	+	1	99	c.30C>T	c.(28-30)gcC>gcT	p.A10A	IPO9_ENST00000464348.1_3'UTR|IPO9-AS1_ENST00000421159.1_RNA|IPO9-AS1_ENST00000421449.1_RNA|IPO9-AS1_ENST00000413035.1_RNA	NM_018085.4	NP_060555.2	Q96P70	IPO9_HUMAN	importin 9	10					protein import into nucleus (GO:0006606)	cytoplasm (GO:0005737)|membrane (GO:0016020)|nucleus (GO:0005634)	histone binding (GO:0042393)|protein transporter activity (GO:0008565)			cervix(1)|endometrium(5)|kidney(4)|large_intestine(5)|lung(16)|ovary(2)|prostate(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)	38						CTGGTGCGGCCTCCGGGCTGC	0.711													C|||	1	0.000199681	0.0	0.0	5008	,	,		9698	0.0		0.0	False		,,,				2504	0.001				p.A10A		Atlas-SNP	.											.	IPO9	98	.	0			c.C30T						PASS	.						10.0	12.0	12.0					1																	201798367		2164	4234	6398	SO:0001819	synonymous_variant	55705	exon1			TGCGGCCTCCGGG	AF410465	CCDS1415.1	1q31.3	2008-02-05			ENSG00000198700	ENSG00000198700		"""Importins"""	19425	protein-coding gene	gene with protein product						11823430, 10574461	Standard	NM_018085		Approved	Imp9, FLJ10402	uc001gwz.3	Q96P70	OTTHUMG00000035805	ENST00000361565.4:c.30C>T	1.37:g.201798367C>T		44.0	0.0	0		60.0	19.0	0.316667	NM_018085	B1ASV5|Q8N1Y1|Q8N3I2|Q8NCG9|Q96SU6|Q9NW01|Q9P0A8|Q9ULM8	Silent	SNP	ENST00000361565.4	37	CCDS1415.1																																																																																			.	.	none		0.711	IPO9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000087088.1	NM_018085	
DYNC1H1	1778	hgsc.bcm.edu	37	14	102508056	102508056	+	Missense_Mutation	SNP	C	C	A	rs10129889	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr14:102508056C>A	ENST00000360184.4	+	65	12251	c.12087C>A	c.(12085-12087)caC>caA	p.H4029Q	RP11-1017G21.4_ENST00000557242.1_RNA|RP11-1017G21.4_ENST00000553701.1_RNA|RP11-1017G21.4_ENST00000557551.1_RNA	NM_001376.4	NP_001367.2	Q14204	DYHC1_HUMAN	dynein, cytoplasmic 1, heavy chain 1	4029	AAA 6. {ECO:0000250}.		H -> Q (in dbSNP:rs10129889). {ECO:0000269|PubMed:9205841, ECO:0000269|Ref.4}.		antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|cell death (GO:0008219)|cytoplasmic mRNA processing body assembly (GO:0033962)|G2/M transition of mitotic cell cycle (GO:0000086)|microtubule-based movement (GO:0007018)|mitotic cell cycle (GO:0000278)|mitotic spindle organization (GO:0007052)|stress granule assembly (GO:0034063)|transport (GO:0006810)	centrosome (GO:0005813)|cytoplasmic dynein complex (GO:0005868)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|filopodium (GO:0030175)|membrane (GO:0016020)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)|poly(A) RNA binding (GO:0044822)			NS(1)|biliary_tract(1)|breast(4)|central_nervous_system(5)|cervix(1)|endometrium(21)|haematopoietic_and_lymphoid_tissue(3)|kidney(10)|large_intestine(28)|lung(60)|ovary(9)|pancreas(1)|prostate(6)|skin(7)|stomach(3)|upper_aerodigestive_tract(4)|urinary_tract(2)	166						ACCTGACCCACATTGTGGGCA	0.602													C|||	496	0.0990415	0.2784	0.0519	5008	,	,		19868	0.002		0.0696	False		,,,				2504	0.0204				p.H4029Q		Atlas-SNP	.											.	DYNC1H1	395	.	0			c.C12087A						PASS	.	C	GLN/HIS	1199,3207	418.7+/-338.4	164,871,1168	59.0	61.0	60.0		12087	4.6	1.0	14	dbSNP_119	60	534,8066	148.8+/-204.0	20,494,3786	yes	missense	DYNC1H1	NM_001376.4	24	184,1365,4954	AA,AC,CC		6.2093,27.2129,13.3246	benign	4029/4647	102508056	1733,11273	2203	4300	6503	SO:0001583	missense	1778	exon65			GACCCACATTGTG	AB002323	CCDS9966.1	14q32.31	2006-12-21	2005-11-24	2005-11-24		ENSG00000197102		"""Cytoplasmic dyneins"""	2961	protein-coding gene	gene with protein product		600112	"""dynein, cytoplasmic, heavy polypeptide 1"""	DNECL, DNCL, DNCH1		16260502, 8666668	Standard	NM_001376		Approved	Dnchc1, HL-3, p22, DHC1	uc001yks.2	Q14204		ENST00000360184.4:c.12087C>A	14.37:g.102508056C>A	ENSP00000348965:p.His4029Gln	131.0	0.0	0		143.0	48.0	0.335664	NM_001376	B0I1R0|Q6DKQ7|Q8WU28|Q92814|Q9Y4G5	Missense_Mutation	SNP	ENST00000360184.4	37	CCDS9966.1	203	0.09294871794871795	138	0.2804878048780488	20	0.055248618784530384	0	0.0	45	0.059366754617414245	C	7.360	0.624576	0.14193	0.272129	0.062093	ENSG00000197102	ENST00000360184	T	0.07908	3.15	5.61	4.59	0.56863	Dynein heavy chain (1);	0.094690	0.64402	D	0.000001	T	0.00012	0.0000	N	0.03154	-0.405	0.22112	P	0.999354976	B	0.06786	0.001	B	0.04013	0.001	T	0.48570	-0.9024	9	0.18710	T	0.47	.	8.1177	0.30953	0.0:0.7299:0.0:0.2701	rs10129889;rs17292699;rs17292706;rs17541554;rs57501843;rs10129889	4029	Q14204	DYHC1_HUMAN	Q	4029	ENSP00000348965:H4029Q	ENSP00000348965:H4029Q	H	+	3	2	DYNC1H1	101577809	0.995000	0.38212	0.984000	0.44739	0.984000	0.73092	0.450000	0.21762	1.256000	0.44068	0.655000	0.94253	CAC	C|0.882;A|0.118	0.118	strong		0.602	DYNC1H1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000414574.1	NM_001376	
AHNAK2	113146	hgsc.bcm.edu	37	14	105413649	105413649	+	Silent	SNP	A	A	G	rs201545349	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr14:105413649A>G	ENST00000333244.5	-	7	8258	c.8139T>C	c.(8137-8139)gaT>gaC	p.D2713D	AHNAK2_ENST00000557457.1_Intron	NM_138420.2	NP_612429.2	Q8IVF2	AHNK2_HUMAN	AHNAK nucleoprotein 2	2713						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)			GGAGTTTCACATCCACCTGGC	0.612													.|||	29	0.00579073	0.0174	0.0	5008	,	,		17337	0.0		0.0	False		,,,				2504	0.0061				p.D2713D		Atlas-SNP	.											AHNAK2_ENST00000333244,NS,carcinoma,-2,1	AHNAK2	719	1	0			c.T8139C						scavenged	.						130.0	144.0	139.0					14																	105413649		1936	4121	6057	SO:0001819	synonymous_variant	113146	exon7			TTTCACATCCACC	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.8139T>C	14.37:g.105413649A>G		239.0	2.0	0.0083682		281.0	13.0	0.0462633	NM_138420	Q5BKX7|Q7Z343|Q7Z358|Q7Z394|Q7Z3G0|Q86WQ6|Q8IYY1|Q8N3G4|Q96EX9	Silent	SNP	ENST00000333244.5	37	CCDS45177.1																																																																																			A|0.998;G|0.002	0.002	weak		0.612	AHNAK2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000410300.1	NM_138420	
TMEM8A	58986	hgsc.bcm.edu	37	16	427452	427452	+	Missense_Mutation	SNP	C	C	T	rs146645376	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr16:427452C>T	ENST00000431232.2	-	3	593	c.433G>A	c.(433-435)Gtt>Att	p.V145I	TMEM8A_ENST00000250930.3_5'UTR|TMEM8A_ENST00000476735.1_5'UTR	NM_021259.2	NP_067082.2	Q9HCN3	TMM8A_HUMAN	transmembrane protein 8A	145					cell adhesion (GO:0007155)	extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|lysosomal membrane (GO:0005765)				central_nervous_system(2)|endometrium(2)|kidney(1)|large_intestine(2)|lung(5)|pancreas(1)|prostate(1)	14						GGGTGGGAAACGTTGACGGAG	0.692											OREG0003703	type=REGULATORY REGION|Gene=TMEM8|Dataset=Stanford ENCODE Dataset|EvidenceSubtype=Transient transfection luciferase assay	C|||	3	0.000599042	0.0	0.0014	5008	,	,		15162	0.0		0.002	False		,,,				2504	0.0				p.V145I		Atlas-SNP	.											.	TMEM8A	49	.	0			c.G433A						PASS	.	C	ILE/VAL	1,4383		0,1,2191	20.0	21.0	21.0		433	-2.8	0.7	16	dbSNP_134	21	21,8571		0,21,4275	yes	missense	TMEM8A	NM_021259.2	29	0,22,6466	TT,TC,CC		0.2444,0.0228,0.1695	benign	145/772	427452	22,12954	2192	4296	6488	SO:0001583	missense	58986	exon3			GGGAAACGTTGAC	AB045292	CCDS10407.1	16p13.3	2009-06-12	2009-06-12	2009-06-12	ENSG00000129925	ENSG00000129925			17205	protein-coding gene	gene with protein product			"""transmembrane protein 6"", ""transmembrane protein 8 (five membrane-spanning domains)"""	TMEM6, TMEM8		11006113	Standard	NM_021259		Approved	M83	uc002cgu.4	Q9HCN3	OTTHUMG00000047996	ENST00000431232.2:c.433G>A	16.37:g.427452C>T	ENSP00000401338:p.Val145Ile	124.0	0.0	0	588	166.0	76.0	0.457831	NM_021259	D3DU49|Q4TT35|Q8WU24|Q96S25|Q9BR03|Q9BT97|Q9H7B9	Missense_Mutation	SNP	ENST00000431232.2	37	CCDS10407.1	4	0.0018315018315018315	0	0.0	2	0.0055248618784530384	0	0.0	2	0.002638522427440633	C	2.751	-0.260131	0.05791	2.28E-4	0.002444	ENSG00000129925	ENST00000431232	T	0.22945	1.93	4.59	-2.78	0.05859	.	0.629806	0.14558	N	0.312254	T	0.09158	0.0226	N	0.16833	0.445	0.80722	D	1	B	0.16396	0.017	B	0.06405	0.002	T	0.28364	-1.0046	10	0.15066	T	0.55	-0.0054	12.862	0.57918	0.0:0.1718:0.0:0.8282	.	145	Q9HCN3	TMM8A_HUMAN	I	145	ENSP00000401338:V145I	ENSP00000401338:V145I	V	-	1	0	TMEM8A	367453	0.069000	0.21087	0.699000	0.30290	0.293000	0.27360	-0.831000	0.04405	-0.760000	0.04677	0.563000	0.77884	GTT	C|0.998;T|0.002	0.002	strong		0.692	TMEM8A-001	KNOWN	basic|appris_candidate_longest|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000109257.2	NM_021259	
BRD1	23774	hgsc.bcm.edu	37	22	50187853	50187853	+	Missense_Mutation	SNP	C	C	T	rs35331092	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr22:50187853C>T	ENST00000216267.8	-	6	2674	c.2188G>A	c.(2188-2190)Gct>Act	p.A730T	BRD1_ENST00000342989.5_Missense_Mutation_p.A325T|BRD1_ENST00000404034.1_Missense_Mutation_p.A730T|BRD1_ENST00000542442.1_Missense_Mutation_p.A418T|BRD1_ENST00000404760.1_Missense_Mutation_p.A730T|BRD1_ENST00000457780.2_Missense_Mutation_p.A730T	NM_014577.1	NP_055392.1	O95696	BRD1_HUMAN	bromodomain containing 1	730			A -> T (in dbSNP:rs35331092).		histone H3 acetylation (GO:0043966)	MOZ/MORF histone acetyltransferase complex (GO:0070776)|nucleus (GO:0005634)	histone binding (GO:0042393)|zinc ion binding (GO:0008270)			endometrium(6)|kidney(3)|large_intestine(5)|lung(17)|ovary(1)|pancreas(1)|prostate(3)|skin(1)	37		all_cancers(38;6.11e-10)|all_epithelial(38;8.06e-09)|all_lung(38;6.64e-05)|Lung NSC(38;0.0011)|Breast(42;0.00235)|Ovarian(80;0.0139)|Lung SC(80;0.164)		UCEC - Uterine corpus endometrioid carcinoma (28;0.0369)|BRCA - Breast invasive adenocarcinoma(115;0.21)		GACTTCATAGCGCAGGTGAGG	0.607													C|||	342	0.0682907	0.0825	0.0317	5008	,	,		18559	0.003		0.0596	False		,,,				2504	0.1513				p.A730T		Atlas-SNP	.											.	BRD1	144	.	0			c.G2188A						PASS	.	C	THR/ALA	422,3984	206.5+/-228.1	21,380,1802	59.0	63.0	62.0		2188	-0.9	0.4	22	dbSNP_126	62	590,8010	156.4+/-210.3	24,542,3734	yes	missense	BRD1	NM_014577.1	58	45,922,5536	TT,TC,CC		6.8605,9.5778,7.781	benign	730/1059	50187853	1012,11994	2203	4300	6503	SO:0001583	missense	23774	exon6			TCATAGCGCAGGT	AF005067	CCDS14080.1	22q13.33	2008-07-01	2002-01-14		ENSG00000100425	ENSG00000100425			1102	protein-coding gene	gene with protein product	"""BR140-like"""	604589	"""bromodomain-containing 1"""			10591208, 10602503	Standard	NM_014577		Approved	BRL, BRPF2	uc003biv.3	O95696	OTTHUMG00000150288	ENST00000216267.8:c.2188G>A	22.37:g.50187853C>T	ENSP00000216267:p.Ala730Thr	110.0	0.0	0		100.0	59.0	0.59	NM_014577	A6ZJA4	Missense_Mutation	SNP	ENST00000216267.8	37	CCDS14080.1	96	0.04395604395604396	41	0.08333333333333333	12	0.03314917127071823	0	0.0	43	0.05672823218997362	C	14.17	2.456934	0.43634	0.095778	0.068605	ENSG00000100425	ENST00000216267;ENST00000404034;ENST00000404760;ENST00000457780;ENST00000542442;ENST00000342989;ENST00000419212	T;T;T;T;T;T	0.28255	2.57;2.57;2.58;2.44;1.62;2.01	5.4	-0.94	0.10405	.	0.418477	0.26248	N	0.025479	T	0.00754	0.0025	L	0.39898	1.24	0.28355	P	0.9207138	P;P;P;D	0.54964	0.948;0.63;0.788;0.969	B;B;B;B	0.43728	0.247;0.12;0.169;0.429	T	0.07654	-1.0761	9	0.31617	T	0.26	.	21.7236	0.99959	0.1644:0.8356:0.0:0.0	rs35331092	730;325;730;730	Q86X06;B7Z926;O95696;O95696-2	.;.;BRD1_HUMAN;.	T	730;730;730;730;418;325;190	ENSP00000216267:A730T;ENSP00000384076:A730T;ENSP00000385858:A730T;ENSP00000410042:A730T;ENSP00000437514:A418T;ENSP00000345886:A325T	ENSP00000216267:A730T	A	-	1	0	BRD1	48573857	0.065000	0.20965	0.369000	0.25952	0.980000	0.70556	0.428000	0.21395	-0.460000	0.07003	0.655000	0.94253	GCT	C|0.936;T|0.064	0.064	strong		0.607	BRD1-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000317402.1	NM_014577	
CTRC	11330	hgsc.bcm.edu	37	1	15772212	15772212	+	Missense_Mutation	SNP	C	C	T	rs121909293	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr1:15772212C>T	ENST00000375949.4	+	7	786	c.760C>T	c.(760-762)Cgg>Tgg	p.R254W	CTRC_ENST00000483406.1_3'UTR|CTRC_ENST00000375943.2_3'UTR	NM_007272.2	NP_009203.2	Q99895	CTRC_HUMAN	chymotrypsin C (caldecrin)	254	Peptidase S1. {ECO:0000255|PROSITE- ProRule:PRU00274}.		Missing (in PCTT; associated with disease susceptibility; results in reduced protein secretion and loss of activity). {ECO:0000269|PubMed:18172691}.|R -> Q (found in a patient with chronic pancreatitis; unknown pathological significance; mutant protein secretion, activity and trypsin-mediated degradation are comparable to those of wild-type). {ECO:0000269|PubMed:19407484}.|R -> W (in PCTT; associated with susceptibility to disease; results in reduced secretion; normal activity; the mutant undergoes proteolytic degradation during trypsin-mediated activation; dbSNP:rs121909293). {ECO:0000269|PubMed:18059268, ECO:0000269|PubMed:18172691, ECO:0000269|PubMed:22580415, ECO:0000269|PubMed:23135764}.		proteolysis (GO:0006508)		peptidase activity (GO:0008233)|serine-type endopeptidase activity (GO:0004252)			endometrium(3)|kidney(1)|large_intestine(2)|lung(6)|prostate(1)	13		Breast(348;0.000207)|all_lung(284;0.00021)|Colorectal(325;0.000257)|Lung NSC(340;0.000269)|Renal(390;0.000518)|Ovarian(437;0.0129)|Myeloproliferative disorder(586;0.0255)|Hepatocellular(190;0.0634)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0228)|Colorectal(212;5.96e-07)|COAD - Colon adenocarcinoma(227;3.56e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000115)|KIRC - Kidney renal clear cell carcinoma(229;0.00244)|STAD - Stomach adenocarcinoma(313;0.0072)|READ - Rectum adenocarcinoma(331;0.0649)		AGTCTACACCCGGGTGTCCGC	0.632													C|||	8	0.00159744	0.0	0.0	5008	,	,		15935	0.0		0.008	False		,,,				2504	0.0				p.R254W		Atlas-SNP	.											.	CTRC	28	.	0			c.C760T	GRCh37	CM080169	CTRC	M	rs121909293	PASS	.	C	TRP/ARG	1,4405	2.1+/-5.4	0,1,2202	81.0	82.0	82.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	760	4.7	1.0	1	dbSNP_133	82	33,8567	22.8+/-68.1	0,33,4267	yes	missense	CTRC	NM_007272.2	101	0,34,6469	TT,TC,CC		0.3837,0.0227,0.2614	probably-damaging	254/269	15772212	34,12972	2203	4300	6503	SO:0001583	missense	11330	exon7			TACACCCGGGTGT	BC015118	CCDS156.1	1p36.21	2009-02-18			ENSG00000162438	ENSG00000162438	3.4.21.2		2523	protein-coding gene	gene with protein product	"""elastase 4"""	601405				8635596	Standard	NM_007272		Approved	CLCR, ELA4	uc001awi.1	Q99895	OTTHUMG00000002255	ENST00000375949.4:c.760C>T	1.37:g.15772212C>T	ENSP00000365116:p.Arg254Trp	63.0	0.0	0		37.0	10.0	0.27027	NM_007272	A8K082|O00765|Q9NUH5	Missense_Mutation	SNP	ENST00000375949.4	37	CCDS156.1	9	0.004120879120879121	0	0.0	0	0.0	0	0.0	9	0.011873350923482849	C	19.97	3.925157	0.73213	2.27E-4	0.003837	ENSG00000162438	ENST00000375949	D	0.94793	-3.52	4.68	4.68	0.58851	Peptidase cysteine/serine, trypsin-like (1);Peptidase S1/S6, chymotrypsin/Hap (3);	0.053971	0.85682	D	0.000000	D	0.97244	0.9099	H	0.94808	3.585	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.96153	0.9109	10	0.87932	D	0	-43.8301	16.7021	0.85357	0.0:1.0:0.0:0.0	.	254	Q99895	CTRC_HUMAN	W	254	ENSP00000365116:R254W	ENSP00000365116:R254W	R	+	1	2	CTRC	15644799	0.930000	0.31532	1.000000	0.80357	0.586000	0.36452	1.189000	0.32114	2.606000	0.88127	0.650000	0.86243	CGG	C|0.997;T|0.003	0.003	strong		0.632	CTRC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000006435.1	NM_007272	
PIK3C2A	5286	hgsc.bcm.edu	37	11	17158120	17158120	+	Missense_Mutation	SNP	C	C	T	rs61733866	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr11:17158120C>T	ENST00000265970.7	-	8	1756	c.1757G>A	c.(1756-1758)aGt>aAt	p.S586N	PIK3C2A_ENST00000531428.1_Intron|PIK3C2A_ENST00000540361.1_Missense_Mutation_p.S206N	NM_002645.2	NP_002636.2	O00443	P3C2A_HUMAN	phosphatidylinositol-4-phosphate 3-kinase, catalytic subunit type 2 alpha	586					clathrin coat assembly (GO:0048268)|endocytosis (GO:0006897)|epidermal growth factor receptor signaling pathway (GO:0007173)|exocytosis (GO:0006887)|insulin receptor signaling pathway (GO:0008286)|phosphatidylinositol biosynthetic process (GO:0006661)|phosphatidylinositol-mediated signaling (GO:0048015)|phospholipid metabolic process (GO:0006644)|platelet-derived growth factor receptor signaling pathway (GO:0048008)|small molecule metabolic process (GO:0044281)|vascular smooth muscle contraction (GO:0014829)	cytoplasm (GO:0005737)|cytoplasmic vesicle (GO:0031410)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|membrane (GO:0016020)|nucleus (GO:0005634)|phosphatidylinositol 3-kinase complex (GO:0005942)|plasma membrane (GO:0005886)|vesicle (GO:0031982)	1-phosphatidylinositol-3-kinase activity (GO:0016303)|1-phosphatidylinositol-4-phosphate 3-kinase activity (GO:0035005)|ATP binding (GO:0005524)|phosphatidylinositol 3-kinase activity (GO:0035004)|phosphatidylinositol binding (GO:0035091)			central_nervous_system(4)|endometrium(5)|kidney(5)|large_intestine(7)|lung(24)|ovary(3)|prostate(4)|skin(2)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	58						ATCTAAAGCACTACAGATTTT	0.328													C|||	32	0.00638978	0.0	0.0043	5008	,	,		16548	0.0		0.005	False		,,,				2504	0.0245				p.S586N		Atlas-SNP	.											.	PIK3C2A	148	.	0			c.G1757A						PASS	.	C	ASN/SER	8,4390	15.5+/-35.6	0,8,2191	114.0	109.0	111.0		1757	4.6	1.0	11	dbSNP_129	111	97,8489	53.1+/-113.8	0,97,4196	yes	missense	PIK3C2A	NM_002645.2	46	0,105,6387	TT,TC,CC		1.1297,0.1819,0.8087	benign	586/1687	17158120	105,12879	2199	4293	6492	SO:0001583	missense	5286	exon8			AAAGCACTACAGA	Y13367	CCDS7824.1	11p15.5-p14	2012-07-13	2012-07-13			ENSG00000011405	2.7.1.154		8971	protein-coding gene	gene with protein product		603601	"""phosphoinositide-3-kinase, class 2, alpha polypeptide"""			9337861	Standard	NM_002645		Approved	PI3K-C2alpha	uc001mmq.4	O00443		ENST00000265970.7:c.1757G>A	11.37:g.17158120C>T	ENSP00000265970:p.Ser586Asn	104.0	0.0	0		77.0	39.0	0.506494	NM_002645	B0LPH2|B4E2G4|Q14CQ9	Missense_Mutation	SNP	ENST00000265970.7	37	CCDS7824.1	9	0.004120879120879121	0	0.0	4	0.011049723756906077	0	0.0	5	0.006596306068601583	C	11.39	1.626054	0.28978	0.001819	0.011297	ENSG00000011405	ENST00000265970;ENST00000540361;ENST00000544896	T;T	0.62788	0.0;0.38	5.5	4.58	0.56647	.	0.440892	0.29995	N	0.010680	T	0.36908	0.0984	L	0.35723	1.085	0.32142	N	0.585417	B	0.23735	0.09	B	0.21360	0.034	T	0.43393	-0.9394	10	0.10377	T	0.69	-8.3308	7.5542	0.27814	0.0:0.7019:0.1477:0.1504	.	586	O00443	P3C2A_HUMAN	N	586;206;586	ENSP00000265970:S586N;ENSP00000438687:S206N	ENSP00000265970:S586N	S	-	2	0	PIK3C2A	17114696	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	2.729000	0.47327	1.459000	0.47892	0.561000	0.74099	AGT	C|0.992;T|0.008	0.008	strong		0.328	PIK3C2A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000387553.1	NM_002645	
AMDHD2	51005	hgsc.bcm.edu	37	16	2577943	2577943	+	Missense_Mutation	SNP	A	A	C	rs182580356	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr16:2577943A>C	ENST00000293971.6	+	5	679	c.585A>C	c.(583-585)gaA>gaC	p.E195D	AMDHD2_ENST00000565570.1_Intron|ATP6C_ENST00000569317.1_Missense_Mutation_p.E148D|AMDHD2_ENST00000413459.3_Missense_Mutation_p.E195D|AMDHD2_ENST00000302956.4_Missense_Mutation_p.E195D|CEMP1_ENST00000382350.1_Intron	NM_015944.3	NP_057028.2	Q9Y303	NAGA_HUMAN	amidohydrolase domain containing 2	195					carbohydrate metabolic process (GO:0005975)|N-acetylglucosamine metabolic process (GO:0006044)|N-acetylneuraminate catabolic process (GO:0019262)	nucleus (GO:0005634)	metal ion binding (GO:0046872)|N-acetylglucosamine-6-phosphate deacetylase activity (GO:0008448)			breast(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(1)|lung(5)|prostate(3)|skin(2)|urinary_tract(2)	19						GTAGCCACGAAGTGATCCGGG	0.682													G|||	5	0.000998403	0.0	0.0043	5008	,	,		13543	0.0		0.002	False		,,,				2504	0.0				p.E195D		Atlas-SNP	.											.	AMDHD2	33	.	0			c.A585C						PASS	.	A	ASP/GLU,ASP/GLU	2,4356		0,2,2177	11.0	15.0	13.0		585,585	-1.5	0.9	16		13	22,8546		0,22,4262	yes	missense,missense	AMDHD2	NM_001145815.1,NM_015944.3	45,45	0,24,6439	CC,CA,AA		0.2568,0.0459,0.1857	benign,benign	195/595,195/440	2577943	24,12902	2179	4284	6463	SO:0001583	missense	51005	exon5			CCACGAAGTGATC	AF132948	CCDS10471.1, CCDS53984.1	16p13.3	2008-02-05			ENSG00000162066	ENSG00000162066			24262	protein-coding gene	gene with protein product						10810093	Standard	NM_001145815		Approved	CGI-14	uc010uwc.2	Q9Y303	OTTHUMG00000128866	ENST00000293971.6:c.585A>C	16.37:g.2577943A>C	ENSP00000293971:p.Glu195Asp	39.0	0.0	0		18.0	10.0	0.555556	NM_001145815	B4DL77|Q8WV54	Missense_Mutation	SNP	ENST00000293971.6	37		3	0.0013736263736263737	0	0.0	3	0.008287292817679558	0	0.0	0	0.0	A	11.47	1.647305	0.29246	4.59E-4	0.002568	ENSG00000162066	ENST00000413459;ENST00000302956;ENST00000293971	D;D;D	0.99948	-8.65;-8.65;-8.65	5.32	-1.49	0.08718	Amidohydrolase 1 (1);Metal-dependent hydrolase, composite domain (1);	0.163396	0.52532	D	0.000061	D	0.99420	0.9795	L	0.35414	1.06	0.80722	D	1	B;B;B	0.19706	0.038;0.002;0.002	B;B;B	0.28553	0.091;0.029;0.017	D	0.99978	1.2301	10	0.27082	T	0.32	-22.327	10.5895	0.45302	0.3942:0.0:0.6058:0.0	.	195;195;195	Q9Y303-3;Q9Y303;Q9Y303-2	.;NAGA_HUMAN;.	D	195	ENSP00000391596:E195D;ENSP00000307481:E195D;ENSP00000293971:E195D	ENSP00000293971:E195D	E	+	3	2	AMDHD2	2517944	1.000000	0.71417	0.855000	0.33649	0.188000	0.23474	0.819000	0.27308	-0.235000	0.09767	-0.146000	0.13790	GAA	A|0.999;C|0.001	0.001	strong		0.682	AMDHD2-004	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000435652.1	NM_015944	
NOLC1	9221	hgsc.bcm.edu	37	10	103919738	103919738	+	Silent	SNP	G	G	A	rs143372447	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr10:103919738G>A	ENST00000605788.1	+	8	1180	c.945G>A	c.(943-945)aaG>aaA	p.K315K	NOLC1_ENST00000603742.1_Silent_p.K34K|NOLC1_ENST00000405356.1_Silent_p.K325K|NOLC1_ENST00000488254.2_Silent_p.K316K	NM_001284389.1|NM_004741.3	NP_001271318.1|NP_004732.2	Q14978	NOLC1_HUMAN	nucleolar and coiled-body phosphoprotein 1	315	11 X 12 AA approximate repeats of an acidic serine cluster.|Interacts with RPA194.				cell cycle (GO:0007049)|mitotic nuclear division (GO:0007067)|nucleolus organization (GO:0007000)|rRNA processing (GO:0006364)	Cajal body (GO:0015030)|cytoplasm (GO:0005737)|nucleolus (GO:0005730)	ATP binding (GO:0005524)|GTP binding (GO:0005525)|poly(A) RNA binding (GO:0044822)			breast(1)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(10)|lung(12)|ovary(1)|upper_aerodigestive_tract(1)	31		Colorectal(252;0.122)		Epithelial(162;5.19e-08)|all cancers(201;9.43e-07)		CTGTGGAGAAGCAGCAGCCTG	0.572													G|||	15	0.00299521	0.0	0.0014	5008	,	,		18044	0.0		0.004	False		,,,				2504	0.0102				p.K315K		Atlas-SNP	.											.	NOLC1	61	.	0			c.G945A						PASS	.	G		7,4399	12.9+/-30.5	0,7,2196	38.0	40.0	39.0		945	4.7	1.0	10	dbSNP_134	39	30,8570	19.8+/-62.0	0,30,4270	no	coding-synonymous	NOLC1	NM_004741.3		0,37,6466	AA,AG,GG		0.3488,0.1589,0.2845		315/700	103919738	37,12969	2203	4300	6503	SO:0001819	synonymous_variant	9221	exon8			GGAGAAGCAGCAG	Z34289	CCDS7530.1, CCDS65925.1, CCDS65926.1	10q24.32	2008-08-01			ENSG00000166197	ENSG00000166197			15608	protein-coding gene	gene with protein product		602394				7657714, 10567578	Standard	XM_005270273		Approved	P130, KIAA0035, NOPP140, NOPP130	uc001kuo.2	Q14978	OTTHUMG00000018944	ENST00000605788.1:c.945G>A	10.37:g.103919738G>A		53.0	0.0	0		73.0	16.0	0.219178	NM_004741	Q15030|Q5VV70|Q9BUV3	Silent	SNP	ENST00000605788.1	37	CCDS7530.1																																																																																			G|0.998;A|0.002	0.002	strong		0.572	NOLC1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000050012.2	NM_004741	
MAP3K4	4216	hgsc.bcm.edu	37	6	161508880	161508880	+	Missense_Mutation	SNP	A	A	C	rs35533223	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr6:161508880A>C	ENST00000392142.4	+	10	2865	c.2717A>C	c.(2716-2718)cAc>cCc	p.H906P	MAP3K4_ENST00000366920.2_Missense_Mutation_p.H906P|MAP3K4_ENST00000366919.2_Missense_Mutation_p.H906P|MAP3K4_ENST00000348824.7_Missense_Mutation_p.H906P	NM_005922.2	NP_005913	Q9Y6R4	M3K4_HUMAN	mitogen-activated protein kinase kinase kinase 4	906			H -> P (in dbSNP:rs35533223). {ECO:0000269|PubMed:17344846}.		activation of MAPKK activity (GO:0000186)|chorionic trophoblast cell differentiation (GO:0060718)|intracellular signal transduction (GO:0035556)|male germ-line sex determination (GO:0019100)|MAPK cascade (GO:0000165)|placenta development (GO:0001890)|positive regulation of JUN kinase activity (GO:0043507)|positive regulation of p38MAPK cascade (GO:1900745)|regulation of gene expression (GO:0010468)|response to UV-C (GO:0010225)	cytoplasm (GO:0005737)	ATP binding (GO:0005524)|MAP kinase kinase kinase activity (GO:0004709)|metal ion binding (GO:0046872)			breast(6)|cervix(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(8)|large_intestine(20)|lung(28)|ovary(3)|skin(2)|stomach(1)	77		Breast(66;0.000776)|Ovarian(120;0.0367)|Prostate(117;0.0771)		OV - Ovarian serous cystadenocarcinoma(65;1.85e-18)|BRCA - Breast invasive adenocarcinoma(81;3.04e-05)		CTGACCAAGCACGGTGATCGA	0.512													A|||	57	0.0113818	0.0023	0.0159	5008	,	,		20328	0.0		0.0278	False		,,,				2504	0.0153				p.H906P		Atlas-SNP	.											.	MAP3K4	364	.	0			c.A2717C						PASS	.	A	PRO/HIS,PRO/HIS	36,4370	40.8+/-73.8	0,36,2167	139.0	112.0	121.0		2717,2717	2.0	0.0	6	dbSNP_126	121	344,8256	117.7+/-177.3	5,334,3961	yes	missense,missense	MAP3K4	NM_005922.2,NM_006724.2	77,77	5,370,6128	CC,CA,AA		4.0,0.8171,2.9217	possibly-damaging,possibly-damaging	906/1609,906/1559	161508880	380,12626	2203	4300	6503	SO:0001583	missense	4216	exon10			CCAAGCACGGTGA	AF002715	CCDS34565.1, CCDS34566.1, CCDS75544.1	6q26	2012-10-02			ENSG00000085511	ENSG00000085511		"""Mitogen-activated protein kinase cascade / Kinase kinase kinases"""	6856	protein-coding gene	gene with protein product		602425		MEKK4		9305639	Standard	XM_005266988		Approved	MTK1, MAPKKK4, KIAA0213	uc003qtn.3	Q9Y6R4	OTTHUMG00000015968	ENST00000392142.4:c.2717A>C	6.37:g.161508880A>C	ENSP00000375986:p.His906Pro	101.0	0.0	0		116.0	60.0	0.517241	NM_006724	A6H8W0|B7ZLD3|B9EG75|Q5VTT8|Q5VTT9|Q92612|Q9H408	Missense_Mutation	SNP	ENST00000392142.4	37	CCDS34565.1	32	0.014652014652014652	2	0.0040650406504065045	8	0.022099447513812154	0	0.0	22	0.029023746701846966	A	13.59	2.282961	0.40394	0.008171	0.04	ENSG00000085511	ENST00000366919;ENST00000392142;ENST00000540111;ENST00000366920;ENST00000348824	T;T;T;T	0.70749	-0.5;-0.49;-0.49;-0.51	5.73	1.95	0.26073	.	0.192782	0.44483	D	0.000443	T	0.48696	0.1514	L	0.60455	1.87	0.33817	D	0.628597	B;P;P	0.42993	0.305;0.797;0.472	B;B;B	0.43623	0.245;0.425;0.261	T	0.40059	-0.9583	10	0.33141	T	0.24	-6.8869	6.1099	0.20094	0.7457:0.0:0.1333:0.121	rs35533223	906;906;906	F5H538;Q9Y6R4-2;Q9Y6R4	.;.;M3K4_HUMAN	P	906	ENSP00000355886:H906P;ENSP00000375986:H906P;ENSP00000355887:H906P;ENSP00000297332:H906P	ENSP00000297332:H906P	H	+	2	0	MAP3K4	161428870	1.000000	0.71417	0.000000	0.03702	0.003000	0.03518	4.880000	0.63107	0.483000	0.27608	0.533000	0.62120	CAC	A|0.976;C|0.024	0.024	strong		0.512	MAP3K4-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000042988.3		
SLFN12	55106	hgsc.bcm.edu	37	17	33749758	33749758	+	Missense_Mutation	SNP	A	A	G	rs138003670	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr17:33749758A>G	ENST00000394562.1	-	4	813	c.290T>C	c.(289-291)aTg>aCg	p.M97T	SLFN12_ENST00000452764.3_Missense_Mutation_p.M97T|SLFN12_ENST00000304905.5_Missense_Mutation_p.M97T|SLFN12_ENST00000460530.1_5'Flank			Q8IYM2	SLN12_HUMAN	schlafen family member 12	97							ATP binding (GO:0005524)			breast(1)|kidney(2)|large_intestine(3)|lung(8)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	18		Ovarian(249;0.17)		UCEC - Uterine corpus endometrioid carcinoma (308;0.0182)		ACCATTCTGCATGAAGTCTAA	0.358													A|||	8	0.00159744	0.0	0.0	5008	,	,		20665	0.0		0.006	False		,,,				2504	0.002				p.M97T		Atlas-SNP	.											.	SLFN12	56	.	0			c.T290C						PASS	.	A	THR/MET	3,4403	6.2+/-15.9	0,3,2200	70.0	70.0	70.0		290	0.7	0.1	17	dbSNP_134	70	31,8569	21.6+/-65.8	0,31,4269	yes	missense	SLFN12	NM_018042.3	81	0,34,6469	GG,GA,AA		0.3605,0.0681,0.2614	benign	97/579	33749758	34,12972	2203	4300	6503	SO:0001583	missense	55106	exon2			TTCTGCATGAAGT	AK001122	CCDS11295.1	17q12	2006-04-05			ENSG00000172123	ENSG00000172123			25500	protein-coding gene	gene with protein product		614955				12477932	Standard	NM_018042		Approved	FLJ10260	uc002hji.4	Q8IYM2	OTTHUMG00000132952	ENST00000394562.1:c.290T>C	17.37:g.33749758A>G	ENSP00000378063:p.Met97Thr	146.0	0.0	0		117.0	53.0	0.452991	NM_018042	A8K711|Q9NP47	Missense_Mutation	SNP	ENST00000394562.1	37	CCDS11295.1	5	0.0022893772893772895	0	0.0	0	0.0	0	0.0	5	0.006596306068601583	a	12.33	1.906264	0.33628	6.81E-4	0.003605	ENSG00000172123	ENST00000394562;ENST00000304905;ENST00000452764;ENST00000447040	T;T;T;T	0.22945	3.79;3.79;3.79;1.93	3.27	0.658	0.17855	.	.	.	.	.	T	0.19406	0.0466	L	0.58583	1.82	0.09310	N	1	P	0.51791	0.948	P	0.46362	0.514	T	0.09975	-1.0650	9	0.46703	T	0.11	.	5.5093	0.16872	0.5168:0.0:0.0:0.4831	.	97	Q8IYM2	SLN12_HUMAN	T	97	ENSP00000378063:M97T;ENSP00000302077:M97T;ENSP00000394903:M97T;ENSP00000398315:M97T	ENSP00000302077:M97T	M	-	2	0	SLFN12	30773871	0.062000	0.20869	0.071000	0.20095	0.053000	0.15095	0.162000	0.16501	-0.026000	0.13895	0.358000	0.22013	ATG	A|0.998;G|0.002	0.002	strong		0.358	SLFN12-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256491.1	NM_018042	
ELK3	2004	hgsc.bcm.edu	37	12	96641452	96641452	+	Silent	SNP	C	C	T			TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr12:96641452C>T	ENST00000228741.3	+	3	1268	c.942C>T	c.(940-942)atC>atT	p.I314I	ELK3_ENST00000552142.1_Intron	NM_005230.2	NP_005221.2	P41970	ELK3_HUMAN	ELK3, ETS-domain protein (SRF accessory protein 2)	314					angiogenesis (GO:0001525)|cell differentiation (GO:0030154)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|signal transduction (GO:0007165)|transcription from RNA polymerase II promoter (GO:0006366)|wound healing (GO:0042060)	intracellular membrane-bounded organelle (GO:0043231)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	purine-rich negative regulatory element binding (GO:0032422)|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 RNA polymerase II transcription factor activity (GO:0000981)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription corepressor activity (GO:0003714)			breast(2)|cervix(1)|endometrium(1)|kidney(1)|large_intestine(4)|liver(1)|lung(5)|ovary(2)|prostate(1)|stomach(2)	20	all_cancers(2;0.00173)					TCGGCTCCATCGCCCTCAACA	0.592																																					p.I314I		Atlas-SNP	.											.	ELK3	36	.	0			c.C942T						PASS	.						37.0	35.0	36.0					12																	96641452		2203	4299	6502	SO:0001819	synonymous_variant	2004	exon3			CTCCATCGCCCTC	BC017371	CCDS9060.1	12q23	2006-12-30				ENSG00000111145			3325	protein-coding gene	gene with protein product		600247				7851904	Standard	NM_005230		Approved	ERP, NET, SAP2	uc001teo.1	P41970		ENST00000228741.3:c.942C>T	12.37:g.96641452C>T		24.0	0.0	0		19.0	9.0	0.473684	NM_005230	B2R6S6|Q6FG57|Q6GU29|Q9UD17	Silent	SNP	ENST00000228741.3	37	CCDS9060.1																																																																																			.	.	none		0.592	ELK3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000408694.1	NM_005230	
TRIM56	81844	hgsc.bcm.edu	37	7	100730707	100730707	+	Silent	SNP	T	T	C	rs372702476		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr7:100730707T>C	ENST00000306085.6	+	3	411	c.114T>C	c.(112-114)caT>caC	p.H38H		NM_030961.1	NP_112223.1	Q9BRZ2	TRI56_HUMAN	tripartite motif containing 56	38					defense response to virus (GO:0051607)|innate immune response (GO:0045087)|interferon-beta production (GO:0032608)|negative regulation of viral entry into host cell (GO:0046597)|negative regulation of viral release from host cell (GO:1902187)|positive regulation of type I interferon production (GO:0032481)|protein K63-linked ubiquitination (GO:0070534)|regulation of type I interferon production (GO:0032479)|response to type I interferon (GO:0034340)	cytoplasm (GO:0005737)|cytosol (GO:0005829)	ligase activity (GO:0016874)|poly(A) RNA binding (GO:0044822)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			breast(1)|central_nervous_system(1)|cervix(1)|kidney(1)|large_intestine(4)|lung(7)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	18	Lung NSC(181;0.136)|all_lung(186;0.182)					CCTGCCTGCATACCTACTGCC	0.687																																					p.H38H	Ovarian(89;1092 1379 22756 38989 39611)	Atlas-SNP	.											.	TRIM56	123	.	0			c.T114C						PASS	.	T		0,4242		0,0,2121	51.0	62.0	58.0		114	-1.4	1.0	7		58	2,8486		0,2,4242	no	coding-synonymous	TRIM56	NM_030961.1		0,2,6363	CC,CT,TT		0.0236,0.0,0.0157		38/756	100730707	2,12728	2121	4244	6365	SO:0001819	synonymous_variant	81844	exon3			CCTGCATACCTAC	BK000511	CCDS43625.1	7q11.2	2013-01-09	2011-01-25		ENSG00000169871	ENSG00000169871		"""Tripartite motif containing / Tripartite motif containing"", ""RING-type (C3HC4) zinc fingers"""	19028	protein-coding gene	gene with protein product			"""tripartite motif-containing 56"""				Standard	NM_030961		Approved	RNF109	uc003uxq.3	Q9BRZ2	OTTHUMG00000157032	ENST00000306085.6:c.114T>C	7.37:g.100730707T>C		60.0	0.0	0		67.0	20.0	0.298507	NM_030961	Q6PJS5|Q86VT6|Q8N2H8|Q8NAC0|Q9H031	Silent	SNP	ENST00000306085.6	37	CCDS43625.1																																																																																			.	.	weak		0.687	TRIM56-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347185.1	NM_030961	
POLR3D	661	hgsc.bcm.edu	37	8	22107986	22107986	+	Silent	SNP	A	A	G	rs75142930	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr8:22107986A>G	ENST00000397802.4	+	8	1367	c.1152A>G	c.(1150-1152)gtA>gtG	p.V384V	POLR3D_ENST00000306433.4_Silent_p.V384V			P05423	RPC4_HUMAN	polymerase (RNA) III (DNA directed) polypeptide D, 44kDa	384					defense response to virus (GO:0051607)|gene expression (GO:0010467)|innate immune response (GO:0045087)|positive regulation of innate immune response (GO:0045089)|positive regulation of interferon-beta production (GO:0032728)|positive regulation of type I interferon production (GO:0032481)|termination of RNA polymerase III transcription (GO:0006386)|transcription elongation from RNA polymerase III promoter (GO:0006385)|transcription from RNA polymerase III promoter (GO:0006383)	cytosol (GO:0005829)|DNA-directed RNA polymerase III complex (GO:0005666)|nuclear chromatin (GO:0000790)|nucleoplasm (GO:0005654)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)|DNA-directed RNA polymerase activity (GO:0003899)	p.V384V(1)		central_nervous_system(1)|endometrium(1)|large_intestine(4)|lung(5)|prostate(1)|stomach(1)	13				Colorectal(74;0.0146)|COAD - Colon adenocarcinoma(73;0.061)		ACAAACTTGTATGTTCCCCTG	0.552													A|||	158	0.0315495	0.0038	0.1124	5008	,	,		19379	0.006		0.0507	False		,,,				2504	0.0184				p.V384V		Atlas-SNP	.											POLR3D,NS,adenoma,0,2	POLR3D	26	2	1	Substitution - coding silent(1)	stomach(1)	c.A1152G						PASS	.	A		52,4354	52.9+/-88.7	0,52,2151	213.0	183.0	193.0		1152	-4.8	1.0	8	dbSNP_132	193	454,8146	136.7+/-193.7	6,442,3852	no	coding-synonymous	POLR3D	NM_001722.2		6,494,6003	GG,GA,AA		5.2791,1.1802,3.8905		384/399	22107986	506,12500	2203	4300	6503	SO:0001819	synonymous_variant	661	exon9			ACTTGTATGTTCC	M17754	CCDS34858.1	8q21	2013-01-21	2003-04-01	2003-04-04	ENSG00000168495	ENSG00000168495		"""RNA polymerase subunits"""	1080	protein-coding gene	gene with protein product		187280	"""BN51 (BHK21) temperature sensitivity complementing"""	BN51T		12391170, 11279001	Standard	NM_001722		Approved	TSBN51, RPC4	uc003xbl.3	P05423	OTTHUMG00000163778	ENST00000397802.4:c.1152A>G	8.37:g.22107986A>G		124.0	0.0	0		186.0	53.0	0.284946	NM_001722	Q6FI28|Q9BPV7|Q9BPZ1|Q9BXB3	Silent	SNP	ENST00000397802.4	37	CCDS34858.1																																																																																			A|0.958;G|0.042	0.042	strong		0.552	POLR3D-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000375434.2	NM_001722	
MAPK8IP1	9479	hgsc.bcm.edu	37	11	45924057	45924057	+	Missense_Mutation	SNP	C	C	T	rs117665789	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr11:45924057C>T	ENST00000241014.2	+	5	909	c.739C>T	c.(739-741)Cct>Tct	p.P247S	MAPK8IP1_ENST00000395629.2_Missense_Mutation_p.P237S	NM_005456.3	NP_005447.1	Q9UQF2	JIP1_HUMAN	mitogen-activated protein kinase 8 interacting protein 1	247	JNK-binding domain (JBD).				JUN phosphorylation (GO:0007258)|negative regulation of apoptotic process (GO:0043066)|negative regulation of intrinsic apoptotic signaling pathway (GO:2001243)|negative regulation of JNK cascade (GO:0046329)|negative regulation of JUN kinase activity (GO:0043508)|positive regulation of signal transduction (GO:0009967)|regulation of JNK cascade (GO:0046328)|regulation of transcription, DNA-templated (GO:0006355)|vesicle-mediated transport (GO:0016192)	axonal growth cone (GO:0044295)|cell body (GO:0044297)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|dendritic growth cone (GO:0044294)|dentate gyrus mossy fiber (GO:0044302)|endoplasmic reticulum (GO:0005783)|membrane (GO:0016020)|mitochondrion (GO:0005739)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|synapse (GO:0045202)	kinesin binding (GO:0019894)|MAP-kinase scaffold activity (GO:0005078)|protein kinase inhibitor activity (GO:0004860)			breast(1)|endometrium(2)|kidney(2)|large_intestine(7)|lung(7)|ovary(2)|prostate(1)|skin(2)	24				GBM - Glioblastoma multiforme(35;0.231)		CCAGATGGCACCTCCGGGTGG	0.706													C|||	16	0.00319489	0.0	0.0029	5008	,	,		13357	0.0		0.0109	False		,,,				2504	0.0031				p.P247S		Atlas-SNP	.											.	MAPK8IP1	51	.	0			c.C739T						PASS	.	C	SER/PRO	7,4359		0,7,2176	11.0	14.0	13.0		739	4.5	0.9	11	dbSNP_132	13	88,8478		0,88,4195	yes	missense	MAPK8IP1	NM_005456.3	74	0,95,6371	TT,TC,CC		1.0273,0.1603,0.7346	possibly-damaging	247/712	45924057	95,12837	2183	4283	6466	SO:0001583	missense	9479	exon5			ATGGCACCTCCGG		CCDS7916.1	11p11.2	2009-07-24			ENSG00000121653	ENSG00000121653			6882	protein-coding gene	gene with protein product		604641		PRKM8IP		9235893, 9442013	Standard	NM_005456		Approved	IB1, JIP-1, JIP1	uc001nbr.3	Q9UQF2	OTTHUMG00000134324	ENST00000241014.2:c.739C>T	11.37:g.45924057C>T	ENSP00000241014:p.Pro247Ser	114.0	0.0	0		72.0	37.0	0.513889	NM_005456	D3DQP4|O43407	Missense_Mutation	SNP	ENST00000241014.2	37	CCDS7916.1	10	0.004578754578754579	0	0.0	0	0.0	2	0.0034965034965034965	8	0.010554089709762533	C	13.85	2.358998	0.41801	0.001603	0.010273	ENSG00000121653	ENST00000241014;ENST00000395629	T;T	0.36699	1.24;1.25	4.51	4.51	0.55191	.	0.065445	0.64402	D	0.000011	T	0.18551	0.0445	N	0.24115	0.695	0.45541	D	0.998496	P	0.43750	0.816	B	0.37267	0.245	T	0.03514	-1.1029	10	0.27785	T	0.31	-3.6985	17.7712	0.88493	0.0:1.0:0.0:0.0	.	247	Q9UQF2	JIP1_HUMAN	S	247;237	ENSP00000241014:P247S;ENSP00000378991:P237S	ENSP00000241014:P247S	P	+	1	0	MAPK8IP1	45880633	0.428000	0.25522	0.877000	0.34402	0.627000	0.37826	3.856000	0.55964	2.504000	0.84457	0.561000	0.74099	CCT	C|0.993;T|0.007	0.007	strong		0.706	MAPK8IP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000259405.1	NM_005456	
ZKSCAN5	23660	hgsc.bcm.edu	37	7	99129744	99129744	+	Missense_Mutation	SNP	G	G	C	rs150395462	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr7:99129744G>C	ENST00000394170.2	+	7	2643	c.2392G>C	c.(2392-2394)Gag>Cag	p.E798Q	ZKSCAN5_ENST00000326775.5_Missense_Mutation_p.E798Q|ZKSCAN5_ENST00000451158.1_Missense_Mutation_p.E798Q	NM_014569.3	NP_055384.1	Q9Y2L8	ZKSC5_HUMAN	zinc finger with KRAB and SCAN domains 5	798					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|sequence-specific DNA binding transcription factor activity (GO:0003700)|zinc ion binding (GO:0008270)			breast(3)|endometrium(1)|kidney(1)|large_intestine(6)|lung(6)|ovary(1)|prostate(1)|skin(1)|urinary_tract(1)	21	all_cancers(62;2.54e-08)|all_epithelial(64;2.55e-09)|Lung NSC(181;0.0053)|all_lung(186;0.00895)|Esophageal squamous(72;0.0166)					CCATACTGGTGAGAAACCTTT	0.398													G|||	4	0.000798722	0.0	0.0014	5008	,	,		20675	0.0		0.003	False		,,,				2504	0.0				p.E798Q		Atlas-SNP	.											.	ZKSCAN5	63	.	0			c.G2392C						PASS	.	G	GLN/GLU,GLN/GLU	5,4401	11.4+/-27.6	0,5,2198	85.0	91.0	89.0		2392,2392	5.0	1.0	7	dbSNP_134	89	61,8539	38.8+/-94.9	1,59,4240	yes	missense,missense	ZKSCAN5	NM_014569.3,NM_145102.2	29,29	1,64,6438	CC,CG,GG		0.7093,0.1135,0.5075	probably-damaging,probably-damaging	798/840,798/840	99129744	66,12940	2203	4300	6503	SO:0001583	missense	23660	exon7			ACTGGTGAGAAAC	AF170025	CCDS5667.1	7q22	2013-01-09	2007-02-20	2007-02-20	ENSG00000196652	ENSG00000196652		"""Zinc fingers, C2H2-type"", ""-"", ""-"", ""-"""	12867	protein-coding gene	gene with protein product		611272	"""zinc finger protein homologous to Zfp95 in mouse"", ""zinc finger protein 95 homolog (mouse)"""	ZFP95		10585779	Standard	NM_014569		Approved	ZNF914, ZSCAN37	uc003uqv.3	Q9Y2L8	OTTHUMG00000156749	ENST00000394170.2:c.2392G>C	7.37:g.99129744G>C	ENSP00000377725:p.Glu798Gln	77.0	0.0	0		100.0	54.0	0.54	NM_145102	A4D280|D6W5S9	Missense_Mutation	SNP	ENST00000394170.2	37	CCDS5667.1	4	0.0018315018315018315	0	0.0	1	0.0027624309392265192	0	0.0	3	0.00395778364116095	G	23.4	4.411517	0.83340	0.001135	0.007093	ENSG00000196652	ENST00000326775;ENST00000451158;ENST00000394170	T;T;T	0.25912	1.77;1.77;1.77	5.03	5.03	0.67393	Zinc finger, C2H2 (1);Zinc finger, C2H2-type/integrase, DNA-binding (1);	0.116325	0.38720	N	0.001586	T	0.42177	0.1191	M	0.70595	2.14	0.50171	D	0.99985	D;D	0.76494	0.999;0.999	D;D	0.70935	0.971;0.971	T	0.45556	-0.9253	10	0.72032	D	0.01	.	16.2692	0.82607	0.0:0.0:1.0:0.0	.	798;798	Q8N718;Q9Y2L8	.;ZKSC5_HUMAN	Q	798	ENSP00000322872:E798Q;ENSP00000392104:E798Q;ENSP00000377725:E798Q	ENSP00000322872:E798Q	E	+	1	0	ZKSCAN5	98967680	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	5.485000	0.66850	2.782000	0.95742	0.655000	0.94253	GAG	G|0.996;C|0.004	0.004	strong		0.398	ZKSCAN5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000345597.1	NM_014569	
RFTN1	23180	hgsc.bcm.edu	37	3	16419238	16419238	+	Missense_Mutation	SNP	C	C	G			TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr3:16419238C>G	ENST00000334133.4	-	5	1085	c.813G>C	c.(811-813)gaG>gaC	p.E271D	RFTN1_ENST00000432519.1_Missense_Mutation_p.E235D	NM_015150.1	NP_055965.1	Q14699	RFTN1_HUMAN	raftlin, lipid raft linker 1	271					B cell receptor signaling pathway (GO:0050853)|dsRNA transport (GO:0033227)|growth (GO:0040007)|interleukin-17 production (GO:0032620)|membrane raft assembly (GO:0001765)|protein localization to membrane raft (GO:1903044)|protein transport into membrane raft (GO:0032596)|response to exogenous dsRNA (GO:0043330)|T cell antigen processing and presentation (GO:0002457)|T cell receptor signaling pathway (GO:0050852)|toll-like receptor 3 signaling pathway (GO:0034138)	cytoplasm (GO:0005737)|endosome (GO:0005768)|extracellular vesicular exosome (GO:0070062)|membrane raft (GO:0045121)|plasma membrane (GO:0005886)|protein complex (GO:0043234)	double-stranded RNA binding (GO:0003725)			central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(5)|kidney(3)|large_intestine(8)|lung(8)|ovary(4)|prostate(2)|skin(1)|upper_aerodigestive_tract(2)	38						CTGAGAGTGGCTCTTCATGCA	0.512																																					p.E271D		Atlas-SNP	.											.	RFTN1	79	.	0			c.G813C						PASS	.						64.0	68.0	67.0					3																	16419238		2203	4300	6503	SO:0001583	missense	23180	exon5			GAGTGGCTCTTCA	D42043	CCDS33712.1	3p24.3	2010-04-09			ENSG00000131378	ENSG00000131378			30278	protein-coding gene	gene with protein product	"""raft-linking protein"""					7788527, 12805216	Standard	NM_015150		Approved	MIG2, KIAA0084, FLJ23866, Raftlin	uc003cay.3	Q14699	OTTHUMG00000156973	ENST00000334133.4:c.813G>C	3.37:g.16419238C>G	ENSP00000334153:p.Glu271Asp	101.0	0.0	0		135.0	37.0	0.274074	NM_015150	Q0D2G0|Q496Y2|Q4QQI7|Q5JB48|Q7Z7P2	Missense_Mutation	SNP	ENST00000334133.4	37	CCDS33712.1	.	.	.	.	.	.	.	.	.	.	C	14.13	2.443891	0.43429	.	.	ENSG00000131378	ENST00000432519;ENST00000334133;ENST00000451036	T;T;T	0.49139	1.5;1.5;0.79	4.67	-0.787	0.10943	.	0.907323	0.09628	N	0.776624	T	0.33527	0.0866	L	0.36672	1.1	0.21290	N	0.999731	B;B	0.18461	0.028;0.028	B;B	0.16722	0.016;0.016	T	0.27971	-1.0058	10	0.44086	T	0.13	-34.4945	5.6878	0.17813	0.0:0.4135:0.1371:0.4494	.	235;271	G3XAJ6;Q14699	.;RFTN1_HUMAN	D	235;271;271	ENSP00000403926:E235D;ENSP00000334153:E271D;ENSP00000403997:E271D	ENSP00000334153:E271D	E	-	3	2	RFTN1	16394242	0.002000	0.14202	0.103000	0.21229	0.791000	0.44710	-0.043000	0.12043	-0.073000	0.12842	0.561000	0.74099	GAG	.	.	none		0.512	RFTN1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000346908.1	NM_015150	
FURIN	5045	hgsc.bcm.edu	37	15	91424029	91424029	+	Silent	SNP	C	C	T	rs142489043	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr15:91424029C>T	ENST00000268171.3	+	14	1944	c.1665C>T	c.(1663-1665)agC>agT	p.S555S		NM_002569.2	NP_002560.1	P09958	FURIN_HUMAN	furin (paired basic amino acid cleaving enzyme)	555					cell proliferation (GO:0008283)|cellular protein metabolic process (GO:0044267)|collagen catabolic process (GO:0030574)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|negative regulation of endopeptidase activity (GO:0010951)|negative regulation of low-density lipoprotein particle receptor catabolic process (GO:0032804)|negative regulation of transforming growth factor beta1 production (GO:0032911)|nerve growth factor processing (GO:0032455)|nerve growth factor production (GO:0032902)|neurotrophin TRK receptor signaling pathway (GO:0048011)|Notch signaling pathway (GO:0007219)|peptide biosynthetic process (GO:0043043)|peptide hormone processing (GO:0016486)|peptidyl-glutamic acid carboxylation (GO:0017187)|positive regulation of membrane protein ectodomain proteolysis (GO:0051044)|post-translational protein modification (GO:0043687)|protein processing (GO:0016485)|proteolysis (GO:0006508)|regulation of endopeptidase activity (GO:0052548)|regulation of protein catabolic process (GO:0042176)|secretion by cell (GO:0032940)|signal peptide processing (GO:0006465)|transforming growth factor beta receptor signaling pathway (GO:0007179)|viral life cycle (GO:0019058)|viral process (GO:0016032)|viral protein processing (GO:0019082)|virion assembly (GO:0019068)	cell surface (GO:0009986)|extracellular vesicular exosome (GO:0070062)|Golgi lumen (GO:0005796)|Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|membrane raft (GO:0045121)|plasma membrane (GO:0005886)|trans-Golgi network (GO:0005802)|trans-Golgi network transport vesicle (GO:0030140)	endopeptidase activity (GO:0004175)|metal ion binding (GO:0046872)|nerve growth factor binding (GO:0048406)|peptidase activity (GO:0008233)|peptide binding (GO:0042277)|protease binding (GO:0002020)|serine-type endopeptidase activity (GO:0004252)|serine-type endopeptidase inhibitor activity (GO:0004867)			breast(1)|central_nervous_system(4)|endometrium(4)|large_intestine(3)|liver(2)|lung(13)|ovary(2)|prostate(3)|skin(1)|urinary_tract(3)	36	Lung NSC(78;0.0771)|all_lung(78;0.137)		Lung(145;0.189)			AAAACACCAGCGAAGCCAACA	0.557													C|||	4	0.000798722	0.0	0.0	5008	,	,		19315	0.0		0.004	False		,,,				2504	0.0				p.S555S		Atlas-SNP	.											.	FURIN	85	.	0			c.C1665T						PASS	.	C		0,4396		0,0,2198	85.0	83.0	84.0		1665	-7.6	0.8	15	dbSNP_134	84	36,8560	25.1+/-72.6	0,36,4262	no	coding-synonymous	FURIN	NM_002569.2		0,36,6460	TT,TC,CC		0.4188,0.0,0.2771		555/795	91424029	36,12956	2198	4298	6496	SO:0001819	synonymous_variant	5045	exon14			CACCAGCGAAGCC	X17094	CCDS10364.1	15q26.1	2007-01-24	2002-12-04	2002-12-06	ENSG00000140564	ENSG00000140564			8568	protein-coding gene	gene with protein product		136950	"""paired basic amino acid cleaving enzyme (furin, membrane associated receptor protein)"""	PCSK3, FUR, PACE		2251280, 1741956	Standard	NM_002569		Approved	SPC1	uc002bpu.1	P09958	OTTHUMG00000149831	ENST00000268171.3:c.1665C>T	15.37:g.91424029C>T		195.0	0.0	0		143.0	30.0	0.20979	NM_002569	Q14336|Q6LBS3|Q9UCZ5	Silent	SNP	ENST00000268171.3	37	CCDS10364.1																																																																																			C|0.997;T|0.003	0.003	strong		0.557	FURIN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000313492.1	NM_002569	
FERMT1	55612	hgsc.bcm.edu	37	20	6078246	6078246	+	Silent	SNP	C	C	T	rs149893089		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr20:6078246C>T	ENST00000217289.4	-	7	1670	c.882G>A	c.(880-882)gaG>gaA	p.E294E	FERMT1_ENST00000536936.1_Silent_p.E37E	NM_017671.4	NP_060141.3	Q9BQL6	FERM1_HUMAN	fermitin family member 1	294	FERM.				cell adhesion (GO:0007155)|establishment of epithelial cell polarity (GO:0090162)|keratinocyte migration (GO:0051546)|keratinocyte proliferation (GO:0043616)	cell junction (GO:0030054)|cell projection (GO:0042995)|cytosol (GO:0005829)|filamentous actin (GO:0031941)|focal adhesion (GO:0005925)|plasma membrane (GO:0005886)				NS(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(3)|lung(3)|ovary(1)|pancreas(1)|prostate(2)|skin(2)	17						ACCTGGCTTGCTCATAGAGTT	0.393													T|||	1	0.000199681	0.0	0.0	5008	,	,		15796	0.0		0.0	False		,,,				2504	0.001				p.E294E		Atlas-SNP	.											.	FERMT1	106	.	0			c.G882A						PASS	.	T		1,4405	826.1+/-416.6	0,1,2202	143.0	135.0	138.0		882	0.8	1.0	20	dbSNP_134	138	5,8595	819.0+/-406.8	0,5,4295	no	coding-synonymous	FERMT1	NM_017671.4		0,6,6497	TT,TC,CC		0.0581,0.0227,0.0461		294/678	6078246	6,13000	2203	4300	6503	SO:0001819	synonymous_variant	55612	exon7			GGCTTGCTCATAG	AK000123	CCDS13098.1	20p12.3	2013-01-10	2010-06-24	2007-12-14	ENSG00000101311	ENSG00000101311		"""Fermitins"", ""Pleckstrin homology (PH) domain containing"""	15889	protein-coding gene	gene with protein product	"""kindlin-1"", ""kinderlin"""	607900	"""chromosome 20 open reading frame 42"", ""fermitin family homolog 1 (Drosophila)"""	C20orf42		12697302, 12789646	Standard	NM_017671		Approved	FLJ20116, URP1, KIND1, UNC112A	uc002wmr.3	Q9BQL6	OTTHUMG00000031826	ENST00000217289.4:c.882G>A	20.37:g.6078246C>T		159.0	0.0	0		157.0	74.0	0.471338	NM_017671	D3DW10|Q8IX34|Q8IYH2|Q9NWM2|Q9NXQ3	Silent	SNP	ENST00000217289.4	37	CCDS13098.1																																																																																			C|0.999;T|0.001	0.001	strong		0.393	FERMT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000077908.2	NM_017671	
CEP250	11190	hgsc.bcm.edu	37	20	34092076	34092076	+	Missense_Mutation	SNP	G	G	A	rs56259282	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr20:34092076G>A	ENST00000397527.1	+	30	6599	c.5879G>A	c.(5878-5880)cGg>cAg	p.R1960Q	CEP250_ENST00000342580.4_Missense_Mutation_p.R1904Q	NM_007186.3	NP_009117.2	Q9BV73	CP250_HUMAN	centrosomal protein 250kDa	1960	Gln/Glu-rich.				centriole-centriole cohesion (GO:0010457)|G2/M transition of mitotic cell cycle (GO:0000086)|mitotic cell cycle (GO:0000278)|protein localization (GO:0008104)|protein localization to organelle (GO:0033365)|regulation of centriole-centriole cohesion (GO:0030997)	centriole (GO:0005814)|centrosome (GO:0005813)|cilium (GO:0005929)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|microtubule organizing center (GO:0005815)|protein complex (GO:0043234)|spindle pole centrosome (GO:0031616)	protein C-terminus binding (GO:0008022)|protein domain specific binding (GO:0019904)|protein kinase binding (GO:0019901)			NS(1)|breast(2)|central_nervous_system(3)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(13)|lung(13)|ovary(4)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	45	Lung NSC(9;0.00156)|all_lung(11;0.00243)		BRCA - Breast invasive adenocarcinoma(18;0.0106)			GAGGCTGCCCGGGCCCGGGCT	0.657													G|||	24	0.00479233	0.0008	0.0115	5008	,	,		18767	0.0		0.0119	False		,,,				2504	0.0031				p.R1960Q		Atlas-SNP	.											.	CEP250	141	.	0			c.G5879A						PASS	.	G	GLN/ARG	9,4369		0,9,2180	9.0	11.0	10.0		5879	-4.0	0.0	20	dbSNP_129	10	103,8479		2,99,4190	yes	missense	CEP250	NM_007186.3	43	2,108,6370	AA,AG,GG		1.2002,0.2056,0.8642	benign	1960/2443	34092076	112,12848	2189	4291	6480	SO:0001583	missense	11190	exon30			CTGCCCGGGCCCG	AF022655	CCDS13255.1	20q11.22	2014-02-20	2006-01-11	2006-01-11	ENSG00000126001	ENSG00000126001			1859	protein-coding gene	gene with protein product		609689	"""centrosomal protein 2"""	CEP2		9506584, 9647649	Standard	NM_007186		Approved	C-NAP1	uc021wco.1	Q9BV73	OTTHUMG00000032343	ENST00000397527.1:c.5879G>A	20.37:g.34092076G>A	ENSP00000380661:p.Arg1960Gln	43.0	0.0	0		40.0	19.0	0.475	NM_007186	E1P5Q3|O14812|O60588|Q9H450	Missense_Mutation	SNP	ENST00000397527.1	37	CCDS13255.1	15	0.006868131868131868	0	0.0	8	0.022099447513812154	0	0.0	7	0.009234828496042216	G	2.257	-0.370208	0.05069	0.002056	0.012002	ENSG00000126001	ENST00000397527;ENST00000342580;ENST00000422671	T;T;T	0.41065	3.05;3.04;1.01	4.95	-4.04	0.04010	.	1.940040	0.02640	N	0.105311	T	0.11836	0.0288	L	0.29908	0.895	0.09310	N	1	B	0.13594	0.008	B	0.08055	0.003	T	0.05550	-1.0878	10	0.12430	T	0.62	.	0.1713	0.00113	0.3233:0.1493:0.21:0.3175	rs56259282	1960	Q9BV73	CP250_HUMAN	Q	1960;1904;448	ENSP00000380661:R1960Q;ENSP00000341541:R1904Q;ENSP00000395992:R448Q	ENSP00000341541:R1904Q	R	+	2	0	CEP250	33555490	0.000000	0.05858	0.000000	0.03702	0.025000	0.11179	-0.281000	0.08456	-0.484000	0.06763	-0.733000	0.03571	CGG	G|0.993;A|0.007	0.007	strong		0.657	CEP250-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078877.7	NM_007186	
ZNF217	7764	hgsc.bcm.edu	37	20	52192595	52192595	+	Missense_Mutation	SNP	C	C	T	rs61748378	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr20:52192595C>T	ENST00000371471.2	-	4	3133	c.2708G>A	c.(2707-2709)cGg>cAg	p.R903Q	RP4-724E16.2_ENST00000424252.1_RNA|ZNF217_ENST00000302342.3_Missense_Mutation_p.R903Q			O75362	ZN217_HUMAN	zinc finger protein 217	903					negative regulation of transcription, DNA-templated (GO:0045892)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	histone deacetylase complex (GO:0000118)|nucleoplasm (GO:0005654)	metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription regulatory region DNA binding (GO:0044212)			NS(1)|breast(3)|central_nervous_system(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(13)|lung(17)|ovary(1)|prostate(4)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	50	all_cancers(1;6.75e-17)|all_epithelial(1;1.76e-18)|Breast(2;3.83e-14)|Lung NSC(4;9.04e-07)|all_lung(4;2.5e-06)|Ovarian(1;0.0398)		BRCA - Breast invasive adenocarcinoma(1;9.88e-17)|Epithelial(1;1.56e-14)|all cancers(1;9.44e-13)|STAD - Stomach adenocarcinoma(23;0.0474)|Colorectal(105;0.198)			GCTGGCACTCCGATTACAGAA	0.562													C|||	57	0.0113818	0.0008	0.0231	5008	,	,		18605	0.0		0.0368	False		,,,				2504	0.0031				p.R903Q		Atlas-SNP	.											.	ZNF217	227	.	0			c.G2708A						PASS	.	C	GLN/ARG	36,4370	40.8+/-73.8	0,36,2167	63.0	61.0	62.0		2708	5.3	0.1	20	dbSNP_129	62	340,8260	117.6+/-177.1	6,328,3966	yes	missense	ZNF217	NM_006526.2	43	6,364,6133	TT,TC,CC		3.9535,0.8171,2.891	probably-damaging	903/1049	52192595	376,12630	2203	4300	6503	SO:0001583	missense	7764	exon3			GCACTCCGATTAC	AF041259	CCDS13443.1	20q13.2	2013-01-08			ENSG00000171940	ENSG00000171940		"""Zinc fingers, C2H2-type"""	13009	protein-coding gene	gene with protein product		602967				9671742	Standard	NM_006526		Approved	ZABC1	uc002xwq.4	O75362	OTTHUMG00000032764	ENST00000371471.2:c.2708G>A	20.37:g.52192595C>T	ENSP00000360526:p.Arg903Gln	197.0	1.0	0.00507614		157.0	82.0	0.522293	NM_006526	E1P5Y6|Q14DB8	Missense_Mutation	SNP	ENST00000371471.2	37	CCDS13443.1	40	0.018315018315018316	2	0.0040650406504065045	9	0.024861878453038673	0	0.0	29	0.03825857519788918	C	15.18	2.755994	0.49362	0.008171	0.039535	ENSG00000171940	ENST00000371471;ENST00000302342;ENST00000395971	T;T	0.13196	2.61;2.61	5.26	5.26	0.73747	.	0.510022	0.19366	N	0.116007	T	0.02267	0.0070	L	0.39147	1.195	0.09310	N	0.999997	P	0.43938	0.822	B	0.32342	0.144	T	0.17531	-1.0366	10	0.87932	D	0	-20.7069	13.2311	0.59945	0.0:0.9214:0.0:0.0786	rs61748378	903	O75362	ZN217_HUMAN	Q	903;903;63	ENSP00000360526:R903Q;ENSP00000304308:R903Q	ENSP00000304308:R903Q	R	-	2	0	ZNF217	51626002	0.953000	0.32496	0.078000	0.20375	0.006000	0.05464	2.935000	0.48963	2.450000	0.82876	0.650000	0.86243	CGG	C|0.976;T|0.024	0.024	strong		0.562	ZNF217-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079757.2	NM_006526	
PLEKHH1	57475	hgsc.bcm.edu	37	14	68053807	68053807	+	Missense_Mutation	SNP	T	T	G	rs118013098	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr14:68053807T>G	ENST00000329153.5	+	29	4082	c.3950T>G	c.(3949-3951)tTc>tGc	p.F1317C	PLEKHH1_ENST00000417684.2_Silent_p.L258L	NM_020715.2	NP_065766.1	Q9ULM0	PKHH1_HUMAN	pleckstrin homology domain containing, family H (with MyTH4 domain) member 1	1317	FERM. {ECO:0000255|PROSITE- ProRule:PRU00084}.					cytoskeleton (GO:0005856)				endometrium(2)|kidney(4)|lung(12)|urinary_tract(1)	19				all cancers(60;0.000771)|OV - Ovarian serous cystadenocarcinoma(108;0.00502)|BRCA - Breast invasive adenocarcinoma(234;0.011)		GAAGCTACCTTCATCATGGCC	0.498													T|||	7	0.00139776	0.0	0.0	5008	,	,		18391	0.0		0.007	False		,,,				2504	0.0				p.F1317C		Atlas-SNP	.											.	PLEKHH1	118	.	0			c.T3950G						PASS	.	T	CYS/PHE	4,3938		0,4,1967	61.0	66.0	64.0		3950	5.5	0.9	14	dbSNP_132	64	38,8266		0,38,4114	yes	missense	PLEKHH1	NM_020715.2	205	0,42,6081	GG,GT,TT		0.4576,0.1015,0.343	benign	1317/1365	68053807	42,12204	1971	4152	6123	SO:0001583	missense	57475	exon29			CTACCTTCATCAT	AB033026	CCDS45128.1	14q24.1	2013-01-10				ENSG00000054690		"""Pleckstrin homology (PH) domain containing"""	17733	protein-coding gene	gene with protein product						10574462	Standard	NM_020715		Approved	KIAA1200	uc001xjl.1	Q9ULM0		ENST00000329153.5:c.3950T>G	14.37:g.68053807T>G	ENSP00000330278:p.Phe1317Cys	199.0	0.0	0		255.0	159.0	0.623529	NM_020715	A6H8X6|Q6PJL4|Q6ZWC7	Missense_Mutation	SNP	ENST00000329153.5	37	CCDS45128.1	7	0.003205128205128205	0	0.0	0	0.0	0	0.0	7	0.009234828496042216	T	21.5	4.152327	0.78001	0.001015	0.004576	ENSG00000054690	ENST00000329153	T	0.71461	-0.57	5.54	5.54	0.83059	FERM domain (1);	0.398053	0.28989	N	0.013497	T	0.49508	0.1561	N	0.19112	0.55	0.80722	D	1	B	0.14012	0.009	B	0.12156	0.007	T	0.52351	-0.8587	10	0.48119	T	0.1	.	14.4073	0.67090	0.0:0.0:0.0:1.0	.	1317	Q9ULM0	PKHH1_HUMAN	C	1317	ENSP00000330278:F1317C	ENSP00000330278:F1317C	F	+	2	0	PLEKHH1	67123560	0.960000	0.32886	0.910000	0.35882	0.977000	0.68977	4.841000	0.62824	2.326000	0.78906	0.533000	0.62120	TTC	T|0.997;G|0.003	0.003	strong		0.498	PLEKHH1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000412730.3	XM_031054	
OR51I1	390063	hgsc.bcm.edu	37	11	5461861	5461861	+	Missense_Mutation	SNP	C	C	G	rs76233016	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr11:5461861C>G	ENST00000380211.1	-	1	883	c.884G>C	c.(883-885)aGt>aCt	p.S295T	HBG2_ENST00000380252.1_Intron|HBE1_ENST00000380237.1_Intron|HBG2_ENST00000380259.2_Intron|AC104389.28_ENST00000415970.1_RNA	NM_001005288.2	NP_001005288.1	Q9H343	O51I1_HUMAN	olfactory receptor, family 51, subfamily I, member 1	295					detection of chemical stimulus involved in sensory perception of smell (GO:0050911)|sensory perception of smell (GO:0007608)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			central_nervous_system(1)|endometrium(1)|large_intestine(6)|lung(17)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(2)	30		Medulloblastoma(188;0.0075)|all_neural(188;0.0572)|Breast(177;0.0675)		Epithelial(150;1.92e-09)|BRCA - Breast invasive adenocarcinoma(625;0.135)		GGTTTTCACACTGTAGATGAT	0.478													C|||	18	0.00359425	0.0	0.0086	5008	,	,		19623	0.0		0.0119	False		,,,				2504	0.0				p.S295T		Atlas-SNP	.											.	OR51I1	66	.	0			c.G884C						PASS	.	C	THR/SER	11,4391	17.9+/-39.9	0,11,2190	120.0	114.0	116.0		884	4.5	1.0	11	dbSNP_132	116	50,8544	31.7+/-84.0	0,50,4247	yes	missense	OR51I1	NM_001005288.2	58	0,61,6437	GG,GC,CC		0.5818,0.2499,0.4694	benign	295/315	5461861	61,12935	2201	4297	6498	SO:0001583	missense	390063	exon1			TTCACACTGTAGA	BK004429	CCDS31382.1	11p15.4	2012-08-09			ENSG00000167359	ENSG00000167359		"""GPCR / Class A : Olfactory receptors"""	15200	protein-coding gene	gene with protein product							Standard	NM_001005288		Approved		uc010qze.2	Q9H343	OTTHUMG00000066908	ENST00000380211.1:c.884G>C	11.37:g.5461861C>G	ENSP00000369559:p.Ser295Thr	149.0	0.0	0		125.0	75.0	0.6	NM_001005288	B9EKW2|Q6IF33	Missense_Mutation	SNP	ENST00000380211.1	37	CCDS31382.1	13	0.005952380952380952	0	0.0	3	0.008287292817679558	0	0.0	10	0.013192612137203167	C	10.13	1.265693	0.23136	0.002499	0.005818	ENSG00000167359	ENST00000321307;ENST00000380211	T	0.37752	1.18	5.47	4.54	0.55810	.	0.096735	0.47093	D	0.000243	T	0.26774	0.0655	M	0.75884	2.315	0.25867	N	0.983753	P	0.48764	0.915	B	0.32677	0.15	T	0.37526	-0.9702	10	0.51188	T	0.08	.	14.2494	0.66009	0.0:0.7161:0.2839:0.0	.	295	Q9H343	O51I1_HUMAN	T	292;295	ENSP00000369559:S295T	ENSP00000439622:S292T	S	-	2	0	OR51I1	5418437	0.045000	0.20229	0.998000	0.56505	0.339000	0.28857	2.449000	0.44935	1.289000	0.44618	0.551000	0.68910	AGT	C|0.994;G|0.006	0.006	strong		0.478	OR51I1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000143399.1	NM_001005288	
AGBL1	123624	hgsc.bcm.edu	37	15	86790936	86790936	+	Silent	SNP	C	C	T	rs371409529		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr15:86790936C>T	ENST00000441037.2	+	6	518	c.423C>T	c.(421-423)taC>taT	p.Y141Y	AGBL1_ENST00000421325.2_Silent_p.Y141Y	NM_152336.2	NP_689549.2	Q96MI9	CBPC4_HUMAN	ATP/GTP binding protein-like 1	141					C-terminal protein deglutamylation (GO:0035609)|protein side chain deglutamylation (GO:0035610)	cytoplasm (GO:0005737)	metallocarboxypeptidase activity (GO:0004181)|tubulin binding (GO:0015631)|zinc ion binding (GO:0008270)			NS(3)|breast(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(8)|liver(2)|lung(28)|ovary(2)|prostate(4)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	62						ACCGAGGCTACGTCACCAGCC	0.597																																					p.Y141Y		Atlas-SNP	.											AGBL1,bladder,carcinoma,0,1	AGBL1	151	1	0			c.C423T						PASS	.						25.0	27.0	26.0					15																	86790936		2139	4253	6392	SO:0001819	synonymous_variant	123624	exon6			AGGCTACGTCACC	AK056872	CCDS58398.1	15q25.3	2014-06-23			ENSG00000166748	ENSG00000166748			26504	protein-coding gene	gene with protein product	"""cytosolic carboxypeptidase 4"""	615496				21074048, 24094747	Standard	NM_152336		Approved	FLJ32310, CCP4	uc002blz.1	Q96MI9	OTTHUMG00000149978	ENST00000441037.2:c.423C>T	15.37:g.86790936C>T		135.0	0.0	0		105.0	80.0	0.761905	NM_152336	A1A4X5|A6NJH6|C9JHL5	Silent	SNP	ENST00000441037.2	37	CCDS58398.1																																																																																			.	.	alt		0.597	AGBL1-001	KNOWN	not_organism_supported|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000314929.5	NM_152336	
BAI2	576	hgsc.bcm.edu	37	1	32193185	32193185	+	Missense_Mutation	SNP	G	G	A	rs41263977	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr1:32193185G>A	ENST00000373658.3	-	33	4935	c.4594C>T	c.(4594-4596)Cgc>Tgc	p.R1532C	BAI2_ENST00000398556.3_Missense_Mutation_p.R1447C|BAI2_ENST00000398547.1_Missense_Mutation_p.R1446C|BAI2_ENST00000398538.1_Missense_Mutation_p.R1501C|BAI2_ENST00000398542.1_Missense_Mutation_p.R1413C|BAI2_ENST00000257070.4_Missense_Mutation_p.R1498C|BAI2_ENST00000465256.1_5'UTR|BAI2_ENST00000440175.2_Missense_Mutation_p.R1122C|BAI2_ENST00000373655.2_Missense_Mutation_p.R1531C|BAI2_ENST00000527361.1_Missense_Mutation_p.R1498C	NM_001703.2	NP_001694.2	O60241	BAI2_HUMAN	brain-specific angiogenesis inhibitor 2	1532					G-protein coupled receptor signaling pathway (GO:0007186)|negative regulation of angiogenesis (GO:0016525)|neuropeptide signaling pathway (GO:0007218)|peripheral nervous system development (GO:0007422)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)			breast(5)|central_nervous_system(2)|endometrium(1)|large_intestine(7)|liver(2)|lung(24)|ovary(7)|pancreas(2)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)	55		Myeloproliferative disorder(586;0.0255)|Ovarian(437;0.0606)|all_neural(195;0.0837)|Breast(348;0.174)		STAD - Stomach adenocarcinoma(196;0.0557)		AAGCTGGGGCGCTCCCCAGGG	0.612													G|||	12	0.00239617	0.0	0.0	5008	,	,		14744	0.0		0.0089	False		,,,				2504	0.0031				p.R1532C		Atlas-SNP	.											.	BAI2	128	.	0			c.C4594T						PASS	.	G	CYS/ARG	7,4399	12.9+/-30.5	0,7,2196	20.0	20.0	20.0		4594	3.3	1.0	1	dbSNP_127	20	77,8523	44.9+/-103.4	0,77,4223	yes	missense	BAI2	NM_001703.2	180	0,84,6419	AA,AG,GG		0.8953,0.1589,0.6459	probably-damaging	1532/1586	32193185	84,12922	2203	4300	6503	SO:0001583	missense	576	exon33			TGGGGCGCTCCCC	AB005298	CCDS72746.1, CCDS72747.1	1p35	2014-08-08			ENSG00000121753	ENSG00000121753		"""-"", ""GPCR / Class B : Orphans"""	944	protein-coding gene	gene with protein product		602683				9533023	Standard	XM_006710783		Approved		uc001btn.3	O60241	OTTHUMG00000003885	ENST00000373658.3:c.4594C>T	1.37:g.32193185G>A	ENSP00000362762:p.Arg1532Cys	108.0	0.0	0		78.0	58.0	0.74359	NM_001703	B9EGK9|Q5T6K0|Q8NGW8|Q96GZ9	Missense_Mutation	SNP	ENST00000373658.3	37	CCDS346.2	6	0.0027472527472527475	0	0.0	0	0.0	0	0.0	6	0.0079155672823219	G	14.71	2.616398	0.46736	0.001589	0.008953	ENSG00000121753	ENST00000398556;ENST00000398547;ENST00000373658;ENST00000373655;ENST00000398542;ENST00000257070;ENST00000527361;ENST00000440175;ENST00000398538	T;T;T;T;T;T;T;T;T	0.48201	3.33;1.62;3.33;3.33;1.8;3.33;3.33;1.46;0.82	4.29	3.3	0.37823	.	0.412552	0.18103	N	0.151610	T	0.47911	0.1471	L	0.52011	1.625	0.39636	D	0.970247	P;D;D;P;D;D	0.76494	0.95;0.999;0.981;0.95;0.999;0.988	B;P;P;B;P;B	0.59825	0.409;0.864;0.608;0.409;0.735;0.295	T	0.58267	-0.7666	10	0.87932	D	0	.	11.0708	0.48002	0.0:0.0:0.8153:0.1847	rs41263977	1498;1520;1122;1531;1532;1501	O60241-4;O60241-3;B4DKC3;O60241-2;O60241;A2A3C2	.;.;.;.;BAI2_HUMAN;.	C	1447;1446;1532;1531;1413;1498;1498;1122;1501	ENSP00000381564:R1447C;ENSP00000381555:R1446C;ENSP00000362762:R1532C;ENSP00000362759:R1531C;ENSP00000381550:R1413C;ENSP00000257070:R1498C;ENSP00000435397:R1498C;ENSP00000391071:R1122C;ENSP00000381548:R1501C	ENSP00000257070:R1498C	R	-	1	0	BAI2	31965772	0.999000	0.42202	0.997000	0.53966	0.941000	0.58515	4.208000	0.58486	2.401000	0.81631	0.561000	0.74099	CGC	G|0.994;A|0.006	0.006	strong		0.612	BAI2-015	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000381838.1	NM_001703	
SCN7A	6332	hgsc.bcm.edu	37	2	167319011	167319011	+	Missense_Mutation	SNP	T	T	A			TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr2:167319011T>A	ENST00000409855.1	-	9	1097	c.971A>T	c.(970-972)aAa>aTa	p.K324I		NM_002976.3	NP_002967.2	Q01118	SCN7A_HUMAN	sodium channel, voltage-gated, type VII, alpha subunit	324					membrane depolarization during action potential (GO:0086010)|muscle contraction (GO:0006936)|neuronal action potential (GO:0019228)|sodium ion homeostasis (GO:0055078)|sodium ion transmembrane transport (GO:0035725)|sodium ion transport (GO:0006814)	glial cell projection (GO:0097386)|plasma membrane (GO:0005886)|voltage-gated sodium channel complex (GO:0001518)	voltage-gated sodium channel activity (GO:0005248)			breast(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(1)|lung(30)|prostate(4)|soft_tissue(1)|urinary_tract(1)	44					Valproic Acid(DB00313)	TATGCCAGCTTTTACACACAC	0.373																																					p.K324I		Atlas-SNP	.											.	SCN7A	410	.	0			c.A971T						PASS	.						71.0	63.0	66.0					2																	167319011		1845	4102	5947	SO:0001583	missense	6332	exon9			CCAGCTTTTACAC	M91556	CCDS46442.1	2q21-q23	2012-03-05	2012-02-28	2002-06-14	ENSG00000136546	ENSG00000136546		"""Sodium channels"", ""Voltage-gated ion channels / Sodium channels"""	10594	protein-coding gene	gene with protein product		182392	"""sodium channel, voltage-gated, type VI, alpha"", ""sodium channel, voltage-gated, type VII, alpha"""	SCN6A		10198179	Standard	NM_002976		Approved	Nav2.1, Nav2.2, NaG	uc002udu.2	Q01118	OTTHUMG00000154078	ENST00000409855.1:c.971A>T	2.37:g.167319011T>A	ENSP00000386796:p.Lys324Ile	137.0	0.0	0		112.0	59.0	0.526786	NM_002976		Missense_Mutation	SNP	ENST00000409855.1	37	CCDS46442.1	.	.	.	.	.	.	.	.	.	.	T	25.1	4.598912	0.87055	.	.	ENSG00000136546	ENST00000409855;ENST00000259060;ENST00000419992;ENST00000441411	D;D;D	0.98717	-5.09;-5.09;-5.09	4.43	4.43	0.53597	Ion transport (1);	0.000000	0.52532	D	0.000071	D	0.99010	0.9662	M	0.83603	2.65	0.42436	D	0.992693	D	0.89917	1.0	D	0.91635	0.999	D	0.99839	1.1060	10	0.87932	D	0	.	12.8081	0.57626	0.0:0.0:0.0:1.0	.	324	Q01118	SCN7A_HUMAN	I	324	ENSP00000386796:K324I;ENSP00000413699:K324I;ENSP00000403846:K324I	ENSP00000259060:K324I	K	-	2	0	SCN7A	167027257	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	5.043000	0.64208	1.747000	0.51819	0.477000	0.44152	AAA	.	.	none		0.373	SCN7A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000333745.1		
CLVS1	157807	hgsc.bcm.edu	37	8	62370916	62370916	+	Silent	SNP	T	T	G	rs72657068	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr8:62370916T>G	ENST00000519846.1	+	6	1264	c.792T>G	c.(790-792)ccT>ccG	p.P264P	CLVS1_ENST00000325897.4_Silent_p.P264P|CLVS1_ENST00000518592.1_5'UTR			Q8IUQ0	CLVS1_HUMAN	clavesin 1	264	CRAL-TRIO. {ECO:0000255|PROSITE- ProRule:PRU00056}.				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						TAATACACCCTGAATTTTTGC	0.408													T|||	8	0.00159744	0.0	0.0029	5008	,	,		18914	0.0		0.002	False		,,,				2504	0.0041				p.P264P		Atlas-SNP	.											.	CLVS1	74	.	0			c.T792G						PASS	.	T		0,4406		0,0,2203	128.0	121.0	123.0		792	-0.0	1.0	8	dbSNP_130	123	28,8572	19.8+/-62.0	0,28,4272	no	coding-synonymous	CLVS1	NM_173519.2		0,28,6475	GG,GT,TT		0.3256,0.0,0.2153		264/355	62370916	28,12978	2203	4300	6503	SO:0001819	synonymous_variant	157807	exon5			ACACCCTGAATTT	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.792T>G	8.37:g.62370916T>G		47.0	0.0	0		24.0	8.0	0.333333	NM_173519	B2R7M5|C8UZT3|Q8NB32	Silent	SNP	ENST00000519846.1	37	CCDS6176.1																																																																																			T|0.998;G|0.002	0.002	strong		0.408	CLVS1-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000378323.1	NM_173519	
MUC17	140453	hgsc.bcm.edu	37	7	100680490	100680490	+	Missense_Mutation	SNP	A	A	G	rs199605653		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr7:100680490A>G	ENST00000306151.4	+	3	5857	c.5793A>G	c.(5791-5793)atA>atG	p.I1931M		NM_001040105.1	NP_001035194.1	Q685J3	MUC17_HUMAN	mucin 17, cell surface associated	1931	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)					TAACAAGTATACCTGTCAGCA	0.483																																					p.I1931M		Atlas-SNP	.											.	MUC17	804	.	0			c.A5793G						PASS	.						242.0	240.0	241.0					7																	100680490		2203	4300	6503	SO:0001583	missense	140453	exon3			AAGTATACCTGTC	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.5793A>G	7.37:g.100680490A>G	ENSP00000302716:p.Ile1931Met	152.0	0.0	0		200.0	17.0	0.085	NM_001040105	O14761|Q685J2|Q8TDH7	Missense_Mutation	SNP	ENST00000306151.4	37	CCDS34711.1	.	.	.	.	.	.	.	.	.	.	N	0.006	-2.052456	0.00394	.	.	ENSG00000169876	ENST00000306151	T	0.02631	4.22	0.579	-1.16	0.09678	.	.	.	.	.	T	0.01592	0.0051	N	0.14661	0.345	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.46911	-0.9157	8	0.33940	T	0.23	.	.	.	.	.	1931	Q685J3	MUC17_HUMAN	M	1931	ENSP00000302716:I1931M	ENSP00000302716:I1931M	I	+	3	3	MUC17	100467210	0.000000	0.05858	0.000000	0.03702	0.018000	0.09664	-2.112000	0.01332	-3.327000	0.00186	-1.981000	0.00455	ATA	A|0.999;G|0.001	0.001	weak		0.483	MUC17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347161.1	NM_001040105	
IKBKAP	8518	hgsc.bcm.edu	37	9	111665215	111665215	+	Silent	SNP	A	A	C	rs35054425	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr9:111665215A>C	ENST00000374647.5	-	16	2065	c.1758T>G	c.(1756-1758)ccT>ccG	p.P586P	IKBKAP_ENST00000537196.1_Silent_p.P237P	NM_003640.3	NP_003631.2	O95163	ELP1_HUMAN	inhibitor of kappa light polypeptide gene enhancer in B-cells, kinase complex-associated protein	586					chromatin organization (GO:0006325)|immune response (GO:0006955)|positive regulation of cell migration (GO:0030335)|protein complex assembly (GO:0006461)|protein phosphorylation (GO:0006468)|regulation of protein kinase activity (GO:0045859)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|signal transduction (GO:0007165)|transcription elongation from RNA polymerase II promoter (GO:0006368)	cytoplasm (GO:0005737)|DNA-directed RNA polymerase II, holoenzyme (GO:0016591)|Elongator holoenzyme complex (GO:0033588)|nucleolus (GO:0005730)|transcription elongation factor complex (GO:0008023)	phosphorylase kinase regulator activity (GO:0008607)|signal transducer activity (GO:0004871)			NS(2)|breast(3)|central_nervous_system(1)|cervix(2)|endometrium(5)|kidney(7)|large_intestine(4)|lung(13)|ovary(2)|pancreas(1)|prostate(5)|skin(2)|stomach(3)|upper_aerodigestive_tract(1)|urinary_tract(2)	53						TAGCCAGAGAAGGTGACTCTG	0.423													A|||	73	0.0145767	0.0015	0.0058	5008	,	,		15642	0.0		0.0089	False		,,,				2504	0.0593				p.P586P		Atlas-SNP	.											.	IKBKAP	122	.	0			c.T1758G						PASS	.	A		8,4398	12.9+/-30.5	0,8,2195	84.0	84.0	84.0		1758	-1.3	1.0	9	dbSNP_126	84	131,8469	67.0+/-129.4	1,129,4170	no	coding-synonymous	IKBKAP	NM_003640.3		1,137,6365	CC,CA,AA		1.5233,0.1816,1.0687		586/1333	111665215	139,12867	2203	4300	6503	SO:0001819	synonymous_variant	8518	exon16			CAGAGAAGGTGAC	AF044195	CCDS6773.1	9q31	2014-09-17	2003-12-02		ENSG00000070061	ENSG00000070061		"""Elongator acetyltransferase complex subunits"""	5959	protein-coding gene	gene with protein product	"""elongator acetyltransferase complex subunit 1"""	603722	"""dysautonomia (Riley-Day syndrome, hereditary sensory autonomic neuropathy type III)"""	DYS		9751059, 11179008	Standard	NM_003640		Approved	IKAP, TOT1, ELP1, IKI3	uc004bdm.4	O95163	OTTHUMG00000020465	ENST00000374647.5:c.1758T>G	9.37:g.111665215A>C		133.0	0.0	0		118.0	50.0	0.423729	NM_003640	Q5JSV2|Q9H327|Q9UG87	Silent	SNP	ENST00000374647.5	37	CCDS6773.1																																																																																			A|0.990;C|0.010	0.010	strong		0.423	IKBKAP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053574.1		
CSDE1	7812	hgsc.bcm.edu	37	1	115269685	115269685	+	Silent	SNP	A	A	G	rs150190370	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr1:115269685A>G	ENST00000358528.4	-	13	1809	c.1383T>C	c.(1381-1383)taT>taC	p.Y461Y	CSDE1_ENST00000534699.1_Silent_p.Y461Y|CSDE1_ENST00000438362.2_Silent_p.Y507Y|CSDE1_ENST00000261443.5_Silent_p.Y430Y|CSDE1_ENST00000530886.1_Silent_p.Y331Y|Y_RNA_ENST00000365030.1_RNA|CSDE1_ENST00000369530.1_Silent_p.Y476Y|CSDE1_ENST00000339438.6_Silent_p.Y430Y	NM_001007553.2	NP_001007554.1	O75534	CSDE1_HUMAN	cold shock domain containing E1, RNA-binding	461	CSD 6.				male gonad development (GO:0008584)|nuclear-transcribed mRNA catabolic process, no-go decay (GO:0070966)|regulation of transcription, DNA-templated (GO:0006355)	CRD-mediated mRNA stability complex (GO:0070937)|cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|plasma membrane (GO:0005886)	DNA binding (GO:0003677)|poly(A) RNA binding (GO:0044822)			NS(1)|breast(4)|endometrium(11)|kidney(2)|large_intestine(12)|lung(17)|ovary(2)|skin(1)|upper_aerodigestive_tract(1)	51	all_epithelial(7;5.11e-05)|all_lung(7;0.000179)|Lung NSC(6;0.00195)|Lung SC(450;0.211)	all_cancers(81;2.21e-07)|all_epithelial(167;4.2e-07)|all_lung(203;9.97e-06)|Lung NSC(69;1.74e-05)		Lung(183;0.0234)|Colorectal(144;0.0686)|COAD - Colon adenocarcinoma(174;0.111)|all cancers(265;0.112)|Epithelial(280;0.124)|LUSC - Lung squamous cell carcinoma(189;0.133)		CACAGTCATCATAAGCAATAA	0.368													A|||	7	0.00139776	0.0	0.0	5008	,	,		18398	0.0069		0.0	False		,,,				2504	0.0				p.Y507Y		Atlas-SNP	.											.	CSDE1	145	.	0			c.T1521C						PASS	.						140.0	122.0	128.0					1																	115269685		2203	4300	6503	SO:0001819	synonymous_variant	7812	exon14			GTCATCATAAGCA		CCDS30811.1, CCDS30812.1, CCDS44197.1, CCDS55626.1	1p13.2	2011-11-02			ENSG00000009307	ENSG00000009307			29905	protein-coding gene	gene with protein product	"""upstream of NRAS"""	191510				2204029, 10048485	Standard	NM_007158		Approved	D1S155E, UNR	uc001efi.3	O75534	OTTHUMG00000012060	ENST00000358528.4:c.1383T>C	1.37:g.115269685A>G		181.0	0.0	0		84.0	5.0	0.0595238	NM_001242891	A8K281|E9PGZ0|G5E9Q2|O94961|Q5TF04|Q5TF05|Q68DF1|Q68DI9|Q9Y2S4	Silent	SNP	ENST00000358528.4	37	CCDS30812.1																																																																																			A|0.997;G|0.003	0.003	strong		0.368	CSDE1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000033397.1	NM_007158	
AQP12A	375318	hgsc.bcm.edu	37	2	241631499	241631499	+	Silent	SNP	G	G	A	rs200769008		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr2:241631499G>A	ENST00000337801.4	+	2	201	c.132G>A	c.(130-132)acG>acA	p.T44T	AQP12A_ENST00000429564.1_Silent_p.T56T|AC011298.2_ENST00000407635.2_lincRNA	NM_198998.2	NP_945349.1	Q8IXF9	AQ12A_HUMAN	aquaporin 12A	44						integral component of membrane (GO:0016021)	transporter activity (GO:0005215)			endometrium(2)|kidney(3)|large_intestine(2)|lung(7)	14		all_epithelial(40;7.49e-12)|Breast(86;0.000148)|Renal(207;0.00571)|Ovarian(221;0.104)|all_neural(83;0.107)|all_hematologic(139;0.182)|all_lung(227;0.186)|Melanoma(123;0.238)		Epithelial(32;2.2e-31)|all cancers(36;1.08e-28)|OV - Ovarian serous cystadenocarcinoma(60;2.13e-15)|Kidney(56;3.04e-09)|KIRC - Kidney renal clear cell carcinoma(57;3.23e-08)|BRCA - Breast invasive adenocarcinoma(100;7.52e-06)|Lung(119;0.00163)|LUSC - Lung squamous cell carcinoma(224;0.008)|Colorectal(34;0.0124)|COAD - Colon adenocarcinoma(134;0.0757)		AGATGAGGACGCTGGTCGAGC	0.701													g|||	1	0.000199681	0.0	0.0	5008	,	,		12447	0.0		0.001	False		,,,				2504	0.0				p.T44T		Atlas-SNP	.											AQP12A,NS,carcinoma,+1,1	AQP12A	32	1	0			c.G132A						PASS	.						25.0	37.0	33.0					2																	241631499		2147	4265	6412	SO:0001819	synonymous_variant	375318	exon2			GAGGACGCTGGTC	AB040748		2q37.3	2013-06-03	2005-05-26	2005-05-26	ENSG00000184945	ENSG00000184945		"""Ion channels / Aquaporins"""	19941	protein-coding gene	gene with protein product		609789	"""aquaporin 12"""	AQP12			Standard	NM_198998		Approved		uc002vzu.3	Q8IXF9	OTTHUMG00000183906	ENST00000337801.4:c.132G>A	2.37:g.241631499G>A		191.0	0.0	0		110.0	49.0	0.445455	NM_198998		Silent	SNP	ENST00000337801.4	37																																																																																				G|0.998;A|0.002	0.002	weak		0.701	AQP12A-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000257185.2	NM_198998	
IL21R	50615	hgsc.bcm.edu	37	16	27460436	27460436	+	Silent	SNP	C	C	T	rs3093408		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr16:27460436C>T	ENST00000337929.3	+	9	1922	c.1449C>T	c.(1447-1449)gcC>gcT	p.A483A	IL21R_ENST00000564089.1_Silent_p.A483A|IL21R-AS1_ENST00000563191.1_RNA|IL21R_ENST00000395754.4_Silent_p.A483A|IL21R_ENST00000395755.1_Silent_p.A483A	NM_181078.2	NP_851564.1	Q9HBE5	IL21R_HUMAN	interleukin 21 receptor	483					interleukin-21-mediated signaling pathway (GO:0038114)|natural killer cell activation (GO:0030101)	integral component of membrane (GO:0016021)	interleukin-21 receptor activity (GO:0001532)			breast(2)|large_intestine(3)|lung(1)|ovary(2)	8						CACCCCTGGCCGGCCTGGATA	0.672			T	BCL6	NHL								C|||	1	0.000199681	0.0	0.0014	5008	,	,		18843	0.0		0.0	False		,,,				2504	0.0				p.A505A		Atlas-SNP	.		Dom	yes		16	16p11	50615	interleukin 21 receptor		L	.	IL21R	95	.	0			c.C1515T						PASS	.	C	,,	0,4394		0,0,2197	41.0	38.0	39.0		1449,1449,1515	-7.6	0.0	16	dbSNP_103	39	3,8597	2.2+/-6.3	0,3,4297	no	coding-synonymous,coding-synonymous,coding-synonymous	IL21R	NM_021798.3,NM_181078.2,NM_181079.4	,,	0,3,6494	TT,TC,CC		0.0349,0.0,0.0231	,,	483/539,483/539,505/561	27460436	3,12991	2197	4300	6497	SO:0001819	synonymous_variant	50615	exon10			CCTGGCCGGCCTG	AF254067	CCDS10630.1	16p11	2014-09-17			ENSG00000103522	ENSG00000103522		"""Interleukins and interleukin receptors"", ""CD molecules"""	6006	protein-coding gene	gene with protein product		605383				11081504	Standard	NM_181078		Approved	CD360	uc002dos.2	Q9HBE5	OTTHUMG00000131675	ENST00000337929.3:c.1449C>T	16.37:g.27460436C>T		131.0	0.0	0		105.0	55.0	0.52381	NM_181079	A8K9E8|D3DWF7|Q96HZ1|Q9HB91	Silent	SNP	ENST00000337929.3	37	CCDS10630.1																																																																																			C|0.999;T|0.001	0.001	strong		0.672	IL21R-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254578.2	NM_181078	
JADE1	79960	hgsc.bcm.edu	37	4	129792873	129792873	+	Missense_Mutation	SNP	A	A	G	rs6855813	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr4:129792873A>G	ENST00000226319.6	+	11	2265	c.1985A>G	c.(1984-1986)aAt>aGt	p.N662S	PHF17_ENST00000512960.1_Missense_Mutation_p.N662S|PHF17_ENST00000452328.2_Missense_Mutation_p.N650S	NM_199320.2	NP_955352.1														NS(1)|breast(2)|endometrium(1)|kidney(2)|large_intestine(10)|lung(10)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	29						AGAAGAGACAATCGTTTTCAT	0.423													A|||	112	0.0223642	0.0734	0.0144	5008	,	,		21259	0.001		0.002	False		,,,				2504	0.002				p.N662S		Atlas-SNP	.											.	PHF17	63	.	0			c.A1985G						PASS	.	A	SER/ASN	329,4077	170.5+/-200.9	13,303,1887	77.0	76.0	76.0		1985	2.2	1.0	4	dbSNP_116	76	11,8589	8.4+/-32.0	0,11,4289	yes	missense	PHF17	NM_199320.2	46	13,314,6176	GG,GA,AA		0.1279,7.4671,2.6142	benign	662/843	129792873	340,12666	2203	4300	6503	SO:0001583	missense	79960	exon11			GAGACAATCGTTT																												ENST00000226319.6:c.1985A>G	4.37:g.129792873A>G	ENSP00000226319:p.Asn662Ser	128.0	0.0	0		96.0	21.0	0.21875	NM_199320		Missense_Mutation	SNP	ENST00000226319.6	37	CCDS34062.1	50	0.022893772893772892	43	0.08739837398373984	5	0.013812154696132596	0	0.0	2	0.002638522427440633	A	0.959	-0.703925	0.03255	0.074671	0.001279	ENSG00000077684	ENST00000226319;ENST00000452328;ENST00000512960;ENST00000535321	T;T;T	0.38401	1.14;1.15;1.14	4.59	2.25	0.28309	.	0.840784	0.11323	N	0.575875	T	0.00580	0.0019	N	0.04880	-0.145	0.80722	D	1	B;B	0.02656	0.0;0.0	B;B	0.04013	0.001;0.0	T	0.17349	-1.0372	9	.	.	.	.	7.662	0.28409	0.7588:0.0:0.2412:0.0	rs6855813;rs6855813	650;662	Q6IE81-2;Q6IE81	.;JADE1_HUMAN	S	662;650;662;662	ENSP00000226319:N662S;ENSP00000388015:N650S;ENSP00000425730:N662S	.	N	+	2	0	PHF17	130012323	1.000000	0.71417	1.000000	0.80357	0.991000	0.79684	1.779000	0.38624	0.910000	0.36722	0.533000	0.62120	AAT	A|0.972;G|0.028	0.028	strong		0.423	PHF17-201	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000364280.1		
GBP4	115361	hgsc.bcm.edu	37	1	89655787	89655787	+	Silent	SNP	T	T	C	rs41305862	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr1:89655787T>C	ENST00000355754.6	-	7	1228	c.1131A>G	c.(1129-1131)gaA>gaG	p.E377E		NM_052941.4	NP_443173.2	Q96PP9	GBP4_HUMAN	guanylate binding protein 4	377						cytoplasm (GO:0005737)|nucleus (GO:0005634)	GTP binding (GO:0005525)|GTPase activity (GO:0003924)			central_nervous_system(1)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(4)|lung(19)|skin(1)|stomach(2)|urinary_tract(1)	33				all cancers(265;0.00723)|Epithelial(280;0.0291)		CTGCAATGGCTTCCCTCTCAC	0.532													T|||	109	0.0217652	0.0113	0.0159	5008	,	,		18719	0.0119		0.0278	False		,,,				2504	0.044				p.E377E		Atlas-SNP	.											.	GBP4	89	.	0			c.A1131G						PASS	.	T		52,4354	52.3+/-87.9	0,52,2151	103.0	97.0	99.0		1131	0.2	1.0	1	dbSNP_127	99	216,8384	90.9+/-153.0	1,214,4085	no	coding-synonymous	GBP4	NM_052941.4		1,266,6236	CC,CT,TT		2.5116,1.1802,2.0606		377/641	89655787	268,12738	2203	4300	6503	SO:0001819	synonymous_variant	115361	exon7			AATGGCTTCCCTC	AF288814	CCDS721.1	1p22.2	2008-02-05			ENSG00000162654	ENSG00000162654			20480	protein-coding gene	gene with protein product		612466				16689661	Standard	NM_052941		Approved	Mpa2	uc001dnb.3	Q96PP9	OTTHUMG00000010663	ENST00000355754.6:c.1131A>G	1.37:g.89655787T>C		306.0	0.0	0		166.0	158.0	0.951807	NM_052941	B2R630|Q05D63|Q6NSL0|Q86T99	Silent	SNP	ENST00000355754.6	37	CCDS721.1																																																																																			T|0.977;C|0.023	0.023	strong		0.532	GBP4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000029409.1	NM_052941	
TDP1	55775	hgsc.bcm.edu	37	14	90458308	90458308	+	Missense_Mutation	SNP	T	T	C			TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr14:90458308T>C	ENST00000335725.4	+	13	1664	c.1414T>C	c.(1414-1416)Tgg>Cgg	p.W472R	TDP1_ENST00000357382.3_Missense_Mutation_p.W233R|TDP1_ENST00000393452.3_Missense_Mutation_p.W472R|TDP1_ENST00000555880.1_Missense_Mutation_p.W472R|TDP1_ENST00000393454.2_Missense_Mutation_p.W472R	NM_018319.3	NP_060789.2	Q9NUW8	TYDP1_HUMAN	tyrosyl-DNA phosphodiesterase 1	472					cell death (GO:0008219)|DNA repair (GO:0006281)|double-strand break repair (GO:0006302)|single strand break repair (GO:0000012)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	3'-tyrosyl-DNA phosphodiesterase activity (GO:0017005)|double-stranded DNA binding (GO:0003690)|exonuclease activity (GO:0004527)|single-stranded DNA binding (GO:0003697)			NS(1)|endometrium(3)|kidney(2)|large_intestine(4)|lung(10)|ovary(3)|prostate(1)|urinary_tract(1)	25		all_cancers(154;0.185)		COAD - Colon adenocarcinoma(157;0.23)		AAAACAGAATTGGCTGCATTC	0.318								Repair of DNA-protein crosslinks																													p.W472R		Atlas-SNP	.											.	TDP1	47	.	0			c.T1414C						PASS	.						120.0	124.0	123.0					14																	90458308		2203	4299	6502	SO:0001583	missense	55775	exon13			CAGAATTGGCTGC	AF182002	CCDS9888.1	14q32.11	2008-08-11				ENSG00000042088			18884	protein-coding gene	gene with protein product		607198				11839309, 12244316	Standard	XM_005267847		Approved	FLJ11090, SCAN1	uc001xxz.3	Q9NUW8		ENST00000335725.4:c.1414T>C	14.37:g.90458308T>C	ENSP00000337353:p.Trp472Arg	80.0	0.0	0		89.0	15.0	0.168539	NM_018319	Q2HXX4|Q86TV8|Q96BK7|Q9NZM7|Q9NZM8	Missense_Mutation	SNP	ENST00000335725.4	37	CCDS9888.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	17.69|17.69	3.452357|3.452357	0.63290|0.63290	.|.	.|.	ENSG00000042088|ENSG00000042088	ENST00000556063|ENST00000393452;ENST00000393454;ENST00000335725;ENST00000357382;ENST00000555880	.|T;T;T;T;T	.|0.44881	.|0.91;0.91;0.91;0.91;0.91	5.94|5.94	4.76|4.76	0.60689|0.60689	.|.	.|0.000000	.|0.85682	.|D	.|0.000000	T|T	0.68842|0.68842	0.3045|0.3045	M|M	0.90483|0.90483	3.12|3.12	0.80722|0.80722	D|D	1|1	.|D;D;D;D;D	.|0.89917	.|1.0;1.0;1.0;0.999;1.0	.|D;D;D;D;D	.|0.91635	.|0.998;0.998;0.999;0.99;0.999	T|T	0.73789|0.73789	-0.3872|-0.3872	5|10	.|0.66056	.|D	.|0.02	-23.862|-23.862	11.4452|11.4452	0.50118|0.50118	0.1353:0.0:0.0:0.8647|0.1353:0.0:0.0:0.8647	.|.	.|472;472;472;233;472	.|G3V2F4;E7EPD8;B2RDI0;Q86TV8;Q9NUW8	.|.;.;.;.;TYDP1_HUMAN	S|R	112|472;472;472;233;472	.|ENSP00000377098:W472R;ENSP00000377099:W472R;ENSP00000337353:W472R;ENSP00000349952:W233R;ENSP00000450628:W472R	.|ENSP00000337353:W472R	L|W	+|+	2|1	0|0	TDP1|TDP1	89528061|89528061	1.000000|1.000000	0.71417|0.71417	0.926000|0.926000	0.36857|0.36857	0.998000|0.998000	0.95712|0.95712	6.735000|6.735000	0.74806|0.74806	1.015000|1.015000	0.39444|0.39444	0.459000|0.459000	0.35465|0.35465	TTG|TGG	.	.	none		0.318	TDP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000411239.1	NM_018319	
SRRM2	23524	hgsc.bcm.edu	37	16	2819196	2819196	+	Silent	SNP	G	G	C	rs150110237	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr16:2819196G>C	ENST00000301740.8	+	12	8481	c.7932G>C	c.(7930-7932)tcG>tcC	p.S2644S	AC092117.2_ENST00000581119.1_RNA|SRRM2_ENST00000574593.1_3'UTR	NM_016333.3	NP_057417.3	Q9UQ35	SRRM2_HUMAN	serine/arginine repetitive matrix 2	2644	Ser-rich.				mRNA splicing, via spliceosome (GO:0000398)	Cajal body (GO:0015030)|catalytic step 2 spliceosome (GO:0071013)|nuclear speck (GO:0016607)|nucleus (GO:0005634)	C2H2 zinc finger domain binding (GO:0070742)|poly(A) RNA binding (GO:0044822)|protein N-terminus binding (GO:0047485)			breast(3)|central_nervous_system(1)|cervix(3)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(20)|lung(34)|ovary(6)|pancreas(3)|prostate(2)|skin(6)|upper_aerodigestive_tract(3)|urinary_tract(7)	105						cctcctcctcgtcgtcttcct	0.597													C|||	9	0.00179712	0.0068	0.0	5008	,	,		18150	0.0		0.0	False		,,,				2504	0.0				p.S2644S		Atlas-SNP	.											.	SRRM2	263	.	0			c.G7932C						PASS	.	C		24,4372	823.0+/-416.5	0,24,2174	112.0	112.0	112.0		7932	-3.7	0.1	16	dbSNP_134	112	5,8595	819.0+/-406.8	0,5,4295	no	coding-synonymous	SRRM2	NM_016333.3		0,29,6469	CC,CG,GG		0.0581,0.546,0.2231		2644/2753	2819196	29,12967	2198	4300	6498	SO:0001819	synonymous_variant	23524	exon12			CTCCTCGTCGTCT	AF201422	CCDS32373.1	16p13.3	2012-07-02			ENSG00000167978	ENSG00000167978			16639	protein-coding gene	gene with protein product		606032				10668804, 11004489	Standard	NM_016333		Approved	SRm300, SRL300, KIAA0324, Cwc21	uc002crk.3	Q9UQ35	OTTHUMG00000177358	ENST00000301740.8:c.7932G>C	16.37:g.2819196G>C		83.0	0.0	0		77.0	22.0	0.285714	NM_016333	A6NKB9|D3DU97|O15038|O94803|Q6NSL3|Q6PIM3|Q6PK40|Q8IW17|Q96GY7|Q9P0G1|Q9UHA8|Q9UQ36|Q9UQ37|Q9UQ38|Q9UQ40	Silent	SNP	ENST00000301740.8	37	CCDS32373.1																																																																																			G|0.998;C|0.002	0.002	strong		0.597	SRRM2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000436411.1		
ZNF433	163059	hgsc.bcm.edu	37	19	12126128	12126128	+	Silent	SNP	C	C	T	rs79356451		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr19:12126128C>T	ENST00000344980.6	-	4	1724	c.1554G>A	c.(1552-1554)tcG>tcA	p.S518S	CTD-2006C1.2_ENST00000406892.2_RNA|ZNF433_ENST00000419886.2_Silent_p.S483S|CTD-2006C1.2_ENST00000495324.1_RNA|CTD-2006C1.2_ENST00000476474.1_RNA	NM_001080411.1	NP_001073880.1	Q8N7K0	ZN433_HUMAN	zinc finger protein 433	518					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			breast(1)|central_nervous_system(2)|endometrium(3)|kidney(1)|large_intestine(4)|lung(1)|prostate(1)|skin(1)	14						GAAAGGAGCTCGAACAGTTGA	0.433													C|||	1	0.000199681	0.0	0.0	5008	,	,		23439	0.0		0.001	False		,,,				2504	0.0				p.S518S		Atlas-SNP	.											ZNF433,colon,carcinoma,-1,2	ZNF433	49	2	0			c.G1554A						scavenged	.	C		0,4398		0,0,2199	71.0	76.0	74.0		1554	-2.4	0.0	19	dbSNP_132	74	4,8594	3.7+/-12.6	0,4,4295	no	coding-synonymous	ZNF433	NM_001080411.1		0,4,6494	TT,TC,CC		0.0465,0.0,0.0308		518/674	12126128	4,12992	2199	4299	6498	SO:0001819	synonymous_variant	163059	exon4			GGAGCTCGAACAG	AK098300	CCDS45983.1	19p13.13	2013-01-08			ENSG00000197647	ENSG00000197647		"""Zinc fingers, C2H2-type"", ""-"""	20811	protein-coding gene	gene with protein product							Standard	NM_001080411		Approved	FLJ40981	uc002msy.1	Q8N7K0	OTTHUMG00000156427	ENST00000344980.6:c.1554G>A	19.37:g.12126128C>T		163.0	1.0	0.00613497		153.0	84.0	0.54902	NM_001080411	Q86VX3	Silent	SNP	ENST00000344980.6	37	CCDS45983.1																																																																																			C|0.999;T|0.001	0.001	strong		0.433	ZNF433-005	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000403716.1	NM_152602	
WDR41	55255	hgsc.bcm.edu	37	5	76728996	76728996	+	Silent	SNP	T	T	C	rs72769029	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr5:76728996T>C	ENST00000296679.4	-	13	1719	c.1344A>G	c.(1342-1344)aaA>aaG	p.K448K	WDR41_ENST00000512033.1_5'UTR|WDR41_ENST00000507029.1_Silent_p.K393K|WDR41_ENST00000414719.2_Silent_p.K194K	NM_018268.2	NP_060738.2	Q9HAD4	WDR41_HUMAN	WD repeat domain 41	448						lysosomal membrane (GO:0005765)				NS(1)|autonomic_ganglia(1)|endometrium(3)|kidney(1)|large_intestine(3)|lung(5)	14		all_lung(232;0.000961)|Lung NSC(167;0.0011)|Ovarian(174;0.0105)|Prostate(461;0.059)		OV - Ovarian serous cystadenocarcinoma(54;6.3e-50)|Epithelial(54;2.04e-44)|all cancers(79;6.84e-40)		TCTCCTCTAATTTTTGAAATA	0.368													T|||	83	0.0165735	0.0015	0.0245	5008	,	,		17492	0.0		0.0338	False		,,,				2504	0.0307				p.K448K		Atlas-SNP	.											.	WDR41	29	.	0			c.A1344G						PASS	.	T		21,4383	27.2+/-55.0	0,21,2181	118.0	121.0	120.0		1344	-0.2	1.0	5	dbSNP_130	120	238,8362	96.8+/-158.5	5,228,4067	no	coding-synonymous	WDR41	NM_018268.2		5,249,6248	CC,CT,TT		2.7674,0.4768,1.9917		448/460	76728996	259,12745	2202	4300	6502	SO:0001819	synonymous_variant	55255	exon13			CTCTAATTTTTGA	AF115511	CCDS4038.1	5q14	2013-01-09			ENSG00000164253	ENSG00000164253		"""WD repeat domain containing"""	25601	protein-coding gene	gene with protein product						12477932	Standard	NM_018268		Approved	FLJ10904	uc003kff.1	Q9HAD4	OTTHUMG00000102169	ENST00000296679.4:c.1344A>G	5.37:g.76728996T>C		218.0	2.0	0.00917431		221.0	219.0	0.99095	NM_018268	B4DT55|Q7Z792|Q8IWG3|Q8IXA9|Q8NDA7|Q9NV62	Silent	SNP	ENST00000296679.4	37	CCDS4038.1																																																																																			T|0.979;C|0.021	0.021	strong		0.368	WDR41-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000220014.2	NM_018268	
ZNF235	9310	hgsc.bcm.edu	37	19	44793278	44793278	+	Missense_Mutation	SNP	A	A	G	rs141976678	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr19:44793278A>G	ENST00000291182.4	-	5	412	c.310T>C	c.(310-312)Tca>Cca	p.S104P	ZNF235_ENST00000589248.1_Intron|ZNF235_ENST00000589799.1_Intron	NM_004234.4	NP_004225.3	Q14590	ZN235_HUMAN	zinc finger protein 235	104					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)			NS(1)|endometrium(1)|kidney(1)|large_intestine(7)|lung(15)|ovary(2)|skin(1)|upper_aerodigestive_tract(1)	29		Prostate(69;0.0352)|all_neural(266;0.116)				TGCCAGCATGAAAGCTCTCCC	0.418																																					p.S104P		Atlas-SNP	.											.	ZNF235	60	.	0			c.T310C						PASS	.	A	PRO/SER	3,4403	4.2+/-10.8	0,3,2200	56.0	58.0	57.0		310	0.9	0.6	19	dbSNP_134	57	8,8592	4.3+/-15.6	0,8,4292	yes	missense	ZNF235	NM_004234.4	74	0,11,6492	GG,GA,AA		0.093,0.0681,0.0846	benign	104/739	44793278	11,12995	2203	4300	6503	SO:0001583	missense	9310	exon5			AGCATGAAAGCTC	X78929	CCDS33048.1	19q13.2	2013-01-08	2002-11-04	2002-11-08	ENSG00000159917	ENSG00000159917		"""Zinc fingers, C2H2-type"", ""-"""	12866	protein-coding gene	gene with protein product		604749	"""zinc finger protein homologous to Zfp93 in mouse"""	ZNF270, ZFP93		7865130, 9570955	Standard	NM_004234		Approved	HZF6, ANF270	uc002oza.4	Q14590		ENST00000291182.4:c.310T>C	19.37:g.44793278A>G	ENSP00000291182:p.Ser104Pro	133.0	0.0	0		121.0	62.0	0.512397	NM_004234	B4DTQ7|O14898|O14899|Q17RR8	Missense_Mutation	SNP	ENST00000291182.4	37	CCDS33048.1	.	.	.	.	.	.	.	.	.	.	A	11.66	1.706086	0.30232	6.81E-4	9.3E-4	ENSG00000159917	ENST00000433015;ENST00000391957;ENST00000291182;ENST00000359844	T	0.05855	3.38	4.18	0.951	0.19579	.	0.487586	0.15465	N	0.260936	T	0.03695	0.0105	N	0.13003	0.285	0.20074	N	0.999938	B;B	0.06786	0.001;0.001	B;B	0.08055	0.003;0.001	T	0.42068	-0.9473	10	0.33940	T	0.23	.	7.7635	0.28965	0.7099:0.0:0.2901:0.0	.	100;104	Q14590-2;Q14590	.;ZN235_HUMAN	P	100;104;104;26	ENSP00000291182:S104P	ENSP00000291182:S104P	S	-	1	0	ZNF235	49485118	0.001000	0.12720	0.635000	0.29338	0.938000	0.57974	0.195000	0.17155	0.279000	0.22186	0.379000	0.24179	TCA	A|0.999;G|0.001	0.001	strong		0.418	ZNF235-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000460732.1		
CDKL3	51265	hgsc.bcm.edu	37	5	133655067	133655067	+	Silent	SNP	C	C	T	rs373913998	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr5:133655067C>T	ENST00000265334.4	-	6	892	c.774G>A	c.(772-774)ttG>ttA	p.L258L	CTD-2410N18.4_ENST00000518409.1_RNA|CDKL3_ENST00000435211.1_Silent_p.L258L|CDKL3_ENST00000536186.1_Intron|CDKL3_ENST00000609654.1_Silent_p.L69L|CDKL3_ENST00000523054.1_Silent_p.L69L|CDKL3_ENST00000521755.1_Intron|CDKL3_ENST00000521118.1_Silent_p.L258L|CDKL3_ENST00000435240.2_5'UTR|CDKL3_ENST00000609383.1_Intron|CDKL3_ENST00000522501.1_5'UTR|CDKL3_ENST00000523832.1_Silent_p.L258L	NM_001113575.1	NP_001107047.1	Q8IVW4	CDKL3_HUMAN	cyclin-dependent kinase-like 3	258	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				cellular protein modification process (GO:0006464)	cytoplasm (GO:0005737)	ATP binding (GO:0005524)|cyclin-dependent protein serine/threonine kinase activity (GO:0004693)|protein kinase activity (GO:0004672)			breast(1)|central_nervous_system(1)|endometrium(1)|large_intestine(2)|lung(3)|prostate(3)	11			KIRC - Kidney renal clear cell carcinoma(527;0.0186)|Kidney(363;0.0365)			TATCTGCCAACAATCCATTAA	0.428													C|||	3	0.000599042	0.0	0.0014	5008	,	,		15912	0.0		0.002	False		,,,				2504	0.0				p.L258L		Atlas-SNP	.											.	CDKL3	76	.	0			c.G774A						PASS	.	C	,	0,3060		0,0,1530	87.0	84.0	85.0		774,774	1.5	1.0	5		85	13,6839		0,13,3413	no	coding-synonymous,coding-synonymous	CDKL3	NM_001113575.1,NM_016508.3	,	0,13,4943	TT,TC,CC		0.1897,0.0,0.1312	,	258/593,258/456	133655067	13,9899	1530	3426	4956	SO:0001819	synonymous_variant	51265	exon6			TGCCAACAATCCA	AF130372	CCDS47264.1, CCDS47265.1, CCDS75303.1	5q31.1	2014-09-09			ENSG00000006837	ENSG00000006837	2.7.11.22	"""Cyclin-dependent kinases"""	15483	protein-coding gene	gene with protein product	"""serine-threonine protein kinase NKIAMRE"""	608459				10463609	Standard	NM_016508		Approved	NKIAMRE	uc003kzf.4	Q8IVW4	OTTHUMG00000186341	ENST00000265334.4:c.774G>A	5.37:g.133655067C>T		23.0	0.0	0		42.0	21.0	0.5	NM_001113575	D3DQA0|D3DQA1|Q9P114	Silent	SNP	ENST00000265334.4	37	CCDS47264.1																																																																																			.	.	weak		0.428	CDKL3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000377697.1	NM_001113575	
FAM135B	51059	hgsc.bcm.edu	37	8	139263158	139263158	+	Missense_Mutation	SNP	G	G	T			TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr8:139263158G>T	ENST00000395297.1	-	6	638	c.468C>A	c.(466-468)ttC>ttA	p.F156L		NM_015912.3	NP_056996.2	Q49AJ0	F135B_HUMAN	family with sequence similarity 135, member B	156										NS(3)|breast(9)|endometrium(21)|kidney(5)|large_intestine(28)|liver(1)|lung(135)|ovary(9)|pancreas(1)|prostate(7)|skin(9)|stomach(1)|upper_aerodigestive_tract(8)|urinary_tract(1)	238	all_epithelial(106;8.29e-14)|Lung NSC(106;6.88e-06)|all_lung(105;1.44e-05)|Ovarian(258;0.00672)|Acute lymphoblastic leukemia(118;0.155)		BRCA - Breast invasive adenocarcinoma(115;0.0805)			GGAAATAGTCGAACATGACCG	0.597										HNSCC(54;0.14)																											p.F156L		Atlas-SNP	.											.	FAM135B	423	.	0			c.C468A						PASS	.						128.0	140.0	136.0					8																	139263158		2096	4217	6313	SO:0001583	missense	51059	exon6			ATAGTCGAACATG	AB196635	CCDS6375.2	8q24.23	2008-11-05			ENSG00000147724	ENSG00000147724			28029	protein-coding gene	gene with protein product						8619474, 9110174	Standard	NM_015912		Approved	C8ORFK32	uc003yuy.3	Q49AJ0	OTTHUMG00000149864	ENST00000395297.1:c.468C>A	8.37:g.139263158G>T	ENSP00000378710:p.Phe156Leu	122.0	0.0	0		137.0	74.0	0.540146	NM_015912	B5MDB3|O95879|Q2WGJ7|Q3KP46	Missense_Mutation	SNP	ENST00000395297.1	37	CCDS6375.2	.	.	.	.	.	.	.	.	.	.	G	22.8	4.340691	0.81911	.	.	ENSG00000147724	ENST00000395297	T	0.72282	-0.64	5.47	-3.38	0.04883	.	0.000000	0.85682	D	0.000000	D	0.82449	0.5039	M	0.84585	2.705	0.44652	D	0.99763	D	0.89917	1.0	D	0.91635	0.999	D	0.83531	0.0091	10	0.87932	D	0	-21.2002	14.2536	0.66035	0.5756:0.0:0.4243:0.0	.	156	Q49AJ0	F135B_HUMAN	L	156	ENSP00000378710:F156L	ENSP00000276737:F156L	F	-	3	2	FAM135B	139332340	0.004000	0.15560	0.973000	0.42090	0.969000	0.65631	-0.976000	0.03786	-0.602000	0.05775	-0.254000	0.11334	TTC	.	.	none		0.597	FAM135B-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000313590.3	NM_015912	
DBX2	440097	hgsc.bcm.edu	37	12	45444426	45444426	+	Silent	SNP	G	G	A			TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr12:45444426G>A	ENST00000332700.6	-	1	456	c.285C>T	c.(283-285)gcC>gcT	p.A95A	RP11-478B9.1_ENST00000548424.1_RNA	NM_001004329.2	NP_001004329.2	Q6ZNG2	DBX2_HUMAN	developing brain homeobox 2	95					regulation of transcription, DNA-templated (GO:0006355)	nucleus (GO:0005634)	sequence-specific DNA binding (GO:0043565)			endometrium(3)|kidney(1)|large_intestine(3)|lung(9)|prostate(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(2)	22	Lung SC(27;0.192)	Lung NSC(34;0.142)		GBM - Glioblastoma multiforme(48;0.0515)		AGGGCGCCCCGGCGGGGCTAA	0.721																																					p.A95A		Atlas-SNP	.											.	DBX2	45	.	0			c.C285T						PASS	.						4.0	5.0	5.0					12																	45444426		1972	3943	5915	SO:0001819	synonymous_variant	440097	exon1			CGCCCCGGCGGGG		CCDS31781.1	12q12	2011-06-20				ENSG00000185610		"""Homeoboxes / ANTP class : NKL subclass"""	33186	protein-coding gene	gene with protein product						11239429	Standard	NM_001004329		Approved	FLJ16139	uc001rok.1	Q6ZNG2	OTTHUMG00000169559	ENST00000332700.6:c.285C>T	12.37:g.45444426G>A		84.0	0.0	0		68.0	21.0	0.308824	NM_001004329		Silent	SNP	ENST00000332700.6	37	CCDS31781.1																																																																																			.	.	none		0.721	DBX2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000404810.1	NM_001004329	
BTBD11	121551	hgsc.bcm.edu	37	12	108011971	108011971	+	Silent	SNP	G	G	A	rs56296886	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr12:108011971G>A	ENST00000280758.5	+	10	2796	c.2268G>A	c.(2266-2268)aaG>aaA	p.K756K	BTBD11_ENST00000490090.2_Silent_p.K756K|BTBD11_ENST00000420571.2_Intron|BTBD11_ENST00000357167.4_Silent_p.K293K|RP11-128P10.1_ENST00000548473.1_RNA	NM_001018072.1	NP_001018082.1	A6QL63	BTBDB_HUMAN	BTB (POZ) domain containing 11	756						integral component of membrane (GO:0016021)				NS(1)|breast(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(13)|lung(18)|ovary(1)|prostate(2)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	53						AGCCAGAGAAGGAGAAGAGTG	0.597													G|||	9	0.00179712	0.0015	0.0043	5008	,	,		20060	0.0		0.003	False		,,,				2504	0.001				p.K756K		Atlas-SNP	.											.	BTBD11	122	.	0			c.G2268A						PASS	.	G	,	6,4400	11.4+/-27.6	0,6,2197	62.0	65.0	64.0		879,2268	4.7	1.0	12	dbSNP_129	64	70,8530	41.7+/-99.0	0,70,4230	no	coding-synonymous,coding-synonymous	BTBD11	NM_001017523.1,NM_001018072.1	,	0,76,6427	AA,AG,GG		0.814,0.1362,0.5843	,	293/642,756/1105	108011971	76,12930	2203	4300	6503	SO:0001819	synonymous_variant	121551	exon10			AGAGAAGGAGAAG	AK091276	CCDS31893.1, CCDS41827.1	12q24.11	2013-10-02			ENSG00000151136	ENSG00000151136		"""BTB/POZ domain containing"", ""Ankyrin repeat domain containing"""	23844	protein-coding gene	gene with protein product							Standard	XM_005268645		Approved	FLJ33957, ABTB2B	uc001tmk.1	A6QL63	OTTHUMG00000150413	ENST00000280758.5:c.2268G>A	12.37:g.108011971G>A		82.0	0.0	0		64.0	28.0	0.4375	NM_001018072	A4FU41|B3KXG3|C9J019|C9JK80|E9PHS4|Q3ZTQ4|Q52M89|Q6ZV99|Q8N245	Silent	SNP	ENST00000280758.5	37	CCDS31893.1																																																																																			G|0.996;A|0.004	0.004	strong		0.597	BTBD11-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000318003.1	NM_152322	
ZDHHC20	253832	hgsc.bcm.edu	37	13	21976996	21976996	+	Missense_Mutation	SNP	T	T	C			TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr13:21976996T>C	ENST00000400590.3	-	5	578	c.380A>G	c.(379-381)tAt>tGt	p.Y127C	ZDHHC20_ENST00000320220.9_Missense_Mutation_p.Y127C|ZDHHC20_ENST00000415724.1_Missense_Mutation_p.Y127C|ZDHHC20_ENST00000382466.3_Missense_Mutation_p.Y127C|ZDHHC20_ENST00000494731.1_5'UTR|ZDHHC20_ENST00000542645.1_Missense_Mutation_p.Y64C			Q5W0Z9	ZDH20_HUMAN	zinc finger, DHHC-type containing 20	127					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)		TTTTTCACAATATCTGATAGC	0.353																																					p.Y127C		Atlas-SNP	.											.	ZDHHC20	36	.	0			c.A380G						PASS	.						65.0	62.0	63.0					13																	21976996		1862	4106	5968	SO:0001583	missense	253832	exon5			TCACAATATCTGA	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.380A>G	13.37:g.21976996T>C	ENSP00000383433:p.Tyr127Cys	41.0	0.0	0		51.0	32.0	0.627451	NM_153251	A8MTV9|C9JG20|I6L9D4|Q2TB82|Q6NVU8	Missense_Mutation	SNP	ENST00000400590.3	37		.	.	.	.	.	.	.	.	.	.	T	19.89	3.910520	0.72983	.	.	ENSG00000180776	ENST00000400590;ENST00000320220;ENST00000382466;ENST00000542645;ENST00000415724	T;T;T;T;T	0.27256	1.68;1.68;1.68;1.68;1.68	5.17	5.17	0.71159	.	0.000000	0.85682	D	0.000000	T	0.62270	0.2414	H	0.96489	3.83	0.80722	D	1	D;P	0.63046	0.992;0.812	P;D	0.63381	0.908;0.914	T	0.76348	-0.2992	10	0.87932	D	0	-33.8396	15.3153	0.74069	0.0:0.0:0.0:1.0	.	64;127	B4DRN8;Q5W0Z9-3	.;.	C	127;127;127;64;127	ENSP00000383433:Y127C;ENSP00000313583:Y127C;ENSP00000371905:Y127C;ENSP00000443236:Y64C;ENSP00000401232:Y127C	ENSP00000313583:Y127C	Y	-	2	0	ZDHHC20	20874996	1.000000	0.71417	0.973000	0.42090	0.820000	0.46376	4.578000	0.60929	2.069000	0.61940	0.533000	0.62120	TAT	.	.	none		0.353	ZDHHC20-001	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000045994.1	NM_153251	
CSMD3	114788	hgsc.bcm.edu	37	8	113363466	113363466	+	Missense_Mutation	SNP	G	G	A			TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr8:113363466G>A	ENST00000297405.5	-	40	6507	c.6263C>T	c.(6262-6264)tCt>tTt	p.S2088F	CSMD3_ENST00000352409.3_Missense_Mutation_p.S2018F|CSMD3_ENST00000455883.2_Missense_Mutation_p.S1984F|CSMD3_ENST00000343508.3_Missense_Mutation_p.S2048F	NM_198123.1	NP_937756.1	Q7Z407	CSMD3_HUMAN	CUB and Sushi multiple domains 3	2088	Sushi 11. {ECO:0000255|PROSITE- ProRule:PRU00302}.					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						TGTAATGTGAGAGTGACCCTA	0.294										HNSCC(6;0.00088)|TCGA Ovarian(7;0.080)																											p.S2088F		Atlas-SNP	.											.	CSMD3	2325	.	0			c.C6263T						PASS	.						120.0	122.0	121.0					8																	113363466		2203	4292	6495	SO:0001583	missense	114788	exon40			ATGTGAGAGTGAC	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.6263C>T	8.37:g.113363466G>A	ENSP00000297405:p.Ser2088Phe	80.0	0.0	0		89.0	20.0	0.224719	NM_198123	Q96PZ3	Missense_Mutation	SNP	ENST00000297405.5	37	CCDS6315.1	.	.	.	.	.	.	.	.	.	.	G	22.0	4.226833	0.79576	.	.	ENSG00000164796	ENST00000343508;ENST00000297405;ENST00000339701;ENST00000455883;ENST00000352409	T;T;T;T;T	0.65549	-0.16;-0.16;-0.16;-0.16;-0.16	4.32	4.32	0.51571	Complement control module (2);Sushi/SCR/CCP (3);	0.087525	0.48286	D	0.000186	T	0.79919	0.4529	M	0.81614	2.55	0.54753	D	0.999985	D;P;D	0.89917	0.973;0.921;1.0	P;P;D	0.79784	0.847;0.722;0.993	T	0.82573	-0.0390	10	0.54805	T	0.06	.	17.3411	0.87296	0.0:0.0:1.0:0.0	.	1984;2088;2048	Q7Z407-3;Q7Z407;Q7Z407-2	.;CSMD3_HUMAN;.	F	2048;2088;1358;1984;2018	ENSP00000345799:S2048F;ENSP00000297405:S2088F;ENSP00000341558:S1358F;ENSP00000412263:S1984F;ENSP00000343124:S2018F	ENSP00000297405:S2088F	S	-	2	0	CSMD3	113432642	1.000000	0.71417	1.000000	0.80357	0.938000	0.57974	7.772000	0.85439	2.380000	0.81148	0.650000	0.86243	TCT	.	.	none		0.294	CSMD3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347141.1	NM_052900	
ASTN2	23245	hgsc.bcm.edu	37	9	119770495	119770495	+	Silent	SNP	G	G	A	rs61736198	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr9:119770495G>A	ENST00000313400.4	-	7	1567	c.1467C>T	c.(1465-1467)tcC>tcT	p.S489S	ASTN2_ENST00000361477.3_5'UTR|ASTN2_ENST00000373996.3_Silent_p.S489S|ASTN2_ENST00000361209.2_Silent_p.S438S			O75129	ASTN2_HUMAN	astrotactin 2	489					negative regulation of protein localization to cell surface (GO:2000009)	cell pole (GO:0060187)|endosome (GO:0005768)|integral component of membrane (GO:0016021)				breast(3)|endometrium(7)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(21)|lung(45)|ovary(4)|pancreas(2)|prostate(2)|skin(9)|stomach(1)|urinary_tract(1)	102						TTAACCAGTCGGAGATGTCCA	0.512													G|||	38	0.00758786	0.0008	0.0058	5008	,	,		20493	0.0159		0.0089	False		,,,				2504	0.0082				p.S438S		Atlas-SNP	.											.	ASTN2	307	.	0			c.C1314T						PASS	.	G		8,4398	14.3+/-33.2	0,8,2195	112.0	96.0	101.0		1314	-9.3	0.4	9	dbSNP_129	101	42,8558	28.5+/-78.6	1,40,4259	no	coding-synonymous	ASTN2	NM_014010.4		1,48,6454	AA,AG,GG		0.4884,0.1816,0.3844		438/1289	119770495	50,12956	2203	4300	6503	SO:0001819	synonymous_variant	23245	exon6			CCAGTCGGAGATG	AF116574	CCDS6814.1, CCDS6815.1, CCDS48009.1, CCDS48009.2, CCDS55334.1	9q33	2008-02-05			ENSG00000148219	ENSG00000148219			17021	protein-coding gene	gene with protein product		612856				9734811	Standard	NM_014010		Approved	KIAA0634	uc004bjt.2	O75129	OTTHUMG00000021013	ENST00000313400.4:c.1467C>T	9.37:g.119770495G>A		189.0	0.0	0		225.0	101.0	0.448889	NM_014010	A2A2T7|A2A2T9|Q52LQ2|Q5JVX8|Q5JVX9|Q5JVY1|Q5VXG8|Q5VZX6|Q8N6P8|Q8WV47|Q96FL4|Q9UHW6	Silent	SNP	ENST00000313400.4	37																																																																																				G|0.994;A|0.006	0.006	strong		0.512	ASTN2-201	KNOWN	basic	protein_coding	protein_coding		NM_014010	
CYP27C1	339761	hgsc.bcm.edu	37	2	127956964	127956964	+	Silent	SNP	G	G	A	rs149542135	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr2:127956964G>A	ENST00000335247.7	-	4	670	c.540C>T	c.(538-540)gcC>gcT	p.A180A	CYP27C1_ENST00000409327.1_Silent_p.A180A	NM_001001665.3	NP_001001665.3	Q4G0S4	C27C1_HUMAN	cytochrome P450, family 27, subfamily C, polypeptide 1	180						membrane (GO:0016020)	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)			central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(4)|lung(5)|prostate(1)|stomach(1)	16	Colorectal(110;0.1)			BRCA - Breast invasive adenocarcinoma(221;0.071)		TGTCGACGCCGGCCAGCAGCA	0.582													G|||	2	0.000399361	0.0	0.0	5008	,	,		19906	0.0		0.002	False		,,,				2504	0.0				p.A180A		Atlas-SNP	.											.	CYP27C1	52	.	0			c.C540T						PASS	.	G		1,4405	2.1+/-5.4	0,1,2202	158.0	139.0	145.0		540	-2.6	0.9	2	dbSNP_134	145	16,8584	11.2+/-40.8	1,14,4285	no	coding-synonymous	CYP27C1	NM_001001665.3		1,15,6487	AA,AG,GG		0.186,0.0227,0.1307		180/373	127956964	17,12989	2203	4300	6503	SO:0001819	synonymous_variant	339761	exon4			GACGCCGGCCAGC	AC027142	CCDS33285.1	2q14.3	2008-05-14	2007-05-18		ENSG00000186684	ENSG00000186684		"""Cytochrome P450s"""	33480	protein-coding gene	gene with protein product							Standard	NM_001001665		Approved	FLJ16008	uc002tod.2	Q4G0S4	OTTHUMG00000153400	ENST00000335247.7:c.540C>T	2.37:g.127956964G>A		175.0	0.0	0		141.0	72.0	0.510638	NM_001001665	Q6ZNI7	Silent	SNP	ENST00000335247.7	37	CCDS33285.1																																																																																			G|0.999;A|0.001	0.001	strong		0.582	CYP27C1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000331046.1	NM_001001665	
TCHH	7062	hgsc.bcm.edu	37	1	152083806	152083806	+	Silent	SNP	C	C	T	rs200947543	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr1:152083806C>T	ENST00000368804.1	-	2	1886	c.1887G>A	c.(1885-1887)agG>agA	p.R629R		NM_007113.2	NP_009044.2	Q07283	TRHY_HUMAN	trichohyalin	629	9 X 28 AA approximate tandem repeats.				keratinization (GO:0031424)	cytoskeleton (GO:0005856)	calcium ion binding (GO:0005509)			NS(2)|breast(4)|central_nervous_system(1)|cervix(1)|endometrium(20)|kidney(9)|large_intestine(16)|lung(33)|ovary(3)|pancreas(1)|prostate(4)|skin(5)|upper_aerodigestive_tract(2)|urinary_tract(4)	105	Hepatocellular(266;0.0877)|Melanoma(130;0.116)|all_hematologic(923;0.127)		LUSC - Lung squamous cell carcinoma(543;0.206)			GCTGCTGGCGCCTCTCTTCCT	0.677													c|||	18	0.00359425	0.0008	0.0043	5008	,	,		15925	0.0		0.0129	False		,,,				2504	0.001				p.R629R		Atlas-SNP	.											.	TCHH	275	.	0			c.G1887A						PASS	.			8,3992		0,8,1992	34.0	40.0	38.0		1887	-0.7	0.0	1	dbSNP_134	38	85,8265		1,83,4091	no	coding-synonymous	TCHH	NM_007113.2		1,91,6083	TT,TC,CC		1.018,0.2,0.753		629/1944	152083806	93,12257	2000	4175	6175	SO:0001819	synonymous_variant	7062	exon3			CTGGCGCCTCTCT	L09190	CCDS41396.1	1q21-q23	2013-01-10		2006-01-27	ENSG00000159450	ENSG00000159450		"""EF-hand domain containing"""	11791	protein-coding gene	gene with protein product		190370		THH		1431214	Standard	NM_007113		Approved		uc001ezp.3	Q07283	OTTHUMG00000013066	ENST00000368804.1:c.1887G>A	1.37:g.152083806C>T		136.0	0.0	0		206.0	127.0	0.616505	NM_007113	Q5VUI3	Silent	SNP	ENST00000368804.1	37	CCDS41396.1																																																																																			C|0.993;T|0.007	0.007	strong		0.677	TCHH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000036671.2	NM_007113	
MTNR1A	4543	hgsc.bcm.edu	37	4	187455329	187455329	+	Silent	SNP	G	G	A	rs8192549	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr4:187455329G>A	ENST00000307161.5	-	2	768	c.567C>T	c.(565-567)atC>atT	p.I189I	RP11-215A19.2_ENST00000509111.1_Intron	NM_005958.3	NP_005949.1	P48039	MTR1A_HUMAN	melatonin receptor 1A	189					circadian rhythm (GO:0007623)|G-protein coupled receptor signaling pathway, coupled to cyclic nucleotide second messenger (GO:0007187)|mating behavior (GO:0007617)|positive regulation of cGMP biosynthetic process (GO:0030828)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	hormone binding (GO:0042562)|melatonin receptor activity (GO:0008502)|organic cyclic compound binding (GO:0097159)			breast(1)|central_nervous_system(1)|endometrium(3)|large_intestine(1)|lung(4)|ovary(1)|pancreas(1)|prostate(1)|skin(1)	14		all_cancers(14;6.39e-56)|all_epithelial(14;1.48e-41)|all_lung(41;2.45e-15)|Lung NSC(41;7.26e-15)|Melanoma(20;1.91e-06)|Hepatocellular(41;0.00335)|Prostate(90;0.00996)|all_hematologic(60;0.014)|Colorectal(36;0.0161)|Renal(120;0.0183)|all_neural(102;0.202)		OV - Ovarian serous cystadenocarcinoma(60;7.63e-12)|BRCA - Breast invasive adenocarcinoma(30;6.68e-07)|GBM - Glioblastoma multiforme(59;3.44e-05)|LUSC - Lung squamous cell carcinoma(40;0.000106)|STAD - Stomach adenocarcinoma(60;0.000279)|READ - Rectum adenocarcinoma(43;0.159)	Agomelatine(DB06594)|Melatonin(DB01065)|Ramelteon(DB00980)	CCACCACGGCGATGGTGTAGG	0.577													G|||	48	0.00958466	0.0015	0.0101	5008	,	,		20839	0.001		0.0298	False		,,,				2504	0.0082				p.I189I		Atlas-SNP	.											.	MTNR1A	46	.	0			c.C567T						PASS	.	G		29,4377	36.0+/-67.5	0,29,2174	136.0	131.0	133.0		567	-9.9	0.0	4	dbSNP_117	133	312,8288	111.0+/-171.3	3,306,3991	no	coding-synonymous	MTNR1A	NM_005958.3		3,335,6165	AA,AG,GG		3.6279,0.6582,2.6219		189/351	187455329	341,12665	2203	4300	6503	SO:0001819	synonymous_variant	4543	exon2			CACGGCGATGGTG		CCDS3848.1	4q35	2012-08-08				ENSG00000168412		"""GPCR / Class A : Melatonin receptors"""	7463	protein-coding gene	gene with protein product		600665				7558006	Standard	NM_005958		Approved	MEL-1A-R	uc003izd.1	P48039		ENST00000307161.5:c.567C>T	4.37:g.187455329G>A		83.0	0.0	0		65.0	13.0	0.2	NM_005958	A0AVC5|B0M0L2	Silent	SNP	ENST00000307161.5	37	CCDS3848.1																																																																																			G|0.977;A|0.023	0.023	strong		0.577	MTNR1A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000360189.1		
HMG20A	10363	hgsc.bcm.edu	37	15	77750802	77750802	+	Missense_Mutation	SNP	A	A	G			TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr15:77750802A>G	ENST00000381714.3	+	3	481	c.53A>G	c.(52-54)gAc>gGc	p.D18G	HMG20A_ENST00000336216.4_Missense_Mutation_p.D18G	NM_018200.2	NP_060670.1	Q9NP66	HM20A_HUMAN	high mobility group 20A	18					chromatin modification (GO:0016568)|chromatin organization (GO:0006325)|negative regulation of neuron differentiation (GO:0045665)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|sequence-specific DNA binding transcription factor activity (GO:0003700)			central_nervous_system(1)|endometrium(4)|kidney(1)|large_intestine(5)|lung(4)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)	18						GCAGATGAAGACGGTTCCAAG	0.423																																					p.D18G		Atlas-SNP	.											.	HMG20A	48	.	0			c.A53G						PASS	.						94.0	94.0	94.0					15																	77750802		2196	4294	6490	SO:0001583	missense	10363	exon3			ATGAAGACGGTTC	AF146222	CCDS10295.1	15q24	2011-07-01	2011-04-05		ENSG00000140382	ENSG00000140382		"""High mobility group / Non-canonical"""	5001	protein-coding gene	gene with protein product	"""HMG box domain containing 1"""	605534	"""high-mobility group 20A"""			10773667	Standard	NM_018200		Approved	HMGX1, FLJ10739, HMGXB1	uc002bcr.3	Q9NP66	OTTHUMG00000143729	ENST00000381714.3:c.53A>G	15.37:g.77750802A>G	ENSP00000371133:p.Asp18Gly	88.0	0.0	0		63.0	5.0	0.0793651	NM_018200	A6NHY3|D3DW78|Q53G31|Q9NSF6	Missense_Mutation	SNP	ENST00000381714.3	37	CCDS10295.1	.	.	.	.	.	.	.	.	.	.	A	15.39	2.820448	0.50633	.	.	ENSG00000140382	ENST00000336216;ENST00000381714	T;T	0.70986	-0.53;-0.53	5.76	5.76	0.90799	.	0.067632	0.64402	D	0.000012	T	0.67011	0.2848	N	0.24115	0.695	0.44816	D	0.997829	B;P	0.46395	0.247;0.877	B;P	0.49829	0.053;0.623	T	0.71431	-0.4595	10	0.66056	D	0.02	-17.0189	14.3238	0.66505	1.0:0.0:0.0:0.0	.	18;18	Q9NP66;Q9NP66-2	HM20A_HUMAN;.	G	18	ENSP00000336856:D18G;ENSP00000371133:D18G	ENSP00000336856:D18G	D	+	2	0	HMG20A	75537857	1.000000	0.71417	1.000000	0.80357	0.988000	0.76386	5.672000	0.68102	2.200000	0.70718	0.460000	0.39030	GAC	.	.	none		0.423	HMG20A-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000419512.2	NM_018200	
HNF1A	6927	hgsc.bcm.edu	37	12	121437114	121437114	+	Silent	SNP	G	G	A	rs55834942	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr12:121437114G>A	ENST00000257555.6	+	8	1771	c.1545G>A	c.(1543-1545)acG>acA	p.T515T	HNF1A_ENST00000541395.1_Silent_p.T515T|RP11-216P16.2_ENST00000606238.1_RNA|HNF1A_ENST00000544413.1_Silent_p.T515T			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						PASS	.	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		230.0	1.0	0.00434783		241.0	117.0	0.485477	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	
ARHGAP42	143872	hgsc.bcm.edu	37	11	100803982	100803982	+	Silent	SNP	C	C	T	rs79213484	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr11:100803982C>T	ENST00000298815.8	+	7	696	c.693C>T	c.(691-693)aaC>aaT	p.N231N	ARHGAP42_ENST00000524892.2_Silent_p.N197N|snoU13_ENST00000459511.1_RNA	NM_152432.2	NP_689645.2	A6NI28	RHG42_HUMAN	Rho GTPase activating protein 42	231	BAR.				signal transduction (GO:0007165)	intracellular (GO:0005622)	GTPase activator activity (GO:0005096)			endometrium(3)|skin(2)	5						TGCAGTTCAACTTGCAGAATG	0.388													C|||	41	0.0081869	0.0015	0.0115	5008	,	,		15042	0.0		0.0268	False		,,,				2504	0.0041				p.N231N		Atlas-SNP	.											.	ARHGAP42	32	.	0			c.C693T						PASS	.	C		6,1378		0,6,686	132.0	102.0	111.0		693	4.6	1.0	11	dbSNP_132	111	99,3083		1,97,1493	no	coding-synonymous	ARHGAP42	NM_152432.2		1,103,2179	TT,TC,CC		3.1113,0.4335,2.2996		231/875	100803982	105,4461	692	1591	2283	SO:0001819	synonymous_variant	143872	exon7			GTTCAACTTGCAG			11q22.1	2012-04-19			ENSG00000165895	ENSG00000165895		"""Rho GTPase activating proteins"""	26545	protein-coding gene	gene with protein product		615936				18954304	Standard	NM_152432		Approved	FLJ32810, GRAF3	uc001pge.2	A6NI28	OTTHUMG00000167530	ENST00000298815.8:c.693C>T	11.37:g.100803982C>T		126.0	0.0	0		211.0	56.0	0.265403	NM_152432	Q96M56	Silent	SNP	ENST00000298815.8	37																																																																																				C|0.983;T|0.017	0.017	strong		0.388	ARHGAP42-201	KNOWN	basic|appris_principal	protein_coding	protein_coding		NM_152432	
COL21A1	81578	hgsc.bcm.edu	37	6	56035495	56035495	+	Silent	SNP	G	G	A	rs41271846	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr6:56035495G>A	ENST00000244728.5	-	5	1375	c.978C>T	c.(976-978)agC>agT	p.S326S	COL21A1_ENST00000535941.1_Silent_p.S326S|COL21A1_ENST00000370819.1_Silent_p.S326S	NM_030820.3	NP_110447.2	Q96P44	COLA1_HUMAN	collagen, type XXI, alpha 1	326	Laminin G-like.				extracellular matrix organization (GO:0030198)	collagen trimer (GO:0005581)|endoplasmic reticulum lumen (GO:0005788)|extracellular region (GO:0005576)|proteinaceous extracellular matrix (GO:0005578)				breast(1)|endometrium(1)|kidney(3)|large_intestine(11)|lung(21)|ovary(2)|prostate(2)	41	Lung NSC(77;0.0483)		LUSC - Lung squamous cell carcinoma(124;0.181)			CATTAATTACGCTGGTTGTTG	0.358													G|||	9	0.00179712	0.0	0.0	5008	,	,		17653	0.0		0.005	False		,,,				2504	0.0041				p.S326S		Atlas-SNP	.											.	COL21A1	201	.	0			c.C978T						PASS	.	G		7,3729		0,7,1861	79.0	71.0	74.0		978	1.5	0.6	6	dbSNP_127	74	72,8136		1,70,4033	no	coding-synonymous	COL21A1	NM_030820.3		1,77,5894	AA,AG,GG		0.8772,0.1874,0.6614		326/958	56035495	79,11865	1868	4104	5972	SO:0001819	synonymous_variant	81578	exon5			AATTACGCTGGTT	AF330693	CCDS55025.1	6p12.3-p11.2	2013-01-16			ENSG00000124749	ENSG00000124749		"""Collagens"""	17025	protein-coding gene	gene with protein product		610002				11566190	Standard	XR_241922		Approved		uc003pcs.3	Q96P44	OTTHUMG00000014907	ENST00000244728.5:c.978C>T	6.37:g.56035495G>A		118.0	0.0	0		113.0	53.0	0.469027	NM_030820	A6NIX5|B2R8J9|Q49A51|Q71RF4|Q8WXV8|Q9H0V3	Silent	SNP	ENST00000244728.5	37	CCDS55025.1																																																																																			G|0.997;A|0.003	0.003	strong		0.358	COL21A1-001	KNOWN	non_canonical_conserved|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000041004.2		
PTPN23	25930	hgsc.bcm.edu	37	3	47453659	47453659	+	Silent	SNP	G	G	T	rs147959396	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr3:47453659G>T	ENST00000265562.4	+	22	4226	c.4149G>T	c.(4147-4149)ccG>ccT	p.P1383P	PTPN23_ENST00000431726.1_Silent_p.P1257P	NM_015466.2	NP_056281.1	Q9H3S7	PTN23_HUMAN	protein tyrosine phosphatase, non-receptor type 23	1383	Tyrosine-protein phosphatase. {ECO:0000255|PROSITE-ProRule:PRU00160}.				cilium morphogenesis (GO:0060271)|negative regulation of epithelial cell migration (GO:0010633)|peptidyl-tyrosine dephosphorylation (GO:0035335)|positive regulation of adherens junction organization (GO:1903393)|positive regulation of early endosome to late endosome transport (GO:2000643)|positive regulation of homophilic cell adhesion (GO:1903387)|protein transport (GO:0015031)|ubiquitin-dependent protein catabolic process via the multivesicular body sorting pathway (GO:0043162)	ciliary basal body (GO:0036064)|cytoplasm (GO:0005737)|cytoplasmic vesicle (GO:0031410)|early endosome (GO:0005769)|endosome (GO:0005768)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)	protein kinase binding (GO:0019901)|protein tyrosine phosphatase activity (GO:0004725)			breast(3)|central_nervous_system(1)|large_intestine(5)|lung(7)|prostate(2)|skin(4)|upper_aerodigestive_tract(1)	23				BRCA - Breast invasive adenocarcinoma(193;0.000271)|KIRC - Kidney renal clear cell carcinoma(197;0.00558)|Kidney(197;0.00632)		ATCAGCGGCCGCTGCACACGC	0.627													G|||	5	0.000998403	0.0	0.0043	5008	,	,		20941	0.0		0.002	False		,,,				2504	0.0				p.P1383P		Atlas-SNP	.											.	PTPN23	85	.	0			c.G4149T						PASS	.	G		6,4400	11.4+/-27.6	0,6,2197	53.0	52.0	53.0		4149	-1.4	1.0	3	dbSNP_134	53	35,8565	24.0+/-70.4	0,35,4265	no	coding-synonymous	PTPN23	NM_015466.2		0,41,6462	TT,TG,GG		0.407,0.1362,0.3152		1383/1637	47453659	41,12965	2203	4300	6503	SO:0001819	synonymous_variant	25930	exon22			GCGGCCGCTGCAC	AB025194	CCDS2754.1	3p21.3	2011-06-09			ENSG00000076201	ENSG00000076201		"""Protein tyrosine phosphatases / Class I Cys-based PTPs : Non-receptor"""	14406	protein-coding gene	gene with protein product		606584				11095967	Standard	NM_015466		Approved	DKFZP564F0923, KIAA1471, HD-PTP	uc003crf.1	Q9H3S7	OTTHUMG00000133520	ENST00000265562.4:c.4149G>T	3.37:g.47453659G>T		175.0	0.0	0		259.0	140.0	0.540541	NM_015466	A8K0D7|Q7KZF8|Q8N6Z5|Q9BSR5|Q9P257|Q9UG03|Q9UMZ4	Silent	SNP	ENST00000265562.4	37	CCDS2754.1																																																																																			G|0.997;T|0.003	0.003	strong		0.627	PTPN23-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257492.2	NM_015466	
PRF1	5551	hgsc.bcm.edu	37	10	72358722	72358722	+	Missense_Mutation	SNP	T	T	C	rs28933375	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr10:72358722T>C	ENST00000441259.1	-	3	915	c.755A>G	c.(754-756)aAc>aGc	p.N252S	PRF1_ENST00000373209.2_Missense_Mutation_p.N252S	NM_001083116.1|NM_005041.4	NP_001076585.1|NP_005032.2	P14222	PERF_HUMAN	perforin 1 (pore forming protein)	252	MACPF. {ECO:0000255|PROSITE- ProRule:PRU00745}.		N -> S (in FHL2; dbSNP:rs28933375). {ECO:0000269|PubMed:10583959}.		apoptotic process (GO:0006915)|cellular defense response (GO:0006968)|cytolysis (GO:0019835)|defense response to tumor cell (GO:0002357)|defense response to virus (GO:0051607)|immune response to tumor cell (GO:0002418)|protein homooligomerization (GO:0051260)|transmembrane transport (GO:0055085)	cytolytic granule (GO:0044194)|cytoplasmic membrane-bounded vesicle (GO:0016023)|endosome (GO:0005768)|extracellular region (GO:0005576)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|wide pore channel activity (GO:0022829)			breast(1)|central_nervous_system(1)|endometrium(1)|large_intestine(2)|lung(11)|ovary(1)|prostate(3)|urinary_tract(3)	23						CTCCACCTCGTTGTCCGTGAG	0.632			M			"""various leukaemia, lymphoma"""	Type 2 familial hemophagocytic lymphohistiocytosis		Familial Hemophagocytic Lymphohistiocytosis				T|||	38	0.00758786	0.0106	0.0058	5008	,	,		18685	0.0		0.0109	False		,,,				2504	0.0092				p.N252S		Atlas-SNP	.	yes	Rec			10	10q22	5551	perforin 1 (pore forming protein)		L	.	PRF1	64	.	0			c.A755G	GRCh37	CM992952	PRF1	M	rs28933375	PASS	.	T	SER/ASN,SER/ASN	40,4366	43.8+/-77.6	0,40,2163	123.0	88.0	100.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	755,755	4.7	0.0	10	dbSNP_125	100	70,8530	41.7+/-99.0	0,70,4230	yes	missense,missense	PRF1	NM_001083116.1,NM_005041.4	46,46	0,110,6393	CC,CT,TT		0.814,0.9079,0.8458	benign,benign	252/556,252/556	72358722	110,12896	2203	4300	6503	SO:0001583	missense	5551	exon3	Familial Cancer Database	FHLH, FHL, Familial Hemophagocytic Reticulosis, FHR	ACCTCGTTGTCCG	BC047695	CCDS7305.1	10q22	2014-09-17			ENSG00000180644	ENSG00000180644			9360	protein-coding gene	gene with protein product	"""Perforin"", ""perforin 1 (preforming protein)"""	170280				1505959, 2592021	Standard	NM_005041		Approved	PFP, P1, HPLH2	uc001jrf.4	P14222	OTTHUMG00000018412	ENST00000441259.1:c.755A>G	10.37:g.72358722T>C	ENSP00000398568:p.Asn252Ser	124.0	0.0	0		77.0	59.0	0.766234	NM_001083116	B2R6X4|Q59F57|Q86WX7	Missense_Mutation	SNP	ENST00000441259.1	37	CCDS7305.1	13	0.005952380952380952	5	0.01016260162601626	2	0.0055248618784530384	0	0.0	6	0.0079155672823219	T	4.521	0.096594	0.08681	0.009079	0.00814	ENSG00000180644	ENST00000373209;ENST00000441259;ENST00000318971	D;D	0.82803	-1.65;-1.65	5.83	4.69	0.59074	Membrane attack complex component/perforin (MACPF) domain (3);	0.677027	0.15448	N	0.261829	T	0.50326	0.1609	N	0.01168	-0.975	0.09310	A	8.34466e-13	B	0.02656	0.0	B	0.06405	0.002	T	0.57207	-0.7851	9	0.21540	T	0.41	-13.5412	10.0841	0.42408	0.0:0.0793:0.0:0.9206	rs28933375	252	P14222	PERF_HUMAN	S	252	ENSP00000362305:N252S;ENSP00000398568:N252S	ENSP00000316746:N252S	N	-	2	0	PRF1	72028728	0.000000	0.05858	0.003000	0.11579	0.010000	0.07245	0.743000	0.26231	1.021000	0.39600	0.533000	0.62120	AAC	T|0.994;C|0.006	0.006	strong		0.632	PRF1-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048517.2	NM_005041	
PCDHA12	56137	hgsc.bcm.edu	37	5	140256920	140256920	+	Silent	SNP	G	G	C	rs115718636	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr5:140256920G>C	ENST00000398631.2	+	1	1863	c.1863G>C	c.(1861-1863)ccG>ccC	p.P621P	PCDHA1_ENST00000394633.3_Intron|PCDHA2_ENST00000526136.1_Intron|PCDHA10_ENST00000307360.5_Intron|PCDHA5_ENST00000529859.1_Intron|PCDHA1_ENST00000504120.2_Intron|PCDHA4_ENST00000512229.2_Intron|PCDHA5_ENST00000529619.1_Intron|PCDHA10_ENST00000506939.2_Intron|PCDHA11_ENST00000398640.2_Intron|PCDHA7_ENST00000525929.1_Intron|PCDHA6_ENST00000527624.1_Intron|PCDHA6_ENST00000529310.1_Intron|PCDHA3_ENST00000522353.2_Intron|PCDHA8_ENST00000531613.1_Intron|PCDHA9_ENST00000532602.1_Intron|PCDHA4_ENST00000530339.1_Intron	NM_018903.2|NM_031864.2	NP_061726.1|NP_114070.1	Q9UN75	PCDAC_HUMAN	protocadherin alpha 12	621	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)			NS(4)|breast(2)|cervix(1)|endometrium(19)|kidney(8)|large_intestine(8)|liver(2)|lung(25)|prostate(1)|skin(3)|upper_aerodigestive_tract(4)|urinary_tract(1)	78			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			CGCACATCCCGTTCCACGTGG	0.672													.|||	111	0.0221645	0.0129	0.0303	5008	,	,		17234	0.0		0.0656	False		,,,				2504	0.0072				p.P621P	Pancreas(113;759 1672 13322 24104 50104)	Atlas-SNP	.											PCDHA12,colon,carcinoma,0,2	PCDHA12	196	2	0			c.G1863C						PASS	.	G	,,,,,,,,,,,,,,,	117,4289	87.8+/-126.4	0,117,2086	228.0	205.0	213.0		,,,1863,,,,,,,,,,,,1863	-0.7	0.9	5	dbSNP_132	213	437,8161	133.5+/-191.0	11,415,3873	no	intron,intron,intron,coding-synonymous,intron,intron,intron,intron,intron,intron,intron,intron,intron,intron,intron,coding-synonymous	PCDHA9,PCDHA12,PCDHA11,PCDHA10,PCDHA8,PCDHA7,PCDHA6,PCDHA5,PCDHA4,PCDHA3,PCDHA2,PCDHA1	NM_018900.2,NM_018901.2,NM_018902.3,NM_018903.2,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_031864.1	,,,,,,,,,,,,,,,	11,532,5959	CC,CG,GG		5.0826,2.6555,4.2602	,,,,,,,,,,,,,,,	,,,621/942,,,,,,,,,,,,621/793	140256920	554,12450	2203	4299	6502	SO:0001819	synonymous_variant	56137	exon1			CATCCCGTTCCAC	AF152477	CCDS47285.1, CCDS75327.1	5q31	2010-11-26			ENSG00000251664	ENSG00000251664		"""Cadherins / Protocadherins : Clustered"""	8666	other	complex locus constituent	"""KIAA0345-like 2"""	606318				10380929	Standard	NM_018903		Approved	PCDH-ALPHA12	uc003lic.2	Q9UN75	OTTHUMG00000163366	ENST00000398631.2:c.1863G>C	5.37:g.140256920G>C		368.0	1.0	0.00271739		298.0	150.0	0.503356	NM_018903	O75278|Q2M1N8	Silent	SNP	ENST00000398631.2	37	CCDS47285.1																																																																																			G|0.959;C|0.041	0.041	strong		0.672	PCDHA12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000372882.2	NM_018903	
C15orf41	84529	hgsc.bcm.edu	37	15	36989578	36989578	+	Silent	SNP	C	C	T	rs117638434	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr15:36989578C>T	ENST00000566621.1	+	8	781	c.531C>T	c.(529-531)aaC>aaT	p.N177N	C15orf41_ENST00000567389.1_Silent_p.N79N|C15orf41_ENST00000437989.2_Silent_p.N177N|C15orf41_ENST00000565792.1_3'UTR|C15orf41_ENST00000562877.1_Silent_p.N79N|C15orf41_ENST00000338183.4_Silent_p.N79N|C15orf41_ENST00000569302.1_Silent_p.N177N	NM_001130010.1	NP_001123482.1	Q9Y2V0	CO041_HUMAN	chromosome 15 open reading frame 41	177										kidney(1)|large_intestine(3)|lung(6)|ovary(1)|pancreas(1)	12		all_epithelial(112;3.06e-10)|Lung NSC(122;6.48e-08)|all_lung(180;8.31e-07)|Melanoma(134;0.222)		all cancers(64;1.76e-19)|GBM - Glioblastoma multiforme(113;5.03e-07)|BRCA - Breast invasive adenocarcinoma(123;0.11)		TAGAGAAAAACCTGTCCTTCC	0.408													C|||	22	0.00439297	0.0	0.0014	5008	,	,		15677	0.0		0.0209	False		,,,				2504	0.0				p.N177N		Atlas-SNP	.											.	C15orf41	24	.	0			c.C531T						PASS	.	C	,	17,3791		0,17,1887	183.0	184.0	184.0		531,237	-0.8	1.0	15	dbSNP_132	184	99,8177		1,97,4040	no	coding-synonymous,coding-synonymous	C15orf41	NM_001130010.1,NM_032499.4	,	1,114,5927	TT,TC,CC		1.1962,0.4464,0.9599	,	177/282,79/184	36989578	116,11968	1904	4138	6042	SO:0001819	synonymous_variant	84529	exon8			GAAAAACCTGTCC	BC006254	CCDS45215.1, CCDS45216.1	15q14	2012-05-31			ENSG00000186073	ENSG00000186073			26929	protein-coding gene	gene with protein product		615626					Standard	XM_005254719		Approved	HH114, MGC11326, FLJ22851	uc001zje.4	Q9Y2V0	OTTHUMG00000172659	ENST00000566621.1:c.531C>T	15.37:g.36989578C>T		196.0	0.0	0		110.0	84.0	0.763636	NM_001130010	B2RD87	Silent	SNP	ENST00000566621.1	37	CCDS45215.1																																																																																			C|0.992;T|0.008	0.008	strong		0.408	C15orf41-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000419741.1	NM_032499	
DDX20	11218	hgsc.bcm.edu	37	1	112309230	112309230	+	Silent	SNP	C	C	T			TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr1:112309230C>T	ENST00000369702.4	+	11	2804	c.2184C>T	c.(2182-2184)agC>agT	p.S728S	DDX20_ENST00000475700.1_Silent_p.S336S	NM_007204.4	NP_009135.4	Q9UHI6	DDX20_HUMAN	DEAD (Asp-Glu-Ala-Asp) box polypeptide 20	728					ATP catabolic process (GO:0006200)|gene expression (GO:0010467)|ncRNA metabolic process (GO:0034660)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|oogenesis (GO:0048477)|positive regulation of apoptotic process (GO:0043065)|regulation of steroid biosynthetic process (GO:0050810)|RNA metabolic process (GO:0016070)|RNA processing (GO:0006396)|spliceosomal snRNP assembly (GO:0000387)|spliceosomal tri-snRNP complex assembly (GO:0000244)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|membrane (GO:0016020)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|SMN complex (GO:0032797)|SMN-Sm protein complex (GO:0034719)|transcriptional repressor complex (GO:0017053)	ATP binding (GO:0005524)|ATP-dependent RNA helicase activity (GO:0004004)|DNA binding (GO:0003677)			endometrium(3)|kidney(7)|large_intestine(6)|lung(3)|pancreas(1)|prostate(1)	21		all_cancers(81;1.06e-05)|all_epithelial(167;7.36e-06)|all_lung(203;2.44e-05)|Lung NSC(69;4.15e-05)		Lung(183;0.0234)|Colorectal(144;0.0282)|all cancers(265;0.0614)|Epithelial(280;0.0999)|COAD - Colon adenocarcinoma(174;0.111)|LUSC - Lung squamous cell carcinoma(189;0.133)		AGGGGGCTAGCCAGAGAGCTA	0.483																																					p.S728S		Atlas-SNP	.											.	DDX20	50	.	0			c.C2184T						PASS	.						65.0	67.0	66.0					1																	112309230		2203	4300	6503	SO:0001819	synonymous_variant	11218	exon11			GGCTAGCCAGAGA	AF106019	CCDS842.1	1p21.1-p13.2	2008-02-05	2003-06-13		ENSG00000064703	ENSG00000064703		"""DEAD-boxes"""	2743	protein-coding gene	gene with protein product		606168	"""DEAD/H (Asp-Glu-Ala-Asp/His) box polypeptide 20, 103kD"""			10383418	Standard	NM_007204		Approved	DP103, GEMIN3	uc001ebs.3	Q9UHI6	OTTHUMG00000011956	ENST00000369702.4:c.2184C>T	1.37:g.112309230C>T		132.0	0.0	0		87.0	4.0	0.045977	NM_007204	B4DWV7|Q96F72|Q9NVM3|Q9UF59|Q9UIY0|Q9Y659	Silent	SNP	ENST00000369702.4	37	CCDS842.1																																																																																			.	.	none		0.483	DDX20-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000033063.2	NM_007204	
RBM48	84060	hgsc.bcm.edu	37	7	92158154	92158154	+	Silent	SNP	G	G	A	rs117787377	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr7:92158154G>A	ENST00000265732.5	+	1	68	c.27G>A	c.(25-27)ggG>ggA	p.G9G	PEX1_ENST00000438045.1_5'Flank|PEX1_ENST00000428214.1_5'Flank|RBM48_ENST00000481551.1_Silent_p.G9G|PEX1_ENST00000248633.4_5'Flank	NM_032120.2	NP_115496.2	Q5RL73	RBM48_HUMAN	RNA binding motif protein 48	9						nucleus (GO:0005634)	RNA binding (GO:0003723)										GGGAGCTAGGGAGTTTATTTG	0.552													G|||	20	0.00399361	0.0008	0.0029	5008	,	,		17571	0.0		0.0149	False		,,,				2504	0.002				p.G9G		Atlas-SNP	.											.	.	.	.	0			c.G27A						PASS	.	G		18,3950		0,18,1966	70.0	75.0	74.0		27	-4.0	0.0	7	dbSNP_132	74	123,8149		0,123,4013	no	coding-synonymous	C7orf64	NM_032120.2		0,141,5979	AA,AG,GG		1.4869,0.4536,1.152		9/368	92158154	141,12099	1984	4136	6120	SO:0001819	synonymous_variant	84060	exon1			GCTAGGGAGTTTA	AL136619	CCDS43615.1	7q21.2	2013-02-12	2011-12-09	2011-12-09	ENSG00000127993	ENSG00000127993		"""RNA binding motif (RRM) containing"""	21785	protein-coding gene	gene with protein product			"""chromosome 7 open reading frame 64"""	C7orf64			Standard	NM_032120		Approved	DKFZp564O0523, HSPC304	uc003ulz.3	Q5RL73	OTTHUMG00000159535	ENST00000265732.5:c.27G>A	7.37:g.92158154G>A		172.0	0.0	0		266.0	167.0	0.62782	NM_032120	B7Z2K5|B7ZL51|Q5H9T2|Q8IYW7|Q96NS0|Q9H0V7	Silent	SNP	ENST00000265732.5	37	CCDS43615.1																																																																																			G|0.992;A|0.008	0.008	strong		0.552	RBM48-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000356076.1	NM_032120	
HAPLN3	145864	hgsc.bcm.edu	37	15	89424765	89424765	+	Missense_Mutation	SNP	C	C	T	rs140982817	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr15:89424765C>T	ENST00000359595.3	-	3	530	c.316G>A	c.(316-318)Ggg>Agg	p.G106R	HAPLN3_ENST00000562889.1_Missense_Mutation_p.G168R	NM_178232.2	NP_839946.1	Q96S86	HPLN3_HUMAN	hyaluronan and proteoglycan link protein 3	106	Ig-like V-type. {ECO:0000305}.				cell adhesion (GO:0007155)	extracellular space (GO:0005615)|proteinaceous extracellular matrix (GO:0005578)	hyaluronic acid binding (GO:0005540)			endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(5)|lung(7)|ovary(1)|prostate(1)	17	Lung NSC(78;0.0392)|all_lung(78;0.077)				Hyaluronan(DB08818)	TGCCTCAGCCCGATGGCCACC	0.662													C|||	3	0.000599042	0.0	0.0029	5008	,	,		18397	0.0		0.001	False		,,,				2504	0.0				p.G106R		Atlas-SNP	.											HAPLN3,caecum,carcinoma,0,1	HAPLN3	43	1	0			c.G316A						PASS	.	C	ARG/GLY	2,4398	4.2+/-10.8	0,2,2198	95.0	76.0	83.0		316	4.2	0.4	15	dbSNP_134	83	55,8543	34.8+/-89.0	0,55,4244	yes	missense	HAPLN3	NM_178232.2	125	0,57,6442	TT,TC,CC		0.6397,0.0455,0.4385	probably-damaging	106/361	89424765	57,12941	2200	4299	6499	SO:0001583	missense	145864	exon3			TCAGCCCGATGGC	AY262759	CCDS10346.1	15q26.1	2013-01-11			ENSG00000140511	ENSG00000140511		"""Immunoglobulin superfamily / V-set domain containing"""	21446	protein-coding gene	gene with protein product			"""extracellular link domain containing, 1"""	EXLD1		12663660	Standard	NM_178232		Approved	HsT19883	uc002bnc.3	Q96S86	OTTHUMG00000148680	ENST00000359595.3:c.316G>A	15.37:g.89424765C>T	ENSP00000352606:p.Gly106Arg	112.0	0.0	0		70.0	21.0	0.3	NM_178232	A8K7P0	Missense_Mutation	SNP	ENST00000359595.3	37	CCDS10346.1	2	9.157509157509158E-4	0	0.0	0	0.0	0	0.0	2	0.002638522427440633	C	17.60	3.429872	0.62844	4.55E-4	0.006397	ENSG00000140511	ENST00000359595	T	0.65364	-0.15	4.21	4.21	0.49690	Immunoglobulin subtype (1);Immunoglobulin V-set (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	0.000000	0.85682	D	0.000000	T	0.77705	0.4170	M	0.90369	3.11	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.91635	0.999;0.999	D	0.85370	0.1113	10	0.87932	D	0	-31.7116	15.5717	0.76345	0.0:1.0:0.0:0.0	.	106;106	A8K7T8;Q96S86	.;HPLN3_HUMAN	R	106	ENSP00000352606:G106R	ENSP00000352606:G106R	G	-	1	0	HAPLN3	87225769	1.000000	0.71417	0.441000	0.26858	0.188000	0.23474	7.032000	0.76498	1.870000	0.54199	0.650000	0.86243	GGG	C|0.998;T|0.002	0.002	strong		0.662	HAPLN3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000309070.1	NM_178232	
IFNA21	3452	hgsc.bcm.edu	37	9	21166423	21166423	+	Silent	SNP	C	C	T	rs1053884	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr9:21166423C>T	ENST00000380225.1	-	1	236	c.189G>A	c.(187-189)caG>caA	p.Q63Q		NM_002175.2	NP_002166.2	P01568	IFN21_HUMAN	interferon, alpha 21	63					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)|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)|cytokine receptor binding (GO:0005126)|type I interferon receptor binding (GO:0005132)			NS(1)|central_nervous_system(1)|endometrium(1)|kidney(2)|large_intestine(1)|lung(5)|skin(3)	14				GBM - Glioblastoma multiforme(5;1.93e-187)|Lung(24;2.12e-22)|LUSC - Lung squamous cell carcinoma(38;1.4e-13)		CAAACTCCTCCTGGGGGAATC	0.502													C|||	25	0.00499201	0.0151	0.0072	5008	,	,		20179	0.0		0.0	False		,,,				2504	0.0				p.Q63Q		Atlas-SNP	.											.	IFNA21	25	.	0			c.G189A						PASS	.	C		49,4357		0,49,2154	135.0	136.0	135.0		189	3.1	0.0	9	dbSNP_86	135	7,8593		0,7,4293	no	coding-synonymous	IFNA21	NM_002175.2		0,56,6447	TT,TC,CC		0.0814,1.1121,0.4306		63/190	21166423	56,12950	2203	4300	6503	SO:0001819	synonymous_variant	3452	exon1			CTCCTCCTGGGGG		CCDS6497.1	9p22	2010-12-10			ENSG00000137080	ENSG00000137080		"""Interferons"""	5424	protein-coding gene	gene with protein product	"""leukocyte interferon protein"""	147584				1385305	Standard	NM_002175		Approved	IFN-alphaI	uc003zom.2	P01568	OTTHUMG00000019653	ENST00000380225.1:c.189G>A	9.37:g.21166423C>T		243.0	0.0	0		232.0	121.0	0.521552	NM_002175	Q14608|Q5VWD1|Q7M4Q4	Silent	SNP	ENST00000380225.1	37	CCDS6497.1																																																																																			C|0.996;T|0.004	0.004	strong		0.502	IFNA21-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051882.1	NM_002175	
CAPN3	825	hgsc.bcm.edu	37	15	42702836	42702836	+	Silent	SNP	C	C	T	rs147774793	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr15:42702836C>T	ENST00000397163.3	+	21	2454	c.2235C>T	c.(2233-2235)taC>taT	p.Y745Y	CAPN3_ENST00000561817.1_Silent_p.Y80Y|CAPN3_ENST00000349748.3_Silent_p.Y653Y|CAPN3_ENST00000562199.1_3'UTR|CAPN3_ENST00000397204.4_Silent_p.Y80Y|CAPN3_ENST00000569136.1_Silent_p.Y80Y|CAPN3_ENST00000357568.3_Silent_p.Y739Y|RP11-164J13.1_ENST00000495723.1_RNA|CAPN3_ENST00000337571.4_Silent_p.Y80Y|CAPN3_ENST00000356316.3_Silent_p.Y652Y|CAPN3_ENST00000397200.4_Silent_p.Y233Y|CAPN3_ENST00000318023.7_Silent_p.Y739Y	NM_000070.2	NP_000061.1	P20807	CAN3_HUMAN	calpain 3, (p94)	745	Domain IV.|EF-hand 3. {ECO:0000255|PROSITE- ProRule:PRU00448}.				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)		TCAACAGCTACGAGATGCGAA	0.517																																					p.Y745Y		Atlas-SNP	.											.	CAPN3	172	.	0			c.C2235T	GRCh37	CM051887	CAPN3	M	rs147774793	PASS	.	C	,,,,,	2,4404	4.2+/-10.8	0,2,2201	65.0	59.0	61.0		2235,2217,1959,699,240,240	-3.8	1.0	15	dbSNP_134	61	9,8589	7.1+/-27.0	0,9,4290	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	CAPN3	NM_000070.2,NM_024344.1,NM_173087.1,NM_173088.1,NM_173089.1,NM_173090.1	,,,,,	0,11,6491	TT,TC,CC		0.1047,0.0454,0.0846	,,,,,	745/822,739/816,653/730,233/310,80/157,80/157	42702836	11,12993	2203	4299	6502	SO:0001819	synonymous_variant	825	exon21			CAGCTACGAGATG	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.2235C>T	15.37:g.42702836C>T		116.0	0.0	0		89.0	20.0	0.224719	NM_000070	A6H8K6|Q7L4R0|Q9BQC8|Q9BTU4|Q9Y5S6|Q9Y5S7	Silent	SNP	ENST00000397163.3	37	CCDS45245.1																																																																																			C|0.999;T|0.001	0.001	strong		0.517	CAPN3-009	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000421075.1		
LRRK1	79705	hgsc.bcm.edu	37	15	101567971	101567971	+	Silent	SNP	C	C	T	rs41535348	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr15:101567971C>T	ENST00000388948.3	+	19	3014	c.2655C>T	c.(2653-2655)aaC>aaT	p.N885N	LRRK1_ENST00000284395.5_Silent_p.N882N	NM_024652.3	NP_078928.3			leucine-rich repeat kinase 1											breast(2)|central_nervous_system(6)|endometrium(12)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(14)|lung(25)|ovary(4)|prostate(1)|skin(1)	72	Melanoma(26;0.00505)|Lung NSC(78;0.00793)|all_lung(78;0.0094)		OV - Ovarian serous cystadenocarcinoma(32;0.000932)|LUSC - Lung squamous cell carcinoma(107;0.187)|Lung(145;0.23)			CGCCCGACAACGACATCAAGG	0.632													C|||	18	0.00359425	0.0008	0.0029	5008	,	,		18583	0.0		0.008	False		,,,				2504	0.0072				p.N885N		Atlas-SNP	.											.	LRRK1	310	.	0			c.C2655T						PASS	.	C		6,4338		0,6,2166	26.0	37.0	34.0		2655	-8.9	0.0	15	dbSNP_127	34	87,8451		0,87,4182	no	coding-synonymous	LRRK1	NM_024652.3		0,93,6348	TT,TC,CC		1.019,0.1381,0.7219		885/2016	101567971	93,12789	2172	4269	6441	SO:0001819	synonymous_variant	79705	exon19			CGACAACGACATC	AB058693	CCDS42086.1	15q26.3	2007-01-29			ENSG00000154237	ENSG00000154237			18608	protein-coding gene	gene with protein product		610986				11347906, 14654223	Standard	XM_005254979		Approved	FLJ23119, KIAA1790, Roco1, RIPK6	uc002bwr.3	Q38SD2	OTTHUMG00000165514	ENST00000388948.3:c.2655C>T	15.37:g.101567971C>T		183.0	0.0	0		129.0	31.0	0.24031	NM_024652		Silent	SNP	ENST00000388948.3	37	CCDS42086.1																																																																																			C|0.995;T|0.005	0.005	strong		0.632	LRRK1-003	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000384567.2	NM_024652	
CACNA1A	773	hgsc.bcm.edu	37	19	13409407	13409407	+	Missense_Mutation	SNP	C	C	T	rs16024	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr19:13409407C>T	ENST00000360228.5	-	19	3039	c.3040G>A	c.(3040-3042)Gag>Aag	p.E1014K	CACNA1A_ENST00000573710.2_Missense_Mutation_p.E1015K	NM_000068.3|NM_001127222.1|NM_001174080.1|NM_023035.2	NP_000059.3|NP_001120694.1|NP_001167551.1|NP_075461.2	O00555	CAC1A_HUMAN	calcium channel, voltage-dependent, P/Q type, alpha 1A subunit	1015					adult walking behavior (GO:0007628)|behavioral response to pain (GO:0048266)|calcium ion import (GO:0070509)|calcium ion-dependent exocytosis (GO:0017156)|calcium ion-dependent exocytosis of neurotransmitter (GO:0048791)|cell death (GO:0008219)|cell growth (GO:0016049)|cellular chloride ion homeostasis (GO:0030644)|cerebellar molecular layer development (GO:0021679)|cerebellar Purkinje cell differentiation (GO:0021702)|cerebellum maturation (GO:0021590)|dendrite morphogenesis (GO:0048813)|energy reserve metabolic process (GO:0006112)|gamma-aminobutyric acid secretion (GO:0014051)|gamma-aminobutyric acid signaling pathway (GO:0007214)|glucose metabolic process (GO:0006006)|hormone metabolic process (GO:0042445)|membrane depolarization (GO:0051899)|membrane depolarization during action potential (GO:0086010)|musculoskeletal movement, spinal reflex action (GO:0050883)|negative regulation of hormone biosynthetic process (GO:0032353)|negative regulation of neuron apoptotic process (GO:0043524)|neuromuscular process controlling balance (GO:0050885)|neuromuscular synaptic transmission (GO:0007274)|neurotransmitter metabolic process (GO:0042133)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|receptor clustering (GO:0043113)|regulation of acetylcholine secretion, neurotransmission (GO:0014056)|regulation of axonogenesis (GO:0050770)|regulation of calcium ion-dependent exocytosis (GO:0017158)|regulation of insulin secretion (GO:0050796)|rhythmic synaptic transmission (GO:0060024)|small molecule metabolic process (GO:0044281)|spinal cord motor neuron differentiation (GO:0021522)|sulfur amino acid metabolic process (GO:0000096)|synapse assembly (GO:0007416)|synaptic transmission (GO:0007268)|synaptic transmission, glutamatergic (GO:0035249)|transmission of nerve impulse (GO:0019226)|vestibular nucleus development (GO:0021750)	cell projection (GO:0042995)|cytoplasm (GO:0005737)|dendrite (GO:0030425)|integral component of membrane (GO:0016021)|neuronal cell body (GO:0043025)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|voltage-gated calcium channel complex (GO:0005891)	high voltage-gated calcium channel activity (GO:0008331)|metal ion binding (GO:0046872)|syntaxin binding (GO:0019905)|voltage-gated calcium channel activity (GO:0005245)			breast(2)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(3)|lung(25)|prostate(2)|urinary_tract(1)	42			OV - Ovarian serous cystadenocarcinoma(19;5.07e-21)		Bepridil(DB01244)|Loperamide(DB00836)|Pregabalin(DB00230)|Spironolactone(DB00421)|Verapamil(DB00661)	GCGTCCCCCTCGTACGTGGCT	0.687													C|||	6	0.00119808	0.0008	0.0029	5008	,	,		9081	0.0		0.003	False		,,,				2504	0.0				p.E1015K		Atlas-SNP	.											.	CACNA1A	715	.	0			c.G3043A						PASS	.	C	LYS/GLU,LYS/GLU,LYS/GLU,LYS/GLU,LYS/GLU	0,3196		0,0,1598	22.0	22.0	22.0		3052,3043,3040,3043,3052	3.5	0.0	19	dbSNP_54	22	35,6103		0,35,3034	yes	missense,missense,missense,missense,missense	CACNA1A	NM_000068.3,NM_001127221.1,NM_001127222.1,NM_001174080.1,NM_023035.2	56,56,56,56,56	0,35,4632	TT,TC,CC		0.5702,0.0,0.375	benign,benign,benign,benign,benign	1018/2267,1015/2262,1014/2507,1015/2264,1018/2513	13409407	35,9299	1598	3069	4667	SO:0001583	missense	773	exon19			CCCCCTCGTACGT	U79666	CCDS45998.1, CCDS45999.1	19p13	2014-09-17			ENSG00000141837	ENSG00000141837		"""Calcium channel subunits"", ""Voltage-gated ion channels / Calcium channels"""	1388	protein-coding gene	gene with protein product		601011		CACNL1A4, SCA6, MHP1, MHP		8825650, 16382099, 23827678	Standard	NM_000068		Approved	Cav2.1, EA2, APCA, HPCA, FHM	uc010xne.2	O00555	OTTHUMG00000044590	ENST00000360228.5:c.3040G>A	19.37:g.13409407C>T	ENSP00000353362:p.Glu1014Lys	141.0	0.0	0		122.0	58.0	0.47541	NM_001127221	J3KP41|P78510|P78511|Q16290|Q92690|Q99790|Q99791|Q99792|Q99793|Q9NS88|Q9UDC4	Missense_Mutation	SNP	ENST00000360228.5	37	CCDS45998.1	4	0.0018315018315018315	0	0.0	2	0.0055248618784530384	0	0.0	2	0.002638522427440633	C	8.418	0.845757	0.16963	0.0	0.005702	ENSG00000141837	ENST00000360228;ENST00000418012;ENST00000357018;ENST00000325084	D	0.95853	-3.83	3.54	3.54	0.40534	.	2.783830	0.01492	N	0.017126	D	0.89213	0.6651	L	0.36672	1.1	0.34650	D	0.721503	B;B;B	0.31599	0.0;0.33;0.222	B;B;B	0.17098	0.0;0.017;0.015	T	0.74842	-0.3527	10	0.06236	T	0.91	.	13.8911	0.63740	0.0:1.0:0.0:0.0	rs16024;rs16024	1015;1018;1014	O00555;E9PD31;Q9NS88	CAC1A_HUMAN;.;.	K	1014;1018;1015;1015	ENSP00000353362:E1014K	ENSP00000317661:E1015K	E	-	1	0	CACNA1A	13270407	0.456000	0.25744	0.039000	0.18376	0.035000	0.12851	1.820000	0.39032	1.541000	0.49316	0.462000	0.41574	GAG	C|0.997;T|0.003	0.003	strong		0.687	CACNA1A-001	KNOWN	non_canonical_U12|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000104062.2	NM_000068	
PARP14	54625	hgsc.bcm.edu	37	3	122419292	122419292	+	Missense_Mutation	SNP	A	A	G	rs7632072	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr3:122419292A>G	ENST00000474629.2	+	6	2157	c.1891A>G	c.(1891-1893)Act>Gct	p.T631A		NM_017554.2	NP_060024.2	Q460N5	PAR14_HUMAN	poly (ADP-ribose) polymerase family, member 14	631					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|membrane (GO:0016020)|nucleus (GO:0005634)	NAD+ ADP-ribosyltransferase activity (GO:0003950)			NS(2)|breast(5)|cervix(2)|endometrium(7)|kidney(5)|large_intestine(8)|lung(14)|ovary(2)|pancreas(1)|prostate(2)|skin(1)|urinary_tract(1)	50				GBM - Glioblastoma multiforme(114;0.0531)		CTCCCCAAACACTGTAATCAT	0.348													A|||	278	0.0555112	0.1218	0.0576	5008	,	,		21423	0.001		0.0487	False		,,,				2504	0.0276				p.T631A		Atlas-SNP	.											.	PARP14	242	.	0			c.A1891G						PASS	.	A	ALA/THR	342,3342		18,306,1518	31.0	30.0	31.0		1891	2.1	0.0	3	dbSNP_116	31	361,7841		5,351,3745	yes	missense	PARP14	NM_017554.2	58	23,657,5263	GG,GA,AA		4.4014,9.2834,5.9145	probably-damaging	631/1802	122419292	703,11183	1842	4101	5943	SO:0001583	missense	54625	exon6			CCAAACACTGTAA	AB033094	CCDS46894.1	3q21	2010-02-16			ENSG00000173193	ENSG00000173193		"""Poly (ADP-ribose) polymerases"""	29232	protein-coding gene	gene with protein product		610028				15273990	Standard	NM_017554		Approved	KIAA1268, pART8	uc003efq.4	Q460N5	OTTHUMG00000159552	ENST00000474629.2:c.1891A>G	3.37:g.122419292A>G	ENSP00000418194:p.Thr631Ala	104.0	0.0	0		72.0	32.0	0.444444	NM_017554	B4E2H0|Q460N4|Q8J027|Q9H9X9|Q9NV60|Q9ULF2	Missense_Mutation	SNP	ENST00000474629.2	37	CCDS46894.1	111	0.050824175824175824	49	0.09959349593495935	22	0.06077348066298342	1	0.0017482517482517483	39	0.051451187335092345	A	13.04	2.119612	0.37436	0.092834	0.044014	ENSG00000173193	ENST00000474629;ENST00000398162	T	0.10099	2.91	6.06	2.12	0.27331	.	0.174182	0.39759	N	0.001269	T	0.00271	0.0008	M	0.66939	2.045	0.09310	N	1	P;B	0.38827	0.649;0.376	B;B	0.33690	0.168;0.055	T	0.30268	-0.9984	10	0.36615	T	0.2	.	3.82	0.08832	0.663:0.1354:0.0717:0.1299	rs7632072;rs52827643;rs7632072	631;631	Q460N5-4;Q460N5	.;PAR14_HUMAN	A	631;550	ENSP00000418194:T631A	ENSP00000381228:T550A	T	+	1	0	PARP14	123901982	0.014000	0.17966	0.001000	0.08648	0.003000	0.03518	1.250000	0.32850	0.497000	0.27926	0.533000	0.62120	ACT	A|0.950;G|0.050	0.050	strong		0.348	PARP14-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000356173.2	NM_017554	
THEM6	51337	hgsc.bcm.edu	37	8	143816828	143816828	+	Missense_Mutation	SNP	G	G	A	rs11540544	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr8:143816828G>A	ENST00000336138.3	+	2	742	c.598G>A	c.(598-600)Ggg>Agg	p.G200R		NM_016647.2	NP_057731.1	Q8WUY1	THEM6_HUMAN	thioesterase superfamily member 6	200						extracellular region (GO:0005576)											CATGGAGAGTGGGCTCAGTGA	0.637													G|||	11	0.00219649	0.0	0.0029	5008	,	,		18322	0.0		0.008	False		,,,				2504	0.001				p.G200R		Atlas-SNP	.											.	.	.	.	0			c.G598A						PASS	.	G	ARG/GLY	6,4386		0,6,2190	63.0	44.0	50.0		598	4.1	1.0	8	dbSNP_120	50	109,8471		1,107,4182	yes	missense	C8orf55	NM_016647.2	125	1,113,6372	AA,AG,GG		1.2704,0.1366,0.8865	probably-damaging	200/209	143816828	115,12857	2196	4290	6486	SO:0001583	missense	51337	exon2			GAGAGTGGGCTCA	BC001311	CCDS6386.1	8q24.3	2012-05-03	2012-04-13	2012-04-13	ENSG00000130193	ENSG00000130193			29656	protein-coding gene	gene with protein product			"""chromosome 8 open reading frame 55"""	C8orf55		12477932	Standard	XM_005250955		Approved	DSCD75	uc003yww.1	Q8WUY1	OTTHUMG00000164673	ENST00000336138.3:c.598G>A	8.37:g.143816828G>A	ENSP00000338607:p.Gly200Arg	99.0	0.0	0		139.0	66.0	0.47482	NM_016647	B2RDN6|Q8NBN2|Q9NYI2	Missense_Mutation	SNP	ENST00000336138.3	37	CCDS6386.1	6	0.0027472527472527475	0	0.0	0	0.0	0	0.0	6	0.0079155672823219	G	10.94	1.491689	0.26774	0.001366	0.012704	ENSG00000130193	ENST00000336138	T	0.44083	0.93	4.07	4.07	0.47477	.	0.000000	0.64402	D	0.000001	T	0.48822	0.1521	L	0.53249	1.67	0.52099	D	0.999946	D;B	0.89917	1.0;0.062	D;B	0.97110	1.0;0.023	T	0.55457	-0.8138	10	0.56958	D	0.05	-30.9737	11.6462	0.51263	0.0:0.0:1.0:0.0	rs11540544	147;200	B4DWJ7;Q8WUY1	.;CH055_HUMAN	R	200	ENSP00000338607:G200R	ENSP00000338607:G200R	G	+	1	0	C8orf55	143813830	0.996000	0.38824	0.962000	0.40283	0.097000	0.18754	2.712000	0.47186	2.104000	0.64026	0.563000	0.77884	GGG	G|0.992;A|0.008	0.008	strong		0.637	THEM6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000379706.1	NM_016647	
EYA3	2140	hgsc.bcm.edu	37	1	28304899	28304899	+	Missense_Mutation	SNP	T	T	C			TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr1:28304899T>C	ENST00000373871.3	-	17	1867	c.1627A>G	c.(1627-1629)Att>Gtt	p.I543V	EYA3_ENST00000540618.1_Missense_Mutation_p.I497V|EYA3_ENST00000373863.3_Missense_Mutation_p.I497V|EYA3_ENST00000436342.2_Missense_Mutation_p.I417V|EYA3_ENST00000373864.1_Missense_Mutation_p.I386V|EYA3_ENST00000545175.1_Missense_Mutation_p.I490V	NM_001282561.1|NM_001282562.1	NP_001269490.1|NP_001269491.1	Q99504	EYA3_HUMAN	EYA transcriptional coactivator and phosphatase 3	543					anatomical structure morphogenesis (GO:0009653)|double-strand break repair (GO:0006302)|histone dephosphorylation (GO:0016576)|multicellular organismal development (GO:0007275)|peptidyl-tyrosine dephosphorylation (GO:0035335)|positive regulation of DNA repair (GO:0045739)|regulation of transcription, DNA-templated (GO:0006355)|response to ionizing radiation (GO:0010212)|transcription, DNA-templated (GO:0006351)|visual perception (GO:0007601)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	chromatin binding (GO:0003682)|metal ion binding (GO:0046872)|protein tyrosine phosphatase activity (GO:0004725)|protein tyrosine/serine/threonine phosphatase activity (GO:0008138)			breast(1)|kidney(1)|large_intestine(2)|lung(5)|ovary(2)|skin(3)|upper_aerodigestive_tract(1)	15		Colorectal(325;3.46e-05)|all_lung(284;0.000414)|Lung NSC(340;0.000432)|Renal(390;0.00121)|Breast(348;0.00345)|Ovarian(437;0.00503)|all_neural(195;0.0208)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0484)|OV - Ovarian serous cystadenocarcinoma(117;1.25e-24)|Colorectal(126;2.96e-08)|COAD - Colon adenocarcinoma(152;2.8e-06)|STAD - Stomach adenocarcinoma(196;0.00364)|KIRC - Kidney renal clear cell carcinoma(1967;0.00378)|BRCA - Breast invasive adenocarcinoma(304;0.00718)|READ - Rectum adenocarcinoma(331;0.0642)		TTGGCTGCAATTTCTTCATCT	0.368																																					p.I543V		Atlas-SNP	.											.	EYA3	38	.	0			c.A1627G						PASS	.						207.0	200.0	202.0					1																	28304899		2203	4300	6503	SO:0001583	missense	2140	exon17			CTGCAATTTCTTC	U81602	CCDS316.1, CCDS60050.1, CCDS60051.1, CCDS60052.1	1p36	2014-06-19	2014-06-19		ENSG00000158161	ENSG00000158161		"""Protein tyrosine phosphatases / Asp-based PTPs"""	3521	protein-coding gene	gene with protein product		601655	"""eyes absent (Drosophila) homolog 3"", ""eyes absent homolog 3 (Drosophila)"""			9020840	Standard	NM_001990		Approved	DKFZp686C132	uc001bpi.2	Q99504	OTTHUMG00000003916	ENST00000373871.3:c.1627A>G	1.37:g.28304899T>C	ENSP00000362978:p.Ile543Val	253.0	0.0	0		155.0	40.0	0.258065	NM_001990	A8K190|B4DIR7|B4DNZ7|O95463|Q8IVX7|Q99813	Missense_Mutation	SNP	ENST00000373871.3	37	CCDS316.1	.	.	.	.	.	.	.	.	.	.	T	8.394	0.840482	0.16891	.	.	ENSG00000158161	ENST00000373871;ENST00000436342;ENST00000373864;ENST00000540618;ENST00000545175;ENST00000373863	D;D;D;D;D;D	0.88046	-2.33;-2.33;-2.33;-2.33;-2.33;-2.33	5.54	5.54	0.83059	EYA (1);Haloacid dehalogenase-like hydrolase (1);	0.254205	0.46145	D	0.000317	T	0.77805	0.4185	N	0.22421	0.69	0.28710	N	0.903603	B;B;B	0.06786	0.0;0.001;0.001	B;B;B	0.06405	0.001;0.001;0.002	T	0.67074	-0.5762	10	0.28530	T	0.3	-12.8991	10.8241	0.46622	0.0:0.0757:0.0:0.9243	.	497;497;543	B4DIR7;Q8IVX7;Q99504	.;.;EYA3_HUMAN	V	543;417;386;497;490;497	ENSP00000362978:I543V;ENSP00000405587:I417V;ENSP00000362971:I386V;ENSP00000442558:I497V;ENSP00000442280:I490V;ENSP00000362970:I497V	ENSP00000362970:I497V	I	-	1	0	EYA3	28177486	1.000000	0.71417	1.000000	0.80357	0.982000	0.71751	2.160000	0.42348	2.107000	0.64212	0.402000	0.26972	ATT	.	.	none		0.368	EYA3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000011184.1	NM_001990	
GATAD2A	54815	hgsc.bcm.edu	37	19	19612027	19612027	+	Silent	SNP	C	C	T			TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr19:19612027C>T	ENST00000360315.3	+	9	1614	c.1302C>T	c.(1300-1302)ggC>ggT	p.G434G	GATAD2A_ENST00000252577.5_Silent_p.G434G|GATAD2A_ENST00000358713.3_Silent_p.G434G|GATAD2A_ENST00000537887.1_Silent_p.G63G|GATAD2A_ENST00000429563.2_Silent_p.G262G|GATAD2A_ENST00000404158.1_Silent_p.G435G	NM_017660.3	NP_060130.3	Q86YP4	P66A_HUMAN	GATA zinc finger domain containing 2A	434	CR2; histone tail-binding.				anterior neuropore closure (GO:0021506)|blood vessel development (GO:0001568)|DNA methylation (GO:0006306)|embryonic body morphogenesis (GO:0010172)|in utero embryonic development (GO:0001701)|negative regulation of transcription, DNA-templated (GO:0045892)|neural fold formation (GO:0001842)|programmed cell death (GO:0012501)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)|NuRD complex (GO:0016581)	protein binding, bridging (GO:0030674)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|zinc ion binding (GO:0008270)			endometrium(2)|kidney(1)|large_intestine(2)|lung(6)|ovary(1)|urinary_tract(1)	13						AGAAGAGCGGCGCCATCATGT	0.627																																					p.G434G		Atlas-SNP	.											GATAD2A_ENST00000360315,colon,carcinoma,+2,2	GATAD2A	81	2	0			c.C1302T						PASS	.						49.0	40.0	43.0					19																	19612027		2203	4300	6503	SO:0001819	synonymous_variant	54815	exon9			GAGCGGCGCCATC	AL390164	CCDS12402.2	19p13.11	2013-01-25			ENSG00000167491	ENSG00000167491		"""GATA zinc finger domain containing"""	29989	protein-coding gene	gene with protein product	"""p66 alpha"""	614997				12183469	Standard	NM_017660		Approved	p66alpha	uc010xqt.2	Q86YP4	OTTHUMG00000152541	ENST00000360315.3:c.1302C>T	19.37:g.19612027C>T		228.0	1.0	0.00438596		226.0	108.0	0.477876	NM_017660	B5MC40|Q7L3J2|Q96F28|Q9NPU2|Q9NXS1	Silent	SNP	ENST00000360315.3	37	CCDS12402.2	.	.	.	.	.	.	.	.	.	.	C	7.688	0.690376	0.15039	.	.	ENSG00000167491	ENST00000418032	.	.	.	5.76	-11.5	0.00074	.	.	.	.	.	T	0.34279	0.0892	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.52087	-0.8622	4	.	.	.	-20.9578	3.2541	0.06826	0.2384:0.4298:0.078:0.2537	.	.	.	.	C	61	.	.	R	+	1	0	GATAD2A	19473027	0.000000	0.05858	0.006000	0.13384	0.808000	0.45660	-5.377000	0.00127	-4.065000	0.00077	-0.158000	0.13435	CGC	.	.	none		0.627	GATAD2A-202	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000326671.4	NM_017660	
PTPN4	5775	hgsc.bcm.edu	37	2	120734589	120734589	+	Silent	SNP	T	T	A			TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr2:120734589T>A	ENST00000263708.2	+	27	3495	c.2724T>A	c.(2722-2724)atT>atA	p.I908I	PTPN4_ENST00000544261.1_Silent_p.I541I	NM_002830.3	NP_002821.1	P29074	PTN4_HUMAN	protein tyrosine phosphatase, non-receptor type 4 (megakaryocyte)	908	Tyrosine-protein phosphatase. {ECO:0000255|PROSITE-ProRule:PRU00160}.				peptidyl-tyrosine dephosphorylation (GO:0035335)|protein dephosphorylation (GO:0006470)	cytoplasm (GO:0005737)|cytoplasmic side of plasma membrane (GO:0009898)|cytoskeleton (GO:0005856)	non-membrane spanning protein tyrosine phosphatase activity (GO:0004726)			endometrium(3)|kidney(2)|large_intestine(7)|lung(15)|ovary(2)|urinary_tract(1)	30					Alendronate(DB00630)	GTGAAGCTATTTTGAAAGTTT	0.328																																					p.I908I		Atlas-SNP	.											PTPN4,NS,carcinoma,+2,1	PTPN4	89	1	0			c.T2724A						PASS	.						53.0	54.0	54.0					2																	120734589		2202	4299	6501	SO:0001819	synonymous_variant	5775	exon27			AGCTATTTTGAAA		CCDS2129.1	2q14.2	2011-06-09			ENSG00000088179	ENSG00000088179		"""Protein tyrosine phosphatases / Class I Cys-based PTPs : Non-receptor"""	9656	protein-coding gene	gene with protein product		176878				1648233	Standard	NM_002830		Approved	PTPMEG	uc002tmf.2	P29074	OTTHUMG00000131436	ENST00000263708.2:c.2724T>A	2.37:g.120734589T>A		119.0	0.0	0		133.0	51.0	0.383459	NM_002830	B2RBV8|Q9UDA7	Silent	SNP	ENST00000263708.2	37	CCDS2129.1	.	.	.	.	.	.	.	.	.	.	T	4.925	0.171834	0.09391	.	.	ENSG00000088179	ENST00000441089	.	.	.	5.12	3.96	0.45880	.	.	.	.	.	T	0.55016	0.1894	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.50048	-0.8873	4	.	.	.	.	6.0894	0.19985	0.1433:0.0767:0.0:0.78	.	.	.	.	I	201	.	.	F	+	1	0	PTPN4	120451059	1.000000	0.71417	0.998000	0.56505	0.996000	0.88848	2.465000	0.45075	0.798000	0.33994	0.528000	0.53228	TTT	.	.	none		0.328	PTPN4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254233.2		
MUC5B	727897	hgsc.bcm.edu	37	11	1269655	1269655	+	Missense_Mutation	SNP	T	T	G			TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr11:1269655T>G	ENST00000529681.1	+	31	11603	c.11545T>G	c.(11545-11547)Tct>Gct	p.S3849A	RP11-532E4.2_ENST00000532061.2_RNA|MUC5B_ENST00000447027.1_Missense_Mutation_p.S3852A	NM_002458.2	NP_002449.2	Q9HC84	MUC5B_HUMAN	mucin 5B, oligomeric mucus/gel-forming	3849	11 X approximate tandem repeats, Ser/Thr- rich.|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)		GGCCACCGGCTCTGTGGCCAC	0.642																																					p.S3849A		Atlas-SNP	.											.	MUC5B	473	.	0			c.T11545G						PASS	.						118.0	137.0	131.0					11																	1269655		2065	4172	6237	SO:0001583	missense	727897	exon31			ACCGGCTCTGTGG	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.11545T>G	11.37:g.1269655T>G	ENSP00000436812:p.Ser3849Ala	219.0	0.0	0		341.0	98.0	0.28739	NM_002458	O00447|O00573|O14985|O15494|O95291|O95451|Q14881|Q7M4S5|Q99552|Q9UE28	Missense_Mutation	SNP	ENST00000529681.1	37	CCDS44515.2	.	.	.	.	.	.	.	.	.	.	T	1.973	-0.435940	0.04636	.	.	ENSG00000117983	ENST00000529681;ENST00000447027;ENST00000349637;ENST00000406844	T;T	0.21031	2.03;2.21	0.58	-1.16	0.09678	.	.	.	.	.	T	0.17152	0.0412	M	0.75264	2.295	0.09310	N	1	P;P	0.40476	0.718;0.718	B;B	0.28385	0.089;0.089	T	0.10154	-1.0642	9	0.87932	D	0	.	4.7328	0.12974	0.0:0.2164:0.0:0.7836	.	4377;3852	A7Y9J9;E9PBJ0	.;.	A	3849;3852;3793;3754	ENSP00000436812:S3849A;ENSP00000415793:S3852A	ENSP00000343037:S3793A	S	+	1	0	MUC5B	1226231	0.000000	0.05858	0.001000	0.08648	0.009000	0.06853	-5.111000	0.00150	-0.567000	0.06046	0.163000	0.16589	TCT	.	.	none		0.642	MUC5B-002	NOVEL	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000390041.2	XM_001126093	
MED12	9968	hgsc.bcm.edu	37	X	70351982	70351982	+	Silent	SNP	A	A	C	rs376058351		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chrX:70351982A>C	ENST00000374080.3	+	30	4211	c.4179A>C	c.(4177-4179)tcA>tcC	p.S1393S	MED12_ENST00000374102.1_Silent_p.S1393S|MED12_ENST00000333646.6_Silent_p.S1393S			Q93074	MED12_HUMAN	mediator complex subunit 12	1393					androgen receptor signaling pathway (GO:0030521)|axis elongation involved in somitogenesis (GO:0090245)|canonical Wnt signaling pathway (GO:0060070)|gene expression (GO:0010467)|heart development (GO:0007507)|intracellular steroid hormone receptor signaling pathway (GO:0030518)|negative regulation of Wnt signaling pathway (GO:0030178)|neural tube closure (GO:0001843)|oligodendrocyte development (GO:0014003)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|Schwann cell development (GO:0014044)|stem cell maintenance (GO:0019827)|transcription initiation from RNA polymerase II promoter (GO:0006367)|Wnt signaling pathway, planar cell polarity pathway (GO:0060071)	mediator complex (GO:0016592)|membrane (GO:0016020)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	chromatin binding (GO:0003682)|ligand-dependent nuclear receptor transcription coactivator activity (GO:0030374)|protein C-terminus binding (GO:0008022)|protein domain specific binding (GO:0019904)|receptor activity (GO:0004872)|RNA polymerase II distal enhancer sequence-specific DNA binding (GO:0000980)|RNA polymerase II transcription cofactor activity (GO:0001104)|RNA polymerase II transcription factor binding transcription factor activity involved in positive regulation of transcription (GO:0001190)|thyroid hormone receptor binding (GO:0046966)|transcription coactivator activity (GO:0003713)|transcription cofactor activity (GO:0003712)|vitamin D receptor binding (GO:0042809)			breast(6)|central_nervous_system(2)|endometrium(22)|kidney(5)|large_intestine(8)|lung(31)|ovary(2)|pancreas(1)|prostate(11)|skin(5)|soft_tissue(323)|upper_aerodigestive_tract(1)|urinary_tract(3)	420	Renal(35;0.156)					TCCAACAGTCAGCAGAGACAG	0.512			"""M, S"""		uterine leiomyoma		Opitz-Kaveggia Syndrome																														p.S1393S		Atlas-SNP	.		Dom	yes		X	Xq13	9968	mediator complex subunit 12	Yes	M	.	MED12	984	.	0			c.A4179C						PASS	.	A		0,3657		0,0,1543,571	83.0	76.0	78.0		4179	-8.8	0.4	X		78	2,6605		0,2,2395,1813	no	coding-synonymous	MED12	NM_005120.2		0,2,3938,2384	CC,CA,AA,A		0.0303,0.0,0.0195		1393/2178	70351982	2,10262	2114	4210	6324	SO:0001819	synonymous_variant	9968	exon30			ACAGTCAGCAGAG	U80742	CCDS43970.1	Xq13	2011-02-14	2007-07-30	2004-11-26	ENSG00000184634	ENSG00000184634			11957	protein-coding gene	gene with protein product		300188	"""trinucleotide repeat containing 11 (THR-associated protein, 230kDa subunit)"", ""mediator of RNA polymerase II transcription, subunit 12 homolog (S. cerevisiae)"", ""FG syndrome 1"""	TNRC11, FGS1		9225980, 10198638, 17334363, 20507344	Standard	NM_005120		Approved	CAGH45, HOPA, OPA1, TRAP230, KIAA0192, OKS	uc004dyy.3	Q93074	OTTHUMG00000021788	ENST00000374080.3:c.4179A>C	X.37:g.70351982A>C		429.0	0.0	0		213.0	207.0	0.971831	NM_005120	O15410|O75557|Q9UHV6|Q9UND7	Silent	SNP	ENST00000374080.3	37	CCDS43970.1																																																																																			.	.	weak		0.512	MED12-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000057105.1	NM_005120	
C1orf43	25912	hgsc.bcm.edu	37	1	154184993	154184993	+	Missense_Mutation	SNP	G	G	A	rs144385115	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr1:154184993G>A	ENST00000368521.5	-	5	646	c.448C>T	c.(448-450)Cgc>Tgc	p.R150C	C1orf43_ENST00000350592.3_Missense_Mutation_p.R116C|C1orf43_ENST00000368516.1_Missense_Mutation_p.R116C|C1orf43_ENST00000368518.1_Missense_Mutation_p.R150C|C1orf43_ENST00000362076.4_Missense_Mutation_p.R98C|C1orf43_ENST00000368519.1_Missense_Mutation_p.R132C	NM_001098616.1	NP_001092086.1	Q9BWL3	CA043_HUMAN	chromosome 1 open reading frame 43	150						integral component of membrane (GO:0016021)	coenzyme binding (GO:0050662)|oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor (GO:0016616)			cervix(1)|endometrium(1)|kidney(2)|large_intestine(2)|lung(3)|ovary(1)	10	all_lung(78;1.98e-30)|Lung NSC(65;2.87e-28)|Hepatocellular(266;0.0877)					AGTGCTTTGCGTACACCCTTG	0.498													G|||	22	0.00439297	0.0008	0.0101	5008	,	,		19963	0.0		0.0119	False		,,,				2504	0.002				p.R150C		Atlas-SNP	.											.	C1orf43	36	.	0			c.C448T						PASS	.	G	CYS/ARG,CYS/ARG,CYS/ARG	6,4400	11.4+/-27.6	0,6,2197	90.0	82.0	85.0		448,346,292	3.5	1.0	1	dbSNP_134	85	70,8530	41.7+/-99.0	0,70,4230	yes	missense,missense,missense	C1orf43	NM_001098616.1,NM_015449.2,NM_138740.2	180,180,180	0,76,6427	AA,AG,GG		0.814,0.1362,0.5843	benign,benign,benign	150/254,116/220,98/202	154184993	76,12930	2203	4300	6503	SO:0001583	missense	25912	exon5			CTTTGCGTACACC	AF077036	CCDS1061.1, CCDS1062.1, CCDS41404.1, CCDS72924.1	1q21.2	2012-06-25			ENSG00000143612	ENSG00000143612			29876	protein-coding gene	gene with protein product						11042152, 11230159	Standard	XM_005245077		Approved	NICE-3, DKFZp586G1722	uc001fei.2	Q9BWL3	OTTHUMG00000035981	ENST00000368521.5:c.448C>T	1.37:g.154184993G>A	ENSP00000357507:p.Arg150Cys	168.0	0.0	0		156.0	84.0	0.538462	NM_001098616	A8K3G8|D3DV72|D3DV74|Q5M801|Q5VU73|Q5VU83|Q96HP7|Q9UFU2|Q9UGL7|Q9UGL8|Q9Y2R6	Missense_Mutation	SNP	ENST00000368521.5	37	CCDS41404.1	16	0.007326007326007326	0	0.0	5	0.013812154696132596	0	0.0	11	0.014511873350923483	G	15.45	2.837975	0.50951	0.001362	0.00814	ENSG00000143612	ENST00000350592;ENST00000368521;ENST00000362076;ENST00000368519;ENST00000368518;ENST00000368516	.	.	.	5.39	3.5	0.40072	Dehydrogenase, multihelical (1);	0.150760	0.64402	D	0.000008	T	0.32466	0.0830	L	0.58101	1.795	0.53005	D	0.999961	B;B;B;B;B	0.14012	0.007;0.007;0.004;0.003;0.009	B;B;B;B;B	0.14023	0.002;0.002;0.01;0.002;0.003	T	0.31503	-0.9941	9	0.54805	T	0.06	-17.9839	5.6172	0.17438	0.0749:0.1395:0.6412:0.1444	.	132;116;150;98;116	Q9BWL3-5;Q9BWL3-2;Q9BWL3;Q9BWL3-4;Q09GN0	.;.;CA043_HUMAN;.;.	C	116;150;98;132;150;116	.	ENSP00000271925:R116C	R	-	1	0	C1orf43	152451617	1.000000	0.71417	0.998000	0.56505	0.792000	0.44763	4.784000	0.62411	0.821000	0.34540	0.585000	0.79938	CGC	G|0.994;A|0.006	0.006	strong		0.498	C1orf43-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000087664.2	NM_015449	
HTR3B	9177	hgsc.bcm.edu	37	11	113803108	113803108	+	Missense_Mutation	SNP	A	A	C	rs72466469	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr11:113803108A>C	ENST00000260191.2	+	5	723	c.466A>C	c.(466-468)Agt>Cgt	p.S156R	HTR3B_ENST00000537778.1_Missense_Mutation_p.S145R	NM_006028.4	NP_006019.1	O95264	5HT3B_HUMAN	5-hydroxytryptamine (serotonin) receptor 3B, ionotropic	156			S -> R (in dbSNP:rs72466469). {ECO:0000269|PubMed:15293096, ECO:0000269|PubMed:15389765, ECO:0000269|PubMed:21179162}.		cation transmembrane transport (GO:0098655)|ion transmembrane transport (GO:0034220)|synaptic transmission (GO:0007268)|transmembrane transport (GO:0055085)|transport (GO:0006810)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)	ion channel activity (GO:0005216)|serotonin receptor activity (GO:0004993)|serotonin-activated cation-selective channel activity (GO:0005232)			endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(7)|lung(11)	20		all_cancers(61;6.81e-18)|all_epithelial(67;6.67e-11)|all_hematologic(158;4.67e-05)|Melanoma(852;0.000316)|Acute lymphoblastic leukemia(157;0.000976)|Breast(348;0.0101)|Prostate(24;0.0154)|all_neural(223;0.0281)|Medulloblastoma(222;0.0425)		BRCA - Breast invasive adenocarcinoma(274;3.04e-06)|Epithelial(105;1.98e-05)|all cancers(92;0.000201)|OV - Ovarian serous cystadenocarcinoma(223;0.151)	Ergoloid mesylate(DB01049)	CTCTGCGTGCAGTTTAGAGAC	0.438													A|||	9	0.00179712	0.0	0.0043	5008	,	,		21219	0.0		0.006	False		,,,				2504	0.0				p.S156R		Atlas-SNP	.											.	HTR3B	50	.	0			c.A466C	GRCh37	CM083528	HTR3B	M	rs72466469	PASS	.	A	ARG/SER	2,4400	2.1+/-5.4	0,2,2199	179.0	153.0	162.0		466	0.7	0.2	11	dbSNP_130	162	69,8523	41.7+/-99.0	2,65,4229	yes	missense	HTR3B	NM_006028.4	110	2,67,6428	CC,CA,AA		0.8031,0.0454,0.5464	possibly-damaging	156/442	113803108	71,12923	2201	4296	6497	SO:0001583	missense	9177	exon5			GCGTGCAGTTTAG	AF080582	CCDS8364.1	11q23.1	2012-05-22	2012-02-03		ENSG00000149305	ENSG00000149305		"""5-HT (serotonin) receptors"", ""Ligand-gated ion channels / 5-HT (serotonin) receptors, ionotropic"""	5298	protein-coding gene	gene with protein product		604654	"""5-hydroxytryptamine (serotonin) receptor 3B"""			9950429, 10521471	Standard	NM_006028		Approved	5-HT3B	uc001pok.3	O95264	OTTHUMG00000168210	ENST00000260191.2:c.466A>C	11.37:g.113803108A>C	ENSP00000260191:p.Ser156Arg	245.0	1.0	0.00408163		345.0	220.0	0.637681	NM_006028	B0YJ23|Q0VJC3	Missense_Mutation	SNP	ENST00000260191.2	37	CCDS8364.1	6	0.0027472527472527475	0	0.0	1	0.0027624309392265192	0	0.0	5	0.006596306068601583	A	16.36	3.101980	0.56183	4.54E-4	0.008031	ENSG00000149305	ENST00000260191;ENST00000537778	T;T	0.79554	-1.28;-1.28	5.82	0.729	0.18266	Neurotransmitter-gated ion-channel ligand-binding (3);	0.421195	0.29473	N	0.012047	T	0.75317	0.3833	L	0.52905	1.665	0.33014	D	0.527966	D;P	0.56287	0.975;0.934	P;P	0.59643	0.861;0.643	T	0.77107	-0.2710	10	0.37606	T	0.19	-0.5361	4.9411	0.13965	0.6577:0.0:0.2158:0.1265	.	145;156	O95264-2;O95264	.;5HT3B_HUMAN	R	156;145	ENSP00000260191:S156R;ENSP00000443118:S145R	ENSP00000260191:S156R	S	+	1	0	HTR3B	113308318	0.181000	0.23161	0.166000	0.22797	0.877000	0.50540	0.873000	0.28052	0.144000	0.18951	-0.376000	0.06991	AGT	A|0.996;C|0.004	0.004	strong		0.438	HTR3B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000398842.1	NM_006028	
OSGIN1	29948	hgsc.bcm.edu	37	16	83998922	83998922	+	Silent	SNP	G	G	A	rs146347192		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr16:83998922G>A	ENST00000343939.2	+	7	1376	c.993G>A	c.(991-993)acG>acA	p.T331T	OSGIN1_ENST00000393306.1_Silent_p.T248T|OSGIN1_ENST00000361711.3_Silent_p.T248T			Q9UJX0	OSGI1_HUMAN	oxidative stress induced growth inhibitor 1	331					cell differentiation (GO:0030154)|multicellular organismal development (GO:0007275)|negative regulation of cell growth (GO:0030308)|positive regulation of apoptotic process (GO:0043065)		growth factor activity (GO:0008083)			autonomic_ganglia(1)|large_intestine(1)|lung(7)|prostate(2)|upper_aerodigestive_tract(1)	12						CCACAGGCACGTTCGACAGCC	0.697																																					p.T248T		Atlas-SNP	.											OSGIN1,NS,carcinoma,+2,1	OSGIN1	33	1	0			c.G744A						scavenged	.	G	,,	0,4398		0,0,2199	26.0	31.0	29.0		993,744,744	-8.1	0.0	16	dbSNP_134	29	2,8580		0,2,4289	no	coding-synonymous,coding-synonymous,coding-synonymous	OSGIN1	NM_013370.3,NM_182980.2,NM_182981.2	,,	0,2,6488	AA,AG,GG		0.0233,0.0,0.0154	,,	331/561,248/478,248/478	83998922	2,12978	2199	4291	6490	SO:0001819	synonymous_variant	29948	exon6			AGGCACGTTCGAC	AY258066	CCDS10939.1	16q23.3	2010-11-23			ENSG00000140961	ENSG00000140961			30093	protein-coding gene	gene with protein product	"""bone marrow stromal cell-derived growth inhibitor"", ""pregnancy induced growth inhibitor"""	607975				11459809, 14570898	Standard	NM_182981		Approved	BDGI, OKL38	uc002fhc.3	Q9UJX0	OTTHUMG00000137640	ENST00000343939.2:c.993G>A	16.37:g.83998922G>A		35.0	0.0	0		28.0	4.0	0.142857	NM_182981	Q52M33|Q86UQ1|Q96S88|Q9BZ70	Silent	SNP	ENST00000343939.2	37																																																																																				G|1.000;A|0.000	0.000	weak		0.697	OSGIN1-001	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000269081.1	NM_013370	
PCDHA4	56144	hgsc.bcm.edu	37	5	140188356	140188356	+	Silent	SNP	A	A	G	rs144593807	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr5:140188356A>G	ENST00000530339.1	+	1	1584	c.1584A>G	c.(1582-1584)ctA>ctG	p.L528L	PCDHA4_ENST00000356878.4_Silent_p.L528L|PCDHA1_ENST00000504120.2_Intron|PCDHA2_ENST00000526136.1_Intron|PCDHA1_ENST00000394633.3_Intron|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						PASS	.	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		133.0	0.0	0		63.0	11.0	0.174603	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	
LY75	4065	hgsc.bcm.edu	37	2	160735174	160735174	+	Missense_Mutation	SNP	C	C	T	rs147820690	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr2:160735174C>T	ENST00000263636.4	-	10	1601	c.1574G>A	c.(1573-1575)gGa>gAa	p.G525E	LY75-CD302_ENST00000504764.1_Missense_Mutation_p.G525E|LY75_ENST00000553424.1_Missense_Mutation_p.G525E|LY75-CD302_ENST00000505052.1_Missense_Mutation_p.G525E|LY75_ENST00000554112.1_Missense_Mutation_p.G525E	NM_002349.3	NP_002340.2	O60449	LY75_HUMAN	lymphocyte antigen 75	525	C-type lectin 3. {ECO:0000255|PROSITE- ProRule:PRU00040}.				endocytosis (GO:0006897)|immune response (GO:0006955)|inflammatory response (GO:0006954)	extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)	carbohydrate binding (GO:0030246)|receptor activity (GO:0004872)			NS(2)|central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(9)|lung(22)|prostate(7)|skin(6)|stomach(3)|upper_aerodigestive_tract(3)|urinary_tract(1)	59				COAD - Colon adenocarcinoma(177;0.132)		GCAGTTTGTTCCAAAAGGGAC	0.388													C|||	3	0.000599042	0.0	0.0014	5008	,	,		20519	0.0		0.002	False		,,,				2504	0.0				p.G525E		Atlas-SNP	.											.	LY75	151	.	0			c.G1574A						PASS	.	C	GLU/GLY,GLU/GLY,GLU/GLY	5,4401	9.9+/-24.2	0,5,2198	173.0	156.0	162.0		1574,1574,1574	4.4	1.0	2	dbSNP_134	162	23,8577	16.6+/-54.9	0,23,4277	yes	missense,missense,missense	LY75,LY75-CD302	NM_001198759.1,NM_001198760.1,NM_002349.3	98,98,98	0,28,6475	TT,TC,CC		0.2674,0.1135,0.2153	probably-damaging,probably-damaging,probably-damaging	525/1874,525/1818,525/1723	160735174	28,12978	2203	4300	6503	SO:0001583	missense	4065	exon10			TTTGTTCCAAAAG	AF011333	CCDS2211.1	2q24	2011-08-30			ENSG00000054219	ENSG00000054219		"""CD molecules"", ""C-type lectin domain containing"""	6729	protein-coding gene	gene with protein product		604524				9553150	Standard	NM_002349		Approved	DEC-205, CLEC13B, CD205		O60449	OTTHUMG00000132025	ENST00000263636.4:c.1574G>A	2.37:g.160735174C>T	ENSP00000263636:p.Gly525Glu	209.0	0.0	0		220.0	125.0	0.568182	NM_002349	O75913|Q53R46|Q53TF5|Q7Z575|Q7Z577	Missense_Mutation	SNP	ENST00000263636.4	37	CCDS2211.1	3	0.0013736263736263737	0	0.0	1	0.0027624309392265192	0	0.0	2	0.002638522427440633	C	19.40	3.820467	0.71028	0.001135	0.002674	ENSG00000054219;ENSG00000054219;ENSG00000054219;ENSG00000248672;ENSG00000248672	ENST00000554112;ENST00000553424;ENST00000263636;ENST00000504764;ENST00000505052	T;T;T;T;T	0.51817	0.69;2.98;2.96;0.69;2.98	5.31	4.43	0.53597	C-type lectin fold (1);C-type lectin-like (1);C-type lectin (2);	0.234809	0.21795	N	0.069012	T	0.66877	0.2834	M	0.73598	2.24	0.48901	D	0.999726	B;D;D;D	0.89917	0.41;1.0;1.0;1.0	P;D;D;D	0.97110	0.45;0.999;1.0;1.0	T	0.67313	-0.5702	10	0.41790	T	0.15	-18.7866	13.1585	0.59531	0.0:0.9209:0.0:0.0791	.	143;525;525;525	Q59H44;O60449-3;O60449;O60449-2	.;.;LY75_HUMAN;.	E	525	ENSP00000451511:G525E;ENSP00000451446:G525E;ENSP00000263636:G525E;ENSP00000423463:G525E;ENSP00000421035:G525E	ENSP00000423463:G525E	G	-	2	0	LY75;LY75-CD302	160443420	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	3.886000	0.56190	1.367000	0.46095	0.650000	0.86243	GGA	C|0.998;T|0.002	0.002	strong		0.388	LY75-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000255035.1		
CCDC66	285331	hgsc.bcm.edu	37	3	56628033	56628033	+	Nonsense_Mutation	SNP	C	C	T	rs150364083	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr3:56628033C>T	ENST00000394672.3	+	10	1451	c.1381C>T	c.(1381-1383)Cga>Tga	p.R461*	CCDC66_ENST00000436465.2_Nonsense_Mutation_p.R461*|CCDC66_ENST00000326595.7_Nonsense_Mutation_p.R427*	NM_001012506.4|NM_001141947.1	NP_001012524.4|NP_001135419.1	A2RUB6	CCD66_HUMAN	coiled-coil domain containing 66	461					post-embryonic retina morphogenesis in camera-type eye (GO:0060060)|retinal rod cell development (GO:0046548)					breast(1)|kidney(1)|large_intestine(2)|liver(1)|lung(4)|skin(2)|urinary_tract(1)	12				KIRC - Kidney renal clear cell carcinoma(284;0.0478)|Kidney(284;0.0597)|OV - Ovarian serous cystadenocarcinoma(275;0.233)		AGACAGACGACGACAAAAACA	0.373													C|||	3	0.000599042	0.0	0.0014	5008	,	,		20246	0.0		0.002	False		,,,				2504	0.0				p.R461X		Atlas-SNP	.											.	CCDC66	145	.	0			c.C1381T						PASS	.	C	stop/ARG,stop/ARG	4,4402	9.9+/-24.2	0,4,2199	180.0	168.0	172.0		1279,1381	4.9	1.0	3	dbSNP_134	172	66,8534	39.8+/-96.3	0,66,4234	yes	stop-gained,stop-gained	CCDC66	NM_001012506.4,NM_001141947.1	,	0,70,6433	TT,TC,CC		0.7674,0.0908,0.5382	,	427/915,461/949	56628033	70,12936	2203	4300	6503	SO:0001587	stop_gained	285331	exon10			AGACGACGACAAA	AL832692	CCDS33770.2, CCDS46852.1	3p14.3	2006-03-27			ENSG00000180376	ENSG00000180376			27709	protein-coding gene	gene with protein product						14702039	Standard	NR_024460		Approved	DKFZp686C0433	uc003dhz.3	A2RUB6	OTTHUMG00000155748	ENST00000394672.3:c.1381C>T	3.37:g.56628033C>T	ENSP00000378167:p.Arg461*	163.0	0.0	0		125.0	51.0	0.408	NM_001141947	B3KWL8|Q4VC34|Q8N949	Nonsense_Mutation	SNP	ENST00000394672.3	37	CCDS46852.1	1	4.578754578754579E-4	0	0.0	0	0.0	0	0.0	1	0.0013192612137203166	C	37	6.393245	0.97529	9.08E-4	0.007674	ENSG00000180376	ENST00000422222;ENST00000394672;ENST00000326595;ENST00000436465	.	.	.	5.81	4.86	0.63082	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-14.6425	15.6712	0.77279	0.1457:0.8543:0.0:0.0	.	.	.	.	X	417;461;427;461	.	ENSP00000326050:R427X	R	+	1	2	CCDC66	56603073	1.000000	0.71417	0.994000	0.49952	0.977000	0.68977	3.573000	0.53856	2.739000	0.93911	0.585000	0.79938	CGA	C|0.996;T|0.004	0.004	strong		0.373	CCDC66-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000341473.1	NM_001012506	
MKI67	4288	hgsc.bcm.edu	37	10	129909929	129909929	+	Missense_Mutation	SNP	T	T	G			TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr10:129909929T>G	ENST00000368654.3	-	11	2615	c.2240A>C	c.(2239-2241)gAc>gCc	p.D747A	MKI67_ENST00000368653.3_Missense_Mutation_p.D387A|MKI67_ENST00000484853.1_5'UTR	NM_002417.4	NP_002408.3	P46013	KI67_HUMAN	marker of proliferation Ki-67	747					cell proliferation (GO:0008283)|cellular response to heat (GO:0034605)|DNA metabolic process (GO:0006259)|hyaluronan metabolic process (GO:0030212)|meiotic nuclear division (GO:0007126)|organ regeneration (GO:0031100)|response to organic cyclic compound (GO:0014070)	chromosome, centromeric region (GO:0000775)|condensed chromosome (GO:0000793)|cytoplasm (GO:0005737)|membrane (GO:0016020)|nucleolus (GO:0005730)|nucleus (GO:0005634)	ATP binding (GO:0005524)|poly(A) RNA binding (GO:0044822)|protein C-terminus binding (GO:0008022)			NS(2)|autonomic_ganglia(1)|breast(2)|central_nervous_system(2)|cervix(2)|endometrium(14)|haematopoietic_and_lymphoid_tissue(5)|kidney(7)|large_intestine(30)|lung(64)|ovary(4)|pancreas(1)|prostate(4)|skin(2)|soft_tissue(1)|stomach(10)|upper_aerodigestive_tract(4)|urinary_tract(4)	159		all_epithelial(44;2.12e-05)|all_lung(145;0.00679)|Lung NSC(174;0.00998)|all_neural(114;0.0936)|Colorectal(57;0.14)|Breast(234;0.166)|Melanoma(40;0.203)				TTCCTTAAAGTCCATTTTTTG	0.348																																					p.D747A		Atlas-SNP	.											.	MKI67	363	.	0			c.A2240C						PASS	.						99.0	97.0	97.0					10																	129909929		2203	4300	6503	SO:0001583	missense	4288	exon11			TTAAAGTCCATTT	X65550	CCDS7659.1, CCDS53588.1	10q26.2	2014-06-12	2013-10-10		ENSG00000148773	ENSG00000148773			7107	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 105"""	176741	"""antigen identified by monoclonal antibody Ki-67"""			2571566, 16206250	Standard	NM_002417		Approved	MIB-, PPP1R105	uc001lke.3	P46013	OTTHUMG00000019255	ENST00000368654.3:c.2240A>C	10.37:g.129909929T>G	ENSP00000357643:p.Asp747Ala	85.0	0.0	0		67.0	28.0	0.41791	NM_002417	Q5VWH2	Missense_Mutation	SNP	ENST00000368654.3	37	CCDS7659.1	.	.	.	.	.	.	.	.	.	.	T	17.07	3.295801	0.60086	.	.	ENSG00000148773	ENST00000368654;ENST00000368653;ENST00000537609;ENST00000368652	T;T	0.01584	4.77;4.75	5.18	4.01	0.46588	.	0.000000	0.45867	D	0.000331	T	0.06872	0.0175	M	0.64404	1.975	0.09310	N	1	D;D;D	0.89917	1.0;0.999;1.0	D;D;D	0.79784	0.993;0.973;0.976	T	0.09975	-1.0650	10	0.72032	D	0.01	.	7.2985	0.26408	0.0:0.0771:0.1574:0.7655	.	746;387;747	F5H4V4;P46013-2;P46013	.;.;KI67_HUMAN	A	747;387;746;322	ENSP00000357643:D747A;ENSP00000357642:D387A	ENSP00000357641:D322A	D	-	2	0	MKI67	129799919	0.017000	0.18338	0.150000	0.22450	0.353000	0.29299	1.086000	0.30853	0.937000	0.37394	0.533000	0.62120	GAC	.	.	none		0.348	MKI67-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000050999.1	NM_002417	
SRSF1	6426	hgsc.bcm.edu	37	17	56083705	56083705	+	Splice_Site	SNP	A	A	G			TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr17:56083705A>G	ENST00000258962.4	-	2	586	c.378T>C	c.(376-378)tcT>tcC	p.S126S	SRSF1_ENST00000582730.2_Splice_Site_p.S126S|SRSF1_ENST00000584773.1_Splice_Site_p.S126S|RP11-159D12.5_ENST00000578794.1_5'Flank|SRSF1_ENST00000585096.1_Intron|SRSF1_ENST00000581497.1_5'Flank	NM_006924.4	NP_008855.1	Q07955	SRSF1_HUMAN	serine/arginine-rich splicing factor 1	126	RRM 2. {ECO:0000255|PROSITE- ProRule:PRU00176}.				cardiac muscle contraction (GO:0060048)|gene expression (GO:0010467)|in utero embryonic development (GO:0001701)|mRNA 3'-end processing (GO:0031124)|mRNA 5'-splice site recognition (GO:0000395)|mRNA export from nucleus (GO:0006406)|mRNA processing (GO:0006397)|mRNA splice site selection (GO:0006376)|mRNA splicing, via spliceosome (GO:0000398)|regulation of mRNA splicing, via spliceosome (GO:0048024)|regulation of mRNA stability (GO:0043488)|regulation of transcription, DNA-templated (GO:0006355)|regulation of translation (GO:0006417)|RNA splicing (GO:0008380)|termination of RNA polymerase II transcription (GO:0006369)|transcription from RNA polymerase II promoter (GO:0006366)	catalytic step 2 spliceosome (GO:0071013)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|nuclear speck (GO:0016607)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	mRNA binding (GO:0003729)|nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)			breast(1)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(1)|lung(7)|ovary(2)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	24						TACACTCACCAGAGACAACCA	0.527																																					p.S126S		Atlas-SNP	.											.	SRSF1	41	.	0			c.T378C						PASS	.						44.0	53.0	50.0					17																	56083705		2125	4165	6290	SO:0001630	splice_region_variant	6426	exon2			CTCACCAGAGACA		CCDS11600.1, CCDS58580.1	17q22	2013-02-12	2010-06-22	2010-06-22	ENSG00000136450	ENSG00000136450		"""Serine/arginine-rich splicing factors"", ""RNA binding motif (RRM) containing"""	10780	protein-coding gene	gene with protein product	"""splicing factor 2"", ""pre-mRNA-splicing factor SF2, P33 subunit"", ""alternate splicing factor"", ""SR splicing factor 1"""	600812	"""splicing factor, arginine/serine-rich 1"""	SFRS1		8530103, 20516191	Standard	NM_006924		Approved	ASF, SF2, SRp30a, SF2p33, MGC5228	uc002ivi.3	Q07955		ENST00000258962.4:c.379+1T>C	17.37:g.56083705A>G		197.0	0.0	0		174.0	56.0	0.321839	NM_006924	B2R6Z7|D3DTZ3|Q13809	Silent	SNP	ENST00000258962.4	37	CCDS11600.1																																																																																			.	.	none		0.527	SRSF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000443335.1	NM_006924	Silent
COQ9	57017	hgsc.bcm.edu	37	16	57490480	57490480	+	Missense_Mutation	SNP	A	A	C	rs191446011		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr16:57490480A>C	ENST00000262507.6	+	4	512	c.443A>C	c.(442-444)cAt>cCt	p.H148P	COQ9_ENST00000567933.1_Intron|COQ9_ENST00000567072.1_Missense_Mutation_p.H148P	NM_020312.3	NP_064708.1	O75208	COQ9_HUMAN	coenzyme Q9	148					mitochondrial electron transport, NADH to ubiquinone (GO:0006120)|ubiquinone biosynthetic process (GO:0006744)	mitochondrion (GO:0005739)				breast(1)|cervix(1)|endometrium(3)|kidney(1)|large_intestine(3)|lung(6)|prostate(1)	16						CTAATACTGCATTTTGTGACC	0.532													A|||	1	0.000199681	0.0	0.0	5008	,	,		22372	0.0		0.001	False		,,,				2504	0.0				p.H148P		Atlas-SNP	.											.	COQ9	30	.	0			c.A443C						PASS	.	A	PRO/HIS	0,4396		0,0,2198	143.0	123.0	130.0		443	5.6	1.0	16		130	2,8598	2.2+/-6.3	0,2,4298	no	missense	COQ9	NM_020312.3	77	0,2,6496	CC,CA,AA		0.0233,0.0,0.0154	probably-damaging	148/319	57490480	2,12994	2198	4300	6498	SO:0001583	missense	57017	exon4			TACTGCATTTTGT	BC064946	CCDS32459.1	16q13	2013-10-18	2013-10-18	2006-01-13	ENSG00000088682	ENSG00000088682			25302	protein-coding gene	gene with protein product		612837	"""chromosome 16 open reading frame 49"", ""coenzyme Q9 homolog (yeast)"", ""coenzyme Q9 homolog (S. cerevisiae)"""	C16orf49		19375058	Standard	NM_020312		Approved	DKFZP434K046	uc002elq.3	O75208		ENST00000262507.6:c.443A>C	16.37:g.57490480A>C	ENSP00000262507:p.His148Pro	163.0	0.0	0		175.0	24.0	0.137143	NM_020312	A8K3L2|Q7L5V7|Q7Z5T6|Q8NBL4|Q9NTJ2|Q9P056	Missense_Mutation	SNP	ENST00000262507.6	37	CCDS32459.1	1	4.578754578754579E-4	0	0.0	0	0.0	0	0.0	1	0.0013192612137203166	A	23.2	4.387434	0.82902	0.0	2.33E-4	ENSG00000088682	ENST00000262507	.	.	.	5.57	5.57	0.84162	.	0.000000	0.85682	D	0.000000	D	0.84133	0.5405	M	0.88450	2.955	0.80722	D	1	D;D;D;D	0.89917	1.0;1.0;1.0;1.0	D;D;D;D	0.87578	0.998;0.996;0.998;0.998	D	0.86577	0.1851	9	0.54805	T	0.06	-11.6483	14.9239	0.70862	1.0:0.0:0.0:0.0	.	148;148;148;148	B4E0U3;B4DIV2;B4DEE3;O75208	.;.;.;COQ9_HUMAN	P	148	.	ENSP00000262507:H148P	H	+	2	0	COQ9	56047981	1.000000	0.71417	1.000000	0.80357	0.880000	0.50808	8.700000	0.91322	2.117000	0.64856	0.460000	0.39030	CAT	A|1.000;C|0.000	0.000	strong		0.532	COQ9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000432598.3	NM_020312	
URB1	9875	hgsc.bcm.edu	37	21	33688855	33688855	+	Missense_Mutation	SNP	G	G	A			TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr21:33688855G>A	ENST00000382751.3	-	38	6671	c.6556C>T	c.(6556-6558)Cgg>Tgg	p.R2186W		NM_014825.2	NP_055640.2	O60287	NPA1P_HUMAN	URB1 ribosome biogenesis 1 homolog (S. cerevisiae)	2186						nucleolus (GO:0005730)	poly(A) RNA binding (GO:0044822)			NS(1)|autonomic_ganglia(1)|breast(2)|central_nervous_system(1)|endometrium(9)|kidney(3)|skin(1)|stomach(1)	19						CTCCCTGCCCGGCCCTGGGCA	0.627																																					p.R2186W		Atlas-SNP	.											.	URB1	176	.	0			c.C6556T						PASS	.						21.0	25.0	24.0					21																	33688855		692	1590	2282	SO:0001583	missense	9875	exon38			CTGCCCGGCCCTG	AB011111	CCDS46645.1	21q22.11	2006-11-28	2006-11-28	2006-11-28	ENSG00000142207	ENSG00000142207			17344	protein-coding gene	gene with protein product	nucleolar preribosomal-associated protein 1	608865	"""chromosome 21 open reading frame 108"""	C21orf108		9628581	Standard	NM_014825		Approved	KIAA0539, NPA1	uc002ypn.2	O60287	OTTHUMG00000064919	ENST00000382751.3:c.6556C>T	21.37:g.33688855G>A	ENSP00000372199:p.Arg2186Trp	92.0	0.0	0		114.0	71.0	0.622807	NM_014825	D3DSE5|Q96NX1|Q9NYQ1	Missense_Mutation	SNP	ENST00000382751.3	37	CCDS46645.1	.	.	.	.	.	.	.	.	.	.	G	6.936	0.542407	0.13250	.	.	ENSG00000142207	ENST00000382751	T	0.32753	1.44	5.31	1.28	0.21552	.	1.121610	0.06416	N	0.721426	T	0.21186	0.0510	N	0.22421	0.69	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.28996	-1.0026	10	0.49607	T	0.09	-6.2552	6.3726	0.21489	0.1371:0.0:0.4702:0.3927	.	2186	O60287	NPA1P_HUMAN	W	2186	ENSP00000372199:R2186W	ENSP00000372199:R2186W	R	-	1	2	URB1	32610726	0.005000	0.15991	0.001000	0.08648	0.137000	0.21094	0.545000	0.23268	-0.048000	0.13401	-1.319000	0.01295	CGG	.	.	none		0.627	URB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000139400.2		
ABCC3	8714	hgsc.bcm.edu	37	17	48745035	48745035	+	Silent	SNP	A	A	C	rs11568601	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr17:48745035A>C	ENST00000285238.8	+	12	1632	c.1552A>C	c.(1552-1554)Agg>Cgg	p.R518R	ABCC3_ENST00000427699.1_Silent_p.R518R	NM_003786.3	NP_003777.2	O15438	MRP3_HUMAN	ATP-binding cassette, sub-family C (CFTR/MRP), member 3	518	ABC transmembrane type-1 1. {ECO:0000255|PROSITE-ProRule:PRU00441}.				bile acid and bile salt transport (GO:0015721)|bile acid metabolic process (GO:0008206)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)|transport (GO:0006810)	integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|ATPase activity, coupled to transmembrane movement of substances (GO:0042626)|organic anion transmembrane transporter activity (GO:0008514)			breast(1)|central_nervous_system(2)|endometrium(2)|kidney(1)|large_intestine(6)|liver(1)|lung(11)|prostate(3)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(2)	33			BRCA - Breast invasive adenocarcinoma(22;3.05e-09)		Cisplatin(DB00515)|Clotrimazole(DB00257)|Conjugated Estrogens(DB00286)|Cyclosporine(DB00091)|Doxorubicin(DB00997)|Etoposide(DB00773)|Ezetimibe(DB00973)|Fluorouracil(DB00544)|Folic Acid(DB00158)|Gadoxetate(DB08884)|Glutathione(DB00143)|Glyburide(DB01016)|Indomethacin(DB00328)|Lamivudine(DB00709)|Leucovorin(DB00650)|Methotrexate(DB00563)|Metyrapone(DB01011)|Nifedipine(DB01115)|Omeprazole(DB00338)|Phenobarbital(DB01174)|Probenecid(DB01032)|Rifampicin(DB01045)|Sulfinpyrazone(DB01138)|Verapamil(DB00661)|Vincristine(DB00541)	GGAGGGCATCAGGCAGGGTGA	0.622													A|||	26	0.00519169	0.0015	0.0058	5008	,	,		22136	0.0		0.0189	False		,,,				2504	0.001				p.R518R		Atlas-SNP	.											.	ABCC3	138	.	0			c.A1552C						PASS	.	A	,	21,4385	28.1+/-56.4	0,21,2182	72.0	58.0	63.0		1552,1552	1.7	1.0	17	dbSNP_126	63	219,8381	91.1+/-153.3	3,213,4084	no	coding-synonymous,coding-synonymous	ABCC3	NM_001144070.1,NM_003786.3	,	3,234,6266	CC,CA,AA		2.5465,0.4766,1.8453	,	518/573,518/1528	48745035	240,12766	2203	4300	6503	SO:0001819	synonymous_variant	8714	exon12			GGCATCAGGCAGG	Y17151	CCDS32681.1, CCDS45739.1	17q21	2012-03-14			ENSG00000108846	ENSG00000108846		"""ATP binding cassette transporters / subfamily C"""	54	protein-coding gene	gene with protein product	"""canalicular multispecific organic anion transporter 2"""	604323				8894702, 9827529	Standard	NM_003786		Approved	MRP3, cMOAT2, EST90757, MLP2, MOAT-D	uc002isl.3	O15438	OTTHUMG00000162245	ENST00000285238.8:c.1552A>C	17.37:g.48745035A>C		80.0	0.0	0		100.0	45.0	0.45	NM_003786	B2RPA9|D3DTX9|O60265|O60922|O75621|O95078|O95289|O95290|Q86X85|Q9UN52	Silent	SNP	ENST00000285238.8	37	CCDS32681.1																																																																																			A|0.984;C|0.016	0.016	strong		0.622	ABCC3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000368083.2	NM_020038	
CDC23	8697	hgsc.bcm.edu	37	5	137533901	137533901	+	Silent	SNP	C	C	T			TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr5:137533901C>T	ENST00000394886.2	-	9	1029	c.999G>A	c.(997-999)acG>acA	p.T333T		NM_004661.3	NP_004652.2	Q9UJX2	CDC23_HUMAN	cell division cycle 23	333					anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process (GO:0031145)|metaphase/anaphase transition of mitotic cell cycle (GO:0007091)|mitotic cell cycle (GO:0000278)|mitotic metaphase plate congression (GO:0007080)|mitotic nuclear division (GO:0007067)|mitotic spindle assembly checkpoint (GO:0007094)|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 K11-linked ubiquitination (GO:0070979)|regulation of exit from mitosis (GO:0007096)|regulation of mitotic metaphase/anaphase transition (GO:0030071)|regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051439)|ubiquitin-dependent protein catabolic process (GO:0006511)	anaphase-promoting complex (GO:0005680)|cytosol (GO:0005829)|intracellular (GO:0005622)|nucleoplasm (GO:0005654)	ubiquitin-protein transferase activity (GO:0004842)			autonomic_ganglia(1)|endometrium(2)|kidney(2)|large_intestine(9)|lung(6)|prostate(2)|skin(1)	23			KIRC - Kidney renal clear cell carcinoma(527;0.0101)|Kidney(363;0.0109)			TTACACAGCACGTTTCTACAC	0.313																																					p.T333T		Atlas-SNP	.											.	CDC23	46	.	0			c.G999A						PASS	.						77.0	81.0	79.0					5																	137533901		2203	4300	6503	SO:0001819	synonymous_variant	8697	exon9			ACAGCACGTTTCT	AF053977	CCDS4200.2	5q31	2013-01-17	2013-01-17		ENSG00000094880	ENSG00000094880		"""Anaphase promoting complex subunits"", ""Tetratricopeptide (TTC) repeat domain containing"""	1724	protein-coding gene	gene with protein product	"""anaphase promoting complex subunit 8"""	603462	"""CDC23 (cell division cycle 23, yeast, homolog)"", ""cell division cycle 23 homolog (S. cerevisiae)"""			9790767	Standard	NM_004661		Approved	APC8, ANAPC8, CUT23	uc003lcl.3	Q9UJX2	OTTHUMG00000129198	ENST00000394886.2:c.999G>A	5.37:g.137533901C>T		80.0	0.0	0		93.0	48.0	0.516129	NM_004661	A8K6E5|B4E3A2|B7WP05|D3DQB7|O75433|Q53FN2|Q9BS73	Silent	SNP	ENST00000394886.2	37	CCDS4200.2																																																																																			.	.	none		0.313	CDC23-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251275.2		
ZNF91	7644	hgsc.bcm.edu	37	19	23544515	23544515	+	Silent	SNP	A	A	T			TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr19:23544515A>T	ENST00000300619.7	-	4	1471	c.1266T>A	c.(1264-1266)acT>acA	p.T422T	ZNF91_ENST00000596528.1_5'Flank|ZNF91_ENST00000397082.2_Silent_p.T390T|ZNF91_ENST00000599743.1_Intron	NM_003430.2	NP_003421.2	Q05481	ZNF91_HUMAN	zinc finger protein 91	422					transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|sequence-specific DNA binding transcription factor activity (GO:0003700)|zinc ion binding (GO:0008270)						all_lung(12;0.0349)|Lung NSC(12;0.0538)|all_epithelial(12;0.0611)				ACTTATGTATAGTAAGATTTG	0.338																																					p.T422T		Atlas-SNP	.											ZNF91_ENST00000300619,NS,lymphoid_neoplasm,-1,2	ZNF91	349	2	0			c.T1266A						PASS	.						13.0	13.0	13.0					19																	23544515		1849	4026	5875	SO:0001819	synonymous_variant	7644	exon4			ATGTATAGTAAGA	M61871	CCDS42541.1, CCDS74322.1	19p12	2014-02-04	2006-05-12		ENSG00000167232	ENSG00000167232		"""Zinc fingers, C2H2-type"", ""-"""	13166	protein-coding gene	gene with protein product		603971	"""zinc finger protein 91 (HPF7, HTF10)"""			2023909, 2505992	Standard	XR_430154		Approved	HPF7, HTF10	uc002nre.3	Q05481	OTTHUMG00000183268	ENST00000300619.7:c.1266T>A	19.37:g.23544515A>T		115.0	0.0	0		111.0	37.0	0.333333	NM_003430	A8K5E1|B7Z6G6	Silent	SNP	ENST00000300619.7	37	CCDS42541.1																																																																																			.	.	none		0.338	ZNF91-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000465891.1	NM_003430	
MYH6	4624	hgsc.bcm.edu	37	14	23862710	23862710	+	Silent	SNP	C	C	T	rs145274612	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr14:23862710C>T	ENST00000356287.3	-	22	2975	c.2946G>A	c.(2944-2946)gaG>gaA	p.E982E	MYH6_ENST00000405093.3_Silent_p.E982E			P13533	MYH6_HUMAN	myosin, heavy chain 6, cardiac muscle, alpha	982					adult heart development (GO:0007512)|ATP catabolic process (GO:0006200)|atrial cardiac muscle tissue morphogenesis (GO:0055009)|BMP signaling pathway (GO:0030509)|canonical Wnt signaling pathway (GO:0060070)|cardiac muscle fiber development (GO:0048739)|in utero embryonic development (GO:0001701)|muscle contraction (GO:0006936)|muscle filament sliding (GO:0030049)|myofibril assembly (GO:0030239)|regulation of ATPase activity (GO:0043462)|regulation of blood pressure (GO:0008217)|regulation of heart contraction (GO:0008016)|regulation of heart growth (GO:0060420)|regulation of heart rate (GO:0002027)|regulation of the force of heart contraction (GO:0002026)|sarcomere organization (GO:0045214)|striated muscle contraction (GO:0006941)|ventricular cardiac muscle tissue morphogenesis (GO:0055010)|visceral muscle development (GO:0007522)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|focal adhesion (GO:0005925)|muscle myosin complex (GO:0005859)|myofibril (GO:0030016)|myosin complex (GO:0016459)|myosin filament (GO:0032982)|nucleus (GO:0005634)|sarcomere (GO:0030017)|stress fiber (GO:0001725)|Z disc (GO:0030018)	actin-dependent ATPase activity (GO:0030898)|ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microfilament motor activity (GO:0000146)|protein kinase binding (GO:0019901)			breast(4)|cervix(2)|endometrium(8)|kidney(2)|large_intestine(16)|liver(1)|lung(60)|ovary(2)|pancreas(3)|prostate(6)|skin(6)|stomach(3)|upper_aerodigestive_tract(4)|urinary_tract(2)	119	all_cancers(95;2.54e-05)			GBM - Glioblastoma multiforme(265;0.00764)|READ - Rectum adenocarcinoma(4;0.0289)|Colorectal(4;0.0441)		CAGCCATCTCCTCTGTTAGGT	0.537													C|||	21	0.00419329	0.0	0.0101	5008	,	,		22617	0.0		0.0119	False		,,,				2504	0.002				p.E982E		Atlas-SNP	.											.	MYH6	274	.	0			c.G2946A						PASS	.	C		9,4397	15.5+/-35.6	0,9,2194	181.0	177.0	178.0		2946	3.3	1.0	14	dbSNP_134	178	103,8497	56.0+/-117.1	0,103,4197	no	coding-synonymous	MYH6	NM_002471.3		0,112,6391	TT,TC,CC		1.1977,0.2043,0.8611		982/1940	23862710	112,12894	2203	4300	6503	SO:0001819	synonymous_variant	4624	exon23			CATCTCCTCTGTT	D00943	CCDS9600.1	14q11.2-q13	2014-09-17	2008-08-01		ENSG00000197616	ENSG00000197616		"""Myosins / Myosin superfamily : Class II"""	7576	protein-coding gene	gene with protein product	"""cardiomyopathy, hypertrophic 1"""	160710	"""myosin, heavy polypeptide 6, cardiac muscle, alpha (cardiomyopathy, hypertrophic 1)"""			2144212	Standard	NM_002471		Approved		uc001wjv.3	P13533	OTTHUMG00000028753	ENST00000356287.3:c.2946G>A	14.37:g.23862710C>T		306.0	1.0	0.00326797		422.0	277.0	0.656398	NM_002471	A2RTX1|D9YZU2|Q13943|Q14906|Q14907	Silent	SNP	ENST00000356287.3	37	CCDS9600.1																																																																																			C|0.992;T|0.008	0.008	strong		0.537	MYH6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000071796.3		
ADAM7	8756	hgsc.bcm.edu	37	8	24333985	24333985	+	Nonsense_Mutation	SNP	C	C	T			TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr8:24333985C>T	ENST00000175238.6	+	8	756	c.673C>T	c.(673-675)Cga>Tga	p.R225*	RP11-624C23.1_ENST00000519689.1_RNA|RP11-624C23.1_ENST00000523578.1_RNA|ADAM7_ENST00000520720.1_5'UTR|ADAM7_ENST00000380789.1_Nonsense_Mutation_p.R225*	NM_003817.3	NP_003808.2	Q9H2U9	ADAM7_HUMAN	ADAM metallopeptidase domain 7	225	Peptidase M12B. {ECO:0000255|PROSITE- ProRule:PRU00276}.					integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	metalloendopeptidase activity (GO:0004222)|zinc ion binding (GO:0008270)			NS(1)|endometrium(5)|kidney(1)|large_intestine(17)|lung(24)|ovary(1)|skin(15)	64		Prostate(55;0.0181)		Colorectal(74;0.0199)|COAD - Colon adenocarcinoma(73;0.0754)|BRCA - Breast invasive adenocarcinoma(99;0.182)		ACTAAGGAACCGAATTTGGGG	0.328																																					p.R225X		Atlas-SNP	.											ADAM7,NS,carcinoma,-1,4	ADAM7	165	4	0			c.C673T						PASS	.						114.0	106.0	109.0					8																	24333985		2203	4300	6503	SO:0001587	stop_gained	8756	exon8			AGGAACCGAATTT	AF090327	CCDS6045.1	8p21.2	2005-08-18	2005-08-18		ENSG00000069206	ENSG00000069206		"""ADAM metallopeptidase domain containing"""	214	protein-coding gene	gene with protein product		607310	"""a disintegrin and metalloproteinase domain 7"""				Standard	NM_003817		Approved	GP-83, EAPI	uc003xeb.3	Q9H2U9	OTTHUMG00000097859	ENST00000175238.6:c.673C>T	8.37:g.24333985C>T	ENSP00000175238:p.Arg225*	69.0	0.0	0		103.0	37.0	0.359223	NM_003817	A8K8X7|O75959|Q6PEJ6	Nonsense_Mutation	SNP	ENST00000175238.6	37	CCDS6045.1	.	.	.	.	.	.	.	.	.	.	C	37	6.589310	0.97688	.	.	ENSG00000069206	ENST00000175238;ENST00000380789;ENST00000335595	.	.	.	5.38	2.32	0.28847	.	0.000000	0.46145	D	0.000301	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	10.9142	0.47126	0.496:0.504:0.0:0.0	.	.	.	.	X	225;225;40	.	ENSP00000175238:R225X	R	+	1	2	ADAM7	24389875	0.428000	0.25522	0.898000	0.35279	0.991000	0.79684	0.270000	0.18607	0.721000	0.32231	0.591000	0.81541	CGA	.	.	none		0.328	ADAM7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000215150.1	NM_003817	
SACS	26278	hgsc.bcm.edu	37	13	23904298	23904298	+	Missense_Mutation	SNP	T	T	G	rs34382952	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr13:23904298T>G	ENST00000382292.3	-	9	13990	c.13717A>C	c.(13717-13719)Aat>Cat	p.N4573H	SACS_ENST00000402364.1_Missense_Mutation_p.N3823H|SACS_ENST00000382298.3_Missense_Mutation_p.N4573H			Q9NZJ4	SACS_HUMAN	sacsin molecular chaperone	4573					cell death (GO:0008219)|negative regulation of inclusion body assembly (GO:0090084)|protein folding (GO:0006457)	axon (GO:0030424)|cell body fiber (GO:0070852)|cytoplasm (GO:0005737)|dendrite (GO:0030425)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	chaperone binding (GO:0051087)|Hsp70 protein binding (GO:0030544)|proteasome binding (GO:0070628)			NS(1)|biliary_tract(1)|breast(3)|central_nervous_system(2)|endometrium(22)|haematopoietic_and_lymphoid_tissue(1)|kidney(15)|large_intestine(54)|lung(49)|ovary(7)|pancreas(1)|prostate(4)|skin(10)|stomach(2)|upper_aerodigestive_tract(6)|urinary_tract(11)	189		all_cancers(29;1.51e-22)|all_epithelial(30;7.82e-19)|all_lung(29;4.71e-18)|Lung SC(185;0.0225)|Breast(139;0.128)		all cancers(112;0.00197)|Epithelial(112;0.00854)|OV - Ovarian serous cystadenocarcinoma(117;0.0298)|Lung(94;0.189)		TGCATAAAATTTTCAAGTTTT	0.348													T|||	15	0.00299521	0.0008	0.0058	5008	,	,		9531	0.0		0.0099	False		,,,				2504	0.0				p.N4573H		Atlas-SNP	.											.	SACS	871	.	0			c.A13717C						PASS	.	T	HIS/ASN	5,4401	9.9+/-24.2	0,5,2198	66.0	67.0	67.0		13717	5.8	1.0	13	dbSNP_126	67	40,8560	26.3+/-74.7	0,40,4260	yes	missense	SACS	NM_014363.4	68	0,45,6458	GG,GT,TT		0.4651,0.1135,0.346	possibly-damaging	4573/4580	23904298	45,12961	2203	4300	6503	SO:0001583	missense	26278	exon10			TAAAATTTTCAAG	AF193556	CCDS9300.2	13q11	2014-06-13	2014-01-30		ENSG00000151835	ENSG00000151835		"""Heat shock proteins / DNAJ (HSP40)"""	10519	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 138"""	604490	"""spastic ataxia of Charlevoix-Saguenay (sacsin)"""			10610707, 15057823, 21726565	Standard	NM_001278055		Approved	ARSACS, KIAA0730, DKFZp686B15167, DNAJC29, SPAX6, PPP1R138	uc001uon.3	Q9NZJ4	OTTHUMG00000016562	ENST00000382292.3:c.13717A>C	13.37:g.23904298T>G	ENSP00000371729:p.Asn4573His	85.0	0.0	0		124.0	50.0	0.403226	NM_014363	O94835|Q5T9J5|Q5T9J7|Q5T9J8|Q68DF5|Q6MZR4|Q8NBF9	Missense_Mutation	SNP	ENST00000382292.3	37	CCDS9300.2	8	0.003663003663003663	0	0.0	3	0.008287292817679558	0	0.0	5	0.006596306068601583	T	18.35	3.603679	0.66445	0.001135	0.004651	ENSG00000151835	ENST00000382292;ENST00000402364;ENST00000382298	D;D;D	0.86366	-2.11;-2.11;-2.11	5.85	5.85	0.93711	.	0.089079	0.85682	D	0.000000	T	0.79627	0.4478	N	0.03608	-0.345	0.35519	D	0.801247	D	0.56521	0.976	P	0.59595	0.86	D	0.88793	0.3279	10	0.59425	D	0.04	.	16.2271	0.82306	0.0:0.0:0.0:1.0	rs34382952	4573	Q9NZJ4	SACS_HUMAN	H	4573;3823;4573	ENSP00000371729:N4573H;ENSP00000385844:N3823H;ENSP00000371735:N4573H	ENSP00000371729:N4573H	N	-	1	0	SACS	22802298	1.000000	0.71417	1.000000	0.80357	0.913000	0.54294	6.258000	0.72487	2.234000	0.73211	0.460000	0.39030	AAT	T|0.997;G|0.003	0.003	strong		0.348	SACS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044148.3	NM_014363	
TRPM5	29850	hgsc.bcm.edu	37	11	2434799	2434799	+	Missense_Mutation	SNP	C	C	A			TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr11:2434799C>A	ENST00000155858.6	-	13	1918	c.1910G>T	c.(1909-1911)tGg>tTg	p.W637L	TRPM5_ENST00000452833.1_Missense_Mutation_p.W639L|TRPM5_ENST00000533060.1_Missense_Mutation_p.W637L|TRPM5_ENST00000528453.1_Missense_Mutation_p.W637L	NM_014555.3	NP_055370.1			transient receptor potential cation channel, subfamily M, member 5											breast(1)|central_nervous_system(1)|endometrium(4)|liver(1)|lung(8)|ovary(2)|prostate(2)|skin(2)|urinary_tract(2)	23		Medulloblastoma(188;0.0049)|Breast(177;0.00586)|all_epithelial(84;0.0075)|Ovarian(85;0.0256)|all_neural(188;0.0311)		BRCA - Breast invasive adenocarcinoma(625;0.00147)|LUSC - Lung squamous cell carcinoma(625;0.191)		GTCCCCCCACCAGATCCTGGT	0.642																																					p.W637L	NSCLC(1;49 61 17205 18850 43201)	Atlas-SNP	.											.	TRPM5	86	.	0			c.G1910T						PASS	.						54.0	53.0	53.0					11																	2434799		2202	4299	6501	SO:0001583	missense	29850	exon13			CCCCACCAGATCC	AF177473	CCDS31340.1	11p15.5	2011-12-14			ENSG00000070985	ENSG00000070985		"""Voltage-gated ion channels / Transient receptor potential cation channels"""	14323	protein-coding gene	gene with protein product		604600				10607831, 16382100	Standard	NM_014555		Approved	LTRPC5, MTR1	uc001lwm.4	Q9NZQ8	OTTHUMG00000009896	ENST00000155858.6:c.1910G>T	11.37:g.2434799C>A	ENSP00000155858:p.Trp637Leu	388.0	1.0	0.00257732		392.0	126.0	0.321429	NM_014555		Missense_Mutation	SNP	ENST00000155858.6	37	CCDS31340.1	.	.	.	.	.	.	.	.	.	.	C	21.3	4.130183	0.77549	.	.	ENSG00000070985	ENST00000533881;ENST00000155858;ENST00000452833;ENST00000533060;ENST00000528453;ENST00000437542	T;T;T;T;T	0.80738	-1.41;-1.41;-1.41;-1.41;-1.41	3.97	3.97	0.46021	.	0.000000	0.64402	D	0.000001	D	0.90448	0.7009	M	0.87381	2.88	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.91635	0.999;0.999;0.995	D	0.92548	0.6047	10	0.87932	D	0	-15.2033	15.4027	0.74855	0.0:1.0:0.0:0.0	.	637;639;637	E9PRW0;Q9NZQ8-2;Q9NZQ8	.;.;TRPM5_HUMAN	L	631;637;639;637;637;637	ENSP00000434383:W631L;ENSP00000155858:W637L;ENSP00000387965:W639L;ENSP00000434121:W637L;ENSP00000436809:W637L	ENSP00000155858:W637L	W	-	2	0	TRPM5	2391375	1.000000	0.71417	1.000000	0.80357	0.754000	0.42855	7.383000	0.79741	1.940000	0.56252	0.313000	0.20887	TGG	.	.	none		0.642	TRPM5-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000027378.1	NM_014555	
IKZF1	10320	hgsc.bcm.edu	37	7	50459542	50459542	+	Silent	SNP	T	T	C			TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr7:50459542T>C	ENST00000331340.3	+	7	986	c.831T>C	c.(829-831)tcT>tcC	p.S277S	IKZF1_ENST00000343574.5_Silent_p.S190S|IKZF1_ENST00000438033.1_Silent_p.S190S|IKZF1_ENST00000439701.1_Silent_p.S235S|IKZF1_ENST00000346667.4_Intron|IKZF1_ENST00000359197.5_Silent_p.S235S|IKZF1_ENST00000440768.2_3'UTR|IKZF1_ENST00000357364.4_Intron|IKZF1_ENST00000349824.4_Intron	NM_001220769.1|NM_001220772.1|NM_001220773.1|NM_001220775.1|NM_006060.4	NP_001207698.1|NP_001207701.1|NP_001207702.1|NP_001207704.1|NP_006051.1	Q13422	IKZF1_HUMAN	IKAROS family zinc finger 1 (Ikaros)	277					B cell differentiation (GO:0030183)|cell cycle (GO:0007049)|chromatin modification (GO:0016568)|forebrain development (GO:0030900)|lymph node development (GO:0048535)|mesoderm development (GO:0007498)|natural killer cell differentiation (GO:0001779)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|Peyer's patch development (GO:0048541)|positive regulation of multicellular organism growth (GO:0040018)|positive regulation of neutrophil differentiation (GO:0045660)|positive regulation of NK T cell differentiation (GO:0051138)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|retina development in camera-type eye (GO:0060041)|T cell differentiation (GO:0030217)|thymus development (GO:0048538)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|pericentric heterochromatin (GO:0005721)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.?(131)		haematopoietic_and_lymphoid_tissue(275)|lung(1)	276	Glioma(55;0.08)|all_neural(89;0.245)	Acute lymphoblastic leukemia(4;7.29e-10)|all_hematologic(4;4.8e-07)				GTAAGAGCTCTATGCCTCAGA	0.413			"""D,T"""	BCL6	"""ALL, DLBCL"""																																p.S277S		Atlas-SNP	.		"""Rec,Dom"""	yes		7	7p12.2	10320	IKAROS family zinc finger 1		L	.	IKZF1	613	.	131	Unknown(131)	haematopoietic_and_lymphoid_tissue(131)	c.T831C						PASS	.						60.0	59.0	59.0					7																	50459542		1858	4109	5967	SO:0001819	synonymous_variant	10320	exon7			GAGCTCTATGCCT	U40462	CCDS59055.1, CCDS69299.1, CCDS75596.1, CCDS75597.1	7p12.2	2014-06-12	2006-08-25	2006-08-25	ENSG00000185811	ENSG00000185811		"""Zinc fingers, C2H2-type"", ""IKAROS zinc fingers"""	13176	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 92"""	603023	"""zinc finger protein, subfamily 1A, 1 (Ikaros)"""	ZNFN1A1		1439790, 7935426	Standard	NM_006060		Approved	hIk-1, LyF-1, Hs.54452, IKAROS, PPP1R92	uc003tow.4	Q13422	OTTHUMG00000155907	ENST00000331340.3:c.831T>C	7.37:g.50459542T>C		83.0	0.0	0		80.0	4.0	0.05	NM_006060	A4D260|B4E0Z1|D3DVM5|O00598|Q53XL2|Q69BM4|Q8WVA3	Silent	SNP	ENST00000331340.3	37																																																																																				.	.	none		0.413	IKZF1-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000342242.1	NM_006060	
TSHZ1	10194	hgsc.bcm.edu	37	18	72998296	72998296	+	Missense_Mutation	SNP	T	T	C			TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr18:72998296T>C	ENST00000580243.1	+	2	1282	c.934T>C	c.(934-936)Tgt>Cgt	p.C312R	TSHZ1_ENST00000322038.5_Missense_Mutation_p.C267R			Q6ZSZ6	TSH1_HUMAN	teashirt zinc finger homeobox 1	312					anterior/posterior pattern specification (GO:0009952)|middle ear morphogenesis (GO:0042474)|regulation of transcription, DNA-templated (GO:0006355)|soft palate development (GO:0060023)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			NS(1)|breast(2)|central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(11)|liver(1)|lung(14)|ovary(1)|skin(6)|upper_aerodigestive_tract(2)	42		Esophageal squamous(42;0.129)|Prostate(75;0.142)|Melanoma(33;0.211)		Colorectal(1;0.000501)|READ - Rectum adenocarcinoma(2;0.00226)|BRCA - Breast invasive adenocarcinoma(31;0.246)		GTGCATGTACTGTGGACACTC	0.557																																					p.C267R		Atlas-SNP	.											.	TSHZ1	104	.	0			c.T799C						PASS	.						150.0	122.0	131.0					18																	72998296		2203	4300	6503	SO:0001583	missense	10194	exon2			ATGTACTGTGGAC	AF039698	CCDS12009.1	18q22.3	2013-11-20	2007-07-16	2006-03-14	ENSG00000179981	ENSG00000179981		"""Teashirt zinc fingers"", ""Homeoboxes / ZF class"", ""Zinc fingers, C2H2-type"""	10669	protein-coding gene	gene with protein product		614427	"""serologically defined colon cancer antigen 33"", ""teashirt zinc finger 1"", ""teashirt family zinc finger 1"""	SDCCAG33		17586487	Standard	NM_005786		Approved	NY-CO-33, TSH1	uc002lly.4	Q6ZSZ6	OTTHUMG00000132859	ENST00000580243.1:c.934T>C	18.37:g.72998296T>C	ENSP00000464391:p.Cys312Arg	199.0	0.0	0		159.0	50.0	0.314465	NM_005786	O60534|Q4LE29|Q53EU4	Missense_Mutation	SNP	ENST00000580243.1	37		.	.	.	.	.	.	.	.	.	.	T	10.93	1.490440	0.26686	.	.	ENSG00000179981	ENST00000322038	D	0.83755	-1.76	5.38	5.38	0.77491	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);	0.000000	0.85682	D	0.000000	D	0.89942	0.6861	M	0.65498	2.005	0.80722	D	1	D	0.76494	0.999	D	0.91635	0.999	D	0.90801	0.4694	10	0.87932	D	0	-17.6812	15.4172	0.74980	0.0:0.0:0.0:1.0	.	312	Q6ZSZ6	TSH1_HUMAN	R	267	ENSP00000323584:C267R	ENSP00000323584:C267R	C	+	1	0	TSHZ1	71127284	1.000000	0.71417	0.989000	0.46669	0.982000	0.71751	7.694000	0.84235	2.512000	0.84698	0.561000	0.74099	TGT	.	.	none		0.557	TSHZ1-005	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000444913.1	NM_005786	
IMPAD1	54928	hgsc.bcm.edu	37	8	57906042	57906042	+	Missense_Mutation	SNP	G	G	A			TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr8:57906042G>A	ENST00000262644.4	-	1	361	c.103C>T	c.(103-105)Cgc>Tgc	p.R35C		NM_017813.4	NP_060283.3	Q9NX62	IMPA3_HUMAN	inositol monophosphatase domain containing 1	35					chondrocyte development (GO:0002063)|chondroitin sulfate metabolic process (GO:0030204)|embryonic digit morphogenesis (GO:0042733)|endochondral ossification (GO:0001958)|inositol biosynthetic process (GO:0006021)|phosphatidylinositol phosphorylation (GO:0046854)|post-embryonic development (GO:0009791)	Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|membrane (GO:0016020)	3'(2'),5'-bisphosphate nucleotidase activity (GO:0008441)|3'-nucleotidase activity (GO:0008254)|inositol monophosphate 1-phosphatase activity (GO:0008934)|inositol monophosphate 3-phosphatase activity (GO:0052832)|inositol monophosphate 4-phosphatase activity (GO:0052833)|metal ion binding (GO:0046872)			kidney(1)|large_intestine(2)|lung(2)|ovary(1)|skin(1)	7		all_cancers(86;0.175)|all_lung(136;0.0321)|Lung NSC(129;0.0417)|all_epithelial(80;0.0448)				AGGCTGAAGCGGCCGGCCAAG	0.741																																					p.R35C		Atlas-SNP	.											.	IMPAD1	27	.	0			c.C103T						PASS	.						2.0	2.0	2.0					8																	57906042		1082	2103	3185	SO:0001583	missense	54928	exon1			TGAAGCGGCCGGC		CCDS6169.1	8q12.1	2013-05-16			ENSG00000104331	ENSG00000104331			26019	protein-coding gene	gene with protein product		614010				21549340	Standard	NM_017813		Approved	FLJ20421, IMPA3, gPAPP	uc003xte.4	Q9NX62	OTTHUMG00000164415	ENST00000262644.4:c.103C>T	8.37:g.57906042G>A	ENSP00000262644:p.Arg35Cys	11.0	0.0	0		8.0	6.0	0.75	NM_017813	Q6NVY7	Missense_Mutation	SNP	ENST00000262644.4	37	CCDS6169.1	.	.	.	.	.	.	.	.	.	.	G	15.72	2.915816	0.52546	.	.	ENSG00000104331	ENST00000262644	T	0.52983	0.64	5.05	4.17	0.49024	.	0.059812	0.64402	D	0.000007	T	0.36771	0.0979	N	0.24115	0.695	0.80722	D	1	D	0.69078	0.997	P	0.47470	0.548	T	0.24512	-1.0158	10	0.72032	D	0.01	-34.6783	7.4777	0.27387	0.0852:0.0:0.7506:0.1642	.	35	Q9NX62	IMPA3_HUMAN	C	35	ENSP00000262644:R35C	ENSP00000262644:R35C	R	-	1	0	IMPAD1	58068596	1.000000	0.71417	1.000000	0.80357	0.001000	0.01503	2.643000	0.46604	1.123000	0.41961	-0.266000	0.10368	CGC	.	.	none		0.741	IMPAD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000378665.1	NM_017813	
HECTD2	143279	hgsc.bcm.edu	37	10	93221018	93221018	+	Missense_Mutation	SNP	G	G	A	rs61754655	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr10:93221018G>A	ENST00000298068.5	+	4	509	c.415G>A	c.(415-417)Gta>Ata	p.V139I	HECTD2_ENST00000371681.4_Missense_Mutation_p.V139I|HECTD2_ENST00000536715.1_5'Flank|HECTD2_ENST00000446394.1_Missense_Mutation_p.V139I	NM_182765.3	NP_877497	Q5U5R9	HECD2_HUMAN	HECT domain containing E3 ubiquitin protein ligase 2	139					protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:0042787)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)			breast(2)|endometrium(2)|kidney(4)|large_intestine(10)|lung(7)|skin(1)|urinary_tract(1)	27						TAGGGAAGATGTAGAAAAAGT	0.284													G|||	4	0.000798722	0.0	0.0029	5008	,	,		12787	0.0		0.002	False		,,,				2504	0.0				p.V139I	NSCLC(12;376 469 1699 39910 41417)	Atlas-SNP	.											.	HECTD2	60	.	0			c.G415A						PASS	.	G	ILE/VAL,ILE/VAL	4,4400	8.1+/-20.4	0,4,2198	101.0	114.0	109.0		415,415	-0.3	1.0	10	dbSNP_129	109	54,8530	34.3+/-88.2	0,54,4238	yes	missense,missense	HECTD2	NM_173497.2,NM_182765.3	29,29	0,58,6436	AA,AG,GG		0.6291,0.0908,0.4466	benign,benign	139/208,139/777	93221018	58,12930	2202	4292	6494	SO:0001583	missense	143279	exon4			GAAGATGTAGAAA	AK094625	CCDS7414.1, CCDS7415.1, CCDS60591.1	10q23.32	2013-09-20	2012-02-23		ENSG00000165338	ENSG00000165338			26736	protein-coding gene	gene with protein product			"""HECT domain containing 2"""			8619474, 9110174	Standard	NM_001284274		Approved	FLJ37306	uc001khl.2	Q5U5R9	OTTHUMG00000018742	ENST00000298068.5:c.415G>A	10.37:g.93221018G>A	ENSP00000298068:p.Val139Ile	176.0	0.0	0		101.0	76.0	0.752475	NM_173497	Q5VZ97|Q5VZ98|Q5VZ99|Q8N1X7|Q8TCP5	Missense_Mutation	SNP	ENST00000298068.5	37	CCDS7414.1	1	4.578754578754579E-4	0	0.0	0	0.0	0	0.0	1	0.0013192612137203166	G	10.46	1.357431	0.24598	9.08E-4	0.006291	ENSG00000165338	ENST00000446394;ENST00000371681;ENST00000298068	T;T;T	0.46819	1.19;0.86;1.2	5.1	-0.347	0.12617	.	0.414930	0.24467	N	0.038276	T	0.18383	0.0441	L	0.27053	0.805	0.80722	D	1	B;B;B	0.16603	0.0;0.0;0.018	B;B;B	0.10450	0.0;0.0;0.005	T	0.05402	-1.0887	10	0.15499	T	0.54	.	4.2595	0.10733	0.4162:0.0:0.3307:0.2531	rs61754655	139;139;139	E7ERR3;Q5U5R9;Q5VZ98	.;HECD2_HUMAN;.	I	139	ENSP00000401023:V139I;ENSP00000360746:V139I;ENSP00000298068:V139I	ENSP00000298068:V139I	V	+	1	0	HECTD2	93210998	0.670000	0.27512	0.997000	0.53966	0.982000	0.71751	-0.199000	0.09491	-0.086000	0.12550	0.467000	0.42956	GTA	G|0.997;A|0.003	0.003	strong		0.284	HECTD2-005	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000098620.1		
CEP72	55722	hgsc.bcm.edu	37	5	637637	637637	+	Missense_Mutation	SNP	A	A	G	rs62000999	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr5:637637A>G	ENST00000264935.5	+	7	1000	c.910A>G	c.(910-912)Atg>Gtg	p.M304V	CEP72_ENST00000444221.1_3'UTR	NM_018140.3	NP_060610.2	Q9P209	CEP72_HUMAN	centrosomal protein 72kDa	304					G2/M transition of mitotic cell cycle (GO:0000086)|gamma-tubulin complex localization (GO:0033566)|mitotic cell cycle (GO:0000278)|spindle organization (GO:0007051)	centrosome (GO:0005813)|cytosol (GO:0005829)				autonomic_ganglia(1)|central_nervous_system(1)|cervix(1)|endometrium(1)|large_intestine(1)|liver(1)|lung(5)|ovary(2)|prostate(3)|skin(1)|stomach(1)|urinary_tract(2)	20			Epithelial(17;0.000339)|all cancers(22;0.00137)|OV - Ovarian serous cystadenocarcinoma(19;0.00153)|Lung(60;0.0863)			CTCAGACTCCATGGATACCGA	0.527													G|||	22	0.00439297	0.0008	0.0043	5008	,	,		20995	0.0		0.0169	False		,,,				2504	0.001				p.M304V		Atlas-SNP	.											.	CEP72	53	.	0			c.A910G						PASS	.	G	VAL/MET	8,4398	822.5+/-416.5	0,8,2195	64.0	69.0	67.0		910	-9.5	0.0	5	dbSNP_129	67	180,8420	810.6+/-407.1	1,178,4121	yes	missense	CEP72	NM_018140.3	21	1,186,6316	GG,GA,AA		2.093,0.1816,1.4455	benign	304/648	637637	188,12818	2203	4300	6503	SO:0001583	missense	55722	exon7			GACTCCATGGATA	BC000132	CCDS34126.1	5p15.33	2014-02-20			ENSG00000112877	ENSG00000112877			25547	protein-coding gene	gene with protein product						10819331	Standard	NM_018140		Approved	KIAA1519, FLJ10565	uc003jbf.3	Q9P209	OTTHUMG00000161745	ENST00000264935.5:c.910A>G	5.37:g.637637A>G	ENSP00000264935:p.Met304Val	221.0	0.0	0		193.0	91.0	0.471503	NM_018140	B4DR26|Q9BV03|Q9BWM3|Q9NVR4	Missense_Mutation	SNP	ENST00000264935.5	37	CCDS34126.1	13	0.005952380952380952	1	0.0020325203252032522	1	0.0027624309392265192	0	0.0	11	0.014511873350923483	G	0.015	-1.560185	0.00910	0.001816	0.02093	ENSG00000112877	ENST00000264935	T	0.06768	3.26	4.76	-9.52	0.00578	.	2.230810	0.01420	N	0.014329	T	0.01029	0.0034	N	0.00926	-1.1	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.34104	-0.9842	10	0.02654	T	1	0.5272	10.8012	0.46489	0.691:0.1782:0.1307:0.0	rs62000999	304	Q9P209	CEP72_HUMAN	V	304	ENSP00000264935:M304V	ENSP00000264935:M304V	M	+	1	0	CEP72	690637	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-2.554000	0.00926	-2.567000	0.00470	-1.050000	0.02344	ATG	A|0.989;G|0.011	0.011	strong		0.527	CEP72-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000365967.3	NM_018140	
MMP8	4317	hgsc.bcm.edu	37	11	102593273	102593273	+	Silent	SNP	T	T	G	rs12803000	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr11:102593273T>G	ENST00000236826.3	-	2	332	c.234A>C	c.(232-234)ccA>ccC	p.P78P		NM_002424.2	NP_002415.1	P22894	MMP8_HUMAN	matrix metallopeptidase 8 (neutrophil collagenase)	78					collagen catabolic process (GO:0030574)|endodermal cell differentiation (GO:0035987)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|proteolysis (GO:0006508)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|proteinaceous extracellular matrix (GO:0005578)	calcium ion binding (GO:0005509)|metalloendopeptidase activity (GO:0004222)|serine-type endopeptidase activity (GO:0004252)|zinc ion binding (GO:0008270)			autonomic_ganglia(1)|breast(3)|kidney(1)|large_intestine(4)|lung(11)|ovary(4)|skin(6)|stomach(1)|urinary_tract(1)	32	all_cancers(8;0.00092)|all_epithelial(12;0.00389)|Lung NSC(15;0.227)	all_hematologic(158;0.00092)|Acute lymphoblastic leukemia(157;0.000967)	Epithelial(9;0.0555)|Lung(13;0.0828)|LUSC - Lung squamous cell carcinoma(19;0.151)|all cancers(10;0.189)	BRCA - Breast invasive adenocarcinoma(274;0.0141)	Marimastat(DB00786)	TTTCCTCATTTGGCTTCCCCG	0.458													T|||	131	0.0261581	0.0015	0.036	5008	,	,		21789	0.0089		0.0417	False		,,,				2504	0.0542				p.P78P		Atlas-SNP	.											MMP8,face,malignant_melanoma,-2,1	MMP8	68	1	0			c.A234C						PASS	.	T		38,4368	43.1+/-76.7	0,38,2165	179.0	174.0	175.0		234	-5.5	0.0	11	dbSNP_121	175	441,8155	133.6+/-191.1	13,415,3870	no	coding-synonymous	MMP8	NM_002424.2		13,453,6035	GG,GT,TT		5.1303,0.8625,3.684		78/468	102593273	479,12523	2203	4298	6501	SO:0001819	synonymous_variant	4317	exon2			CTCATTTGGCTTC	J05556	CCDS8320.1	11q21-q22	2008-02-05	2005-08-08		ENSG00000118113	ENSG00000118113	3.4.24.34		7175	protein-coding gene	gene with protein product		120355	"""matrix metalloproteinase 8 (neutrophil collagenase)"""	CLG1			Standard	NM_002424		Approved		uc001phe.2	P22894	OTTHUMG00000167587	ENST00000236826.3:c.234A>C	11.37:g.102593273T>G		343.0	0.0	0		579.0	141.0	0.243523	NM_002424	Q45F99	Silent	SNP	ENST00000236826.3	37	CCDS8320.1	50	0.022893772893772892	1	0.0020325203252032522	15	0.04143646408839779	3	0.005244755244755245	31	0.040897097625329816	T	9.744	1.165560	0.21538	0.008625	0.051303	ENSG00000118113	ENST00000438475	.	.	.	5.73	-5.47	0.02600	.	.	.	.	.	T	0.02571	0.0078	.	.	.	0.28932	N	0.891481	.	.	.	.	.	.	T	0.28586	-1.0039	4	.	.	.	.	1.8071	0.03083	0.1913:0.251:0.3608:0.1968	rs12803000;rs12803000	.	.	.	Q	54	.	.	K	-	1	0	MMP8	102098483	0.000000	0.05858	0.021000	0.16686	0.916000	0.54674	-2.650000	0.00858	-0.504000	0.06577	0.533000	0.62120	AAA	T|0.966;G|0.034	0.034	strong		0.458	MMP8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000395223.1	NM_002424	
HOXD10	3236	hgsc.bcm.edu	37	2	176983923	176983923	+	Silent	SNP	G	G	C	rs33913965	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr2:176983923G>C	ENST00000249501.4	+	2	1242	c.987G>C	c.(985-987)cgG>cgC	p.R329R	HOXD-AS2_ENST00000440016.2_RNA|HOXD10_ENST00000490088.2_3'UTR	NM_002148.3	NP_002139.2	P28358	HXD10_HUMAN	homeobox D10	329					adult locomotory behavior (GO:0008344)|anterior/posterior pattern specification (GO:0009952)|embryonic limb morphogenesis (GO:0030326)|embryonic skeletal system morphogenesis (GO:0048704)|forelimb morphogenesis (GO:0035136)|hindlimb morphogenesis (GO:0035137)|neuromuscular process (GO:0050905)|peripheral nervous system neuron development (GO:0048935)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|proximal/distal pattern formation (GO:0009954)|single fertilization (GO:0007338)|skeletal muscle tissue development (GO:0007519)|spinal cord motor neuron cell fate specification (GO:0021520)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	chromatin binding (GO:0003682)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)			endometrium(2)|kidney(1)|large_intestine(2)|lung(8)|ovary(3)|upper_aerodigestive_tract(1)	17			OV - Ovarian serous cystadenocarcinoma(117;0.0207)|Epithelial(96;0.18)	Colorectal(32;0.0226)|READ - Rectum adenocarcinoma(9;0.0556)		GAGAGAACCGGATCCGAGAAC	0.562													G|||	37	0.00738818	0.0015	0.0187	5008	,	,		10062	0.0		0.0209	False		,,,				2504	0.001				p.R329R		Atlas-SNP	.											.	HOXD10	65	.	0			c.G987C						PASS	.	G		18,4388	25.3+/-52.1	0,18,2185	45.0	48.0	47.0		987	3.9	1.0	2	dbSNP_126	47	193,8407	84.8+/-147.2	1,191,4108	no	coding-synonymous	HOXD10	NM_002148.3		1,209,6293	CC,CG,GG		2.2442,0.4085,1.6223		329/341	176983923	211,12795	2203	4300	6503	SO:0001819	synonymous_variant	3236	exon2			GAACCGGATCCGA		CCDS2266.1	2q31.1	2014-09-17	2005-12-22		ENSG00000128710	ENSG00000128710		"""Homeoboxes / ANTP class : HOXL subclass"""	5133	protein-coding gene	gene with protein product		142984	"""homeo box D10"""	HOX4, HOX4D		1973146, 1358459	Standard	NM_002148		Approved		uc002ukj.3	P28358	OTTHUMG00000132511	ENST00000249501.4:c.987G>C	2.37:g.176983923G>C		128.0	0.0	0		159.0	77.0	0.484277	NM_002148	Q6NT10	Silent	SNP	ENST00000249501.4	37	CCDS2266.1																																																																																			G|0.984;C|0.016	0.016	strong		0.562	HOXD10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255692.2		
KIAA1731	85459	hgsc.bcm.edu	37	11	93433289	93433289	+	Silent	SNP	A	A	G	rs374656563		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr11:93433289A>G	ENST00000325212.6	+	15	5373	c.5211A>G	c.(5209-5211)acA>acG	p.T1737T	KIAA1731_ENST00000531700.1_Intron|KIAA1731_ENST00000344196.4_5'UTR|KIAA1731_ENST00000411936.1_Silent_p.T1737T			Q9C0D2	K1731_HUMAN	KIAA1731	1737						centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)				breast(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)	11		Acute lymphoblastic leukemia(157;2.31e-05)|all_hematologic(158;0.00824)				AGAGACAAACAGCATTGCAGC	0.368																																					p.T1737T		Atlas-SNP	.											.	KIAA1731	173	.	0			c.A5211G						PASS	.	A		0,1384		0,0,692	64.0	55.0	58.0		5211	0.1	0.0	11		58	2,3180		0,2,1589	no	coding-synonymous	KIAA1731	NM_033395.1		0,2,2281	GG,GA,AA		0.0629,0.0,0.0438		1737/2602	93433289	2,4564	692	1591	2283	SO:0001819	synonymous_variant	85459	exon15			ACAAACAGCATTG	AB051518	CCDS44708.1	11q21	2014-03-11			ENSG00000166004	ENSG00000166004			29366	protein-coding gene	gene with protein product						20844083	Standard	NM_033395		Approved		uc009ywb.1	Q9C0D2	OTTHUMG00000167449	ENST00000325212.6:c.5211A>G	11.37:g.93433289A>G		137.0	0.0	0		236.0	142.0	0.601695	NM_033395	C9J5H9|C9JQY8|Q8N7L4|Q8N919|Q8N9B0|Q96LT8	Silent	SNP	ENST00000325212.6	37	CCDS44708.1																																																																																			.	.	weak		0.368	KIAA1731-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000394640.1	NM_033395	
NOP9	161424	hgsc.bcm.edu	37	14	24772373	24772373	+	Missense_Mutation	SNP	C	C	T	rs147123517	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr14:24772373C>T	ENST00000267425.3	+	6	1330	c.1237C>T	c.(1237-1239)Cgc>Tgc	p.R413C	NOP9_ENST00000396802.3_Missense_Mutation_p.R413C	NM_174913.1	NP_777573.1	Q86U38	NOP9_HUMAN	NOP9 nucleolar protein	413							poly(A) RNA binding (GO:0044822)										GGGGGCCTGTCGCAGAGTTGG	0.557													C|||	8	0.00159744	0.0	0.0014	5008	,	,		16884	0.0		0.007	False		,,,				2504	0.0				p.R413C		Atlas-SNP	.											.	.	.	.	0			c.C1237T						PASS	.	C	CYS/ARG	4,4402	6.2+/-15.9	0,4,2199	70.0	71.0	71.0		1237	4.2	1.0	14	dbSNP_134	71	45,8555	30.1+/-81.4	0,45,4255	yes	missense	C14orf21	NM_174913.1	180	0,49,6454	TT,TC,CC		0.5233,0.0908,0.3767	probably-damaging	413/637	24772373	49,12957	2203	4300	6503	SO:0001583	missense	161424	exon6			GCCTGTCGCAGAG		CCDS9624.1, CCDS66616.1	14q12	2012-12-10	2012-12-10	2012-06-06	ENSG00000196943	ENSG00000196943			19826	protein-coding gene	gene with protein product			"""chromosome 14 open reading frame 21"", ""NOP9 nucleolar protein homolog (yeast)"""	C14orf21		21653694	Standard	XM_005267385		Approved		uc001wol.1	Q86U38	OTTHUMG00000029342	ENST00000267425.3:c.1237C>T	14.37:g.24772373C>T	ENSP00000267425:p.Arg413Cys	156.0	0.0	0		281.0	94.0	0.33452	NM_174913	A8MY76|Q8IVF0|Q8TBS6	Missense_Mutation	SNP	ENST00000267425.3	37	CCDS9624.1	4	0.0018315018315018315	0	0.0	1	0.0027624309392265192	0	0.0	3	0.00395778364116095	C	18.19	3.567896	0.65651	9.08E-4	0.005233	ENSG00000196943	ENST00000267425;ENST00000396802	T;T	0.32753	1.48;1.44	5.16	4.25	0.50352	.	0.224065	0.38897	N	0.001525	T	0.35189	0.0923	L	0.54323	1.7	0.43536	D	0.995829	D	0.76494	0.999	P	0.59288	0.855	T	0.23013	-1.0200	10	0.52906	T	0.07	-4.9362	11.1833	0.48642	0.4521:0.5479:0.0:0.0	.	413	Q86U38	CN021_HUMAN	C	413	ENSP00000267425:R413C;ENSP00000380020:R413C	ENSP00000267425:R413C	R	+	1	0	C14orf21	23842213	0.869000	0.29996	1.000000	0.80357	0.909000	0.53808	0.630000	0.24553	1.356000	0.45884	0.563000	0.77884	CGC	C|0.996;T|0.004	0.004	strong		0.557	NOP9-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000073186.2		
FAM149A	25854	hgsc.bcm.edu	37	4	187088399	187088399	+	Missense_Mutation	SNP	G	G	T	rs111681837	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr4:187088399G>T	ENST00000356371.5	+	13	2231	c.2231G>T	c.(2230-2232)gGt>gTt	p.G744V	FAM149A_ENST00000227065.4_Missense_Mutation_p.G453V|FAM149A_ENST00000389354.5_Missense_Mutation_p.G453V|FAM149A_ENST00000502970.1_Missense_Mutation_p.G453V|FAM149A_ENST00000514153.1_Missense_Mutation_p.G453V|FAM149A_ENST00000503432.1_Missense_Mutation_p.G453V			A5PLN7	F149A_HUMAN	family with sequence similarity 149, member A	744										breast(2)|endometrium(1)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(8)|lung(8)|pancreas(1)|prostate(1)|skin(2)	25		all_cancers(14;4.27e-52)|all_epithelial(14;7.69e-39)|all_lung(41;1.34e-13)|Lung NSC(41;3.58e-13)|Melanoma(20;1.91e-06)|Colorectal(36;0.0066)|Hepatocellular(41;0.00886)|Renal(120;0.00988)|Prostate(90;0.00996)|all_hematologic(60;0.014)|all_neural(102;0.243)		OV - Ovarian serous cystadenocarcinoma(60;1.19e-10)|BRCA - Breast invasive adenocarcinoma(30;1.22e-05)|GBM - Glioblastoma multiforme(59;0.000122)|STAD - Stomach adenocarcinoma(60;0.000288)|LUSC - Lung squamous cell carcinoma(40;0.00241)|READ - Rectum adenocarcinoma(43;0.166)		ACATGGACAGGTCAAAGTATT	0.373													G|||	8	0.00159744	0.0008	0.0014	5008	,	,		20278	0.0		0.006	False		,,,				2504	0.0				p.G453V		Atlas-SNP	.											.	FAM149A	52	.	0			c.G1358T						PASS	.	G	VAL/GLY,VAL/GLY	7,4399	12.9+/-30.5	0,7,2196	126.0	128.0	128.0		1358,1358	4.8	1.0	4	dbSNP_132	128	58,8542	35.9+/-90.5	0,58,4242	yes	missense,missense	FAM149A	NM_001006655.2,NM_015398.2	109,109	0,65,6438	TT,TG,GG		0.6744,0.1589,0.4998	probably-damaging,probably-damaging	453/483,453/483	187088399	65,12941	2203	4300	6503	SO:0001583	missense	25854	exon12			GGACAGGTCAAAG	AK057166	CCDS34117.1	4q35.1	2012-04-19			ENSG00000109794	ENSG00000109794			24527	protein-coding gene	gene with protein product							Standard	NM_015398		Approved	DKFZP564J102, MST119, MSTP119	uc010isl.3	A5PLN7	OTTHUMG00000160565	ENST00000356371.5:c.2231G>T	4.37:g.187088399G>T	ENSP00000348732:p.Gly744Val	276.0	0.0	0		165.0	48.0	0.290909	NM_001006655	B5MDB8|Q2TAN6|Q7Z2S5|Q9Y4T9	Missense_Mutation	SNP	ENST00000356371.5	37		6|6|6	0.0027472527472527475|0.0027472527472527475|0.0027472527472527475	0|0|0	0.0|0.0|0.0	1|1|1	0.0027624309392265192|0.0027624309392265192|0.0027624309392265192	0|0|0	0.0|0.0|0.0	5|5|5	0.006596306068601583|0.006596306068601583|0.006596306068601583	G|G|G	20.2|20.2|20.2	3.945034|3.945034|3.945034	0.73672|0.73672|0.73672	0.001589|0.001589|0.001589	0.006744|0.006744|0.006744	ENSG00000109794|ENSG00000109794|ENSG00000109794	ENST00000503432;ENST00000356371;ENST00000227065;ENST00000502970;ENST00000514153;ENST00000389354|ENST00000512271|ENST00000510843;ENST00000502894	T;T;T;T;T;T|.|.	0.15372|.|.	2.56;2.43;2.56;2.56;2.56;2.56|.|.	5.62|5.62|5.62	4.77|4.77|4.77	0.60923|0.60923|0.60923	.|.|.	0.309873|.|.	0.32518|.|.	N|.|.	0.005996|.|.	T|T|T	0.64360|0.64360|0.64360	0.2591|0.2591|0.2591	M|M|M	0.65975|0.65975|0.65975	2.015|2.015|2.015	0.52501|0.52501|0.52501	D|D|D	0.999951|0.999951|0.999951	D;D|.|.	0.76494|.|.	0.999;0.999|.|.	D;D|.|.	0.74023|.|.	0.982;0.961|.|.	T|T|T	0.67356|0.67356|0.67356	-0.5691|-0.5691|-0.5691	10|5|5	0.87932|.|.	D|.|.	0|.|.	-13.1821|-13.1821|-13.1821	13.7969|13.7969|13.7969	0.63177|0.63177|0.63177	0.0766:0.0:0.9234:0.0|0.0766:0.0:0.9234:0.0|0.0766:0.0:0.9234:0.0	.|.|.	743;744|.|.	A5PLN7-3;A5PLN7|.|.	.;F149A_HUMAN|.|.	V|S|F	453;744;453;453;453;453|129|131;14	ENSP00000426835:G453V;ENSP00000348732:G744V;ENSP00000227065:G453V;ENSP00000427155:G453V;ENSP00000424380:G453V;ENSP00000374005:G453V|.|.	ENSP00000227065:G453V|.|.	G|R|V	+|+|+	2|3|1	0|2|0	FAM149A|FAM149A|FAM149A	187325393|187325393|187325393	1.000000|1.000000|1.000000	0.71417|0.71417|0.71417	1.000000|1.000000|1.000000	0.80357|0.80357|0.80357	0.965000|0.965000|0.965000	0.64279|0.64279|0.64279	4.047000|4.047000|4.047000	0.57383|0.57383|0.57383	2.652000|2.652000|2.652000	0.90054|0.90054|0.90054	0.591000|0.591000|0.591000	0.81541|0.81541|0.81541	GGT|AGG|GTC	G|0.995;T|0.005	0.005	strong		0.373	FAM149A-201	KNOWN	basic	protein_coding	protein_coding		NM_001006655	
TSHZ3	57616	hgsc.bcm.edu	37	19	31769293	31769293	+	Missense_Mutation	SNP	T	T	C	rs143453460	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr19:31769293T>C	ENST00000240587.4	-	2	1733	c.1406A>G	c.(1405-1407)gAg>gGg	p.E469G		NM_020856.2	NP_065907.2	Q63HK5	TSH3_HUMAN	teashirt zinc finger homeobox 3	469			E -> G (in dbSNP:rs143453460). {ECO:0000269|PubMed:17974005, ECO:0000269|PubMed:19745106}.		in utero embryonic development (GO:0001701)|kidney morphogenesis (GO:0060993)|kidney smooth muscle cell differentiation (GO:0072195)|lung development (GO:0030324)|metanephros development (GO:0001656)|musculoskeletal movement (GO:0050881)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of smooth muscle cell differentiation (GO:0051152)|regulation of respiratory gaseous exchange by neurological system process (GO:0002087)|sensory perception of touch (GO:0050975)|transcription, DNA-templated (GO:0006351)|ureter smooth muscle cell differentiation (GO:0072193)|ureteric bud development (GO:0001657)|ureteric peristalsis (GO:0072105)	growth cone (GO:0030426)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)|metal ion binding (GO:0046872)			breast(4)|endometrium(15)|kidney(9)|large_intestine(20)|lung(60)|ovary(4)|pancreas(2)|prostate(4)|skin(5)	123	Esophageal squamous(110;0.226)					CTTCTTGACCTCCACATTCAG	0.542													T|||	18	0.00359425	0.0	0.0086	5008	,	,		18888	0.0		0.0099	False		,,,				2504	0.002				p.E469G		Atlas-SNP	.											TSHZ3_ENST00000240587,NS,carcinoma,+1,2	TSHZ3	549	2	0			c.A1406G						PASS	.	T	GLY/GLU	8,4398	12.9+/-30.5	0,8,2195	152.0	154.0	153.0		1406	5.6	1.0	19	dbSNP_134	153	102,8498	54.8+/-115.7	0,102,4198	yes	missense	TSHZ3	NM_020856.2	98	0,110,6393	CC,CT,TT		1.186,0.1816,0.8458	probably-damaging	469/1082	31769293	110,12896	2203	4300	6503	SO:0001583	missense	57616	exon2			TTGACCTCCACAT	AL136805	CCDS12421.2	19q13.11	2013-11-20	2007-07-16	2006-03-14	ENSG00000121297	ENSG00000121297		"""Teashirt zinc fingers"", ""Homeoboxes / ZF class"", ""Zinc fingers, C2H2-type"""	30700	protein-coding gene	gene with protein product	"""teashirt 3"""	614119	"""zinc finger protein 537"", ""teashirt family zinc finger 3"""	ZNF537			Standard	NM_020856		Approved	KIAA1474, TSH3	uc002nsy.4	Q63HK5	OTTHUMG00000150184	ENST00000240587.4:c.1406A>G	19.37:g.31769293T>C	ENSP00000240587:p.Glu469Gly	209.0	1.0	0.00478469		199.0	108.0	0.542714	NM_020856	Q9H0G6|Q9P254	Missense_Mutation	SNP	ENST00000240587.4	37	CCDS12421.2	11	0.005036630036630037	0	0.0	5	0.013812154696132596	0	0.0	6	0.0079155672823219	T	18.15	3.560653	0.65538	0.001816	0.01186	ENSG00000121297	ENST00000240587	T	0.38077	1.16	5.55	5.55	0.83447	.	0.052145	0.85682	D	0.000000	T	0.49898	0.1584	M	0.67397	2.05	0.80722	D	1	D	0.71674	0.998	D	0.72982	0.979	T	0.54957	-0.8215	10	0.44086	T	0.13	-30.6092	15.7178	0.77681	0.0:0.0:0.0:1.0	.	469	Q63HK5	TSH3_HUMAN	G	469	ENSP00000240587:E469G	ENSP00000240587:E469G	E	-	2	0	TSHZ3	36461133	1.000000	0.71417	1.000000	0.80357	0.865000	0.49528	5.849000	0.69465	2.099000	0.63709	0.533000	0.62120	GAG	T|0.991;C|0.009	0.009	strong		0.542	TSHZ3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000316743.2	NM_020856	
TCP1	6950	hgsc.bcm.edu	37	6	160201577	160201577	+	Missense_Mutation	SNP	G	G	C	rs148556538	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr6:160201577G>C	ENST00000321394.7	-	9	1275	c.995C>G	c.(994-996)gCc>gGc	p.A332G	SNORA20_ENST00000384662.1_RNA|TCP1_ENST00000420894.2_Missense_Mutation_p.A332G|TCP1_ENST00000392168.2_Missense_Mutation_p.A177G|TCP1_ENST00000544255.1_Missense_Mutation_p.A108G	NM_030752.2	NP_110379.2	P17987	TCPA_HUMAN	t-complex 1	332					'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)|tubulin complex assembly (GO:0007021)	acrosomal vesicle (GO:0001669)|cell body (GO:0044297)|centrosome (GO:0005813)|chaperonin-containing T-complex (GO:0005832)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|microtubule (GO:0005874)|nuclear heterochromatin (GO:0005720)|pericentriolar material (GO:0000242)|zona pellucida receptor complex (GO:0002199)	ATP binding (GO:0005524)|poly(A) RNA binding (GO:0044822)|unfolded protein binding (GO:0051082)			breast(1)|endometrium(4)|large_intestine(3)|lung(2)	10		Breast(66;1.53e-05)|Ovarian(120;0.024)		OV - Ovarian serous cystadenocarcinoma(65;4.05e-20)|BRCA - Breast invasive adenocarcinoma(81;1.1e-06)		TTCCAAATTGGCCAGGGTTGA	0.388													G|||	9	0.00179712	0.0068	0.0	5008	,	,		19426	0.0		0.0	False		,,,				2504	0.0				p.A332G		Atlas-SNP	.											.	TCP1	37	.	0			c.C995G						PASS	.	G	GLY/ALA,GLY/ALA	13,4393	17.9+/-39.9	0,13,2190	101.0	102.0	102.0		530,995	5.8	1.0	6	dbSNP_134	102	1,8599	1.2+/-3.3	0,1,4299	yes	missense,missense	TCP1	NM_001008897.1,NM_030752.2	60,60	0,14,6489	CC,CG,GG		0.0116,0.2951,0.1076	possibly-damaging,possibly-damaging	177/402,332/557	160201577	14,12992	2203	4300	6503	SO:0001583	missense	6950	exon9			AAATTGGCCAGGG	X52882	CCDS5269.1, CCDS43522.1	6q25-q27	2012-10-02			ENSG00000120438	ENSG00000120438		"""Heat Shock Proteins / Chaperonins"""	11655	protein-coding gene	gene with protein product		186980				3476253, 3653076	Standard	NM_030752		Approved	D6S230E, CCT1, Ccta	uc003qsr.3	P17987	OTTHUMG00000015937	ENST00000321394.7:c.995C>G	6.37:g.160201577G>C	ENSP00000317334:p.Ala332Gly	209.0	1.0	0.00478469		196.0	101.0	0.515306	NM_030752	E1P5B2|Q15556|Q5TCM3	Missense_Mutation	SNP	ENST00000321394.7	37	CCDS5269.1	.	.	.	.	.	.	.	.	.	.	G	22.1	4.242607	0.79912	0.002951	1.16E-4	ENSG00000120438	ENST00000321394;ENST00000544255;ENST00000420894;ENST00000392168;ENST00000539756	T;T;T;T;T	0.77489	-1.1;-1.1;-1.1;-1.1;-1.1	5.76	5.76	0.90799	.	0.140834	0.64402	D	0.000003	T	0.81683	0.4874	M	0.84683	2.71	0.58432	D	0.999999	P;P	0.43024	0.798;0.53	P;P	0.45538	0.484;0.456	D	0.83565	0.0109	10	0.56958	D	0.05	-13.3037	20.3242	0.98691	0.0:0.0:1.0:0.0	.	332;332	E7ERF2;P17987	.;TCPA_HUMAN	G	332;108;332;177;130	ENSP00000317334:A332G;ENSP00000439447:A108G;ENSP00000390159:A332G;ENSP00000376008:A177G;ENSP00000441345:A130G	ENSP00000317334:A332G	A	-	2	0	TCP1	160121567	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	7.269000	0.78482	2.882000	0.98803	0.655000	0.94253	GCC	G|0.999;C|0.001	0.001	strong		0.388	TCP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042917.2	NM_030752	
CCBL1	883	hgsc.bcm.edu	37	9	131600394	131600394	+	Missense_Mutation	SNP	A	A	G	rs371451324		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr9:131600394A>G	ENST00000302586.3	-	5	536	c.374T>C	c.(373-375)tTt>tCt	p.F125S	CCBL1_ENST00000436267.2_Missense_Mutation_p.F219S|CCBL1_ENST00000483599.1_5'UTR|CCBL1_ENST00000320665.6_Missense_Mutation_p.F75S	NM_001122671.1|NM_004059.4	NP_001116143.1|NP_004050.3	Q16773	KAT1_HUMAN	cysteine conjugate-beta lyase, cytoplasmic	125					cellular amino acid biosynthetic process (GO:0008652)|cellular modified amino acid metabolic process (GO:0006575)|cellular nitrogen compound metabolic process (GO:0034641)|kynurenine metabolic process (GO:0070189)|L-kynurenine catabolic process (GO:0097053)|L-phenylalanine catabolic process (GO:0006559)|small molecule metabolic process (GO:0044281)|tryptophan catabolic process (GO:0006569)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleus (GO:0005634)	cysteine-S-conjugate beta-lyase activity (GO:0047804)|glutamine-phenylpyruvate transaminase activity (GO:0047316)|kynurenine-oxoglutarate transaminase activity (GO:0016212)|L-glutamine:pyruvate aminotransferase activity (GO:0047945)|L-phenylalanine-oxaloacetate transaminase activity (GO:0036141)|L-phenylalanine:pyruvate aminotransferase activity (GO:0047312)|protein homodimerization activity (GO:0042803)|pyridoxal phosphate binding (GO:0030170)|transaminase activity (GO:0008483)			endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(3)|lung(10)|ovary(1)|prostate(1)|skin(1)	18					L-Glutamine(DB00130)	GTAGCAGTCAAAAAAGGGTTC	0.542																																					p.F125S		Atlas-SNP	.											.	CCBL1	36	.	0			c.T374C						PASS	.	A	SER/PHE,SER/PHE,SER/PHE	0,4402		0,0,2201	165.0	174.0	171.0		374,224,374	5.1	1.0	9		171	1,8585	1.2+/-3.3	0,1,4292	no	missense,missense,missense	CCBL1	NM_001122671.1,NM_001122672.1,NM_004059.4	155,155,155	0,1,6493	GG,GA,AA		0.0116,0.0,0.0077	probably-damaging,probably-damaging,probably-damaging	125/423,75/373,125/423	131600394	1,12987	2201	4293	6494	SO:0001583	missense	883	exon5			CAGTCAAAAAAGG	Y17448	CCDS43884.1, CCDS48038.1, CCDS75915.1	9q34.11	2008-03-11	2008-03-11		ENSG00000171097	ENSG00000171097	2.6.1.64		1564	protein-coding gene	gene with protein product	"""glutamine transaminase K"", ""kyneurenine aminotransferase"""	600547	"""cysteine conjugate-beta lyase; cytoplasmic (glutamine transaminase K, kyneurenine aminotransferase)"""			7883047	Standard	NM_001122671		Approved	KATI, GTK	uc004bwh.3	Q16773	OTTHUMG00000020767	ENST00000302586.3:c.374T>C	9.37:g.131600394A>G	ENSP00000302227:p.Phe125Ser	234.0	1.0	0.0042735		197.0	99.0	0.502538	NM_001122671	Q5T275|Q8N191	Missense_Mutation	SNP	ENST00000302586.3	37	CCDS43884.1	.	.	.	.	.	.	.	.	.	.	A	26.0	4.698125	0.88830	0.0	1.16E-4	ENSG00000171097	ENST00000302586;ENST00000320665;ENST00000436267;ENST00000451800;ENST00000416084	D;D;D;D;D	0.91351	-2.83;-2.83;-2.83;-2.83;-2.83	5.12	5.12	0.69794	Aminotransferase, class I/classII (1);Pyridoxal phosphate-dependent transferase, major region, subdomain 1 (1);Pyridoxal phosphate-dependent transferase, major domain (1);	0.000000	0.85682	D	0.000000	D	0.96731	0.8933	H	0.95950	3.745	0.80722	D	1	D;D;D;D;D	0.89917	1.0;1.0;1.0;1.0;1.0	D;D;D;D;D	0.97110	1.0;1.0;0.999;1.0;1.0	D	0.97818	1.0255	10	0.87932	D	0	-33.2894	13.7717	0.63029	1.0:0.0:0.0:0.0	.	219;125;75;125;125	B7Z4W5;A8K563;Q16773-2;Q16773;Q5T278	.;.;.;KAT1_HUMAN;.	S	125;75;219;125;125	ENSP00000302227:F125S;ENSP00000317342:F75S;ENSP00000399415:F219S;ENSP00000390377:F125S;ENSP00000412402:F125S	ENSP00000302227:F125S	F	-	2	0	CCBL1	130640215	1.000000	0.71417	0.977000	0.42913	0.944000	0.59088	6.220000	0.72237	1.927000	0.55829	0.528000	0.53228	TTT	.	.	weak		0.542	CCBL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054521.2		
LILRA4	23547	hgsc.bcm.edu	37	19	54848826	54848826	+	Missense_Mutation	SNP	C	C	T	rs145556773	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr19:54848826C>T	ENST00000291759.4	-	5	853	c.797G>A	c.(796-798)cGc>cAc	p.R266H	AC008984.2_ENST00000507363.1_RNA	NM_012276.3	NP_036408.3	P59901	LIRA4_HUMAN	leukocyte immunoglobulin-like receptor, subfamily A (with TM domain), member 4	266	Ig-like C2-type 3.				immune system process (GO:0002376)	integral component of membrane (GO:0016021)				NS(2)|breast(1)|central_nervous_system(2)|endometrium(2)|large_intestine(5)|lung(13)|prostate(3)|skin(1)|upper_aerodigestive_tract(3)	32	Ovarian(34;0.19)			GBM - Glioblastoma multiforme(193;0.0565)		CCGGCCAGGGCGCTGGGGGAG	0.657													C|||	7	0.00139776	0.0	0.0029	5008	,	,		12832	0.0		0.005	False		,,,				2504	0.0				p.R266H		Atlas-SNP	.											.	LILRA4	91	.	0			c.G797A						PASS	.	C	HIS/ARG	1,4403		0,1,2201	22.0	24.0	23.0		797	-5.0	0.0	19	dbSNP_134	23	56,8542		0,56,4243	yes	missense	LILRA4	NM_012276.3	29	0,57,6444	TT,TC,CC		0.6513,0.0227,0.4384	benign	266/500	54848826	57,12945	2202	4299	6501	SO:0001583	missense	23547	exon5			CCAGGGCGCTGGG	AF041261	CCDS12890.1	19q13.4	2013-01-11			ENSG00000239961	ENSG00000239961		"""Leukocyte immunoglobulin-like receptors"", ""CD molecules"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	15503	protein-coding gene	gene with protein product		607517				10941842	Standard	NM_012276		Approved	ILT7, CD85g	uc002qfj.3	P59901	OTTHUMG00000065355	ENST00000291759.4:c.797G>A	19.37:g.54848826C>T	ENSP00000291759:p.Arg266His	205.0	0.0	0		175.0	95.0	0.542857	NM_012276	Q32MC4	Missense_Mutation	SNP	ENST00000291759.4	37	CCDS12890.1	4	0.0018315018315018315	0	0.0	2	0.0055248618784530384	0	0.0	2	0.002638522427440633	.	0.012	-1.661083	0.00772	2.27E-4	0.006513	ENSG00000239961	ENST00000291759	T	0.12879	2.64	2.51	-5.02	0.02982	Immunoglobulin subtype (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	2.356960	0.01819	N	0.033919	T	0.07593	0.0191	L	0.46157	1.445	0.09310	N	1	B	0.12630	0.006	B	0.18561	0.022	T	0.26326	-1.0106	10	0.18710	T	0.47	.	3.0012	0.06015	0.1276:0.1549:0.1272:0.5903	.	266	P59901	LIRA4_HUMAN	H	266	ENSP00000291759:R266H	ENSP00000291759:R266H	R	-	2	0	LILRA4	59540638	0.000000	0.05858	0.000000	0.03702	0.041000	0.13682	-2.350000	0.01092	-2.651000	0.00424	-0.391000	0.06502	CGC	C|0.997;T|0.003	0.003	strong		0.657	LILRA4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000140229.2	NM_012276	
C15orf52	388115	hgsc.bcm.edu	37	15	40629995	40629995	+	Missense_Mutation	SNP	G	G	A	rs149438052	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr15:40629995G>A	ENST00000559313.1	-	6	760	c.745C>T	c.(745-747)Cgc>Tgc	p.R249C	C15orf52_ENST00000557973.1_5'Flank|C15orf52_ENST00000397536.2_Missense_Mutation_p.R39C	NM_207380.2	NP_997263.2	Q6ZUT6	CO052_HUMAN	chromosome 15 open reading frame 52	249							poly(A) RNA binding (GO:0044822)			central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(4)|lung(9)|urinary_tract(1)	19		all_cancers(109;9.35e-19)|all_epithelial(112;1.18e-15)|Lung NSC(122;2.45e-11)|all_lung(180;6.47e-10)|Melanoma(134;0.0574)|Ovarian(310;0.0822)|Colorectal(260;0.117)		GBM - Glioblastoma multiforme(113;9.06e-06)|Colorectal(105;0.0107)|BRCA - Breast invasive adenocarcinoma(123;0.0505)|READ - Rectum adenocarcinoma(2;0.0649)|Lung(196;0.0781)|LUAD - Lung adenocarcinoma(183;0.0841)		CGGGCGAGGCGGGCTAGGTCG	0.711																																					p.R249C		Atlas-SNP	.											.	C15orf52	47	.	0			c.C745T						PASS	.						23.0	24.0	24.0					15																	40629995		2202	4298	6500	SO:0001583	missense	388115	exon6			CGAGGCGGGCTAG	AK124643	CCDS10055.2	15q15.1	2007-06-14			ENSG00000188549	ENSG00000188549			33488	protein-coding gene	gene with protein product							Standard	NM_207380		Approved	FLJ43339	uc001zlh.4	Q6ZUT6	OTTHUMG00000129981	ENST00000559313.1:c.745C>T	15.37:g.40629995G>A	ENSP00000453969:p.Arg249Cys	93.0	0.0	0		48.0	18.0	0.375	NM_207380	B9EIQ8|Q68DG9|Q6ZTM3|Q6ZU22	Missense_Mutation	SNP	ENST00000559313.1	37	CCDS10055.2	.	.	.	.	.	.	.	.	.	.	G	26.7	4.764787	0.90020	.	.	ENSG00000188549	ENST00000382688;ENST00000397536;ENST00000397535	T	0.72942	-0.7	4.63	4.63	0.57726	.	0.092822	0.45867	D	0.000338	D	0.82637	0.5080	M	0.74258	2.255	0.58432	D	0.999992	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.91635	0.999;0.998;0.999	D	0.84930	0.0859	10	0.87932	D	0	-13.7074	12.996	0.58646	0.0:0.0:1.0:0.0	.	39;181;249	Q6ZUT6-2;Q6ZUT6-3;Q6ZUT6	.;.;CO052_HUMAN	C	249;39;181	ENSP00000380670:R39C	ENSP00000372135:R249C	R	-	1	0	C15orf52	38417287	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	1.805000	0.38883	2.097000	0.63578	0.563000	0.77884	CGC	A|0.001;G|0.999	0.001	strong		0.711	C15orf52-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000319567.2	NM_207380	
TRAP1	10131	hgsc.bcm.edu	37	16	3724365	3724365	+	Missense_Mutation	SNP	C	C	T	rs145715008		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr16:3724365C>T	ENST00000246957.5	-	9	1107	c.1019G>A	c.(1018-1020)cGc>cAc	p.R340H	TRAP1_ENST00000573872.1_5'UTR|TRAP1_ENST00000575671.1_Missense_Mutation_p.R131H|TRAP1_ENST00000538171.1_Missense_Mutation_p.R287H	NM_016292.2	NP_057376.2	Q12931	TRAP1_HUMAN	TNF receptor-associated protein 1	340					chaperone-mediated protein folding (GO:0061077)|negative regulation of cellular respiration (GO:1901856)|negative regulation of oxidative stress-induced intrinsic apoptotic signaling pathway (GO:1902176)|regulation of reactive oxygen species metabolic process (GO:2000377)|response to stress (GO:0006950)	extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|mitochondrial inner membrane (GO:0005743)|mitochondrial intermembrane space (GO:0005758)|mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	ATP binding (GO:0005524)|poly(A) RNA binding (GO:0044822)|protein kinase binding (GO:0019901)|tumor necrosis factor receptor binding (GO:0005164)			central_nervous_system(2)|endometrium(3)|kidney(2)|large_intestine(3)|lung(7)|skin(1)|upper_aerodigestive_tract(1)	19		Ovarian(90;0.0261)				GAAGATGCTGCGGATGTTGAG	0.602													C|||	1	0.000199681	0.0	0.0	5008	,	,		20813	0.001		0.0	False		,,,				2504	0.0				p.R340H		Atlas-SNP	.											TRAP1,colon,carcinoma,-1,1	TRAP1	53	1	0			c.G1019A						PASS	.	C	HIS/ARG	2,4392	4.2+/-10.8	0,2,2195	160.0	102.0	122.0		1019	5.8	1.0	16	dbSNP_134	122	9,8591	7.1+/-27.0	0,9,4291	yes	missense	TRAP1	NM_016292.2	29	0,11,6486	TT,TC,CC		0.1047,0.0455,0.0847	possibly-damaging	340/705	3724365	11,12983	2197	4300	6497	SO:0001583	missense	10131	exon9			ATGCTGCGGATGT	AF154108	CCDS10508.1, CCDS61824.1	16p13.3	2011-09-02			ENSG00000126602	ENSG00000126602		"""Heat shock proteins / HSPC"""	16264	protein-coding gene	gene with protein product		606219				10652318, 7876093	Standard	NM_016292		Approved	HSP75, HSP90L	uc002cvt.4	Q12931	OTTHUMG00000129427	ENST00000246957.5:c.1019G>A	16.37:g.3724365C>T	ENSP00000246957:p.Arg340His	138.0	0.0	0		163.0	90.0	0.552147	NM_016292	B4DR68|D3DUC8|F5H897|O43642|O75235|Q9UHL5	Missense_Mutation	SNP	ENST00000246957.5	37	CCDS10508.1	1	4.578754578754579E-4	0	0.0	0	0.0	1	0.0017482517482517483	0	0.0	C	21.3	4.131985	0.77662	4.55E-4	0.001047	ENSG00000126602	ENST00000246957;ENST00000538171	T;T	0.12569	2.67;2.67	5.82	5.82	0.92795	Ribosomal protein S5 domain 2-type fold (1);	0.000000	0.85682	D	0.000000	T	0.18759	0.0450	L	0.49256	1.55	0.80722	D	1	P;P	0.36944	0.518;0.574	B;B	0.36922	0.152;0.236	T	0.00768	-1.1574	10	0.87932	D	0	-32.3858	19.0936	0.93240	0.0:1.0:0.0:0.0	.	287;340	F5H897;Q12931	.;TRAP1_HUMAN	H	340;287	ENSP00000246957:R340H;ENSP00000442070:R287H	ENSP00000246957:R340H	R	-	2	0	TRAP1	3664366	1.000000	0.71417	1.000000	0.80357	0.202000	0.24057	7.424000	0.80242	2.757000	0.94681	0.655000	0.94253	CGC	C|0.999;T|0.001	0.001	strong		0.602	TRAP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251586.2	NM_016292	
USP43	124739	hgsc.bcm.edu	37	17	9580092	9580092	+	Missense_Mutation	SNP	C	C	G			TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr17:9580092C>G	ENST00000285199.7	+	5	959	c.863C>G	c.(862-864)tCt>tGt	p.S288C	USP43_ENST00000570827.2_3'UTR|USP43_ENST00000570475.1_Missense_Mutation_p.S288C	NM_001267576.1|NM_153210.4	NP_001254505.1|NP_694942.3	Q70EL4	UBP43_HUMAN	ubiquitin specific peptidase 43	288	USP.				ubiquitin-dependent protein catabolic process (GO:0006511)		cysteine-type peptidase activity (GO:0008234)|ubiquitinyl hydrolase activity (GO:0036459)			breast(2)|central_nervous_system(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(4)|lung(5)|ovary(2)|upper_aerodigestive_tract(3)|urinary_tract(2)	26						GTCTTCCCCTCTAAGAGCCAG	0.542																																					p.S288C		Atlas-SNP	.											.	USP43	65	.	0			c.C863G						PASS	.						91.0	93.0	93.0					17																	9580092		2015	4165	6180	SO:0001583	missense	124739	exon5			TCCCCTCTAAGAG	AK055188	CCDS45610.1, CCDS58516.1	17p12	2005-08-08	2005-08-08			ENSG00000154914		"""Ubiquitin-specific peptidases"""	20072	protein-coding gene	gene with protein product			"""ubiquitin specific protease 43"""			12838346	Standard	NM_153210		Approved	FLJ30626	uc010cod.4	Q70EL4		ENST00000285199.7:c.863C>G	17.37:g.9580092C>G	ENSP00000285199:p.Ser288Cys	264.0	0.0	0		256.0	28.0	0.109375	NM_001267576	A6NDT9|B7ZLT9|B7ZVX5|Q8N2C5|Q96DQ6	Missense_Mutation	SNP	ENST00000285199.7	37	CCDS45610.1	.	.	.	.	.	.	.	.	.	.	C	12.78	2.041149	0.35989	.	.	ENSG00000154914	ENST00000285199	T	0.10099	2.91	4.62	2.55	0.30701	Peptidase C19, ubiquitin carboxyl-terminal hydrolase 2 (2);	0.387701	0.24601	N	0.037138	T	0.12475	0.0303	L	0.50847	1.595	0.09310	N	0.999998	B;B	0.12630	0.001;0.006	B;B	0.23852	0.01;0.049	T	0.18999	-1.0319	10	0.52906	T	0.07	-3.9205	12.7709	0.57421	0.0:0.7264:0.2736:0.0	.	288;288	B7ZVX5;Q70EL4	.;UBP43_HUMAN	C	288	ENSP00000285199:S288C	ENSP00000285199:S288C	S	+	2	0	USP43	9520817	0.587000	0.26791	0.707000	0.30419	0.997000	0.91878	2.000000	0.40816	0.537000	0.28751	0.555000	0.69702	TCT	.	.	none		0.542	USP43-006	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000439855.3	NM_153210	
DDX60L	91351	hgsc.bcm.edu	37	4	169294859	169294859	+	Silent	SNP	C	C	T	rs13133439	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr4:169294859C>T	ENST00000511577.1	-	35	4981	c.4734G>A	c.(4732-4734)ggG>ggA	p.G1578G	DDX60L_ENST00000260184.7_Silent_p.G1578G			Q5H9U9	DDX6L_HUMAN	DEAD (Asp-Glu-Ala-Asp) box polypeptide 60-like	1578							ATP binding (GO:0005524)|helicase activity (GO:0004386)|RNA binding (GO:0003723)			breast(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(7)|lung(23)|ovary(2)|prostate(1)|skin(1)|stomach(1)	43		Prostate(90;0.00876)|Renal(120;0.0183)|all_neural(102;0.0837)|Melanoma(52;0.132)		GBM - Glioblastoma multiforme(119;0.175)		TATCTGTGTTCCCCGAAAGAC	0.408													C|||	44	0.00878594	0.0008	0.013	5008	,	,		21270	0.0		0.0298	False		,,,				2504	0.0041				p.G1578G		Atlas-SNP	.											DDX60L,NS,carcinoma,-2,1	DDX60L	116	1	0			c.G4734A						PASS	.	C		31,4315	30.8+/-60.4	0,31,2142	266.0	268.0	267.0		4734	-2.0	0.1	4	dbSNP_121	267	333,8255	111.4+/-171.7	8,317,3969	no	coding-synonymous	DDX60L	NM_001012967.1		8,348,6111	TT,TC,CC		3.8775,0.7133,2.8143		1578/1707	169294859	364,12570	2173	4294	6467	SO:0001819	synonymous_variant	91351	exon35			TGTGTTCCCCGAA	AK092461	CCDS47161.1	4q32.3	2008-01-08				ENSG00000181381			26429	protein-coding gene	gene with protein product							Standard	XM_005263341		Approved	FLJ31033	uc003irq.4	Q5H9U9		ENST00000511577.1:c.4734G>A	4.37:g.169294859C>T		373.0	0.0	0		210.0	51.0	0.242857	NM_001012967	Q96ND6	Silent	SNP	ENST00000511577.1	37																																																																																				C|0.979;T|0.021	0.021	strong		0.408	DDX60L-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000364839.1	NM_001012967	
LPHN1	22859	hgsc.bcm.edu	37	19	14288369	14288369	+	Silent	SNP	C	C	T	rs146417164	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr19:14288369C>T	ENST00000340736.6	-	3	555	c.258G>A	c.(256-258)ccG>ccA	p.P86P	LPHN1_ENST00000361434.3_Silent_p.P86P	NM_001008701.2	NP_001008701.1	O94910	LPHN1_HUMAN	latrophilin 1	86	SUEL-type lectin. {ECO:0000255|PROSITE- ProRule:PRU00260}.				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						TGAAGGCGTCCGGCAGGTAGC	0.572													C|||	26	0.00519169	0.0	0.0086	5008	,	,		18398	0.002		0.0179	False		,,,				2504	0.0				p.P86P		Atlas-SNP	.											.	LPHN1	107	.	0			c.G258A						PASS	.	C	,	8,4398	14.3+/-33.2	0,8,2195	137.0	114.0	122.0		258,258	-9.7	0.0	19	dbSNP_134	122	104,8496	57.2+/-118.5	1,102,4197	no	coding-synonymous,coding-synonymous	LPHN1	NM_001008701.2,NM_014921.4	,	1,110,6392	TT,TC,CC		1.2093,0.1816,0.8611	,	86/1475,86/1470	14288369	112,12894	2203	4300	6503	SO:0001819	synonymous_variant	22859	exon3			GGCGTCCGGCAGG	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.258G>A	19.37:g.14288369C>T		140.0	0.0	0		119.0	62.0	0.521008	NM_001008701	Q96IE7|Q9BU07|Q9HAR3	Silent	SNP	ENST00000340736.6	37	CCDS32928.1																																																																																			C|0.992;T|0.008	0.008	strong		0.572	LPHN1-001	KNOWN	overlapping_uORF|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000459696.1	NM_014921	
LGALS16	148003	hgsc.bcm.edu	37	19	40151098	40151098	+	Missense_Mutation	SNP	A	A	C	rs181925874	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr19:40151098A>C	ENST00000392051.3	+	4	435	c.367A>C	c.(367-369)Atg>Ctg	p.M123L		NM_001190441.1	NP_001177370.1			lectin, galactoside-binding, soluble, 16																		ATATGTGAAGATGATTCAAGT	0.428													A|||	2	0.000399361	0.0	0.0014	5008	,	,		23434	0.0		0.001	False		,,,				2504	0.0				p.M123L		Atlas-SNP	.											.	LGALS16	6	.	0			c.A367C						PASS	.																																			SO:0001583	missense	148003	exon4			GTGAAGATGATTC		CCDS54267.1	19q13.2	2011-08-04			ENSG00000249861	ENSG00000249861		"""Lectins, galactoside-binding"""	40039	protein-coding gene	gene with protein product						19497882	Standard	NM_001190441		Approved		uc021uun.1	A8MUM7		ENST00000392051.3:c.367A>C	19.37:g.40151098A>C	ENSP00000375904:p.Met123Leu	23.0	0.0	0		29.0	9.0	0.310345	NM_001190441		Missense_Mutation	SNP	ENST00000392051.3	37	CCDS54267.1	1	4.578754578754579E-4	0	0.0	1	0.0027624309392265192	0	0.0	0	0.0	.	11.38	1.621495	0.28889	.	.	ENSG00000249861	ENST00000392051	T	0.15834	2.39	1.21	-0.276	0.12902	.	.	.	.	.	T	0.14657	0.0354	L	0.46670	1.46	0.09310	N	1	P	0.46706	0.883	P	0.44860	0.462	T	0.13150	-1.0520	9	0.38643	T	0.18	.	3.0591	0.06194	0.6127:0.0:0.0:0.3873	.	123	A8MUM7	LEG16_HUMAN	L	123	ENSP00000375904:M123L	ENSP00000375904:M123L	M	+	1	0	LGALS16	44842938	0.014000	0.17966	0.032000	0.17829	0.295000	0.27426	0.444000	0.21661	-0.500000	0.06614	0.163000	0.16589	ATG	A|1.000;C|0.000	0.000	strong		0.428	LGALS16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000465022.1		
KCNU1	157855	hgsc.bcm.edu	37	8	36788597	36788597	+	Missense_Mutation	SNP	G	G	C	rs190224798	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr8:36788597G>C	ENST00000399881.3	+	25	2902	c.2865G>C	c.(2863-2865)ttG>ttC	p.L955F	KCNU1_ENST00000518904.1_3'UTR	NM_001031836.2	NP_001027006.2	A8MYU2	KCNU1_HUMAN	potassium channel, subfamily U, member 1	955					multicellular organism reproduction (GO:0032504)|potassium ion transmembrane transport (GO:0071805)|single fertilization (GO:0007338)|sperm-egg recognition (GO:0035036)	plasma membrane (GO:0005886)|voltage-gated potassium channel complex (GO:0008076)	large conductance calcium-activated potassium channel activity (GO:0060072)|potassium channel activity (GO:0005267)|voltage-gated potassium channel activity (GO:0005249)			breast(4)|central_nervous_system(1)|cervix(1)|endometrium(8)|kidney(1)|large_intestine(9)|lung(31)|ovary(1)|urinary_tract(1)	57				KIRC - Kidney renal clear cell carcinoma(67;0.0504)|Kidney(114;0.0634)		CGTCGCTCTTGTCTGGAAGAA	0.443													G|||	3	0.000599042	0.0008	0.0014	5008	,	,		17383	0.0		0.0	False		,,,				2504	0.001				p.L955F		Atlas-SNP	.											.	KCNU1	359	.	0			c.G2865C						PASS	.	G	PHE/LEU	4,3820		0,4,1908	137.0	131.0	133.0		2865	0.5	0.0	8		133	18,8248		0,18,4115	yes	missense	KCNU1	NM_001031836.2	22	0,22,6023	CC,CG,GG		0.2178,0.1046,0.182	possibly-damaging	955/1150	36788597	22,12068	1912	4133	6045	SO:0001583	missense	157855	exon25			GCTCTTGTCTGGA	BC028701	CCDS55220.1	8p11.2	2012-07-05				ENSG00000215262		"""Potassium channels"", ""Voltage-gated ion channels / Potassium channels, calcium-activated"""	18867	protein-coding gene	gene with protein product		615215				16382103	Standard	NM_001031836		Approved	KCa5.1, Slo3, KCNMC1, Kcnma3	uc010lvw.3	A8MYU2		ENST00000399881.3:c.2865G>C	8.37:g.36788597G>C	ENSP00000382770:p.Leu955Phe	156.0	0.0	0		218.0	61.0	0.279817	NM_001031836		Missense_Mutation	SNP	ENST00000399881.3	37	CCDS55220.1	1	4.578754578754579E-4	0	0.0	1	0.0027624309392265192	0	0.0	0	0.0	G	11.00	1.510137	0.27036	0.001046	0.002178	ENSG00000215262	ENST00000399881	T	0.39229	1.09	5.41	0.468	0.16732	.	2.385820	0.03106	U	0.161774	T	0.44705	0.1306	M	0.73962	2.25	0.09310	N	1	B	0.12013	0.005	B	0.10450	0.005	T	0.34453	-0.9828	10	0.87932	D	0	0.6019	4.979	0.14155	0.0865:0.1259:0.6256:0.162	.	955	A8MYU2	KCNU1_HUMAN	F	955	ENSP00000382770:L955F	ENSP00000382770:L955F	L	+	3	2	KCNU1	36907755	0.001000	0.12720	0.000000	0.03702	0.009000	0.06853	0.833000	0.27504	-0.142000	0.11354	0.650000	0.86243	TTG	G|1.000;C|0.000	0.000	strong		0.443	KCNU1-001	KNOWN	non_canonical_conserved|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000376631.1	NM_001031836	
ASPHD1	253982	hgsc.bcm.edu	37	16	29917177	29917177	+	Missense_Mutation	SNP	G	G	A			TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr16:29917177G>A	ENST00000308748.5	+	3	1384	c.1132G>A	c.(1132-1134)Gag>Aag	p.E378K	ASPHD1_ENST00000483405.1_Missense_Mutation_p.E97K	NM_181718.3	NP_859069.2	Q5U4P2	ASPH1_HUMAN	aspartate beta-hydroxylase domain containing 1	378					peptidyl-amino acid modification (GO:0018193)	integral component of membrane (GO:0016021)	dioxygenase activity (GO:0051213)			endometrium(4)|large_intestine(2)|lung(1)|prostate(1)	8						GGCAGGGGCTGAGCGCCAGGC	0.637																																					p.E378K		Atlas-SNP	.											.	ASPHD1	28	.	0			c.G1132A						PASS	.						70.0	60.0	64.0					16																	29917177		2197	4300	6497	SO:0001583	missense	253982	exon3			GGGGCTGAGCGCC	AF070642	CCDS10660.1	16p11.2	2008-02-05			ENSG00000174939	ENSG00000174939			27380	protein-coding gene	gene with protein product							Standard	NM_181718		Approved		uc002dut.3	Q5U4P2	OTTHUMG00000132121	ENST00000308748.5:c.1132G>A	16.37:g.29917177G>A	ENSP00000311447:p.Glu378Lys	111.0	0.0	0		99.0	56.0	0.565657	NM_181718	A0AVE3|B7ZLZ3|Q8IW63|Q8N316|Q96H00	Missense_Mutation	SNP	ENST00000308748.5	37	CCDS10660.1	.	.	.	.	.	.	.	.	.	.	G	36	5.897740	0.97081	.	.	ENSG00000174939	ENST00000414952;ENST00000308748	T;T	0.59364	0.27;0.27	5.76	5.76	0.90799	.	0.000000	0.64402	D	0.000001	T	0.80177	0.4575	M	0.86953	2.85	0.80722	D	1	D	0.76494	0.999	D	0.75020	0.985	T	0.82938	-0.0209	10	0.87932	D	0	-22.1497	18.742	0.91777	0.0:0.0:1.0:0.0	.	378	Q5U4P2	ASPH1_HUMAN	K	378	ENSP00000388036:E378K;ENSP00000311447:E378K	ENSP00000311447:E378K	E	+	1	0	ASPHD1	29824678	1.000000	0.71417	0.923000	0.36655	0.980000	0.70556	9.149000	0.94659	2.728000	0.93425	0.655000	0.94253	GAG	.	.	none		0.637	ASPHD1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000255163.2	NM_181718	
CPED1	79974	hgsc.bcm.edu	37	7	120737809	120737809	+	Missense_Mutation	SNP	C	C	T	rs144805034	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr7:120737809C>T	ENST00000310396.5	+	6	1140	c.673C>T	c.(673-675)Ccg>Tcg	p.P225S	CPED1_ENST00000450913.2_Missense_Mutation_p.P225S|CPED1_ENST00000423795.1_Missense_Mutation_p.P5S	NM_024913.4	NP_079189.4	A4D0V7	CPED1_HUMAN	cadherin-like and PC-esterase domain containing 1	225						endoplasmic reticulum (GO:0005783)											GCAATTAAAGCCGAGTACTTC	0.428													C|||	5	0.000998403	0.0	0.0	5008	,	,		18641	0.0		0.005	False		,,,				2504	0.0				p.P225S		Atlas-SNP	.											.	.	.	.	0			c.C673T						PASS	.	C	SER/PRO,SER/PRO	6,4400	11.4+/-27.6	0,6,2197	148.0	144.0	146.0		673,673	4.8	0.0	7	dbSNP_134	146	58,8542	36.4+/-91.3	0,58,4242	yes	missense,missense	C7orf58	NM_001105533.1,NM_024913.4	74,74	0,64,6439	TT,TC,CC		0.6744,0.1362,0.4921	possibly-damaging,possibly-damaging	225/784,225/1027	120737809	64,12942	2203	4300	6503	SO:0001583	missense	79974	exon5			TTAAAGCCGAGTA		CCDS34739.1, CCDS47690.1	7q31.31	2012-06-12	2012-06-12	2012-06-12	ENSG00000106034	ENSG00000106034			26159	protein-coding gene	gene with protein product			"""chromosome 7 open reading frame 58"""	C7orf58		20056006	Standard	NM_024913		Approved	FLJ21986	uc003vjq.4	A4D0V7	OTTHUMG00000156982	ENST00000310396.5:c.673C>T	7.37:g.120737809C>T	ENSP00000309772:p.Pro225Ser	171.0	0.0	0		89.0	73.0	0.820225	NM_001105533	A8K1R3|Q6UXT1|Q86T76|Q86T84|Q8N2T5|Q96NC9	Missense_Mutation	SNP	ENST00000310396.5	37	CCDS34739.1	4	0.0018315018315018315	0	0.0	0	0.0	0	0.0	4	0.005277044854881266	C	13.55	2.271428	0.40194	0.001362	0.006744	ENSG00000106034	ENST00000310396;ENST00000428526;ENST00000450913;ENST00000423795;ENST00000443817	T;T;T;T;T	0.43294	0.95;0.95;0.95;2.02;1.61	5.75	4.82	0.62117	.	1.300280	0.04908	N	0.452653	T	0.30324	0.0761	L	0.40543	1.245	0.24671	N	0.993418	P;B;B	0.39216	0.664;0.435;0.116	B;B;B	0.38500	0.275;0.157;0.043	T	0.11767	-1.0574	10	0.18710	T	0.47	-16.7029	11.2559	0.49054	0.1821:0.8179:0.0:0.0	.	5;225;225	G5E9U2;A4D0V7-2;A4D0V7	.;.;CG058_HUMAN	S	225;225;225;5;5	ENSP00000309772:P225S;ENSP00000398082:P225S;ENSP00000406122:P225S;ENSP00000415573:P5S;ENSP00000391952:P5S	ENSP00000309772:P225S	P	+	1	0	C7orf58	120525045	0.038000	0.19896	0.015000	0.15790	0.699000	0.40488	0.642000	0.24735	2.710000	0.92621	0.557000	0.71058	CCG	C|0.996;T|0.004	0.004	strong		0.428	CPED1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000346959.1	NM_024913	
VSIG1	340547	hgsc.bcm.edu	37	X	107320447	107320447	+	Missense_Mutation	SNP	C	C	T			TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chrX:107320447C>T	ENST00000217957.5	+	7	1117	c.1000C>T	c.(1000-1002)Cca>Tca	p.P334S	VSIG1_ENST00000415430.3_Missense_Mutation_p.P370S	NM_182607.4	NP_872413.1	Q86XK7	VSIG1_HUMAN	V-set and immunoglobulin domain containing 1	334						integral component of membrane (GO:0016021)				breast(1)|endometrium(3)|kidney(1)|large_intestine(4)|lung(6)|ovary(1)|upper_aerodigestive_tract(1)	17						agagcctgccccagGATCAGA	0.562																																					p.P370S		Atlas-SNP	.											.	VSIG1	126	.	0			c.C1108T						PASS	.						75.0	69.0	71.0					X																	107320447		2203	4300	6503	SO:0001583	missense	340547	exon8			CCTGCCCCAGGAT	BX648658	CCDS14535.1, CCDS55474.1	Xq22.3	2013-01-29			ENSG00000101842	ENSG00000101842		"""Immunoglobulin superfamily / V-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	28675	protein-coding gene	gene with protein product		300620				12477932	Standard	NM_182607		Approved	MGC44287	uc011msk.2	Q86XK7	OTTHUMG00000022175	ENST00000217957.5:c.1000C>T	X.37:g.107320447C>T	ENSP00000217957:p.Pro334Ser	127.0	0.0	0		71.0	4.0	0.056338	NM_001170553	C9J4P2|Q6MZS4	Missense_Mutation	SNP	ENST00000217957.5	37	CCDS14535.1	.	.	.	.	.	.	.	.	.	.	C	4.558	0.103573	0.08731	.	.	ENSG00000101842	ENST00000415430;ENST00000217957	T;T	0.61274	0.12;0.12	3.5	-7.0	0.01599	.	1.931450	0.02302	N	0.071290	T	0.38427	0.1040	L	0.43152	1.355	0.09310	N	1	B;B	0.06786	0.001;0.001	B;B	0.04013	0.001;0.001	T	0.48445	-0.9035	10	0.05436	T	0.98	.	3.3355	0.07100	0.1048:0.1372:0.4102:0.3478	.	370;334	C9J4P2;Q86XK7	.;VSIG1_HUMAN	S	370;334	ENSP00000402219:P370S;ENSP00000217957:P334S	ENSP00000217957:P334S	P	+	1	0	VSIG1	107207103	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-4.489000	0.00226	-2.917000	0.00306	-4.471000	0.00005	CCA	.	.	none		0.562	VSIG1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000057858.1	NM_182607	
OR5AS1	219447	hgsc.bcm.edu	37	11	55798278	55798278	+	Silent	SNP	C	C	T	rs148523609	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr11:55798278C>T	ENST00000313555.1	+	1	384	c.384C>T	c.(382-384)aaC>aaT	p.N128N		NM_001001921.1	NP_001001921.1	Q8N127	O5AS1_HUMAN	olfactory receptor, family 5, subfamily AS, member 1	128						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			endometrium(7)|large_intestine(7)|liver(1)|lung(22)|ovary(3)|prostate(4)|skin(3)|stomach(1)	48	Esophageal squamous(21;0.00693)					CCATCTGCAACCCACTGCTCT	0.468													C|||	14	0.00279553	0.0008	0.0014	5008	,	,		20153	0.0		0.0089	False		,,,				2504	0.0031				p.N128N		Atlas-SNP	.											.	OR5AS1	121	.	0			c.C384T						PASS	.	C		12,4390	21.2+/-45.6	0,12,2189	150.0	122.0	132.0		384	-1.9	0.3	11	dbSNP_134	132	106,8486	57.5+/-118.9	1,104,4191	no	coding-synonymous	OR5AS1	NM_001001921.1		1,116,6380	TT,TC,CC		1.2337,0.2726,0.9081		128/325	55798278	118,12876	2201	4296	6497	SO:0001819	synonymous_variant	219447	exon1			CTGCAACCCACTG	AB065543	CCDS31516.1	11q11	2012-08-09			ENSG00000181785	ENSG00000181785		"""GPCR / Class A : Olfactory receptors"""	15261	protein-coding gene	gene with protein product							Standard	NM_001001921		Approved		uc010riw.2	Q8N127	OTTHUMG00000166830	ENST00000313555.1:c.384C>T	11.37:g.55798278C>T		335.0	1.0	0.00298507		295.0	136.0	0.461017	NM_001001921	Q6IFB8	Silent	SNP	ENST00000313555.1	37	CCDS31516.1																																																																																			C|0.993;T|0.007	0.007	strong		0.468	OR5AS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391538.1	NM_001001921	
SRRM2	23524	hgsc.bcm.edu	37	16	2816519	2816519	+	Missense_Mutation	SNP	G	G	A	rs138447860	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr16:2816519G>A	ENST00000301740.8	+	11	6539	c.5990G>A	c.(5989-5991)cGc>cAc	p.R1997H		NM_016333.3	NP_057417.3	Q9UQ35	SRRM2_HUMAN	serine/arginine repetitive matrix 2	1997	Arg-rich.|Ser-rich.				mRNA splicing, via spliceosome (GO:0000398)	Cajal body (GO:0015030)|catalytic step 2 spliceosome (GO:0071013)|nuclear speck (GO:0016607)|nucleus (GO:0005634)	C2H2 zinc finger domain binding (GO:0070742)|poly(A) RNA binding (GO:0044822)|protein N-terminus binding (GO:0047485)			breast(3)|central_nervous_system(1)|cervix(3)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(20)|lung(34)|ovary(6)|pancreas(3)|prostate(2)|skin(6)|upper_aerodigestive_tract(3)|urinary_tract(7)	105						TCTCGATCTCGCACATCTCCA	0.577													G|||	10	0.00199681	0.0	0.0043	5008	,	,		17504	0.0		0.007	False		,,,				2504	0.0				p.R1997H		Atlas-SNP	.											.	SRRM2	263	.	0			c.G5990A						PASS	.	G	HIS/ARG	3,4393	6.2+/-15.9	0,3,2195	71.0	75.0	74.0		5990	5.3	1.0	16	dbSNP_134	74	50,8550	32.3+/-84.9	0,50,4250	yes	missense	SRRM2	NM_016333.3	29	0,53,6445	AA,AG,GG		0.5814,0.0682,0.4078	probably-damaging	1997/2753	2816519	53,12943	2198	4300	6498	SO:0001583	missense	23524	exon11			GATCTCGCACATC	AF201422	CCDS32373.1	16p13.3	2012-07-02			ENSG00000167978	ENSG00000167978			16639	protein-coding gene	gene with protein product		606032				10668804, 11004489	Standard	NM_016333		Approved	SRm300, SRL300, KIAA0324, Cwc21	uc002crk.3	Q9UQ35	OTTHUMG00000177358	ENST00000301740.8:c.5990G>A	16.37:g.2816519G>A	ENSP00000301740:p.Arg1997His	87.0	0.0	0		99.0	48.0	0.484848	NM_016333	A6NKB9|D3DU97|O15038|O94803|Q6NSL3|Q6PIM3|Q6PK40|Q8IW17|Q96GY7|Q9P0G1|Q9UHA8|Q9UQ36|Q9UQ37|Q9UQ38|Q9UQ40	Missense_Mutation	SNP	ENST00000301740.8	37	CCDS32373.1	4	0.0018315018315018315	0	0.0	1	0.0027624309392265192	0	0.0	3	0.00395778364116095	G	11.77	1.736455	0.30774	6.82E-4	0.005814	ENSG00000167978	ENST00000301740;ENST00000382301;ENST00000544933	T	0.24908	1.83	5.26	5.26	0.73747	.	0.000000	0.53938	D	0.000043	T	0.23572	0.0570	N	0.08118	0	0.35761	D	0.820188	D	0.76494	0.999	D	0.69654	0.965	T	0.48198	-0.9056	10	0.62326	D	0.03	-6.3676	16.354	0.83228	0.0:0.0:1.0:0.0	.	1997	Q9UQ35	SRRM2_HUMAN	H	1997;1997;1249	ENSP00000301740:R1997H	ENSP00000301740:R1997H	R	+	2	0	SRRM2	2756520	0.967000	0.33354	0.988000	0.46212	0.988000	0.76386	3.451000	0.52964	2.466000	0.83321	0.650000	0.86243	CGC	G|0.997;A|0.003	0.003	strong		0.577	SRRM2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000436411.1		
PLEC	5339	hgsc.bcm.edu	37	8	145006143	145006143	+	Missense_Mutation	SNP	T	T	C	rs189137260	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr8:145006143T>C	ENST00000322810.4	-	18	2720	c.2551A>G	c.(2551-2553)Atc>Gtc	p.I851V	PLEC_ENST00000345136.3_Missense_Mutation_p.I714V|PLEC_ENST00000357649.2_Missense_Mutation_p.I718V|PLEC_ENST00000354589.3_Missense_Mutation_p.I714V|PLEC_ENST00000436759.2_Missense_Mutation_p.I741V|PLEC_ENST00000354958.2_Missense_Mutation_p.I692V|PLEC_ENST00000356346.3_Missense_Mutation_p.I700V|PLEC_ENST00000398774.2_Missense_Mutation_p.I682V|PLEC_ENST00000527096.1_Missense_Mutation_p.I737V	NM_201380.2	NP_958782.1	Q15149	PLEC_HUMAN	plectin	851	Globular 1.				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						TGTGCCTCGATACAGCAGCAC	0.682													T|||	7	0.00139776	0.0	0.0	5008	,	,		12293	0.0069		0.0	False		,,,				2504	0.0				p.I851V		Atlas-SNP	.											.	PLEC	1144	.	0			c.A2551G						PASS	.						18.0	23.0	21.0					8																	145006143		2101	4235	6336	SO:0001583	missense	5339	exon18			CCTCGATACAGCA	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.2551A>G	8.37:g.145006143T>C	ENSP00000323856:p.Ile851Val	114.0	0.0	0		154.0	83.0	0.538961	NM_201380	Q15148|Q16640|Q6S376|Q6S377|Q6S378|Q6S379|Q6S380|Q6S381|Q6S382|Q6S383	Missense_Mutation	SNP	ENST00000322810.4	37	CCDS43772.1	11	0.005036630036630037	1	0.0020325203252032522	1	0.0027624309392265192	7	0.012237762237762238	2	0.002638522427440633	T	10.35	1.327031	0.24080	.	.	ENSG00000178209	ENST00000345136;ENST00000357649;ENST00000354589;ENST00000398774;ENST00000322810;ENST00000354958;ENST00000356346;ENST00000436759;ENST00000527096	D;D;D;D;D;D;D;D;D	0.88975	-2.45;-2.45;-2.45;-2.45;-2.45;-2.45;-2.45;-2.45;-2.45	4.2	0.331	0.15933	.	0.000000	0.64402	U	0.000016	T	0.69949	0.3168	N	0.21545	0.675	0.34771	D	0.73369	B;B;B;B;B;B;B;B	0.06786	0.001;0.001;0.001;0.001;0.001;0.001;0.001;0.001	B;B;B;B;B;B;B;B	0.09377	0.004;0.004;0.004;0.002;0.004;0.004;0.004;0.004	T	0.62872	-0.6762	10	0.23302	T	0.38	.	5.975	0.19373	0.0:0.1853:0.1515:0.6631	.	741;700;692;851;682;714;718;714	Q15149-2;Q15149-9;Q15149-8;Q15149;Q15149-7;Q15149-5;Q15149-6;Q15149-4	.;.;.;PLEC_HUMAN;.;.;.;.	V	714;718;714;682;851;692;700;741;737	ENSP00000344848:I714V;ENSP00000350277:I718V;ENSP00000346602:I714V;ENSP00000381756:I682V;ENSP00000323856:I851V;ENSP00000347044:I692V;ENSP00000348702:I700V;ENSP00000388180:I741V;ENSP00000434583:I737V	ENSP00000323856:I851V	I	-	1	0	PLEC	145078131	0.157000	0.22836	0.190000	0.23270	0.782000	0.44232	0.054000	0.14205	0.208000	0.20626	0.372000	0.22366	ATC	T|0.995;C|0.005	0.005	strong		0.682	PLEC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000383281.1	NM_000445	
KIAA1683	80726	hgsc.bcm.edu	37	19	18377981	18377981	+	Silent	SNP	C	C	G	rs61740692	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr19:18377981C>G	ENST00000600328.3	-	3	562	c.369G>C	c.(367-369)ctG>ctC	p.L123L	KIAA1683_ENST00000392413.4_Silent_p.L123L|KIAA1683_ENST00000600359.3_Silent_p.L77L			Q9H0B3	K1683_HUMAN	KIAA1683	123	IQ 1. {ECO:0000255|PROSITE- ProRule:PRU00116}.					mitochondrion (GO:0005739)|nucleus (GO:0005634)				breast(1)|endometrium(7)|kidney(2)|large_intestine(7)|lung(11)|ovary(2)|prostate(3)|skin(3)|upper_aerodigestive_tract(1)	37						TCTGGGAAATCAGCTTCTGCC	0.562													C|||	9	0.00179712	0.0015	0.0014	5008	,	,		17364	0.0		0.006	False		,,,				2504	0.0				p.L123L		Atlas-SNP	.											.	KIAA1683	190	.	0			c.G369C						PASS	.	C	,,	8,4398	14.3+/-33.2	0,8,2195	57.0	57.0	57.0		369,231,369	-8.1	0.0	19	dbSNP_129	57	112,8488	60.6+/-122.4	0,112,4188	no	coding-synonymous,coding-synonymous,coding-synonymous	KIAA1683	NM_001145304.1,NM_001145305.1,NM_025249.3	,,	0,120,6383	GG,GC,CC		1.3023,0.1816,0.9227	,,	123/1368,77/1135,123/1181	18377981	120,12886	2203	4300	6503	SO:0001819	synonymous_variant	80726	exon3			GGAAATCAGCTTC	AB051470	CCDS32958.1, CCDS46017.1, CCDS46018.1	19p13.1	2008-02-05				ENSG00000130518			29350	protein-coding gene	gene with protein product						11214970, 11230166	Standard	NM_025249		Approved		uc010ebn.2	Q9H0B3		ENST00000600328.3:c.369G>C	19.37:g.18377981C>G		208.0	0.0	0		194.0	94.0	0.484536	NM_001145304	B4DYH2|E9PDE0|E9PH54|Q2KHR5|Q8N4G8|Q96M14|Q9C0I0	Silent	SNP	ENST00000600328.3	37	CCDS32958.1																																																																																			C|0.984;G|0.016	0.016	strong		0.562	KIAA1683-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000466312.3		
YPEL3	83719	hgsc.bcm.edu	37	16	30106716	30106716	+	5'UTR	SNP	C	C	A	rs184524218	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr16:30106716C>A	ENST00000398838.4	-	0	187				RP11-455F5.3_ENST00000515455.2_RNA|YPEL3_ENST00000398841.1_Missense_Mutation_p.V30L|YPEL3_ENST00000562641.1_Missense_Mutation_p.V30L|YPEL3_ENST00000566595.1_5'UTR|YPEL3_ENST00000565479.1_Intron|YPEL3_ENST00000563788.1_5'UTR|YPEL3_ENST00000566134.1_5'UTR	NM_001145524.1	NP_001138996.1	P61236	YPEL3_HUMAN	yippee-like 3 (Drosophila)							nucleus (GO:0005634)				endometrium(1)|lung(2)	3						AGTGGCCCCACGCGGGGAGCG	0.672													C|||	16	0.00319489	0.0	0.0014	5008	,	,		14972	0.0		0.0129	False		,,,				2504	0.002				p.V30L		Atlas-SNP	.											.	YPEL3	5	.	0			c.G88T						PASS	.	C	,LEU/VAL	6,3864		0,6,1929	23.0	26.0	25.0		,88	3.5	1.0	16		25	108,8124		0,108,4008	yes	utr-5,missense	YPEL3	NM_001145524.1,NM_031477.4	,32	0,114,5937	AA,AC,CC		1.312,0.155,0.942	,	,30/158	30106716	114,11988	1935	4116	6051	SO:0001623	5_prime_UTR_variant	83719	exon1			GCCCCACGCGGGG	AF305622	CCDS42147.1, CCDS45459.1	16p11	2008-02-05							18327	protein-coding gene	gene with protein product		609724					Standard	NM_031477		Approved	MGC10500	uc002dwm.3	P61236		ENST00000398838.4:c.-27G>T	16.37:g.30106716C>A		44.0	0.0	0		37.0	24.0	0.648649	NM_031477	Q65Z99|Q86VK6|Q9BSJ4|Q9CQB6	Missense_Mutation	SNP	ENST00000398838.4	37	CCDS45459.1	9	0.004120879120879121	0	0.0	1	0.0027624309392265192	0	0.0	8	0.010554089709762533	C	13.01	2.110837	0.37242	0.00155	0.01312	ENSG00000090238	ENST00000398841	.	.	.	3.52	3.52	0.40303	.	0.000000	0.30109	N	0.010388	T	0.16128	0.0388	.	.	.	0.21627	N	0.999613	B	0.06786	0.001	B	0.06405	0.002	T	0.11591	-1.0581	8	0.10902	T	0.67	-5.6356	10.7694	0.46314	0.0:0.8051:0.1949:0.0	.	30	P61236-2	.	L	30	.	ENSP00000381821:V30L	V	-	1	0	YPEL3	30014217	1.000000	0.71417	1.000000	0.80357	0.976000	0.68499	2.998000	0.49465	1.811000	0.52892	0.561000	0.74099	GTG	C|0.995;A|0.005	0.005	strong		0.672	YPEL3-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000434043.1	NM_031477	
VPS13C	54832	hgsc.bcm.edu	37	15	62253954	62253954	+	Missense_Mutation	SNP	G	G	T			TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr15:62253954G>T	ENST00000261517.5	-	35	3815	c.3742C>A	c.(3742-3744)Ccg>Acg	p.P1248T	VPS13C_ENST00000395898.3_Missense_Mutation_p.P1205T|VPS13C_ENST00000395896.4_Missense_Mutation_p.P1248T|VPS13C_ENST00000249837.3_Missense_Mutation_p.P1205T	NM_020821.2	NP_065872.1			vacuolar protein sorting 13 homolog C (S. cerevisiae)											NS(3)|breast(4)|endometrium(4)|kidney(9)|large_intestine(26)|lung(46)|ovary(5)|prostate(6)|skin(6)|stomach(5)|upper_aerodigestive_tract(2)|urinary_tract(1)	117						ACTATAACCGGTGCTTTCAAA	0.458																																					p.P1248T		Atlas-SNP	.											.	VPS13C	506	.	0			c.C3742A						PASS	.						111.0	110.0	111.0					15																	62253954		2203	4300	6503	SO:0001583	missense	54832	exon35			TAACCGGTGCTTT	AJ608770	CCDS10180.1, CCDS32257.1, CCDS45272.1, CCDS58367.1	15q21.3	2009-07-09	2006-04-04		ENSG00000129003	ENSG00000129003			23594	protein-coding gene	gene with protein product		608879	"""vacuolar protein sorting 13C (yeast)"""				Standard	NM_018080		Approved	FLJ20136, FLJ10381, KIAA1421	uc002agz.3	Q709C8	OTTHUMG00000132801	ENST00000261517.5:c.3742C>A	15.37:g.62253954G>T	ENSP00000261517:p.Pro1248Thr	168.0	0.0	0		109.0	8.0	0.0733945	NM_020821		Missense_Mutation	SNP	ENST00000261517.5	37	CCDS32257.1	.	.	.	.	.	.	.	.	.	.	G	21.7	4.186000	0.78789	.	.	ENSG00000129003	ENST00000249837;ENST00000261517;ENST00000395896;ENST00000395898	T;T;T	0.14893	2.47;2.47;2.47	5.76	4.85	0.62838	.	0.000000	0.85682	D	0.000000	T	0.49474	0.1559	M	0.90309	3.105	0.80722	D	1	D;D;D;D	0.89917	1.0;1.0;0.999;1.0	D;D;D;D	0.76071	0.987;0.982;0.974;0.971	T	0.61520	-0.7046	10	0.87932	D	0	.	14.8531	0.70313	0.0689:0.0:0.9311:0.0	.	1205;1248;1205;1248	Q709C8-4;Q709C8-2;Q709C8-3;Q709C8	.;.;.;VP13C_HUMAN	T	1205;1248;1248;1248	ENSP00000249837:P1205T;ENSP00000261517:P1248T;ENSP00000379233:P1248T	ENSP00000249837:P1205T	P	-	1	0	VPS13C	60041246	1.000000	0.71417	0.936000	0.37596	0.978000	0.69477	9.476000	0.97823	1.434000	0.47414	0.563000	0.77884	CCG	.	.	none		0.458	VPS13C-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000415997.1	NM_017684	
HIST1H1E	3008	hgsc.bcm.edu	37	6	26157009	26157009	+	Missense_Mutation	SNP	C	C	T			TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr6:26157009C>T	ENST00000304218.3	+	1	451	c.391C>T	c.(391-393)Cca>Tca	p.P131S	HIST1H2BD_ENST00000377777.4_5'Flank|HIST1H2BD_ENST00000289316.2_5'Flank	NM_005321.2	NP_005312.1	P10412	H14_HUMAN	histone cluster 1, H1e	131					nucleosome assembly (GO:0006334)|nucleosome positioning (GO:0016584)	extracellular vesicular exosome (GO:0070062)|nuclear heterochromatin (GO:0005720)|nucleosome (GO:0000786)|nucleus (GO:0005634)	chromatin DNA binding (GO:0031490)|poly(A) RNA binding (GO:0044822)			NS(2)|central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(1)|liver(1)|lung(9)|ovary(2)|prostate(1)|skin(3)|upper_aerodigestive_tract(2)	26						GGCCAAGAAGCCAGCAGGAGC	0.642																																					p.P131S		Atlas-SNP	.											.	HIST1H1E	69	.	0			c.C391T						PASS	.						16.0	22.0	20.0					6																	26157009		2201	4297	6498	SO:0001583	missense	3008	exon1			AAGAAGCCAGCAG	M60748	CCDS4586.1	6p22.1	2012-05-04	2006-10-11	2003-02-21	ENSG00000168298	ENSG00000168298		"""Histones / Replication-dependent"""	4718	protein-coding gene	gene with protein product		142220	"""H1 histone family, member 4"", ""histone 1, H1e"""	H1F4		1916825, 12408966	Standard	NM_005321		Approved	H1.4, H1e, H1s-4	uc003ngq.3	P10412	OTTHUMG00000014422	ENST00000304218.3:c.391C>T	6.37:g.26157009C>T	ENSP00000307705:p.Pro131Ser	103.0	0.0	0		109.0	35.0	0.321101	NM_005321	Q4VB25	Missense_Mutation	SNP	ENST00000304218.3	37	CCDS4586.1	.	.	.	.	.	.	.	.	.	.	.	3.113	-0.182313	0.06340	.	.	ENSG00000168298	ENST00000304218	T	0.25579	1.79	5.51	-0.293	0.12835	.	0.186307	0.47455	N	0.000233	T	0.04634	0.0126	L	0.38175	1.15	0.48975	D	0.999731	B	0.10296	0.003	B	0.08055	0.003	T	0.29731	-1.0002	10	0.11182	T	0.66	0.2785	3.53	0.07773	0.114:0.485:0.2269:0.1741	.	131	P10412	H14_HUMAN	S	131	ENSP00000307705:P131S	ENSP00000307705:P131S	P	+	1	0	HIST1H1E	26264988	0.865000	0.29922	0.579000	0.28588	0.041000	0.13682	0.334000	0.19787	0.052000	0.16007	0.561000	0.74099	CCA	.	.	none		0.642	HIST1H1E-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040084.1	NM_005321	
XKR8	55113	hgsc.bcm.edu	37	1	28290155	28290155	+	Silent	SNP	G	G	A	rs142513353	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr1:28290155G>A	ENST00000373884.5	+	2	1049	c.441G>A	c.(439-441)acG>acA	p.T147T	XKR8_ENST00000481387.1_3'UTR	NM_018053.2	NP_060523.2	Q9H6D3	XKR8_HUMAN	XK, Kell blood group complex subunit-related family, member 8	147					engulfment of apoptotic cell (GO:0043652)|phosphatidylserine exposure on apoptotic cell surface (GO:0070782)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				endometrium(1)|large_intestine(2)|lung(1)	4		Colorectal(325;0.000147)|Renal(390;0.00357)|Lung NSC(340;0.00588)|all_lung(284;0.00645)|Breast(348;0.0174)|Myeloproliferative disorder(586;0.0393)|Ovarian(437;0.0545)|all_neural(195;0.0557)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0416)|OV - Ovarian serous cystadenocarcinoma(117;4.72e-24)|Colorectal(126;1.52e-08)|COAD - Colon adenocarcinoma(152;1.7e-06)|KIRC - Kidney renal clear cell carcinoma(1967;0.00269)|STAD - Stomach adenocarcinoma(196;0.00303)|BRCA - Breast invasive adenocarcinoma(304;0.00572)|READ - Rectum adenocarcinoma(331;0.0526)		CACAGCTCACGCTGGTGCTGG	0.627													G|||	10	0.00199681	0.0	0.0043	5008	,	,		17805	0.0		0.007	False		,,,				2504	0.0				p.T147T		Atlas-SNP	.											.	XKR8	15	.	0			c.G441A						PASS	.	G		3,4403	4.2+/-10.8	0,3,2200	23.0	20.0	21.0		441	-1.9	1.0	1	dbSNP_134	21	31,8569	19.8+/-62.0	0,31,4269	no	coding-synonymous	XKR8	NM_018053.2		0,34,6469	AA,AG,GG		0.3605,0.0681,0.2614		147/396	28290155	34,12972	2203	4300	6503	SO:0001819	synonymous_variant	55113	exon2			GCTCACGCTGGTG	AK091615	CCDS315.1	1p35.3	2008-02-05	2006-01-12		ENSG00000158156	ENSG00000158156			25508	protein-coding gene	gene with protein product			"""X Kell blood group precursor-related family, member 8"""			12477932	Standard	NM_018053		Approved	FLJ10307	uc001bph.1	Q9H6D3	OTTHUMG00000003912	ENST00000373884.5:c.441G>A	1.37:g.28290155G>A		201.0	0.0	0		128.0	16.0	0.125	NM_018053		Silent	SNP	ENST00000373884.5	37	CCDS315.1																																																																																			G|0.997;A|0.003	0.003	strong		0.627	XKR8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000011175.1	NM_018053	
CD1B	910	hgsc.bcm.edu	37	1	158299358	158299358	+	Missense_Mutation	SNP	A	A	G			TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr1:158299358A>G	ENST00000368168.3	-	4	795	c.688T>C	c.(688-690)Tac>Cac	p.Y230H		NM_001764.2	NP_001755.1	P29016	CD1B_HUMAN	CD1b molecule	230	Ig-like.				antigen processing and presentation (GO:0019882)|immune response (GO:0006955)	cell surface (GO:0009986)|endosome (GO:0005768)|integral component of membrane (GO:0016021)|lysosome (GO:0005764)|plasma membrane (GO:0005886)				breast(2)|large_intestine(2)|lung(17)|ovary(2)|prostate(5)|skin(1)|upper_aerodigestive_tract(1)	30	all_hematologic(112;0.0378)					GGCTTTGGGTAGAATCCTGAG	0.587																																					p.Y230H		Atlas-SNP	.											CD1B,colon,carcinoma,+1,1	CD1B	78	1	0			c.T688C						PASS	.						91.0	87.0	88.0					1																	158299358		2203	4300	6503	SO:0001583	missense	910	exon4			TTGGGTAGAATCC	M28826	CCDS1176.1	1q23.1	2014-01-14	2006-03-28		ENSG00000158485	ENSG00000158485		"""CD molecules"", ""Immunoglobulin superfamily / C1-set domain containing"""	1635	protein-coding gene	gene with protein product		188360	"""CD1B antigen, b polypeptide"", ""CD1b antigen"""	CD1		2447586	Standard	NM_001764		Approved		uc001frx.3	P29016	OTTHUMG00000017513	ENST00000368168.3:c.688T>C	1.37:g.158299358A>G	ENSP00000357150:p.Tyr230His	325.0	0.0	0		396.0	231.0	0.583333	NM_001764	Q5TDK9|Q5TDL0|Q9UMM2	Missense_Mutation	SNP	ENST00000368168.3	37	CCDS1176.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	12.94|12.94	2.086996|2.086996	0.36855|0.36855	.|.	.|.	ENSG00000158485|ENSG00000158485	ENST00000451207|ENST00000368168	.|T	.|0.03920	.|3.76	4.26|4.26	1.9|1.9	0.25705|0.25705	.|Immunoglobulin-like (1);MHC class I-like antigen recognition (1);Immunoglobulin C1-set (2);	.|0.196307	.|0.25509	.|N	.|0.030200	T|T	0.04952|0.04952	0.0133|0.0133	M|M	0.64080|0.64080	1.96|1.96	0.28660|0.28660	N|N	0.9062|0.9062	.|D;P	.|0.54397	.|0.966;0.888	.|P;P	.|0.59546	.|0.859;0.668	T|T	0.22556|0.22556	-1.0213|-1.0213	5|10	.|0.44086	.|T	.|0.13	-8.3888|-8.3888	5.8437|5.8437	0.18647|0.18647	0.7803:0.0:0.2197:0.0|0.7803:0.0:0.2197:0.0	.|.	.|230;230	.|P29016;P29016-2	.|CD1B_HUMAN;.	P|H	197|230	.|ENSP00000357150:Y230H	.|ENSP00000357150:Y230H	L|Y	-|-	2|1	0|0	CD1B|CD1B	156565982|156565982	1.000000|1.000000	0.71417|0.71417	0.997000|0.997000	0.53966|0.53966	0.977000|0.977000	0.68977|0.68977	0.587000|0.587000	0.23909|0.23909	0.280000|0.280000	0.22209|0.22209	0.533000|0.533000	0.62120|0.62120	CTA|TAC	.	.	none		0.587	CD1B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000046350.2	NM_001764	
SLC39A13	91252	hgsc.bcm.edu	37	11	47431764	47431764	+	Missense_Mutation	SNP	G	G	A	rs35741412	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr11:47431764G>A	ENST00000362021.4	+	2	161	c.119G>A	c.(118-120)cGg>cAg	p.R40Q	RP11-750H9.5_ENST00000532943.1_RNA|SLC39A13_ENST00000354884.4_Missense_Mutation_p.R40Q|SLC39A13_ENST00000524928.1_Missense_Mutation_p.R40Q|RP11-750H9.5_ENST00000532340.1_RNA|SLC39A13_ENST00000533076.1_Missense_Mutation_p.R40Q|SLC39A13_ENST00000531974.1_Missense_Mutation_p.R40Q	NM_001128225.2	NP_001121697	Q96H72	S39AD_HUMAN	solute carrier family 39 (zinc transporter), member 13	40					cellular zinc ion homeostasis (GO:0006882)|connective tissue development (GO:0061448)|zinc ion transmembrane transport (GO:0071577)	Golgi apparatus (GO:0005794)|integral component of Golgi membrane (GO:0030173)|integral component of membrane (GO:0016021)|perinuclear region of cytoplasm (GO:0048471)	protein homodimerization activity (GO:0042803)|zinc ion transmembrane transporter activity (GO:0005385)			breast(1)|kidney(1)|lung(1)|prostate(1)	4				Lung(87;0.0936)		CTCCGGAGCCGGGGGACTGCG	0.687													G|||	38	0.00758786	0.0015	0.013	5008	,	,		13659	0.0		0.0258	False		,,,				2504	0.001				p.R40Q		Atlas-SNP	.											.	SLC39A13	18	.	0			c.G119A						PASS	.	G	GLN/ARG,GLN/ARG	15,4387	20.2+/-43.8	0,15,2186	30.0	36.0	34.0		119,119	2.8	0.9	11	dbSNP_126	34	214,8382	84.5+/-147.0	2,210,4086	yes	missense,missense	SLC39A13	NM_001128225.2,NM_152264.4	43,43	2,225,6272	AA,AG,GG		2.4895,0.3408,1.7618	benign,benign	40/372,40/365	47431764	229,12769	2201	4298	6499	SO:0001583	missense	91252	exon2			GGAGCCGGGGGAC		CCDS7934.1, CCDS44592.1	11p11.2	2013-05-22			ENSG00000165915	ENSG00000165915		"""Solute carriers"""	20859	protein-coding gene	gene with protein product		608735	"""solute carrier family 39 (metal ion transporter), member 13"""			12659941	Standard	NM_001128225		Approved	FLJ25785	uc009ylq.3	Q96H72	OTTHUMG00000166890	ENST00000362021.4:c.119G>A	11.37:g.47431764G>A	ENSP00000354689:p.Arg40Gln	131.0	0.0	0		98.0	54.0	0.55102	NM_152264	D3DQR6|D3DQR7|E9PLY1|E9PQV3|Q659D9|Q8N7C9|Q8WV10	Missense_Mutation	SNP	ENST00000362021.4	37	CCDS44592.1	25	0.011446886446886446	2	0.0040650406504065045	6	0.016574585635359115	0	0.0	17	0.022427440633245383	G	12.31	1.899337	0.33535	0.003408	0.024895	ENSG00000165915	ENST00000533076;ENST00000531974;ENST00000531419;ENST00000531865;ENST00000362021;ENST00000354884;ENST00000526614;ENST00000527091;ENST00000524928	T;T;T;T;T;T;T;T;T	0.70869	-0.49;0.97;0.96;-0.52;-0.38;-0.19;-0.03;0.97;0.91	5.05	2.85	0.33270	.	1.028510	0.07690	N	0.938611	T	0.29850	0.0746	N	0.14661	0.345	0.21527	N	0.999657	B;B;B	0.21688	0.019;0.013;0.059	B;B;B	0.13407	0.001;0.003;0.009	T	0.31194	-0.9952	10	0.07813	T	0.8	-1.9191	2.8954	0.05689	0.0997:0.1541:0.5026:0.2436	rs35741412;rs61897433	40;40;40	Q96H72;Q96H72-2;E9PNE7	S39AD_HUMAN;.;.	Q	40	ENSP00000434290:R40Q;ENSP00000435845:R40Q;ENSP00000432302:R40Q;ENSP00000434684:R40Q;ENSP00000354689:R40Q;ENSP00000346956:R40Q;ENSP00000432499:R40Q;ENSP00000435076:R40Q;ENSP00000437186:R40Q	ENSP00000346956:R40Q	R	+	2	0	SLC39A13	47388340	1.000000	0.71417	0.932000	0.37286	0.500000	0.33767	1.734000	0.38166	0.884000	0.36064	0.491000	0.48974	CGG	G|0.984;A|0.016	0.016	strong		0.687	SLC39A13-012	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000395652.1	NM_152264	
KLC4	89953	hgsc.bcm.edu	37	6	43039340	43039340	+	Missense_Mutation	SNP	C	C	T	rs41274918	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr6:43039340C>T	ENST00000394056.2	+	11	1786	c.1291C>T	c.(1291-1293)Cgg>Tgg	p.R431W	KLC4_ENST00000347162.5_Missense_Mutation_p.R431W|KLC4_ENST00000259708.3_Missense_Mutation_p.R449W|KLC4_ENST00000453940.2_Missense_Mutation_p.R354W|KLC4_ENST00000479388.1_Missense_Mutation_p.R431W|RP11-387M24.5_ENST00000606123.1_RNA|KLC4_ENST00000394058.1_Missense_Mutation_p.R431W			Q9NSK0	KLC4_HUMAN	kinesin light chain 4	431						cytoplasm (GO:0005737)|kinesin complex (GO:0005871)|microtubule (GO:0005874)	microtubule motor activity (GO:0003777)	p.R431W(1)		endometrium(2)|large_intestine(7)|lung(5)|ovary(1)|pancreas(1)|skin(3)|urinary_tract(4)	23			all cancers(41;0.00169)|Colorectal(64;0.00245)|COAD - Colon adenocarcinoma(64;0.00536)|OV - Ovarian serous cystadenocarcinoma(102;0.0376)|KIRC - Kidney renal clear cell carcinoma(2;0.0453)			TGCAGAGGAGCGGGAGGAAAT	0.587													C|||	3	0.000599042	0.0	0.0	5008	,	,		17649	0.0		0.002	False		,,,				2504	0.001				p.R449W		Atlas-SNP	.											KLC4,colon,carcinoma,0,1	KLC4	89	1	1	Substitution - Missense(1)	large_intestine(1)	c.C1345T						scavenged	.	C	TRP/ARG,TRP/ARG,TRP/ARG	1,4405	2.1+/-5.4	0,1,2202	59.0	61.0	60.0		1291,1291,1345	5.8	1.0	6	dbSNP_127	60	1,8599	1.2+/-3.3	0,1,4299	yes	missense,missense,missense	KLC4	NM_201521.1,NM_201522.1,NM_201523.1	101,101,101	0,2,6501	TT,TC,CC		0.0116,0.0227,0.0154	probably-damaging,probably-damaging,probably-damaging	431/620,431/620,449/638	43039340	2,13004	2203	4300	6503	SO:0001583	missense	89953	exon10			GAGGAGCGGGAGG	AK055293	CCDS4882.1, CCDS4883.1, CCDS47429.1, CCDS75459.1	6p21.1	2013-01-10	2005-09-13	2005-09-13	ENSG00000137171	ENSG00000137171		"""Tetratricopeptide (TTC) repeat domain containing"""	21624	protein-coding gene	gene with protein product			"""kinesin-like 8"""	KNSL8			Standard	NM_001289034		Approved	bA387M24.3	uc003otw.1	Q9NSK0	OTTHUMG00000014720	ENST00000394056.2:c.1291C>T	6.37:g.43039340C>T	ENSP00000377620:p.Arg431Trp	280.0	2.0	0.00714286		251.0	134.0	0.533865	NM_201523	B3KNY4|B3KPI3|B3KSQ3|B4DME9|Q66K28|Q96EG6	Missense_Mutation	SNP	ENST00000394056.2	37	CCDS4883.1	1	4.578754578754579E-4	0	0.0	0	0.0	0	0.0	1	0.0013192612137203166	C	17.58	3.423957	0.62733	2.27E-4	1.16E-4	ENSG00000137171	ENST00000347162;ENST00000453940;ENST00000259708;ENST00000479388;ENST00000394056;ENST00000394058	T;T;T;T;T;T	0.80824	-1.4;-1.38;-1.42;-1.4;-1.4;-1.4	5.83	5.83	0.93111	.	0.000000	0.56097	D	0.000022	D	0.88381	0.6421	M	0.85859	2.78	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.91635	0.937;0.999;0.998	D	0.87053	0.2148	10	0.36615	T	0.2	-22.2004	14.7934	0.69860	0.1783:0.8217:0.0:0.0	rs41274918	354;449;431	B4DME9;Q9NSK0-3;Q9NSK0	.;.;KLC4_HUMAN	W	431;354;449;431;431;431	ENSP00000340221:R431W;ENSP00000395806:R354W;ENSP00000259708:R449W;ENSP00000418031:R431W;ENSP00000377620:R431W;ENSP00000377622:R431W	ENSP00000259708:R449W	R	+	1	2	KLC4	43147318	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	1.659000	0.37387	2.765000	0.95021	0.555000	0.69702	CGG	C|0.999;T|0.001	0.001	strong		0.587	KLC4-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040579.2	NM_138343	
BAI2	576	hgsc.bcm.edu	37	1	32196453	32196453	+	Missense_Mutation	SNP	C	C	T			TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr1:32196453C>T	ENST00000373658.3	-	29	4669	c.4328G>A	c.(4327-4329)cGg>cAg	p.R1443Q	BAI2_ENST00000398556.3_Missense_Mutation_p.R1358Q|BAI2_ENST00000398547.1_Missense_Mutation_p.R1376Q|BAI2_ENST00000398538.1_Missense_Mutation_p.R1431Q|BAI2_ENST00000398542.1_Missense_Mutation_p.R1343Q|BAI2_ENST00000257070.4_Missense_Mutation_p.R1410Q|BAI2_ENST00000465256.1_5'UTR|BAI2_ENST00000440175.2_Missense_Mutation_p.R1052Q|BAI2_ENST00000373655.2_Missense_Mutation_p.R1443Q|BAI2_ENST00000527361.1_Missense_Mutation_p.R1410Q	NM_001703.2	NP_001694.2	O60241	BAI2_HUMAN	brain-specific angiogenesis inhibitor 2	1443					G-protein coupled receptor signaling pathway (GO:0007186)|negative regulation of angiogenesis (GO:0016525)|neuropeptide signaling pathway (GO:0007218)|peripheral nervous system development (GO:0007422)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)	p.R1443Q(1)		breast(5)|central_nervous_system(2)|endometrium(1)|large_intestine(7)|liver(2)|lung(24)|ovary(7)|pancreas(2)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)	55		Myeloproliferative disorder(586;0.0255)|Ovarian(437;0.0606)|all_neural(195;0.0837)|Breast(348;0.174)		STAD - Stomach adenocarcinoma(196;0.0557)		AGGCATGGTCCGGCTGCGCTC	0.632																																					p.R1443Q		Atlas-SNP	.											BAI2,colon,carcinoma,0,1	BAI2	128	1	1	Substitution - Missense(1)	large_intestine(1)	c.G4328A						PASS	.						40.0	51.0	47.0					1																	32196453		2202	4299	6501	SO:0001583	missense	576	exon29			ATGGTCCGGCTGC	AB005298	CCDS72746.1, CCDS72747.1	1p35	2014-08-08			ENSG00000121753	ENSG00000121753		"""-"", ""GPCR / Class B : Orphans"""	944	protein-coding gene	gene with protein product		602683				9533023	Standard	XM_006710783		Approved		uc001btn.3	O60241	OTTHUMG00000003885	ENST00000373658.3:c.4328G>A	1.37:g.32196453C>T	ENSP00000362762:p.Arg1443Gln	85.0	0.0	0		39.0	4.0	0.102564	NM_001703	B9EGK9|Q5T6K0|Q8NGW8|Q96GZ9	Missense_Mutation	SNP	ENST00000373658.3	37	CCDS346.2	.	.	.	.	.	.	.	.	.	.	C	26.3	4.729029	0.89390	.	.	ENSG00000121753	ENST00000398556;ENST00000398547;ENST00000373658;ENST00000373655;ENST00000398542;ENST00000257070;ENST00000527361;ENST00000440175;ENST00000398538	T;T;T;T;T;T;T;T;T	0.47528	1.52;1.76;0.92;0.92;1.89;0.84;0.84;1.55;0.95	5.74	5.74	0.90152	.	0.000000	0.39274	N	0.001419	T	0.61763	0.2373	L	0.48642	1.525	0.51767	D	0.999934	D;D;D;D;D;D;D	0.89917	0.996;0.996;0.999;1.0;0.996;0.994;1.0	P;P;P;D;P;P;D	0.63957	0.883;0.77;0.743;0.92;0.883;0.594;0.92	T	0.52902	-0.8513	10	0.31617	T	0.26	.	19.9066	0.97010	0.0:1.0:0.0:0.0	.	1410;1431;1052;1358;1443;1443;1431	O60241-4;O60241-3;B4DKC3;A2A3C6;O60241-2;O60241;A2A3C2	.;.;.;.;.;BAI2_HUMAN;.	Q	1358;1376;1443;1443;1343;1410;1410;1052;1431	ENSP00000381564:R1358Q;ENSP00000381555:R1376Q;ENSP00000362762:R1443Q;ENSP00000362759:R1443Q;ENSP00000381550:R1343Q;ENSP00000257070:R1410Q;ENSP00000435397:R1410Q;ENSP00000391071:R1052Q;ENSP00000381548:R1431Q	ENSP00000257070:R1410Q	R	-	2	0	BAI2	31969040	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	4.447000	0.60020	2.884000	0.98904	0.655000	0.94253	CGG	.	.	none		0.632	BAI2-015	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000381838.1	NM_001703	
PDE6A	5145	hgsc.bcm.edu	37	5	149265875	149265875	+	Silent	SNP	G	G	A	rs61733360	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr5:149265875G>A	ENST00000255266.5	-	14	1910	c.1791C>T	c.(1789-1791)ttC>ttT	p.F597F		NM_000440.2	NP_000431.2	P16499	PDE6A_HUMAN	phosphodiesterase 6A, cGMP-specific, rod, alpha	597					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)	p.F597F(1)		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)	TGTCATGGCAGAAAGCAGCAG	0.527													G|||	133	0.0265575	0.003	0.0749	5008	,	,		20466	0.0119		0.0308	False		,,,				2504	0.0348				p.F597F		Atlas-SNP	.											PDE6A,NS,carcinoma,0,1	PDE6A	98	1	1	Substitution - coding silent(1)	stomach(1)	c.C1791T						PASS	.	G		37,4369	43.1+/-76.7	0,37,2166	155.0	130.0	138.0		1791	5.7	1.0	5	dbSNP_129	138	325,8275	114.6+/-174.5	8,309,3983	no	coding-synonymous	PDE6A	NM_000440.2		8,346,6149	AA,AG,GG		3.7791,0.8398,2.7833		597/861	149265875	362,12644	2203	4300	6503	SO:0001819	synonymous_variant	5145	exon14			ATGGCAGAAAGCA		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.1791C>T	5.37:g.149265875G>A		159.0	0.0	0		163.0	79.0	0.484663	NM_000440	Q0P638	Silent	SNP	ENST00000255266.5	37	CCDS4299.1																																																																																			G|0.969;A|0.031	0.031	strong		0.527	PDE6A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252326.2		
HNRNPL	3191	hgsc.bcm.edu	37	19	39331198	39331198	+	Splice_Site	SNP	A	A	T			TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr19:39331198A>T	ENST00000221419.5	-	7	1248	c.882T>A	c.(880-882)ggT>ggA	p.G294G	AC104534.3_ENST00000594769.1_5'Flank|HNRNPL_ENST00000600873.1_Splice_Site_p.G161G	NM_001533.2	NP_001524.2	P14866	HNRPL_HUMAN	heterogeneous nuclear ribonucleoprotein L	294					gene expression (GO:0010467)|mRNA splicing, via spliceosome (GO:0000398)|RNA processing (GO:0006396)|RNA splicing (GO:0008380)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|pronucleus (GO:0045120)|ribonucleoprotein complex (GO:0030529)	nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)|transcription regulatory region DNA binding (GO:0044212)			NS(1)|breast(1)|central_nervous_system(2)|endometrium(4)|large_intestine(10)|lung(9)|ovary(1)|prostate(1)|urinary_tract(1)	30	all_cancers(60;6.83e-06)|Ovarian(47;0.0454)		Lung(45;0.00342)|LUSC - Lung squamous cell carcinoma(53;0.00575)			TGCCAGGGTCACCTGTGGAGA	0.602																																					p.G294G		Atlas-SNP	.											.	HNRNPL	67	.	0			c.T882A						PASS	.						27.0	27.0	27.0					19																	39331198		2199	4299	6498	SO:0001630	splice_region_variant	3191	exon7			AGGGTCACCTGTG	X16135	CCDS33015.1, CCDS33016.1	19q13.2	2013-06-12		2007-08-16	ENSG00000104824	ENSG00000104824		"""RNA binding motif (RRM) containing"""	5045	protein-coding gene	gene with protein product		603083		HNRPL		2687284	Standard	NM_001533		Approved		uc021uuh.1	P14866	OTTHUMG00000182612	ENST00000221419.5:c.881-1T>A	19.37:g.39331198A>T		94.0	0.0	0		90.0	30.0	0.333333	NM_001533	A6ND69|A6NIT8|Q9H3P3	Silent	SNP	ENST00000221419.5	37	CCDS33015.1																																																																																			.	.	none		0.602	HNRNPL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000462670.1		Silent
ATXN2	6311	hgsc.bcm.edu	37	12	111907956	111907956	+	Nonsense_Mutation	SNP	G	G	C			TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr12:111907956G>C	ENST00000377617.3	-	20	3433	c.3272C>G	c.(3271-3273)tCa>tGa	p.S1091*	ATXN2_ENST00000608853.1_Nonsense_Mutation_p.S931*|ATXN2_ENST00000550104.1_3'UTR|ATXN2_ENST00000389153.4_Nonsense_Mutation_p.S828*|ATXN2_ENST00000542287.2_Nonsense_Mutation_p.S826*|ATXN2_ENST00000535949.1_Nonsense_Mutation_p.S802*	NM_002973.3	NP_002964.3	Q99700	ATX2_HUMAN	ataxin 2	1091					cell death (GO:0008219)|cerebellar Purkinje cell differentiation (GO:0021702)|cytoplasmic mRNA processing body assembly (GO:0033962)|homeostasis of number of cells (GO:0048872)|negative regulation of multicellular organism growth (GO:0040015)|negative regulation of receptor internalization (GO:0002091)|neuromuscular process (GO:0050905)|neuron projection morphogenesis (GO:0048812)|regulation of translation (GO:0006417)|RNA metabolic process (GO:0016070)|RNA transport (GO:0050658)|stress granule assembly (GO:0034063)	cytoplasm (GO:0005737)|cytoplasmic stress granule (GO:0010494)|Golgi apparatus (GO:0005794)|membrane (GO:0016020)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|polysome (GO:0005844)|ribonucleoprotein complex (GO:0030529)|trans-Golgi network (GO:0005802)	epidermal growth factor receptor binding (GO:0005154)|poly(A) RNA binding (GO:0044822)|protein C-terminus binding (GO:0008022)|RNA binding (GO:0003723)			NS(1)|breast(2)|central_nervous_system(2)|cervix(1)|endometrium(6)|kidney(5)|large_intestine(8)|lung(6)|ovary(1)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)	37						CTGAGTTGCTGAAGAAGATAC	0.453																																					p.S1091X		Atlas-SNP	.											.	ATXN2	99	.	0			c.C3272G						PASS	.						218.0	172.0	188.0					12																	111907956		2203	4300	6503	SO:0001587	stop_gained	6311	exon20			GTTGCTGAAGAAG	U80749	CCDS31902.1	12q23-q24.1	2014-09-17	2004-08-12	2004-08-13	ENSG00000204842	ENSG00000204842		"""Ataxins"""	10555	protein-coding gene	gene with protein product	"""trinucleotide repeat containing 13"""	601517	"""spinocerebellar ataxia 2 (olivopontocerebellar ataxia 2, autosomal dominant, ataxin 2)"""	SCA2, TNRC13		8358438, 9225980	Standard	NM_002973		Approved	ATX2	uc001tsj.3	Q99700	OTTHUMG00000133475	ENST00000377617.3:c.3272C>G	12.37:g.111907956G>C	ENSP00000366843:p.Ser1091*	183.0	0.0	0		174.0	54.0	0.310345	NM_002973	A6NLD4|Q6ZQZ7|Q99493	Nonsense_Mutation	SNP	ENST00000377617.3	37	CCDS31902.1	.	.	.	.	.	.	.	.	.	.	G	41	8.647790	0.98899	.	.	ENSG00000204842	ENST00000389154;ENST00000389153;ENST00000377617;ENST00000482777;ENST00000542287;ENST00000535949;ENST00000550844	.	.	.	5.46	5.46	0.80206	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.39692	T	0.17	-12.4094	19.6783	0.95946	0.0:0.0:1.0:0.0	.	.	.	.	X	146;828;1091;110;826;802;16	.	ENSP00000366843:S1091X	S	-	2	0	ATXN2	110392339	1.000000	0.71417	0.973000	0.42090	0.782000	0.44232	9.301000	0.96167	2.724000	0.93272	0.585000	0.79938	TCA	.	.	none		0.453	ATXN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257351.3	NM_002973	
DNAJC13	23317	hgsc.bcm.edu	37	3	132241682	132241682	+	Missense_Mutation	SNP	C	C	T	rs145242123	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr3:132241682C>T	ENST00000260818.6	+	49	5932	c.5684C>T	c.(5683-5685)aCg>aTg	p.T1895M		NM_015268.3	NP_056083.3	O75165	DJC13_HUMAN	DnaJ (Hsp40) homolog, subfamily C, member 13	1895					osteoblast differentiation (GO:0001649)	extracellular vesicular exosome (GO:0070062)|lysosomal membrane (GO:0005765)|membrane (GO:0016020)				breast(4)|endometrium(2)|kidney(2)|large_intestine(5)|lung(15)|ovary(1)|pancreas(2)|prostate(2)|urinary_tract(1)	34						GTTCGAATTACGTTAATGAAA	0.333													C|||	3	0.000599042	0.0	0.0029	5008	,	,		18811	0.0		0.001	False		,,,				2504	0.0				p.T1895M		Atlas-SNP	.											.	DNAJC13	253	.	0			c.C5684T						PASS	.	C	MET/THR	1,4405	2.1+/-5.4	0,1,2202	51.0	51.0	51.0		5684	5.2	1.0	3	dbSNP_134	51	12,8588	8.4+/-32.0	0,12,4288	yes	missense	DNAJC13	NM_015268.3	81	0,13,6490	TT,TC,CC		0.1395,0.0227,0.1	benign	1895/2244	132241682	13,12993	2203	4300	6503	SO:0001583	missense	23317	exon49			GAATTACGTTAAT	AB014578	CCDS33857.1	3q22.1	2011-09-02			ENSG00000138246	ENSG00000138246		"""Heat shock proteins / DNAJ (HSP40)"""	30343	protein-coding gene	gene with protein product		614334				12438707	Standard	NM_015268		Approved	RME8, KIAA0678	uc003eor.3	O75165	OTTHUMG00000159674	ENST00000260818.6:c.5684C>T	3.37:g.132241682C>T	ENSP00000260818:p.Thr1895Met	138.0	0.0	0		125.0	70.0	0.56	NM_015268	Q3L0T1|Q6PI82|Q6UJ77|Q6ZSW1|Q6ZUT5|Q86XG3|Q96DC1|Q9BWK9	Missense_Mutation	SNP	ENST00000260818.6	37	CCDS33857.1	2	9.157509157509158E-4	0	0.0	1	0.0027624309392265192	0	0.0	1	0.0013192612137203166	C	8.466	0.856381	0.17106	2.27E-4	0.001395	ENSG00000138246	ENST00000260818;ENST00000538066	T	0.49720	0.77	6.08	5.2	0.72013	Armadillo-like helical (1);Armadillo-type fold (1);	0.122360	0.56097	N	0.000036	T	0.42720	0.1215	L	0.58810	1.83	0.31740	N	0.635937	B	0.13145	0.007	B	0.06405	0.002	T	0.47156	-0.9139	10	0.33940	T	0.23	.	9.9625	0.41704	0.0:0.7534:0.0:0.2466	.	1895	O75165	DJC13_HUMAN	M	1895;542	ENSP00000260818:T1895M	ENSP00000260818:T1895M	T	+	2	0	DNAJC13	133724372	0.797000	0.28877	0.995000	0.50966	0.605000	0.37080	1.532000	0.36029	0.919000	0.36945	-0.797000	0.03246	ACG	C|0.998;T|0.002	0.002	strong		0.333	DNAJC13-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000356807.2	NM_015268	
FLT3	2322	hgsc.bcm.edu	37	13	28623525	28623525	+	Silent	SNP	G	G	A	rs146983744	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr13:28623525G>A	ENST00000241453.7	-	8	1113	c.1032C>T	c.(1030-1032)atC>atT	p.I344I	FLT3_ENST00000537084.1_Silent_p.I344I|FLT3_ENST00000380982.4_Silent_p.I344I	NM_004119.2	NP_004110.2	P36888	FLT3_HUMAN	fms-related tyrosine kinase 3	344					B cell differentiation (GO:0030183)|cellular response to cytokine stimulus (GO:0071345)|common myeloid progenitor cell proliferation (GO:0035726)|cytokine-mediated signaling pathway (GO:0019221)|dendritic cell differentiation (GO:0097028)|hemopoiesis (GO:0030097)|leukocyte homeostasis (GO:0001776)|lymphocyte proliferation (GO:0046651)|myeloid progenitor cell differentiation (GO:0002318)|negative regulation of B cell differentiation (GO:0045578)|negative regulation of cell proliferation (GO:0008285)|peptidyl-tyrosine phosphorylation (GO:0018108)|positive regulation of cell proliferation (GO:0008284)|positive regulation of MAP kinase activity (GO:0043406)|positive regulation of MAPK cascade (GO:0043410)|positive regulation of phosphatidylinositol 3-kinase activity (GO:0043552)|positive regulation of phosphatidylinositol 3-kinase signaling (GO:0014068)|positive regulation of tyrosine phosphorylation of STAT protein (GO:0042531)|pro-B cell differentiation (GO:0002328)|pro-T cell differentiation (GO:0002572)|protein autophosphorylation (GO:0046777)|regulation of apoptotic process (GO:0042981)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)|vascular endothelial growth factor signaling pathway (GO:0038084)	endoplasmic reticulum (GO:0005783)|external side of plasma membrane (GO:0009897)|integral component of plasma membrane (GO:0005887)	ATP binding (GO:0005524)|cytokine receptor activity (GO:0004896)|protein homodimerization activity (GO:0042803)|transmembrane receptor protein tyrosine kinase activity (GO:0004714)|vascular endothelial growth factor-activated receptor activity (GO:0005021)			NS(1)|breast(3)|central_nervous_system(2)|endometrium(1)|haematopoietic_and_lymphoid_tissue(12329)|kidney(2)|large_intestine(8)|lung(30)|ovary(4)|prostate(1)|skin(5)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	12390	Acute lymphoblastic leukemia(6;0.04)	Lung SC(185;0.0156)|Ovarian(182;0.0392)	Colorectal(13;0.000157)|READ - Rectum adenocarcinoma(15;0.105)	OV - Ovarian serous cystadenocarcinoma(117;0.00154)|all cancers(112;0.00459)|GBM - Glioblastoma multiforme(144;0.00562)|Epithelial(112;0.0959)|Lung(94;0.212)	Ponatinib(DB08901)|Sorafenib(DB00398)|Sunitinib(DB01268)	CATTACCTACGATGGTAACCA	0.398			"""Mis, O"""		"""AML, ALL"""																																p.I344I		Atlas-SNP	.		Dom	yes		13	13q12	2322	fms-related tyrosine kinase 3		L	.	FLT3	15525	.	0			c.C1032T						PASS	.	G		1,4405	2.1+/-5.4	0,1,2202	245.0	216.0	226.0		1032	3.8	1.0	13	dbSNP_134	226	6,8594	5.0+/-18.6	0,6,4294	no	coding-synonymous	FLT3	NM_004119.2		0,7,6496	AA,AG,GG		0.0698,0.0227,0.0538		344/994	28623525	7,12999	2203	4300	6503	SO:0001819	synonymous_variant	2322	exon8			ACCTACGATGGTA	U02687	CCDS31953.1	13q12	2014-09-17			ENSG00000122025	ENSG00000122025	2.7.10.1	"""CD molecules"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	3765	protein-coding gene	gene with protein product		136351				8394751	Standard	NM_004119		Approved	STK1, FLK2, CD135	uc001urw.3	P36888	OTTHUMG00000016646	ENST00000241453.7:c.1032C>T	13.37:g.28623525G>A		145.0	0.0	0		133.0	74.0	0.556391	NM_004119	A0AVG9|B7ZLT7|B7ZLT8|F5H0A0|Q13414	Silent	SNP	ENST00000241453.7	37	CCDS31953.1																																																																																			G|0.999;A|0.001	0.001	strong		0.398	FLT3-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000044319.2		
NPC1	4864	hgsc.bcm.edu	37	18	21123523	21123523	+	Missense_Mutation	SNP	C	C	T	rs375047023		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr18:21123523C>T	ENST00000269228.5	-	14	2695	c.2141G>A	c.(2140-2142)cGt>cAt	p.R714H	NPC1_ENST00000540608.1_5'UTR|NPC1_ENST00000412552.2_Missense_Mutation_p.R396H	NM_000271.4	NP_000262.2	O15118	NPC1_HUMAN	Niemann-Pick disease, type C1	714	SSD. {ECO:0000255|PROSITE- ProRule:PRU00199}.				adult walking behavior (GO:0007628)|autophagy (GO:0006914)|bile acid metabolic process (GO:0008206)|cellular response to low-density lipoprotein particle stimulus (GO:0071404)|cellular response to steroid hormone stimulus (GO:0071383)|cholesterol efflux (GO:0033344)|cholesterol homeostasis (GO:0042632)|cholesterol metabolic process (GO:0008203)|cholesterol transport (GO:0030301)|endocytosis (GO:0006897)|establishment of protein localization to membrane (GO:0090150)|lysosomal transport (GO:0007041)|membrane raft organization (GO:0031579)|negative regulation of cell death (GO:0060548)|negative regulation of macroautophagy (GO:0016242)|protein glycosylation (GO:0006486)|response to cadmium ion (GO:0046686)|response to drug (GO:0042493)|signal transduction (GO:0007165)	endoplasmic reticulum (GO:0005783)|endosome (GO:0005768)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|lysosomal membrane (GO:0005765)|lysosome (GO:0005764)|membrane (GO:0016020)|membrane raft (GO:0045121)|nuclear envelope (GO:0005635)|perinuclear region of cytoplasm (GO:0048471)	cholesterol binding (GO:0015485)|hedgehog receptor activity (GO:0008158)|receptor activity (GO:0004872)|sterol transporter activity (GO:0015248)|transmembrane signaling receptor activity (GO:0004888)			breast(1)|cervix(1)|endometrium(4)|kidney(6)|large_intestine(10)|lung(13)|ovary(2)|stomach(1)	38	all_cancers(21;0.000106)|all_epithelial(16;6.57e-07)|Lung NSC(20;0.00166)|all_lung(20;0.00536)|Colorectal(14;0.0202)|Ovarian(20;0.127)					CCCTTGAAGACGTTCATCTCT	0.403																																					p.R714H		Atlas-SNP	.											.	NPC1	114	.	0			c.G2141A						PASS	.	C	HIS/ARG	1,4405	2.1+/-5.4	0,1,2202	64.0	66.0	65.0		2141	4.9	1.0	18		65	1,8599	1.2+/-3.3	0,1,4299	no	missense	NPC1	NM_000271.4	29	0,2,6501	TT,TC,CC		0.0116,0.0227,0.0154	probably-damaging	714/1279	21123523	2,13004	2203	4300	6503	SO:0001583	missense	4864	exon14			TGAAGACGTTCAT	AF002020	CCDS11878.1	18q11.2	2014-06-17			ENSG00000141458	ENSG00000141458			7897	protein-coding gene	gene with protein product		607623				8446622	Standard	NM_000271		Approved		uc002kum.4	O15118	OTTHUMG00000131873	ENST00000269228.5:c.2141G>A	18.37:g.21123523C>T	ENSP00000269228:p.Arg714His	21.0	0.0	0		15.0	9.0	0.6	NM_000271	B4DET3|Q9P130	Missense_Mutation	SNP	ENST00000269228.5	37	CCDS11878.1	.	.	.	.	.	.	.	.	.	.	C	26.2	4.719159	0.89205	2.27E-4	1.16E-4	ENSG00000141458	ENST00000269228;ENST00000412552;ENST00000540608	D;D	0.95949	-3.86;-3.86	5.79	4.93	0.64822	Sterol-sensing domain (1);	0.000000	0.85682	D	0.000000	D	0.95918	0.8671	L	0.60067	1.865	0.80722	D	1	D;D	0.61697	0.99;0.99	P;P	0.54889	0.679;0.763	D	0.95741	0.8783	10	0.56958	D	0.05	-14.1977	14.8323	0.70156	0.0:0.9311:0.0:0.0689	.	725;714	Q59GR1;O15118	.;NPC1_HUMAN	H	714;396;559	ENSP00000269228:R714H;ENSP00000408606:R396H	ENSP00000269228:R714H	R	-	2	0	NPC1	19377521	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	7.448000	0.80631	1.472000	0.48140	-0.142000	0.14014	CGT	.	.	weak		0.403	NPC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254823.2	NM_000271	
PIP5K1C	23396	hgsc.bcm.edu	37	19	3633473	3633473	+	Missense_Mutation	SNP	C	C	T	rs35014191	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr19:3633473C>T	ENST00000335312.3	-	17	2054	c.1966G>A	c.(1966-1968)Gcc>Acc	p.A656T	PIP5K1C_ENST00000539785.1_Intron	NM_001195733.1|NM_012398.2	NP_001182662.1|NP_036530.1	O60331	PI51C_HUMAN	phosphatidylinositol-4-phosphate 5-kinase, type I, gamma	656	Mediates interaction with TLN2.				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)		GGGGCCTGGGCGCTATAGTGG	0.701													C|||	34	0.00678914	0.0129	0.0058	5008	,	,		11951	0.0		0.006	False		,,,				2504	0.0072				p.A656T	Esophageal Squamous(135;99 1744 12852 27186 39851)	Atlas-SNP	.											PIP5K1C_ENST00000335312,NS,carcinoma,+1,1	PIP5K1C	63	1	0			c.G1966A						PASS	.	C	,THR/ALA	21,4373		0,21,2176	17.0	22.0	20.0		,1966	-6.2	0.2	19	dbSNP_126	20	101,8487		0,101,4193	no	intron,missense	PIP5K1C	NM_001195733.1,NM_012398.2	,58	0,122,6369	TT,TC,CC		1.1761,0.4779,0.9398	,benign	,656/669	3633473	122,12860	2197	4294	6491	SO:0001583	missense	23396	exon17			CCTGGGCGCTATA	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.1966G>A	19.37:g.3633473C>T	ENSP00000335333:p.Ala656Thr	111.0	0.0	0		95.0	53.0	0.557895	NM_012398	B7Z9E7|C6GIJ7|C6GIJ8|Q7LE07	Missense_Mutation	SNP	ENST00000335312.3	37	CCDS32872.1	12	0.005494505494505495	7	0.014227642276422764	1	0.0027624309392265192	0	0.0	4	0.005277044854881266	C	6.504	0.461201	0.12342	0.004779	0.011761	ENSG00000186111	ENST00000335312	T	0.25912	1.77	3.39	-6.18	0.02085	.	0.500976	0.17660	N	0.166351	T	0.05227	0.0139	N	0.03608	-0.345	0.58432	D	0.999999	B	0.02656	0.0	B	0.01281	0.0	T	0.37979	-0.9682	10	0.07813	T	0.8	-8.2929	12.3675	0.55236	0.0:0.2685:0.0:0.7315	rs35014191	656	O60331	PI51C_HUMAN	T	656	ENSP00000335333:A656T	ENSP00000335333:A656T	A	-	1	0	PIP5K1C	3584473	0.551000	0.26497	0.185000	0.23176	0.746000	0.42486	-0.496000	0.06436	-1.205000	0.02645	-0.657000	0.03884	GCC	C|0.992;T|0.008	0.008	strong		0.701	PIP5K1C-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000453432.2	NM_012398	
MUC17	140453	hgsc.bcm.edu	37	7	100677355	100677355	+	Silent	SNP	A	A	C			TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr7:100677355A>C	ENST00000306151.4	+	3	2722	c.2658A>C	c.(2656-2658)tcA>tcC	p.S886S		NM_001040105.1	NP_001035194.1	Q685J3	MUC17_HUMAN	mucin 17, cell surface associated	886	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)					GCACCCTTTCAACAACTCCTG	0.498																																					p.S886S		Atlas-SNP	.											.	MUC17	804	.	0			c.A2658C						PASS	.						292.0	289.0	290.0					7																	100677355		2203	4300	6503	SO:0001819	synonymous_variant	140453	exon3			CCTTTCAACAACT	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.2658A>C	7.37:g.100677355A>C		162.0	0.0	0		302.0	23.0	0.0761589	NM_001040105	O14761|Q685J2|Q8TDH7	Silent	SNP	ENST00000306151.4	37	CCDS34711.1																																																																																			.	.	none		0.498	MUC17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347161.1	NM_001040105	
PNKP	11284	hgsc.bcm.edu	37	19	50364914	50364914	+	Missense_Mutation	SNP	C	C	T			TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr19:50364914C>T	ENST00000322344.3	-	15	1446	c.1337G>A	c.(1336-1338)cGc>cAc	p.R446H	PNKP_ENST00000600573.1_Missense_Mutation_p.R415H|AC018766.5_ENST00000601893.1_RNA|PNKP_ENST00000596014.1_Missense_Mutation_p.R446H|AC018766.5_ENST00000599259.1_RNA|PNKP_ENST00000600910.1_Silent_p.P409P|AC018766.5_ENST00000593654.1_RNA|AC018766.4_ENST00000596624.1_RNA	NM_007254.3	NP_009185.2	Q96T60	PNKP_HUMAN	polynucleotide kinase 3'-phosphatase	446	Kinase. {ECO:0000250}.				dephosphorylation (GO:0016311)|DNA damage response, detection of DNA damage (GO:0042769)|DNA repair (GO:0006281)|DNA-dependent DNA replication (GO:0006261)|nucleic acid phosphodiester bond hydrolysis (GO:0090305)|nucleotide phosphorylation (GO:0046939)|nucleotide-excision repair, DNA damage removal (GO:0000718)|polynucleotide 3' dephosphorylation (GO:0098506)|response to oxidative stress (GO:0006979)|response to radiation (GO:0009314)	membrane (GO:0016020)|nucleolus (GO:0005730)|nucleus (GO:0005634)	ATP binding (GO:0005524)|ATP-dependent polydeoxyribonucleotide 5'-hydroxyl-kinase activity (GO:0046404)|damaged DNA binding (GO:0003684)|double-stranded DNA binding (GO:0003690)|endonuclease activity (GO:0004519)|nucleotide kinase activity (GO:0019201)|polynucleotide 3'-phosphatase activity (GO:0046403)|purine nucleotide binding (GO:0017076)			breast(1)|cervix(1)|endometrium(2)|kidney(2)|large_intestine(1)|lung(10)|ovary(1)|urinary_tract(1)	19		all_lung(116;1.05e-05)|Lung NSC(112;3.77e-05)|all_neural(266;0.107)|Ovarian(192;0.231)		GBM - Glioblastoma multiforme(134;0.0118)|OV - Ovarian serous cystadenocarcinoma(262;0.0134)		GAGGAAGCAGCGGCAGGGGAC	0.741								Other BER factors																													p.R446H		Atlas-SNP	.											.	PNKP	71	.	0			c.G1337A						PASS	.						4.0	8.0	7.0					19																	50364914		1965	3897	5862	SO:0001583	missense	11284	exon15			AAGCAGCGGCAGG	AF126486	CCDS12783.1	19q13.3-q13.4	2008-02-05				ENSG00000039650			9154	protein-coding gene	gene with protein product		605610				10446192, 10446193	Standard	NM_007254		Approved	PNK	uc002pqj.3	Q96T60		ENST00000322344.3:c.1337G>A	19.37:g.50364914C>T	ENSP00000323511:p.Arg446His	25.0	0.0	0		24.0	4.0	0.166667	NM_007254	Q9BUL2|Q9P1V2|Q9UKU8|Q9UNF8|Q9UNI0	Missense_Mutation	SNP	ENST00000322344.3	37	CCDS12783.1	.	.	.	.	.	.	.	.	.	.	C	28.0	4.885414	0.91814	.	.	ENSG00000039650	ENST00000322344	T	0.48201	0.82	3.96	3.96	0.45880	.	0.000000	0.64402	D	0.000003	T	0.66626	0.2808	M	0.77313	2.365	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;1.0	T	0.69435	-0.5146	10	0.54805	T	0.06	-17.9148	11.6883	0.51499	0.0:1.0:0.0:0.0	.	407;446	Q9BUL2;Q96T60	.;PNKP_HUMAN	H	446	ENSP00000323511:R446H	ENSP00000323511:R446H	R	-	2	0	PNKP	55056726	1.000000	0.71417	1.000000	0.80357	0.916000	0.54674	3.989000	0.56958	2.226000	0.72624	0.557000	0.71058	CGC	.	.	none		0.741	PNKP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000465830.1	NM_007254	
CHAT	1103	hgsc.bcm.edu	37	10	50854637	50854637	+	Missense_Mutation	SNP	G	G	A	rs8178991	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr10:50854637G>A	ENST00000337653.2	+	8	1351	c.1198G>A	c.(1198-1200)Gac>Aac	p.D400N	CHAT_ENST00000351556.3_Missense_Mutation_p.D282N|CHAT_ENST00000455728.2_Missense_Mutation_p.D282N|CHAT_ENST00000395559.2_Missense_Mutation_p.D282N|CHAT_ENST00000339797.1_Missense_Mutation_p.D282N|CHAT_ENST00000395562.2_Missense_Mutation_p.D318N	NM_001142929.1|NM_020549.4	NP_001136401.1|NP_065574	P28329	CLAT_HUMAN	choline O-acetyltransferase	400			D -> N (in dbSNP:rs8178991).		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)	GGAGCTCAGCGACACCCACAG	0.637													G|||	30	0.00599042	0.0015	0.0101	5008	,	,		20906	0.0		0.0199	False		,,,				2504	0.001				p.D400N		Atlas-SNP	.											.	CHAT	162	.	0			c.G1198A						PASS	.	G	ASN/ASP,ASN/ASP,ASN/ASP,ASN/ASP,ASN/ASP,ASN/ASP,ASN/ASP	21,4385	29.0+/-57.7	0,21,2182	92.0	81.0	84.0		844,952,844,1198,844,844,844	4.3	0.9	10	dbSNP_117	84	189,8411	85.0+/-147.5	4,181,4115	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	23,23,23,23,23,23,23	4,202,6297	AA,AG,GG		2.1977,0.4766,1.6146	benign,benign,benign,benign,benign,benign,benign	282/631,318/667,282/631,400/749,282/631,282/631,282/631	50854637	210,12796	2203	4300	6503	SO:0001583	missense	1103	exon8			CTCAGCGACACCC	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.1198G>A	10.37:g.50854637G>A	ENSP00000337103:p.Asp400Asn	141.0	0.0	0		104.0	104.0	1	NM_020549	A2BDF4|A2BDF5|Q16488|Q9BQ23|Q9BQ35|Q9BQE1	Missense_Mutation	SNP	ENST00000337653.2	37	CCDS7232.1	19	0.0086996336996337	1	0.0020325203252032522	3	0.008287292817679558	0	0.0	15	0.01978891820580475	G	19.11	3.763636	0.69878	0.004766	0.021977	ENSG00000070748	ENST00000339797;ENST00000351556;ENST00000395559;ENST00000337653;ENST00000395562;ENST00000455728	T;T;T;T;T;T	0.81415	-1.49;-1.49;-1.49;-1.49;-1.49;-1.49	5.27	4.34	0.51931	.	0.099000	0.64402	D	0.000003	T	0.72277	0.3440	M	0.78223	2.4	0.58432	D	0.999996	B;D	0.56968	0.339;0.978	B;P	0.48524	0.096;0.58	T	0.78738	-0.2087	10	0.51188	T	0.08	-24.4513	10.8728	0.46894	0.0727:0.1312:0.7961:0.0	rs8178991	282;400	F8W8I2;P28329	.;CLAT_HUMAN	N	282;282;282;400;318;282	ENSP00000343486:D282N;ENSP00000345878:D282N;ENSP00000378926:D282N;ENSP00000337103:D400N;ENSP00000378929:D318N;ENSP00000390521:D282N	ENSP00000337103:D400N	D	+	1	0	CHAT	50524643	1.000000	0.71417	0.898000	0.35279	0.926000	0.56050	4.110000	0.57831	1.162000	0.42619	0.655000	0.94253	GAC	G|0.986;A|0.014	0.014	strong		0.637	CHAT-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000047997.1	NM_020549	
KRTAP19-6	337973	hgsc.bcm.edu	37	21	31914019	31914019	+	Missense_Mutation	SNP	C	C	T	rs77807247	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr21:31914019C>T	ENST00000334046.5	-	1	164	c.134G>A	c.(133-135)cGc>cAc	p.R45H		NM_181612.2	NP_853643.1	Q3LI70	KR196_HUMAN	keratin associated protein 19-6	45						intermediate filament (GO:0005882)				breast(1)|large_intestine(2)|lung(5)|upper_aerodigestive_tract(1)	9						GCATGATGGGCGGCAGCAGCC	0.498													c|||	161	0.0321486	0.1135	0.0115	5008	,	,		14661	0.0		0.001	False		,,,				2504	0.002				p.R45H		Atlas-SNP	.											.	KRTAP19-6	16	.	0			c.G134A						PASS	.	C	HIS/ARG	371,4035	188.5+/-214.9	13,345,1845	110.0	120.0	116.0		134	-6.1	0.0	21	dbSNP_131	116	12,8588	9.8+/-36.6	0,12,4288	yes	missense	KRTAP19-6	NM_181612.2	29	13,357,6133	TT,TC,CC		0.1395,8.4203,2.9448	benign	45/59	31914019	383,12623	2203	4300	6503	SO:0001583	missense	337973	exon1			GATGGGCGGCAGC	AP001708	CCDS13598.1	21q22.1	2010-09-30			ENSG00000186925	ENSG00000186925		"""Keratin associated proteins"""	18941	protein-coding gene	gene with protein product						12359730	Standard	NM_181612		Approved	KAP19.6	uc002yok.1	Q3LI70	OTTHUMG00000057779	ENST00000334046.5:c.134G>A	21.37:g.31914019C>T	ENSP00000375107:p.Arg45His	111.0	0.0	0		141.0	47.0	0.333333	NM_181612	Q3LI71	Missense_Mutation	SNP	ENST00000334046.5	37	CCDS13598.1	64	0.029304029304029304	58	0.11788617886178862	6	0.016574585635359115	0	0.0	0	0.0	c	6.926	0.540492	0.13250	0.084203	0.001395	ENSG00000186925	ENST00000334046;ENST00000437381	T	0.11169	2.8	4.39	-6.09	0.02145	.	0.598882	0.13443	N	0.387478	T	0.00109	0.0003	.	.	.	0.09310	N	1	B	0.12013	0.005	B	0.04013	0.001	T	0.32587	-0.9901	9	0.87932	D	0	-1.818	7.3473	0.26670	0.1168:0.3112:0.0:0.5719	.	45	Q3LI70	KR196_HUMAN	H	45	ENSP00000375107:R45H	ENSP00000375107:R45H	R	-	2	0	KRTAP19-6	30835890	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-0.929000	0.03976	-1.347000	0.02208	-1.903000	0.00527	CGC	C|0.969;T|0.031	0.031	strong		0.498	KRTAP19-6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000128231.4		
KPNB1	3837	hgsc.bcm.edu	37	17	45734285	45734285	+	Silent	SNP	T	T	C			TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr17:45734285T>C	ENST00000290158.4	+	4	749	c.342T>C	c.(340-342)gcT>gcC	p.A114A	KPNB1_ENST00000537679.1_5'Flank|KPNB1_ENST00000540627.1_5'UTR|KPNB1_ENST00000535458.2_5'UTR|KPNB1_ENST00000577918.1_3'UTR	NM_001276453.1|NM_002265.4	NP_001263382.1|NP_002256.2	Q14974	IMB1_HUMAN	karyopherin (importin) beta 1	114					apoptotic DNA fragmentation (GO:0006309)|apoptotic process (GO:0006915)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|cytokine-mediated signaling pathway (GO:0019221)|intracellular transport of virus (GO:0075733)|NLS-bearing protein import into nucleus (GO:0006607)|protein import into nucleus (GO:0006606)|protein import into nucleus, translocation (GO:0000060)|ribosomal protein import into nucleus (GO:0006610)|small molecule metabolic process (GO:0044281)|viral life cycle (GO:0019058)|viral process (GO:0016032)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|endoplasmic reticulum tubular network (GO:0071782)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|nuclear envelope (GO:0005635)|nuclear membrane (GO:0031965)|nuclear pore (GO:0005643)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	enzyme binding (GO:0019899)|nuclear localization sequence binding (GO:0008139)|poly(A) RNA binding (GO:0044822)|protein domain specific binding (GO:0019904)|protein transporter activity (GO:0008565)|zinc ion binding (GO:0008270)			breast(1)|ovary(1)|pancreas(1)|skin(1)	4						AGTGTGTGGCTGGTATTGCTT	0.468																																					p.H114H		Atlas-SNP	.											.	KPNB1	58	.	0			c.C342C						PASS	.						138.0	121.0	127.0					17																	45734285		2203	4300	6503	SO:0001819	synonymous_variant	3837	exon4			TGTGGCTGGTATT	L39793	CCDS11513.1, CCDS62228.1	17q21.32	2013-02-14			ENSG00000108424	ENSG00000108424		"""Importins"", ""Armadillo repeat containing"""	6400	protein-coding gene	gene with protein product	"""importin 1"""	602738				7615630, 7627554	Standard	NM_002265		Approved	NTF97, IPOB, MGC2155, MGC2156, MGC2157, IMB1, Impnb, IPO1	uc002ilt.2	Q14974	OTTHUMG00000036957	ENST00000290158.4:c.342T>C	17.37:g.45734285T>C		146.0	0.0	0		111.0	46.0	0.414414	NM_002265	B7ZAV6|D3DTT3|Q14637|Q53XN2|Q96J27	Silent	SNP	ENST00000290158.4	37	CCDS11513.1																																																																																			.	.	none		0.468	KPNB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000089755.2	NM_002265	
KIAA2018	205717	hgsc.bcm.edu	37	3	113376113	113376113	+	Silent	SNP	C	C	T	rs62265537|rs59601191|rs112313093|rs59990801|rs397990842|rs10606566		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr3:113376113C>T	ENST00000478658.1	-	5	4433	c.4416G>A	c.(4414-4416)caG>caA	p.Q1472Q	KIAA2018_ENST00000316407.4_Silent_p.Q1472Q|KIAA2018_ENST00000491165.1_Intron			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		106.0	0.0	0		69.0	3.0	0.0434783	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	
CREBBP	1387	hgsc.bcm.edu	37	16	3808872	3808872	+	Nonsense_Mutation	SNP	G	G	A			TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr16:3808872G>A	ENST00000262367.5	-	17	4161	c.3352C>T	c.(3352-3354)Cag>Tag	p.Q1118*	CREBBP_ENST00000382070.3_Nonsense_Mutation_p.Q1080*	NM_004380.2	NP_004371.2	Q92793	CBP_HUMAN	CREB binding protein	1118	Bromo. {ECO:0000255|PROSITE- ProRule:PRU00035}.				cellular lipid metabolic process (GO:0044255)|cellular response to hypoxia (GO:0071456)|chromatin organization (GO:0006325)|embryonic digit morphogenesis (GO:0042733)|gene expression (GO:0010467)|germ-line stem cell maintenance (GO:0030718)|histone acetylation (GO:0016573)|homeostatic process (GO:0042592)|innate immune response (GO:0045087)|N-terminal peptidyl-lysine acetylation (GO:0018076)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|Notch signaling pathway (GO:0007219)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of type I interferon production (GO:0032481)|protein complex assembly (GO:0006461)|regulation of smoothened signaling pathway (GO:0008589)|regulation of transcription from RNA polymerase II promoter in response to hypoxia (GO:0061418)|regulation of transcription, DNA-templated (GO:0006355)|response to hypoxia (GO:0001666)|rhythmic process (GO:0048511)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)|transcription initiation from RNA polymerase II promoter (GO:0006367)|viral process (GO:0016032)	condensed chromosome outer kinetochore (GO:0000940)|cytoplasm (GO:0005737)|histone acetyltransferase complex (GO:0000123)|nuclear body (GO:0016604)|nuclear chromatin (GO:0000790)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	acetyltransferase activity (GO:0016407)|chromatin binding (GO:0003682)|core promoter proximal region sequence-specific DNA binding (GO:0000987)|histone acetyltransferase activity (GO:0004402)|MRF binding (GO:0043426)|p53 binding (GO:0002039)|RNA polymerase II activating transcription factor binding (GO:0001102)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in negative regulation of transcription (GO:0001078)|RNA polymerase II transcription coactivator activity (GO:0001105)|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)|signal transducer activity (GO:0004871)|transcription coactivator activity (GO:0003713)|transcription factor binding (GO:0008134)|zinc ion binding (GO:0008270)			NS(1)|breast(5)|central_nervous_system(4)|cervix(3)|endometrium(12)|haematopoietic_and_lymphoid_tissue(125)|kidney(5)|large_intestine(32)|lung(43)|ovary(18)|pancreas(2)|prostate(6)|skin(9)|soft_tissue(1)|stomach(3)|upper_aerodigestive_tract(5)|urinary_tract(21)	295		Ovarian(90;0.0266)		OV - Ovarian serous cystadenocarcinoma(1;3.54e-05)		CCGAGGAGCTGGGGATCTACA	0.433			"""T, N, F, Mis, O"""	"""MLL, MORF, RUNXBP2"""	"""ALL, AML, DLBCL, B-NHL """		Rubinstein-Taybi syndrome																														p.Q1118X		Atlas-SNP	.		Dom/Rec	yes		16	16p13.3	1387	CREB binding protein (CBP)	yes	L	.	CREBBP	546	.	0			c.C3352T						PASS	.						83.0	81.0	81.0					16																	3808872		2197	4300	6497	SO:0001587	stop_gained	1387	exon17			GGAGCTGGGGATC	U85962	CCDS10509.1, CCDS45399.1	16p13.3	2011-07-01	2008-08-01		ENSG00000005339	ENSG00000005339		"""Chromatin-modifying enzymes / K-acetyltransferases"""	2348	protein-coding gene	gene with protein product		600140	"""Rubinstein-Taybi syndrome"""	RSTS		8413673	Standard	NM_001079846		Approved	RTS, CBP, KAT3A	uc002cvv.3	Q92793	OTTHUMG00000129431	ENST00000262367.5:c.3352C>T	16.37:g.3808872G>A	ENSP00000262367:p.Gln1118*	136.0	0.0	0		141.0	44.0	0.312057	NM_004380	D3DUC9|O00147|Q16376|Q4LE28	Nonsense_Mutation	SNP	ENST00000262367.5	37	CCDS10509.1	.	.	.	.	.	.	.	.	.	.	G	49	15.347356	0.99831	.	.	ENSG00000005339	ENST00000262367;ENST00000543883;ENST00000382070	.	.	.	5.05	5.05	0.67936	.	0.000000	0.64402	D	0.000003	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.16420	T	0.52	-9.7097	18.7675	0.91879	0.0:0.0:1.0:0.0	.	.	.	.	X	1118;1148;1080	.	ENSP00000262367:Q1118X	Q	-	1	0	CREBBP	3748873	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	5.034000	0.64152	2.499000	0.84300	0.561000	0.74099	CAG	.	.	none		0.433	CREBBP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251591.2	NM_004380	
FMO4	2329	hgsc.bcm.edu	37	1	171303626	171303626	+	Missense_Mutation	SNP	G	G	A	rs573059844		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr1:171303626G>A	ENST00000367749.3	+	8	1234	c.904G>A	c.(904-906)Gtg>Atg	p.V302M		NM_002022.1	NP_002013.1	P31512	FMO4_HUMAN	flavin containing monooxygenase 4	302					drug catabolic process (GO:0042737)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)	flavin adenine dinucleotide binding (GO:0050660)|N,N-dimethylaniline monooxygenase activity (GO:0004499)|NADP binding (GO:0050661)			NS(1)|breast(1)|central_nervous_system(1)|endometrium(3)|kidney(2)|large_intestine(7)|lung(12)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	33	all_cancers(6;3.9e-08)|all_hematologic(923;0.088)|Acute lymphoblastic leukemia(37;0.181)					GAAAACCAGCGTGATTGAATT	0.378																																					p.V302M	Pancreas(24;816 862 7754 7993 32832)	Atlas-SNP	.											FMO4,caecum,carcinoma,0,1	FMO4	64	1	0			c.G904A						PASS	.						70.0	73.0	72.0					1																	171303626		2203	4300	6503	SO:0001583	missense	2329	exon8			ACCAGCGTGATTG	BC002780	CCDS1295.1	1q24.3	2011-08-04			ENSG00000076258	ENSG00000076258	1.14.13.8		3772	protein-coding gene	gene with protein product		136131		FMO2		8311461	Standard	NM_002022		Approved		uc001gho.3	P31512	OTTHUMG00000035506	ENST00000367749.3:c.904G>A	1.37:g.171303626G>A	ENSP00000356723:p.Val302Met	133.0	0.0	0		170.0	51.0	0.3	NM_002022	Q53XR0	Missense_Mutation	SNP	ENST00000367749.3	37	CCDS1295.1	.	.	.	.	.	.	.	.	.	.	G	13.75	2.331649	0.41297	.	.	ENSG00000076258	ENST00000367749	T	0.61040	0.14	5.66	4.76	0.60689	.	0.135375	0.48286	D	0.000184	T	0.74680	0.3748	M	0.92880	3.355	0.46954	D	0.999265	D	0.89917	1.0	D	0.85130	0.997	T	0.80939	-0.1158	10	0.72032	D	0.01	-15.5018	10.7486	0.46196	0.1469:0.0:0.8531:0.0	.	302	P31512	FMO4_HUMAN	M	302	ENSP00000356723:V302M	ENSP00000356723:V302M	V	+	1	0	FMO4	169570250	0.823000	0.29233	0.380000	0.26093	0.043000	0.13939	1.146000	0.31589	1.387000	0.46486	-0.128000	0.14901	GTG	.	.	none		0.378	FMO4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000086223.1	NM_002022	
C14orf37	145407	hgsc.bcm.edu	37	14	58605734	58605734	+	Missense_Mutation	SNP	T	T	C	rs61741497	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr14:58605734T>C	ENST00000267485.7	-	2	537	c.343A>G	c.(343-345)Act>Gct	p.T115A	C14orf37_ENST00000334342.5_5'UTR	NM_001001872.2	NP_001001872.2	Q86TY3	CN037_HUMAN	chromosome 14 open reading frame 37	115						integral component of membrane (GO:0016021)				breast(7)|central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(4)|lung(16)|pancreas(1)|skin(1)	33						CCTGACTCAGTAGGTGTGGAA	0.478													T|||	8	0.00159744	0.0	0.0029	5008	,	,		21817	0.0		0.006	False		,,,				2504	0.0				p.T115A		Atlas-SNP	.											.	C14orf37	87	.	0			c.A343G						PASS	.	T	ALA/THR	8,4398	15.5+/-35.6	0,8,2195	85.0	81.0	82.0		343	2.1	0.1	14	dbSNP_129	82	62,8538	37.4+/-92.8	3,56,4241	yes	missense	C14orf37	NM_001001872.2	58	3,64,6436	CC,CT,TT		0.7209,0.1816,0.5382	possibly-damaging	115/775	58605734	70,12936	2203	4300	6503	SO:0001583	missense	145407	exon2			ACTCAGTAGGTGT		CCDS32089.1	14q23.1	2012-09-03			ENSG00000139971	ENSG00000139971			19846	protein-coding gene	gene with protein product							Standard	NM_001001872		Approved		uc001xdc.3	Q86TY3	OTTHUMG00000171173	ENST00000267485.7:c.343A>G	14.37:g.58605734T>C	ENSP00000267485:p.Thr115Ala	153.0	1.0	0.00653595		212.0	140.0	0.660377	NM_001001872	A8K8Z8|Q6P5Q1|Q86TY1	Missense_Mutation	SNP	ENST00000267485.7	37	CCDS32089.1	7	0.003205128205128205	0	0.0	1	0.0027624309392265192	0	0.0	6	0.0079155672823219	T	9.312	1.055831	0.19907	0.001816	0.007209	ENSG00000139971	ENST00000267485;ENST00000438670	T	0.21734	1.99	5.82	2.06	0.26882	.	0.429079	0.24436	N	0.038557	T	0.13415	0.0325	M	0.62723	1.935	0.19300	N	0.99997	B;P;B;B	0.40970	0.208;0.734;0.208;0.208	B;B;B;B	0.39503	0.084;0.301;0.084;0.084	T	0.09729	-1.0661	10	0.37606	T	0.19	-2.845	4.9334	0.13928	0.0:0.2244:0.1493:0.6264	.	153;115;115;115	B4DMS4;Q86TY3-2;A8K990;Q86TY3	.;.;.;CN037_HUMAN	A	115;153	ENSP00000267485:T115A	ENSP00000267485:T115A	T	-	1	0	C14orf37	57675487	0.014000	0.17966	0.120000	0.21714	0.017000	0.09413	-0.048000	0.11944	0.106000	0.17784	0.533000	0.62120	ACT	T|0.995;C|0.005	0.005	strong		0.478	C14orf37-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000412059.1	NM_001001872	
CEACAM20	125931	hgsc.bcm.edu	37	19	45024535	45024535	+	RNA	SNP	T	T	C	rs200961907		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr19:45024535T>C	ENST00000454753.1	-	0	1281							Q6UY09	CEA20_HUMAN	carcinoembryonic antigen-related cell adhesion molecule 20							integral component of membrane (GO:0016021)				central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(2)|lung(8)|prostate(1)	15		Prostate(69;0.0352)				AGGGGCTCACTCCGGGCCCGG	0.592																																					p.S335G		Atlas-SNP	.											.	CEACAM20	31	.	0			c.A1003G						PASS	.		GLY/SER,GLY/SER,GLY/SER,GLY/SER	1,3869		0,1,1934	45.0	47.0	46.0		1003,1003,1003,1003	4.3	0.0	19		46	7,8257		0,7,4125	yes	missense,missense,missense,missense	CEACAM20	NM_001102597.1,NM_001102598.1,NM_001102599.1,NM_001102600.1	56,56,56,56	0,8,6059	CC,CT,TT		0.0847,0.0258,0.0659	probably-damaging,probably-damaging,probably-damaging,probably-damaging	335/597,335/492,335/504,335/585	45024535	8,12126	1935	4132	6067			125931	exon5			GCTCACTCCGGGC	AY358129	CCDS74390.1, CCDS74391.1, CCDS74392.1, CCDS74393.1	19q13.31	2013-01-30			ENSG00000176395	ENSG00000273777		"""Immunoglobulin superfamily / Immunoglobulin-like domain containing"", ""Immunoglobulin superfamily / I-set domain containing"""	24879	protein-coding gene	gene with protein product						12975309	Standard	NM_001102600		Approved	UNQ9366	uc010ejo.1	Q6UY09	OTTHUMG00000151532		19.37:g.45024535T>C		70.0	0.0	0		86.0	43.0	0.5	NM_001102600		Missense_Mutation	SNP	ENST00000454753.1	37																																																																																				T|0.996;C|0.004	0.004	weak		0.592	CEACAM20-001	KNOWN	basic	processed_transcript	processed_transcript	OTTHUMT00000323032.1	NM_198444	
DHRS4	10901	hgsc.bcm.edu	37	14	24424346	24424346	+	Silent	SNP	G	G	A	rs4981491		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr14:24424346G>A	ENST00000313250.5	+	2	434	c.231G>A	c.(229-231)caG>caA	p.Q77Q	DHRS4_ENST00000559632.1_Silent_p.Q77Q|DHRS4_ENST00000397075.3_Silent_p.Q77Q|DHRS4_ENST00000558263.1_Silent_p.Q77Q|DHRS4_ENST00000421831.1_Silent_p.Q59Q|DHRS4_ENST00000558581.1_Silent_p.Q77Q|DHRS4_ENST00000543741.2_Silent_p.Q77Q|DHRS4_ENST00000308178.8_Silent_p.Q59Q|DHRS4_ENST00000382761.3_Silent_p.Q59Q|DHRS4-AS1_ENST00000556379.1_RNA|DHRS4_ENST00000397074.3_Silent_p.Q77Q|DHRS4_ENST00000397073.2_Silent_p.Q59Q	NM_021004.2	NP_066284.2	Q9BTZ2	DHRS4_HUMAN	dehydrogenase/reductase (SDR family) member 4	77					alcohol metabolic process (GO:0006066)|cellular ketone metabolic process (GO:0042180)|oxidation-reduction process (GO:0055114)|protein tetramerization (GO:0051262)|steroid metabolic process (GO:0008202)	extracellular vesicular exosome (GO:0070062)|intracellular membrane-bounded organelle (GO:0043231)|mitochondrion (GO:0005739)|nuclear membrane (GO:0031965)|nucleus (GO:0005634)|peroxisomal membrane (GO:0005778)|peroxisome (GO:0005777)	3-keto sterol reductase activity (GO:0000253)|alcohol dehydrogenase [NAD(P)+] activity (GO:0018455)|carbonyl reductase (NADPH) activity (GO:0004090)|oxidoreductase activity, acting on NAD(P)H, quinone or similar compound as acceptor (GO:0016655)|receptor binding (GO:0005102)			central_nervous_system(2)|endometrium(1)|kidney(3)|large_intestine(1)|lung(4)|ovary(1)|skin(1)|upper_aerodigestive_tract(1)	14				GBM - Glioblastoma multiforme(265;0.00962)	Vitamin A(DB00162)	CCACGCTGCAGGGGGAGGGGC	0.701																																					p.Q77Q		Atlas-SNP	.											.	DHRS4	22	.	0			c.G231A						PASS	.						37.0	42.0	40.0					14																	24424346		2203	4299	6502	SO:0001819	synonymous_variant	10901	exon2			GCTGCAGGGGGAG	AF044127	CCDS9605.1, CCDS61408.1, CCDS61409.1, CCDS61410.1, CCDS61411.1, CCDS61412.1	14q11.2	2013-06-14			ENSG00000157326	ENSG00000157326	1.1.1.184	"""Short chain dehydrogenase/reductase superfamily / Classical SDR fold cluster 1"""	16985	protein-coding gene	gene with protein product	"""short chain dehydrogenase/reductase family 25C, member 2"""	611596				10333503, 19027726	Standard	NM_021004		Approved	SCAD-SRL, SDR-SRL, humNRDR, FLJ11008, SDR25C2	uc001wla.3	Q9BTZ2	OTTHUMG00000028777	ENST00000313250.5:c.231G>A	14.37:g.24424346G>A		324.0	0.0	0		432.0	92.0	0.212963	NM_021004	B2RB10|B7WNS9|D3YTB8|E2QRL8|O95162|Q20CR0|Q2LC19|Q2LE81|Q58IU4|Q6E0Y1|Q6UWU3|Q71UQ6|Q8TD03|Q9H3N5|Q9NV08	Silent	SNP	ENST00000313250.5	37	CCDS9605.1																																																																																			.	.	weak		0.701	DHRS4-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000071857.3		
RFX2	5990	hgsc.bcm.edu	37	19	6013057	6013057	+	Missense_Mutation	SNP	C	C	T			TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr19:6013057C>T	ENST00000303657.5	-	8	988	c.839G>A	c.(838-840)cGg>cAg	p.R280Q	RFX2_ENST00000592546.1_Missense_Mutation_p.R255Q|CTC-232P5.1_ENST00000587836.1_RNA|RFX2_ENST00000359161.3_Missense_Mutation_p.R280Q	NM_000635.3	NP_000626.2	P48378	RFX2_HUMAN	regulatory factor X, 2 (influences HLA class II expression)	280					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)			breast(4)|central_nervous_system(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(4)|lung(4)|ovary(1)|pancreas(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)	21						CTCCTGCAGCCGGTTCAGTGG	0.612																																					p.R280Q	Colon(38;171 817 19800 47433 48051)	Atlas-SNP	.											.	RFX2	60	.	0			c.G839A						PASS	.						126.0	122.0	123.0					19																	6013057		2203	4300	6503	SO:0001583	missense	5990	exon8			TGCAGCCGGTTCA		CCDS12157.1, CCDS12158.1	19p13.3	2011-11-23			ENSG00000087903	ENSG00000087903			9983	protein-coding gene	gene with protein product	"""trans-acting regulatory factor 2"", ""DNA binding protein RFX2"", ""HLA class II regulatory factor RFX2"""	142765				1505960	Standard	NM_000635		Approved	FLJ14226	uc002meb.3	P48378		ENST00000303657.5:c.839G>A	19.37:g.6013057C>T	ENSP00000306335:p.Arg280Gln	42.0	0.0	0		56.0	25.0	0.446429	NM_000635	A8K581|B3KNC4|Q6IQ44|Q8SNA2	Missense_Mutation	SNP	ENST00000303657.5	37	CCDS12157.1	.	.	.	.	.	.	.	.	.	.	C	19.57	3.851655	0.71719	.	.	ENSG00000087903	ENST00000303657;ENST00000359161;ENST00000537791	T;D	0.92149	-0.1;-2.98	4.99	2.84	0.33178	.	0.059667	0.64402	D	0.000002	D	0.88385	0.6422	M	0.65320	2	0.80722	D	1	P;P	0.41848	0.763;0.651	B;B	0.37387	0.248;0.087	D	0.84345	0.0529	10	0.37606	T	0.19	-48.0962	9.5849	0.39510	0.0:0.7782:0.1427:0.0791	.	255;280	P48378-2;P48378	.;RFX2_HUMAN	Q	280;255;67	ENSP00000306335:R280Q;ENSP00000352076:R255Q	ENSP00000306335:R280Q	R	-	2	0	RFX2	5964057	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	4.746000	0.62133	0.611000	0.30052	0.557000	0.71058	CGG	.	.	none		0.612	RFX2-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000452687.1	NM_000635	
VN1R2	317701	hgsc.bcm.edu	37	19	53761857	53761857	+	Missense_Mutation	SNP	G	G	T	rs112986288	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr19:53761857G>T	ENST00000341702.3	+	1	313	c.229G>T	c.(229-231)Gtc>Ttc	p.V77F		NM_173856.2	NP_776255.2	Q8NFZ6	VN1R2_HUMAN	vomeronasal 1 receptor 2	77					response to pheromone (GO:0019236)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	pheromone receptor activity (GO:0016503)			breast(2)|central_nervous_system(1)|endometrium(2)|kidney(3)|large_intestine(6)|lung(15)|skin(1)|upper_aerodigestive_tract(1)	31				GBM - Glioblastoma multiforme(134;0.00301)		acactctcttgtctctgcaca	0.483													G|||	37	0.00738818	0.0	0.0072	5008	,	,		16666	0.0		0.0139	False		,,,				2504	0.0184				p.V77F		Atlas-SNP	.											.	VN1R2	71	.	0			c.G229T						PASS	.	G	PHE/VAL	8,4376		0,8,2184	35.0	35.0	35.0		229	0.1	0.0	19	dbSNP_132	35	78,8498		1,76,4211	no	missense	VN1R2	NM_173856.2	50	1,84,6395	TT,TG,GG		0.9095,0.1825,0.6636	benign	77/396	53761857	86,12874	2192	4288	6480	SO:0001583	missense	317701	exon1			TCTCTTGTCTCTG	AF370359	CCDS12862.1	19q13.42	2012-08-22			ENSG00000196131	ENSG00000196131		"""Vomeronasal receptors / Type 1"", ""GPCR / Unclassified : Vomeronasal receptors, type 1"""	19872	protein-coding gene	gene with protein product						12123587	Standard	NM_173856		Approved	V1RL2	uc002qbi.2	Q8NFZ6		ENST00000341702.3:c.229G>T	19.37:g.53761857G>T	ENSP00000351244:p.Val77Phe	65.0	0.0	0		55.0	22.0	0.4	NM_173856	A1L411|Q8TDU4	Missense_Mutation	SNP	ENST00000341702.3	37	CCDS12862.1	13	0.005952380952380952	0	0.0	4	0.011049723756906077	0	0.0	9	0.011873350923482849	G	5.291	0.239112	0.10023	0.001825	0.009095	ENSG00000196131	ENST00000341702	T	0.10192	2.9	0.0465	0.0465	0.14256	.	.	.	.	.	T	0.02929	0.0087	N	0.08118	0	0.09310	N	1	B	0.25169	0.119	B	0.12837	0.008	T	0.38001	-0.9681	9	0.72032	D	0.01	.	2.6651	0.05041	0.4852:0.0:0.5147:0.0	.	77	Q8NFZ6	VN1R2_HUMAN	F	77	ENSP00000351244:V77F	ENSP00000351244:V77F	V	+	1	0	VN1R2	58453669	0.000000	0.05858	0.022000	0.16811	0.022000	0.10575	-1.105000	0.03323	0.132000	0.18615	0.134000	0.15878	GTC	G|0.994;T|0.006	0.006	strong		0.483	VN1R2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000464285.1	NM_173856	
MAN2A2	4122	hgsc.bcm.edu	37	15	91452566	91452566	+	Silent	SNP	G	G	A	rs148266546		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr15:91452566G>A	ENST00000559717.1	+	9	1665	c.1206G>A	c.(1204-1206)ctG>ctA	p.L402L	MAN2A2_ENST00000430376.2_5'Flank|MAN2A2_ENST00000431652.2_5'UTR|MAN2A2_ENST00000360468.3_Silent_p.L402L			P49641	MA2A2_HUMAN	mannosidase, alpha, class 2A, member 2	402					cellular protein metabolic process (GO:0044267)|mannose metabolic process (GO:0006013)|post-translational protein modification (GO:0043687)|protein N-linked glycosylation via asparagine (GO:0018279)	Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)	carbohydrate binding (GO:0030246)|hydrolase activity, hydrolyzing N-glycosyl compounds (GO:0016799)|mannosyl-oligosaccharide 1,3-1,6-alpha-mannosidase activity (GO:0004572)|zinc ion binding (GO:0008270)			NS(1)|autonomic_ganglia(1)|breast(2)|central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(9)|lung(13)|ovary(4)|prostate(1)|skin(3)|upper_aerodigestive_tract(2)|urinary_tract(1)	47	Lung NSC(78;0.0771)|all_lung(78;0.137)		Lung(145;0.229)			GGGCAGCCCTGCTTCTGGACC	0.572													G|||	1	0.000199681	0.0	0.0014	5008	,	,		17474	0.0		0.0	False		,,,				2504	0.0				p.L402L		Atlas-SNP	.											.	MAN2A2	99	.	0			c.G1206A						PASS	.	G		0,4396		0,0,2198	56.0	55.0	55.0		1206	4.8	1.0	15	dbSNP_134	55	4,8592	3.7+/-12.6	0,4,4294	no	coding-synonymous	MAN2A2	NM_006122.2		0,4,6492	AA,AG,GG		0.0465,0.0,0.0308		402/1151	91452566	4,12988	2198	4298	6496	SO:0001819	synonymous_variant	4122	exon8			AGCCCTGCTTCTG	L28821	CCDS32332.1	15q25	2011-06-30			ENSG00000196547	ENSG00000196547			6825	protein-coding gene	gene with protein product		600988				8524845	Standard	NM_006122		Approved	MANA2X, HsT19662	uc002bqc.3	P49641		ENST00000559717.1:c.1206G>A	15.37:g.91452566G>A		101.0	0.0	0		62.0	6.0	0.0967742	NM_006122	A6NH12|A8K1E8|Q13754	Silent	SNP	ENST00000559717.1	37	CCDS32332.1																																																																																			G|1.000;A|0.000	0.000	strong		0.572	MAN2A2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000418246.5	NM_006122	
MUC4	4585	hgsc.bcm.edu	37	3	195509722	195509722	+	Missense_Mutation	SNP	G	G	T			TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr3:195509722G>T	ENST00000463781.3	-	2	9188	c.8729C>A	c.(8728-8730)aCc>aAc	p.T2910N	MUC4_ENST00000349607.4_Intron|MUC4_ENST00000346145.4_Intron|MUC4_ENST00000475231.1_Missense_Mutation_p.T2910N	NM_018406.6	NP_060876.5	Q99102	MUC4_HUMAN	mucin 4, cell surface associated	0					cell-matrix adhesion (GO:0007160)|cellular protein metabolic process (GO:0044267)|maintenance of gastrointestinal epithelium (GO:0030277)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|Golgi lumen (GO:0005796)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|proteinaceous extracellular matrix (GO:0005578)|vesicle (GO:0031982)	ErbB-2 class receptor binding (GO:0005176)|extracellular matrix constituent, lubricant activity (GO:0030197)			NS(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(3)|kidney(1)|large_intestine(5)|lung(23)|ovary(3)|prostate(8)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	51	all_cancers(143;1.11e-08)|Ovarian(172;0.0634)|Breast(254;0.206)	Lung NSC(153;0.191)	Epithelial(36;3.72e-24)|all cancers(36;6.22e-22)|OV - Ovarian serous cystadenocarcinoma(49;1.1e-18)|Lung(62;4.65e-05)|LUSC - Lung squamous cell carcinoma(58;5.31e-05)	GBM - Glioblastoma multiforme(46;2.37e-05)		AAGAGGCGTGGTGTCACCTGT	0.587																																					p.T2910N		Atlas-SNP	.											.	MUC4	1505	.	0			c.C8729A						PASS	.						13.0	9.0	10.0					3																	195509722		674	1529	2203	SO:0001583	missense	4585	exon2			GGCGTGGTGTCAC	AJ276359	CCDS3310.1, CCDS3311.1, CCDS54700.1	3q29	2007-01-19	2006-03-14		ENSG00000145113	ENSG00000145113		"""Mucins"""	7514	protein-coding gene	gene with protein product		158372	"""mucin 4, tracheobronchial"""			1673336	Standard	NM_004532		Approved		uc021xjp.1	Q99102	OTTHUMG00000151827	ENST00000463781.3:c.8729C>A	3.37:g.195509722G>T	ENSP00000417498:p.Thr2910Asn	327.0	0.0	0		520.0	83.0	0.159615	NM_018406	O95938|Q9GZM2|Q9GZV6|Q9H481|Q9H482|Q9H483|Q9H484|Q9H485|Q9H486|Q9H487|Q9H4D6|Q9H4D8|Q9NPJ0|Q9NY09|Q9NY75|Q9NY76|Q9NY77|Q9NY78|Q9NY79|Q9NY80|Q9NY81	Missense_Mutation	SNP	ENST00000463781.3	37	CCDS54700.1	.	.	.	.	.	.	.	.	.	.	g	5.988	0.366151	0.11352	.	.	ENSG00000145113	ENST00000463781;ENST00000475231	T;T	0.33216	1.42;1.46	.	.	.	.	.	.	.	.	T	0.19167	0.0460	N	0.19112	0.55	0.09310	N	1	P	0.39094	0.659	B	0.42959	0.403	T	0.17930	-1.0353	7	.	.	.	.	4.6597	0.12636	0.0:0.0:1.0:0.0	.	2782	E7ESK3	.	N	2910	ENSP00000417498:T2910N;ENSP00000420243:T2910N	.	T	-	2	0	MUC4	196994501	0.003000	0.15002	0.000000	0.03702	0.000000	0.00434	-0.816000	0.04477	-0.000000	0.14550	0.000000	0.15137	ACC	.	.	none		0.587	MUC4-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000324081.6	NM_018406	
FARP2	9855	hgsc.bcm.edu	37	2	242396209	242396209	+	Missense_Mutation	SNP	C	C	A	rs145630778		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr2:242396209C>A	ENST00000264042.3	+	14	1629	c.1459C>A	c.(1459-1461)Ccc>Acc	p.P487T	FARP2_ENST00000373287.4_Missense_Mutation_p.P487T|FARP2_ENST00000545004.1_Missense_Mutation_p.P487T	NM_014808.2	NP_055623.1	O94887	FARP2_HUMAN	FERM, RhoGEF and pleckstrin domain protein 2	487	Pro-rich.				actin cytoskeleton reorganization (GO:0031532)|axon guidance (GO:0007411)|cell adhesion (GO:0007155)|neuron remodeling (GO:0016322)|osteoclast differentiation (GO:0030316)|podosome assembly (GO:0071800)|positive regulation of Rac GTPase activity (GO:0032855)|positive regulation of Rho GTPase activity (GO:0032321)|Rac protein signal transduction (GO:0016601)|regulation of integrin activation (GO:0033623)|regulation of Rac GTPase activity (GO:0032314)|semaphorin-plexin signaling pathway (GO:0071526)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|extrinsic component of membrane (GO:0019898)	Rac guanyl-nucleotide exchange factor activity (GO:0030676)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)			breast(1)|central_nervous_system(2)|cervix(1)|endometrium(5)|kidney(1)|large_intestine(8)|lung(18)|ovary(2)|skin(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	43		all_cancers(19;4.88e-34)|all_epithelial(40;4.81e-14)|Breast(86;0.000141)|Renal(207;0.0143)|all_lung(227;0.0344)|Lung NSC(271;0.0886)|Ovarian(221;0.0905)|Esophageal squamous(248;0.131)|all_hematologic(139;0.182)|Melanoma(123;0.238)		Epithelial(32;1.81e-33)|all cancers(36;1.61e-30)|OV - Ovarian serous cystadenocarcinoma(60;6.83e-15)|Kidney(56;1.19e-08)|KIRC - Kidney renal clear cell carcinoma(57;8.98e-08)|BRCA - Breast invasive adenocarcinoma(100;1.49e-06)|Lung(119;0.000152)|LUSC - Lung squamous cell carcinoma(224;0.00125)|Colorectal(34;0.0199)|COAD - Colon adenocarcinoma(134;0.121)		CCGGAAGAGCCCCCTGAGTCT	0.617													C|||	1	0.000199681	0.0	0.0	5008	,	,		17269	0.0		0.001	False		,,,				2504	0.0				p.P487T		Atlas-SNP	.											.	FARP2	92	.	0			c.C1459A						PASS	.	C	THR/PRO	0,4406		0,0,2203	85.0	85.0	85.0		1459	3.0	0.2	2	dbSNP_134	85	1,8599	2.2+/-6.3	0,1,4299	yes	missense	FARP2	NM_014808.2	38	0,1,6502	AA,AC,CC		0.0116,0.0,0.0077	benign	487/1055	242396209	1,13005	2203	4300	6503	SO:0001583	missense	9855	exon14			AAGAGCCCCCTGA	AB018336	CCDS33424.1, CCDS63197.1	2q37.3	2013-01-10			ENSG00000006607	ENSG00000006607		"""Rho guanine nucleotide exchange factors"", ""Pleckstrin homology (PH) domain containing"""	16460	protein-coding gene	gene with protein product						9872452, 12351724	Standard	NM_001282984		Approved	KIAA0793, FIR, PLEKHC3, FRG	uc002wbi.2	O94887	OTTHUMG00000151574	ENST00000264042.3:c.1459C>A	2.37:g.242396209C>A	ENSP00000264042:p.Pro487Thr	266.0	1.0	0.0037594		258.0	120.0	0.465116	NM_014808	B7Z6J8|F5GZ84|Q53QM5|Q8WU27|Q9UFE7	Missense_Mutation	SNP	ENST00000264042.3	37	CCDS33424.1	1	4.578754578754579E-4	0	0.0	0	0.0	0	0.0	1	0.0013192612137203166	C	10.91	1.485420	0.26686	0.0	1.16E-4	ENSG00000006607	ENST00000264042;ENST00000545004;ENST00000373287	T;T;D	0.81499	-0.98;-1.49;-1.5	5.18	3.03	0.35002	.	0.717669	0.13260	N	0.401364	T	0.67552	0.2905	L	0.32530	0.975	0.26033	N	0.981711	P;B;B	0.34724	0.465;0.328;0.22	B;B;B	0.34242	0.178;0.124;0.058	T	0.53322	-0.8455	10	0.12103	T	0.63	.	9.2186	0.37362	0.0:0.7326:0.0:0.2674	.	487;487;487	O94887-2;F5GZ84;O94887	.;.;FARP2_HUMAN	T	487	ENSP00000264042:P487T;ENSP00000443876:P487T;ENSP00000362384:P487T	ENSP00000264042:P487T	P	+	1	0	FARP2	242044882	1.000000	0.71417	0.234000	0.24042	0.857000	0.48899	3.646000	0.54396	1.195000	0.43115	-0.192000	0.12808	CCC	C|1.000;A|0.000	0.000	strong		0.617	FARP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000323153.1		
MYBPC2	4606	hgsc.bcm.edu	37	19	50944294	50944294	+	Missense_Mutation	SNP	C	C	T	rs374005339		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr19:50944294C>T	ENST00000357701.5	+	8	781	c.730C>T	c.(730-732)Cgg>Tgg	p.R244W		NM_004533.3	NP_004524.3	Q14324	MYPC2_HUMAN	myosin binding protein C, fast type	244					cell adhesion (GO:0007155)|muscle filament sliding (GO:0030049)	cytosol (GO:0005829)|myosin filament (GO:0032982)	structural constituent of muscle (GO:0008307)			breast(1)	1		all_neural(266;0.057)		OV - Ovarian serous cystadenocarcinoma(262;0.0079)|GBM - Glioblastoma multiforme(134;0.0144)		CATGCTGAAGCGGCTGAAAAA	0.602																																					p.R244W		Atlas-SNP	.											.	MYBPC2	103	.	0			c.C730T						PASS	.		TRP/ARG	1,4181		0,1,2090	32.0	34.0	34.0		730	2.2	1.0	19		34	1,8491		0,1,4245	no	missense	MYBPC2	NM_004533.3	101	0,2,6335	TT,TC,CC		0.0118,0.0239,0.0158	probably-damaging	244/1142	50944294	2,12672	2091	4246	6337	SO:0001583	missense	4606	exon8			CTGAAGCGGCTGA		CCDS46152.1	19q13.33	2013-02-11	2001-11-28		ENSG00000086967	ENSG00000086967		"""Myosin binding proteins"", ""Immunoglobulin superfamily / I-set domain containing"", ""Fibronectin type III domain containing"""	7550	protein-coding gene	gene with protein product	"""fast-type muscle myosin-binding-protein C"""	160793	"""myosin-binding protein C, fast-type"""			8375400	Standard	NM_004533		Approved	MYBPCF, MYBPC, MGC163408	uc002psf.2	Q14324		ENST00000357701.5:c.730C>T	19.37:g.50944294C>T	ENSP00000350332:p.Arg244Trp	178.0	0.0	0		203.0	12.0	0.0591133	NM_004533	A1L4G9	Missense_Mutation	SNP	ENST00000357701.5	37	CCDS46152.1	.	.	.	.	.	.	.	.	.	.	.	15.42	2.829530	0.50845	2.39E-4	1.18E-4	ENSG00000086967	ENST00000357701	T	0.59638	0.25	3.33	2.23	0.28157	.	0.000000	0.33477	U	0.004875	T	0.69975	0.3171	M	0.66297	2.02	0.35743	D	0.818838	D	0.89917	1.0	D	0.97110	1.0	T	0.76391	-0.2976	10	0.66056	D	0.02	.	9.7381	0.40401	0.368:0.632:0.0:0.0	.	244	Q14324	MYPC2_HUMAN	W	244	ENSP00000350332:R244W	ENSP00000350332:R244W	R	+	1	2	MYBPC2	55636106	1.000000	0.71417	0.999000	0.59377	0.797000	0.45037	1.612000	0.36889	0.910000	0.36722	0.298000	0.19748	CGG	.	.	weak		0.602	MYBPC2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000464751.1	NM_004533	
GLI2	2736	hgsc.bcm.edu	37	2	121742307	121742307	+	Silent	SNP	C	C	T	rs13008360	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr2:121742307C>T	ENST00000452319.1	+	12	2004	c.1944C>T	c.(1942-1944)acC>acT	p.T648T	GLI2_ENST00000314490.11_Silent_p.T320T|GLI2_ENST00000361492.4_Silent_p.T648T|GLI2_ENST00000435313.2_3'UTR					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)				CCATCAAGACCGAGAGCTCCG	0.701													C|||	40	0.00798722	0.0015	0.0101	5008	,	,		16587	0.0		0.0308	False		,,,				2504	0.0				p.T648T		Atlas-SNP	.											GLI2,NS,carcinoma,0,1	GLI2	187	1	0			c.C1944T						scavenged	.	C		26,4366		0,26,2170	21.0	22.0	22.0		1944	-5.5	1.0	2	dbSNP_121	22	229,8367		4,221,4073	no	coding-synonymous	GLI2	NM_005270.4		4,247,6243	TT,TC,CC		2.664,0.592,1.9634		648/1587	121742307	255,12733	2196	4298	6494	SO:0001819	synonymous_variant	2736	exon11			CAAGACCGAGAGC		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.1944C>T	2.37:g.121742307C>T		126.0	1.0	0.00793651		84.0	47.0	0.559524	NM_005270		Silent	SNP	ENST00000452319.1	37	CCDS33283.1																																																																																			C|0.984;T|0.016	0.016	strong		0.701	GLI2-009	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000332293.3	NM_005270	
HOXB8	3218	hgsc.bcm.edu	37	17	46690777	46690777	+	Silent	SNP	A	A	G	rs45441492	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr17:46690777A>G	ENST00000239144.4	-	2	753	c.519T>C	c.(517-519)cgT>cgC	p.R173R	HOXB8_ENST00000576562.1_Silent_p.R172R|HOXB7_ENST00000239165.7_5'Flank|HOXB7_ENST00000567101.2_Intron	NM_024016.3	NP_076921.1	P17481	HXB8_HUMAN	homeobox B8	173					adult locomotory behavior (GO:0008344)|anterior/posterior pattern specification (GO:0009952)|dorsal spinal cord development (GO:0021516)|embryonic skeletal system morphogenesis (GO:0048704)|grooming behavior (GO:0007625)|negative regulation of myeloid cell differentiation (GO:0045638)|sensory perception of pain (GO:0019233)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)			large_intestine(1)|lung(8)|urinary_tract(2)	11						TTCGCCGCTTACGAGTCAGAT	0.557													G|||	304	0.0607029	0.1536	0.0519	5008	,	,		8833	0.001		0.0278	False		,,,				2504	0.0368				p.R173R		Atlas-SNP	.											.	HOXB8	26	.	0			c.T519C						PASS	.	G		658,3748	764.6+/-413.3	52,554,1597	106.0	101.0	102.0		519	3.1	1.0	17	dbSNP_127	102	459,8141	798.8+/-407.4	16,427,3857	no	coding-synonymous	HOXB8	NM_024016.3		68,981,5454	GG,GA,AA		5.3372,14.9342,8.5883		173/244	46690777	1117,11889	2203	4300	6503	SO:0001819	synonymous_variant	3218	exon2			CCGCTTACGAGTC		CCDS11533.1	17q21.32	2011-06-20	2005-12-22		ENSG00000120068	ENSG00000120068		"""Homeoboxes / ANTP class : HOXL subclass"""	5119	protein-coding gene	gene with protein product		142963	"""homeo box B8"""	HOX2, HOX2D		1973146, 1358459	Standard	XM_005257286		Approved		uc002inw.3	P17481	OTTHUMG00000159904	ENST00000239144.4:c.519T>C	17.37:g.46690777A>G		221.0	1.0	0.00452489		182.0	180.0	0.989011	NM_024016	Q9H1I2	Silent	SNP	ENST00000239144.4	37	CCDS11533.1																																																																																			A|0.924;G|0.076	0.076	strong		0.557	HOXB8-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000358092.3		
PARD3	56288	hgsc.bcm.edu	37	10	34630575	34630575	+	Silent	SNP	T	T	A	rs141191270	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr10:34630575T>A	ENST00000374789.3	-	16	2722	c.2397A>T	c.(2395-2397)gcA>gcT	p.A799A	PARD3_ENST00000545260.1_Silent_p.A739A|PARD3_ENST00000545693.1_Silent_p.A783A|PARD3_ENST00000346874.4_Silent_p.A799A|PARD3_ENST00000350537.4_Silent_p.A783A|PARD3_ENST00000374794.3_Silent_p.A739A|PARD3_ENST00000374773.1_Silent_p.A796A|PARD3_ENST00000374790.3_Silent_p.A739A|PARD3_ENST00000374776.1_Silent_p.A783A|PARD3_ENST00000544292.1_Silent_p.A513A|PARD3_ENST00000374788.3_Silent_p.A796A|PARD3_ENST00000340077.5_Silent_p.A796A	NM_019619.3	NP_062565.2	Q8TEW0	PARD3_HUMAN	par-3 family cell polarity regulator	799	Interacts with PRKCI and PRKCZ. {ECO:0000250}.				apical constriction (GO:0003383)|asymmetric cell division (GO:0008356)|axonogenesis (GO:0007409)|cell cycle (GO:0007049)|cell junction assembly (GO:0034329)|cell-cell junction organization (GO:0045216)|centrosome localization (GO:0051642)|establishment of epithelial cell polarity (GO:0090162)|establishment or maintenance of cell polarity (GO:0007163)|microtubule cytoskeleton organization (GO:0000226)|myelination in peripheral nervous system (GO:0022011)|negative regulation of peptidyl-threonine phosphorylation (GO:0010801)|positive regulation of myelination (GO:0031643)|protein complex assembly (GO:0006461)|protein kinase C-activating G-protein coupled receptor signaling pathway (GO:0007205)|protein targeting to membrane (GO:0006612)|regulation of actin filament-based process (GO:0032970)|regulation of cellular localization (GO:0060341)|tight junction assembly (GO:0070830)|transforming growth factor beta receptor signaling pathway (GO:0007179)|wound healing, spreading of cells (GO:0044319)	apical part of cell (GO:0045177)|axonal growth cone (GO:0044295)|cell cortex (GO:0005938)|cell junction (GO:0030054)|cell-cell adherens junction (GO:0005913)|cell-cell junction (GO:0005911)|cytosol (GO:0005829)|internode region of axon (GO:0033269)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)|protein complex (GO:0043234)|spindle (GO:0005819)|tight junction (GO:0005923)	phosphatidylinositol-3,4,5-trisphosphate binding (GO:0005547)|phosphatidylinositol-3-phosphate binding (GO:0032266)|phosphatidylinositol-4,5-bisphosphate binding (GO:0005546)			NS(2)|breast(4)|central_nervous_system(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(11)|lung(21)|ovary(2)|pancreas(1)|prostate(1)|skin(4)|upper_aerodigestive_tract(2)	63		Breast(68;0.0707)				AATCACTGATTGCAGCCTTGG	0.478																																					p.A799A		Atlas-SNP	.											.	PARD3	131	.	0			c.A2397T						PASS	.	T	,,,,,,,,,,	3,4403	6.2+/-15.9	0,3,2200	128.0	117.0	120.0		2388,2349,2397,2349,2349,2217,2217,2388,2388,2349,2397	-11.3	0.0	10	dbSNP_134	120	2,8598	3.0+/-9.4	0,2,4298	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	PARD3	NM_001184785.1,NM_001184786.1,NM_001184787.1,NM_001184788.1,NM_001184789.1,NM_001184790.1,NM_001184791.1,NM_001184792.1,NM_001184793.1,NM_001184794.1,NM_019619.3	,,,,,,,,,,	0,5,6498	AA,AT,TT		0.0233,0.0681,0.0384	,,,,,,,,,,	796/1354,783/1341,799/1320,783/1311,783/1274,739/1267,739/1245,796/1032,796/1001,783/989,799/1357	34630575	5,13001	2203	4300	6503	SO:0001819	synonymous_variant	56288	exon16			ACTGATTGCAGCC	AF252293	CCDS7178.1, CCDS53509.1, CCDS53510.1, CCDS53511.1, CCDS53512.1, CCDS53513.1, CCDS53514.1, CCDS53515.1, CCDS53516.1	10p11.22	2014-06-13	2013-08-28		ENSG00000148498	ENSG00000148498			16051	protein-coding gene	gene with protein product	"""atypical PKC isotype-specific interacting protein"", ""par-3 family cell polarity regulator alpha"", ""protein phosphatase 1, regulatory subunit 118"""	606745	"""par-3 (partitioning defective 3, C.elegans) homolog"", ""par-3 partitioning defective 3 homolog (C. elegans)"""			10934474	Standard	NM_001184790		Approved	PAR3, PARD3A, Bazooka, Baz, ASIP, PPP1R118	uc010qej.2	Q8TEW0	OTTHUMG00000017948	ENST00000374789.3:c.2397A>T	10.37:g.34630575T>A		118.0	0.0	0		88.0	69.0	0.784091	NM_001184787	F5H5T0|Q5T2U1|Q5VUA2|Q5VUA3|Q5VWV0|Q5VWV1|Q5VWV3|Q5VWV4|Q5VWV5|Q6IQ47|Q8TCZ9|Q8TEW1|Q8TEW2|Q8TEW3|Q96K28|Q96RM6|Q96RM7|Q9BY57|Q9BY58|Q9HC48|Q9NWL4|Q9NYE6	Silent	SNP	ENST00000374789.3	37	CCDS7178.1																																																																																			T|0.999;A|0.001	0.001	strong		0.478	PARD3-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000047527.1	NM_019619	
SWSAP1	126074	hgsc.bcm.edu	37	19	11486354	11486354	+	Missense_Mutation	SNP	C	C	A	rs146815699	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr19:11486354C>A	ENST00000312423.2	+	2	411	c.352C>A	c.(352-354)Ctt>Att	p.L118I	CTD-2342J14.6_ENST00000590399.1_RNA	NM_175871.3	NP_787067.2	Q6NVH7	SWAP1_HUMAN	SWIM-type zinc finger 7 associated protein 1	118					ATP catabolic process (GO:0006200)|double-strand break repair via homologous recombination (GO:0000724)|protein stabilization (GO:0050821)	nucleus (GO:0005634)|Shu complex (GO:0097196)	ATPase activity (GO:0016887)|single-stranded DNA binding (GO:0003697)										CATTGCCTTACTTCTAGACAC	0.652													C|||	3	0.000599042	0.0	0.0014	5008	,	,		17164	0.0		0.002	False		,,,				2504	0.0				p.L118I		Atlas-SNP	.											.	.	.	.	0			c.C352A						PASS	.	C	ILE/LEU	5,4401	9.9+/-24.2	0,5,2198	73.0	72.0	72.0		352	5.3	1.0	19	dbSNP_134	72	39,8561	26.8+/-75.7	0,39,4261	yes	missense	C19orf39	NM_175871.3	5	0,44,6459	AA,AC,CC		0.4535,0.1135,0.3383	possibly-damaging	118/230	11486354	44,12962	2203	4300	6503	SO:0001583	missense	126074	exon2			GCCTTACTTCTAG	AK092438	CCDS12259.1	19p13.2	2011-11-24	2011-11-24	2011-11-24	ENSG00000173928	ENSG00000173928			26638	protein-coding gene	gene with protein product	"""zinc finger, SWIM-type containing 7 associated protein 1"", ""SWS1-associated protein 1"""	614536	"""chromosome 19 open reading frame 39"""	C19orf39		21965664	Standard	NM_175871		Approved	FLJ35119, ZSWIM7AP1, SWS1AP1	uc002mrg.1	Q6NVH7		ENST00000312423.2:c.352C>A	19.37:g.11486354C>A	ENSP00000310008:p.Leu118Ile	70.0	0.0	0		66.0	25.0	0.378788	NM_175871	Q8NAM1	Missense_Mutation	SNP	ENST00000312423.2	37	CCDS12259.1	3	0.0013736263736263737	0	0.0	1	0.0027624309392265192	0	0.0	2	0.002638522427440633	C	24.3	4.520751	0.85495	0.001135	0.004535	ENSG00000173928	ENST00000312423	T	0.41400	1.0	5.32	5.32	0.75619	.	0.000000	0.64402	D	0.000007	T	0.63307	0.2500	M	0.65975	2.015	0.45216	D	0.998223	D	0.76494	0.999	D	0.87578	0.998	T	0.65038	-0.6265	10	0.59425	D	0.04	-11.7403	15.9252	0.79611	0.0:1.0:0.0:0.0	.	118	Q6NVH7	CS039_HUMAN	I	118	ENSP00000310008:L118I	ENSP00000310008:L118I	L	+	1	0	C19orf39	11347354	1.000000	0.71417	0.998000	0.56505	0.762000	0.43233	4.466000	0.60148	2.489000	0.83994	0.655000	0.94253	CTT	C|0.997;A|0.003	0.003	strong		0.652	SWSAP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000458789.1	NM_175871	
C5orf42	65250	hgsc.bcm.edu	37	5	37153871	37153871	+	Missense_Mutation	SNP	G	G	T	rs77014998	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr5:37153871G>T	ENST00000508244.1	-	40	8275	c.8182C>A	c.(8182-8184)Cct>Act	p.P2728T	C5orf42_ENST00000274258.7_Missense_Mutation_p.P1626T|C5orf42_ENST00000425232.2_Missense_Mutation_p.P2728T			Q9H799	CE042_HUMAN	chromosome 5 open reading frame 42	2728						integral component of membrane (GO:0016021)				breast(5)|endometrium(3)|kidney(8)|large_intestine(24)|lung(28)|ovary(4)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(3)	79	all_lung(31;0.000616)		COAD - Colon adenocarcinoma(61;0.14)|Epithelial(62;0.177)|Colorectal(62;0.202)			AGCATTTCAGGCTTGGGGAAA	0.358													G|||	13	0.00259585	0.0	0.0058	5008	,	,		19975	0.0		0.0089	False		,,,				2504	0.0				p.P2728T		Atlas-SNP	.											.	C5orf42	422	.	0			c.C8182A						PASS	.	G	THR/PRO	20,4386	27.2+/-55.0	0,20,2183	93.0	83.0	86.0		8182	2.3	0.0	5	dbSNP_131	86	99,8501	54.4+/-115.2	1,97,4202	yes	missense	C5orf42	NM_023073.3	38	1,117,6385	TT,TG,GG		1.1512,0.4539,0.915	benign	2728/3198	37153871	119,12887	2203	4300	6503	SO:0001583	missense	65250	exon41			TTTCAGGCTTGGG		CCDS34146.1, CCDS34146.2	5p13.2	2014-01-28			ENSG00000197603	ENSG00000197603			25801	protein-coding gene	gene with protein product		614571				22264561	Standard	NM_023073		Approved	FLJ13231, JBTS17	uc011cpa.1	Q9H799	OTTHUMG00000160492	ENST00000508244.1:c.8182C>A	5.37:g.37153871G>T	ENSP00000421690:p.Pro2728Thr	122.0	0.0	0		90.0	34.0	0.377778	NM_023073	A8MUB7|B7ZLV7|Q4G174|Q6DK46|Q8N8L4|Q9H5T1|Q9H8T9	Missense_Mutation	SNP	ENST00000508244.1	37	CCDS34146.2	9	0.004120879120879121	0	0.0	2	0.0055248618784530384	0	0.0	7	0.009234828496042216	G	3.383	-0.126029	0.06795	0.004539	0.011512	ENSG00000197603	ENST00000508244;ENST00000425232;ENST00000274258;ENST00000514429;ENST00000388739	T;T;T;T	0.17854	2.25;2.25;2.35;2.34	5.41	2.29	0.28610	.	1.705140	0.03544	N	0.224372	T	0.07052	0.0179	N	0.14661	0.345	0.09310	N	1	B;B	0.06786	0.001;0.001	B;B	0.06405	0.002;0.002	T	0.29274	-1.0017	10	0.16420	T	0.52	.	4.6926	0.12788	0.1913:0.0:0.5443:0.2644	.	2728;1626	E9PH94;Q9H799	.;CE042_HUMAN	T	2728;2728;1626;1794;1662	ENSP00000421690:P2728T;ENSP00000389014:P2728T;ENSP00000274258:P1626T;ENSP00000424223:P1794T	ENSP00000274258:P1626T	P	-	1	0	C5orf42	37189628	0.000000	0.05858	0.000000	0.03702	0.592000	0.36648	0.288000	0.18939	0.645000	0.30675	0.591000	0.81541	CCT	G|0.992;T|0.008	0.008	strong		0.358	C5orf42-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000360806.1	NM_023073	
VPS13B	157680	hgsc.bcm.edu	37	8	100874154	100874154	+	Missense_Mutation	SNP	G	G	A	rs149318176	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr8:100874154G>A	ENST00000358544.2	+	58	11381	c.11270G>A	c.(11269-11271)cGg>cAg	p.R3757Q	VPS13B_ENST00000395996.1_3'UTR|VPS13B_ENST00000357162.2_Missense_Mutation_p.R3732Q	NM_017890.4	NP_060360.3	Q7Z7G8	VP13B_HUMAN	vacuolar protein sorting 13 homolog B (yeast)	3757					protein transport (GO:0015031)					NS(1)|autonomic_ganglia(1)|breast(6)|central_nervous_system(4)|cervix(3)|endometrium(11)|haematopoietic_and_lymphoid_tissue(4)|kidney(10)|large_intestine(37)|lung(78)|ovary(8)|pancreas(3)|prostate(5)|skin(9)|upper_aerodigestive_tract(4)|urinary_tract(9)	193	Breast(36;3.73e-07)		OV - Ovarian serous cystadenocarcinoma(57;0.00636)			GGCCTGTCCCGGCTGGGCATC	0.677													G|||	5	0.000998403	0.0	0.0014	5008	,	,		14908	0.0		0.001	False		,,,				2504	0.0031				p.R3757Q	Colon(161;2205 2542 7338 31318)	Atlas-SNP	.											.	VPS13B	811	.	0			c.G11270A						PASS	.	G	GLN/ARG,GLN/ARG	0,4392		0,0,2196	16.0	18.0	18.0		11270,11195	5.8	1.0	8	dbSNP_134	18	23,8565		0,23,4271	yes	missense,missense	VPS13B	NM_017890.3,NM_152564.3	43,43	0,23,6467	AA,AG,GG		0.2678,0.0,0.1772	probably-damaging,probably-damaging	3757/4023,3732/3998	100874154	23,12957	2196	4294	6490	SO:0001583	missense	157680	exon58			TGTCCCGGCTGGG	AJ608772	CCDS6280.1, CCDS6281.1, CCDS6283.1, CCDS47903.1	8q22-q23	2014-09-17	2006-12-19	2005-04-08	ENSG00000132549	ENSG00000132549			2183	protein-coding gene	gene with protein product		607817	"""Cohen syndrome 1"""	CHS1, COH1		7920642, 15498460	Standard	NM_181661		Approved		uc003yiv.4	Q7Z7G8	OTTHUMG00000140383	ENST00000358544.2:c.11270G>A	8.37:g.100874154G>A	ENSP00000351346:p.Arg3757Gln	61.0	0.0	0		83.0	28.0	0.337349	NM_017890	C9JD30|Q709C6|Q709C7|Q7Z7G4|Q7Z7G5|Q7Z7G6|Q7Z7G7|Q8NB77|Q9NWV1|Q9Y4E7	Missense_Mutation	SNP	ENST00000358544.2	37	CCDS6280.1	.	.	.	.	.	.	.	.	.	.	G	35	5.463122	0.96257	0.0	0.002678	ENSG00000132549	ENST00000357162;ENST00000358544	T;T	0.69306	-0.39;-0.39	5.78	5.78	0.91487	Autophagy-related, C-terminal (1);	0.000000	0.85682	D	0.000000	T	0.77260	0.4104	L	0.40543	1.245	0.80722	D	1	D;D	0.89917	0.997;1.0	D;D	0.87578	0.948;0.998	T	0.74873	-0.3516	10	0.41790	T	0.15	.	20.0204	0.97499	0.0:0.0:1.0:0.0	.	3732;3757	Q7Z7G8-2;Q7Z7G8	.;VP13B_HUMAN	Q	3732;3757	ENSP00000349685:R3732Q;ENSP00000351346:R3757Q	ENSP00000349685:R3732Q	R	+	2	0	VPS13B	100943330	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	7.628000	0.83189	2.729000	0.93468	0.650000	0.86243	CGG	G|0.998;A|0.002	0.002	strong		0.677	VPS13B-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000277138.1	NM_184042	
ALG6	29929	hgsc.bcm.edu	37	1	63902524	63902524	+	Missense_Mutation	SNP	C	C	G	rs41285372	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr1:63902524C>G	ENST00000371108.4	+	15	1662	c.1357C>G	c.(1357-1359)Ctg>Gtg	p.L453V	ALG6_ENST00000263440.4_Missense_Mutation_p.L455V|ALG6_ENST00000494765.1_3'UTR	NM_013339.3	NP_037471.2	Q9Y672	ALG6_HUMAN	ALG6, alpha-1,3-glucosyltransferase	453					cellular protein metabolic process (GO:0044267)|dolichol-linked oligosaccharide biosynthetic process (GO:0006488)|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 membrane (GO:0016021)|membrane (GO:0016020)	glucosyltransferase activity (GO:0046527)			endometrium(1)|large_intestine(4)|lung(5)|prostate(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	13						TATGGTGCTTCTGACGTTGAT	0.383													C|||	21	0.00419329	0.0008	0.0043	5008	,	,		18422	0.0		0.0159	False		,,,				2504	0.001				p.L453V		Atlas-SNP	.											.	ALG6	33	.	0			c.C1357G						PASS	.	C	VAL/LEU	24,4382	30.8+/-60.4	1,22,2180	227.0	214.0	219.0		1357	3.2	1.0	1	dbSNP_127	219	152,8448	72.9+/-135.5	1,150,4149	yes	missense	ALG6	NM_013339.3	32	2,172,6329	GG,GC,CC		1.7674,0.5447,1.3532	possibly-damaging	453/508	63902524	176,12830	2203	4300	6503	SO:0001583	missense	29929	exon15			GTGCTTCTGACGT	AF063604	CCDS30735.1	1p31.3	2013-03-01	2013-03-01		ENSG00000088035	ENSG00000088035	2.4.1.267		23157	protein-coding gene	gene with protein product	"""dolichyl-P-Glc:Man(9)GlcNAc(2)-PP-dolichol alpha- 1->3-glucosyltransferase"""	604566	"""asparagine-linked glycosylation 6 homolog (yeast, alpha-1,3-glucosyltransferase)"", ""asparagine-linked glycosylation 6, alpha-1,3-glucosyltransferase homolog (S. cerevisiae)"""			10359825, 11875054	Standard	NM_013339		Approved		uc021oof.1	Q9Y672	OTTHUMG00000009140	ENST00000371108.4:c.1357C>G	1.37:g.63902524C>G	ENSP00000360149:p.Leu453Val	275.0	0.0	0		180.0	135.0	0.75	NM_013339	B3KMU2|Q5SXR9|Q9H3I0	Missense_Mutation	SNP	ENST00000371108.4	37	CCDS30735.1	13	0.005952380952380952	1	0.0020325203252032522	2	0.0055248618784530384	0	0.0	10	0.013192612137203167	C	16.45	3.125406	0.56721	0.005447	0.017674	ENSG00000088035	ENST00000371108;ENST00000263440;ENST00000423077	D;D	0.83755	-1.76;-1.76	5.06	3.19	0.36642	.	0.079049	0.53938	D	0.000045	D	0.86100	0.5852	M	0.73962	2.25	0.58432	D	0.999999	D;D	0.89917	1.0;0.977	D;D	0.87578	0.998;0.919	D	0.85509	0.1196	10	0.45353	T	0.12	-16.66	11.1039	0.48190	0.0:0.8472:0.0:0.1528	rs41285372	200;455	B4DHV8;A2A2G4	.;.	V	453;455;200	ENSP00000360149:L453V;ENSP00000263440:L455V	ENSP00000263440:L455V	L	+	1	2	ALG6	63675112	0.985000	0.35326	0.997000	0.53966	0.749000	0.42624	2.010000	0.40913	0.647000	0.30713	0.484000	0.47621	CTG	C|0.987;G|0.013	0.013	strong		0.383	ALG6-001	KNOWN	non_canonical_conserved|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000025330.2	NM_013339	
IFNA1	3439	hgsc.bcm.edu	37	9	21440916	21440916	+	Missense_Mutation	SNP	C	C	T	rs2230050	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr9:21440916C>T	ENST00000276927.1	+	1	477	c.410C>T	c.(409-411)gCg>gTg	p.A137V		NM_024013.2	NP_076918.1	P01562	IFNA1_HUMAN	interferon, alpha 1	137			A -> V (in alpha-1B; dbSNP:rs2230050). {ECO:0000269|Ref.9}.		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)|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)			kidney(1)|large_intestine(1)|lung(3)|ovary(2)	7				Lung(24;7.66e-27)|LUSC - Lung squamous cell carcinoma(38;1.4e-13)|OV - Ovarian serous cystadenocarcinoma(39;0.0173)		CTGATGAATGCGGACTCCATC	0.498													c|||	118	0.0235623	0.0764	0.013	5008	,	,		18884	0.001		0.005	False		,,,				2504	0.002				p.A137V		Atlas-SNP	.											IFNA1,NS,carcinoma,-1,1	IFNA1	21	1	0			c.C410T						scavenged	.	C	VAL/ALA	264,3734		11,242,1746	17.0	21.0	19.0		410	0.5	0.0	9	dbSNP_134	19	25,8205		0,25,4090	no	missense	IFNA1	NM_024013.2	64	11,267,5836	TT,TC,CC		0.3038,6.6033,2.3634	benign	137/190	21440916	289,11939	1999	4115	6114	SO:0001583	missense	3439	exon1			TGAATGCGGACTC		CCDS6508.1	9p22	2010-12-10			ENSG00000197919	ENSG00000197919		"""Interferons"""	5417	protein-coding gene	gene with protein product	"""IFN-alpha 1b"", ""interferon alpha 1b"""	147660				1385305	Standard	NM_024013		Approved	IFNA@, IFL, IFN, IFN-ALPHA, IFNA13, IFN-alphaD	uc003zpd.2	P01562	OTTHUMG00000019673	ENST00000276927.1:c.410C>T	9.37:g.21440916C>T	ENSP00000276927:p.Ala137Val	714.0	0.0	0		634.0	176.0	0.277603	NM_024013	D4Q9M8|Q14605|Q2M1L8|Q52LB8|Q5VYQ2|Q7M4Q1|Q8WZ68|Q9UMJ3	Missense_Mutation	SNP	ENST00000276927.1	37	CCDS6508.1	.	.	.	.	.	.	.	.	.	.	C	7.309	0.614657	0.14129	0.066033	0.003038	ENSG00000197919	ENST00000276927	T	0.05580	3.42	3.12	0.511	0.16989	Four-helical cytokine-like, core (1);Four-helical cytokine, core (1);	0.388379	0.22170	N	0.063657	T	0.00271	0.0008	N	0.11927	0.2	0.09310	N	1	B	0.09022	0.002	B	0.13407	0.009	T	0.43702	-0.9375	10	0.39692	T	0.17	.	3.5529	0.07853	0.5394:0.2403:0.0:0.2203	.	137	P01562	IFNA1_HUMAN	V	137	ENSP00000276927:A137V	ENSP00000276927:A137V	A	+	2	0	IFNA1	21430916	0.000000	0.05858	0.000000	0.03702	0.002000	0.02628	0.127000	0.15790	-0.015000	0.14150	-0.607000	0.04081	GCG	C|0.946;T|0.054	0.054	strong		0.498	IFNA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051902.1	NM_024013	
TELO2	9894	hgsc.bcm.edu	37	16	1555505	1555505	+	Missense_Mutation	SNP	C	C	T			TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr16:1555505C>T	ENST00000262319.6	+	16	2216	c.1937C>T	c.(1936-1938)cCa>cTa	p.P646L	TELO2_ENST00000564507.1_3'UTR	NM_016111.3	NP_057195.2	Q9Y4R8	TELO2_HUMAN	telomere maintenance 2	646					regulation of TOR signaling (GO:0032006)	chromosome, telomeric region (GO:0000781)|cytoplasm (GO:0005737)|intracellular (GO:0005622)|membrane (GO:0016020)|nucleus (GO:0005634)|TORC1 complex (GO:0031931)|TORC2 complex (GO:0031932)	protein complex binding (GO:0032403)			NS(1)|endometrium(1)|kidney(5)|lung(9)|ovary(1)|skin(1)|urinary_tract(1)	19		Hepatocellular(780;0.219)				CCGTGCCTGCCAGAGGCAGCC	0.667																																					p.P646L		Atlas-SNP	.											.	TELO2	44	.	0			c.C1937T						PASS	.						33.0	37.0	36.0					16																	1555505		2198	4297	6495	SO:0001583	missense	9894	exon16			GCCTGCCAGAGGC	AL080126	CCDS32363.1	16p13.3	2013-08-06	2013-08-06		ENSG00000100726	ENSG00000100726			29099	protein-coding gene	gene with protein product		611140	"""TEL2, telomere maintenance 2, homolog (S. cerevisiae)"""			9734811, 11230166, 12670948	Standard	NM_016111		Approved	KIAA0683, hCLK2, TEL2	uc002cly.3	Q9Y4R8	OTTHUMG00000044471	ENST00000262319.6:c.1937C>T	16.37:g.1555505C>T	ENSP00000262319:p.Pro646Leu	102.0	0.0	0		131.0	61.0	0.465649	NM_016111	D3DU73|O75168|Q7LDV4|Q9BR21	Missense_Mutation	SNP	ENST00000262319.6	37	CCDS32363.1	.	.	.	.	.	.	.	.	.	.	C	9.403	1.078424	0.20227	.	.	ENSG00000100726	ENST00000437914;ENST00000262319	T	0.14893	2.47	3.64	1.62	0.23740	.	0.309815	0.24107	N	0.041482	T	0.12305	0.0299	L	0.50333	1.59	0.21147	N	0.999776	B	0.26635	0.155	B	0.20384	0.029	T	0.27706	-1.0066	10	0.22706	T	0.39	-0.0024	5.4471	0.16541	0.1965:0.693:0.0:0.1106	.	646	Q9Y4R8	TELO2_HUMAN	L	169;646	ENSP00000262319:P646L	ENSP00000262319:P646L	P	+	2	0	TELO2	1495506	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	0.334000	0.19787	0.069000	0.16605	-1.436000	0.01078	CCA	.	.	none		0.667	TELO2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000103602.2	NM_016111	
MMP8	4317	hgsc.bcm.edu	37	11	102595579	102595579	+	Missense_Mutation	SNP	G	G	C	rs17099450	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr11:102595579G>C	ENST00000236826.3	-	1	106	c.8C>G	c.(7-9)tCc>tGc	p.S3C		NM_002424.2	NP_002415.1	P22894	MMP8_HUMAN	matrix metallopeptidase 8 (neutrophil collagenase)	3			S -> C (in dbSNP:rs17099450). {ECO:0000269|Ref.2}.		collagen catabolic process (GO:0030574)|endodermal cell differentiation (GO:0035987)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|proteolysis (GO:0006508)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|proteinaceous extracellular matrix (GO:0005578)	calcium ion binding (GO:0005509)|metalloendopeptidase activity (GO:0004222)|serine-type endopeptidase activity (GO:0004252)|zinc ion binding (GO:0008270)			autonomic_ganglia(1)|breast(3)|kidney(1)|large_intestine(4)|lung(11)|ovary(4)|skin(6)|stomach(1)|urinary_tract(1)	32	all_cancers(8;0.00092)|all_epithelial(12;0.00389)|Lung NSC(15;0.227)	all_hematologic(158;0.00092)|Acute lymphoblastic leukemia(157;0.000967)	Epithelial(9;0.0555)|Lung(13;0.0828)|LUSC - Lung squamous cell carcinoma(19;0.151)|all cancers(10;0.189)	BRCA - Breast invasive adenocarcinoma(274;0.0141)	Marimastat(DB00786)	CGTCTTCAGGGAGAACATGAT	0.468													G|||	199	0.0397364	0.0514	0.0389	5008	,	,		18266	0.0089		0.0417	False		,,,				2504	0.0542				p.S3C		Atlas-SNP	.											.	MMP8	68	.	0			c.C8G						PASS	.	G	CYS/SER	213,4193	130.2+/-166.9	7,199,1997	147.0	154.0	152.0		8	-10.2	0.0	11	dbSNP_123	152	441,8157	133.9+/-191.4	13,415,3871	yes	missense	MMP8	NM_002424.2	112	20,614,5868	CC,CG,GG		5.1291,4.8343,5.0292	benign	3/468	102595579	654,12350	2203	4299	6502	SO:0001583	missense	4317	exon1			TTCAGGGAGAACA	J05556	CCDS8320.1	11q21-q22	2008-02-05	2005-08-08		ENSG00000118113	ENSG00000118113	3.4.24.34		7175	protein-coding gene	gene with protein product		120355	"""matrix metalloproteinase 8 (neutrophil collagenase)"""	CLG1			Standard	NM_002424		Approved		uc001phe.2	P22894	OTTHUMG00000167587	ENST00000236826.3:c.8C>G	11.37:g.102595579G>C	ENSP00000236826:p.Ser3Cys	200.0	0.0	0		335.0	80.0	0.238806	NM_002424	Q45F99	Missense_Mutation	SNP	ENST00000236826.3	37	CCDS8320.1	73	0.033424908424908424	23	0.046747967479674794	16	0.04419889502762431	3	0.005244755244755245	31	0.040897097625329816	G	11.83	1.756524	0.31137	0.048343	0.051291	ENSG00000118113	ENST00000236826	T	0.13901	2.55	5.26	-10.2	0.00374	.	5.605950	0.00166	N	0.000000	T	0.00815	0.0027	N	0.14661	0.345	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.24368	-1.0162	10	0.52906	T	0.07	.	0.229	0.00177	0.2519:0.1874:0.2546:0.3061	rs17099450;rs52812571;rs17099450	3	P22894	MMP8_HUMAN	C	3	ENSP00000236826:S3C	ENSP00000236826:S3C	S	-	2	0	MMP8	102100789	0.000000	0.05858	0.000000	0.03702	0.002000	0.02628	-1.482000	0.02320	-1.792000	0.01259	-1.067000	0.02272	TCC	G|0.946;C|0.054	0.054	strong		0.468	MMP8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000395223.1	NM_002424	
EGFR	1956	hgsc.bcm.edu	37	7	55268916	55268916	+	Silent	SNP	C	C	T	rs2293347|rs587778251	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr7:55268916C>T	ENST00000275493.2	+	25	3159	c.2982C>T	c.(2980-2982)gaC>gaT	p.D994D	EGFR_ENST00000454757.2_Silent_p.D941D|EGFR_ENST00000442591.1_Intron|EGFR_ENST00000455089.1_Silent_p.D949D	NM_005228.3	NP_005219.2	P00533	EGFR_HUMAN	epidermal growth factor receptor	994					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)	GTCCTACAGACTCCAACTTCT	0.512		8	"""A, O, Mis"""		"""glioma, NSCLC"""	NSCLC			Lung Cancer, Familial Clustering of	TCGA GBM(3;<1E-08)|TSP Lung(4;<1E-08)			t|||	710	0.141773	0.0129	0.1542	5008	,	,		18651	0.247		0.1113	False		,,,				2504	0.2301				p.D994D		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	20426	.	0			c.C2982T						PASS	.	T		121,4285	90.6+/-129.3	1,119,2083	151.0	139.0	143.0		2982	3.8	1.0	7	dbSNP_100	143	795,7805	185.7+/-233.4	42,711,3547	no	coding-synonymous	EGFR	NM_005228.3		43,830,5630	TT,TC,CC		9.2442,2.7463,7.0429		994/1211	55268916	916,12090	2203	4300	6503	SO:0001819	synonymous_variant	1956	exon25	Familial Cancer Database	incl. Hereditary Lung cancer, Hereditary Non-Small Cell Lung cancer	TACAGACTCCAAC		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.2982C>T	7.37:g.55268916C>T		206.0	0.0	0		252.0	85.0	0.337302	NM_005228	O00688|O00732|P06268|Q14225|Q68GS5|Q92795|Q9BZS2|Q9GZX1|Q9H2C9|Q9H3C9|Q9UMD7|Q9UMD8|Q9UMG5	Silent	SNP	ENST00000275493.2	37	CCDS5514.1																																																																																			C|0.894;T|0.106	0.106	strong		0.512	EGFR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251456.2	NM_005228	
SSUH2	51066	hgsc.bcm.edu	37	3	8675447	8675447	+	Missense_Mutation	SNP	C	C	T	rs112366230	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr3:8675447C>T	ENST00000317371.4	-	11	1403	c.178G>A	c.(178-180)Gcc>Acc	p.A60T	SSUH2_ENST00000341795.3_Missense_Mutation_p.A60T|SSUH2_ENST00000415132.1_Missense_Mutation_p.A60T|SSUH2_ENST00000544814.1_Missense_Mutation_p.A82T			Q9Y2M2	SSUH2_HUMAN	ssu-2 homolog (C. elegans)	60						cytoplasm (GO:0005737)											CTGAGGAGGGCTTCCCGGGCC	0.657													C|||	67	0.0133786	0.0424	0.0086	5008	,	,		13880	0.0		0.003	False		,,,				2504	0.002				p.A82T		Atlas-SNP	.											.	.	.	.	0			c.G244A						PASS	.	C	THR/ALA	156,4248		3,150,2049	27.0	30.0	29.0		178	5.1	1.0	3	dbSNP_132	29	73,8519		1,71,4224	yes	missense	C3orf32	NM_015931.1	58	4,221,6273	TT,TC,CC		0.8496,3.5422,1.7621	probably-damaging	60/354	8675447	229,12767	2202	4296	6498	SO:0001583	missense	51066	exon4			GGAGGGCTTCCCG	AB024705	CCDS2568.1, CCDS58815.1	3p25.3	2012-11-05	2012-11-05	2012-11-05	ENSG00000125046	ENSG00000125046			24809	protein-coding gene	gene with protein product			"""chromosome 3 open reading frame 32"""	C3orf32		20205943	Standard	NM_001256748		Approved	fls485, ssu-2	uc011atg.3	Q9Y2M2	OTTHUMG00000122075	ENST00000317371.4:c.178G>A	3.37:g.8675447C>T	ENSP00000324551:p.Ala60Thr	157.0	0.0	0		182.0	96.0	0.527473	NM_001256748	A6NFA9|B3KS84|B7Z6E3|F5H2S5|Q7Z7K4	Missense_Mutation	SNP	ENST00000317371.4	37	CCDS2568.1	16	0.007326007326007326	13	0.026422764227642278	3	0.008287292817679558	0	0.0	0	0.0	C	21.1	4.092595	0.76756	0.035422	0.008496	ENSG00000125046	ENST00000341795;ENST00000317371;ENST00000415132;ENST00000544814;ENST00000427408	T;T;T;T;T	0.54675	0.61;0.61;0.59;0.61;0.56	5.14	5.14	0.70334	.	0.000000	0.85682	D	0.000000	T	0.43897	0.1268	M	0.83953	2.67	0.46061	D	0.998843	D;D	0.89917	1.0;1.0	D;D	0.87578	0.998;0.998	T	0.68416	-0.5414	10	0.72032	D	0.01	-39.6842	14.128	0.65235	0.0:1.0:0.0:0.0	.	82;60	F5H2S5;Q9Y2M2	.;CC032_HUMAN	T	60;60;60;82;82	ENSP00000339150:A60T;ENSP00000324551:A60T;ENSP00000410757:A60T;ENSP00000439378:A82T;ENSP00000401289:A82T	ENSP00000324551:A60T	A	-	1	0	C3orf32	8650447	1.000000	0.71417	1.000000	0.80357	0.339000	0.28857	4.952000	0.63618	2.407000	0.81776	0.484000	0.47621	GCC	C|0.986;T|0.014	0.014	strong		0.657	SSUH2-005	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000337900.1	NM_015931	
CABIN1	23523	hgsc.bcm.edu	37	22	24567795	24567795	+	Missense_Mutation	SNP	C	C	T	rs145513360	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr22:24567795C>T	ENST00000398319.2	+	34	6257	c.5872C>T	c.(5872-5874)Cgg>Tgg	p.R1958W	CABIN1_ENST00000405822.2_Missense_Mutation_p.R1879W|CABIN1_ENST00000263119.5_Missense_Mutation_p.R1958W|CABIN1_ENST00000485008.1_3'UTR|CABIN1_ENST00000337989.7_Missense_Mutation_p.R383W	NM_001199281.1	NP_001186210.1	Q9Y6J0	CABIN_HUMAN	calcineurin binding protein 1	1958					cell surface receptor signaling pathway (GO:0007166)|chromatin modification (GO:0016568)|DNA replication-independent nucleosome assembly (GO:0006336)|negative regulation of catalytic activity (GO:0043086)	aggresome (GO:0016235)|cytoplasm (GO:0005737)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	protein phosphatase inhibitor activity (GO:0004864)			breast(2)|central_nervous_system(2)|endometrium(6)|kidney(6)|large_intestine(13)|liver(1)|lung(18)|ovary(5)|pancreas(3)|prostate(1)|skin(6)|upper_aerodigestive_tract(1)|urinary_tract(1)	65						CTCTGTCCAGCGGCCCAGTGA	0.607													C|||	3	0.000599042	0.0	0.0	5008	,	,		19053	0.0		0.003	False		,,,				2504	0.0				p.R1958W		Atlas-SNP	.											.	CABIN1	153	.	0			c.C5872T						PASS	.	C	TRP/ARG,TRP/ARG,TRP/ARG	0,4406		0,0,2203	123.0	115.0	118.0		5872,5722,5872	2.7	0.9	22	dbSNP_134	118	4,8596	3.7+/-12.6	0,4,4296	yes	missense,missense,missense	CABIN1	NM_001199281.1,NM_001201429.1,NM_012295.3	101,101,101	0,4,6499	TT,TC,CC		0.0465,0.0,0.0308	probably-damaging,probably-damaging,probably-damaging	1958/2221,1908/2171,1958/2221	24567795	4,13002	2203	4300	6503	SO:0001583	missense	23523	exon34			GTCCAGCGGCCCA	AF072441	CCDS13823.1, CCDS74830.1	22q11.23	2008-09-16			ENSG00000099991	ENSG00000099991			24187	protein-coding gene	gene with protein product		604251				9655484, 9205841	Standard	NM_001199281		Approved	KIAA0330, PPP3IN	uc002zzi.1	Q9Y6J0	OTTHUMG00000150797	ENST00000398319.2:c.5872C>T	22.37:g.24567795C>T	ENSP00000381364:p.Arg1958Trp	141.0	0.0	0		160.0	94.0	0.5875	NM_001199281	G5E9F3|Q6PHY0|Q9Y460	Missense_Mutation	SNP	ENST00000398319.2	37	CCDS13823.1	2	9.157509157509158E-4	0	0.0	0	0.0	0	0.0	2	0.002638522427440633	C	17.75	3.465698	0.63513	0.0	4.65E-4	ENSG00000099991	ENST00000263119;ENST00000405822;ENST00000398319;ENST00000337989;ENST00000403176	T;T;T;T	0.19806	2.12;2.12;2.12;2.12	4.9	2.7	0.31948	.	0.150708	0.43110	D	0.000609	T	0.30008	0.0751	N	0.24115	0.695	0.39027	D	0.959857	D;D	0.89917	0.999;1.0	P;D	0.79784	0.9;0.993	T	0.12192	-1.0557	10	0.72032	D	0.01	.	12.406	0.55441	0.3019:0.698:0.0:0.0	.	1879;1958	G5E9F3;Q9Y6J0	.;CABIN_HUMAN	W	1958;1879;1958;383;382	ENSP00000263119:R1958W;ENSP00000384694:R1879W;ENSP00000381364:R1958W;ENSP00000336991:R383W	ENSP00000263119:R1958W	R	+	1	2	CABIN1	22897795	0.011000	0.17503	0.915000	0.36163	0.505000	0.33919	0.127000	0.15790	0.689000	0.31550	0.650000	0.86243	CGG	C|0.999;T|0.001	0.001	strong		0.607	CABIN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000320161.2	NM_012295	
B2M	567	hgsc.bcm.edu	37	15	45003746	45003746	+	Start_Codon_SNP	SNP	T	T	G			TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr15:45003746T>G	ENST00000558401.1	+	1	72	c.2T>G	c.(1-3)aTg>aGg	p.M1R	B2M_ENST00000544417.1_Start_Codon_SNP_p.M1R|B2M_ENST00000559916.1_Start_Codon_SNP_p.M1R|PATL2_ENST00000558573.1_5'Flank	NM_004048.2	NP_004039.1	P61769	B2MG_HUMAN	beta-2-microglobulin	1					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)	p.M1R(3)|p.M1K(2)|p.M1T(2)|p.?(1)		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)		CGGGCCGAGATGTCTCGCTCC	0.612																																					p.M1R		Atlas-SNP	.											B2M,caecum,carcinoma,-1,17	B2M	99	17	8	Substitution - Missense(7)|Unknown(1)	haematopoietic_and_lymphoid_tissue(7)|lung(1)	c.T2G						PASS	.						126.0	92.0	104.0					15																	45003746		2198	4298	6496	SO:0001582	initiator_codon_variant	567	exon1			CCGAGATGTCTCG	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.2T>G	15.37:g.45003746T>G	ENSP00000452780:p.Met1Arg	113.0	0.0	0		75.0	38.0	0.506667	NM_004048	P01884|Q540F8|Q6IAT8|Q9UCK0|Q9UD48|Q9UDF4	Missense_Mutation	SNP	ENST00000558401.1	37	CCDS10113.1	.	.	.	.	.	.	.	.	.	.	T	17.67	3.446958	0.63178	.	.	ENSG00000166710	ENST00000349264;ENST00000544417;ENST00000396754	T	0.01304	5.03	5.35	4.22	0.49857	.	.	.	.	.	T	0.04907	0.0132	.	.	.	0.80722	D	1	D;D;D	0.63880	0.989;0.993;0.981	P;P;P	0.59288	0.847;0.855;0.708	T	0.21415	-1.0246	8	0.87932	D	0	.	8.1513	0.31143	0.0:0.0894:0.0:0.9106	.	1;1;1	F5H6I0;A6XMH4;P61769	.;.;B2MG_HUMAN	R	1	ENSP00000437604:M1R	ENSP00000340858:M1R	M	+	2	0	B2M	42791038	0.961000	0.32948	0.428000	0.26697	0.026000	0.11368	1.415000	0.34748	1.147000	0.42369	0.533000	0.62120	ATG	.	.	none		0.612	B2M-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000254007.2	NM_004048	Missense_Mutation
PPP1R42	286187	hgsc.bcm.edu	37	8	67926717	67926717	+	Silent	SNP	T	T	C			TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr8:67926717T>C	ENST00000324682.5	-	3	384	c.240A>G	c.(238-240)caA>caG	p.Q80Q	PPP1R42_ENST00000522909.1_Silent_p.Q80Q|PPP1R42_ENST00000517834.1_Intron	NM_001013626.2	NP_001013648.1	Q7Z4L9	PPR42_HUMAN	protein phosphatase 1, regulatory subunit 42	80					regulation of phosphatase activity (GO:0010921)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|manchette (GO:0002177)|microtubule cytoskeleton (GO:0015630)|microtubule organizing center (GO:0005815)	actin binding (GO:0003779)|dynein binding (GO:0045502)|tubulin binding (GO:0015631)										TACAATTGTTTTGTAGGTACA	0.274																																					p.Q80Q		Atlas-SNP	.											.	PPP1R42	2	.	0			c.A240G						PASS	.						97.0	109.0	105.0					8																	67926717		2203	4294	6497	SO:0001819	synonymous_variant	286187	exon3			ATTGTTTTGTAGG	BC055413	CCDS34902.1	8q13.1-q13.2	2012-04-17	2011-10-11	2011-10-11	ENSG00000178125	ENSG00000178125		"""Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"""	33732	protein-coding gene	gene with protein product	"""testis leucine-rich repeat"""		"""leucine rich repeat containing 67"""	LRRC67			Standard	NM_001013626		Approved	dtr, TLLR	uc003xxc.3	Q7Z4L9	OTTHUMG00000164745	ENST00000324682.5:c.240A>G	8.37:g.67926717T>C		127.0	0.0	0		73.0	60.0	0.821918	NM_001013626		Silent	SNP	ENST00000324682.5	37	CCDS34902.1																																																																																			.	.	none		0.274	PPP1R42-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000380034.2	NM_001013626	
PLXNC1	10154	hgsc.bcm.edu	37	12	94631496	94631496	+	Silent	SNP	C	C	T	rs2230755	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr12:94631496C>T	ENST00000258526.4	+	10	2286	c.2037C>T	c.(2035-2037)aaC>aaT	p.N679N		NM_005761.2	NP_005752.1	O60486	PLXC1_HUMAN	plexin C1	679					axon guidance (GO:0007411)|cell adhesion (GO:0007155)|signal transduction (GO:0007165)	integral component of membrane (GO:0016021)|intracellular (GO:0005622)|membrane (GO:0016020)|plasma membrane (GO:0005886)	receptor activity (GO:0004872)|receptor binding (GO:0005102)			breast(2)|central_nervous_system(1)|cervix(2)|endometrium(4)|kidney(4)|large_intestine(12)|lung(30)|ovary(2)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	64						GGAAAAGCAACGTGATAGTAA	0.398													C|||	306	0.0611022	0.1566	0.0591	5008	,	,		21079	0.0119		0.0298	False		,,,				2504	0.0164				p.N679N		Atlas-SNP	.											.	PLXNC1	135	.	0			c.C2037T						PASS	.	C		589,3817	259.5+/-263.1	47,495,1661	94.0	80.0	85.0		2037	-3.6	0.9	12	dbSNP_98	85	296,8304	108.8+/-169.4	5,286,4009	no	coding-synonymous	PLXNC1	NM_005761.2		52,781,5670	TT,TC,CC		3.4419,13.3681,6.8046		679/1569	94631496	885,12121	2203	4300	6503	SO:0001819	synonymous_variant	10154	exon10			AAGCAACGTGATA	AF030339	CCDS9049.1	12q23	2009-04-17				ENSG00000136040		"""CD molecules"", ""Plexins"""	9106	protein-coding gene	gene with protein product		604259					Standard	NR_037687		Approved	VESPR, CD232	uc001tdc.3	O60486	OTTHUMG00000170235	ENST00000258526.4:c.2037C>T	12.37:g.94631496C>T		82.0	0.0	0		54.0	12.0	0.222222	NM_005761	Q59H25	Silent	SNP	ENST00000258526.4	37	CCDS9049.1																																																																																			C|0.929;T|0.071	0.071	strong		0.398	PLXNC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000408126.2		
CFAP221	200373	hgsc.bcm.edu	37	2	120383248	120383248	+	Silent	SNP	A	A	G			TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr2:120383248A>G	ENST00000413369.3	+	15	1587	c.1500A>G	c.(1498-1500)aaA>aaG	p.K500K	PCDP1_ENST00000602047.1_Silent_p.K214K|PCDP1_ENST00000597189.1_3'UTR	NM_001271049.1	NP_001257978																Colorectal(110;0.196)					GCCAAGCAAAACAATCGATAG	0.428																																					p.K500K		Atlas-SNP	.											.	.	.	.	0			c.A1500G						PASS	.						130.0	111.0	117.0					2																	120383248		2203	4300	6503	SO:0001819	synonymous_variant	0	exon15			AGCAAAACAATCG																												ENST00000413369.3:c.1500A>G	2.37:g.120383248A>G		134.0	0.0	0		113.0	36.0	0.318584	NM_001271049		Silent	SNP	ENST00000413369.3	37	CCDS33282.2	.	.	.	.	.	.	.	.	.	.	A	2.807	-0.247935	0.05867	.	.	ENSG00000163075	ENST00000443972;ENST00000413057	.	.	.	4.45	0.852	0.18995	.	.	.	.	.	T	0.30885	0.0779	.	.	.	0.09310	N	1	.	.	.	.	.	.	T	0.25082	-1.0142	4	.	.	.	-6.3731	6.1027	0.20057	0.6942:0.0:0.3058:0.0	.	.	.	.	S	59;48	.	.	N	+	2	0	AC069154.2	120099718	0.000000	0.05858	0.000000	0.03702	0.036000	0.12997	0.160000	0.16462	0.142000	0.18901	0.533000	0.62120	AAC	.	.	none		0.428	PCDP1-006	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000464236.1		
TSPAN32	10077	hgsc.bcm.edu	37	11	2325427	2325427	+	Missense_Mutation	SNP	T	T	C	rs61744929	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr11:2325427T>C	ENST00000182290.4	+	3	409	c.272T>C	c.(271-273)aTg>aCg	p.M91T	C11orf21_ENST00000470369.1_5'Flank|TSPAN32_ENST00000483227.1_3'UTR|C11orf21_ENST00000381153.3_5'Flank|TSPAN32_ENST00000451520.2_Missense_Mutation_p.M80T|TSPAN32_ENST00000381121.3_Missense_Mutation_p.M91T	NM_139022.2	NP_620591.3	Q96QS1	TSN32_HUMAN	tetraspanin 32	91					cell-cell signaling (GO:0007267)|cytoskeleton organization (GO:0007010)|defense response to protozoan (GO:0042832)|integrin-mediated signaling pathway (GO:0007229)|negative regulation of cell proliferation (GO:0008285)|negative regulation of myeloid dendritic cell activation (GO:0030886)|platelet aggregation (GO:0070527)|regulation of defense response to virus (GO:0050688)	cell surface (GO:0009986)|integrin alphaIIb-beta3 complex (GO:0070442)|intracellular (GO:0005622)				breast(1)|central_nervous_system(1)|lung(4)|ovary(1)|skin(1)	8		all_epithelial(84;4.89e-05)|Breast(177;0.000962)|Medulloblastoma(188;0.00106)|Ovarian(85;0.0014)|all_neural(188;0.00791)|Lung NSC(207;0.209)		BRCA - Breast invasive adenocarcinoma(625;0.000533)|LUSC - Lung squamous cell carcinoma(625;0.082)|Lung(200;0.153)		CAGGGCCTCATGGCAGGGGTG	0.632													T|||	19	0.00379393	0.0015	0.0043	5008	,	,		16077	0.0		0.0099	False		,,,				2504	0.0041				p.M91T		Atlas-SNP	.											.	TSPAN32	19	.	0			c.T272C						PASS	.	T	THR/MET	8,4390		0,8,2191	37.0	34.0	35.0		272	4.1	1.0	11	dbSNP_129	35	119,8465		0,119,4173	yes	missense	TSPAN32	NM_139022.2	81	0,127,6364	CC,CT,TT		1.3863,0.1819,0.9783	benign	91/321	2325427	127,12855	2199	4292	6491	SO:0001583	missense	10077	exon3			GCCTCATGGCAGG	AF176070	CCDS7733.1	11p15	2013-02-14	2005-08-16	2005-08-16	ENSG00000064201	ENSG00000064201		"""Tetraspanins"""	13410	protein-coding gene	gene with protein product		603853	"""pan-hematopoietic expression"""	TSSC6, PHEMX		10072438, 10950922	Standard	NM_139022		Approved		uc001lvy.1	Q96QS1	OTTHUMG00000009762	ENST00000182290.4:c.272T>C	11.37:g.2325427T>C	ENSP00000182290:p.Met91Thr	36.0	0.0	0		36.0	14.0	0.388889	NM_139022	Q96KX4|Q9HC50|Q9HC51|Q9Y5U1	Missense_Mutation	SNP	ENST00000182290.4	37	CCDS7733.1	8	0.003663003663003663	1	0.0020325203252032522	1	0.0027624309392265192	0	0.0	6	0.0079155672823219	T	10.19	1.282156	0.23392	0.001819	0.013863	ENSG00000064201	ENST00000182290;ENST00000381121;ENST00000451520;ENST00000444307;ENST00000381117	T;T;T;T	0.79554	-1.28;-1.28;-1.28;-1.24	4.12	4.12	0.48240	.	0.146307	0.30649	N	0.009173	T	0.78572	0.4304	L	0.51422	1.61	0.31276	N	0.691117	D;D;P;D;P;D	0.63880	0.993;0.978;0.936;0.991;0.948;0.978	P;P;P;P;P;P	0.60609	0.877;0.649;0.556;0.736;0.684;0.733	T	0.80294	-0.1443	10	0.42905	T	0.14	-24.6332	9.7847	0.40668	0.0:0.0:0.0:1.0	rs61744929	78;91;61;91;91;80	B4DQ90;Q96QS1-5;G3XAG6;Q96QS1-3;Q96QS1;F8WCN6	.;.;.;.;TSN32_HUMAN;.	T	91;91;80;61;61	ENSP00000182290:M91T;ENSP00000370513:M91T;ENSP00000405205:M80T;ENSP00000370509:M61T	ENSP00000182290:M91T	M	+	2	0	TSPAN32	2282003	0.988000	0.35896	1.000000	0.80357	0.169000	0.22640	0.386000	0.20702	1.636000	0.50526	0.443000	0.29094	ATG	T|0.992;C|0.008	0.008	strong		0.632	TSPAN32-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000026912.2	NM_139024	
MUC17	140453	hgsc.bcm.edu	37	7	100682156	100682156	+	Missense_Mutation	SNP	A	A	G			TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr7:100682156A>G	ENST00000306151.4	+	3	7523	c.7459A>G	c.(7459-7461)Atg>Gtg	p.M2487V		NM_001040105.1	NP_001035194.1	Q685J3	MUC17_HUMAN	mucin 17, cell surface associated	2487	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)					CAGCACACCTATGACCACTTC	0.493																																					p.M2487V		Atlas-SNP	.											MUC17,bladder,carcinoma,-2,2	MUC17	804	2	0			c.A7459G						scavenged	.						285.0	288.0	287.0					7																	100682156		2203	4300	6503	SO:0001583	missense	140453	exon3			ACACCTATGACCA	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.7459A>G	7.37:g.100682156A>G	ENSP00000302716:p.Met2487Val	214.0	0.0	0		268.0	13.0	0.0485075	NM_001040105	O14761|Q685J2|Q8TDH7	Missense_Mutation	SNP	ENST00000306151.4	37	CCDS34711.1	.	.	.	.	.	.	.	.	.	.	N	0.296	-0.976703	0.02215	.	.	ENSG00000169876	ENST00000306151	T	0.02032	4.49	1.06	-2.02	0.07388	.	.	.	.	.	T	0.00906	0.0030	N	0.02539	-0.55	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.46261	-0.9204	9	0.15952	T	0.53	.	4.2578	0.10726	0.345:0.2168:0.4382:0.0	.	2487	Q685J3	MUC17_HUMAN	V	2487	ENSP00000302716:M2487V	ENSP00000302716:M2487V	M	+	1	0	MUC17	100468876	0.000000	0.05858	0.000000	0.03702	0.011000	0.07611	-3.180000	0.00569	-1.550000	0.01708	-1.389000	0.01157	ATG	.	.	none		0.493	MUC17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347161.1	NM_001040105	
ZNF697	90874	hgsc.bcm.edu	37	1	120166528	120166528	+	Silent	SNP	A	A	G	rs374393078		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr1:120166528A>G	ENST00000421812.2	-	3	557	c.438T>C	c.(436-438)caT>caC	p.H146H		NM_001080470.1	NP_001073939.1	Q5TEC3	ZN697_HUMAN	zinc finger protein 697	146					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			ovary(2)	2	all_neural(166;0.219)	all_lung(203;3.66e-05)|Lung NSC(69;0.000202)|all_epithelial(167;0.0266)		Lung(183;0.011)|LUSC - Lung squamous cell carcinoma(189;0.0577)		CCAGGGAGAGATGTCGCCTCC	0.706																																					p.H146H		Atlas-SNP	.											.	ZNF697	26	.	0			c.T438C						PASS	.	A		1,3997		0,1,1998	15.0	19.0	18.0		438	-2.7	0.9	1		18	0,8274		0,0,4137	no	coding-synonymous	ZNF697	NM_001080470.1		0,1,6135	GG,GA,AA		0.0,0.025,0.0081		146/546	120166528	1,12271	1999	4137	6136	SO:0001819	synonymous_variant	90874	exon3			GGAGAGATGTCGC	AK027019, BC033126	CCDS44202.1	1p12	2013-01-08			ENSG00000143067	ENSG00000143067		"""Zinc fingers, C2H2-type"""	32034	protein-coding gene	gene with protein product							Standard	NM_001080470		Approved	MGC45731	uc001ehy.1	Q5TEC3	OTTHUMG00000012962	ENST00000421812.2:c.438T>C	1.37:g.120166528A>G		158.0	0.0	0		162.0	40.0	0.246914	NM_001080470	Q96IT2	Silent	SNP	ENST00000421812.2	37	CCDS44202.1																																																																																			.	.	none		0.706	ZNF697-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000036349.3	XM_371286	
TFG	10342	hgsc.bcm.edu	37	3	100455433	100455433	+	Silent	SNP	T	T	G	rs12562	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr3:100455433T>G	ENST00000240851.4	+	6	934	c.594T>G	c.(592-594)gcT>gcG	p.A198A	TFG_ENST00000418917.2_Silent_p.A198A|TFG_ENST00000476228.1_Silent_p.A198A|TFG_ENST00000490574.1_Silent_p.A198A	NM_001195478.1|NM_001195479.1|NM_006070.5	NP_001182407.1|NP_001182408.1|NP_006061.2	Q92734	TFG_HUMAN	TRK-fused gene	198					cell death (GO:0008219)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)	signal transducer activity (GO:0004871)		TFG/NR4A3(2)|TFG/NTRK1_ENST00000392302(5)|TFG/ALK(9)	large_intestine(4)|lung(2)|prostate(1)|stomach(1)	8						CACCCAGTGCTCCTGCAGAAG	0.507			T	"""NTRK1, ALK"""	"""papillary thyroid, ALCL, NSCLC"""								T|||	2	0.000399361	0.0	0.0	5008	,	,		17057	0.0		0.002	False		,,,				2504	0.0				p.A198A		Atlas-SNP	.		Dom	yes		3	3q11-q12	10342	TRK-fused gene		"""E, L"""	.	TFG	42	.	0			c.T594G						PASS	.	T	,,,	9,4397	15.5+/-35.6	0,9,2194	69.0	63.0	65.0		594,594,594,594	2.6	1.0	3	dbSNP_52	65	69,8531	41.7+/-99.0	0,69,4231	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	TFG	NM_001007565.2,NM_001195478.1,NM_001195479.1,NM_006070.5	,,,	0,78,6425	GG,GT,TT		0.8023,0.2043,0.5997	,,,	198/401,198/401,198/397,198/401	100455433	78,12928	2203	4300	6503	SO:0001819	synonymous_variant	10342	exon6			CAGTGCTCCTGCA	BC009241	CCDS2939.1, CCDS56266.1	3q12.2	2013-03-13	2001-12-04		ENSG00000114354	ENSG00000114354			11758	protein-coding gene	gene with protein product		602498				9169129, 23479643	Standard	NM_001007565		Approved	TF6, FLJ36137, SPG57	uc003dui.3	Q92734	OTTHUMG00000159085	ENST00000240851.4:c.594T>G	3.37:g.100455433T>G		244.0	0.0	0		256.0	132.0	0.515625	NM_006070	D3DN49|G5E9V1|Q15656|Q969I2	Silent	SNP	ENST00000240851.4	37	CCDS2939.1																																																																																			T|0.993;G|0.007	0.007	strong		0.507	TFG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000353242.1	NM_006070	
FMO4	2329	hgsc.bcm.edu	37	1	171303810	171303810	+	Missense_Mutation	SNP	C	C	T	rs144578261	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr1:171303810C>T	ENST00000367749.3	+	8	1418	c.1088C>T	c.(1087-1089)gCg>gTg	p.A363V		NM_002022.1	NP_002013.1	P31512	FMO4_HUMAN	flavin containing monooxygenase 4	363					drug catabolic process (GO:0042737)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)	flavin adenine dinucleotide binding (GO:0050660)|N,N-dimethylaniline monooxygenase activity (GO:0004499)|NADP binding (GO:0050661)			NS(1)|breast(1)|central_nervous_system(1)|endometrium(3)|kidney(2)|large_intestine(7)|lung(12)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	33	all_cancers(6;3.9e-08)|all_hematologic(923;0.088)|Acute lymphoblastic leukemia(37;0.181)					CTAGAGAGAGCGACATTAGCC	0.403													C|||	2	0.000399361	0.0	0.0	5008	,	,		19559	0.0		0.0	False		,,,				2504	0.002				p.A363V	Pancreas(24;816 862 7754 7993 32832)	Atlas-SNP	.											FMO4,NS,NS,-1,1	FMO4	64	1	0			c.C1088T						scavenged	.	C	VAL/ALA	1,4405	2.1+/-5.4	0,1,2202	87.0	88.0	88.0		1088	5.6	0.1	1	dbSNP_134	88	3,8597	3.0+/-9.4	0,3,4297	yes	missense	FMO4	NM_002022.1	64	0,4,6499	TT,TC,CC		0.0349,0.0227,0.0308	benign	363/559	171303810	4,13002	2203	4300	6503	SO:0001583	missense	2329	exon8			AGAGAGCGACATT	BC002780	CCDS1295.1	1q24.3	2011-08-04			ENSG00000076258	ENSG00000076258	1.14.13.8		3772	protein-coding gene	gene with protein product		136131		FMO2		8311461	Standard	NM_002022		Approved		uc001gho.3	P31512	OTTHUMG00000035506	ENST00000367749.3:c.1088C>T	1.37:g.171303810C>T	ENSP00000356723:p.Ala363Val	111.0	1.0	0.00900901		156.0	63.0	0.403846	NM_002022	Q53XR0	Missense_Mutation	SNP	ENST00000367749.3	37	CCDS1295.1	.	.	.	.	.	.	.	.	.	.	C	15.89	2.966086	0.53507	2.27E-4	3.49E-4	ENSG00000076258	ENST00000367749	T	0.58060	0.36	5.63	5.63	0.86233	.	0.633406	0.17137	N	0.185613	T	0.43919	0.1269	M	0.66939	2.045	0.38079	D	0.936608	P	0.38048	0.616	B	0.33568	0.166	T	0.56780	-0.7922	10	0.87932	D	0	-2.4899	19.2618	0.93971	0.0:1.0:0.0:0.0	.	363	P31512	FMO4_HUMAN	V	363	ENSP00000356723:A363V	ENSP00000356723:A363V	A	+	2	0	FMO4	169570434	0.106000	0.21978	0.117000	0.21633	0.428000	0.31595	3.801000	0.55545	2.632000	0.89209	0.650000	0.86243	GCG	C|1.000;T|0.000	0.000	weak		0.403	FMO4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000086223.1	NM_002022	
PSG11	5680	hgsc.bcm.edu	37	19	43528921	43528921	+	Missense_Mutation	SNP	C	C	G	rs558961472	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr19:43528921C>G	ENST00000401740.1	-	2	455	c.352G>C	c.(352-354)Gga>Cga	p.G118R	PSG11_ENST00000403486.1_Intron|PSG11_ENST00000306322.7_Intron|PSG11_ENST00000320078.7_Missense_Mutation_p.G118R			Q00887	PSG9_HUMAN	pregnancy specific beta-1-glycoprotein 11	118	Ig-like V-type.				female pregnancy (GO:0007565)	extracellular region (GO:0005576)				breast(1)|endometrium(2)|kidney(1)|large_intestine(3)|lung(15)|prostate(2)|stomach(1)|upper_aerodigestive_tract(1)	26		Prostate(69;0.00682)				GTGTAGGATCCTGCGTCCTCC	0.458													.|||	2	0.000399361	0.0	0.0	5008	,	,		20669	0.0		0.0	False		,,,				2504	0.002				p.G118R		Atlas-SNP	.											PSG11,NS,carcinoma,+2,1	PSG11	57	1	0			c.G352C						scavenged	.						154.0	147.0	150.0					19																	43528921		2199	4294	6493	SO:0001583	missense	5680	exon2			AGGATCCTGCGTC	U25988	CCDS12614.2, CCDS12615.2	19q13.2	2013-01-29			ENSG00000243130	ENSG00000243130		"""Immunoglobulin superfamily / V-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	9516	protein-coding gene	gene with protein product	"""pregnancy specific beta-1-glycoprotein 13"""	176401		PSG13, PSG14		7794280	Standard	NM_001113410		Approved	MGC22484	uc002ovm.1	Q9UQ72	OTTHUMG00000151546	ENST00000401740.1:c.352G>C	19.37:g.43528921C>G	ENSP00000384995:p.Gly118Arg	310.0	0.0	0		359.0	27.0	0.0752089	NM_002785	B2R869|Q15227|Q15236|Q15237|Q8WW78|Q9UQ73	Missense_Mutation	SNP	ENST00000401740.1	37	CCDS12614.2	.	.	.	.	.	.	.	.	.	.	c	10.99	1.507740	0.27036	.	.	ENSG00000243130	ENST00000320078;ENST00000401740	T;T	0.11821	2.74;2.74	0.929	0.929	0.19449	Immunoglobulin subtype (1);Immunoglobulin V-set (1);Immunoglobulin-like fold (1);	.	.	.	.	T	0.32912	0.0845	M	0.79805	2.47	0.09310	N	1	D	0.89917	1.0	D	0.97110	1.0	T	0.05354	-1.0890	9	0.59425	D	0.04	.	5.2086	0.15304	0.0:1.0:0.0:0.0	.	118	Q9UQ72	PSG11_HUMAN	R	118	ENSP00000319140:G118R;ENSP00000384995:G118R	ENSP00000319140:G118R	G	-	1	0	PSG11	48220761	0.007000	0.16637	0.011000	0.14972	0.029000	0.11900	0.559000	0.23485	0.795000	0.33922	0.184000	0.17185	GGA	.	.	none		0.458	PSG11-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000323079.1	NM_002785	
MUT	4594	hgsc.bcm.edu	37	6	49425446	49425446	+	Silent	SNP	T	T	C	rs138085432	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr6:49425446T>C	ENST00000274813.3	-	3	838	c.711A>G	c.(709-711)ccA>ccG	p.P237P		NM_000255.3	NP_000246.2	P22033	MUTA_HUMAN	methylmalonyl CoA mutase	237					cellular lipid metabolic process (GO:0044255)|cobalamin metabolic process (GO:0009235)|fatty acid beta-oxidation (GO:0006635)|homocysteine metabolic process (GO:0050667)|post-embryonic development (GO:0009791)|short-chain fatty acid catabolic process (GO:0019626)|small molecule metabolic process (GO:0044281)|vitamin metabolic process (GO:0006766)|water-soluble vitamin metabolic process (GO:0006767)	mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)	cobalamin binding (GO:0031419)|metal ion binding (GO:0046872)|methylmalonyl-CoA mutase activity (GO:0004494)|modified amino acid binding (GO:0072341)			endometrium(2)|kidney(1)|large_intestine(4)|lung(17)|ovary(1)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)	30	Lung NSC(77;0.0376)				Cyanocobalamin(DB00115)|Hydroxocobalamin(DB00200)	TTTTCATGGATGGTTCTGGAG	0.313													T|||	53	0.0105831	0.0023	0.0101	5008	,	,		17146	0.0		0.0129	False		,,,				2504	0.0307				p.P237P		Atlas-SNP	.											.	MUT	70	.	0			c.A711G						PASS	.	T		23,4379	28.1+/-56.4	0,23,2178	57.0	51.0	53.0		711	0.7	1.0	6	dbSNP_134	53	115,8475	58.3+/-119.8	1,113,4181	no	coding-synonymous	MUT	NM_000255.3		1,136,6359	CC,CT,TT		1.3388,0.5225,1.0622		237/751	49425446	138,12854	2201	4295	6496	SO:0001819	synonymous_variant	4594	exon3			CATGGATGGTTCT		CCDS4924.1	6p21	2012-10-02	2010-04-30		ENSG00000146085	ENSG00000146085	5.4.99.2		7526	protein-coding gene	gene with protein product		609058	"""methylmalonyl Coenzyme A mutase"""			2907507, 9503014	Standard	NM_000255		Approved		uc003ozg.4	P22033	OTTHUMG00000014814	ENST00000274813.3:c.711A>G	6.37:g.49425446T>C		69.0	0.0	0		117.0	46.0	0.393162	NM_000255	A8K953|Q5SYZ3|Q96B11|Q9UD64	Silent	SNP	ENST00000274813.3	37	CCDS4924.1																																																																																			T|0.991;C|0.009	0.009	strong		0.313	MUT-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040854.1		
SSH1	54434	hgsc.bcm.edu	37	12	109198832	109198832	+	Splice_Site	SNP	G	G	A	rs140151008	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr12:109198832G>A	ENST00000326495.5	-	10	1047	c.954C>T	c.(952-954)ctC>ctT	p.L318L	SSH1_ENST00000551165.1_Splice_Site_p.L318L|SSH1_ENST00000326470.5_Splice_Site_p.L329L|SSH1_ENST00000360239.3_Splice_Site_p.S22L	NM_018984.3	NP_061857.3	Q8WYL5	SSH1_HUMAN	slingshot protein phosphatase 1	318	Tyrosine-protein phosphatase.				actin cytoskeleton organization (GO:0030036)|cell morphogenesis (GO:0000902)|cellular response to ATP (GO:0071318)|protein dephosphorylation (GO:0006470)|regulation of actin polymerization or depolymerization (GO:0008064)|regulation of axonogenesis (GO:0050770)|regulation of cellular protein metabolic process (GO:0032268)|regulation of lamellipodium assembly (GO:0010591)	cell projection (GO:0042995)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	actin binding (GO:0003779)|DNA binding (GO:0003677)|phosphoprotein phosphatase activity (GO:0004721)|protein tyrosine phosphatase activity (GO:0004725)|protein tyrosine/serine/threonine phosphatase activity (GO:0008138)			breast(1)|endometrium(5)|kidney(3)|large_intestine(9)|lung(8)|ovary(4)|prostate(2)|skin(4)|upper_aerodigestive_tract(1)|urinary_tract(1)	38						TGCCTCTTACGAGATAAAGAT	0.433													G|||	17	0.00339457	0.0	0.0	5008	,	,		19464	0.0		0.004	False		,,,				2504	0.0133				p.L329L		Atlas-SNP	.											.	SSH1	144	.	0			c.C987T						PASS	.	G	,,	6,4400	12.9+/-30.5	0,6,2197	125.0	118.0	120.0		954,987,954	-1.8	1.0	12	dbSNP_134	120	63,8537	38.8+/-94.9	0,63,4237	yes	coding-synonymous-near-splice,coding-synonymous-near-splice,coding-synonymous-near-splice	SSH1	NM_001161330.1,NM_001161331.1,NM_018984.3	,,	0,69,6434	AA,AG,GG		0.7326,0.1362,0.5305	,,	318/693,329/704,318/1050	109198832	69,12937	2203	4300	6503	SO:0001630	splice_region_variant	54434	exon9			TCTTACGAGATAA	BC062341	CCDS9121.1, CCDS53825.1, CCDS55882.1	12q24.12	2013-03-05	2013-03-05			ENSG00000084112		"""Protein tyrosine phosphatases / Class I Cys-based PTPs : Slingshots"""	30579	protein-coding gene	gene with protein product		606778	"""slingshot homolog 1 (Drosophila)"""			10718198, 11832213	Standard	NM_018984		Approved	KIAA1298	uc001tnm.3	Q8WYL5	OTTHUMG00000169371	ENST00000326495.5:c.954+1C>T	12.37:g.109198832G>A		132.0	0.0	0		132.0	63.0	0.477273	NM_001161331	Q6P6C0|Q8N9A7|Q8WYL3|Q8WYL4|Q9P2P8	Silent	SNP	ENST00000326495.5	37	CCDS9121.1	2	9.157509157509158E-4	0	0.0	0	0.0	0	0.0	2	0.002638522427440633	G	18.44	3.625527	0.66901	0.001362	0.007326	ENSG00000084112	ENST00000360239	D	0.86164	-2.08	5.13	-1.82	0.07857	.	.	.	.	.	T	0.67268	0.2875	.	.	.	0.27735	N	0.944678	B	0.19935	0.04	B	0.06405	0.002	T	0.55798	-0.8084	7	.	.	.	-29.1082	7.2487	0.26138	0.3231:0.4661:0.2108:0.0	.	22	Q8WYL5-4	.	L	22	ENSP00000353374:S22L	.	S	-	2	0	SSH1	107722961	1.000000	0.71417	0.998000	0.56505	0.994000	0.84299	1.002000	0.29796	-0.089000	0.12484	0.655000	0.94253	TCG	G|0.996;A|0.004	0.004	strong		0.433	SSH1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000403724.1	NM_018984	Silent
USP25	29761	hgsc.bcm.edu	37	21	17181168	17181168	+	Nonsense_Mutation	SNP	T	T	G			TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr21:17181168T>G	ENST00000285679.6	+	8	1190	c.821T>G	c.(820-822)tTa>tGa	p.L274*	USP25_ENST00000547201.1_3'UTR|USP25_ENST00000285681.2_Nonsense_Mutation_p.L274*|USP25_ENST00000351097.5_Intron|USP25_ENST00000400183.2_Nonsense_Mutation_p.L274*	NM_013396.3	NP_037528.3	Q9UHP3	UBP25_HUMAN	ubiquitin specific peptidase 25	274	USP.				cellular protein modification process (GO:0006464)|protein K48-linked deubiquitination (GO:0071108)|protein K63-linked deubiquitination (GO:0070536)|proteolysis (GO:0006508)|ubiquitin-dependent protein catabolic process (GO:0006511)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	peptidase activity (GO:0008233)|SUMO binding (GO:0032183)|ubiquitin-specific protease activity (GO:0004843)			breast(4)|endometrium(6)|kidney(2)|large_intestine(13)|liver(5)|lung(14)|ovary(4)|prostate(1)|skin(1)|urinary_tract(2)	52				Epithelial(23;7.55e-05)|all cancers(11;0.000429)|COAD - Colon adenocarcinoma(22;0.00543)|OV - Ovarian serous cystadenocarcinoma(11;0.00743)|Colorectal(24;0.0116)|Lung(58;0.0853)|LUSC - Lung squamous cell carcinoma(23;0.0889)		TTAGATTGGTTAGAAGATGCC	0.333																																					p.L274X		Atlas-SNP	.											.	USP25	156	.	0			c.T821G						PASS	.						76.0	73.0	74.0					21																	17181168		2203	4300	6503	SO:0001587	stop_gained	29761	exon8			ATTGGTTAGAAGA	AF170562	CCDS33515.1, CCDS63336.1, CCDS63337.1	21q11.2	2011-02-24	2005-08-08		ENSG00000155313	ENSG00000155313		"""Ubiquitin-specific peptidases"""	12624	protein-coding gene	gene with protein product		604736	"""ubiquitin specific protease 25"""			12838346, 10612803	Standard	NM_013396		Approved	USP21	uc002yjy.1	Q9UHP3	OTTHUMG00000074343	ENST00000285679.6:c.821T>G	21.37:g.17181168T>G	ENSP00000285679:p.Leu274*	55.0	0.0	0		80.0	15.0	0.1875	NM_013396	C0LSZ0|Q6DHZ9|Q9H9W1	Nonsense_Mutation	SNP	ENST00000285679.6	37	CCDS33515.1	.	.	.	.	.	.	.	.	.	.	T	39	7.408059	0.98265	.	.	ENSG00000155313	ENST00000285681;ENST00000285679;ENST00000400183	.	.	.	4.83	4.83	0.62350	.	0.000000	0.64402	D	0.000001	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	14.7222	0.69314	0.0:0.0:0.0:1.0	.	.	.	.	X	274	.	ENSP00000285679:L274X	L	+	2	0	USP25	16103039	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.651000	0.83577	1.928000	0.55862	0.482000	0.46254	TTA	.	.	none		0.333	USP25-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000157964.1		
KRT77	374454	hgsc.bcm.edu	37	12	53090181	53090181	+	Silent	SNP	G	G	A			TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr12:53090181G>A	ENST00000341809.3	-	3	820	c.792C>T	c.(790-792)agC>agT	p.S264S	KRT77_ENST00000537195.1_Silent_p.S31S|RP11-641A6.3_ENST00000547533.1_RNA	NM_175078.2	NP_778253.2	Q7Z794	K2C1B_HUMAN	keratin 77	264	Coil 1B.|Rod.					cytoskeleton (GO:0005856)|extracellular vesicular exosome (GO:0070062)|keratin filament (GO:0045095)	structural molecule activity (GO:0005198)	p.S264S(1)		NS(2)|endometrium(2)|large_intestine(3)|lung(11)|ovary(2)|skin(1)|stomach(2)|upper_aerodigestive_tract(2)	25						AGTCATTCTCGCTGCCAGTCC	0.567																																					p.S264S		Atlas-SNP	.											KRT77,NS,carcinoma,0,1	KRT77	58	1	1	Substitution - coding silent(1)	lung(1)	c.C792T						scavenged	.						176.0	125.0	142.0					12																	53090181		2203	4300	6503	SO:0001819	synonymous_variant	374454	exon3			ATTCTCGCTGCCA	BK000975	CCDS8837.1	12q13.13	2013-06-25	2006-07-17	2006-07-17	ENSG00000189182	ENSG00000189182		"""-"", ""Intermediate filaments type II, keratins (basic)"""	20411	protein-coding gene	gene with protein product		611158	"""keratin 1B"""	KRT1B		11683385, 16831889	Standard	NM_175078		Approved		uc001saw.3	Q7Z794	OTTHUMG00000169450	ENST00000341809.3:c.792C>T	12.37:g.53090181G>A		51.0	1.0	0.0196078		56.0	27.0	0.482143	NM_175078	Q7RTS8	Silent	SNP	ENST00000341809.3	37	CCDS8837.1																																																																																			.	.	none		0.567	KRT77-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000404111.1	NM_175078	
TBC1D2	55357	hgsc.bcm.edu	37	9	100971024	100971024	+	Silent	SNP	G	G	A	rs148143158	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr9:100971024G>A	ENST00000375064.1	-	9	2114	c.2076C>T	c.(2074-2076)ccC>ccT	p.P692P	TBC1D2_ENST00000342112.5_Silent_p.P474P|TBC1D2_ENST00000375066.5_Silent_p.P692P|TBC1D2_ENST00000493589.2_5'UTR|TBC1D2_ENST00000375063.1_Silent_p.P232P	NM_001267571.1	NP_001254500.1	Q9BYX2	TBD2A_HUMAN	TBC1 domain family, member 2	692	Rab-GAP TBC. {ECO:0000255|PROSITE- ProRule:PRU00163}.				positive regulation of Rab GTPase activity (GO:0032851)	cell junction (GO:0030054)|cytoplasmic vesicle (GO:0031410)	cadherin binding (GO:0045296)|Rab GTPase activator activity (GO:0005097)			breast(1)|endometrium(5)|kidney(2)|large_intestine(7)|ovary(3)|prostate(4)|skin(1)|upper_aerodigestive_tract(1)	24		Myeloproliferative disorder(762;0.0255)		OV - Ovarian serous cystadenocarcinoma(323;2.55e-37)		GGAGCTTGTCGGGGAAGCTGG	0.642													G|||	16	0.00319489	0.0	0.0043	5008	,	,		18428	0.0		0.004	False		,,,				2504	0.0092				p.P692P		Atlas-SNP	.											TBC1D2_ENST00000375063,NS,carcinoma,0,2	TBC1D2	70	2	0			c.C2076T						PASS	.	G		9,4397	14.3+/-33.2	0,9,2194	90.0	89.0	90.0		2076	-2.2	1.0	9	dbSNP_134	90	37,8563	24.6+/-71.5	0,37,4263	yes	coding-synonymous	TBC1D2	NM_018421.3		0,46,6457	AA,AG,GG		0.4302,0.2043,0.3537		692/918	100971024	46,12960	2203	4300	6503	SO:0001819	synonymous_variant	55357	exon9			CTTGTCGGGGAAG	AY026527	CCDS35080.1, CCDS59137.1, CCDS75865.1	9q22.32	2011-11-30			ENSG00000095383	ENSG00000095383			18026	protein-coding gene	gene with protein product	"""prostate antigen recognized and identified by SEREX"""	609871					Standard	NM_018421		Approved	PARIS1, TBC1D2A, Armus	uc011lvb.2	Q9BYX2	OTTHUMG00000020343	ENST00000375064.1:c.2076C>T	9.37:g.100971024G>A		243.0	0.0	0		245.0	121.0	0.493878	NM_001267571	B3KWD1|B4DQ05|B9A6J7|Q59EU0|Q5TBQ5|Q6IPC7|Q7L1K8|Q8WYT1|Q9H6A2|Q9NSH4	Silent	SNP	ENST00000375064.1	37																																																																																				G|0.996;A|0.004	0.004	strong		0.642	TBC1D2-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000053366.1	NM_018421	
TENM4	26011	hgsc.bcm.edu	37	11	78369573	78369573	+	Missense_Mutation	SNP	C	C	T	rs75922333	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr11:78369573C>T	ENST00000278550.7	-	34	8302	c.7840G>A	c.(7840-7842)Gtg>Atg	p.V2614M		NM_001098816.2	NP_001092286.2	Q6N022	TEN4_HUMAN	teneurin transmembrane protein 4	2614					cardiac cell fate specification (GO:0060912)|cardiac muscle cell proliferation (GO:0060038)|central nervous system myelin formation (GO:0032289)|gastrulation with mouth forming second (GO:0001702)|neuron development (GO:0048666)|positive regulation of gastrulation (GO:2000543)|positive regulation of myelination (GO:0031643)|positive regulation of oligodendrocyte differentiation (GO:0048714)|self proteolysis (GO:0097264)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)|integral component of plasma membrane (GO:0005887)|neuron projection (GO:0043005)|nucleus (GO:0005634)	protein homodimerization activity (GO:0042803)										TGGGTATCCACCCCATCAATG	0.557													C|||	17	0.00339457	0.0023	0.0014	5008	,	,		20854	0.0		0.0129	False		,,,				2504	0.0				p.V2614M		Atlas-SNP	.											.	.	.	.	0			c.G7840A						PASS	.	C	MET/VAL	16,4072		0,16,2028	44.0	47.0	46.0		7840	1.8	0.7	11	dbSNP_131	46	155,8247		2,151,4048	yes	missense	ODZ4	NM_001098816.2	21	2,167,6076	TT,TC,CC		1.8448,0.3914,1.3691	benign	2614/2770	78369573	171,12319	2044	4201	6245	SO:0001583	missense	26011	exon34			TATCCACCCCATC	AB037723	CCDS44688.1	11q13	2012-10-02	2012-10-02	2012-10-02		ENSG00000149256			29945	protein-coding gene	gene with protein product		610084	"""odz, odd Oz/ten-m homolog 4 (Drosophila)"""	ODZ4		12000766, 10625539	Standard	NM_001098816		Approved	KIAA1302, Ten-M4	uc001ozl.4	Q6N022		ENST00000278550.7:c.7840G>A	11.37:g.78369573C>T	ENSP00000278550:p.Val2614Met	106.0	0.0	0		105.0	47.0	0.447619	NM_001098816	A6ND26|Q7Z3C7|Q96MS6|Q9P2P4|Q9Y4S2	Missense_Mutation	SNP	ENST00000278550.7	37	CCDS44688.1	14	0.00641025641025641	3	0.006097560975609756	1	0.0027624309392265192	0	0.0	10	0.013192612137203167	C	9.623	1.134402	0.21123	0.003914	0.018448	ENSG00000149256	ENST00000278550	D	0.89485	-2.52	5.65	1.78	0.24846	.	0.375145	0.29273	N	0.012631	T	0.59595	0.2205	N	0.08118	0	0.27241	N	0.959155	B	0.13145	0.007	B	0.09377	0.004	T	0.54022	-0.8355	9	.	.	.	.	9.0578	0.36416	0.0:0.5855:0.0:0.4145	.	2614	Q6N022	TEN4_HUMAN	M	2614	ENSP00000278550:V2614M	.	V	-	1	0	ODZ4	78047221	0.005000	0.15991	0.705000	0.30386	0.942000	0.58702	-0.244000	0.08903	0.185000	0.20105	-0.137000	0.14449	GTG	C|0.990;T|0.010	0.010	strong		0.557	TENM4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391406.2		
SF3A2	8175	hgsc.bcm.edu	37	19	2248185	2248185	+	Silent	SNP	A	A	T			TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr19:2248185A>T	ENST00000221494.5	+	9	1453	c.1035A>T	c.(1033-1035)ccA>ccT	p.P345P	AMH_ENST00000221496.4_5'Flank|MIR4321_ENST00000592276.1_RNA	NM_007165.4	NP_009096.2	Q15428	SF3A2_HUMAN	splicing factor 3a, subunit 2, 66kDa	345	Pro-rich.				gene expression (GO:0010467)|mRNA 3'-splice site recognition (GO:0000389)|mRNA processing (GO:0006397)|mRNA splicing, via spliceosome (GO:0000398)|RNA splicing (GO:0008380)	catalytic step 2 spliceosome (GO:0071013)|nucleoplasm (GO:0005654)|small nuclear ribonucleoprotein complex (GO:0030532)|spliceosomal complex (GO:0005681)	poly(A) RNA binding (GO:0044822)|zinc ion binding (GO:0008270)			NS(1)|large_intestine(1)|lung(2)	4		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)		GGGTTCACCCACCAGCCCCCG	0.741																																					p.P345P		Atlas-SNP	.											SF3A2,colon,carcinoma,0,1	SF3A2	22	1	0			c.A1035T						scavenged	.						2.0	3.0	3.0					19																	2248185		1454	3177	4631	SO:0001819	synonymous_variant	8175	exon9			TCACCCACCAGCC	L21990	CCDS12084.1	19p13.3	2012-10-02	2002-08-29		ENSG00000104897	ENSG00000104897			10766	protein-coding gene	gene with protein product		600796	"""splicing factor 3a, subunit 2, 66kD"""			8211113, 8541848	Standard	NM_007165		Approved	SF3a66, SAP62, PRPF11, Prp11	uc002lvg.3	Q15428	OTTHUMG00000180414	ENST00000221494.5:c.1035A>T	19.37:g.2248185A>T		24.0	0.0	0		15.0	10.0	0.666667	NM_007165	B2RBU1|D6W605|O75245	Silent	SNP	ENST00000221494.5	37	CCDS12084.1																																																																																			.	.	none		0.741	SF3A2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000451268.3		
TET2	54790	hgsc.bcm.edu	37	4	106196819	106196819	+	Missense_Mutation	SNP	G	G	T	rs142312318	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr4:106196819G>T	ENST00000540549.1	+	11	6012	c.5152G>T	c.(5152-5154)Gta>Tta	p.V1718L	TET2_ENST00000380013.4_Missense_Mutation_p.V1718L|TET2_ENST00000545826.1_3'UTR|TET2_ENST00000513237.1_Missense_Mutation_p.V1739L			Q6N021	TET2_HUMAN	tet methylcytosine dioxygenase 2	1718			V -> L (in refractory anemia with ringed sideroblasts; somatic mutation in an acute myeloid leukemia sample; dbSNP:rs142312318). {ECO:0000269|PubMed:19372255, ECO:0000269|PubMed:19420352}.		5-methylcytosine catabolic process (GO:0006211)|cell cycle (GO:0007049)|DNA demethylation (GO:0080111)|histone H3-K4 trimethylation (GO:0080182)|kidney development (GO:0001822)|myeloid cell differentiation (GO:0030099)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|post-embryonic development (GO:0009791)|protein O-linked glycosylation (GO:0006493)		DNA binding (GO:0003677)|ferrous iron binding (GO:0008198)|methylcytosine dioxygenase activity (GO:0070579)|zinc ion binding (GO:0008270)	p.V1718L(6)		NS(1)|breast(2)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1272)|kidney(3)|large_intestine(11)|lung(10)|ovary(1)|pancreas(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	1314		Myeloproliferative disorder(5;0.0393)		OV - Ovarian serous cystadenocarcinoma(123;7.18e-08)		TGTACATCATGTAGGGAAATT	0.418			"""Mis N, F"""		MDS								G|||	3	0.000599042	0.0	0.0014	5008	,	,		23074	0.0		0.001	False		,,,				2504	0.001				p.V1718L		Atlas-SNP	.		Rec	yes		4	4q24	54790	tet oncogene family member 2		L	TET2,NS,lymphoid_neoplasm,0,8	TET2	1762	8	6	Substitution - Missense(6)	haematopoietic_and_lymphoid_tissue(6)	c.G5152T						PASS	.	G	LEU/VAL	1,1383		0,1,691	114.0	95.0	101.0		5152	-2.3	0.0	4	dbSNP_134	101	21,3161		0,21,1570	yes	missense	TET2	NM_001127208.2	32	0,22,2261	TT,TG,GG		0.66,0.0723,0.4818	possibly-damaging	1718/2003	106196819	22,4544	692	1591	2283	SO:0001583	missense	54790	exon11			CATCATGTAGGGA	AB046766	CCDS3666.1, CCDS47120.1	4q24	2014-09-17	2011-09-30	2008-03-12	ENSG00000168769	ENSG00000168769			25941	protein-coding gene	gene with protein product		612839	"""KIAA1546"", ""tet oncogene family member 2"""	KIAA1546		10997877, 12646957	Standard	NM_017628		Approved	FLJ20032	uc003hxk.3	Q6N021	OTTHUMG00000131213	ENST00000540549.1:c.5152G>T	4.37:g.106196819G>T	ENSP00000442788:p.Val1718Leu	263.0	0.0	0		200.0	95.0	0.475	NM_001127208	B5MDU0|Q2TB88|Q3LIB8|Q96JX5|Q9HCM6|Q9NXW0	Missense_Mutation	SNP	ENST00000540549.1	37	CCDS47120.1	2	9.157509157509158E-4	0	0.0	1	0.0027624309392265192	0	0.0	1	0.0013192612137203166	G	0.311	-0.968065	0.02232	7.23E-4	0.0066	ENSG00000168769	ENST00000540549;ENST00000513237;ENST00000380013	T;T;T	0.02158	4.42;4.42;4.42	5.16	-2.29	0.06805	Methylcytosine dioxygenase TET, double-stranded beta helix fold domain (1);	.	.	.	.	T	0.00998	0.0033	N	0.21583	0.68	0.09310	N	1	B;B	0.13145	0.007;0.007	B;B	0.17433	0.018;0.012	T	0.49011	-0.8983	9	0.08837	T	0.75	-0.48	5.6612	0.17670	0.3513:0.2405:0.4082:0.0	.	1739;1718	E7EQS8;Q6N021	.;TET2_HUMAN	L	1718;1739;1718	ENSP00000442788:V1718L;ENSP00000425443:V1739L;ENSP00000369351:V1718L	ENSP00000369351:V1718L	V	+	1	0	TET2	106416268	0.000000	0.05858	0.000000	0.03702	0.066000	0.16364	-0.054000	0.11826	-0.328000	0.08539	-0.373000	0.07131	GTA	G|0.999;T|0.001	0.001	strong		0.418	TET2-202	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000253952.2	NM_017628	
ATM	472	hgsc.bcm.edu	37	11	108106435	108106435	+	Missense_Mutation	SNP	A	A	G	rs148590073	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr11:108106435A>G	ENST00000452508.2	+	6	559	c.370A>G	c.(370-372)Atc>Gtc	p.I124V	ATM_ENST00000278616.4_Missense_Mutation_p.I124V			Q13315	ATM_HUMAN	ATM serine/threonine kinase	124					brain development (GO:0007420)|cell cycle arrest (GO:0007050)|cellular response to DNA damage stimulus (GO:0006974)|cellular response to gamma radiation (GO:0071480)|DNA damage induced protein phosphorylation (GO:0006975)|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest (GO:0006977)|DNA repair (GO:0006281)|double-strand break repair (GO:0006302)|double-strand break repair via homologous recombination (GO:0000724)|heart development (GO:0007507)|histone mRNA catabolic process (GO:0071044)|intrinsic apoptotic signaling pathway in response to DNA damage (GO:0008630)|lipoprotein catabolic process (GO:0042159)|mitotic spindle assembly checkpoint (GO:0007094)|negative regulation of B cell proliferation (GO:0030889)|neuron apoptotic process (GO:0051402)|oocyte development (GO:0048599)|peptidyl-serine phosphorylation (GO:0018105)|phosphatidylinositol-3-phosphate biosynthetic process (GO:0036092)|positive regulation of apoptotic process (GO:0043065)|positive regulation of DNA damage response, signal transduction by p53 class mediator (GO:0043517)|positive regulation of neuron apoptotic process (GO:0043525)|pre-B cell allelic exclusion (GO:0002331)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|reciprocal meiotic recombination (GO:0007131)|replicative senescence (GO:0090399)|response to hypoxia (GO:0001666)|response to ionizing radiation (GO:0010212)|signal transduction (GO:0007165)|signal transduction involved in mitotic G2 DNA damage checkpoint (GO:0072434)|somitogenesis (GO:0001756)|telomere maintenance (GO:0000723)	cytoplasmic vesicle (GO:0031410)|nucleoplasm (GO:0005654)|spindle (GO:0005819)	1-phosphatidylinositol-3-kinase activity (GO:0016303)|ATP binding (GO:0005524)|DNA binding (GO:0003677)|DNA-dependent protein kinase activity (GO:0004677)|histone serine kinase activity (GO:0035174)|protein complex binding (GO:0032403)|protein dimerization activity (GO:0046983)|protein N-terminus binding (GO:0047485)|protein serine/threonine kinase activity (GO:0004674)			NS(4)|breast(23)|central_nervous_system(11)|endometrium(10)|haematopoietic_and_lymphoid_tissue(227)|kidney(19)|large_intestine(53)|liver(5)|lung(62)|ovary(6)|pancreas(4)|prostate(13)|skin(4)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(3)	448		all_cancers(61;9.64e-12)|all_epithelial(67;9.97e-08)|Melanoma(852;2.55e-06)|Acute lymphoblastic leukemia(157;3.95e-05)|all_hematologic(158;0.00014)|Breast(348;0.0258)|all_neural(303;0.072)		Epithelial(105;9.05e-06)|BRCA - Breast invasive adenocarcinoma(274;1.06e-05)|all cancers(92;0.000208)|Colorectal(284;0.116)|OV - Ovarian serous cystadenocarcinoma(223;0.147)	Caffeine(DB00201)	CTTAAATTATATCATGGATAC	0.308			"""D, Mis, N, F, S"""		T-PLL	"""leukemia, lymphoma, medulloblastoma, glioma"""		Genes defective in diseases associated with sensitivity to DNA damaging agents	Ataxia Telangiectasia	TSP Lung(14;0.12)			A|||	7	0.00139776	0.0053	0.0	5008	,	,		18157	0.0		0.0	False		,,,				2504	0.0				p.I124V		Atlas-SNP	.	yes	Rec	yes	Ataxia-telangiectasia	11	11q22.3	472	ataxia telangiectasia mutated		"""L, O"""	.	ATM	1657	.	0			c.A370G	GRCh37	CD000908	ATM	D	rs148590073	PASS	.	A	VAL/ILE	35,4367	40.0+/-72.8	0,35,2166	113.0	116.0	115.0		370	0.4	1.0	11	dbSNP_134	115	0,8596		0,0,4298	yes	missense	ATM	NM_000051.3	29	0,35,6464	GG,GA,AA		0.0,0.7951,0.2693	benign	124/3057	108106435	35,12963	2201	4298	6499	SO:0001583	missense	472	exon5	Familial Cancer Database	AT, Louis-Bar syndrome	AATTATATCATGG	AB209133	CCDS31669.1	11q22-q23	2014-09-17	2014-06-17		ENSG00000149311	ENSG00000149311			795	protein-coding gene	gene with protein product	"""TEL1, telomere maintenance 1, homolog (S. cerevisiae)"""	607585	"""ataxia telangiectasia mutated (includes complementation groups A, C and D)"", ""ataxia telangiectasia mutated"""	ATA, ATDC, ATC, ATD			Standard	XM_005271561		Approved	TEL1, TELO1	uc001pkb.1	Q13315	OTTHUMG00000166480	ENST00000452508.2:c.370A>G	11.37:g.108106435A>G	ENSP00000388058:p.Ile124Val	135.0	0.0	0		212.0	64.0	0.301887	NM_000051	B2RNX5|O15429|Q12758|Q16551|Q93007|Q9NP02|Q9UCX7	Missense_Mutation	SNP	ENST00000452508.2	37	CCDS31669.1	3	0.0013736263736263737	3	0.006097560975609756	0	0.0	0	0.0	0	0.0	A	5.116	0.207058	0.09704	0.007951	0.0	ENSG00000149311	ENST00000527805;ENST00000278616;ENST00000452508	T;T;T	0.70045	-0.45;-0.45;-0.45	5.62	0.39	0.16275	Telomere-length maintenance and DNA damage repair (1);	0.272984	0.36101	N	0.002796	T	0.18130	0.0435	N	0.00801	-1.175	0.22581	N	0.998968	B	0.06786	0.001	B	0.08055	0.003	T	0.31724	-0.9933	10	0.06494	T	0.89	.	5.4836	0.16737	0.294:0.0:0.5308:0.1751	.	124	Q13315	ATM_HUMAN	V	124	ENSP00000435747:I124V;ENSP00000278616:I124V;ENSP00000388058:I124V	ENSP00000278616:I124V	I	+	1	0	ATM	107611645	0.996000	0.38824	0.976000	0.42696	0.990000	0.78478	0.866000	0.27954	0.174000	0.19809	0.477000	0.44152	ATC	A|0.997;G|0.003	0.003	strong		0.308	ATM-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000389938.1	NM_000051	
SIK3	23387	hgsc.bcm.edu	37	11	116719841	116719841	+	Missense_Mutation	SNP	C	C	T			TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr11:116719841C>T	ENST00000292055.4	-	21	3531	c.3496G>A	c.(3496-3498)Gct>Act	p.A1166T	SIK3_ENST00000542607.1_Missense_Mutation_p.A1106T|SIK3_ENST00000488337.1_5'UTR|SIK3_ENST00000446921.2_Missense_Mutation_p.A1164T|SIK3_ENST00000434315.2_Missense_Mutation_p.A1005T|AP006216.12_ENST00000444200.1_RNA|SIK3_ENST00000375288.1_Missense_Mutation_p.A501T|SIK3_ENST00000375300.1_Missense_Mutation_p.A1224T	NM_025164.3	NP_079440.3	Q9Y2K2	SIK3_HUMAN	SIK family kinase 3	1166					protein phosphorylation (GO:0006468)	cytoplasm (GO:0005737)	ATP binding (GO:0005524)|magnesium ion binding (GO:0000287)|protein serine/threonine kinase activity (GO:0004674)			breast(6)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(9)|liver(1)|lung(18)|ovary(4)|pancreas(1)|prostate(2)|skin(3)|stomach(2)|upper_aerodigestive_tract(1)	57						CATACATAAGCATCGTCGCTG	0.602																																					p.A1166T		Atlas-SNP	.											.	SIK3	112	.	0			c.G3496A						PASS	.						170.0	122.0	139.0					11																	116719841		2201	4292	6493	SO:0001583	missense	23387	exon21			CATAAGCATCGTC	AB023216	CCDS8379.1, CCDS60974.1, CCDS8379.2	11q23.3	2010-02-17			ENSG00000160584	ENSG00000160584			29165	protein-coding gene	gene with protein product		614776				10231032, 8889548	Standard	NM_025164		Approved	FLJ12240, L19, KIAA0999, QSK	uc001ppy.3	Q9Y2K2	OTTHUMG00000066628	ENST00000292055.4:c.3496G>A	11.37:g.116719841C>T	ENSP00000292055:p.Ala1166Thr	326.0	1.0	0.00306748		461.0	306.0	0.663774	NM_025164	A1A5A8|Q59FY2|Q5M9N1|Q6P3R6|Q8IYM8|Q9HA50	Missense_Mutation	SNP	ENST00000292055.4	37	CCDS8379.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	28.5|28.5	4.921494|4.921494	0.92249|0.92249	.|.	.|.	ENSG00000160584|ENSG00000160584	ENST00000375300;ENST00000292055;ENST00000375288;ENST00000542607;ENST00000434315|ENST00000445177;ENST00000454905;ENST00000446921	T;T;T;D;T|.	0.81821|.	-1.44;-1.42;0.59;-1.54;-1.17|.	5.26|5.26	4.35|4.35	0.52113|0.52113	.|.	0.000000|.	0.41194|.	U|.	0.000938|.	T|T	0.56108|0.56108	0.1963|0.1963	L|L	0.36672|0.36672	1.1|1.1	0.58432|0.58432	D|D	0.999998|0.999998	D;D;D;B|.	0.89917|.	1.0;1.0;1.0;0.117|.	D;D;D;B|.	0.87578|.	0.998;0.998;0.998;0.138|.	T|T	0.52087|0.52087	-0.8622|-0.8622	10|5	0.87932|.	D|.	0|.	.|.	13.8208|13.8208	0.63320|0.63320	0.0:0.9254:0.0:0.0746|0.0:0.9254:0.0:0.0746	.|.	1106;1005;1166;501|.	A1A5A8;A1A5A9;Q9Y2K2;Q9Y2K2-2|.	.;.;SIK3_HUMAN;.|.	T|Y	1224;1166;501;1106;1005|1265;5;1128	ENSP00000364449:A1224T;ENSP00000292055:A1166T;ENSP00000364437:A501T;ENSP00000438108:A1106T;ENSP00000415873:A1005T|.	ENSP00000292055:A1166T|.	A|C	-|-	1|2	0|0	SIK3|SIK3	116225051|116225051	1.000000|1.000000	0.71417|0.71417	0.978000|0.978000	0.43139|0.43139	0.993000|0.993000	0.82548|0.82548	7.456000|7.456000	0.80751|0.80751	1.223000|1.223000	0.43536|0.43536	0.557000|0.557000	0.71058|0.71058	GCT|TGC	.	.	none		0.602	SIK3-201	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding		NM_025164	
NETO1	81832	hgsc.bcm.edu	37	18	70526301	70526301	+	Missense_Mutation	SNP	T	T	C			TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr18:70526301T>C	ENST00000327305.6	-	4	886	c.229A>G	c.(229-231)Aga>Gga	p.R77G	NETO1_ENST00000580049.1_5'UTR|NETO1_ENST00000299430.2_Missense_Mutation_p.R76G|NETO1_ENST00000397929.1_Missense_Mutation_p.R76G|NETO1_ENST00000583169.1_Missense_Mutation_p.R77G	NM_138966.3	NP_620416	Q8TDF5	NETO1_HUMAN	neuropilin (NRP) and tolloid (TLL)-like 1	77	CUB 1. {ECO:0000255|PROSITE- ProRule:PRU00059}.				memory (GO:0007613)|positive regulation of excitatory postsynaptic membrane potential (GO:2000463)|receptor localization to synapse (GO:0097120)|regulation of long-term neuronal synaptic plasticity (GO:0048169)|visual learning (GO:0008542)	cell junction (GO:0030054)|excitatory synapse (GO:0060076)|extracellular region (GO:0005576)|kainate selective glutamate receptor complex (GO:0032983)|postsynaptic density (GO:0014069)|postsynaptic membrane (GO:0045211)				NS(3)|breast(2)|cervix(1)|endometrium(4)|kidney(1)|large_intestine(7)|lung(36)|ovary(2)|prostate(3)|skin(3)|stomach(1)	63		Esophageal squamous(42;0.129)		READ - Rectum adenocarcinoma(1;0.0487)		ATGCACTGTCTTGGAGCGGCT	0.368																																					p.R77G		Atlas-SNP	.											.	NETO1	178	.	0			c.A229G						PASS	.						57.0	57.0	57.0					18																	70526301		2203	4300	6503	SO:0001583	missense	81832	exon4			ACTGTCTTGGAGC	AF448838	CCDS12000.1, CCDS42444.1	18q22.2	2008-08-01			ENSG00000166342	ENSG00000166342			13823	protein-coding gene	gene with protein product		607973				11943477, 12810072	Standard	NM_138999		Approved	BTCL1, BCTL1	uc002lkw.3	Q8TDF5	OTTHUMG00000132834	ENST00000327305.6:c.229A>G	18.37:g.70526301T>C	ENSP00000313088:p.Arg77Gly	144.0	0.0	0		150.0	51.0	0.34	NM_001201465	Q86W85|Q8ND78|Q8TDF4	Missense_Mutation	SNP	ENST00000327305.6	37	CCDS12000.1	.	.	.	.	.	.	.	.	.	.	T	9.808	1.182281	0.21787	.	.	ENSG00000166342	ENST00000327305;ENST00000299430;ENST00000397929	T;T;T	0.23754	1.89;1.89;2.15	5.35	5.35	0.76521	CUB (5);	0.000000	0.64402	D	0.000003	T	0.23532	0.0569	N	0.01482	-0.84	0.80722	D	1	D;D;P	0.76494	0.999;0.989;0.592	D;D;B	0.80764	0.994;0.985;0.241	T	0.50233	-0.8852	10	0.25751	T	0.34	-24.7403	15.6405	0.76997	0.0:0.0:0.0:1.0	.	76;76;77	Q8TDF5-1;Q8TDF5-2;Q8TDF5	.;.;NETO1_HUMAN	G	77;76;76	ENSP00000313088:R77G;ENSP00000299430:R76G;ENSP00000381024:R76G	ENSP00000299430:R76G	R	-	1	2	NETO1	68677281	1.000000	0.71417	1.000000	0.80357	0.991000	0.79684	4.054000	0.57434	2.159000	0.67721	0.533000	0.62120	AGA	.	.	none		0.368	NETO1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256301.2	NM_138999	
APBA2	321	hgsc.bcm.edu	37	15	29368269	29368269	+	Silent	SNP	G	G	A	rs149285403	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr15:29368269G>A	ENST00000558402.1	+	7	1643	c.1044G>A	c.(1042-1044)gtG>gtA	p.V348V	APBA2_ENST00000561069.1_Silent_p.V348V|APBA2_ENST00000411764.1_Silent_p.V348V|APBA2_ENST00000558259.1_Silent_p.V348V|APBA2_ENST00000558330.1_Silent_p.V348V			Q99767	APBA2_HUMAN	amyloid beta (A4) precursor protein-binding, family A, member 2	348					in utero embryonic development (GO:0001701)|locomotory behavior (GO:0007626)|multicellular organism growth (GO:0035264)|nervous system development (GO:0007399)|protein transport (GO:0015031)|regulation of gene expression (GO:0010468)|synaptic transmission (GO:0007268)	plasma membrane (GO:0005886)	beta-amyloid binding (GO:0001540)			NS(1)|breast(1)|central_nervous_system(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(2)|kidney(4)|large_intestine(7)|liver(2)|lung(33)|stomach(1)|urinary_tract(1)	59		all_lung(180;1.73e-12)|Breast(32;2.89e-05)|Colorectal(260;0.234)		all cancers(64;7.44e-11)|Epithelial(43;5.74e-10)|GBM - Glioblastoma multiforme(186;0.026)|BRCA - Breast invasive adenocarcinoma(123;0.0286)|Lung(196;0.24)		CAAAGAAGGTGGCATCATTTC	0.378																																					p.V348V		Atlas-SNP	.											.	APBA2	132	.	0			c.G1044A						PASS	.	G	,	2,4404	4.2+/-10.8	0,2,2201	185.0	185.0	185.0		1044,1044	3.9	1.0	15	dbSNP_134	185	18,8582	13.3+/-46.6	0,18,4282	no	coding-synonymous,coding-synonymous	APBA2	NM_001130414.1,NM_005503.3	,	0,20,6483	AA,AG,GG		0.2093,0.0454,0.1538	,	348/738,348/750	29368269	20,12986	2203	4300	6503	SO:0001819	synonymous_variant	321	exon5			GAAGGTGGCATCA	AB014719	CCDS10022.1, CCDS45197.1	15q11-q12	2008-07-18	2008-07-18		ENSG00000034053	ENSG00000034053			579	protein-coding gene	gene with protein product		602712	"""X11-like"", ""amyloid beta (A4) precursor protein-binding, family A, member 2 (X11-like)"""	X11L, MINT2		8955346	Standard	NM_005503		Approved	D15S1518E, LIN-10, MGC:14091, HsT16821	uc001zck.3	Q99767	OTTHUMG00000129255	ENST00000558402.1:c.1044G>A	15.37:g.29368269G>A		138.0	0.0	0		95.0	76.0	0.8	NM_005503	E9PGI4|O60571|Q5XKC0	Silent	SNP	ENST00000558402.1	37	CCDS10022.1																																																																																			G|0.999;A|0.001	0.001	strong		0.378	APBA2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251362.3	NM_005503	
ZNF493	284443	hgsc.bcm.edu	37	19	21607296	21607296	+	Missense_Mutation	SNP	G	G	A			TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr19:21607296G>A	ENST00000355504.4	+	2	1717	c.1451G>A	c.(1450-1452)cGa>cAa	p.R484Q	ZNF493_ENST00000392288.2_Missense_Mutation_p.R612Q|CTD-2561J22.3_ENST00000600810.1_Intron	NM_175910.6	NP_787106.4	Q6ZR52	ZN493_HUMAN	zinc finger protein 493	484					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)			central_nervous_system(2)|cervix(1)|endometrium(1)|kidney(1)|large_intestine(6)|lung(10)|ovary(1)|prostate(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	30						GCTTTTAACCGATCTTCAATC	0.368																																					p.R612Q		Atlas-SNP	.											ZNF493_ENST00000392288,NS,carcinoma,0,4	ZNF493	178	4	0			c.G1835A						scavenged	.						33.0	35.0	35.0					19																	21607296		2201	4298	6499	SO:0001583	missense	284443	exon4			TTAACCGATCTTC	AK093823, BC006408, BC022394	CCDS12412.1, CCDS42536.1, CCDS12411.1	19p12	2013-01-08			ENSG00000196268	ENSG00000196268		"""Zinc fingers, C2H2-type"", ""-"""	23708	protein-coding gene	gene with protein product							Standard	NM_001076678		Approved	FLJ36504	uc002npw.3	Q6ZR52	OTTHUMG00000141297	ENST00000355504.4:c.1451G>A	19.37:g.21607296G>A	ENSP00000347691:p.Arg484Gln	70.0	0.0	0		71.0	4.0	0.056338	NM_001076678	G5E974|Q59GM3|Q6ZSF6|Q8N1Z6|Q8N965|Q9BR99	Missense_Mutation	SNP	ENST00000355504.4	37	CCDS12412.1	.	.	.	.	.	.	.	.	.	.	N	0.005	-2.171271	0.00315	.	.	ENSG00000196268	ENST00000392288;ENST00000355504	T;T	0.07567	3.18;3.18	0.859	-1.72	0.08107	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.03136	0.0092	L	0.27944	0.81	0.09310	N	1	B;B	0.31077	0.307;0.199	B;B	0.17979	0.02;0.002	T	0.42292	-0.9460	9	0.02654	T	1	.	1.7831	0.03036	0.3925:0.0:0.3315:0.276	.	484;612	Q6ZR52;Q6ZR52-2	ZN493_HUMAN;.	Q	612;484	ENSP00000376110:R612Q;ENSP00000347691:R484Q	ENSP00000347691:R484Q	R	+	2	0	ZNF493	21399136	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-5.205000	0.00141	-1.052000	0.03222	-1.038000	0.02383	CGA	.	.	none		0.368	ZNF493-003	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000280563.1	NM_175910	
FAM160A1	729830	hgsc.bcm.edu	37	4	152577473	152577473	+	Nonsense_Mutation	SNP	C	C	T	rs367582779		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr4:152577473C>T	ENST00000505231.1	+	10	2800	c.2641C>T	c.(2641-2643)Cag>Tag	p.Q881*	FAM160A1_ENST00000435205.1_Nonsense_Mutation_p.Q881*			Q05DH4	F16A1_HUMAN	family with sequence similarity 160, member A1	881										endometrium(2)|kidney(1)	3						GATCATTACTCAGCTAGCCAG	0.507																																					p.Q881X		Atlas-SNP	.											.	FAM160A1	60	.	0			c.C2641T						PASS	.	C	stop/GLN	0,1384		0,0,692	87.0	76.0	79.0		2641	5.4	0.9	4		79	1,3181		0,1,1590	no	stop-gained	FAM160A1	NM_001109977.1		0,1,2282	TT,TC,CC		0.0314,0.0,0.0219		881/1041	152577473	1,4565	692	1591	2283	SO:0001587	stop_gained	729830	exon12			ATTACTCAGCTAG		CCDS47146.1	4q31.3	2012-11-30			ENSG00000164142	ENSG00000164142			34237	protein-coding gene	gene with protein product							Standard	NM_001109977		Approved	FLJ43373	uc003imj.2	Q05DH4	OTTHUMG00000161675	ENST00000505231.1:c.2641C>T	4.37:g.152577473C>T	ENSP00000421580:p.Gln881*	278.0	1.0	0.00359712		181.0	122.0	0.674033	NM_001109977	Q6ZUS2	Nonsense_Mutation	SNP	ENST00000505231.1	37	CCDS47146.1	.	.	.	.	.	.	.	.	.	.	C	43	10.373391	0.99393	0.0	3.14E-4	ENSG00000164142	ENST00000435205;ENST00000505231	.	.	.	5.45	5.45	0.79879	.	.	.	.	.	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.22706	T	0.39	.	19.281	0.94052	0.0:1.0:0.0:0.0	.	.	.	.	X	881	.	ENSP00000413196:Q881X	Q	+	1	0	FAM160A1	152796923	1.000000	0.71417	0.851000	0.33527	0.980000	0.70556	7.730000	0.84881	2.568000	0.86640	0.561000	0.74099	CAG	.	.	weak		0.507	FAM160A1-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000365691.1	NM_001109977	
FAM98A	25940	hgsc.bcm.edu	37	2	33820635	33820635	+	Silent	SNP	C	C	T	rs72785999	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr2:33820635C>T	ENST00000238823.8	-	2	263	c.123G>A	c.(121-123)gaG>gaA	p.E41E	FAM98A_ENST00000498340.1_5'UTR|FAM98A_ENST00000441530.2_5'UTR|FAM98A_ENST00000403368.1_Silent_p.E41E			Q8NCA5	FA98A_HUMAN	family with sequence similarity 98, member A	41							poly(A) RNA binding (GO:0044822)			NS(1)|breast(1)|cervix(1)|endometrium(2)|kidney(1)|large_intestine(3)|lung(12)|ovary(1)|prostate(1)|skin(1)	24	all_hematologic(175;0.115)					GTTTGGTAAACTCGGGGGAAC	0.448													C|||	15	0.00299521	0.0	0.0029	5008	,	,		15482	0.0		0.0099	False		,,,				2504	0.0031				p.E41E		Atlas-SNP	.											.	FAM98A	42	.	0			c.G123A						PASS	.	C		11,4395	17.9+/-39.9	1,9,2193	105.0	107.0	106.0		123	4.1	1.0	2	dbSNP_130	106	74,8526	42.2+/-99.7	0,74,4226	no	coding-synonymous	FAM98A	NM_015475.3		1,83,6419	TT,TC,CC		0.8605,0.2497,0.6535		41/519	33820635	85,12921	2203	4300	6503	SO:0001819	synonymous_variant	25940	exon2			GGTAAACTCGGGG		CCDS33179.1	2p22.3	2006-11-29		2005-11-20	ENSG00000119812	ENSG00000119812			24520	protein-coding gene	gene with protein product						12477932	Standard	NM_015475		Approved	DKFZP564F0522	uc002rpa.1	Q8NCA5	OTTHUMG00000152152	ENST00000238823.8:c.123G>A	2.37:g.33820635C>T		133.0	0.0	0		171.0	94.0	0.549708	NM_015475	B2RNA2|Q9Y3Y6	Silent	SNP	ENST00000238823.8	37	CCDS33179.1																																																																																			C|0.995;T|0.005	0.005	strong		0.448	FAM98A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000325457.2	NM_015475	
COL6A3	1293	hgsc.bcm.edu	37	2	238280553	238280553	+	Silent	SNP	G	G	A	rs35114079	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr2:238280553G>A	ENST00000295550.4	-	9	4559	c.4107C>T	c.(4105-4107)atC>atT	p.I1369I	COL6A3_ENST00000392003.2_Silent_p.I962I|COL6A3_ENST00000353578.4_Silent_p.I1163I|COL6A3_ENST00000346358.4_Silent_p.I1169I|COL6A3_ENST00000472056.1_Silent_p.I762I|COL6A3_ENST00000409809.1_Silent_p.I1163I|COL6A3_ENST00000347401.3_Silent_p.I1168I|COL6A3_ENST00000392004.3_Silent_p.I1163I	NM_004369.3	NP_004360.2	P12111	CO6A3_HUMAN	collagen, type VI, alpha 3	1369	Nonhelical region.|VWFA 7. {ECO:0000255|PROSITE- ProRule:PRU00219}.				axon guidance (GO:0007411)|cell adhesion (GO:0007155)|collagen catabolic process (GO:0030574)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|muscle organ development (GO:0007517)|response to glucose (GO:0009749)	collagen type VI trimer (GO:0005589)|endoplasmic reticulum lumen (GO:0005788)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|proteinaceous extracellular matrix (GO:0005578)|sarcolemma (GO:0042383)|vesicle (GO:0031982)	serine-type endopeptidase inhibitor activity (GO:0004867)			breast(6)|central_nervous_system(7)|cervix(3)|endometrium(7)|haematopoietic_and_lymphoid_tissue(2)|kidney(13)|large_intestine(64)|lung(62)|ovary(14)|pancreas(2)|prostate(11)|skin(14)|stomach(2)|upper_aerodigestive_tract(6)|urinary_tract(4)	217		Breast(86;0.000301)|Renal(207;0.000966)|all_hematologic(139;0.067)|Ovarian(221;0.0694)|all_lung(227;0.0943)|Melanoma(123;0.203)		Epithelial(121;1.23e-21)|OV - Ovarian serous cystadenocarcinoma(60;1.34e-10)|Kidney(56;5.71e-09)|KIRC - Kidney renal clear cell carcinoma(57;1.51e-07)|BRCA - Breast invasive adenocarcinoma(100;0.00025)|Lung(119;0.0142)|LUSC - Lung squamous cell carcinoma(224;0.034)		CGTTCCTGGCGATCGTGAAAG	0.612													G|||	14	0.00279553	0.0015	0.0014	5008	,	,		16527	0.0		0.006	False		,,,				2504	0.0051				p.I1369I		Atlas-SNP	.											.	COL6A3	608	.	0			c.C4107T						PASS	.	G	,,,,	7,4399	12.9+/-30.5	0,7,2196	60.0	56.0	57.0		4107,2886,3489,2286,3489	-9.3	0.0	2	dbSNP_126	57	71,8529	42.2+/-99.7	0,71,4229	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	COL6A3	NM_004369.3,NM_057164.4,NM_057165.4,NM_057166.4,NM_057167.3	,,,,	0,78,6425	AA,AG,GG		0.8256,0.1589,0.5997	,,,,	1369/3178,962/1037,1163/1238,762/2571,1163/2972	238280553	78,12928	2203	4300	6503	SO:0001819	synonymous_variant	1293	exon9			CCTGGCGATCGTG	X52022	CCDS33409.1, CCDS33410.1, CCDS33411.1, CCDS33412.1, CCDS33410.2, CCDS33411.2, CCDS54439.1	2q37	2014-09-17			ENSG00000163359	ENSG00000163359		"""Collagens"""	2213	protein-coding gene	gene with protein product		120250				1339440, 11992252	Standard	NM_004369		Approved		uc002vwl.2	P12111	OTTHUMG00000150020	ENST00000295550.4:c.4107C>T	2.37:g.238280553G>A		127.0	0.0	0		77.0	28.0	0.363636	NM_004369	A8MT30|B4E3U5|B7ZMJ7|E9PFQ6|E9PGQ9|Q16501|Q53QF4|Q53QF6	Silent	SNP	ENST00000295550.4	37	CCDS33412.1																																																																																			G|0.994;A|0.006	0.006	strong		0.612	COL6A3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000315790.2	NM_004369	
PRF1	5551	hgsc.bcm.edu	37	10	72360197	72360197	+	Silent	SNP	T	T	C	rs116554195	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr10:72360197T>C	ENST00000441259.1	-	2	622	c.462A>G	c.(460-462)gcA>gcG	p.A154A	PRF1_ENST00000373209.2_Silent_p.A154A	NM_001083116.1|NM_005041.4	NP_001076585.1|NP_005032.2	P14222	PERF_HUMAN	perforin 1 (pore forming protein)	154	MACPF. {ECO:0000255|PROSITE- ProRule:PRU00745}.				apoptotic process (GO:0006915)|cellular defense response (GO:0006968)|cytolysis (GO:0019835)|defense response to tumor cell (GO:0002357)|defense response to virus (GO:0051607)|immune response to tumor cell (GO:0002418)|protein homooligomerization (GO:0051260)|transmembrane transport (GO:0055085)	cytolytic granule (GO:0044194)|cytoplasmic membrane-bounded vesicle (GO:0016023)|endosome (GO:0005768)|extracellular region (GO:0005576)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|wide pore channel activity (GO:0022829)			breast(1)|central_nervous_system(1)|endometrium(1)|large_intestine(2)|lung(11)|ovary(1)|prostate(3)|urinary_tract(3)	23						CAAAGTTGGCTGCCTGTGAGT	0.612			M			"""various leukaemia, lymphoma"""	Type 2 familial hemophagocytic lymphohistiocytosis		Familial Hemophagocytic Lymphohistiocytosis				T|||	76	0.0151757	0.0378	0.0086	5008	,	,		17805	0.0		0.0109	False		,,,				2504	0.0092				p.A154A		Atlas-SNP	.	yes	Rec			10	10q22	5551	perforin 1 (pore forming protein)		L	.	PRF1	64	.	0			c.A462G						PASS	.	T	,	135,4271	95.7+/-134.4	1,133,2069	81.0	71.0	74.0		462,462	-8.4	0.0	10	dbSNP_132	74	71,8529	41.7+/-99.0	0,71,4229	no	coding-synonymous,coding-synonymous	PRF1	NM_001083116.1,NM_005041.4	,	1,204,6298	CC,CT,TT		0.8256,3.064,1.5839	,	154/556,154/556	72360197	206,12800	2203	4300	6503	SO:0001819	synonymous_variant	5551	exon2	Familial Cancer Database	FHLH, FHL, Familial Hemophagocytic Reticulosis, FHR	GTTGGCTGCCTGT	BC047695	CCDS7305.1	10q22	2014-09-17			ENSG00000180644	ENSG00000180644			9360	protein-coding gene	gene with protein product	"""Perforin"", ""perforin 1 (preforming protein)"""	170280				1505959, 2592021	Standard	NM_005041		Approved	PFP, P1, HPLH2	uc001jrf.4	P14222	OTTHUMG00000018412	ENST00000441259.1:c.462A>G	10.37:g.72360197T>C		235.0	0.0	0		126.0	92.0	0.730159	NM_001083116	B2R6X4|Q59F57|Q86WX7	Silent	SNP	ENST00000441259.1	37	CCDS7305.1																																																																																			T|0.987;C|0.013	0.013	strong		0.612	PRF1-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048517.2	NM_005041	
MUC2	4583	hgsc.bcm.edu	37	11	1093481	1093481	+	Missense_Mutation	SNP	C	C	T	rs547164370	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr11:1093481C>T	ENST00000441003.2	+	30	5327	c.5300C>T	c.(5299-5301)aCg>aTg	p.T1767M	MUC2_ENST00000333592.6_Missense_Mutation_p.T55M|MUC2_ENST00000361558.6_Intron|MUC2_ENST00000359061.5_Splice_Site_p.T1734M	NM_002457.2	NP_002448.2	Q02817	MUC2_HUMAN	mucin 2, oligomeric mucus/gel-forming	0					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)	accccaaccacggtactcatc	0.612													c|||	7	0.00139776	0.0	0.0014	5008	,	,		26176	0.005		0.001	False		,,,				2504	0.0				p.T1767M		Atlas-SNP	.											.	MUC2	614	.	0			c.C5300T						PASS	.																																			SO:0001583	missense	4583	exon30			CAACCACGGTACT	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.5300C>T	11.37:g.1093481C>T	ENSP00000415183:p.Thr1767Met	72.0	0.0	0		69.0	20.0	0.289855	NM_002457	Q14878	Missense_Mutation	SNP	ENST00000441003.2	37		.	.	.	.	.	.	.	.	.	.	C	3.092	-0.186712	0.06340	.	.	ENSG00000198788	ENST00000441003;ENST00000359061;ENST00000333592	T;T;T	0.12879	2.64;3.12;2.78	1.77	-3.54	0.04653	.	0.173549	0.20316	U	0.094725	T	0.06325	0.0163	.	.	.	0.09310	N	1	B	0.33073	0.396	B	0.24848	0.056	T	0.14952	-1.0454	9	0.66056	D	0.02	.	1.3227	0.02119	0.1446:0.3605:0.1442:0.3508	.	1767	E7EUV1	.	M	1767;1734;55	ENSP00000415183:T1767M;ENSP00000351956:T1734M;ENSP00000331373:T55M	ENSP00000331373:T55M	T	+	2	0	MUC2	1083481	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	0.581000	0.23819	-1.920000	0.01069	-1.152000	0.01820	ACG	.	.	none		0.612	MUC2-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000345894.2	NM_002457	
TRIP6	7205	hgsc.bcm.edu	37	7	100465824	100465824	+	Missense_Mutation	SNP	G	G	A	rs2437100	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr7:100465824G>A	ENST00000200457.4	+	3	692	c.332G>A	c.(331-333)cGg>cAg	p.R111Q		NM_003302.2	NP_003293.2	Q15654	TRIP6_HUMAN	thyroid hormone receptor interactor 6	111			R -> Q (in dbSNP:rs2437100). {ECO:0000269|PubMed:15489334}.		focal adhesion assembly (GO:0048041)|positive regulation of cell migration (GO:0030335)|regulation of transcription, DNA-templated (GO:0006355)|release of cytoplasmic sequestered NF-kappaB (GO:0008588)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|focal adhesion (GO:0005925)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	interleukin-1 receptor binding (GO:0005149)|kinase binding (GO:0019900)|poly(A) RNA binding (GO:0044822)|thyroid hormone receptor binding (GO:0046966)|zinc ion binding (GO:0008270)			breast(1)|central_nervous_system(3)|endometrium(2)|large_intestine(2)|liver(1)|lung(5)	14	Lung NSC(181;0.041)|all_lung(186;0.0581)					AATGGGGGTCGGGGTCATGCG	0.672													G|||	32	0.00638978	0.0008	0.0058	5008	,	,		14361	0.0		0.0268	False		,,,				2504	0.0				p.R111Q		Atlas-SNP	.											.	TRIP6	45	.	0			c.G332A						PASS	.	G	GLN/ARG	21,4385	29.0+/-57.7	0,21,2182	41.0	41.0	41.0		332	4.5	0.8	7	dbSNP_100	41	176,8424	80.6+/-143.3	1,174,4125	yes	missense	TRIP6	NM_003302.2	43	1,195,6307	AA,AG,GG		2.0465,0.4766,1.5147	probably-damaging	111/477	100465824	197,12809	2203	4300	6503	SO:0001583	missense	7205	exon3			GGGGTCGGGGTCA	L40374, AF000974	CCDS5708.1	7q22	2006-09-05			ENSG00000087077	ENSG00000087077			12311	protein-coding gene	gene with protein product		602933				9598321, 7776974	Standard	NM_003302		Approved	ZRP-1, OIP1, MGC10556, MGC10558, MGC29959, MGC3837, MGC4423	uc003uww.3	Q15654	OTTHUMG00000157029	ENST00000200457.4:c.332G>A	7.37:g.100465824G>A	ENSP00000200457:p.Arg111Gln	71.0	0.0	0		105.0	73.0	0.695238	NM_003302	A4D2E7|F2ZC07|F2ZC08|O15170|O15275|Q9BTB2|Q9BUE5|Q9BXP3|Q9UNT4	Missense_Mutation	SNP	ENST00000200457.4	37	CCDS5708.1	26	0.011904761904761904	1	0.0020325203252032522	2	0.0055248618784530384	0	0.0	23	0.030343007915567283	G	18.42	3.619897	0.66787	0.004766	0.020465	ENSG00000087077	ENST00000200457	T	0.59502	0.26	4.53	4.53	0.55603	.	0.374538	0.26931	N	0.021774	T	0.33089	0.0851	L	0.47716	1.5	0.28405	N	0.918477	D	0.69078	0.997	P	0.53518	0.728	T	0.40646	-0.9552	10	0.11794	T	0.64	.	12.7393	0.57241	0.0:0.0:1.0:0.0	rs2437100	111	Q15654	TRIP6_HUMAN	Q	111	ENSP00000200457:R111Q	ENSP00000200457:R111Q	R	+	2	0	TRIP6	100303760	0.997000	0.39634	0.757000	0.31301	0.054000	0.15201	3.870000	0.56070	2.074000	0.62210	0.455000	0.32223	CGG	G|0.985;A|0.015	0.015	strong		0.672	TRIP6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347151.2	NM_003302	
GNB5	10681	hgsc.bcm.edu	37	15	52446260	52446260	+	Silent	SNP	C	C	T	rs35581121	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr15:52446260C>T	ENST00000261837.7	-	4	317	c.252G>A	c.(250-252)gcG>gcA	p.A84A	GNB5_ENST00000560116.1_Silent_p.A42A|GNB5_ENST00000396335.4_Silent_p.A42A|GNB5_ENST00000358784.7_Silent_p.A42A	NM_016194.3	NP_057278.2	O14775	GBB5_HUMAN	guanine nucleotide binding protein (G protein), beta 5	84					GTP catabolic process (GO:0006184)|negative regulation of voltage-gated calcium channel activity (GO:1901386)|phototransduction, visible light (GO:0007603)|regulation of rhodopsin mediated signaling pathway (GO:0022400)|rhodopsin mediated signaling pathway (GO:0016056)|signal transduction (GO:0007165)	nucleus (GO:0005634)|plasma membrane (GO:0005886)	chaperone binding (GO:0051087)|G-protein gamma-subunit binding (GO:0031682)|GTPase activity (GO:0003924)|signal transducer activity (GO:0004871)			large_intestine(1)|lung(1)	2				all cancers(107;0.0163)		CCACCCGCTCCGCCACCTGGT	0.562													C|||	84	0.0167732	0.0008	0.0389	5008	,	,		18869	0.001		0.0378	False		,,,				2504	0.0174				p.A84A		Atlas-SNP	.											.	GNB5	28	.	0			c.G252A						PASS	.	C	,	36,4354	40.0+/-72.8	1,34,2160	79.0	67.0	71.0		126,252	-11.1	0.0	15	dbSNP_126	71	317,8269	112.5+/-172.7	4,309,3980	no	coding-synonymous,coding-synonymous	GNB5	NM_006578.3,NM_016194.3	,	5,343,6140	TT,TC,CC		3.6921,0.82,2.7204	,	42/354,84/396	52446260	353,12623	2195	4293	6488	SO:0001819	synonymous_variant	10681	exon4			CCGCTCCGCCACC	AF017656	CCDS10149.1, CCDS45261.1	15q21.1	2013-01-10			ENSG00000069966	ENSG00000069966		"""WD repeat domain containing"""	4401	protein-coding gene	gene with protein product		604447				9606987	Standard	NM_016194		Approved	GB5	uc031qrz.1	O14775	OTTHUMG00000131892	ENST00000261837.7:c.252G>A	15.37:g.52446260C>T		51.0	0.0	0		26.0	6.0	0.230769	NM_016194	B2RBR5|Q9HAU9|Q9UFT3	Silent	SNP	ENST00000261837.7	37	CCDS10149.1																																																																																			C|0.973;T|0.027	0.027	strong		0.562	GNB5-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000254842.1		
GBP7	388646	hgsc.bcm.edu	37	1	89613280	89613280	+	Silent	SNP	G	G	A	rs115454072	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr1:89613280G>A	ENST00000294671.2	-	8	1473	c.1335C>T	c.(1333-1335)gaC>gaT	p.D445D		NM_207398.2	NP_997281.2	Q8N8V2	GBP7_HUMAN	guanylate binding protein 7	445						membrane (GO:0016020)	GTP binding (GO:0005525)|GTPase activity (GO:0003924)			NS(1)|breast(2)|central_nervous_system(1)|endometrium(2)|large_intestine(9)|lung(5)|ovary(1)|pancreas(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	27		Lung NSC(277;0.0908)		all cancers(265;0.00835)|Epithelial(280;0.0322)		CTAGTGTATAGTCCTGTTCAA	0.443													G|||	115	0.0229633	0.0166	0.0159	5008	,	,		18197	0.0119		0.0278	False		,,,				2504	0.0429				p.D445D		Atlas-SNP	.											.	GBP7	57	.	0			c.C1335T						PASS	.	G		71,4335	64.1+/-101.4	0,71,2132	171.0	171.0	171.0		1335	-0.8	0.0	1	dbSNP_132	171	215,8385	90.6+/-152.8	1,213,4086	no	coding-synonymous	GBP7	NM_207398.2		1,284,6218	AA,AG,GG		2.5,1.6114,2.199		445/639	89613280	286,12720	2203	4300	6503	SO:0001819	synonymous_variant	388646	exon8			TGTATAGTCCTGT	AK096141	CCDS720.1	1p22.2	2008-02-05			ENSG00000213512	ENSG00000213512			29606	protein-coding gene	gene with protein product		612468					Standard	NM_207398		Approved	FLJ38822, GBP4L	uc001dna.2	Q8N8V2	OTTHUMG00000010659	ENST00000294671.2:c.1335C>T	1.37:g.89613280G>A		300.0	0.0	0		159.0	158.0	0.993711	NM_207398		Silent	SNP	ENST00000294671.2	37	CCDS720.1																																																																																			G|0.976;A|0.024	0.024	strong		0.443	GBP7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000029401.1	NM_207398	
ACSL1	2180	hgsc.bcm.edu	37	4	185724503	185724503	+	Missense_Mutation	SNP	C	C	T	rs114493597	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr4:185724503C>T	ENST00000515030.1	-	2	491	c.166G>A	c.(166-168)Gac>Aac	p.D56N	ACSL1_ENST00000437665.3_5'UTR|ACSL1_ENST00000454703.2_Intron|ACSL1_ENST00000513317.1_Missense_Mutation_p.D56N|ACSL1_ENST00000504900.1_Missense_Mutation_p.D56N|ACSL1_ENST00000281455.2_Missense_Mutation_p.D56N|ACSL1_ENST00000507295.1_Missense_Mutation_p.D56N|ACSL1_ENST00000504342.1_Missense_Mutation_p.D56N			P33121	ACSL1_HUMAN	acyl-CoA synthetase long-chain family member 1	56				CD -> WH (in Ref. 2; AAB00959). {ECO:0000305}.	adiponectin-activated signaling pathway (GO:0033211)|alpha-linolenic acid metabolic process (GO:0036109)|cellular lipid metabolic process (GO:0044255)|linoleic acid metabolic process (GO:0043651)|lipid biosynthetic process (GO:0008610)|long-chain fatty acid import (GO:0044539)|long-chain fatty acid metabolic process (GO:0001676)|long-chain fatty-acyl-CoA biosynthetic process (GO:0035338)|positive regulation of protein serine/threonine kinase activity (GO:0071902)|response to drug (GO:0042493)|response to nutrient (GO:0007584)|response to oleic acid (GO:0034201)|response to organic cyclic compound (GO:0014070)|small molecule metabolic process (GO:0044281)|triglyceride biosynthetic process (GO:0019432)|unsaturated fatty acid metabolic process (GO:0033559)|xenobiotic catabolic process (GO:0042178)	endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|mitochondrial outer membrane (GO:0005741)|mitochondrion (GO:0005739)|peroxisomal membrane (GO:0005778)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|long-chain fatty acid-CoA ligase activity (GO:0004467)			NS(1)|central_nervous_system(1)|cervix(1)|endometrium(3)|kidney(3)|large_intestine(6)|liver(1)|lung(17)|ovary(2)|prostate(1)|skin(2)	38		all_lung(41;7.57e-14)|Lung NSC(41;1.81e-13)|Colorectal(36;0.00172)|Hepatocellular(41;0.00826)|Renal(120;0.00988)|Prostate(90;0.0235)|all_hematologic(60;0.0315)|all_neural(102;0.107)|Medulloblastoma(177;0.146)		all cancers(43;1.33e-28)|Epithelial(43;5.3e-25)|OV - Ovarian serous cystadenocarcinoma(60;4.88e-11)|Colorectal(24;3.59e-06)|STAD - Stomach adenocarcinoma(60;2.72e-05)|GBM - Glioblastoma multiforme(59;2.83e-05)|BRCA - Breast invasive adenocarcinoma(30;7.66e-05)|COAD - Colon adenocarcinoma(29;0.000538)|LUSC - Lung squamous cell carcinoma(40;0.008)|READ - Rectum adenocarcinoma(43;0.0419)	Adenosine monophosphate(DB00131)|Adenosine triphosphate(DB00171)	ATGGAGAGGTCGCATGGCGGC	0.592													C|||	3	0.000599042	0.0	0.0	5008	,	,		18362	0.0		0.003	False		,,,				2504	0.0				p.D56N		Atlas-SNP	.											.	ACSL1	77	.	0			c.G166A						PASS	.	C	ASN/ASP	3,4403	6.2+/-15.9	0,3,2200	64.0	58.0	60.0		166	5.0	1.0	4	dbSNP_133	60	33,8567	22.2+/-67.0	0,33,4267	yes	missense	ACSL1	NM_001995.2	23	0,36,6467	TT,TC,CC		0.3837,0.0681,0.2768	possibly-damaging	56/699	185724503	36,12970	2203	4300	6503	SO:0001583	missense	2180	exon2			AGAGGTCGCATGG	BC026290	CCDS3839.1, CCDS68825.1, CCDS68826.1, CCDS75213.1	4q35.1	2014-08-08	2004-02-19	2004-02-20	ENSG00000151726	ENSG00000151726	6.2.1.3	"""Acyl-CoA synthetase family"""	3569	protein-coding gene	gene with protein product	"""lignoceroyl-CoA synthase"", ""long-chain fatty-acid-coenzyme A ligase 1"""	152425	"""fatty-acid-Coenzyme A ligase, long-chain 2"""	FACL2		2341402, 1531127	Standard	XM_005262828		Approved	LACS2, LACS, ACS1, LACS1, FACL1	uc003iwu.1	P33121	OTTHUMG00000160547	ENST00000515030.1:c.166G>A	4.37:g.185724503C>T	ENSP00000422607:p.Asp56Asn	126.0	0.0	0		93.0	64.0	0.688172	NM_001995	B7Z452|D3DP57|P41215|Q8N8V7|Q8TA99	Missense_Mutation	SNP	ENST00000515030.1	37	CCDS3839.1	1	4.578754578754579E-4	0	0.0	0	0.0	0	0.0	1	0.0013192612137203166	C	19.38	3.815734	0.70912	6.81E-4	0.003837	ENSG00000151726	ENST00000515030;ENST00000281455;ENST00000507295;ENST00000504342;ENST00000513317;ENST00000504900	T;T;T;T;T;T	0.23950	2.07;2.07;1.88;2.07;2.0;2.2	5.04	5.04	0.67666	.	0.045032	0.85682	D	0.000000	T	0.49253	0.1546	M	0.69463	2.115	0.80722	D	1	B;B;D;B	0.89917	0.312;0.02;1.0;0.037	B;B;D;B	0.71870	0.052;0.035;0.975;0.035	T	0.33033	-0.9884	10	0.31617	T	0.26	-33.9469	18.5929	0.91220	0.0:1.0:0.0:0.0	.	56;56;56;56	E7EPM6;B7Z452;D6RER0;P33121	.;.;.;ACSL1_HUMAN	N	56	ENSP00000422607:D56N;ENSP00000281455:D56N;ENSP00000426244:D56N;ENSP00000425006:D56N;ENSP00000426150:D56N;ENSP00000424935:D56N	ENSP00000281455:D56N	D	-	1	0	ACSL1	185961497	1.000000	0.71417	0.998000	0.56505	0.995000	0.86356	7.213000	0.77950	2.614000	0.88457	0.655000	0.94253	GAC	C|0.998;T|0.002	0.002	strong		0.592	ACSL1-011	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000361112.2	NM_001995	
KIAA0754	643314	hgsc.bcm.edu	37	1	39879340	39879340	+	Missense_Mutation	SNP	G	G	C	rs141110458	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr1:39879340G>C	ENST00000530275.1	+	1	3190	c.2995G>C	c.(2995-2997)Gct>Cct	p.A999P	MACF1_ENST00000564288.1_Intron|MACF1_ENST00000539005.1_Intron|MACF1_ENST00000317713.7_Intron|MACF1_ENST00000545844.1_Intron|MACF1_ENST00000567887.1_Intron|MACF1_ENST00000361689.2_Intron|MACF1_ENST00000289893.4_Intron|MACF1_ENST00000372915.3_Intron	NM_015038.1	NP_055853.1	O94854	K0754_HUMAN	KIAA0754	999	Ala-rich.									central_nervous_system(1)|large_intestine(6)|skin(1)	8	Lung NSC(20;5.57e-06)|Ovarian(52;0.00769)|Acute lymphoblastic leukemia(166;0.074)	Myeloproliferative disorder(586;0.0393)	OV - Ovarian serous cystadenocarcinoma(33;7.78e-19)|Epithelial(16;1.73e-17)|all cancers(16;2.49e-16)|LUSC - Lung squamous cell carcinoma(16;0.00146)|Lung(16;0.00204)			CTCCCCAGCTGCTGCAGTGCC	0.711													G|||	13	0.00259585	0.0	0.0029	5008	,	,		10576	0.001		0.006	False		,,,				2504	0.0041				p.A1135P		Atlas-SNP	.											.	KIAA0754	93	.	0			c.G3403C						PASS	.	G	,PRO/ALA,	5,3513		0,5,1754	6.0	9.0	8.0		,3403,	0.2	0.0	1	dbSNP_134	8	77,7935		0,77,3929	no	intron,missense,intron	MACF1,KIAA0754	NM_012090.4,NM_015038.1,NM_033044.3	,27,	0,82,5683	CC,CG,GG		0.9611,0.1421,0.7112	,probably-damaging,	,1135/1428,	39879340	82,11448	1759	4006	5765	SO:0001583	missense	643314	exon1			CCAGCTGCTGCAG			1p34.2	2009-07-09				ENSG00000255103			29111	protein-coding gene	gene with protein product						9872452	Standard	NM_015038		Approved		uc009vvt.1	O94854		ENST00000530275.1:c.2995G>C	1.37:g.39879340G>C	ENSP00000431179:p.Ala999Pro	140.0	0.0	0		61.0	37.0	0.606557	NM_015038	E9PMC2|Q6ZSB2	Missense_Mutation	SNP	ENST00000530275.1	37		22	0.010073260073260074	7	0.014227642276422764	5	0.013812154696132596	7	0.012237762237762238	3	0.00395778364116095	G	13.78	2.338002	0.41398	0.001421	0.009611	ENSG00000255103	ENST00000530275	T	0.24151	1.87	4.56	0.241	0.15494	.	.	.	.	.	T	0.13243	0.0321	N	0.14661	0.345	0.09310	N	1	D	0.56968	0.978	P	0.54706	0.759	T	0.10337	-1.0634	9	0.25751	T	0.34	.	2.6328	0.04949	0.0953:0.1583:0.4215:0.3249	.	999	O94854	K0754_HUMAN	P	999	ENSP00000431179:A999P	ENSP00000431179:A999P	A	+	1	0	RP4-562N20.1	39651927	0.000000	0.05858	0.001000	0.08648	0.011000	0.07611	-0.456000	0.06754	0.200000	0.20447	0.498000	0.49722	GCT	G|0.990;C|0.010	0.010	strong		0.711	KIAA0754-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000392100.1	NM_015038	
LTF	4057	hgsc.bcm.edu	37	3	46496910	46496910	+	Silent	SNP	G	G	A	rs145526650	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr3:46496910G>A	ENST00000231751.4	-	5	817	c.522C>T	c.(520-522)gcC>gcT	p.A174A	LTF_ENST00000417439.1_Silent_p.A174A|LTF_ENST00000426532.2_Silent_p.A130A	NM_002343.3	NP_002334.2	P02788	TRFL_HUMAN	lactotransferrin	174	Transferrin-like 1. {ECO:0000255|PROSITE- ProRule:PRU00741}.				antibacterial humoral response (GO:0019731)|antifungal humoral response (GO:0019732)|bone morphogenesis (GO:0060349)|humoral immune response (GO:0006959)|innate immune response in mucosa (GO:0002227)|interaction with host (GO:0051701)|iron assimilation by chelation and transport (GO:0033214)|iron ion transport (GO:0006826)|negative regulation of apoptotic process (GO:0043066)|negative regulation of lipopolysaccharide-mediated signaling pathway (GO:0031665)|negative regulation of osteoclast development (GO:2001205)|negative regulation of single-species biofilm formation in or on host organism (GO:1900229)|negative regulation of tumor necrosis factor (ligand) superfamily member 11 production (GO:2000308)|ossification (GO:0001503)|phagosome maturation (GO:0090382)|positive regulation of bone mineralization involved in bone maturation (GO:1900159)|positive regulation of chondrocyte proliferation (GO:1902732)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of osteoblast differentiation (GO:0045669)|positive regulation of osteoblast proliferation (GO:0033690)|positive regulation of protein serine/threonine kinase activity (GO:0071902)|positive regulation of toll-like receptor 4 signaling pathway (GO:0034145)|regulation of cytokine production (GO:0001817)|regulation of tumor necrosis factor production (GO:0032680)|response to host immune response (GO:0052572)|retina homeostasis (GO:0001895)|transcription, DNA-templated (GO:0006351)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)|phagocytic vesicle lumen (GO:0097013)|secretory granule (GO:0030141)|specific granule (GO:0042581)	DNA binding (GO:0003677)|ferric iron binding (GO:0008199)|heparin binding (GO:0008201)|iron ion binding (GO:0005506)|protein serine/threonine kinase activator activity (GO:0043539)|serine-type endopeptidase activity (GO:0004252)	p.A174A(1)		NS(1)|breast(3)|central_nervous_system(3)|endometrium(4)|kidney(3)|large_intestine(5)|lung(13)|ovary(1)|prostate(1)|skin(4)|upper_aerodigestive_tract(2)	40				all cancers(1;7.55e-14)|GBM - Glioblastoma multiforme(1;2.1e-09)|Epithelial(1;9.25e-07)|Colorectal(1;3.81e-05)|BRCA - Breast invasive adenocarcinoma(193;0.00129)|COAD - Colon adenocarcinoma(1;0.00308)|KIRC - Kidney renal clear cell carcinoma(197;0.0205)|Kidney(197;0.0242)|OV - Ovarian serous cystadenocarcinoma(275;0.089)		GAACACAGCTGGCTGAGAAGA	0.567													G|||	5	0.000998403	0.0008	0.0	5008	,	,		21912	0.0		0.004	False		,,,				2504	0.0				p.A174A		Atlas-SNP	.											LTF,NS,carcinoma,0,1	LTF	98	1	1	Substitution - coding silent(1)	kidney(1)	c.C522T						PASS	.	G	,	5,4401	9.9+/-24.2	0,5,2198	99.0	80.0	86.0		390,522	0.6	0.3	3	dbSNP_134	86	34,8566	23.4+/-69.3	0,34,4266	no	coding-synonymous,coding-synonymous	LTF	NM_001199149.1,NM_002343.3	,	0,39,6464	AA,AG,GG		0.3953,0.1135,0.2999	,	130/667,174/711	46496910	39,12967	2203	4300	6503	SO:0001819	synonymous_variant	4057	exon5			ACAGCTGGCTGAG		CCDS33747.1, CCDS56251.1	3p21.31	2012-10-02			ENSG00000012223	ENSG00000012223			6720	protein-coding gene	gene with protein product		150210				17476971, 3356163	Standard	NM_001199149		Approved	HLF2	uc003cpq.3	P02788	OTTHUMG00000156325	ENST00000231751.4:c.522C>T	3.37:g.46496910G>A		196.0	0.0	0		161.0	80.0	0.496894	NM_002343	A8K9U8|B2MV13|B7Z4X2|E7EQH5|O00756|Q16780|Q16785|Q16786|Q16789|Q5DSM0|Q8IU92|Q8IZH6|Q8TCD2|Q96KZ4|Q96KZ5|Q9H1Z3|Q9UCY5	Silent	SNP	ENST00000231751.4	37	CCDS33747.1	3	0.0013736263736263737	1	0.0020325203252032522	0	0.0	0	0.0	2	0.002638522427440633	G	10.21	1.287664	0.23478	0.001135	0.003953	ENSG00000012223	ENST00000443743	.	.	.	4.89	0.614	0.17603	.	.	.	.	.	T	0.64057	0.2564	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.64972	-0.6281	5	0.72032	D	0.01	0.0819	10.0059	0.41957	0.0:0.428:0.4338:0.1382	.	.	.	.	L	107	.	ENSP00000393737:P107L	P	-	2	0	LTF	46471914	0.807000	0.29009	0.279000	0.24732	0.998000	0.95712	1.015000	0.29963	0.190000	0.20209	0.655000	0.94253	CCA	G|0.998;A|0.002	0.002	strong		0.567	LTF-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000343951.2	NM_002343	
WWC2	80014	hgsc.bcm.edu	37	4	184192231	184192231	+	Splice_Site	SNP	A	A	G			TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr4:184192231A>G	ENST00000403733.3	+	16	2599		c.e16-1		WWC2_ENST00000504005.1_Splice_Site|WWC2_ENST00000513834.1_Splice_Site|WWC2_ENST00000448232.2_Splice_Site	NM_024949.5	NP_079225.5	Q6AWC2	WWC2_HUMAN	WW and C2 domain containing 2						negative regulation of hippo signaling (GO:0035331)|negative regulation of organ growth (GO:0046621)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)	cytosol (GO:0005829)	kinase binding (GO:0019900)|protein complex scaffold (GO:0032947)			NS(1)|breast(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(4)|lung(15)|ovary(2)|prostate(1)|stomach(1)|urinary_tract(3)	32		all_lung(41;5.28e-14)|Lung NSC(41;1.35e-13)|Colorectal(36;0.00681)|Hepatocellular(41;0.00886)|Renal(120;0.00992)|Prostate(90;0.0237)|all_hematologic(60;0.0592)|Esophageal squamous(56;0.179)|all_neural(102;0.202)		all cancers(43;3.38e-24)|Epithelial(43;1.4e-20)|OV - Ovarian serous cystadenocarcinoma(60;1.09e-09)|GBM - Glioblastoma multiforme(59;3.33e-05)|Colorectal(24;3.58e-05)|STAD - Stomach adenocarcinoma(60;4.21e-05)|COAD - Colon adenocarcinoma(29;0.000171)|LUSC - Lung squamous cell carcinoma(40;0.0145)|READ - Rectum adenocarcinoma(43;0.242)		TCACTTACATAGGCTGGAACT	0.318																																					.		Atlas-SNP	.											WWC2,NS,carcinoma,0,1	WWC2	78	1	0			c.2401-2A>G						scavenged	.						30.0	29.0	29.0					4																	184192231		2203	4296	6499	SO:0001630	splice_region_variant	80014	exon16			TTACATAGGCTGG	BC017957	CCDS34109.2	4q35.1	2010-08-05	2006-11-09		ENSG00000151718	ENSG00000151718		"""WW, C2 and coiled-coil domain containing"""	24148	protein-coding gene	gene with protein product			"""WW, C2 and coiled-coil domain containing 2"""			12477932	Standard	NM_024949		Approved	BOMB, FLJ22029	uc010irx.3	Q6AWC2	OTTHUMG00000150685	ENST00000403733.3:c.2401-1A>G	4.37:g.184192231A>G		144.0	0.0	0		68.0	3.0	0.0441176	NM_024949	Q32Q84|Q69YQ1|Q6AWB8|Q6ZSY9|Q6ZU09|Q7Z620|Q8TEB8|Q9H6P0	Splice_Site	SNP	ENST00000403733.3	37	CCDS34109.2	.	.	.	.	.	.	.	.	.	.	A	18.71	3.681262	0.68042	.	.	ENSG00000151718	ENST00000403733;ENST00000513834;ENST00000448232;ENST00000504005	.	.	.	5.33	5.33	0.75918	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	15.4782	0.75501	1.0:0.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	WWC2	184429225	1.000000	0.71417	0.938000	0.37757	0.976000	0.68499	7.743000	0.85020	2.237000	0.73441	0.460000	0.39030	.	.	.	none		0.318	WWC2-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000319608.1	NM_024949	Intron
TCEB3B	51224	hgsc.bcm.edu	37	18	44560337	44560337	+	Silent	SNP	G	G	T	rs3744864	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr18:44560337G>T	ENST00000332567.4	-	1	1651	c.1299C>A	c.(1297-1299)gtC>gtA	p.V433V	KATNAL2_ENST00000245121.5_Intron|KATNAL2_ENST00000592005.1_Intron|KATNAL2_ENST00000356157.7_Intron	NM_016427.2	NP_057511.2	Q8IYF1	ELOA2_HUMAN	transcription elongation factor B polypeptide 3B (elongin A2)	433					regulation of DNA-templated transcription, elongation (GO:0032784)|transcription from RNA polymerase II promoter (GO:0006366)	integral component of membrane (GO:0016021)|nucleus (GO:0005634)	DNA binding (GO:0003677)			breast(1)|cervix(3)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(15)|lung(24)|ovary(2)|pancreas(2)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	58						GGCTTTCCTGGACAGGAGGCA	0.567													G|||	26	0.00519169	0.0	0.0159	5008	,	,		17739	0.001		0.0139	False		,,,				2504	0.0				p.V433V		Atlas-SNP	.											TCEB3B,NS,carcinoma,-1,1	TCEB3B	141	1	0			c.C1299A						PASS	.	G	,	11,4393	16.8+/-37.8	0,11,2191	81.0	78.0	79.0		1299,	1.0	0.0	18	dbSNP_107	79	97,8503	53.6+/-114.3	0,97,4203	no	coding-synonymous,intron	TCEB3B,KATNAL2	NM_016427.2,NM_031303.2	,	0,108,6394	TT,TG,GG		1.1279,0.2498,0.8305	,	433/754,	44560337	108,12896	2202	4300	6502	SO:0001819	synonymous_variant	51224	exon1			TTCCTGGACAGGA	BC036022	CCDS11932.1	18q21.1	2009-08-04			ENSG00000206181	ENSG00000206181			30771	protein-coding gene	gene with protein product	"""transcription elongation factor (SIII) elongin A2"", ""elongin A2"""	609522				7660129, 8244996	Standard	NM_016427		Approved	HsT832, TCEB3L	uc002lcr.1	Q8IYF1	OTTHUMG00000132649	ENST00000332567.4:c.1299C>A	18.37:g.44560337G>T		119.0	0.0	0		122.0	53.0	0.434426	NM_016427	Q9P2V9	Silent	SNP	ENST00000332567.4	37	CCDS11932.1																																																																																			G|0.992;T|0.008	0.008	strong		0.567	TCEB3B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255900.1	NM_016427	
ETV3L	440695	hgsc.bcm.edu	37	1	157069134	157069134	+	Missense_Mutation	SNP	G	G	A	rs61730132	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr1:157069134G>A	ENST00000454449.2	-	2	379	c.95C>T	c.(94-96)tCg>tTg	p.S32L		NM_001004341.2	NP_001004341.1	Q6ZN32	ETV3L_HUMAN	ets variant 3-like	32					cell differentiation (GO:0030154)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription from RNA polymerase II promoter (GO:0006366)	nucleus (GO:0005634)	sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0000981)			breast(1)|central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(2)|lung(9)|ovary(2)|prostate(2)|skin(2)|upper_aerodigestive_tract(2)	24	Hepatocellular(266;0.158)	Prostate(1639;0.184)				GCCTGGGGACGACTCGGCTTT	0.642													G|||	26	0.00519169	0.0008	0.0029	5008	,	,		17095	0.0		0.0109	False		,,,				2504	0.0123				p.S32L		Atlas-SNP	.											.	ETV3L	73	.	0			c.C95T						PASS	.	G	LEU/SER	5,4401	9.9+/-24.2	0,5,2198	51.0	51.0	51.0		95	4.0	1.0	1	dbSNP_129	51	74,8526	43.6+/-101.6	0,74,4226	yes	missense	ETV3L	NM_001004341.2	145	0,79,6424	AA,AG,GG		0.8605,0.1135,0.6074	probably-damaging	32/362	157069134	79,12927	2203	4300	6503	SO:0001583	missense	440695	exon2			GGGGACGACTCGG	AK131392	CCDS30893.1	1q23.1	2013-09-24	2008-09-12		ENSG00000253831	ENSG00000253831			33834	protein-coding gene	gene with protein product			"""ets variant gene 3-like"""				Standard	NM_001004341		Approved	FLJ16478	uc001fqq.2	Q6ZN32	OTTHUMG00000041325	ENST00000454449.2:c.95C>T	1.37:g.157069134G>A	ENSP00000430271:p.Ser32Leu	150.0	0.0	0		231.0	94.0	0.406926	NM_001004341		Missense_Mutation	SNP	ENST00000454449.2	37	CCDS30893.1	11	0.005036630036630037	1	0.0020325203252032522	1	0.0027624309392265192	0	0.0	9	0.011873350923482849	G	24.7	4.556591	0.86231	0.001135	0.008605	ENSG00000253831	ENST00000454449	T	0.12255	2.7	4.96	4.03	0.46877	Winged helix-turn-helix transcription repressor DNA-binding (1);	0.000000	0.32802	N	0.005635	T	0.16685	0.0401	L	0.34521	1.04	0.40492	D	0.980559	D	0.89917	1.0	D	0.78314	0.991	T	0.02625	-1.1132	10	0.87932	D	0	.	14.2718	0.66155	0.0:0.1505:0.8495:0.0	rs61730132	32	Q6ZN32	ETV3L_HUMAN	L	32	ENSP00000430271:S32L	ENSP00000430271:S32L	S	-	2	0	ETV3L	155335758	1.000000	0.71417	0.954000	0.39281	0.918000	0.54935	5.422000	0.66453	1.271000	0.44313	0.655000	0.94253	TCG	G|0.994;A|0.006	0.006	strong		0.642	ETV3L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000099024.2	NM_001004341	
ARID4A	5926	hgsc.bcm.edu	37	14	58831995	58831995	+	Missense_Mutation	SNP	A	A	G	rs377087834		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr14:58831995A>G	ENST00000355431.3	+	20	3561	c.3188A>G	c.(3187-3189)cAa>cGa	p.Q1063R	ARID4A_ENST00000348476.3_Missense_Mutation_p.Q1063R|ARID4A_ENST00000395168.3_Missense_Mutation_p.Q1063R|ARID4A_ENST00000431317.2_Missense_Mutation_p.Q1063R	NM_002892.3	NP_002883.3	P29374	ARI4A_HUMAN	AT rich interactive domain 4A (RBP1-like)	1063					erythrocyte development (GO:0048821)|histone H3-K4 trimethylation (GO:0080182)|histone H3-K9 trimethylation (GO:0036124)|histone H4-K20 trimethylation (GO:0034773)|negative regulation of transcription, DNA-templated (GO:0045892)|regulation of gene expression by genetic imprinting (GO:0006349)|transcription from RNA polymerase II promoter (GO:0006366)	nucleus (GO:0005634)|transcriptional repressor complex (GO:0017053)	DNA binding (GO:0003677)|sequence-specific DNA binding transcription factor activity (GO:0003700)			NS(1)|breast(2)|central_nervous_system(1)|cervix(4)|endometrium(8)|kidney(2)|large_intestine(14)|lung(19)|ovary(3)|skin(4)|upper_aerodigestive_tract(1)|urinary_tract(1)	60						ATAATTGTACAAGAGAGAGAG	0.383																																					p.Q1063R		Atlas-SNP	.											.	ARID4A	222	.	0			c.A3188G						PASS	.	A	ARG/GLN,ARG/GLN,ARG/GLN	1,4395		0,1,2197	59.0	61.0	60.0		3188,3188,3188	4.2	0.6	14		60	2,8576		0,2,4287	no	missense,missense,missense	ARID4A	NM_002892.3,NM_023000.2,NM_023001.2	43,43,43	0,3,6484	GG,GA,AA		0.0233,0.0227,0.0231	benign,benign,benign	1063/1258,1063/1204,1063/1189	58831995	3,12971	2198	4289	6487	SO:0001583	missense	5926	exon20			TTGTACAAGAGAG	S57153	CCDS9732.1, CCDS9733.1, CCDS45114.1	14q22.3	2013-02-07	2004-01-28	2004-01-28	ENSG00000032219	ENSG00000032219		"""-"""	9885	protein-coding gene	gene with protein product		180201	"""retinoblastoma-binding protein 1"""	RBBP1		1857421, 8455946	Standard	NM_023000		Approved	RBP1, RBP-1	uc001xdp.3	P29374	OTTHUMG00000140320	ENST00000355431.3:c.3188A>G	14.37:g.58831995A>G	ENSP00000347602:p.Gln1063Arg	84.0	0.0	0		99.0	42.0	0.424242	NM_002892	Q15991|Q15992|Q15993	Missense_Mutation	SNP	ENST00000355431.3	37	CCDS9732.1	.	.	.	.	.	.	.	.	.	.	A	6.768	0.510652	0.12883	2.27E-4	2.33E-4	ENSG00000032219	ENST00000355431;ENST00000348476;ENST00000395168;ENST00000431317;ENST00000417477	T;T;T;T;T	0.17370	2.43;2.43;2.46;2.43;2.28	5.46	4.25	0.50352	.	0.533378	0.21403	N	0.075117	T	0.12817	0.0311	L	0.44542	1.39	0.30980	N	0.722581	B;B;B	0.06786	0.001;0.001;0.001	B;B;B	0.09377	0.003;0.002;0.004	T	0.08973	-1.0696	10	0.17832	T	0.49	-11.3967	7.5328	0.27693	0.6734:0.2537:0.0729:0.0	.	1063;1063;1063	P29374-3;P29374;P29374-2	.;ARI4A_HUMAN;.	R	1063;1063;1063;1063;741	ENSP00000347602:Q1063R;ENSP00000344556:Q1063R;ENSP00000378597:Q1063R;ENSP00000397368:Q1063R;ENSP00000416053:Q741R	ENSP00000344556:Q1063R	Q	+	2	0	ARID4A	57901748	1.000000	0.71417	0.605000	0.28930	0.958000	0.62258	3.193000	0.50997	2.082000	0.62665	0.455000	0.32223	CAA	.	.	weak		0.383	ARID4A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276927.2	NM_023001	
FAM149A	25854	hgsc.bcm.edu	37	4	187078745	187078745	+	Missense_Mutation	SNP	A	A	G	rs113168248	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr4:187078745A>G	ENST00000356371.5	+	8	1474	c.1474A>G	c.(1474-1476)Aaa>Gaa	p.K492E	FAM149A_ENST00000227065.4_Missense_Mutation_p.K201E|FAM149A_ENST00000389354.5_Missense_Mutation_p.K201E|FAM149A_ENST00000514829.1_3'UTR|FAM149A_ENST00000502970.1_Missense_Mutation_p.K201E|FAM149A_ENST00000514153.1_Missense_Mutation_p.K201E|FAM149A_ENST00000503432.1_Missense_Mutation_p.K201E			A5PLN7	F149A_HUMAN	family with sequence similarity 149, member A	492										breast(2)|endometrium(1)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(8)|lung(8)|pancreas(1)|prostate(1)|skin(2)	25		all_cancers(14;4.27e-52)|all_epithelial(14;7.69e-39)|all_lung(41;1.34e-13)|Lung NSC(41;3.58e-13)|Melanoma(20;1.91e-06)|Colorectal(36;0.0066)|Hepatocellular(41;0.00886)|Renal(120;0.00988)|Prostate(90;0.00996)|all_hematologic(60;0.014)|all_neural(102;0.243)		OV - Ovarian serous cystadenocarcinoma(60;1.19e-10)|BRCA - Breast invasive adenocarcinoma(30;1.22e-05)|GBM - Glioblastoma multiforme(59;0.000122)|STAD - Stomach adenocarcinoma(60;0.000288)|LUSC - Lung squamous cell carcinoma(40;0.00241)|READ - Rectum adenocarcinoma(43;0.166)		AGAAACATTGAAAGTGGCTGG	0.468													A|||	11	0.00219649	0.0008	0.0043	5008	,	,		20772	0.0		0.007	False		,,,				2504	0.0				p.K201E		Atlas-SNP	.											.	FAM149A	52	.	0			c.A601G						PASS	.	A	GLU/LYS,GLU/LYS	6,4400	11.4+/-27.6	0,6,2197	70.0	80.0	77.0		601,601	3.5	0.1	4	dbSNP_132	77	62,8538	37.8+/-93.5	0,62,4238	yes	missense,missense	FAM149A	NM_001006655.2,NM_015398.2	56,56	0,68,6435	GG,GA,AA		0.7209,0.1362,0.5228	benign,benign	201/483,201/483	187078745	68,12938	2203	4300	6503	SO:0001583	missense	25854	exon7			ACATTGAAAGTGG	AK057166	CCDS34117.1	4q35.1	2012-04-19			ENSG00000109794	ENSG00000109794			24527	protein-coding gene	gene with protein product							Standard	NM_015398		Approved	DKFZP564J102, MST119, MSTP119	uc010isl.3	A5PLN7	OTTHUMG00000160565	ENST00000356371.5:c.1474A>G	4.37:g.187078745A>G	ENSP00000348732:p.Lys492Glu	41.0	0.0	0		38.0	5.0	0.131579	NM_001006655	B5MDB8|Q2TAN6|Q7Z2S5|Q9Y4T9	Missense_Mutation	SNP	ENST00000356371.5	37		8	0.003663003663003663	0	0.0	2	0.0055248618784530384	0	0.0	6	0.0079155672823219	A	8.161	0.789539	0.16258	0.001362	0.007209	ENSG00000109794	ENST00000503432;ENST00000356371;ENST00000227065;ENST00000502970;ENST00000514153;ENST00000389354	T;T;T;T;T;T	0.13420	2.68;2.59;2.68;2.68;2.68;2.68	5.97	3.47	0.39725	.	0.209202	0.42821	D	0.000654	T	0.08403	0.0209	L	0.53729	1.69	0.09310	N	1	P;B;P	0.42692	0.525;0.217;0.787	B;B;B	0.40199	0.182;0.089;0.322	T	0.13602	-1.0503	10	0.22706	T	0.39	-18.2705	6.3912	0.21587	0.7847:0.0:0.0763:0.139	.	492;492;201	A5PLN7-3;A5PLN7;B4DHZ9	.;F149A_HUMAN;.	E	201;492;201;201;201;201	ENSP00000426835:K201E;ENSP00000348732:K492E;ENSP00000227065:K201E;ENSP00000427155:K201E;ENSP00000424380:K201E;ENSP00000374005:K201E	ENSP00000227065:K201E	K	+	1	0	FAM149A	187315739	0.986000	0.35501	0.050000	0.19076	0.009000	0.06853	3.318000	0.51975	1.056000	0.40484	0.524000	0.50904	AAA	A|0.995;G|0.005	0.005	strong		0.468	FAM149A-201	KNOWN	basic	protein_coding	protein_coding		NM_001006655	
PAK7	57144	hgsc.bcm.edu	37	20	9523244	9523244	+	Missense_Mutation	SNP	C	C	T	rs150828790	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr20:9523244C>T	ENST00000378429.3	-	10	2539	c.1993G>A	c.(1993-1995)Gac>Aac	p.D665N	PAK7_ENST00000378423.1_Missense_Mutation_p.D665N|PAK7_ENST00000353224.5_Missense_Mutation_p.D665N	NM_020341.3	NP_065074.1	Q9P286	PAK7_HUMAN	p21 protein (Cdc42/Rac)-activated kinase 7	665	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				apoptotic process (GO:0006915)|cell growth (GO:0016049)|cell migration (GO:0016477)|cell proliferation (GO:0008283)|cytoskeleton organization (GO:0007010)|learning (GO:0007612)|locomotory behavior (GO:0007626)|memory (GO:0007613)|negative regulation of extrinsic apoptotic signaling pathway (GO:2001237)|signal transduction (GO:0007165)	mitochondrion (GO:0005739)|nucleus (GO:0005634)	ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)			NS(1)|central_nervous_system(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(10)|lung(44)|ovary(2)|skin(13)|stomach(1)|upper_aerodigestive_tract(3)	81			COAD - Colon adenocarcinoma(9;0.194)			TTGTGTAGGTCCTTCACTCTT	0.478													C|||	3	0.000599042	0.0008	0.0	5008	,	,		20256	0.0		0.002	False		,,,				2504	0.0				p.D665N		Atlas-SNP	.											.	PAK7	194	.	0			c.G1993A						PASS	.	C	ASN/ASP,ASN/ASP	0,4406		0,0,2203	156.0	158.0	157.0		1993,1993	5.5	1.0	20	dbSNP_134	157	18,8582	13.3+/-46.6	0,18,4282	yes	missense,missense	PAK7	NM_020341.3,NM_177990.2	23,23	0,18,6485	TT,TC,CC		0.2093,0.0,0.1384	benign,benign	665/720,665/720	9523244	18,12988	2203	4300	6503	SO:0001583	missense	57144	exon9			GTAGGTCCTTCAC	AB033090	CCDS13107.1	20p12	2008-06-17	2008-06-17		ENSG00000101349	ENSG00000101349			15916	protein-coding gene	gene with protein product		608038	"""p21(CDKN1A)-activated kinase 7"""			11756552, 10574462	Standard	NM_020341		Approved	KIAA1264, PAK5	uc002wnk.2	Q9P286	OTTHUMG00000031857	ENST00000378429.3:c.1993G>A	20.37:g.9523244C>T	ENSP00000367686:p.Asp665Asn	159.0	0.0	0		189.0	96.0	0.507937	NM_177990	A8K5T6|D3DW14|Q5W115|Q9BX09|Q9ULF6	Missense_Mutation	SNP	ENST00000378429.3	37	CCDS13107.1	3	0.0013736263736263737	1	0.0020325203252032522	0	0.0	0	0.0	2	0.002638522427440633	C	13.57	2.276632	0.40294	0.0	0.002093	ENSG00000101349	ENST00000378429;ENST00000353224;ENST00000378423	T;T;T	0.13538	2.58;2.58;2.58	5.48	5.48	0.80851	Serine/threonine-protein kinase-like domain (1);Serine/threonine-protein kinase, catalytic  domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.042605	0.85682	D	0.000000	T	0.12263	0.0298	N	0.25992	0.78	0.58432	D	0.999996	B	0.09022	0.002	B	0.10450	0.005	T	0.15492	-1.0435	9	.	.	.	.	19.3557	0.94412	0.0:1.0:0.0:0.0	.	665	Q9P286	PAK7_HUMAN	N	665	ENSP00000367686:D665N;ENSP00000322957:D665N;ENSP00000367679:D665N	.	D	-	1	0	PAK7	9471244	1.000000	0.71417	1.000000	0.80357	0.991000	0.79684	4.034000	0.57289	2.597000	0.87782	0.655000	0.94253	GAC	C|0.999;T|0.001	0.001	strong		0.478	PAK7-001	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000077962.1		
KLHL34	257240	hgsc.bcm.edu	37	X	21675125	21675125	+	Missense_Mutation	SNP	G	G	A			TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chrX:21675125G>A	ENST00000379499.2	-	1	1323	c.782C>T	c.(781-783)aCg>aTg	p.T261M		NM_153270.1	NP_695002.1	Q8N239	KLH34_HUMAN	kelch-like family member 34	261						extracellular space (GO:0005615)				cervix(1)|endometrium(7)|kidney(1)|large_intestine(3)|lung(11)|ovary(2)|urinary_tract(1)	26						GCGGGAGGGCGTCGTGTGGTA	0.706													G|||	1	0.000264901	0.0	0.0	3775	,	,		9852	0.0		0.0	False		,,,				2504	0.001				p.T261M		Atlas-SNP	.											.	KLHL34	76	.	0			c.C782T						PASS	.						16.0	18.0	17.0					X																	21675125		2197	4282	6479	SO:0001583	missense	257240	exon1			GAGGGCGTCGTGT	AK092279	CCDS14199.1	Xp22.12	2013-02-22	2013-02-22		ENSG00000185915	ENSG00000185915		"""Kelch-like"", ""BTB/POZ domain containing"""	26634	protein-coding gene	gene with protein product			"""kelch-like 34 (Drosophila)"""				Standard	NM_153270		Approved	FLJ34960, RP11-450P7.3	uc004czz.1	Q8N239	OTTHUMG00000021234	ENST00000379499.2:c.782C>T	X.37:g.21675125G>A	ENSP00000368813:p.Thr261Met	203.0	0.0	0		87.0	83.0	0.954023	NM_153270		Missense_Mutation	SNP	ENST00000379499.2	37	CCDS14199.1	.	.	.	.	.	.	.	.	.	.	G	0	-2.747283	0.00086	.	.	ENSG00000185915	ENST00000379499	T	0.72394	-0.65	4.76	3.89	0.44902	.	0.552287	0.18919	N	0.127528	T	0.38480	0.1042	N	0.01168	-0.975	0.09310	N	1	B	0.20887	0.049	B	0.12837	0.008	T	0.24693	-1.0153	10	0.27082	T	0.32	.	8.1602	0.31194	0.0844:0.0:0.7565:0.1591	.	261	Q8N239	KLH34_HUMAN	M	261	ENSP00000368813:T261M	ENSP00000368813:T261M	T	-	2	0	KLHL34	21585046	0.003000	0.15002	0.038000	0.18304	0.365000	0.29674	1.693000	0.37742	0.990000	0.38787	0.422000	0.28245	ACG	.	.	none		0.706	KLHL34-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056022.1	NM_153270	
KCNK16	83795	hgsc.bcm.edu	37	6	39284148	39284148	+	Silent	SNP	C	C	T			TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr6:39284148C>T	ENST00000373229.5	-	5	745	c.732G>A	c.(730-732)ctG>ctA	p.L244L	KCNK16_ENST00000437525.2_Silent_p.L244L|KCNK17_ENST00000373231.4_5'Flank|KCNK16_ENST00000507712.1_Intron|KCNK16_ENST00000425054.2_Intron|KCNK17_ENST00000453413.2_5'Flank|KCNK16_ENST00000373227.4_Intron	NM_032115.3	NP_115491.1	Q96T55	KCNKG_HUMAN	potassium channel, subfamily K, member 16	244					potassium ion transport (GO:0006813)|synaptic transmission (GO:0007268)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	potassium channel activity (GO:0005267)|voltage-gated ion channel activity (GO:0005244)			large_intestine(1)|lung(7)|ovary(2)|prostate(1)|skin(2)	13						CCAGCCACGCCAGGCCCAGGA	0.627																																					p.L244L		Atlas-SNP	.											.	KCNK16	59	.	0			c.G732A						PASS	.						32.0	34.0	33.0					6																	39284148		2203	4300	6503	SO:0001819	synonymous_variant	83795	exon5			CCACGCCAGGCCC	AF358909	CCDS4843.1, CCDS47420.1, CCDS47421.1, CCDS47422.1	6p21.2-p21.1	2012-03-07			ENSG00000095981	ENSG00000095981		"""Potassium channels"", ""Voltage-gated ion channels / Potassium channels, Two-P"""	14464	protein-coding gene	gene with protein product		607369				11263999, 16382106	Standard	NM_032115		Approved	K2p16.1, TALK-1, TALK1	uc003ooq.3	Q96T55	OTTHUMG00000014645	ENST00000373229.5:c.732G>A	6.37:g.39284148C>T		89.0	0.0	0		89.0	46.0	0.516854	NM_001135106	B5TJL9|Q2M2N9|Q5TCF3|Q6X6Z3|Q6X6Z4|Q6X6Z5|Q9H591	Silent	SNP	ENST00000373229.5	37	CCDS4843.1																																																																																			.	.	none		0.627	KCNK16-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000040452.2	NM_032115	
ERMARD	55780	hgsc.bcm.edu	37	6	170169688	170169688	+	Missense_Mutation	SNP	A	A	G	rs61738268	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr6:170169688A>G	ENST00000366773.3	+	12	1145	c.1112A>G	c.(1111-1113)cAt>cGt	p.H371R	ERMARD_ENST00000392095.4_Missense_Mutation_p.H245R|ERMARD_ENST00000418781.3_Missense_Mutation_p.H371R|ERMARD_ENST00000366772.2_Missense_Mutation_p.H371R|RP1-266L20.9_ENST00000586101.1_RNA|ERMARD_ENST00000588451.1_Missense_Mutation_p.H235R	NM_001278532.1|NM_018341.1	NP_001265461.1|NP_060811.1	Q5T6L9	EMARD_HUMAN	ER membrane-associated RNA degradation	371					multicellular organismal development (GO:0007275)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)											ATAAGAGATCATTTAAGCCAC	0.388													A|||	37	0.00738818	0.0	0.013	5008	,	,		16813	0.0		0.0119	False		,,,				2504	0.0164				p.H371R		Atlas-SNP	.											.	C6orf70	63	.	0			c.A1112G						PASS	.	A	ARG/HIS	5,4401		0,5,2198	58.0	54.0	56.0		1112	-4.5	0.0	6	dbSNP_129	56	108,8492		2,104,4194	yes	missense	C6orf70	NM_018341.1	29	2,109,6392	GG,GA,AA		1.2558,0.1135,0.8688	benign	371/679	170169688	113,12893	2203	4300	6503	SO:0001583	missense	55780	exon12			GAGATCATTTAAG	AK002014	CCDS34576.1, CCDS64572.1, CCDS64573.1, CCDS64574.1	6q27	2013-08-28	2013-08-28	2013-08-28	ENSG00000130023	ENSG00000130023			21056	protein-coding gene	gene with protein product		615532	"""chromosome 6 open reading frame 70"""	C6orf70		23768067	Standard	NM_018341		Approved	FLJ11152, dJ266L20.3	uc003qxg.1	Q5T6L9	OTTHUMG00000016067	ENST00000366773.3:c.1112A>G	6.37:g.170169688A>G	ENSP00000355735:p.His371Arg	77.0	0.0	0		61.0	25.0	0.409836	NM_018341	B4DFH0|F8WAF1|Q3ZCS8|Q5T6L8|Q9NUT5|Q9NVU2	Missense_Mutation	SNP	ENST00000366773.3	37	CCDS34576.1	20	0.009157509157509158	0	0.0	8	0.022099447513812154	0	0.0	12	0.0158311345646438	.	0.029	-1.347487	0.01266	0.001135	0.012558	ENSG00000130023	ENST00000366773;ENST00000366772;ENST00000418781;ENST00000392095;ENST00000366771	T;T	0.35605	1.3;1.36	5.34	-4.53	0.03462	.	0.650998	0.14673	N	0.305256	T	0.06690	0.0171	N	0.12502	0.225	0.09310	N	1	B;B;B	0.06786	0.001;0.001;0.0	B;B;B	0.09377	0.004;0.003;0.001	T	0.34254	-0.9836	10	0.20519	T	0.43	.	15.5024	0.75709	0.816:0.0:0.184:0.0	rs61738268	371;371;371	Q5T6L9-3;Q5T6L9-2;Q5T6L9	.;.;CF070_HUMAN	R	371;371;371;245;19	ENSP00000355735:H371R;ENSP00000375945:H245R	ENSP00000355733:H19R	H	+	2	0	C6orf70	169911613	0.000000	0.05858	0.000000	0.03702	0.473000	0.32948	-1.487000	0.02310	-0.732000	0.04856	-0.426000	0.05927	CAT	A|0.991;G|0.009	0.009	strong		0.388	ERMARD-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000043238.2	NM_018341	
CSRP2BP	57325	hgsc.bcm.edu	37	20	18168099	18168099	+	Missense_Mutation	SNP	G	G	A	rs376874386		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr20:18168099G>A	ENST00000435364.3	+	10	2686	c.2345G>A	c.(2344-2346)cGc>cAc	p.R782H	CSRP2BP_ENST00000377681.3_Missense_Mutation_p.R781H|CSRP2BP_ENST00000489634.2_Missense_Mutation_p.R654H	NM_020536.4	NP_065397	Q9H8E8	CSR2B_HUMAN	CSRP2 binding protein	782	N-acetyltransferase. {ECO:0000255|PROSITE-ProRule:PRU00532}.				chromatin organization (GO:0006325)|G2/M transition of mitotic cell cycle (GO:0000086)|histone H3 acetylation (GO:0043966)	Ada2/Gcn5/Ada3 transcription activator complex (GO:0005671)|cytoplasm (GO:0005737)|nucleus (GO:0005634)	histone acetyltransferase activity (GO:0004402)|LIM domain binding (GO:0030274)			NS(1)|breast(1)|endometrium(3)|kidney(3)|large_intestine(7)|lung(12)|ovary(2)|prostate(3)|skin(1)|stomach(1)	34						AGGCTCCGGCGCTGATGCGAA	0.413																																					p.R782H		Atlas-SNP	.											.	CSRP2BP	80	.	0			c.G2345A						PASS	.	G	HIS/ARG	0,4406		0,0,2203	73.0	73.0	73.0		2345	5.9	1.0	20		73	1,8599	1.2+/-3.3	0,1,4299	no	missense	CSRP2BP	NM_020536.4	29	0,1,6502	AA,AG,GG		0.0116,0.0,0.0077	probably-damaging	782/783	18168099	1,13005	2203	4300	6503	SO:0001583	missense	57325	exon10			TCCGGCGCTGATG	AF252257	CCDS13133.1	20p11.23	2012-06-06			ENSG00000149474	ENSG00000149474			15904	protein-coding gene	gene with protein product	"""cysteine rich protein 2 binding protein"", ""ATAC component 2 homolog (Drosophila)"""					9286703, 10924333, 19103755	Standard	NR_028402		Approved	CRP2BP, dJ717M23.1, PRO1194, ATAC2, KAT14	uc021wbb.1	Q9H8E8	OTTHUMG00000031962	ENST00000435364.3:c.2345G>A	20.37:g.18168099G>A	ENSP00000392318:p.Arg782His	66.0	0.0	0		65.0	29.0	0.446154	NM_020536	A2A2I5|Q96GW6|Q96IH3|Q9HBF0|Q9UIY5	Missense_Mutation	SNP	ENST00000435364.3	37	CCDS13133.1	.	.	.	.	.	.	.	.	.	.	G	36	5.598337	0.96614	0.0	1.16E-4	ENSG00000149474	ENST00000278816;ENST00000377681;ENST00000435364;ENST00000489634	T;T;T;T	0.28666	1.6;1.61;1.6;1.63	5.87	5.87	0.94306	GCN5-related N-acetyltransferase (GNAT) domain (1);	0.000000	0.85682	D	0.000000	T	0.58779	0.2146	M	0.72576	2.205	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.91635	0.999;0.998	T	0.58945	-0.7546	10	0.87932	D	0	.	20.2147	0.98293	0.0:0.0:1.0:0.0	.	654;782	Q9H8E8-2;Q9H8E8	.;CSR2B_HUMAN	H	782;781;782;654	ENSP00000278816:R782H;ENSP00000366909:R781H;ENSP00000392318:R782H;ENSP00000425909:R654H	ENSP00000278816:R782H	R	+	2	0	CSRP2BP	18116099	1.000000	0.71417	1.000000	0.80357	0.968000	0.65278	9.750000	0.98875	2.785000	0.95823	0.591000	0.81541	CGC	.	.	weak		0.413	CSRP2BP-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000078152.5	NM_020536	
LILRA4	23547	hgsc.bcm.edu	37	19	54848145	54848145	+	Missense_Mutation	SNP	G	G	A	rs75547479	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr19:54848145G>A	ENST00000291759.4	-	6	1278	c.1222C>T	c.(1222-1224)Cac>Tac	p.H408Y	AC008984.2_ENST00000507363.1_RNA	NM_012276.3	NP_036408.3	P59901	LIRA4_HUMAN	leukocyte immunoglobulin-like receptor, subfamily A (with TM domain), member 4	408	Ig-like C2-type 4.				immune system process (GO:0002376)	integral component of membrane (GO:0016021)				NS(2)|breast(1)|central_nervous_system(2)|endometrium(2)|large_intestine(5)|lung(13)|prostate(3)|skin(1)|upper_aerodigestive_tract(3)	32	Ovarian(34;0.19)			GBM - Glioblastoma multiforme(193;0.0565)		TCACTGGGGTGAGACAGCAGG	0.592													G|||	74	0.0147764	0.0333	0.0014	5008	,	,		17303	0.0		0.001	False		,,,				2504	0.0286				p.H408Y		Atlas-SNP	.											.	LILRA4	91	.	0			c.C1222T						PASS	.						112.0	91.0	98.0					19																	54848145		2203	4300	6503	SO:0001583	missense	23547	exon6			TGGGGTGAGACAG	AF041261	CCDS12890.1	19q13.4	2013-01-11			ENSG00000239961	ENSG00000239961		"""Leukocyte immunoglobulin-like receptors"", ""CD molecules"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	15503	protein-coding gene	gene with protein product		607517				10941842	Standard	NM_012276		Approved	ILT7, CD85g	uc002qfj.3	P59901	OTTHUMG00000065355	ENST00000291759.4:c.1222C>T	19.37:g.54848145G>A	ENSP00000291759:p.His408Tyr	235.0	0.0	0		182.0	19.0	0.104396	NM_012276	Q32MC4	Missense_Mutation	SNP	ENST00000291759.4	37	CCDS12890.1	.	.	.	.	.	.	.	.	.	.	.	6.455	0.452105	0.12283	.	.	ENSG00000239961	ENST00000291759	T	0.00724	5.78	2.4	0.177	0.15054	Immunoglobulin subtype (1);Immunoglobulin-like fold (1);	3.662820	0.00932	N	0.002721	T	0.01523	0.0049	M	0.81341	2.54	0.09310	N	1	B	0.14438	0.01	B	0.09377	0.004	T	0.56056	-0.8042	10	0.20519	T	0.43	.	4.4089	0.11423	0.3496:0.0:0.6504:0.0	.	408	P59901	LIRA4_HUMAN	Y	408	ENSP00000291759:H408Y	ENSP00000291759:H408Y	H	-	1	0	LILRA4	59539957	0.000000	0.05858	0.008000	0.14137	0.035000	0.12851	-1.057000	0.03486	0.109000	0.17891	0.455000	0.32223	CAC	A|0.005;G|0.995	0.005	strong		0.592	LILRA4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000140229.2	NM_012276	
GPR151	134391	hgsc.bcm.edu	37	5	145894882	145894882	+	Silent	SNP	G	G	A			TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr5:145894882G>A	ENST00000311104.2	-	1	871	c.795C>T	c.(793-795)ccC>ccT	p.P265P		NM_194251.2	NP_919227.2	Q8TDV0	GP151_HUMAN	G protein-coupled receptor 151	265						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)			endometrium(2)|large_intestine(1)|lung(6)|ovary(1)|pancreas(1)|skin(1)|urinary_tract(2)	14			KIRC - Kidney renal clear cell carcinoma(527;0.000785)|Kidney(363;0.00101)			CTACCCATTCGGGGAGCCACA	0.507																																					p.P265P	Pancreas(78;420 1386 18535 37114 49710)	Atlas-SNP	.											.	GPR151	35	.	0			c.C795T						PASS	.						54.0	56.0	56.0					5																	145894882		2203	4300	6503	SO:0001819	synonymous_variant	134391	exon1			CCATTCGGGGAGC	AY255557	CCDS34266.1	5q32	2012-08-21						"""GPCR / Class A : Orphans"""	23624	protein-coding gene	gene with protein product	"""galanin receptor 4"""					12679517	Standard	NM_194251		Approved	PGR7, GALR4	uc003lod.1	Q8TDV0		ENST00000311104.2:c.795C>T	5.37:g.145894882G>A		94.0	0.0	0		113.0	32.0	0.283186	NM_194251	Q86SN8|Q8NGV2	Silent	SNP	ENST00000311104.2	37	CCDS34266.1																																																																																			.	.	none		0.507	GPR151-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000373457.1	NM_194251	
PLCL2	23228	hgsc.bcm.edu	37	3	17053613	17053613	+	Silent	SNP	C	C	T	rs61751588	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr3:17053613C>T	ENST00000418129.2	+	2	2862	c.2397C>T	c.(2395-2397)ccC>ccT	p.P799P	PLCL2_ENST00000396755.2_Silent_p.P799P|PLCL2_ENST00000432376.1_Silent_p.P799P	NM_001144382.1	NP_001137854.1	Q9UPR0	PLCL2_HUMAN	phospholipase C-like 2	925	C2. {ECO:0000255|PROSITE- ProRule:PRU00041}.				B cell proliferation involved in immune response (GO:0002322)|B-1a B cell differentiation (GO:0002337)|gamma-aminobutyric acid signaling pathway (GO:0007214)|intracellular signal transduction (GO:0035556)|lipid metabolic process (GO:0006629)|negative regulation of B cell receptor signaling pathway (GO:0050859)|positive regulation of receptor binding (GO:1900122)|regulation of peptidyl-serine phosphorylation (GO:0033135)|regulation of synaptic transmission, GABAergic (GO:0032228)	cytoplasm (GO:0005737)	calcium ion binding (GO:0005509)|GABA receptor binding (GO:0050811)|phosphatidylinositol phospholipase C activity (GO:0004435)|signal transducer activity (GO:0004871)			breast(4)|cervix(1)|endometrium(4)|kidney(1)|large_intestine(9)|lung(13)|ovary(1)|prostate(2)|skin(7)|urinary_tract(1)	43						ATGCCCAGCCCCCTATACGGG	0.438													C|||	34	0.00678914	0.0008	0.0043	5008	,	,		17519	0.0		0.0258	False		,,,				2504	0.0041				p.P799P		Atlas-SNP	.											.	PLCL2	145	.	0			c.C2397T						PASS	.	C	,	19,4387	24.3+/-50.5	1,17,2185	60.0	65.0	64.0		2779,2397	-0.4	1.0	3	dbSNP_129	64	175,8423	75.1+/-137.7	3,169,4127	yes	coding-synonymous,coding-synonymous	PLCL2	NM_001144382.1,NM_015184.5	,	4,186,6312	TT,TC,CC		2.0354,0.4312,1.4918	,	925/1128,799/1002	17053613	194,12810	2203	4299	6502	SO:0001819	synonymous_variant	23228	exon2			CCAGCCCCCTATA	AB029015	CCDS33713.1, CCDS74911.1	3p25.3-p25.1	2008-03-18	2002-02-18	2002-02-22	ENSG00000154822	ENSG00000154822			9064	protein-coding gene	gene with protein product		614276	"""phospholipase C, epsilon 2"""	PLCE2		10470851	Standard	NM_015184		Approved	KIAA1092	uc011awd.2	Q9UPR0	OTTHUMG00000155467	ENST00000418129.2:c.2397C>T	3.37:g.17053613C>T		70.0	0.0	0		51.0	22.0	0.431373	NM_015184	A8K5V4|Q8N498|Q9H8L0|Q9UFP9	Silent	SNP	ENST00000418129.2	37	CCDS33713.1	23	0.010531135531135532	0	0.0	2	0.0055248618784530384	0	0.0	21	0.027704485488126648	C	9.281	1.048206	0.19827	0.004312	0.020354	ENSG00000154822	ENST00000419842	T	0.20069	2.1	5.53	-0.419	0.12340	.	0.164246	0.53938	D	0.000054	T	0.04407	0.0121	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.12142	-1.0559	7	0.10636	T	0.68	.	9.1754	0.37109	0.4233:0.203:0.3736:0.0	rs61751588	.	.	.	L	543	ENSP00000404433:P543L	ENSP00000404433:P543L	P	+	2	0	PLCL2	17028617	0.893000	0.30496	0.989000	0.46669	0.984000	0.73092	-0.009000	0.12765	0.255000	0.21593	0.491000	0.48974	CCC	C|0.987;T|0.013	0.013	strong		0.438	PLCL2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000340250.3		
FN1	2335	hgsc.bcm.edu	37	2	216248820	216248820	+	Missense_Mutation	SNP	G	G	T			TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr2:216248820G>T	ENST00000359671.1	-	29	4809	c.4544C>A	c.(4543-4545)aCc>aAc	p.T1515N	FN1_ENST00000432072.2_Missense_Mutation_p.T1606N|FN1_ENST00000357009.2_Missense_Mutation_p.T1515N|FN1_ENST00000490833.1_5'Flank|FN1_ENST00000323926.6_Missense_Mutation_p.T1606N|FN1_ENST00000354785.4_Missense_Mutation_p.T1606N|FN1_ENST00000421182.1_Missense_Mutation_p.T1515N|FN1_ENST00000336916.4_Missense_Mutation_p.T1515N|FN1_ENST00000346544.3_Missense_Mutation_p.T1515N|FN1_ENST00000357867.4_Missense_Mutation_p.T1515N|FN1_ENST00000345488.5_Missense_Mutation_p.T1515N|FN1_ENST00000356005.4_Missense_Mutation_p.T1515N|FN1_ENST00000446046.1_Missense_Mutation_p.T1515N|FN1_ENST00000443816.1_Missense_Mutation_p.T1515N			P02751	FINC_HUMAN	fibronectin 1	1515	Cell-attachment.|Fibronectin type-III 10. {ECO:0000255|PROSITE-ProRule:PRU00316}.				acute-phase response (GO:0006953)|angiogenesis (GO:0001525)|blood coagulation (GO:0007596)|calcium-independent cell-matrix adhesion (GO:0007161)|cell adhesion (GO:0007155)|cell-substrate junction assembly (GO:0007044)|endodermal cell differentiation (GO:0035987)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|integrin activation (GO:0033622)|leukocyte migration (GO:0050900)|peptide cross-linking (GO:0018149)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|positive regulation of axon extension (GO:0045773)|regulation of cell shape (GO:0008360)|response to wounding (GO:0009611)|substrate adhesion-dependent cell spreading (GO:0034446)	apical plasma membrane (GO:0016324)|basal lamina (GO:0005605)|blood microparticle (GO:0072562)|endoplasmic reticulum-Golgi intermediate compartment (GO:0005793)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|fibrinogen complex (GO:0005577)|platelet alpha granule lumen (GO:0031093)	collagen binding (GO:0005518)|heparin binding (GO:0008201)|integrin binding (GO:0005178)|peptidase activator activity (GO:0016504)|protease binding (GO:0002020)		FN1/ALK(2)	NS(1)|autonomic_ganglia(1)|breast(2)|central_nervous_system(7)|endometrium(9)|kidney(8)|large_intestine(33)|lung(38)|ovary(1)|pancreas(1)|prostate(3)|skin(1)|stomach(2)|upper_aerodigestive_tract(2)	109		Renal(323;0.127)		Epithelial(149;9.59e-07)|all cancers(144;0.000174)|LUSC - Lung squamous cell carcinoma(224;0.008)|Lung(261;0.00948)	Ocriplasmin(DB08888)	CACAGTGATGGTATAATCAAC	0.498																																					p.T1606N		Atlas-SNP	.											.	FN1	521	.	0			c.C4817A						PASS	.						131.0	120.0	123.0					2																	216248820		2203	4300	6503	SO:0001583	missense	2335	exon30			GTGATGGTATAAT		CCDS2399.1, CCDS2400.1, CCDS42813.1, CCDS42814.1, CCDS46510.1, CCDS46512.1	2q34	2014-01-30			ENSG00000115414	ENSG00000115414		"""Fibronectin type III domain containing"", ""Endogenous ligands"""	3778	protein-coding gene	gene with protein product	"""migration-stimulating factor"", ""cold-insoluble globulin"""	135600				2992939, 3003095	Standard	NM_054034		Approved	MSF, CIG, LETS, GFND2, FINC	uc002vfa.3	P02751	OTTHUMG00000133054	ENST00000359671.1:c.4544C>A	2.37:g.216248820G>T	ENSP00000352696:p.Thr1515Asn	114.0	0.0	0		71.0	19.0	0.267606	NM_212482	B7ZLF0|E9PE77|E9PG29|O95609|O95610|Q14312|Q14325|Q14326|Q17RV7|Q564H7|Q585T2|Q59EH1|Q60FE4|Q68DP8|Q68DP9|Q68DT4|Q6LDP6|Q6MZS0|Q6MZU5|Q6N025|Q6N0A6|Q7Z391|Q86T27|Q8IVI8|Q96KP7|Q96KP8|Q96KP9|Q9H1B8|Q9HAP3|Q9UMK2	Missense_Mutation	SNP	ENST00000359671.1	37		.	.	.	.	.	.	.	.	.	.	G	20.8	4.046748	0.75846	.	.	ENSG00000115414	ENST00000421182;ENST00000323926;ENST00000336916;ENST00000357867;ENST00000354785;ENST00000265313;ENST00000359671;ENST00000346544;ENST00000345488;ENST00000357009;ENST00000446046;ENST00000443816;ENST00000432072;ENST00000356005;ENST00000456923	T;T;T;T;T;T;T;T;T;T;T;T;T;T	0.57907	0.37;0.37;0.37;0.37;0.37;0.37;0.37;0.37;0.37;0.37;0.37;0.37;0.37;0.37	5.83	4.94	0.65067	.	0.000000	0.64402	D	0.000001	T	0.63331	0.2502	L	0.39898	1.24	0.27525	N	0.951287	D;D;D;D;D;P;D;D;D;D	0.76494	0.999;0.999;0.999;0.997;0.999;0.922;0.999;0.999;0.999;0.995	D;D;D;D;D;P;D;D;D;D	0.83275	0.977;0.995;0.996;0.969;0.987;0.905;0.987;0.977;0.977;0.969	T	0.56426	-0.7981	10	0.46703	T	0.11	.	14.3418	0.66633	0.0705:0.0:0.9295:0.0	.	1606;1606;1515;1515;1515;1515;1516;1515;1515;1606	P02751-13;P02751-7;P02751-10;P02751-8;E9PE77;P02751-3;E7ERA1;P02751-9;P02751-14;P02751-15	.;.;.;.;.;.;.;.;.;.	N	1515;1606;1515;1515;1606;1516;1515;1515;1515;1515;1515;1515;1606;1515;322	ENSP00000394423:T1515N;ENSP00000323534:T1606N;ENSP00000338200:T1515N;ENSP00000350534:T1515N;ENSP00000346839:T1606N;ENSP00000352696:T1515N;ENSP00000265312:T1515N;ENSP00000273049:T1515N;ENSP00000349509:T1515N;ENSP00000410422:T1515N;ENSP00000415018:T1515N;ENSP00000399538:T1606N;ENSP00000348285:T1515N;ENSP00000416139:T322N	ENSP00000265313:T1516N	T	-	2	0	FN1	215957065	1.000000	0.71417	1.000000	0.80357	0.944000	0.59088	6.391000	0.73208	2.756000	0.94617	0.655000	0.94253	ACC	.	.	none		0.498	FN1-204	KNOWN	basic	protein_coding	protein_coding		NM_212476	
U2AF2	11338	hgsc.bcm.edu	37	19	56181019	56181019	+	Silent	SNP	C	C	T	rs147666260	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr19:56181019C>T	ENST00000308924.4	+	11	1294	c.1254C>T	c.(1252-1254)ccC>ccT	p.P418P	U2AF2_ENST00000590551.1_Silent_p.P250P|CTD-2537I9.12_ENST00000585940.1_RNA|CTD-2537I9.12_ENST00000589456.1_RNA|CTD-2537I9.13_ENST00000592252.1_RNA|U2AF2_ENST00000450554.2_Silent_p.P414P			P26368	U2AF2_HUMAN	U2 small nuclear RNA auxiliary factor 2	418	RRM 3. {ECO:0000255|PROSITE- ProRule:PRU00176}.				gene expression (GO:0010467)|mRNA 3'-end processing (GO:0031124)|mRNA export from nucleus (GO:0006406)|mRNA processing (GO:0006397)|mRNA splicing, via spliceosome (GO:0000398)|negative regulation of mRNA splicing, via spliceosome (GO:0048025)|RNA splicing (GO:0008380)|termination of RNA polymerase II transcription (GO:0006369)|transcription from RNA polymerase II promoter (GO:0006366)	nuclear speck (GO:0016607)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|spliceosomal complex (GO:0005681)	enzyme binding (GO:0019899)|nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)			biliary_tract(1)|central_nervous_system(1)|cervix(1)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(3)|lung(9)|ovary(1)|prostate(1)|urinary_tract(2)	21		Colorectal(82;0.00244)|Ovarian(87;0.133)	BRCA - Breast invasive adenocarcinoma(297;0.18)	GBM - Glioblastoma multiforme(193;0.107)		TCGAGATCCCCCGGCCTGTGG	0.657													C|||	15	0.00299521	0.0	0.0101	5008	,	,		16186	0.0		0.008	False		,,,				2504	0.0				p.P418P		Atlas-SNP	.											.	U2AF2	62	.	0			c.C1254T						PASS	.	C	,	9,4397	15.5+/-35.6	0,9,2194	123.0	111.0	115.0		1242,1254	-0.6	1.0	19	dbSNP_134	115	87,8513	48.5+/-108.0	1,85,4214	no	coding-synonymous,coding-synonymous	U2AF2	NM_001012478.1,NM_007279.2	,	1,94,6408	TT,TC,CC		1.0116,0.2043,0.7381	,	414/472,418/476	56181019	96,12910	2203	4300	6503	SO:0001819	synonymous_variant	11338	exon11			GATCCCCCGGCCT	BC008740	CCDS12933.1, CCDS46197.1	19q13.43	2014-09-17	2006-04-11			ENSG00000063244		"""RNA binding motif (RRM) containing"""	23156	protein-coding gene	gene with protein product	"""U2 small nuclear ribonucleoprotein auxiliary factor (65kD)"", ""splicing factor U2AF 65 kD subunit"", ""U2 snRNP auxiliary factor large subunit"""	191318	"""U2 (RNU2) small nuclear RNA auxiliary factor 2"""			1538748	Standard	XM_006722994		Approved	U2AF65	uc002qlu.3	P26368		ENST00000308924.4:c.1254C>T	19.37:g.56181019C>T		151.0	0.0	0		162.0	81.0	0.5	NM_007279	Q96HC5	Silent	SNP	ENST00000308924.4	37	CCDS12933.1																																																																																			C|0.994;T|0.006	0.006	strong		0.657	U2AF2-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000453599.1	NM_007279	
VEGFC	7424	hgsc.bcm.edu	37	4	177713326	177713326	+	Missense_Mutation	SNP	T	T	A	rs55728985	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr4:177713326T>A	ENST00000280193.2	-	1	555	c.140A>T	c.(139-141)gAg>gTg	p.E47V		NM_005429.2	NP_005420	P49767	VEGFC_HUMAN	vascular endothelial growth factor C	47					angiogenesis (GO:0001525)|blood coagulation (GO:0007596)|induction of positive chemotaxis (GO:0050930)|morphogenesis of embryonic epithelium (GO:0016331)|negative regulation of blood pressure (GO:0045776)|negative regulation of cell proliferation (GO:0008285)|organ morphogenesis (GO:0009887)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|positive chemotaxis (GO:0050918)|positive regulation of angiogenesis (GO:0045766)|positive regulation of blood vessel endothelial cell migration (GO:0043536)|positive regulation of cell division (GO:0051781)|positive regulation of cell proliferation (GO:0008284)|positive regulation of cell-matrix adhesion (GO:0001954)|positive regulation of epithelial cell proliferation (GO:0050679)|positive regulation of lymphangiogenesis (GO:1901492)|positive regulation of mast cell chemotaxis (GO:0060754)|positive regulation of neuroblast proliferation (GO:0002052)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|positive regulation of protein autophosphorylation (GO:0031954)|positive regulation of protein secretion (GO:0050714)|regulation of vascular endothelial growth factor receptor signaling pathway (GO:0030947)|response to drug (GO:0042493)|signal transduction (GO:0007165)|substrate-dependent cell migration (GO:0006929)|vascular endothelial growth factor receptor signaling pathway (GO:0048010)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|membrane (GO:0016020)|platelet alpha granule lumen (GO:0031093)	chemoattractant activity (GO:0042056)			biliary_tract(1)|cervix(1)|large_intestine(6)|lung(28)|pancreas(1)|prostate(2)|skin(2)	41		Breast(14;0.000223)|Renal(120;0.00988)|Prostate(90;0.00996)|Melanoma(52;0.0101)|all_hematologic(60;0.107)|all_neural(102;0.164)		all cancers(43;1.59e-18)|Epithelial(43;3.68e-16)|OV - Ovarian serous cystadenocarcinoma(60;8.52e-09)|GBM - Glioblastoma multiforme(59;0.000546)|STAD - Stomach adenocarcinoma(60;0.00308)|Colorectal(24;0.025)|COAD - Colon adenocarcinoma(29;0.0359)|LUSC - Lung squamous cell carcinoma(193;0.0397)		TACCGTGGCCTCGCCCGCGTC	0.716													T|||	7	0.00139776	0.0	0.0043	5008	,	,		9648	0.0		0.004	False		,,,				2504	0.0				p.E47V		Atlas-SNP	.											VEGFC,NS,carcinoma,-1,1	VEGFC	94	1	0			c.A140T						PASS	.	T	VAL/GLU	1,3751		0,1,1875	18.0	22.0	21.0		140	3.1	1.0	4	dbSNP_129	21	43,8131		0,43,4044	yes	missense	VEGFC	NM_005429.2	121	0,44,5919	AA,AT,TT		0.5261,0.0267,0.3689	benign	47/421	177713326	44,11882	1876	4087	5963	SO:0001583	missense	7424	exon1			GTGGCCTCGCCCG	BC035212	CCDS43285.1	4q34.3	2013-02-18				ENSG00000150630			12682	protein-coding gene	gene with protein product	"""vascular endothelial growth factor-related protein"""	601528				8617204	Standard	NM_005429		Approved	VRP	uc003ius.1	P49767		ENST00000280193.2:c.140A>T	4.37:g.177713326T>A	ENSP00000280193:p.Glu47Val	25.0	0.0	0		15.0	4.0	0.266667	NM_005429	B2R9Q8	Missense_Mutation	SNP	ENST00000280193.2	37	CCDS43285.1	.	.	.	.	.	.	.	.	.	.	T	17.21	3.330343	0.60743	2.67E-4	0.005261	ENSG00000150630	ENST00000280193	.	.	.	4.3	3.13	0.36017	.	0.089559	0.43110	D	0.000613	T	0.44829	0.1312	L	0.57536	1.79	0.38259	D	0.941825	D	0.59357	0.985	P	0.50270	0.636	T	0.57590	-0.7785	9	0.72032	D	0.01	-12.749	6.7656	0.23564	0.0:0.1111:0.0:0.8889	rs55728985;rs62617087	47	P49767	VEGFC_HUMAN	V	47	.	ENSP00000280193:E47V	E	-	2	0	VEGFC	177950320	0.986000	0.35501	0.998000	0.56505	0.332000	0.28634	1.525000	0.35953	1.577000	0.49804	0.254000	0.18369	GAG	T|0.996;A|0.004	0.004	strong		0.716	VEGFC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000361991.1	NM_005429	
CFAP57	149465	hgsc.bcm.edu	37	1	43638436	43638436	+	Silent	SNP	G	G	T	rs6695238	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr1:43638436G>T	ENST00000372492.4	+	2	336	c.12G>T	c.(10-12)gtG>gtT	p.V4V	EBNA1BP2_ENST00000431635.2_5'Flank|EBNA1BP2_ENST00000236051.2_5'Flank|WDR65_ENST00000528956.1_Silent_p.V4V|EBNA1BP2_ENST00000472982.1_5'Flank	NM_001195831.2	NP_001182760.2	Q96MR6	WDR65_HUMAN		4										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)				TGTCAGCCGTGGTAGCTCAGA	0.547													G|||	341	0.0680911	0.1899	0.0576	5008	,	,		10442	0.001		0.0368	False		,,,				2504	0.0123				p.V4V		Atlas-SNP	.											.	WDR65	76	.	0			c.G12T						PASS	.	G	,,	714,3692	295.6+/-283.7	65,584,1554	116.0	104.0	108.0		12,12,12	2.1	1.0	1	dbSNP_116	108	354,8246	119.5+/-178.9	6,342,3952	no	coding-synonymous,coding-synonymous,coding-synonymous	WDR65	NM_001167965.1,NM_001167966.1,NM_152498.3	,,	71,926,5506	TT,TG,GG		4.1163,16.2052,8.2116	,,	4/699,4/699,4/699	43638436	1068,11938	2203	4300	6503	SO:0001819	synonymous_variant	149465	exon2			AGCCGTGGTAGCT																												ENST00000372492.4:c.12G>T	1.37:g.43638436G>T		175.0	0.0	0		69.0	53.0	0.768116	NM_152498	A6NKQ3|Q17RI9|Q5TAI0	Silent	SNP	ENST00000372492.4	37																																																																																				G|0.920;T|0.080	0.080	strong		0.547	WDR65-002	NOVEL	not_organism_supported|basic|appris_principal|exp_conf	protein_coding	protein_coding	OTTHUMT00000384325.1		
FARP2	9855	hgsc.bcm.edu	37	2	242373714	242373714	+	Missense_Mutation	SNP	C	C	T	rs372818608		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr2:242373714C>T	ENST00000264042.3	+	10	1179	c.1009C>T	c.(1009-1011)Cgg>Tgg	p.R337W	FARP2_ENST00000373287.4_Missense_Mutation_p.R337W|FARP2_ENST00000545004.1_Missense_Mutation_p.R337W	NM_014808.2	NP_055623.1	O94887	FARP2_HUMAN	FERM, RhoGEF and pleckstrin domain protein 2	337					actin cytoskeleton reorganization (GO:0031532)|axon guidance (GO:0007411)|cell adhesion (GO:0007155)|neuron remodeling (GO:0016322)|osteoclast differentiation (GO:0030316)|podosome assembly (GO:0071800)|positive regulation of Rac GTPase activity (GO:0032855)|positive regulation of Rho GTPase activity (GO:0032321)|Rac protein signal transduction (GO:0016601)|regulation of integrin activation (GO:0033623)|regulation of Rac GTPase activity (GO:0032314)|semaphorin-plexin signaling pathway (GO:0071526)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|extrinsic component of membrane (GO:0019898)	Rac guanyl-nucleotide exchange factor activity (GO:0030676)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)			breast(1)|central_nervous_system(2)|cervix(1)|endometrium(5)|kidney(1)|large_intestine(8)|lung(18)|ovary(2)|skin(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	43		all_cancers(19;4.88e-34)|all_epithelial(40;4.81e-14)|Breast(86;0.000141)|Renal(207;0.0143)|all_lung(227;0.0344)|Lung NSC(271;0.0886)|Ovarian(221;0.0905)|Esophageal squamous(248;0.131)|all_hematologic(139;0.182)|Melanoma(123;0.238)		Epithelial(32;1.81e-33)|all cancers(36;1.61e-30)|OV - Ovarian serous cystadenocarcinoma(60;6.83e-15)|Kidney(56;1.19e-08)|KIRC - Kidney renal clear cell carcinoma(57;8.98e-08)|BRCA - Breast invasive adenocarcinoma(100;1.49e-06)|Lung(119;0.000152)|LUSC - Lung squamous cell carcinoma(224;0.00125)|Colorectal(34;0.0199)|COAD - Colon adenocarcinoma(134;0.121)		CTTCTTCAGCCGGGGCTCCTC	0.463																																					p.R337W		Atlas-SNP	.											.	FARP2	92	.	0			c.C1009T						PASS	.	C	TRP/ARG	2,4404	4.2+/-10.8	0,2,2201	78.0	81.0	80.0		1009	4.1	1.0	2		80	0,8600		0,0,4300	no	missense	FARP2	NM_014808.2	101	0,2,6501	TT,TC,CC		0.0,0.0454,0.0154	probably-damaging	337/1055	242373714	2,13004	2203	4300	6503	SO:0001583	missense	9855	exon10			TTCAGCCGGGGCT	AB018336	CCDS33424.1, CCDS63197.1	2q37.3	2013-01-10			ENSG00000006607	ENSG00000006607		"""Rho guanine nucleotide exchange factors"", ""Pleckstrin homology (PH) domain containing"""	16460	protein-coding gene	gene with protein product						9872452, 12351724	Standard	NM_001282984		Approved	KIAA0793, FIR, PLEKHC3, FRG	uc002wbi.2	O94887	OTTHUMG00000151574	ENST00000264042.3:c.1009C>T	2.37:g.242373714C>T	ENSP00000264042:p.Arg337Trp	121.0	0.0	0		90.0	4.0	0.0444444	NM_014808	B7Z6J8|F5GZ84|Q53QM5|Q8WU27|Q9UFE7	Missense_Mutation	SNP	ENST00000264042.3	37	CCDS33424.1	.	.	.	.	.	.	.	.	.	.	C	18.78	3.696420	0.68386	4.54E-4	0.0	ENSG00000006607	ENST00000264042;ENST00000545004;ENST00000373287;ENST00000413432	D;D;D;D	0.86432	-2.12;-2.12;-2.12;-2.12	5.04	4.13	0.48395	FERM adjacent (FA) (1);	0.062830	0.64402	D	0.000012	D	0.93851	0.8033	M	0.88105	2.93	0.58432	D	0.999995	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.97110	1.0;0.999;1.0	D	0.94179	0.7430	10	0.66056	D	0.02	.	12.8745	0.57982	0.3929:0.6071:0.0:0.0	.	337;337;337	O94887-2;F5GZ84;O94887	.;.;FARP2_HUMAN	W	337;337;337;24	ENSP00000264042:R337W;ENSP00000443876:R337W;ENSP00000362384:R337W;ENSP00000412772:R24W	ENSP00000264042:R337W	R	+	1	2	FARP2	242022387	1.000000	0.71417	1.000000	0.80357	0.978000	0.69477	1.660000	0.37397	1.023000	0.39654	0.557000	0.71058	CGG	.	.	weak		0.463	FARP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000323153.1		
ZNF732	654254	hgsc.bcm.edu	37	4	289877	289877	+	Missense_Mutation	SNP	G	G	T	rs62619793	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr4:289877G>T	ENST00000419098.1	-	2	81	c.71C>A	c.(70-72)gCc>gAc	p.A24D		NM_001137608.1	NP_001131080.1	B4DXR9	ZN732_HUMAN	zinc finger protein 732	24	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(1)|lung(2)	3						ATTCTGCTGGGCAGGGTCCAG	0.423													.|||	191	0.038139	0.0968	0.0317	5008	,	,		17640	0.0		0.0298	False		,,,				2504	0.0112				p.A23D		Atlas-SNP	.											.	ZNF732	117	.	0			c.C68A						PASS	.						33.0	32.0	32.0					4																	289877		692	1590	2282	SO:0001583	missense	654254	exon1			TGCTGGGCAGGGT	AK302099	CCDS46990.1	4p16.3	2014-02-12	2009-07-22		ENSG00000186777	ENSG00000186777		"""Zinc fingers, C2H2-type"", ""-"""	37138	protein-coding gene	gene with protein product							Standard	NM_001137608		Approved	FLJ59067	uc011buu.1	B4DXR9	OTTHUMG00000159883	ENST00000419098.1:c.71C>A	4.37:g.289877G>T	ENSP00000415774:p.Ala24Asp	326.0	1.0	0.00306748		291.0	138.0	0.474227	NM_001137608		Missense_Mutation	SNP	ENST00000419098.1	37	CCDS46990.1	90	0.04120879120879121	57	0.11585365853658537	11	0.03038674033149171	0	0.0	22	0.029023746701846966	G	6.253	0.414829	0.11870	.	.	ENSG00000186777	ENST00000419098	T	0.02525	4.26	1.22	1.22	0.21188	Krueppel-associated box (4);	.	.	.	.	T	0.00109	0.0003	M	0.88310	2.945	0.80722	P	0.0	B	0.20368	0.044	B	0.28991	0.097	T	0.03566	-1.1024	8	0.72032	D	0.01	.	5.3307	0.15930	0.0:0.0:1.0:0.0	rs62619793	24	B4DXR9	ZN732_HUMAN	D	24	ENSP00000415774:A24D	ENSP00000415774:A24D	A	-	2	0	ZNF732	279877	0.000000	0.05858	0.082000	0.20525	0.084000	0.17831	-1.252000	0.02880	0.300000	0.22699	0.305000	0.20034	GCC	G|0.958;T|0.042	0.042	strong		0.423	ZNF732-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000357937.2	NM_001137608	
COPB1	1315	hgsc.bcm.edu	37	11	14515829	14515829	+	Missense_Mutation	SNP	T	T	C			TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr11:14515829T>C	ENST00000249923.3	-	3	548	c.248A>G	c.(247-249)gAa>gGa	p.E83G	PSMA1_ENST00000419365.2_3'UTR|PSMA1_ENST00000555531.1_3'UTR|COPB1_ENST00000439561.2_Missense_Mutation_p.E83G	NM_016451.4	NP_057535.1	P53618	COPB_HUMAN	coatomer protein complex, subunit beta 1	83					COPI coating of Golgi vesicle (GO:0048205)|intra-Golgi vesicle-mediated transport (GO:0006891)|intracellular protein transport (GO:0006886)|membrane organization (GO:0061024)|retrograde vesicle-mediated transport, Golgi to ER (GO:0006890)|viral process (GO:0016032)	COPI vesicle coat (GO:0030126)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|Golgi apparatus (GO:0005794)|Golgi membrane (GO:0000139)|Golgi-associated vesicle (GO:0005798)|intracellular membrane-bounded organelle (GO:0043231)|membrane (GO:0016020)|plasma membrane (GO:0005886)	structural molecule activity (GO:0005198)			NS(1)|breast(1)|central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(9)|lung(12)|ovary(1)|prostate(1)|skin(1)|stomach(1)|urinary_tract(2)	36						AGGAACAATTTCCCAAAATAC	0.363																																					p.E83G		Atlas-SNP	.											.	COPB1	81	.	0			c.A248G						PASS	.						84.0	88.0	87.0					11																	14515829		2200	4294	6494	SO:0001583	missense	1315	exon3			ACAATTTCCCAAA	BC037280	CCDS7815.1	11p15.2	2011-05-20	2006-06-30	2006-06-30	ENSG00000129083	ENSG00000129083			2231	protein-coding gene	gene with protein product		600959	"""coatomer protein complex, subunit beta"""	COPB		7982906	Standard	NM_016451		Approved		uc001mlg.2	P53618	OTTHUMG00000165824	ENST00000249923.3:c.248A>G	11.37:g.14515829T>C	ENSP00000249923:p.Glu83Gly	112.0	0.0	0		124.0	55.0	0.443548	NM_001144062	D3DQX0|Q6GTT7|Q9NTK2|Q9UNW7	Missense_Mutation	SNP	ENST00000249923.3	37	CCDS7815.1	.	.	.	.	.	.	.	.	.	.	T	29.3	4.997254	0.93167	.	.	ENSG00000129083	ENST00000249923;ENST00000439561;ENST00000534234;ENST00000529866;ENST00000534771	T;T;T;T;T	0.27890	1.64;1.64;1.64;1.64;1.64	5.31	5.31	0.75309	Clathrin/coatomer adaptor, adaptin-like, N-terminal (1);Armadillo-like helical (1);Armadillo-type fold (1);	0.000000	0.85682	D	0.000000	T	0.68540	0.3012	H	0.96142	3.775	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	T	0.80137	-0.1508	10	0.87932	D	0	-14.0469	15.2851	0.73822	0.0:0.0:0.0:1.0	.	83	P53618	COPB_HUMAN	G	83	ENSP00000249923:E83G;ENSP00000397873:E83G;ENSP00000436383:E83G;ENSP00000431530:E83G;ENSP00000436401:E83G	ENSP00000249923:E83G	E	-	2	0	COPB1	14472405	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	8.040000	0.89188	2.004000	0.58718	0.533000	0.62120	GAA	.	.	none		0.363	COPB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000386410.1	NM_016451	
KIAA1731	85459	hgsc.bcm.edu	37	11	93430474	93430474	+	Missense_Mutation	SNP	C	C	G			TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr11:93430474C>G	ENST00000325212.6	+	15	2558	c.2396C>G	c.(2395-2397)cCt>cGt	p.P799R	KIAA1731_ENST00000531700.1_Intron|KIAA1731_ENST00000344196.4_5'UTR|KIAA1731_ENST00000411936.1_Missense_Mutation_p.P799R			Q9C0D2	K1731_HUMAN	KIAA1731	799						centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)				breast(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)	11		Acute lymphoblastic leukemia(157;2.31e-05)|all_hematologic(158;0.00824)				AGTTCTCTGCCTGTTAAAGTT	0.368																																					p.P799R		Atlas-SNP	.											.	KIAA1731	173	.	0			c.C2396G						PASS	.						92.0	72.0	78.0					11																	93430474		692	1591	2283	SO:0001583	missense	85459	exon15			CTCTGCCTGTTAA	AB051518	CCDS44708.1	11q21	2014-03-11			ENSG00000166004	ENSG00000166004			29366	protein-coding gene	gene with protein product						20844083	Standard	NM_033395		Approved		uc009ywb.1	Q9C0D2	OTTHUMG00000167449	ENST00000325212.6:c.2396C>G	11.37:g.93430474C>G	ENSP00000316681:p.Pro799Arg	117.0	0.0	0		229.0	79.0	0.344978	NM_033395	C9J5H9|C9JQY8|Q8N7L4|Q8N919|Q8N9B0|Q96LT8	Missense_Mutation	SNP	ENST00000325212.6	37	CCDS44708.1	.	.	.	.	.	.	.	.	.	.	C	10.15	1.270850	0.23221	.	.	ENSG00000166004	ENST00000325212;ENST00000411936	T;T	0.36520	1.25;1.25	4.06	4.06	0.47325	.	0.167616	0.28889	N	0.013807	T	0.45816	0.1361	L	0.39898	1.24	0.80722	D	1	D	0.61697	0.99	P	0.59487	0.858	T	0.39057	-0.9632	10	0.52906	T	0.07	-2.8388	14.1939	0.65656	0.0:1.0:0.0:0.0	.	799	Q9C0D2	K1731_HUMAN	R	799	ENSP00000316681:P799R;ENSP00000406505:P799R	ENSP00000316681:P799R	P	+	2	0	KIAA1731	93070122	0.138000	0.22547	0.099000	0.21106	0.016000	0.09150	1.386000	0.34419	2.547000	0.85894	0.650000	0.86243	CCT	.	.	none		0.368	KIAA1731-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000394640.1	NM_033395	
EXPH5	23086	hgsc.bcm.edu	37	11	108383560	108383560	+	Missense_Mutation	SNP	T	T	A	rs10890850	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr11:108383560T>A	ENST00000265843.4	-	6	2784	c.2674A>T	c.(2674-2676)Aat>Tat	p.N892Y	EXPH5_ENST00000428840.1_Missense_Mutation_p.N816Y|EXPH5_ENST00000443411.1_Missense_Mutation_p.N704Y|EXPH5_ENST00000524840.1_5'Flank|EXPH5_ENST00000525344.1_Missense_Mutation_p.N885Y	NM_015065.2	NP_055880	Q8NEV8	EXPH5_HUMAN	exophilin 5	892			N -> Y (in dbSNP:rs10890850).		intracellular protein transport (GO:0006886)|keratinocyte development (GO:0003334)|multivesicular body sorting pathway (GO:0071985)|positive regulation of exocytosis (GO:0045921)|positive regulation of protein secretion (GO:0050714)	endosome (GO:0005768)	Rab GTPase binding (GO:0017137)			breast(3)|central_nervous_system(3)|endometrium(6)|haematopoietic_and_lymphoid_tissue(2)|kidney(7)|large_intestine(13)|liver(1)|lung(34)|ovary(3)|pancreas(2)|prostate(2)|skin(11)|stomach(3)|upper_aerodigestive_tract(1)	91		all_cancers(61;3.99e-08)|Acute lymphoblastic leukemia(157;3.97e-05)|Melanoma(852;4.04e-05)|all_epithelial(67;0.000116)|all_hematologic(158;0.000315)|Breast(348;0.104)|all_neural(303;0.16)		Epithelial(105;8.1e-06)|BRCA - Breast invasive adenocarcinoma(274;1.22e-05)|all cancers(92;0.000129)|OV - Ovarian serous cystadenocarcinoma(223;0.11)|Colorectal(284;0.184)		AGGGAAGAATTCTTTGATGGT	0.438													T|||	270	0.0539137	0.1316	0.0115	5008	,	,		19382	0.0119		0.002	False		,,,				2504	0.0757				p.N892Y		Atlas-SNP	.											.	EXPH5	193	.	0			c.A2674T						PASS	.	T	TYR/ASN	493,3909	229.8+/-244.2	29,435,1737	182.0	167.0	172.0		2674	-2.0	0.0	11	dbSNP_120	172	9,8587	7.1+/-27.0	0,9,4289	yes	missense	EXPH5	NM_015065.2	143	29,444,6026	AA,AT,TT		0.1047,11.1995,3.8621	benign	892/1990	108383560	502,12496	2201	4298	6499	SO:0001583	missense	23086	exon6			AAGAATTCTTTGA		CCDS8341.1	11q22.3	2008-02-05			ENSG00000110723	ENSG00000110723			30578	protein-coding gene	gene with protein product	"""synaptotagmin-like homologue lacking C2 domains b"""	612878				9734811, 11773082	Standard	NM_015065		Approved	SLAC2-B	uc001pkk.3	Q8NEV8	OTTHUMG00000166536	ENST00000265843.4:c.2674A>T	11.37:g.108383560T>A	ENSP00000265843:p.Asn892Tyr	152.0	0.0	0		211.0	60.0	0.28436	NM_015065	Q2KHM1|Q9Y4D6	Missense_Mutation	SNP	ENST00000265843.4	37	CCDS8341.1	59	0.027014652014652016	46	0.09349593495934959	5	0.013812154696132596	7	0.012237762237762238	1	0.0013192612137203166	T	14.92	2.680490	0.47886	0.111995	0.001047	ENSG00000110723	ENST00000265843;ENST00000428840;ENST00000443411;ENST00000525344;ENST00000526312;ENST00000533052	T;T;T;T;T;T	0.04603	4.17;4.1;3.95;4.17;4.02;3.59	5.74	-1.97	0.07503	.	0.712890	0.13437	N	0.387972	T	0.00109	0.0003	L	0.44542	1.39	0.09310	N	1	P	0.49090	0.919	B	0.43445	0.42	T	0.40813	-0.9543	10	0.72032	D	0.01	-0.8859	6.5046	0.22188	0.0:0.4682:0.1578:0.3739	rs10890850;rs10890850	892	Q8NEV8	EXPH5_HUMAN	Y	892;816;704;885;816;704	ENSP00000265843:N892Y;ENSP00000391966:N816Y;ENSP00000411390:N704Y;ENSP00000432546:N885Y;ENSP00000432683:N816Y;ENSP00000446434:N704Y	ENSP00000265843:N892Y	N	-	1	0	EXPH5	107888770	0.000000	0.05858	0.002000	0.10522	0.230000	0.25150	-0.173000	0.09854	-0.270000	0.09285	0.460000	0.39030	AAT	T|0.967;A|0.033	0.033	strong		0.438	EXPH5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000390279.1	NM_015065	
ZNF281	23528	hgsc.bcm.edu	37	1	200378495	200378495	+	Silent	SNP	C	C	T	rs374232799	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr1:200378495C>T	ENST00000294740.3	-	2	463	c.339G>A	c.(337-339)tcG>tcA	p.S113S	ZNF281_ENST00000367352.3_Silent_p.S77S|ZNF281_ENST00000367353.1_Silent_p.S113S	NM_001281293.1|NM_001281294.1|NM_012482.4	NP_001268222.1|NP_001268223.1|NP_036614.1	Q9Y2X9	ZN281_HUMAN	zinc finger protein 281	113					embryonic body morphogenesis (GO:0010172)|negative regulation of gene expression (GO:0010629)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of transcription, DNA-templated (GO:0045893)|stem cell differentiation (GO:0048863)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	core promoter binding (GO:0001047)|metal ion binding (GO:0046872)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription corepressor activity (GO:0003714)|transcription regulatory region DNA binding (GO:0044212)			breast(4)|endometrium(3)|kidney(3)|large_intestine(6)|lung(7)|ovary(2)|prostate(1)|upper_aerodigestive_tract(1)	27						AGGTCCTCTGCGAGGGGAAGG	0.662																																					p.S113S		Atlas-SNP	.											.	ZNF281	74	.	0			c.G339A						PASS	.	C		0,4176		0,0,2088	7.0	6.0	6.0		339	3.2	1.0	1		6	2,8178		0,2,4088	no	coding-synonymous	ZNF281	NM_012482.3		0,2,6176	TT,TC,CC		0.0244,0.0,0.0162		113/896	200378495	2,12354	2088	4090	6178	SO:0001819	synonymous_variant	23528	exon2			CCTCTGCGAGGGG	AF125158	CCDS1402.1, CCDS60384.1	1q32.1	2012-08-08			ENSG00000162702	ENSG00000162702		"""Zinc fingers, C2H2-type"""	13075	protein-coding gene	gene with protein product						10448078	Standard	NM_012482		Approved	ZBP-99	uc001gve.3	Q9Y2X9	OTTHUMG00000035724	ENST00000294740.3:c.339G>A	1.37:g.200378495C>T		43.0	0.0	0		38.0	26.0	0.684211	NM_012482	A6NF48|B3KMX2|Q5RKW5|Q9NY92	Silent	SNP	ENST00000294740.3	37	CCDS1402.1																																																																																			.	.	none		0.662	ZNF281-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000086879.2	NM_012482	
C17orf62	79415	hgsc.bcm.edu	37	17	80404555	80404555	+	Missense_Mutation	SNP	G	G	A	rs72857481	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr17:80404555G>A	ENST00000437807.2	-	5	462	c.145C>T	c.(145-147)Ctc>Ttc	p.L49F	C17orf62_ENST00000585080.1_Missense_Mutation_p.L49F|C17orf62_ENST00000306645.5_Missense_Mutation_p.L49F|C17orf62_ENST00000434650.2_Missense_Mutation_p.L35F|C17orf62_ENST00000578913.1_Missense_Mutation_p.L49F|C17orf62_ENST00000577732.1_Missense_Mutation_p.L49F|C17orf62_ENST00000585064.1_Missense_Mutation_p.L49F|C17orf62_ENST00000583617.1_Missense_Mutation_p.L49F|C17orf62_ENST00000342572.8_Intron|C17orf62_ENST00000577436.1_Missense_Mutation_p.L35F|C17orf62_ENST00000336995.7_Intron|C17orf62_ENST00000583359.1_5'UTR|C17orf62_ENST00000578919.1_Missense_Mutation_p.L49F	NM_001193653.1|NM_001193657.1	NP_001180582.1|NP_001180586.1	Q9BQA9	CQ062_HUMAN	chromosome 17 open reading frame 62	49						integral component of membrane (GO:0016021)				breast(2)|large_intestine(2)|skin(2)|urinary_tract(2)	8	Breast(20;0.00106)|all_neural(118;0.0804)		OV - Ovarian serous cystadenocarcinoma(97;0.0143)|BRCA - Breast invasive adenocarcinoma(99;0.0369)			ACGTAGAAGAGCTTCCAGCCC	0.647													G|||	34	0.00678914	0.0	0.0072	5008	,	,		17150	0.0		0.0229	False		,,,				2504	0.0061				p.L49F		Atlas-SNP	.											.	C17orf62	23	.	0			c.C145T						PASS	.	G	PHE/LEU,PHE/LEU,PHE/LEU,PHE/LEU,PHE/LEU,PHE/LEU,PHE/LEU	15,4391	22.3+/-47.3	0,15,2188	96.0	93.0	94.0		145,145,103,145,145,145,145	2.6	1.0	17	dbSNP_130	94	165,8435	77.5+/-140.1	1,163,4136	yes	missense,missense,missense,missense,missense,missense,missense	C17orf62	NM_001033046.3,NM_001100407.2,NM_001100408.2,NM_001193653.1,NM_001193654.1,NM_001193655.1,NM_001193657.1	22,22,22,22,22,22,22	1,178,6324	AA,AG,GG		1.9186,0.3404,1.384	benign,benign,benign,benign,benign,benign,benign	49/188,49/188,35/174,49/188,49/188,49/188,49/188	80404555	180,12826	2203	4300	6503	SO:0001583	missense	79415	exon5			AGAAGAGCTTCCA	AK074950	CCDS32776.1, CCDS45817.1	17q25.3	2014-06-09			ENSG00000178927	ENSG00000178927			28672	protein-coding gene	gene with protein product							Standard	NM_001100407		Approved	MGC4368, FLJ90469	uc021ufr.1	Q9BQA9		ENST00000437807.2:c.145C>T	17.37:g.80404555G>A	ENSP00000388909:p.Leu49Phe	66.0	0.0	0		73.0	31.0	0.424658	NM_001193657	E1B6X3|Q96NR1	Missense_Mutation	SNP	ENST00000437807.2	37	CCDS32776.1	20	0.009157509157509158	0	0.0	2	0.0055248618784530384	0	0.0	18	0.023746701846965697	G	11.50	1.658734	0.29515	0.003404	0.019186	ENSG00000178927	ENST00000437807;ENST00000306645;ENST00000434650	.	.	.	4.96	2.58	0.30949	.	.	.	.	.	T	0.35098	0.0920	L	0.41824	1.3	0.80722	D	1	B;B	0.12013	0.002;0.005	B;B	0.14023	0.006;0.01	T	0.46679	-0.9174	8	0.52906	T	0.07	.	11.0231	0.47730	0.1877:0.0:0.8123:0.0	.	35;49	E1B6X3;Q9BQA9	.;CQ062_HUMAN	F	49;49;35	.	ENSP00000307765:L49F	L	-	1	0	C17orf62	77997844	1.000000	0.71417	1.000000	0.80357	0.608000	0.37181	3.151000	0.50670	1.086000	0.41228	0.561000	0.74099	CTC	G|0.989;A|0.011	0.011	strong		0.647	C17orf62-006	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000443260.1	NM_001033046	
RIMS4	140730	hgsc.bcm.edu	37	20	43386414	43386414	+	Splice_Site	SNP	T	T	A			TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr20:43386414T>A	ENST00000372851.3	-	4	416		c.e4-2		RIMS4_ENST00000541604.2_Splice_Site	NM_001205317.1|NM_182970.3	NP_001192246.1|NP_892015.1	Q9H426	RIMS4_HUMAN	regulating synaptic membrane exocytosis 4						exocytosis (GO:0006887)|neurotransmitter transport (GO:0006836)|regulation of membrane potential (GO:0042391)	cell junction (GO:0030054)|presynaptic active zone (GO:0048786)|synaptic membrane (GO:0097060)				central_nervous_system(1)|cervix(1)|endometrium(4)|kidney(1)|large_intestine(5)|lung(11)|ovary(5)|urinary_tract(1)	29		Myeloproliferative disorder(115;0.0122)				CCACATCCCCTGGAAGAGGCA	0.562																																					.		Atlas-SNP	.											.	RIMS4	47	.	0			c.353-2A>T						PASS	.						83.0	69.0	74.0					20																	43386414		2203	4300	6503	SO:0001630	splice_region_variant	140730	exon5			ATCCCCTGGAAGA		CCDS13338.1, CCDS56191.1	20q13.12	2005-02-03	2003-06-18	2003-06-20	ENSG00000101098	ENSG00000101098			16183	protein-coding gene	gene with protein product		611601	"""chromosome 20 open reading frame 190"""	C20orf190		12620390	Standard	NM_182970		Approved	dJ781B1.3	uc010ggu.3	Q9H426	OTTHUMG00000032546	ENST00000372851.3:c.350-2A>T	20.37:g.43386414T>A		81.0	0.0	0		80.0	26.0	0.325	NM_001205317	A4FU94|E1P613|Q3MI44|Q5JWT7	Splice_Site	SNP	ENST00000372851.3	37	CCDS13338.1	.	.	.	.	.	.	.	.	.	.	T	18.70	3.680306	0.68042	.	.	ENSG00000101098	ENST00000372851;ENST00000541604	.	.	.	5.91	5.91	0.95273	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	16.3453	0.83126	0.0:0.0:0.0:1.0	.	.	.	.	.	-1	.	.	.	-	.	.	RIMS4	42819828	1.000000	0.71417	0.999000	0.59377	0.492000	0.33523	8.040000	0.89188	2.261000	0.74972	0.533000	0.62120	.	.	.	none		0.562	RIMS4-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000101027.2	NM_182970	Intron
LARP4B	23185	hgsc.bcm.edu	37	10	909711	909711	+	Silent	SNP	A	A	G			TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr10:909711A>G	ENST00000316157.3	-	4	442	c.402T>C	c.(400-402)taT>taC	p.Y134Y		NM_015155.1	NP_055970.1	Q92615	LAR4B_HUMAN	La ribonucleoprotein domain family, member 4B	134					positive regulation of translation (GO:0045727)	cytoplasm (GO:0005737)|cytoplasmic stress granule (GO:0010494)|cytosol (GO:0005829)|membrane (GO:0016020)|nucleolus (GO:0005730)|polysomal ribosome (GO:0042788)	poly(A) RNA binding (GO:0044822)			NS(1)|breast(2)|central_nervous_system(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(13)|lung(13)|ovary(2)|skin(2)|urinary_tract(2)	38						GCAGAGAGTCATATTCTGAGG	0.473																																					p.Y134Y		Atlas-SNP	.											.	LARP4B	110	.	0			c.T402C						PASS	.						99.0	100.0	100.0					10																	909711		2203	4300	6503	SO:0001819	synonymous_variant	23185	exon5			AGAGTCATATTCT	D86971	CCDS31131.1	10p15.3	2011-08-24	2009-06-09	2009-06-09	ENSG00000107929	ENSG00000107929		"""La ribonucleoprotein domain containing"""	28987	protein-coding gene	gene with protein product			"""KIAA0217"", ""La ribonucleoprotein domain family, member 5"""	KIAA0217, LARP5		9039502, 20573744	Standard	NM_015155		Approved		uc031ptb.1	Q92615	OTTHUMG00000017534	ENST00000316157.3:c.402T>C	10.37:g.909711A>G		112.0	0.0	0		70.0	10.0	0.142857	NM_015155	A7MD20|Q5T3R3|Q5T3R4|Q5T3R5|Q68CY4	Silent	SNP	ENST00000316157.3	37	CCDS31131.1																																																																																			.	.	none		0.473	LARP4B-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000046395.2	NM_015155	
DOCK8	81704	hgsc.bcm.edu	37	9	304670	304670	+	Missense_Mutation	SNP	C	C	T	rs146490788	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr9:304670C>T	ENST00000453981.1	+	5	606	c.494C>T	c.(493-495)tCg>tTg	p.S165L	DOCK8_ENST00000432829.2_Missense_Mutation_p.S97L|DOCK8_ENST00000469391.1_Missense_Mutation_p.S97L			Q8NF50	DOCK8_HUMAN	dedicator of cytokinesis 8	165					blood coagulation (GO:0007596)|dendritic cell migration (GO:0036336)|immunological synapse formation (GO:0001771)|memory T cell proliferation (GO:0061485)|negative regulation of T cell apoptotic process (GO:0070233)|small GTPase mediated signal transduction (GO:0007264)	cell leading edge (GO:0031252)|cytosol (GO:0005829)|membrane (GO:0016020)	guanyl-nucleotide exchange factor activity (GO:0005085)			breast(1)|central_nervous_system(5)|endometrium(2)|kidney(6)|large_intestine(13)|lung(22)|ovary(3)|prostate(3)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(6)	65		all_cancers(5;2.13e-17)|all_epithelial(5;2.15e-12)|all_lung(10;6.69e-11)|Lung NSC(10;1.08e-10)|Acute lymphoblastic leukemia(5;0.000242)|all_hematologic(5;0.00317)|Breast(48;0.0151)|Prostate(43;0.128)		all cancers(5;9.3e-07)|GBM - Glioblastoma multiforme(5;2.41e-06)|Epithelial(6;0.00557)|Lung(218;0.00942)		ACGTTTGAGTCGGAAACCTTG	0.463																																					p.S165L		Atlas-SNP	.											.	DOCK8	401	.	0			c.C494T						PASS	.	C	LEU/SER,LEU/SER,LEU/SER	3,4403	6.2+/-15.9	0,3,2200	127.0	134.0	132.0		290,290,494	6.0	1.0	9	dbSNP_134	132	7,8593	5.7+/-21.5	0,7,4293	yes	missense,missense,missense	DOCK8	NM_001190458.1,NM_001193536.1,NM_203447.3	145,145,145	0,10,6493	TT,TC,CC		0.0814,0.0681,0.0769	benign,benign,benign	97/2000,97/2032,165/2100	304670	10,12996	2203	4300	6503	SO:0001583	missense	81704	exon5			TTGAGTCGGAAAC	AK090429	CCDS6440.1, CCDS6440.2, CCDS55283.1, CCDS55284.1	9p24.3	2014-09-17			ENSG00000107099	ENSG00000107099			19191	protein-coding gene	gene with protein product		611432				11214971	Standard	NM_203447		Approved	FLJ00026, FLJ00152, ZIR8, FLJ00346	uc003zgf.2	Q8NF50	OTTHUMG00000078789	ENST00000453981.1:c.494C>T	9.37:g.304670C>T	ENSP00000408464:p.Ser165Leu	67.0	0.0	0		58.0	30.0	0.517241	NM_203447	A2A350|A2BDF2|A4FU78|B7ZLP0|E9PH09|Q3MV16|Q5JPJ1|Q8TEP1|Q8WUY2|Q9BYJ5|Q9H1Q2|Q9H1Q3|Q9H308|Q9H7P2	Missense_Mutation	SNP	ENST00000453981.1	37	CCDS6440.2	.	.	.	.	.	.	.	.	.	.	C	18.68	3.676168	0.67928	6.81E-4	8.14E-4	ENSG00000107099	ENST00000453981;ENST00000287364;ENST00000432829;ENST00000487230;ENST00000469391	T;T;T;T	0.32272	2.59;2.59;1.46;2.59	6.02	6.02	0.97574	.	0.139758	0.49916	D	0.000133	T	0.41971	0.1182	N	0.19112	0.55	0.58432	D	0.999999	B;D;B	0.89917	0.158;1.0;0.031	B;D;B	0.83275	0.029;0.996;0.006	T	0.11203	-1.0597	10	0.25751	T	0.34	.	18.7213	0.91694	0.0:1.0:0.0:0.0	.	97;165;165	E9PH09;A2A349;Q8NF50	.;.;DOCK8_HUMAN	L	165;165;97;97;97	ENSP00000408464:S165L;ENSP00000394888:S97L;ENSP00000418318:S97L;ENSP00000419438:S97L	ENSP00000287364:S165L	S	+	2	0	DOCK8	294670	0.999000	0.42202	1.000000	0.80357	0.993000	0.82548	5.226000	0.65299	2.865000	0.98341	0.655000	0.94253	TCG	C|0.999;T|0.001	0.001	strong		0.463	DOCK8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000171792.5	XM_036307	
ZNF285	26974	hgsc.bcm.edu	37	19	44891009	44891009	+	Silent	SNP	C	C	T	rs139913772	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr19:44891009C>T	ENST00000330997.4	-	4	1462	c.1398G>A	c.(1396-1398)gcG>gcA	p.A466A	ZNF285_ENST00000591679.1_Silent_p.A473A|ZNF285_ENST00000544719.2_Silent_p.A466A|CTC-512J12.6_ENST00000588212.1_Intron	NM_152354.3	NP_689567.3	Q96NJ3	ZN285_HUMAN	zinc finger protein 285	466					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			breast(1)|central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(7)|lung(15)|ovary(2)|prostate(5)|skin(5)|upper_aerodigestive_tract(1)|urinary_tract(2)	44						CAGAGCTATACGCAAAATCCT	0.423																																					p.A466A		Atlas-SNP	.											ZNF285,NS,carcinoma,0,2	ZNF285	86	2	0			c.G1398A						PASS	.	T		0,4406		0,0,2203	84.0	85.0	85.0		1398	-6.9	0.0	19	dbSNP_134	85	8,8592	6.4+/-24.3	0,8,4292	no	coding-synonymous	ZNF285	NM_152354.3		0,8,6495	TT,TC,CC		0.093,0.0,0.0615		466/591	44891009	8,12998	2203	4300	6503	SO:0001819	synonymous_variant	26974	exon4			GCTATACGCAAAA	AK055309	CCDS12638.1, CCDS74389.1	19q13.32	2013-01-08	2010-04-14	2010-04-14		ENSG00000267508		"""Zinc fingers, C2H2-type"", ""-"""	13079	protein-coding gene	gene with protein product			"""zinc finger protein 285A"""	ZNF285A			Standard	XM_005258734		Approved			Q96NJ3	OTTHUMG00000178848	ENST00000330997.4:c.1398G>A	19.37:g.44891009C>T		236.0	0.0	0		200.0	84.0	0.42	NM_152354	Q17RJ3|Q6B0A8|Q6ISR5	Silent	SNP	ENST00000330997.4	37	CCDS12638.1																																																																																			C|0.999;T|0.001	0.001	strong		0.423	ZNF285-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000443600.1	NM_152354	
AP3B2	8120	hgsc.bcm.edu	37	15	83378366	83378366	+	Silent	SNP	G	G	A	rs200226421	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr15:83378366G>A	ENST00000261722.3	-	1	300	c.93C>T	c.(91-93)atC>atT	p.I31I	AP3B2_ENST00000535348.1_Silent_p.I31I|AP3B2_ENST00000561455.1_5'Flank|AC105339.1_ENST00000440479.1_lincRNA|AP3B2_ENST00000542200.1_Silent_p.I31I|AP3B2_ENST00000535359.1_Silent_p.I31I	NM_004644.3	NP_004635.2	Q13367	AP3B2_HUMAN	adaptor-related protein complex 3, beta 2 subunit	31					anterograde axon cargo transport (GO:0008089)|anterograde synaptic vesicle transport (GO:0048490)|intracellular protein transport (GO:0006886)|post-Golgi vesicle-mediated transport (GO:0006892)	AP-3 adaptor complex (GO:0030123)|COPI-coated vesicle (GO:0030137)|cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|nucleus (GO:0005634)	transporter activity (GO:0005215)			breast(4)|endometrium(1)|kidney(1)|large_intestine(4)|lung(21)|ovary(4)|pancreas(1)|prostate(3)|urinary_tract(2)	41			BRCA - Breast invasive adenocarcinoma(143;0.229)			CGGAGGAGAAGATGCCGCCGC	0.761													G|||	25	0.00499201	0.0008	0.0029	5008	,	,		8047	0.0		0.0199	False		,,,				2504	0.002				p.I31I		Atlas-SNP	.											.	AP3B2	103	.	0			c.C93T						PASS	.	G		0,2962		0,0,1481	2.0	3.0	3.0		93	1.7	1.0	15		3	42,6932		0,42,3445	no	coding-synonymous	AP3B2	NM_004644.3		0,42,4926	AA,AG,GG		0.6022,0.0,0.4227		31/1083	83378366	42,9894	1481	3487	4968	SO:0001819	synonymous_variant	8120	exon1			GGAGAAGATGCCG	U37673	CCDS45331.1, CCDS61736.1, CCDS61737.1	15q	2008-07-07			ENSG00000103723	ENSG00000103723			567	protein-coding gene	gene with protein product		602166				7671305, 1851215	Standard	NM_004644		Approved	NAPTB	uc010uoh.2	Q13367	OTTHUMG00000168009	ENST00000261722.3:c.93C>T	15.37:g.83378366G>A		10.0	0.0	0		12.0	10.0	0.833333	NM_004644	A4Z4T7|B7ZKR7|B7ZKS0|O14808|Q52LY8	Silent	SNP	ENST00000261722.3	37	CCDS45331.1																																																																																			.	.	weak		0.761	AP3B2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000397463.1		
PRSS41	360226	hgsc.bcm.edu	37	16	2849372	2849372	+	RNA	SNP	C	C	A	rs201777593		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr16:2849372C>A	ENST00000399677.1	+	0	382				SNORA3_ENST00000408792.1_RNA			Q7RTY9	PRS41_HUMAN	protease, serine, 41							anchored component of membrane (GO:0031225)|intracellular organelle (GO:0043229)|plasma membrane (GO:0005886)	serine-type endopeptidase activity (GO:0004252)										CTACAGCAGTCGTTACAAAGT	0.552													C|||	1	0.000199681	0.0	0.0	5008	,	,		17254	0.0		0.001	False		,,,				2504	0.0				p.R128S		Atlas-SNP	.											.	.	.	.	0			c.C382A						PASS	.						176.0	134.0	147.0					16																	2849372		692	1591	2283			360226	exon3			AGCAGTCGTTACA			16p13.3	2014-04-01			ENSG00000215148	ENSG00000215148		"""Serine peptidases / Serine peptidases"""	30715	other	unknown	"""testis serine protease 1"""					12838346	Standard	NM_001135086		Approved	TESSP1	uc010uwi.2	Q7RTY9	OTTHUMG00000128932		16.37:g.2849372C>A		128.0	0.0	0		112.0	54.0	0.482143	NM_001135086		Missense_Mutation	SNP	ENST00000399677.1	37																																																																																				.	.	weak		0.552	PRSS41-002	KNOWN	basic	processed_transcript	pseudogene	OTTHUMT00000436450.1	NM_183379	
HNF1A	6927	hgsc.bcm.edu	37	12	121432117	121432117	+	Silent	SNP	G	G	C	rs56348580	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr12:121432117G>C	ENST00000257555.6	+	4	1090	c.864G>C	c.(862-864)ggG>ggC	p.G288G	HNF1A_ENST00000402929.1_Silent_p.G288G|HNF1A_ENST00000400024.2_Silent_p.G288G|HNF1A_ENST00000541395.1_Silent_p.G288G|HNF1A_ENST00000543427.1_Silent_p.G171G|HNF1A_ENST00000538626.1_Intron|HNF1A_ENST00000544413.1_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		60.0	0.0	0		26.0	26.0	1	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	
DCST1	149095	hgsc.bcm.edu	37	1	155019698	155019698	+	Missense_Mutation	SNP	G	G	A	rs200041699	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr1:155019698G>A	ENST00000295542.1	+	14	1618	c.1522G>A	c.(1522-1524)Ggg>Agg	p.G508R	RP11-307C12.11_ENST00000452962.1_RNA|DCST1_ENST00000368419.2_Missense_Mutation_p.G508R|DCST1_ENST00000392480.1_Missense_Mutation_p.G508R|DCST1_ENST00000423025.2_Missense_Mutation_p.G483R	NM_152494.3	NP_689707.2	Q5T197	DCST1_HUMAN	DC-STAMP domain containing 1	508						integral component of membrane (GO:0016021)	zinc ion binding (GO:0008270)			breast(2)|endometrium(4)|kidney(2)|large_intestine(3)|lung(8)|ovary(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(2)	27	all_epithelial(22;1.43e-30)|all_lung(78;6.64e-28)|all_hematologic(923;0.0359)|Hepatocellular(266;0.0877)		BRCA - Breast invasive adenocarcinoma(34;0.000434)			GGTGAAGGTCGGGGGAGACTC	0.542													G|||	2	0.000399361	0.0015	0.0	5008	,	,		18587	0.0		0.0	False		,,,				2504	0.0				p.G508R		Atlas-SNP	.											.	DCST1	69	.	0			c.G1522A						PASS	.	G	ARG/GLY,ARG/GLY	1,4405	2.1+/-5.4	0,1,2202	82.0	81.0	81.0		1447,1522	4.9	0.0	1		81	0,8600		0,0,4300	no	missense,missense	DCST1	NM_001143687.2,NM_152494.3	125,125	0,1,6502	AA,AG,GG		0.0,0.0227,0.0077	possibly-damaging,possibly-damaging	483/682,508/707	155019698	1,13005	2203	4300	6503	SO:0001583	missense	149095	exon14			AAGGTCGGGGGAG	AK057347	CCDS1083.1, CCDS44235.1	1q22	2008-02-05			ENSG00000163357	ENSG00000163357			26539	protein-coding gene	gene with protein product							Standard	NM_152494		Approved	FLJ32785	uc001fgn.2	Q5T197	OTTHUMG00000041314	ENST00000295542.1:c.1522G>A	1.37:g.155019698G>A	ENSP00000295542:p.Gly508Arg	184.0	0.0	0		253.0	144.0	0.56917	NM_152494	B4DXA0|E9PHV3|Q5T198|Q6P1W6|Q71S70|Q96M70	Missense_Mutation	SNP	ENST00000295542.1	37	CCDS1083.1	.	.	.	.	.	.	.	.	.	.	G	14.31	2.496614	0.44352	2.27E-4	0.0	ENSG00000163357	ENST00000295542;ENST00000392480;ENST00000423025;ENST00000368419	T;T;T;T	0.29397	1.57;1.57;1.57;1.57	4.88	4.88	0.63580	Dendritic cell-specific transmembrane protein-like (1);	0.308295	0.33005	N	0.005381	T	0.20455	0.0492	L	0.40543	1.245	0.19300	N	0.999974	D;P	0.57571	0.98;0.932	P;P	0.54060	0.741;0.741	T	0.06899	-1.0801	10	0.13853	T	0.58	-11.7727	13.7183	0.62712	0.0:0.0:1.0:0.0	.	483;508	E9PHV3;Q5T197	.;DCST1_HUMAN	R	508;508;483;508	ENSP00000295542:G508R;ENSP00000376271:G508R;ENSP00000387369:G483R;ENSP00000357404:G508R	ENSP00000295542:G508R	G	+	1	0	DCST1	153286322	1.000000	0.71417	0.023000	0.16930	0.036000	0.12997	4.814000	0.62627	2.688000	0.91661	0.655000	0.94253	GGG	G|0.999;A|0.001	0.001	weak		0.542	DCST1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000099006.1	NM_152494	
DIDO1	11083	hgsc.bcm.edu	37	20	61528044	61528044	+	Silent	SNP	G	G	A			TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr20:61528044G>A	ENST00000266070.4	-	7	2218	c.1893C>T	c.(1891-1893)tcC>tcT	p.S631S	DIDO1_ENST00000395343.1_Silent_p.S631S|DIDO1_ENST00000395340.1_Silent_p.S631S|DIDO1_ENST00000395335.2_Silent_p.S631S	NM_033081.2	NP_149072.2	Q9BTC0	DIDO1_HUMAN	death inducer-obliterator 1	631					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)					CCAAAGCAGCGGAGCCAGGGA	0.647																																					p.S631S	Melanoma(25;381 482 3385 5362 7955 17159 17174 40604 47095)	Atlas-SNP	.											.	DIDO1	321	.	0			c.C1893T						PASS	.						46.0	52.0	50.0					20																	61528044		2203	4300	6503	SO:0001819	synonymous_variant	11083	exon7			AGCAGCGGAGCCA	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.1893C>T	20.37:g.61528044G>A		91.0	0.0	0		109.0	53.0	0.486239	NM_080797	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																																																																																			.	.	none		0.647	DIDO1-201	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000080091.2	NM_080796	
RBM17	84991	hgsc.bcm.edu	37	10	6139078	6139078	+	Missense_Mutation	SNP	A	A	G			TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr10:6139078A>G	ENST00000446108.1	+	2	694	c.50A>G	c.(49-51)gAa>gGa	p.E17G	RBM17_ENST00000379888.4_Missense_Mutation_p.E17G	NM_001145547.1	NP_001139019.1	Q96I25	SPF45_HUMAN	RNA binding motif protein 17	17					alternative mRNA splicing, via spliceosome (GO:0000380)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|spliceosomal complex (GO:0005681)	nucleotide binding (GO:0000166)|RNA binding (GO:0003723)			NS(1)|breast(3)|cervix(1)|endometrium(1)|kidney(4)|large_intestine(2)|lung(4)|prostate(1)|urinary_tract(2)	19						TCAAAAACAGAAGGCTGGTCC	0.468																																					p.E17G		Atlas-SNP	.											.	RBM17	45	.	0			c.A50G						PASS	.						106.0	106.0	106.0					10																	6139078		2203	4300	6503	SO:0001583	missense	84991	exon2			AAACAGAAGGCTG	AF083384	CCDS7077.1	10p15.1	2013-01-28			ENSG00000134453	ENSG00000134453		"""RNA binding motif (RRM) containing"", ""G patch domain containing"""	16944	protein-coding gene	gene with protein product	"""splicing factor 45kDa"""	606935				9731529	Standard	NM_032905		Approved	SPF45, MGC14439	uc001ijb.3	Q96I25	OTTHUMG00000017618	ENST00000446108.1:c.50A>G	10.37:g.6139078A>G	ENSP00000388638:p.Glu17Gly	174.0	0.0	0		118.0	5.0	0.0423729	NM_001145547	Q96GY6	Missense_Mutation	SNP	ENST00000446108.1	37	CCDS7077.1	.	.	.	.	.	.	.	.	.	.	A	19.61	3.859257	0.71834	.	.	ENSG00000134453	ENST00000379888;ENST00000432931;ENST00000446108;ENST00000418631	T;T;T;T	0.56611	0.45;0.45;0.45;0.45	4.64	3.5	0.40072	.	0.049423	0.85682	N	0.000000	T	0.41534	0.1163	L	0.51422	1.61	0.80722	D	1	P	0.39216	0.664	B	0.32928	0.155	T	0.25502	-1.0130	10	0.40728	T	0.16	-25.6691	10.0431	0.42171	0.9194:0.0:0.0806:0.0	.	17	Q96I25	SPF45_HUMAN	G	17	ENSP00000369218:E17G;ENSP00000408214:E17G;ENSP00000388638:E17G;ENSP00000402303:E17G	ENSP00000369218:E17G	E	+	2	0	RBM17	6179084	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	8.815000	0.91973	0.738000	0.32606	0.377000	0.23210	GAA	.	.	none		0.468	RBM17-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000046635.1	NM_032905	
ZNF33B	7582	hgsc.bcm.edu	37	10	43089370	43089370	+	Missense_Mutation	SNP	T	T	A	rs71505625	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr10:43089370T>A	ENST00000359467.3	-	5	1142	c.1028A>T	c.(1027-1029)cAt>cTt	p.H343L	ZNF33B_ENST00000486187.1_RNA	NM_006955.1	NP_008886.1	Q06732	ZN33B_HUMAN	zinc finger protein 33B	343					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(1)|endometrium(4)|kidney(1)|large_intestine(6)|lung(15)|skin(1)|stomach(1)	29						TCGAGTGAGATGTGACTTCTC	0.413													t|||	7	0.00139776	0.0	0.0014	5008	,	,		22122	0.0		0.004	False		,,,				2504	0.002				p.H343L	Melanoma(137;1247 1767 16772 25727 43810)	Atlas-SNP	.											.	ZNF33B	78	.	0			c.A1028T						PASS	.	T	LEU/HIS	2,4404	4.2+/-10.8	0,2,2201	121.0	119.0	120.0		1028	2.3	1.0	10	dbSNP_130	120	20,8580	14.6+/-50.1	0,20,4280	no	missense	ZNF33B	NM_006955.1	99	0,22,6481	AA,AT,TT		0.2326,0.0454,0.1692	probably-damaging	343/779	43089370	22,12984	2203	4300	6503	SO:0001583	missense	7582	exon5			GTGAGATGTGACT	X68688, AJ491697	CCDS7198.1	10q11.2	2013-01-08	2005-03-18		ENSG00000196693	ENSG00000196693		"""Zinc fingers, C2H2-type"", ""-"""	13097	protein-coding gene	gene with protein product		194522	"""zinc finger protein 33b (KOX 31)"", ""zinc finger protein 11B"""	ZNF11B		2014798	Standard	NM_006955		Approved	KOX31, KOX2	uc001jaf.1	Q06732	OTTHUMG00000018014	ENST00000359467.3:c.1028A>T	10.37:g.43089370T>A	ENSP00000352444:p.His343Leu	215.0	0.0	0		132.0	23.0	0.174242	NM_006955	Q06731|Q32MA2|Q86XY8|Q8NDW3	Missense_Mutation	SNP	ENST00000359467.3	37	CCDS7198.1	4	0.0018315018315018315	0	0.0	1	0.0027624309392265192	0	0.0	3	0.00395778364116095	T	4.540	0.100297	0.08731	4.54E-4	0.002326	ENSG00000196693	ENST00000359467;ENST00000395836	T	0.18338	2.22	2.28	2.28	0.28536	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	0.207772	0.24160	N	0.040988	T	0.09774	0.0240	N	0.20483	0.58	0.09310	N	0.999998	B	0.10296	0.003	B	0.08055	0.003	T	0.24119	-1.0169	10	0.32370	T	0.25	.	8.5071	0.33195	0.0:0.0:0.0:1.0	.	343	Q06732	ZN33B_HUMAN	L	343;309	ENSP00000352444:H343L	ENSP00000352444:H343L	H	-	2	0	ZNF33B	42409376	0.000000	0.05858	0.998000	0.56505	0.966000	0.64601	0.224000	0.17738	1.324000	0.45282	0.341000	0.21757	CAT	T|0.998;A|0.002	0.002	strong		0.413	ZNF33B-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_006955	
STXBP2	6813	hgsc.bcm.edu	37	19	7712050	7712050	+	Silent	SNP	C	C	T	rs146425381	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr19:7712050C>T	ENST00000221283.5	+	17	1486	c.1455C>T	c.(1453-1455)gaC>gaT	p.D485D	STXBP2_ENST00000414284.2_Silent_p.D482D|STXBP2_ENST00000441779.2_Silent_p.D496D|STXBP2_ENST00000602355.1_Silent_p.D20D	NM_006949.2	NP_008880.2	Q15833	STXB2_HUMAN	syntaxin binding protein 2	485					leukocyte mediated cytotoxicity (GO:0001909)|neutrophil degranulation (GO:0043312)|protein transport (GO:0015031)|regulation of mast cell degranulation (GO:0043304)|vesicle docking involved in exocytosis (GO:0006904)	azurophil granule (GO:0042582)|cytolytic granule (GO:0044194)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|plasma membrane (GO:0005886)|specific granule (GO:0042581)|tertiary granule (GO:0070820)	syntaxin-3 binding (GO:0030348)			breast(1)|central_nervous_system(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(2)|lung(7)|pancreas(1)|skin(1)|upper_aerodigestive_tract(1)	23						GCCGCCAGGACGCCGTGGAGG	0.721													C|||	3	0.000599042	0.0	0.0014	5008	,	,		13459	0.0		0.002	False		,,,				2504	0.0				p.D496D		Atlas-SNP	.											.	STXBP2	63	.	0			c.C1488T						PASS	.	C	,	0,4384		0,0,2192	22.0	28.0	26.0		1446,1455	-3.5	0.5	19	dbSNP_134	26	14,8528		0,14,4257	no	coding-synonymous,coding-synonymous	STXBP2	NM_001127396.1,NM_006949.2	,	0,14,6449	TT,TC,CC		0.1639,0.0,0.1083	,	482/591,485/594	7712050	14,12912	2192	4271	6463	SO:0001819	synonymous_variant	6813	exon17			CCAGGACGCCGTG	U63533	CCDS12181.1, CCDS45948.1, CCDS62522.1	19p13.3-p13.2	2014-09-17				ENSG00000076944			11445	protein-coding gene	gene with protein product		601717				8921365	Standard	NM_001127396		Approved	UNC18B, Hunc18b	uc010xjr.3	Q15833		ENST00000221283.5:c.1455C>T	19.37:g.7712050C>T		57.0	0.0	0		50.0	15.0	0.3	NM_001272034	B4E175|E7EQD5|Q9BU65	Silent	SNP	ENST00000221283.5	37	CCDS12181.1																																																																																			C|0.999;T|0.001	0.001	strong		0.721	STXBP2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000460963.1	NM_006949	
SLITRK3	22865	hgsc.bcm.edu	37	3	164906800	164906800	+	Missense_Mutation	SNP	G	G	T			TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr3:164906800G>T	ENST00000475390.1	-	2	2262	c.1819C>A	c.(1819-1821)Ctg>Atg	p.L607M	SLITRK3_ENST00000241274.3_Missense_Mutation_p.L607M			O94933	SLIK3_HUMAN	SLIT and NTRK-like family, member 3	607	LRRCT 2.				axonogenesis (GO:0007409)	integral component of membrane (GO:0016021)				NS(1)|breast(2)|central_nervous_system(1)|cervix(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(14)|lung(66)|ovary(6)|pancreas(1)|prostate(4)|skin(5)|upper_aerodigestive_tract(5)	119						AGAACTTCCAGCTCAATAGTG	0.542										HNSCC(40;0.11)																											p.L607M		Atlas-SNP	.											.	SLITRK3	263	.	0			c.C1819A						PASS	.						61.0	57.0	58.0					3																	164906800		2203	4300	6503	SO:0001583	missense	22865	exon2			CTTCCAGCTCAAT	AB020655	CCDS3197.1	3q26.1	2004-07-28			ENSG00000121871	ENSG00000121871			23501	protein-coding gene	gene with protein product		609679				10048485, 14557068	Standard	NM_014926		Approved	KIAA0848	uc003fek.3	O94933	OTTHUMG00000158072	ENST00000475390.1:c.1819C>A	3.37:g.164906800G>T	ENSP00000420091:p.Leu607Met	111.0	0.0	0		87.0	15.0	0.172414	NM_014926	Q1RMY6	Missense_Mutation	SNP	ENST00000475390.1	37	CCDS3197.1	.	.	.	.	.	.	.	.	.	.	G	6.538	0.467489	0.12402	.	.	ENSG00000121871	ENST00000475390;ENST00000241274	T;T	0.54675	0.56;0.56	5.76	4.8	0.61643	Cysteine-rich flanking region, C-terminal (1);	0.000000	0.30185	N	0.010219	T	0.32133	0.0819	N	0.10809	0.05	0.33093	D	0.538255	B	0.12013	0.005	B	0.11329	0.006	T	0.36890	-0.9729	10	0.45353	T	0.12	-9.1664	9.2667	0.37645	0.0785:0.0:0.7817:0.1398	.	607	O94933	SLIK3_HUMAN	M	607	ENSP00000420091:L607M;ENSP00000241274:L607M	ENSP00000241274:L607M	L	-	1	2	SLITRK3	166389494	0.021000	0.18746	0.997000	0.53966	0.879000	0.50718	0.452000	0.21795	1.403000	0.46800	0.655000	0.94253	CTG	.	.	none		0.542	SLITRK3-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000350126.1	NM_014926	
KLHL17	339451	hgsc.bcm.edu	37	1	899824	899824	+	Silent	SNP	C	C	T	rs201807567	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr1:899824C>T	ENST00000338591.3	+	11	1721	c.1614C>T	c.(1612-1614)aaC>aaT	p.N538N	PLEKHN1_ENST00000379409.2_5'Flank|PLEKHN1_ENST00000379407.3_5'Flank|PLEKHN1_ENST00000379410.3_5'Flank	NM_198317.2	NP_938073.1	Q6TDP4	KLH17_HUMAN	kelch-like family member 17	538	Interaction with F-actin. {ECO:0000250}.				actin cytoskeleton organization (GO:0030036)|brain development (GO:0007420)|protein ubiquitination (GO:0016567)	actin cytoskeleton (GO:0015629)|cell junction (GO:0030054)|dendrite cytoplasm (GO:0032839)|extracellular space (GO:0005615)|neuronal cell body (GO:0043025)|postsynaptic density (GO:0014069)|postsynaptic membrane (GO:0045211)	protein complex scaffold (GO:0032947)			central_nervous_system(1)|kidney(2)|lung(3)|prostate(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	10	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;9.48e-15)|all_lung(118;9.67e-07)|Lung NSC(185;5.59e-05)|Renal(390;0.00571)|Breast(487;0.0183)|Hepatocellular(190;0.0268)|Myeloproliferative disorder(586;0.028)|Ovarian(437;0.127)|Lung SC(97;0.217)		UCEC - Uterine corpus endometrioid carcinoma (11;0.00459)|Epithelial(90;1.52e-38)|OV - Ovarian serous cystadenocarcinoma(86;5.59e-23)|Colorectal(212;0.000155)|COAD - Colon adenocarcinoma(227;0.000193)|BRCA - Breast invasive adenocarcinoma(365;0.000469)|Kidney(185;0.00227)|STAD - Stomach adenocarcinoma(132;0.00644)|KIRC - Kidney renal clear cell carcinoma(229;0.0339)|Lung(427;0.199)		CAGGGGGCAACGACGGCACCA	0.667													C|||	11	0.00219649	0.0	0.0014	5008	,	,		10445	0.001		0.006	False		,,,				2504	0.0031				p.N538N		Atlas-SNP	.											.	KLHL17	31	.	0			c.C1614T						PASS	.	C		1,4119		0,1,2059	15.0	16.0	16.0		1614	-2.8	1.0	1		16	27,8173		0,27,4073	no	coding-synonymous	KLHL17	NM_198317.2		0,28,6132	TT,TC,CC		0.3293,0.0243,0.2273		538/643	899824	28,12292	2060	4100	6160	SO:0001819	synonymous_variant	339451	exon11			GGGCAACGACGGC	AY423763	CCDS30550.1	1p36	2013-01-30	2013-01-30		ENSG00000187961	ENSG00000187961		"""Kelch-like"", ""BTB/POZ domain containing"""	24023	protein-coding gene	gene with protein product	"""actinfilin"""		"""kelch-like 17 (Drosophila)"""			12063253	Standard	NM_198317		Approved		uc001aca.2	Q6TDP4	OTTHUMG00000040721	ENST00000338591.3:c.1614C>T	1.37:g.899824C>T		88.0	0.0	0		48.0	38.0	0.791667	NM_198317	Q5SV94	Silent	SNP	ENST00000338591.3	37	CCDS30550.1																																																																																			C|0.996;T|0.004	0.004	strong		0.667	KLHL17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000097875.3	NM_198317	
EP300	2033	hgsc.bcm.edu	37	22	41546158	41546158	+	Missense_Mutation	SNP	C	C	A	rs148884710	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr22:41546158C>A	ENST00000263253.7	+	14	3992	c.2773C>A	c.(2773-2775)Cct>Act	p.P925T		NM_001429.3	NP_001420.2	Q09472	EP300_HUMAN	E1A binding protein p300	925					apoptotic process (GO:0006915)|cellular response to hypoxia (GO:0071456)|chromatin organization (GO:0006325)|circadian rhythm (GO:0007623)|G2/M transition of mitotic cell cycle (GO:0000086)|heart development (GO:0007507)|histone H2B acetylation (GO:0043969)|histone H4 acetylation (GO:0043967)|innate immune response (GO:0045087)|internal peptidyl-lysine acetylation (GO:0018393)|internal protein amino acid acetylation (GO:0006475)|intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator (GO:0042771)|lung development (GO:0030324)|mitotic cell cycle (GO:0000278)|N-terminal peptidyl-lysine acetylation (GO:0018076)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|nervous system development (GO:0007399)|Notch signaling pathway (GO:0007219)|organ morphogenesis (GO:0009887)|positive regulation by host of viral transcription (GO:0043923)|positive regulation of protein binding (GO:0032092)|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 type I interferon production (GO:0032481)|regulation of androgen receptor signaling pathway (GO:0060765)|regulation of cell cycle (GO:0051726)|regulation of transcription from RNA polymerase II promoter in response to hypoxia (GO:0061418)|regulation of transcription, DNA-templated (GO:0006355)|regulation of tubulin deacetylation (GO:0090043)|response to estrogen (GO:0043627)|response to hypoxia (GO:0001666)|skeletal muscle tissue development (GO:0007519)|somitogenesis (GO:0001756)|transcription, DNA-templated (GO:0006351)|viral process (GO:0016032)	cytoplasm (GO:0005737)|histone acetyltransferase complex (GO:0000123)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	acetyltransferase activity (GO:0016407)|activating transcription factor binding (GO:0033613)|androgen receptor binding (GO:0050681)|beta-catenin binding (GO:0008013)|chromatin binding (GO:0003682)|chromatin DNA binding (GO:0031490)|core promoter binding (GO:0001047)|DNA binding (GO:0003677)|histone acetyltransferase activity (GO:0004402)|lysine N-acetyltransferase activity, acting on acetyl phosphate as donor (GO:0004468)|nuclear hormone receptor binding (GO:0035257)|pre-mRNA intronic binding (GO:0097157)|RNA polymerase II activating transcription factor binding (GO:0001102)|RNA polymerase II core promoter sequence-specific DNA binding (GO:0000979)|transcription coactivator activity (GO:0003713)|transcription factor binding (GO:0008134)|transferase activity, transferring acyl groups (GO:0016746)|zinc ion binding (GO:0008270)	p.P925T(1)		NS(2)|breast(11)|central_nervous_system(7)|cervix(1)|endometrium(10)|haematopoietic_and_lymphoid_tissue(31)|kidney(5)|large_intestine(31)|liver(2)|lung(33)|ovary(2)|pancreas(4)|prostate(1)|skin(6)|stomach(1)|upper_aerodigestive_tract(8)|urinary_tract(16)	171						AGCGTCTGTTCCTACCCCAAC	0.522			"""T,  N, F, Mis, O"""	"""MLL, RUNXBP2"""	"""colorectal, breast, pancreatic, AML, ALL, DLBCL"""				Rubinstein-Taybi syndrome				C|||	8	0.00159744	0.0	0.0014	5008	,	,		20472	0.0		0.007	False		,,,				2504	0.0				p.P925T		Atlas-SNP	.		Rec	yes		22	22q13	2033	300 kd E1A-Binding protein gene		"""L, E"""	EP300,NS,lymphoid_neoplasm,0,1	EP300	367	1	1	Substitution - Missense(1)	haematopoietic_and_lymphoid_tissue(1)	c.C2773A						PASS	.	C	THR/PRO	10,4394	16.8+/-37.8	0,10,2192	64.0	48.0	53.0		2773	3.8	0.9	22	dbSNP_134	53	55,8545	35.3+/-89.8	3,49,4248	yes	missense	EP300	NM_001429.3	38	3,59,6440	AA,AC,CC		0.6395,0.2271,0.4998	benign	925/2415	41546158	65,12939	2202	4300	6502	SO:0001583	missense	2033	exon14	Familial Cancer Database	Broad Thumb-Hallux syndrome	TCTGTTCCTACCC	U01877	CCDS14010.1	22q13.2	2011-07-01			ENSG00000100393	ENSG00000100393		"""Chromatin-modifying enzymes / K-acetyltransferases"""	3373	protein-coding gene	gene with protein product	"""histone acetyltransferase p300"""	602700				7523245	Standard	NM_001429		Approved	p300, KAT3B	uc003azl.4	Q09472	OTTHUMG00000150937	ENST00000263253.7:c.2773C>A	22.37:g.41546158C>A	ENSP00000263253:p.Pro925Thr	59.0	0.0	0		58.0	33.0	0.568965	NM_001429	B1AKC2	Missense_Mutation	SNP	ENST00000263253.7	37	CCDS14010.1	5	0.0022893772893772895	0	0.0	1	0.0027624309392265192	0	0.0	4	0.005277044854881266	C	13.29	2.193769	0.38707	0.002271	0.006395	ENSG00000100393	ENST00000263253	D	0.83992	-1.79	5.92	3.85	0.44370	.	0.135740	0.33401	N	0.004949	T	0.68183	0.2973	L	0.47716	1.5	0.35741	D	0.818666	B	0.13594	0.008	B	0.16722	0.016	T	0.67608	-0.5627	10	0.22706	T	0.39	-8.5427	8.0505	0.30575	0.0:0.7318:0.1307:0.1375	.	925	Q09472	EP300_HUMAN	T	925	ENSP00000263253:P925T	ENSP00000263253:P925T	P	+	1	0	EP300	39876104	0.960000	0.32886	0.934000	0.37439	0.957000	0.61999	1.349000	0.33998	0.859000	0.35456	-0.373000	0.07131	CCT	C|0.995;A|0.005	0.005	strong		0.522	EP300-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000320600.1	NM_001429	
SLAIN1	122060	hgsc.bcm.edu	37	13	78320801	78320801	+	Missense_Mutation	SNP	C	C	G	rs144139933	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr13:78320801C>G	ENST00000466548.1	+	5	1029	c.1003C>G	c.(1003-1005)Cct>Gct	p.P335A	SLAIN1_ENST00000314070.5_Intron|SLAIN1_ENST00000465831.1_3'UTR|SLAIN1_ENST00000267219.8_Missense_Mutation_p.P116A|SLAIN1_ENST00000418532.1_Missense_Mutation_p.P116A|SLAIN1_ENST00000351546.3_Missense_Mutation_p.P72A|SLAIN1_ENST00000358679.3_Missense_Mutation_p.P72A|SLAIN1_ENST00000488699.1_Missense_Mutation_p.P193A	NM_001242868.1	NP_001229797.1	Q8ND83	SLAI1_HUMAN	SLAIN motif family, member 1	335										breast(1)|endometrium(3)|large_intestine(1)|lung(6)|ovary(1)|skin(1)|upper_aerodigestive_tract(1)	14		Acute lymphoblastic leukemia(28;0.0279)|Breast(118;0.037)		GBM - Glioblastoma multiforme(99;0.0853)		TTTGCCACCACCTCAGCCTCG	0.468													C|||	6	0.00119808	0.0	0.0014	5008	,	,		19409	0.0		0.005	False		,,,				2504	0.0				p.P357A		Atlas-SNP	.											.	SLAIN1	43	.	0			c.C1069G						PASS	.	C	ALA/PRO,ALA/PRO,,,ALA/PRO,ALA/PRO	2,4404	4.2+/-10.8	0,2,2201	158.0	150.0	153.0		577,1069,,,211,214	5.9	1.0	13	dbSNP_134	153	21,8579	16.6+/-54.9	0,21,4279	yes	missense,missense,intron,intron,missense,missense	SLAIN1	NM_001040153.3,NM_001242868.1,NM_001242869.1,NM_001242870.1,NM_001242871.1,NM_144595.3	27,27,,,27,27	0,23,6480	GG,GC,CC		0.2442,0.0454,0.1768	probably-damaging,probably-damaging,,,probably-damaging,probably-damaging	193/427,357/591,,,71/305,72/306	78320801	23,12983	2203	4300	6503	SO:0001583	missense	122060	exon4			CCACCACCTCAGC	AK054608	CCDS9460.1, CCDS31995.1, CCDS31995.2, CCDS55901.1, CCDS73588.1, CCDS73589.1	13q22.3	2006-09-12	2006-09-12	2006-09-12	ENSG00000139737	ENSG00000139737			26387	protein-coding gene	gene with protein product		610491	"""chromosome 13 open reading frame 32"""	C13orf32		16546155	Standard	NM_001040153		Approved	FLJ30046	uc001vkk.3	Q8ND83	OTTHUMG00000017110	ENST00000466548.1:c.1003C>G	13.37:g.78320801C>G	ENSP00000419730:p.Pro335Ala	181.0	0.0	0		181.0	95.0	0.524862	NM_001242868	A8K0Z9|B7Z209|Q5T6P4|Q5T6P7|Q8ND10|Q96NV0	Missense_Mutation	SNP	ENST00000466548.1	37		5	0.0022893772893772895	0	0.0	1	0.0027624309392265192	0	0.0	4	0.005277044854881266	C	20.3	3.960845	0.74016	4.54E-4	0.002442	ENSG00000139737	ENST00000466548;ENST00000389459;ENST00000418532;ENST00000442759;ENST00000446759;ENST00000488699;ENST00000267219;ENST00000351546;ENST00000441784;ENST00000462234;ENST00000496045;ENST00000474663;ENST00000358679	.	.	.	5.92	5.92	0.95590	.	0.000000	0.85682	D	0.000000	T	0.73489	0.3593	M	0.69823	2.125	0.80722	D	1	D;D;D	0.76494	0.999;0.999;0.998	D;D;D	0.71414	0.973;0.973;0.96	T	0.74697	-0.3578	8	.	.	.	-15.4977	20.3325	0.98724	0.0:1.0:0.0:0.0	.	71;193;335	B7Z326;B7Z209;Q8ND83	.;.;SLAI1_HUMAN	A	335;335;116;116;166;193;116;72;72;72;72;72;72	.	.	P	+	1	0	SLAIN1	77218802	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	5.733000	0.68571	2.805000	0.96524	0.655000	0.94253	CCT	C|0.999;G|0.001	0.001	strong		0.468	SLAIN1-009	KNOWN	not_organism_supported|basic	protein_coding	protein_coding	OTTHUMT00000355018.1	NM_144595	
SH3TC1	54436	hgsc.bcm.edu	37	4	8229140	8229140	+	Missense_Mutation	SNP	G	G	T	rs141562329	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr4:8229140G>T	ENST00000245105.3	+	12	1786	c.1719G>T	c.(1717-1719)agG>agT	p.R573S	SH3TC1_ENST00000514274.1_3'UTR|SH3TC1_ENST00000539824.1_Missense_Mutation_p.R497S	NM_018986.3	NP_061859	Q8TE82	S3TC1_HUMAN	SH3 domain and tetratricopeptide repeats 1	573										NS(1)|breast(3)|endometrium(4)|kidney(4)|large_intestine(6)|lung(10)|pancreas(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(2)	33						GCAGCAGGAGGCTCAAGCTGT	0.692													G|||	13	0.00259585	0.0	0.0	5008	,	,		15676	0.001		0.003	False		,,,				2504	0.0092				p.R573S	NSCLC(145;2298 2623 35616 37297)	Atlas-SNP	.											.	SH3TC1	105	.	0			c.G1719T						PASS	.	G	SER/ARG	0,4340		0,0,2170	35.0	40.0	38.0		1719	2.4	0.8	4	dbSNP_134	38	18,8450		0,18,4216	yes	missense	SH3TC1	NM_018986.3	110	0,18,6386	TT,TG,GG		0.2126,0.0,0.1405	possibly-damaging	573/1337	8229140	18,12790	2170	4234	6404	SO:0001583	missense	54436	exon12			CAGGAGGCTCAAG	AK074093	CCDS3399.1	4p16.1	2013-01-11			ENSG00000125089	ENSG00000125089		"""Tetratricopeptide (TTC) repeat domain containing"""	26009	protein-coding gene	gene with protein product							Standard	NM_018986		Approved	FLJ20356	uc003gkv.4	Q8TE82	OTTHUMG00000160934	ENST00000245105.3:c.1719G>T	4.37:g.8229140G>T	ENSP00000245105:p.Arg573Ser	97.0	0.0	0		93.0	40.0	0.430108	NM_018986	Q4W5G5	Missense_Mutation	SNP	ENST00000245105.3	37	CCDS3399.1	3	0.0013736263736263737	0	0.0	0	0.0	0	0.0	3	0.00395778364116095	G	15.49	2.849206	0.51270	0.0	0.002126	ENSG00000125089	ENST00000382516;ENST00000245105;ENST00000539824;ENST00000535265	T;T	0.79845	-1.31;-1.31	4.51	2.42	0.29668	Tetratricopeptide-like helical (1);	0.373920	0.30003	N	0.010654	T	0.79639	0.4480	L	0.49126	1.545	0.09310	N	1	P	0.48911	0.917	P	0.50314	0.637	T	0.71394	-0.4606	10	0.66056	D	0.02	-17.1056	10.2336	0.43268	0.2842:0.0:0.7158:0.0	.	573	Q8TE82	S3TC1_HUMAN	S	311;573;497;402	ENSP00000245105:R573S;ENSP00000441045:R497S	ENSP00000245105:R573S	R	+	3	2	SH3TC1	8280040	0.976000	0.34144	0.808000	0.32385	0.871000	0.50021	0.768000	0.26590	0.892000	0.36259	-0.254000	0.11334	AGG	G|0.999;T|0.001	0.001	strong		0.692	SH3TC1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000206991.2	NM_018986	
FAT4	79633	hgsc.bcm.edu	37	4	126241565	126241565	+	Silent	SNP	C	C	T			TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr4:126241565C>T	ENST00000394329.3	+	1	4012	c.3999C>T	c.(3997-3999)ctC>ctT	p.L1333L		NM_024582.4	NP_078858.4	Q6V0I7	FAT4_HUMAN	FAT atypical cadherin 4	1333	Cadherin 13. {ECO:0000255|PROSITE- ProRule:PRU00043}.				branching involved in ureteric bud morphogenesis (GO:0001658)|cerebral cortex development (GO:0021987)|digestive tract development (GO:0048565)|heart morphogenesis (GO:0003007)|heterophilic cell-cell adhesion (GO:0007157)|hippo signaling (GO:0035329)|homophilic cell adhesion (GO:0007156)|inner ear receptor stereocilium organization (GO:0060122)|neurogenesis (GO:0022008)|ossification involved in bone maturation (GO:0043931)|plasma membrane organization (GO:0007009)|regulation of metanephric nephron tubule epithelial cell differentiation (GO:0072307)	apical part of cell (GO:0045177)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)	p.L1333L(4)		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						TTGGTGAACTCGTGTCCTCTG	0.358																																					p.L1333L		Atlas-SNP	.											FAT4_ENST00000394329,NS,carcinoma,0,2	FAT4	1752	2	4	Substitution - coding silent(4)	lung(4)	c.C3999T						PASS	.						139.0	131.0	133.0					4																	126241565		1890	4108	5998	SO:0001819	synonymous_variant	79633	exon1			TGAACTCGTGTCC	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.3999C>T	4.37:g.126241565C>T		154.0	0.0	0		93.0	54.0	0.580645	NM_024582	A8K5Z6|B5MDG4|Q3LIA6|Q8TCK7|Q9H5T6	Silent	SNP	ENST00000394329.3	37	CCDS3732.3																																																																																			.	.	none		0.358	FAT4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256765.2	NM_024582	
MUC17	140453	hgsc.bcm.edu	37	7	100678032	100678032	+	Missense_Mutation	SNP	T	T	C	rs147173571		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr7:100678032T>C	ENST00000306151.4	+	3	3399	c.3335T>C	c.(3334-3336)cTg>cCg	p.L1112P		NM_001040105.1	NP_001035194.1	Q685J3	MUC17_HUMAN	mucin 17, cell surface associated	1112	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)					AGCACCAGGCTGGTGGTCAGT	0.512																																					p.L1112P		Atlas-SNP	.											.	MUC17	804	.	0			c.T3335C						PASS	.						494.0	394.0	428.0					7																	100678032		2203	4300	6503	SO:0001583	missense	140453	exon3			CCAGGCTGGTGGT	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.3335T>C	7.37:g.100678032T>C	ENSP00000302716:p.Leu1112Pro	206.0	0.0	0		753.0	89.0	0.118194	NM_001040105	O14761|Q685J2|Q8TDH7	Missense_Mutation	SNP	ENST00000306151.4	37	CCDS34711.1	.	.	.	.	.	.	.	.	.	.	C	0.149	-1.093913	0.01858	.	.	ENSG00000169876	ENST00000306151	T	0.03212	4.01	0.693	-0.391	0.12446	.	.	.	.	.	T	0.01320	0.0043	N	0.01576	-0.805	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.48055	-0.9068	8	0.25751	T	0.34	.	.	.	.	.	1112	Q685J3	MUC17_HUMAN	P	1112	ENSP00000302716:L1112P	ENSP00000302716:L1112P	L	+	2	0	MUC17	100464752	0.000000	0.05858	0.001000	0.08648	0.004000	0.04260	-6.070000	0.00082	-0.165000	0.10908	-1.364000	0.01208	CTG	.	.	weak		0.512	MUC17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347161.1	NM_001040105	
LAMC1	3915	hgsc.bcm.edu	37	1	183091040	183091040	+	Missense_Mutation	SNP	G	G	A	rs147401305	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr1:183091040G>A	ENST00000258341.4	+	12	2430	c.2173G>A	c.(2173-2175)Gcc>Acc	p.A725T		NM_002293.3	NP_002284.3	P11047	LAMC1_HUMAN	laminin, gamma 1 (formerly LAMB2)	725	Laminin EGF-like 6. {ECO:0000255|PROSITE- ProRule:PRU00460}.				axon guidance (GO:0007411)|cell adhesion (GO:0007155)|cell migration (GO:0016477)|endoderm development (GO:0007492)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|hemidesmosome assembly (GO:0031581)|positive regulation of epithelial cell proliferation (GO:0050679)|protein complex assembly (GO:0006461)|substrate adhesion-dependent cell spreading (GO:0034446)	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)	extracellular matrix structural constituent (GO:0005201)|glycosphingolipid binding (GO:0043208)	p.A725S(1)		NS(2)|breast(5)|central_nervous_system(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(17)|lung(27)|ovary(3)|prostate(2)|skin(3)|upper_aerodigestive_tract(3)	76						TGTGCTTTGCGCCTGCAATGG	0.478																																					p.A725T		Atlas-SNP	.											LAMC1,NS,carcinoma,0,1	LAMC1	176	1	1	Substitution - Missense(1)	lung(1)	c.G2173A						scavenged	.	G	THR/ALA	3,4403	6.2+/-15.9	0,3,2200	132.0	117.0	122.0		2173	1.5	0.5	1	dbSNP_134	122	4,8596	3.7+/-12.6	0,4,4296	yes	missense	LAMC1	NM_002293.3	58	0,7,6496	AA,AG,GG		0.0465,0.0681,0.0538	benign	725/1610	183091040	7,12999	2203	4300	6503	SO:0001583	missense	3915	exon12			CTTTGCGCCTGCA	J03202	CCDS1351.1	1q31	2013-03-01			ENSG00000135862	ENSG00000135862		"""Laminins"""	6492	protein-coding gene	gene with protein product		150290		LAMB2		3234037	Standard	NM_002293		Approved		uc001gpy.4	P11047	OTTHUMG00000035418	ENST00000258341.4:c.2173G>A	1.37:g.183091040G>A	ENSP00000258341:p.Ala725Thr	103.0	1.0	0.00970874		146.0	88.0	0.60274	NM_002293	Q5VYE7	Missense_Mutation	SNP	ENST00000258341.4	37	CCDS1351.1	.	.	.	.	.	.	.	.	.	.	G	1.387	-0.581931	0.03827	6.81E-4	4.65E-4	ENSG00000135862	ENST00000258341	T	0.61627	0.09	5.17	1.54	0.23209	EGF-like, laminin (3);	0.249221	0.46442	N	0.000296	T	0.17959	0.0431	N	0.00621	-1.32	0.19945	N	0.999948	B	0.02656	0.0	B	0.04013	0.001	T	0.29027	-1.0025	10	0.07990	T	0.79	.	5.4496	0.16556	0.6007:0.0:0.2809:0.1184	.	725	P11047	LAMC1_HUMAN	T	725	ENSP00000258341:A725T	ENSP00000258341:A725T	A	+	1	0	LAMC1	181357663	0.001000	0.12720	0.533000	0.28001	0.645000	0.38454	0.530000	0.23036	0.013000	0.14918	-0.946000	0.02672	GCC	G|0.999;A|0.001	0.001	strong		0.478	LAMC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000085954.2	NM_002293	
SUCLG2	8801	hgsc.bcm.edu	37	3	67579535	67579535	+	Missense_Mutation	SNP	T	T	C	rs74675534	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr3:67579535T>C	ENST00000307227.5	-	3	329	c.302A>G	c.(301-303)aAa>aGa	p.K101R	SUCLG2_ENST00000492795.1_Missense_Mutation_p.K101R|SUCLG2_ENST00000493112.1_Missense_Mutation_p.K101R	NM_003848.3	NP_003839.2	Q96I99	SUCB2_HUMAN	succinate-CoA ligase, GDP-forming, beta subunit	101	ATP-grasp.				cellular metabolic process (GO:0044237)|small molecule metabolic process (GO:0044281)|succinate metabolic process (GO:0006105)|succinyl-CoA metabolic process (GO:0006104)|tricarboxylic acid cycle (GO:0006099)	mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)|plasma membrane (GO:0005886)|succinate-CoA ligase complex (GDP-forming) (GO:0045244)	ATP binding (GO:0005524)|GDP binding (GO:0019003)|GTP binding (GO:0005525)|succinate-CoA ligase (GDP-forming) activity (GO:0004776)			central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(1)|lung(3)|skin(1)	10		Renal(2;0.00294)|Lung NSC(201;0.012)|Hepatocellular(537;0.121)		BRCA - Breast invasive adenocarcinoma(55;3.53e-05)|Epithelial(33;0.000153)	Succinic acid(DB00139)	AACACCTCCTTTCAAACCACT	0.383													T|||	9	0.00179712	0.0008	0.0	5008	,	,		17705	0.0		0.007	False		,,,				2504	0.001				p.K101R		Atlas-SNP	.											.	SUCLG2	95	.	0			c.A302G						PASS	.	T	ARG/LYS,ARG/LYS	6,3664		0,6,1829	156.0	147.0	150.0		302,302	5.0	1.0	3	dbSNP_131	150	86,8080		1,84,3998	yes	missense,missense	SUCLG2	NM_001177599.1,NM_003848.3	26,26	1,90,5827	CC,CT,TT		1.0531,0.1635,0.7773	benign,benign	101/441,101/433	67579535	92,11744	1835	4083	5918	SO:0001583	missense	8801	exon3			CCTCCTTTCAAAC	AF058954	CCDS43104.1, CCDS54605.1	3p14.3	2004-05-17			ENSG00000172340	ENSG00000172340	6.2.1.4		11450	protein-coding gene	gene with protein product		603922				9765291	Standard	NM_001177599		Approved		uc003dna.4	Q96I99	OTTHUMG00000158740	ENST00000307227.5:c.302A>G	3.37:g.67579535T>C	ENSP00000307432:p.Lys101Arg	129.0	0.0	0		102.0	57.0	0.558824	NM_001177599	C9JVT2|O95195|Q6NUH7|Q86VX8|Q8WUQ1	Missense_Mutation	SNP	ENST00000307227.5	37	CCDS43104.1	5	0.0022893772893772895	0	0.0	0	0.0	0	0.0	5	0.006596306068601583	T	17.48	3.401307	0.62288	0.001635	0.010531	ENSG00000172340	ENST00000493112;ENST00000307227;ENST00000541608;ENST00000492795	T;T;T	0.70399	-0.48;-0.48;-0.48	5.01	5.01	0.66863	ATP-grasp fold, subdomain 1 (1);ATP-grasp fold, succinyl-CoA synthetase-type (1);	0.143233	0.64402	D	0.000006	T	0.73666	0.3616	M	0.88775	2.98	0.80722	D	1	B	0.25955	0.138	B	0.36766	0.232	T	0.79006	-0.1979	10	0.66056	D	0.02	.	14.7526	0.69536	0.0:0.0:0.0:1.0	.	101	Q96I99	SUCB2_HUMAN	R	101;101;53;101	ENSP00000419325:K101R;ENSP00000307432:K101R;ENSP00000417589:K101R	ENSP00000307432:K101R	K	-	2	0	SUCLG2	67662225	1.000000	0.71417	1.000000	0.80357	0.947000	0.59692	7.957000	0.87870	1.884000	0.54569	0.377000	0.23210	AAA	T|0.993;C|0.007	0.007	strong		0.383	SUCLG2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000351993.1	NM_003848	
PLIN4	729359	hgsc.bcm.edu	37	19	4513549	4513549	+	Silent	SNP	G	G	A	rs146566557	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr19:4513549G>A	ENST00000301286.3	-	3	380	c.381C>T	c.(379-381)agC>agT	p.S127S		NM_001080400.1	NP_001073869.1	Q96Q06	PLIN4_HUMAN	perilipin 4	127	27 X 33 AA approximate tandem repeat.					cytoplasm (GO:0005737)|lipid particle (GO:0005811)|plasma membrane (GO:0005886)				NS(2)|breast(4)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(7)|lung(14)|ovary(1)|skin(2)|soft_tissue(1)|stomach(2)	41						CTGTGACCCCGCTGGACACCA	0.667													G|||	4	0.000798722	0.0008	0.0	5008	,	,		17859	0.001		0.002	False		,,,				2504	0.0				p.S127S		Atlas-SNP	.											.	PLIN4	191	.	0			c.C381T						PASS	.	G		2,3976		0,2,1987	26.0	30.0	29.0		381	-10.7	0.0	19	dbSNP_134	29	37,8263		0,37,4113	no	coding-synonymous	PLIN4	NM_001080400.1		0,39,6100	AA,AG,GG		0.4458,0.0503,0.3176		127/1358	4513549	39,12239	1989	4150	6139	SO:0001819	synonymous_variant	729359	exon3			GACCCCGCTGGAC	AB067468	CCDS45927.1	19p13.3	2009-10-06	2009-08-12	2009-08-12	ENSG00000167676	ENSG00000167676		"""Perilipins"""	29393	protein-coding gene	gene with protein product		613247	"""KIAA1881"""	KIAA1881		11572484, 19638644	Standard	NM_001080400		Approved	S3-12	uc002mar.1	Q96Q06	OTTHUMG00000167571	ENST00000301286.3:c.381C>T	19.37:g.4513549G>A		80.0	0.0	0		89.0	47.0	0.52809	NM_001080400	A6NEI2	Silent	SNP	ENST00000301286.3	37	CCDS45927.1																																																																																			G|0.998;A|0.002	0.002	strong		0.667	PLIN4-001	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000395095.1	XM_170901	
METTL25	84190	hgsc.bcm.edu	37	12	82792792	82792792	+	Missense_Mutation	SNP	T	T	G			TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr12:82792792T>G	ENST00000248306.3	+	4	819	c.750T>G	c.(748-750)aaT>aaG	p.N250K	METTL25_ENST00000547357.1_3'UTR	NM_032230.2	NP_115606.2	Q8N6Q8	MET25_HUMAN	methyltransferase like 25	250							methyltransferase activity (GO:0008168)										AAGTGCAAAATAAAGTTAAAA	0.343																																					p.N250K		Atlas-SNP	.											.	.	.	.	0			c.T750G						PASS	.						60.0	57.0	58.0					12																	82792792		2203	4299	6502	SO:0001583	missense	84190	exon4			GCAAAATAAAGTT	BC029120	CCDS9024.1	12q21.31	2012-08-13	2012-08-13	2012-08-13	ENSG00000127720	ENSG00000127720			26228	protein-coding gene	gene with protein product			"""chromosome 12 open reading frame 26"""	C12orf26			Standard	NM_032230		Approved	FLJ22789	uc001szq.3	Q8N6Q8	OTTHUMG00000170252	ENST00000248306.3:c.750T>G	12.37:g.82792792T>G	ENSP00000248306:p.Asn250Lys	48.0	0.0	0		31.0	11.0	0.354839	NM_032230	Q9H5Y3	Missense_Mutation	SNP	ENST00000248306.3	37	CCDS9024.1	.	.	.	.	.	.	.	.	.	.	T	0.058	-1.231429	0.01505	.	.	ENSG00000127720	ENST00000248306	T	0.29142	1.58	5.39	-0.792	0.10925	.	1.047890	0.07359	N	0.883727	T	0.07548	0.0190	N	0.01352	-0.895	0.09310	N	1	B	0.02656	0.0	B	0.04013	0.001	T	0.30119	-0.9989	10	0.05525	T	0.97	-2.823	1.9271	0.03319	0.1244:0.1816:0.1292:0.5648	.	250	Q8N6Q8	CL026_HUMAN	K	250	ENSP00000248306:N250K	ENSP00000248306:N250K	N	+	3	2	C12orf26	81316923	0.162000	0.22906	0.000000	0.03702	0.023000	0.10783	0.214000	0.17541	-0.265000	0.09352	-0.418000	0.06021	AAT	.	.	none		0.343	METTL25-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000408192.1	NM_032230	
THBS1	7057	hgsc.bcm.edu	37	15	39880818	39880818	+	Silent	SNP	C	C	T	rs41338344	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr15:39880818C>T	ENST00000260356.5	+	10	1728	c.1563C>T	c.(1561-1563)aaC>aaT	p.N521N		NM_003246.2	NP_003237.2	P07996	TSP1_HUMAN	thrombospondin 1	521	TSP type-1 3. {ECO:0000255|PROSITE- ProRule:PRU00210}.				activation of MAPK activity (GO:0000187)|behavioral response to pain (GO:0048266)|blood coagulation (GO:0007596)|cell adhesion (GO:0007155)|cell cycle arrest (GO:0007050)|cell migration (GO:0016477)|cellular response to growth factor stimulus (GO:0071363)|cellular response to heat (GO:0034605)|cellular response to tumor necrosis factor (GO:0071356)|chronic inflammatory response (GO:0002544)|endocardial cushion development (GO:0003197)|engulfment of apoptotic cell (GO:0043652)|extracellular matrix organization (GO:0030198)|growth plate cartilage development (GO:0003417)|immune response (GO:0006955)|negative regulation of angiogenesis (GO:0016525)|negative regulation of antigen processing and presentation of peptide or polysaccharide antigen via MHC class II (GO:0002581)|negative regulation of apoptotic process (GO:0043066)|negative regulation of blood vessel endothelial cell migration (GO:0043537)|negative regulation of cell-matrix adhesion (GO:0001953)|negative regulation of cGMP-mediated signaling (GO:0010754)|negative regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043154)|negative regulation of dendritic cell antigen processing and presentation (GO:0002605)|negative regulation of endothelial cell migration (GO:0010596)|negative regulation of endothelial cell proliferation (GO:0001937)|negative regulation of extrinsic apoptotic signaling pathway (GO:2001237)|negative regulation of fibrinolysis (GO:0051918)|negative regulation of fibroblast growth factor receptor signaling pathway (GO:0040037)|negative regulation of focal adhesion assembly (GO:0051895)|negative regulation of interleukin-12 production (GO:0032695)|negative regulation of nitric oxide mediated signal transduction (GO:0010751)|negative regulation of plasma membrane long-chain fatty acid transport (GO:0010748)|negative regulation of plasminogen activation (GO:0010757)|outflow tract morphogenesis (GO:0003151)|peptide cross-linking (GO:0018149)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|positive regulation of angiogenesis (GO:0045766)|positive regulation of blood coagulation (GO:0030194)|positive regulation of blood vessel endothelial cell migration (GO:0043536)|positive regulation of cell migration (GO:0030335)|positive regulation of cell-substrate adhesion (GO:0010811)|positive regulation of chemotaxis (GO:0050921)|positive regulation of endothelial cell apoptotic process (GO:2000353)|positive regulation of endothelial cell migration (GO:0010595)|positive regulation of extrinsic apoptotic signaling pathway via death domain receptors (GO:1902043)|positive regulation of fibroblast migration (GO:0010763)|positive regulation of macrophage activation (GO:0043032)|positive regulation of macrophage chemotaxis (GO:0010759)|positive regulation of phosphorylation (GO:0042327)|positive regulation of protein kinase B signaling (GO:0051897)|positive regulation of reactive oxygen species metabolic process (GO:2000379)|positive regulation of transforming growth factor beta receptor signaling pathway (GO:0030511)|positive regulation of transforming growth factor beta1 production (GO:0032914)|positive regulation of translation (GO:0045727)|positive regulation of tumor necrosis factor biosynthetic process (GO:0042535)|response to calcium ion (GO:0051592)|response to drug (GO:0042493)|response to endoplasmic reticulum stress (GO:0034976)|response to glucose (GO:0009749)|response to hypoxia (GO:0001666)|response to magnesium ion (GO:0032026)|response to mechanical stimulus (GO:0009612)|response to progesterone (GO:0032570)|response to testosterone (GO:0033574)|response to unfolded protein (GO:0006986)|sprouting angiogenesis (GO:0002040)	cell surface (GO:0009986)|endoplasmic reticulum (GO:0005783)|external side of plasma membrane (GO:0009897)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|fibrinogen complex (GO:0005577)|platelet alpha granule (GO:0031091)|platelet alpha granule lumen (GO:0031093)|sarcoplasmic reticulum (GO:0016529)|secretory granule (GO:0030141)	calcium ion binding (GO:0005509)|collagen V binding (GO:0070052)|fibrinogen binding (GO:0070051)|fibroblast growth factor binding (GO:0017134)|fibronectin binding (GO:0001968)|glycoprotein binding (GO:0001948)|heparin binding (GO:0008201)|identical protein binding (GO:0042802)|integrin binding (GO:0005178)|laminin binding (GO:0043236)|low-density lipoprotein particle binding (GO:0030169)|phosphatidylserine binding (GO:0001786)|proteoglycan binding (GO:0043394)|transforming growth factor beta binding (GO:0050431)			breast(1)|central_nervous_system(3)|endometrium(8)|kidney(5)|large_intestine(15)|lung(9)|ovary(3)|pancreas(1)|prostate(2)|skin(2)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	53		all_cancers(109;1.35e-17)|all_epithelial(112;2.07e-15)|Lung NSC(122;4.44e-11)|all_lung(180;1.11e-09)|Melanoma(134;0.0574)|Colorectal(260;0.117)|Ovarian(310;0.223)		GBM - Glioblastoma multiforme(113;2.77e-06)|BRCA - Breast invasive adenocarcinoma(123;0.105)		TCTGCAACAACCCCACACCCC	0.537													C|||	64	0.0127796	0.003	0.0274	5008	,	,		20155	0.0		0.0318	False		,,,				2504	0.0092				p.N521N		Atlas-SNP	.											.	THBS1	106	.	0			c.C1563T						PASS	.	C		34,4366	39.2+/-71.8	0,34,2166	94.0	89.0	91.0		1563	4.8	1.0	15	dbSNP_127	91	301,8293	109.6+/-170.1	4,293,4000	no	coding-synonymous	THBS1	NM_003246.2		4,327,6166	TT,TC,CC		3.5024,0.7727,2.5781		521/1171	39880818	335,12659	2200	4297	6497	SO:0001819	synonymous_variant	7057	exon10			CAACAACCCCACA		CCDS32194.1	15q15	2009-04-08			ENSG00000137801	ENSG00000137801			11785	protein-coding gene	gene with protein product	"""thrombospondin-1p180"""	188060				2341158, 2335352	Standard	NM_003246		Approved	TSP1, THBS, TSP, THBS-1, TSP-1	uc001zkh.3	P07996	OTTHUMG00000133665	ENST00000260356.5:c.1563C>T	15.37:g.39880818C>T		80.0	0.0	0		54.0	15.0	0.277778	NM_003246	A8K6H4|B4E3J7|B9EGH6|Q15667|Q59E99	Silent	SNP	ENST00000260356.5	37	CCDS32194.1																																																																																			C|0.975;T|0.025	0.025	strong		0.537	THBS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257831.2	NM_003246	
PNLIPRP3	119548	hgsc.bcm.edu	37	10	118231317	118231317	+	Silent	SNP	C	C	T			TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr10:118231317C>T	ENST00000369230.3	+	10	1244	c.1098C>T	c.(1096-1098)agC>agT	p.S366S		NM_001011709.2	NP_001011709.2	Q17RR3	LIPR3_HUMAN	pancreatic lipase-related protein 3	366	PLAT.				lipid catabolic process (GO:0016042)	extracellular region (GO:0005576)	triglyceride lipase activity (GO:0004806)			breast(3)|central_nervous_system(1)|cervix(1)|endometrium(1)|kidney(1)|large_intestine(9)|lung(29)|ovary(2)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	50				all cancers(201;0.0131)		TCAGTGGAAGCGAAGTCACTC	0.453																																					p.S366S		Atlas-SNP	.											.	PNLIPRP3	101	.	0			c.C1098T						PASS	.						203.0	209.0	207.0					10																	118231317		2203	4300	6503	SO:0001819	synonymous_variant	119548	exon10			TGGAAGCGAAGTC	BC015840	CCDS31292.1	10q26.12	2014-03-14			ENSG00000203837	ENSG00000203837	3.1.1.3		23492	protein-coding gene	gene with protein product							Standard	NM_001011709		Approved		uc001lcl.4	Q17RR3	OTTHUMG00000019100	ENST00000369230.3:c.1098C>T	10.37:g.118231317C>T		233.0	0.0	0		200.0	86.0	0.43	NM_001011709		Silent	SNP	ENST00000369230.3	37	CCDS31292.1																																																																																			.	.	none		0.453	PNLIPRP3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050520.1	XM_058404	
ALK	238	hgsc.bcm.edu	37	2	30143499	30143499	+	Silent	SNP	G	G	C	rs4358080	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr2:30143499G>C	ENST00000389048.3	-	1	933	c.27C>G	c.(25-27)ctC>ctG	p.L9L	ALK_ENST00000431873.1_Silent_p.L9L	NM_004304.4	NP_004295.2	Q9UM73	ALK_HUMAN	anaplastic lymphoma receptor tyrosine kinase	9					activation of MAPK activity (GO:0000187)|cell proliferation (GO:0008283)|neuron development (GO:0048666)|NIK/NF-kappaB signaling (GO:0038061)|peptidyl-tyrosine phosphorylation (GO:0018108)|phosphorylation (GO:0016310)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|protein autophosphorylation (GO:0046777)|regulation of apoptotic process (GO:0042981)|signal transduction (GO:0007165)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)	extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|protein complex (GO:0043234)	ATP binding (GO:0005524)|NF-kappaB-inducing kinase activity (GO:0004704)|protein tyrosine kinase activity (GO:0004713)|transmembrane receptor protein tyrosine kinase activity (GO:0004714)		ATIC/ALK(24)|FN1/ALK(2)|C2orf44/ALK(2)|TPM3/ALK(33)|KLC1/ALK(2)|VCL/ALK(4)|TPM4/ALK(12)|KIF5B/ALK(8)|RANBP2/ALK(34)|SQSTM1/ALK(2)|EML4/ALK(543)|PPFIBP1/ALK(3)|SEC31A/ALK(3)|NPM1/ALK(632)|CLTC/ALK(44)|CARS/ALK(5)|MSN/ALK(6)|TFG/ALK(9)	NS(2)|autonomic_ganglia(198)|breast(8)|central_nervous_system(2)|cervix(1)|endometrium(11)|haematopoietic_and_lymphoid_tissue(7)|kidney(4)|large_intestine(25)|lung(61)|ovary(6)|pancreas(1)|prostate(2)|skin(5)|soft_tissue(3)|stomach(2)|thyroid(2)	340	Acute lymphoblastic leukemia(172;0.155)				Adenosine triphosphate(DB00171)|Crizotinib(DB08865)	GCAGCGGCAGGAGCCACAGGA	0.736			"""T, Mis, A"""	"""NPM1, TPM3, TFG, TPM4, ATIC, CLTC, MSN, ALO17, CARS, EML4, KIF5B, C2orf22"""	"""ALCL, NSCLC, Neuroblastoma"""	neuroblastoma			Neuroblastoma, Familial Clustering of;Congenital Central Hypoventilation Syndrome				C|||	4476	0.89377	0.8003	0.938	5008	,	,		12200	0.998		0.8837	False		,,,				2504	0.8916				p.L9L		Atlas-SNP	.	yes	Dom	yes	Familial neuroblastoma	2	2p23	238	anaplastic lymphoma kinase (Ki-1)		"""L, E, M"""	.	ALK	533	.	0			c.C27G						PASS	.	C		2838,380		1249,340,20	3.0	5.0	4.0		27	2.1	1.0	2	dbSNP_111	4	6073,509		2805,463,23	no	coding-synonymous	ALK	NM_004304.4		4054,803,43	CC,CG,GG		7.7332,11.8086,9.0714		9/1621	30143499	8911,889	1609	3291	4900	SO:0001819	synonymous_variant	238	exon1	Familial Cancer Database	Familial Neuroblastoma;CCHS, Ondine Curse, incl. Ondine-Hirschsprung Disease	CGGCAGGAGCCAC	D45915	CCDS33172.1	2p23	2014-09-17	2008-01-23		ENSG00000171094	ENSG00000171094		"""CD molecules"""	427	protein-coding gene	gene with protein product		105590	"""anaplastic lymphoma kinase (Ki-1)"""			8122112	Standard	NM_004304		Approved	CD246	uc002rmy.3	Q9UM73	OTTHUMG00000152034	ENST00000389048.3:c.27C>G	2.37:g.30143499G>C		0.0	0.0	.		4.0	4.0	1	NM_004304	Q4ZFX9|Q53QQ6|Q53RZ4|Q59FI3|Q9Y4K6	Silent	SNP	ENST00000389048.3	37	CCDS33172.1																																																																																			G|0.120;C|0.880	0.880	strong		0.736	ALK-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000324994.1	NM_004304	
IL12B	3593	hgsc.bcm.edu	37	5	158750329	158750329	+	Missense_Mutation	SNP	C	C	T	rs3213096	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr5:158750329C>T	ENST00000231228.2	-	3	552	c.97G>A	c.(97-99)Gta>Ata	p.V33I		NM_002187.2	NP_002178.2	P29460	IL12B_HUMAN	interleukin 12B	33	Ig-like C2-type.		V -> I (in dbSNP:rs3213096). {ECO:0000269|Ref.5}.		cell cycle arrest (GO:0007050)|cell migration (GO:0016477)|cellular response to interferon-gamma (GO:0071346)|cellular response to lipopolysaccharide (GO:0071222)|defense response to Gram-negative bacterium (GO:0050829)|defense response to protozoan (GO:0042832)|defense response to virus (GO:0051607)|interferon-gamma biosynthetic process (GO:0042095)|natural killer cell activation (GO:0030101)|natural killer cell activation involved in immune response (GO:0002323)|negative regulation of growth of symbiont in host (GO:0044130)|negative regulation of inflammatory response to antigenic stimulus (GO:0002862)|negative regulation of interleukin-10 production (GO:0032693)|negative regulation of interleukin-17 production (GO:0032700)|negative regulation of smooth muscle cell proliferation (GO:0048662)|positive regulation of activated T cell proliferation (GO:0042104)|positive regulation of activation of JAK2 kinase activity (GO:0010535)|positive regulation of cell adhesion (GO:0045785)|positive regulation of defense response to virus by host (GO:0002230)|positive regulation of granulocyte macrophage colony-stimulating factor production (GO:0032725)|positive regulation of inflammatory response (GO:0050729)|positive regulation of interferon-gamma biosynthetic process (GO:0045078)|positive regulation of interferon-gamma production (GO:0032729)|positive regulation of interleukin-10 production (GO:0032733)|positive regulation of interleukin-12 production (GO:0032735)|positive regulation of interleukin-17 production (GO:0032740)|positive regulation of lymphocyte proliferation (GO:0050671)|positive regulation of memory T cell differentiation (GO:0043382)|positive regulation of mononuclear cell proliferation (GO:0032946)|positive regulation of natural killer cell activation (GO:0032816)|positive regulation of natural killer cell mediated cytotoxicity directed against tumor cell target (GO:0002860)|positive regulation of natural killer cell proliferation (GO:0032819)|positive regulation of NF-kappaB import into nucleus (GO:0042346)|positive regulation of NK T cell activation (GO:0051135)|positive regulation of NK T cell proliferation (GO:0051142)|positive regulation of osteoclast differentiation (GO:0045672)|positive regulation of smooth muscle cell apoptotic process (GO:0034393)|positive regulation of T cell mediated cytotoxicity (GO:0001916)|positive regulation of T cell proliferation (GO:0042102)|positive regulation of T-helper 1 type immune response (GO:0002827)|positive regulation of T-helper 17 cell lineage commitment (GO:2000330)|positive regulation of T-helper 17 type immune response (GO:2000318)|positive regulation of tissue remodeling (GO:0034105)|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 Stat4 protein (GO:0042520)|positive regulation of tyrosine phosphorylation of Stat5 protein (GO:0042523)|regulation of cytokine biosynthetic process (GO:0042035)|regulation of tyrosine phosphorylation of Stat1 protein (GO:0042510)|response to UV-B (GO:0010224)|sensory perception of pain (GO:0019233)|sexual reproduction (GO:0019953)|T-helper 1 type immune response (GO:0042088)|T-helper cell differentiation (GO:0042093)	cytoplasm (GO:0005737)|extracellular space (GO:0005615)|interleukin-12 complex (GO:0043514)|interleukin-23 complex (GO:0070743)|membrane (GO:0016020)	cytokine receptor activity (GO:0004896)|identical protein binding (GO:0042802)|interleukin-12 alpha subunit binding (GO:0042164)|interleukin-12 receptor binding (GO:0005143)|protein heterodimerization activity (GO:0046982)			cervix(1)|endometrium(1)|large_intestine(5)|lung(4)	11	Renal(175;0.00196)	Medulloblastoma(196;0.0354)|all_neural(177;0.138)	Kidney(164;7.83e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000525)			TCCAATTCTACGACATAAACT	0.502													C|||	19	0.00379393	0.0	0.0043	5008	,	,		20539	0.0		0.0099	False		,,,				2504	0.0061				p.V33I		Atlas-SNP	.											.	IL12B	30	.	0			c.G97A						PASS	.	C	ILE/VAL	7,4399	12.9+/-30.5	0,7,2196	61.0	56.0	58.0		97	5.2	0.9	5	dbSNP_106	58	49,8551	31.2+/-83.2	0,49,4251	yes	missense	IL12B	NM_002187.2	29	0,56,6447	TT,TC,CC		0.5698,0.1589,0.4306	benign	33/329	158750329	56,12950	2203	4300	6503	SO:0001583	missense	3593	exon3			ATTCTACGACATA	M65290	CCDS4346.1	5q31.1-q33.1	2014-09-17	2014-04-04		ENSG00000113302	ENSG00000113302		"""Interleukins and interleukin receptors"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	5970	protein-coding gene	gene with protein product	"""natural killer cell stimulatory factor-2"", ""cytotoxic lymphocyte maturation factor 2, p40"", ""interleukin 12, p40"", ""natural killer cell stimulatory factor, 40 kD subunit"", ""interleukin-12 beta chain"", ""IL12, subunit p40"""	161561	"""interleukin 12B (natural killer cell stimulatory factor 2, cytotoxic lymphocyte maturation factor 2, p40)"""	NKSF2		1673147	Standard	NM_002187		Approved	CLMF, IL-12B, NKSF, CLMF2	uc003lxr.1	P29460	OTTHUMG00000130307	ENST00000231228.2:c.97G>A	5.37:g.158750329C>T	ENSP00000231228:p.Val33Ile	57.0	0.0	0		63.0	29.0	0.460317	NM_002187		Missense_Mutation	SNP	ENST00000231228.2	37	CCDS4346.1	13	0.005952380952380952	0	0.0	3	0.008287292817679558	0	0.0	10	0.013192612137203167	C	9.248	1.040122	0.19669	0.001589	0.005698	ENSG00000113302	ENST00000231228	T	0.22743	1.94	6.02	5.16	0.70880	Immunoglobulin-like (1);Immunoglobulin-like fold (1);	0.054974	0.64402	D	0.000001	T	0.20210	0.0486	M	0.79475	2.455	0.45791	D	0.998676	B	0.09022	0.002	B	0.12156	0.007	T	0.03473	-1.1033	10	0.46703	T	0.11	-3.6912	11.4605	0.50208	0.0:0.9177:0.0:0.0823	rs3213096;rs17056679;rs17875310;rs52806839;rs56592501;rs3213096	33	P29460	IL12B_HUMAN	I	33	ENSP00000231228:V33I	ENSP00000231228:V33I	V	-	1	0	IL12B	158682907	0.822000	0.29219	0.877000	0.34402	0.087000	0.18053	1.240000	0.32731	1.568000	0.49683	-0.137000	0.14449	GTA	C|0.994;T|0.006	0.006	strong		0.502	IL12B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252652.2	NM_002187	
ZNF16	7564	hgsc.bcm.edu	37	8	146157265	146157265	+	Missense_Mutation	SNP	C	C	T	rs80044147	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr8:146157265C>T	ENST00000276816.4	-	4	1094	c.908G>A	c.(907-909)aGc>aAc	p.S303N	ZNF16_ENST00000394909.2_Missense_Mutation_p.S303N	NM_001029976.2	NP_001025147.2	P17020	ZNF16_HUMAN	zinc finger protein 16	303	Required for nuclear localization.				cell cycle (GO:0007049)|cell division (GO:0051301)|cellular response to sodium dodecyl sulfate (GO:0072707)|negative regulation of apoptotic process (GO:0043066)|positive regulation of cell cycle phase transition (GO:1901989)|positive regulation of cell division (GO:0051781)|positive regulation of cell proliferation (GO:0008284)|positive regulation of erythrocyte differentiation (GO:0045648)|positive regulation of kinase activity (GO:0033674)|positive regulation of megakaryocyte differentiation (GO:0045654)|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(1)|kidney(4)|large_intestine(5)|lung(9)|ovary(5)|prostate(1)|skin(1)|urinary_tract(1)	29	all_cancers(97;8.72e-12)|all_epithelial(106;1.07e-10)|Lung NSC(106;7.18e-05)|all_lung(105;0.00021)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155)	Acute lymphoblastic leukemia(644;0.136)	Epithelial(56;3.45e-38)|all cancers(56;3.04e-33)|BRCA - Breast invasive adenocarcinoma(115;0.0424)|Colorectal(110;0.055)	GBM - Glioblastoma multiforme(99;0.02)|KIRC - Kidney renal clear cell carcinoma(644;0.0486)		CGAGTTCTGGCTGAAGGCTTT	0.478													C|||	5	0.000998403	0.0008	0.0	5008	,	,		20412	0.0		0.004	False		,,,				2504	0.0				p.S303N		Atlas-SNP	.											.	ZNF16	80	.	0			c.G908A						PASS	.	C	ASN/SER,ASN/SER	9,4397	15.5+/-35.6	0,9,2194	72.0	72.0	72.0		908,908	3.1	1.0	8	dbSNP_132	72	31,8569	22.2+/-67.0	0,31,4269	yes	missense,missense	ZNF16	NM_001029976.2,NM_006958.2	46,46	0,40,6463	TT,TC,CC		0.3605,0.2043,0.3076	benign,benign	303/683,303/683	146157265	40,12966	2203	4300	6503	SO:0001583	missense	7564	exon3			TTCTGGCTGAAGG	X52340	CCDS6437.1	8q24	2013-01-08	2006-05-10		ENSG00000170631	ENSG00000170631		"""Zinc fingers, C2H2-type"""	12947	protein-coding gene	gene with protein product		601262	"""zinc finger protein 16 (KOX 9)"""				Standard	NM_006958		Approved	KOX9	uc003zeu.3	P17020	OTTHUMG00000165253	ENST00000276816.4:c.908G>A	8.37:g.146157265C>T	ENSP00000276816:p.Ser303Asn	137.0	0.0	0		159.0	48.0	0.301887	NM_006958	B3KXM4|D3DWP2|Q45SH7|Q96FG0|Q9NRA4	Missense_Mutation	SNP	ENST00000276816.4	37	CCDS6437.1	3	0.0013736263736263737	0	0.0	0	0.0	0	0.0	3	0.00395778364116095	C	8.817	0.936690	0.18206	0.002043	0.003605	ENSG00000170631	ENST00000276816;ENST00000394909	T;T	0.19394	2.15;2.15	4.02	3.11	0.35812	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.11110	0.0271	N	0.17594	0.5	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.12268	-1.0554	9	0.42905	T	0.14	.	3.0488	0.06162	0.1772:0.5474:0.1724:0.103	.	303	P17020	ZNF16_HUMAN	N	303	ENSP00000276816:S303N;ENSP00000378369:S303N	ENSP00000276816:S303N	S	-	2	0	ZNF16	146128069	0.000000	0.05858	1.000000	0.80357	0.988000	0.76386	-1.354000	0.02614	2.056000	0.61249	0.563000	0.77884	AGC	C|0.998;T|0.002	0.002	strong		0.478	ZNF16-002	KNOWN	alternative_5_UTR|basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000382978.1	NM_006958	
KRTAP1-1	81851	hgsc.bcm.edu	37	17	39197304	39197304	+	Missense_Mutation	SNP	T	T	C			TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr17:39197304T>C	ENST00000306271.4	-	1	409	c.346A>G	c.(346-348)Atc>Gtc	p.I116V		NM_030967.2	NP_112229.1	Q07627	KRA11_HUMAN	keratin associated protein 1-1	116						keratin filament (GO:0045095)		p.I116V(1)		NS(2)|endometrium(2)|kidney(5)|lung(4)|prostate(1)	14		Breast(137;0.000496)	STAD - Stomach adenocarcinoma(17;0.000371)			CACCACCTGATACGGGTGCTC	0.662																																					p.I116V		Atlas-SNP	.											KRTAP1-1,NS,malignant_melanoma,0,1	KRTAP1-1	23	1	1	Substitution - Missense(1)	NS(1)	c.A346G						PASS	.						22.0	27.0	25.0					17																	39197304		2019	4148	6167	SO:0001583	missense	81851	exon1			ACCTGATACGGGT	AJ406926	CCDS42324.1	17q21.2	2014-06-05			ENSG00000188581	ENSG00000188581		"""Keratin associated proteins"""	16772	protein-coding gene	gene with protein product		608819				11279113	Standard	NM_030967		Approved	KAP1.1B, HB2A, KAP1.1, KAP1.1A	uc002hvw.1	Q07627	OTTHUMG00000133592	ENST00000306271.4:c.346A>G	17.37:g.39197304T>C	ENSP00000305975:p.Ile116Val	156.0	0.0	0		135.0	13.0	0.0962963	NM_030967	A6NC32|Q96S60|Q96S67	Missense_Mutation	SNP	ENST00000306271.4	37	CCDS42324.1	.	.	.	.	.	.	.	.	.	.	T	8.173	0.792133	0.16258	.	.	ENSG00000188581	ENST00000306271;ENST00000543328	T	0.29655	1.56	4.28	-1.23	0.09465	.	.	.	.	.	T	0.12135	0.0295	N	0.03253	-0.375	0.09310	N	1	B	0.02656	0.0	B	0.06405	0.002	T	0.34079	-0.9843	9	0.20046	T	0.44	.	9.4726	0.38851	0.0:0.573:0.0:0.427	.	116	Q07627	KRA11_HUMAN	V	116;106	ENSP00000305975:I116V	ENSP00000305975:I116V	I	-	1	0	KRTAP1-1	36450830	0.132000	0.22450	0.024000	0.17045	0.516000	0.34256	0.017000	0.13399	-0.199000	0.10317	0.529000	0.55759	ATC	.	.	none		0.662	KRTAP1-1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257696.1	NM_030967	
ZNF345	25850	hgsc.bcm.edu	37	19	37369032	37369032	+	Missense_Mutation	SNP	G	G	C			TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr19:37369032G>C	ENST00000529555.1	+	2	2088	c.1300G>C	c.(1300-1302)Gct>Cct	p.A434P	ZNF345_ENST00000420450.1_Missense_Mutation_p.A434P|ZNF345_ENST00000432005.2_Intron|ZNF345_ENST00000589046.1_Missense_Mutation_p.A434P|ZNF345_ENST00000526123.1_Intron			Q14585	ZN345_HUMAN	zinc finger protein 345	434					negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|regulation of transcription from RNA polymerase III promoter (GO:0006359)|regulation of transcription, DNA-templated (GO:0006355)|transcription from RNA polymerase II promoter (GO:0006366)|transcription from RNA polymerase III promoter (GO:0006383)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(1)|endometrium(1)|kidney(1)|large_intestine(13)|lung(5)|ovary(2)|prostate(1)	24	Esophageal squamous(110;0.183)		COAD - Colon adenocarcinoma(19;0.114)|Colorectal(19;0.177)			GTGTGGGAAGGCTTTTTATAG	0.423																																					p.A434P		Atlas-SNP	.											.	ZNF345	68	.	0			c.G1300C						PASS	.						79.0	81.0	80.0					19																	37369032		2203	4300	6503	SO:0001583	missense	25850	exon4			GGGAAGGCTTTTT	X78933	CCDS12497.1	19q13.12	2013-01-08			ENSG00000251247	ENSG00000251247		"""Zinc fingers, C2H2-type"""	16367	protein-coding gene	gene with protein product						7865130	Standard	NM_003419		Approved	HZF10	uc002oey.4	Q14585	OTTHUMG00000048162	ENST00000529555.1:c.1300G>C	19.37:g.37369032G>C	ENSP00000431202:p.Ala434Pro	97.0	0.0	0		101.0	56.0	0.554455	NM_001242476		Missense_Mutation	SNP	ENST00000529555.1	37	CCDS12497.1	.	.	.	.	.	.	.	.	.	.	G	10.40	1.340040	0.24339	.	.	ENSG00000251247	ENST00000420450;ENST00000529555;ENST00000344705	T;T	0.14391	2.51;2.51	3.0	-0.576	0.11731	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.13586	0.0329	M	0.64260	1.97	0.09310	N	1	B	0.26041	0.14	B	0.29663	0.105	T	0.35549	-0.9784	9	0.72032	D	0.01	.	3.2328	0.06754	0.3529:0.0:0.4485:0.1985	.	434	Q14585	ZN345_HUMAN	P	434;434;198	ENSP00000431216:A434P;ENSP00000431202:A434P	ENSP00000442320:A198P	A	+	1	0	ZNF345	42060872	0.000000	0.05858	0.250000	0.24296	0.522000	0.34438	-1.705000	0.01896	-0.091000	0.12440	0.655000	0.94253	GCT	.	.	none		0.423	ZNF345-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000388258.1		
PTCH2	8643	hgsc.bcm.edu	37	1	45294295	45294295	+	Missense_Mutation	SNP	C	C	T			TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr1:45294295C>T	ENST00000372192.3	-	12	1603	c.1473G>A	c.(1471-1473)atG>atA	p.M491I	PTCH2_ENST00000447098.2_Missense_Mutation_p.M491I	NM_003738.4	NP_003729.3	Q9Y6C5	PTC2_HUMAN	patched 2	491	SSD. {ECO:0000255|PROSITE- ProRule:PRU00199}.				epidermis development (GO:0008544)|hair cycle (GO:0042633)|negative regulation of smoothened signaling pathway (GO:0045879)|signal transduction (GO:0007165)	integral component of membrane (GO:0016021)	hedgehog family protein binding (GO:0097108)|hedgehog receptor activity (GO:0008158)|smoothened binding (GO:0005119)			NS(2)|breast(6)|central_nervous_system(3)|cervix(1)|endometrium(5)|kidney(2)|large_intestine(6)|lung(19)|ovary(1)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)	50	Acute lymphoblastic leukemia(166;0.155)					GACACTCGCCCATGCGCTCCT	0.632									Basal Cell Nevus syndrome																												p.M491I		Atlas-SNP	.											.	PTCH2	96	.	0			c.G1473A						PASS	.						71.0	55.0	60.0					1																	45294295		2202	4300	6502	SO:0001583	missense	8643	exon12	Familial Cancer Database	Gorlin syndrome, Gorlin-Golz syndrome, Naevoid Basal Cell Carcinoma syndrome, NBCCS	CTCGCCCATGCGC	AF091501	CCDS516.1, CCDS53312.1	1p34.1	2010-06-24	2010-06-24		ENSG00000117425	ENSG00000117425			9586	protein-coding gene	gene with protein product		603673	"""patched (Drosophila) homolog 2"", ""patched homolog 2 (Drosophila)"""			9811851, 9931336	Standard	NM_003738		Approved		uc010olf.2	Q9Y6C5	OTTHUMG00000008490	ENST00000372192.3:c.1473G>A	1.37:g.45294295C>T	ENSP00000361266:p.Met491Ile	102.0	0.0	0		67.0	4.0	0.0597015	NM_001166292	O95341|O95856|Q53Z57|Q5QP87|Q6UX14	Missense_Mutation	SNP	ENST00000372192.3	37	CCDS516.1	.	.	.	.	.	.	.	.	.	.	C	13.56	2.275107	0.40194	.	.	ENSG00000117425	ENST00000447098;ENST00000372192	D;D	0.94184	-3.37;-3.37	4.47	-3.0	0.05480	Sterol-sensing domain (1);	0.196196	0.35320	N	0.003287	T	0.79776	0.4504	N	0.05467	-0.045	0.29800	N	0.832513	B;B	0.02656	0.0;0.0	B;B	0.09377	0.004;0.003	T	0.68228	-0.5464	10	0.18276	T	0.48	-34.0928	7.4614	0.27298	0.1257:0.1735:0.0:0.7008	.	491;491	Q9Y6C5-2;Q9Y6C5	.;PTC2_HUMAN	I	491	ENSP00000389703:M491I;ENSP00000361266:M491I	ENSP00000361266:M491I	M	-	3	0	PTCH2	45066882	0.000000	0.05858	0.640000	0.29408	0.929000	0.56500	-3.137000	0.00588	-0.491000	0.06697	0.462000	0.41574	ATG	.	.	none		0.632	PTCH2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000023428.4	NM_003738	
BCOR	54880	hgsc.bcm.edu	37	X	39932808	39932808	+	Silent	SNP	G	G	A	rs144606152	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chrX:39932808G>A	ENST00000378444.4	-	4	2019	c.1791C>T	c.(1789-1791)caC>caT	p.H597H	BCOR_ENST00000397354.3_Silent_p.H597H|BCOR_ENST00000342274.4_Silent_p.H597H|BCOR_ENST00000378455.4_Silent_p.H597H	NM_001123385.1	NP_001116857.1	Q6W2J9	BCOR_HUMAN	BCL6 corepressor	597					heart development (GO:0007507)|histone H2A monoubiquitination (GO:0035518)|negative regulation of bone mineralization (GO:0030502)|negative regulation of histone H3-K36 methylation (GO:0000415)|negative regulation of histone H3-K4 methylation (GO:0051572)|negative regulation of tooth mineralization (GO:0070171)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|odontogenesis (GO:0042476)|palate development (GO:0060021)|specification of axis polarity (GO:0065001)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	heat shock protein binding (GO:0031072)|histone deacetylase binding (GO:0042826)|transcription corepressor activity (GO:0003714)|transcription factor binding (GO:0008134)|transcription regulatory region DNA binding (GO:0044212)			breast(4)|central_nervous_system(11)|cervix(1)|endometrium(24)|eye(6)|haematopoietic_and_lymphoid_tissue(33)|kidney(2)|large_intestine(11)|lung(22)|ovary(2)|pancreas(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(3)|urinary_tract(2)	126						GCTGGCCCACGTGCTGAATAA	0.607			"""F, N, S, T"""	RARA	"""retinoblastoma, AML, APL(translocation)"""		oculo-facio-cardio-dental genetic						G|||	63	0.0166887	0.0015	0.0159	3775	,	,		12801	0.0		0.0437	False		,,,				2504	0.0061				p.H597H		Atlas-SNP	.		Rec	yes		X	Xp11.4	54880	BCL6 corepressor	yes		.	BCOR	351	.	0			c.C1791T						PASS	.	G	,,,	22,3811		0,19,3,1612,568	68.0	65.0	66.0		1791,1791,1791,1791	-1.4	0.9	X	dbSNP_134	66	372,6356		5,260,102,2163,1770	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	BCOR	NM_001123383.1,NM_001123384.1,NM_001123385.1,NM_017745.5	,,,	5,279,105,3775,2338	AA,AG,A,GG,G		5.5291,0.574,3.7307	,,,	597/1722,597/1704,597/1756,597/1722	39932808	394,10167	2202	4300	6502	SO:0001819	synonymous_variant	54880	exon4			GCCCACGTGCTGA	AF317391	CCDS14250.1, CCDS48092.1, CCDS48093.1	Xp11.4	2014-09-17	2010-06-10		ENSG00000183337	ENSG00000183337		"""Ankyrin repeat domain containing"""	20893	protein-coding gene	gene with protein product		300485	"""BCL6 co-repressor"""			10898795	Standard	NM_017745		Approved	FLJ20285, KIAA1575	uc004den.4	Q6W2J9	OTTHUMG00000024100	ENST00000378444.4:c.1791C>T	X.37:g.39932808G>A		90.0	0.0	0		38.0	36.0	0.947368	NM_001123385	D3DWB3|D3DWB4|Q29RF6|Q6P4B6|Q7Z2K7|Q8TEB4|Q96DB3|Q9H232|Q9H233|Q9HCJ7|Q9NXF2	Silent	SNP	ENST00000378444.4	37	CCDS48093.1																																																																																			G|0.963;A|0.037	0.037	strong		0.607	BCOR-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000060666.2	NM_017745	
ARAP2	116984	hgsc.bcm.edu	37	4	36230634	36230634	+	Missense_Mutation	SNP	G	G	A	rs141442791	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr4:36230634G>A	ENST00000303965.4	-	2	964	c.475C>T	c.(475-477)Cca>Tca	p.P159S		NM_015230.3	NP_056045.2	Q8WZ64	ARAP2_HUMAN	ArfGAP with RhoGAP domain, ankyrin repeat and PH domain 2	159					regulation of ARF GTPase activity (GO:0032312)|regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)	ARF GTPase activator activity (GO:0008060)|phosphatidylinositol-3,4,5-trisphosphate binding (GO:0005547)|zinc ion binding (GO:0008270)			breast(2)|central_nervous_system(2)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(22)|liver(1)|lung(32)|ovary(2)|pancreas(1)|prostate(3)|skin(7)|urinary_tract(1)	82						TTCAGGTGTGGTTCCTCTGCA	0.393													G|||	7	0.00139776	0.0	0.0014	5008	,	,		20594	0.0		0.006	False		,,,				2504	0.0				p.P159S		Atlas-SNP	.											.	ARAP2	210	.	0			c.C475T						PASS	.	G	SER/PRO	3,4403	4.2+/-10.8	0,3,2200	69.0	65.0	67.0		475	-0.6	0.0	4	dbSNP_134	67	16,8584	11.9+/-42.8	0,16,4284	yes	missense	ARAP2	NM_015230.3	74	0,19,6484	AA,AG,GG		0.186,0.0681,0.1461	benign	159/1705	36230634	19,12987	2203	4300	6503	SO:0001583	missense	116984	exon2			GGTGTGGTTCCTC	AF411982	CCDS3441.1	4p15.1	2013-01-11	2008-09-22	2008-09-22	ENSG00000047365	ENSG00000047365		"""ADP-ribosylation factor GTPase activating proteins"", ""Sterile alpha motif (SAM) domain containing"", ""Pleckstrin homology (PH) domain containing"", ""Ankyrin repeat domain containing"""	16924	protein-coding gene	gene with protein product		606645	"""centaurin, delta 1"""	CENTD1			Standard	NM_015230		Approved	PARX	uc003gsq.2	Q8WZ64	OTTHUMG00000097811	ENST00000303965.4:c.475C>T	4.37:g.36230634G>A	ENSP00000302895:p.Pro159Ser	82.0	0.0	0		94.0	43.0	0.457447	NM_015230	Q4W5D2|Q7Z2L5|Q96L70|Q96P49|Q9Y4E4	Missense_Mutation	SNP	ENST00000303965.4	37	CCDS3441.1	2	9.157509157509158E-4	0	0.0	0	0.0	0	0.0	2	0.002638522427440633	G	5.262	0.233857	0.09969	6.81E-4	0.00186	ENSG00000047365	ENST00000303965	T	0.62639	0.01	5.5	-0.558	0.11796	.	0.647728	0.14546	N	0.312977	T	0.34395	0.0896	N	0.14661	0.345	0.09310	N	1	B;B	0.06786	0.001;0.001	B;B	0.04013	0.0;0.001	T	0.12889	-1.0530	10	0.16420	T	0.52	.	3.6174	0.08082	0.3113:0.0:0.427:0.2617	.	89;159	A7E2A5;Q8WZ64	.;ARAP2_HUMAN	S	159	ENSP00000302895:P159S	ENSP00000302895:P159S	P	-	1	0	ARAP2	35907029	0.888000	0.30383	0.021000	0.16686	0.262000	0.26303	1.029000	0.30140	0.010000	0.14839	0.650000	0.86243	CCA	G|0.998;A|0.002	0.002	strong		0.393	ARAP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000215074.2	NM_015230	
RP1	6101	hgsc.bcm.edu	37	8	55541738	55541738	+	Missense_Mutation	SNP	A	A	C	rs147009600	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr8:55541738A>C	ENST00000220676.1	+	4	5444	c.5296A>C	c.(5296-5298)Aat>Cat	p.N1766H		NM_006269.1	NP_006260.1	P56715	RP1_HUMAN	retinitis pigmentosa 1 (autosomal dominant)	1766					axoneme assembly (GO:0035082)|cellular response to light stimulus (GO:0071482)|intracellular signal transduction (GO:0035556)|photoreceptor cell development (GO:0042461)|photoreceptor cell maintenance (GO:0045494)|photoreceptor cell outer segment organization (GO:0035845)|phototransduction, visible light (GO:0007603)|retinal cone cell development (GO:0046549)|retinal rod cell development (GO:0046548)|visual perception (GO:0007601)	axoneme (GO:0005930)|microtubule (GO:0005874)|microtubule associated complex (GO:0005875)|photoreceptor connecting cilium (GO:0032391)|photoreceptor inner segment (GO:0001917)|photoreceptor outer segment (GO:0001750)	microtubule binding (GO:0008017)			NS(4)|breast(6)|central_nervous_system(2)|cervix(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(4)|kidney(7)|large_intestine(29)|lung(69)|ovary(6)|pancreas(1)|prostate(9)|skin(17)|upper_aerodigestive_tract(3)|urinary_tract(2)	169		all_lung(136;0.0831)|Lung NSC(129;0.109)|all_epithelial(80;0.123)	OV - Ovarian serous cystadenocarcinoma(7;4.4e-07)|Epithelial(17;3.37e-05)|all cancers(17;0.000285)			CATGTGTGGCAATGCAGACAC	0.438													A|||	2	0.000399361	0.0	0.0	5008	,	,		23417	0.0		0.0	False		,,,				2504	0.002				p.N1766H	Colon(91;1014 1389 7634 14542 40420)	Atlas-SNP	.											.	RP1	429	.	0			c.A5296C						PASS	.	A	HIS/ASN	0,4406		0,0,2203	95.0	92.0	93.0		5296	3.5	0.9	8	dbSNP_134	93	6,8594	5.0+/-18.6	0,6,4294	yes	missense	RP1	NM_006269.1	68	0,6,6497	CC,CA,AA		0.0698,0.0,0.0461	benign	1766/2157	55541738	6,13000	2203	4300	6503	SO:0001583	missense	6101	exon4			TGTGGCAATGCAG	AF146592	CCDS6160.1	8q12.1	2013-01-08				ENSG00000104237			10263	protein-coding gene	gene with protein product		603937				1783394	Standard	NM_006269		Approved	DCDC4A	uc003xsd.1	P56715		ENST00000220676.1:c.5296A>C	8.37:g.55541738A>C	ENSP00000220676:p.Asn1766His	184.0	0.0	0		100.0	15.0	0.15	NM_006269		Missense_Mutation	SNP	ENST00000220676.1	37	CCDS6160.1	.	.	.	.	.	.	.	.	.	.	A	8.388	0.839077	0.16891	0.0	6.98E-4	ENSG00000104237	ENST00000220676	T	0.47177	0.85	5.93	3.47	0.39725	.	0.241833	0.28977	N	0.013529	T	0.35941	0.0949	L	0.33485	1.01	0.26317	N	0.977733	B	0.18461	0.028	B	0.15870	0.014	T	0.16041	-1.0416	10	0.30078	T	0.28	.	12.782	0.57483	0.6029:0.397:0.0:0.0	.	1766	P56715	RP1_HUMAN	H	1766	ENSP00000220676:N1766H	ENSP00000220676:N1766H	N	+	1	0	RP1	55704291	0.998000	0.40836	0.854000	0.33618	0.698000	0.40448	3.291000	0.51764	0.454000	0.26884	0.533000	0.62120	AAT	A|0.999;C|0.001	0.001	strong		0.438	RP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000378532.2	NM_006269	
PPHLN1	51535	hgsc.bcm.edu	37	12	42839923	42839923	+	Missense_Mutation	SNP	G	G	A	rs201876048	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr12:42839923G>A	ENST00000395568.2	+	12	1265	c.1181G>A	c.(1180-1182)cGt>cAt	p.R394H	PPHLN1_ENST00000317560.9_Intron|PPHLN1_ENST00000432191.2_Missense_Mutation_p.R370H|PPHLN1_ENST00000256678.8_Missense_Mutation_p.R299H	NM_016488.6	NP_057572.5	Q8NEY8	PPHLN_HUMAN	periphilin 1	394					keratinization (GO:0031424)	cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|intracellular membrane-bounded organelle (GO:0043231)|nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)			breast(5)|kidney(1)|large_intestine(4)|lung(2)|ovary(2)|stomach(1)|upper_aerodigestive_tract(1)	16	all_cancers(12;0.00049)|Breast(8;0.165)	Lung NSC(34;0.123)		GBM - Glioblastoma multiforme(48;0.0875)		aaacgggttcgtcggacgaca	0.622													G|||	3	0.000599042	0.0	0.0014	5008	,	,		11704	0.0		0.002	False		,,,				2504	0.0				p.R394H		Atlas-SNP	.											.	PPHLN1	101	.	0			c.G1181A						PASS	.	G	HIS/ARG,HIS/ARG	1,4325		0,1,2162	7.0	8.0	8.0		1109,1181	0.2	0.1	12		8	18,8426		0,18,4204	yes	missense,missense	PPHLN1	NM_001143787.1,NM_016488.6	29,29	0,19,6366	AA,AG,GG		0.2132,0.0231,0.1488	probably-damaging,probably-damaging	370/435,394/459	42839923	19,12751	2163	4222	6385	SO:0001583	missense	51535	exon12			GGGTTCGTCGGAC	AY157850	CCDS8741.1, CCDS31777.1, CCDS41773.1, CCDS44860.1, CCDS44861.1, CCDS55817.1	12q12	2006-10-24				ENSG00000134283			19369	protein-coding gene	gene with protein product		608150					Standard	NM_016488		Approved		uc001rng.1	Q8NEY8		ENST00000395568.2:c.1181G>A	12.37:g.42839923G>A	ENSP00000378935:p.Arg394His	92.0	0.0	0		93.0	47.0	0.505376	NM_016488	E9PAX8|Q86YT2|Q8IXN3|Q8TB09|Q96NB9|Q9NXL4|Q9P0P6|Q9P0R9	Missense_Mutation	SNP	ENST00000395568.2	37	CCDS31777.1	.	.	.	.	.	.	.	.	.	.	G	5.312	0.242935	0.10077	2.31E-4	0.002132	ENSG00000134283	ENST00000395568;ENST00000256678;ENST00000432191	.	.	.	0.158	0.158	0.14942	.	0.000000	0.85682	U	0.000000	T	0.12263	0.0298	N	0.02011	-0.69	0.09310	N	1	B;B;B;B	0.06786	0.001;0.001;0.001;0.0	B;B;B;B	0.01281	0.0;0.0;0.0;0.0	T	0.20706	-1.0267	8	0.87932	D	0	.	.	.	.	.	299;345;370;394	F8W6A0;B7Z695;Q8NEY8-3;Q8NEY8	.;.;.;PPHLN_HUMAN	H	394;299;370	.	ENSP00000256678:R299H	R	+	2	0	PPHLN1	41126190	0.328000	0.24687	0.148000	0.22405	0.150000	0.21749	0.251000	0.18257	0.202000	0.20498	0.205000	0.17691	CGT	.	.	weak		0.622	PPHLN1-010	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000404047.1	NM_201515	
GDPD5	81544	hgsc.bcm.edu	37	11	75150971	75150971	+	Silent	SNP	G	G	A	rs115438239	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr11:75150971G>A	ENST00000336898.3	-	15	2346	c.1509C>T	c.(1507-1509)gcC>gcT	p.A503A	GDPD5_ENST00000376282.3_Silent_p.A384A|GDPD5_ENST00000533805.1_Silent_p.A258A|GDPD5_ENST00000526177.1_Silent_p.A365A|GDPD5_ENST00000443276.2_3'UTR|GDPD5_ENST00000533784.1_Silent_p.A384A|GDPD5_ENST00000529721.1_Silent_p.A503A	NM_030792.6	NP_110419.5	Q8WTR4	GDPD5_HUMAN	glycerophosphodiester phosphodiesterase domain containing 5	503					cerebral cortex neuron differentiation (GO:0021895)|glycerol metabolic process (GO:0006071)|lipid metabolic process (GO:0006629)|negative regulation of Notch signaling pathway (GO:0045746)|neuron projection development (GO:0031175)|positive regulation of neuron differentiation (GO:0045666)|regulation of timing of cell differentiation (GO:0048505)|spinal cord motor neuron differentiation (GO:0021522)	cell projection (GO:0042995)|cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)	glycerophosphodiester phosphodiesterase activity (GO:0008889)			breast(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(3)|lung(6)|ovary(3)|skin(2)	20						AGACCAGGTCGGCAGTGACCC	0.612													G|||	10	0.00199681	0.0008	0.0	5008	,	,		19335	0.003		0.006	False		,,,				2504	0.0				p.A503A		Atlas-SNP	.											.	GDPD5	49	.	0			c.C1509T						PASS	.	G		2,4398	4.2+/-10.8	0,2,2198	124.0	101.0	109.0		1509	-7.7	0.7	11	dbSNP_132	109	27,8559	19.2+/-60.6	0,27,4266	no	coding-synonymous	GDPD5	NM_030792.6		0,29,6464	AA,AG,GG		0.3145,0.0455,0.2233		503/606	75150971	29,12957	2200	4293	6493	SO:0001819	synonymous_variant	81544	exon15			CAGGTCGGCAGTG	AF318377	CCDS8238.1	11q13.4-q13.5	2011-01-25				ENSG00000158555			28804	protein-coding gene	gene with protein product		609632				18667693, 17275818	Standard	NM_030792		Approved	PP1665, GDE2	uc001owp.4	Q8WTR4		ENST00000336898.3:c.1509C>T	11.37:g.75150971G>A		115.0	0.0	0		117.0	62.0	0.529915	NM_030792	Q49AQ5|Q6UX76|Q7Z4S0|Q8N781|Q8NCB7|Q8TB77	Silent	SNP	ENST00000336898.3	37	CCDS8238.1																																																																																			G|0.997;A|0.003	0.003	strong		0.612	GDPD5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000384409.1	NM_030792	
LVRN	206338	hgsc.bcm.edu	37	5	115351066	115351066	+	Silent	SNP	T	T	A			TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr5:115351066T>A	ENST00000357872.4	+	17	2692	c.2568T>A	c.(2566-2568)atT>atA	p.I856I	AQPEP_ENST00000515454.1_3'UTR	NM_173800.4	NP_776161.3	Q6Q4G3	AMPQ_HUMAN		856						integral component of membrane (GO:0016021)	metallopeptidase activity (GO:0008237)|zinc ion binding (GO:0008270)										AAGAAAAGATTCAACTTGCTT	0.343																																					p.I856I		Atlas-SNP	.											FLJ90650,caecum,carcinoma,0,1	.	.	1	0			c.T2568A						scavenged	.						91.0	87.0	88.0					5																	115351066		2202	4300	6502	SO:0001819	synonymous_variant	0	exon17			AAAGATTCAACTT																												ENST00000357872.4:c.2568T>A	5.37:g.115351066T>A		31.0	0.0	0		35.0	3.0	0.0857143	NM_173800	A8K6J0|C9JGD2|Q32MR1|Q4G0I9|Q4G0V2|Q86XA3|Q8NBZ2	Silent	SNP	ENST00000357872.4	37	CCDS4124.1																																																																																			.	.	none		0.343	AQPEP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250852.1		
ALDH9A1	223	hgsc.bcm.edu	37	1	165664562	165664562	+	Missense_Mutation	SNP	G	G	A			TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr1:165664562G>A	ENST00000354775.4	-	2	558	c.254C>T	c.(253-255)gCt>gTt	p.A85V	ALDH9A1_ENST00000461664.1_5'UTR|ALDH9A1_ENST00000538148.1_5'UTR	NM_000696.3	NP_000687.3	P49189	AL9A1_HUMAN	aldehyde dehydrogenase 9 family, member A1	61					carnitine biosynthetic process (GO:0045329)|cellular aldehyde metabolic process (GO:0006081)|cellular nitrogen compound metabolic process (GO:0034641)|hormone metabolic process (GO:0042445)|kidney development (GO:0001822)|liver development (GO:0001889)|neurotransmitter biosynthetic process (GO:0042136)|oxidation-reduction process (GO:0055114)|small molecule metabolic process (GO:0044281)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|mitochondrion (GO:0005739)	1-pyrroline dehydrogenase activity (GO:0033737)|3-chloroallyl aldehyde dehydrogenase activity (GO:0004028)|4-trimethylammoniobutyraldehyde dehydrogenase activity (GO:0047105)|aldehyde dehydrogenase (NAD) activity (GO:0004029)|amine binding (GO:0043176)|aminobutyraldehyde dehydrogenase activity (GO:0019145)|NAD binding (GO:0051287)			endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(2)|lung(7)|prostate(1)|skin(2)|urinary_tract(1)	21	all_hematologic(923;0.0773)|Acute lymphoblastic leukemia(8;0.155)					TATTTTAAAAGCAGCCTTTGC	0.398																																					p.A85V	Ovarian(179;1583 2014 18106 33801 42447)	Atlas-SNP	.											.	ALDH9A1	75	.	0			c.C254T						PASS	.						99.0	98.0	98.0					1																	165664562		2203	4300	6503	SO:0001583	missense	223	exon2			TTAAAAGCAGCCT	U34252	CCDS1250.2	1q22-q23	2008-02-05			ENSG00000143149	ENSG00000143149		"""Aldehyde dehydrogenases"""	412	protein-coding gene	gene with protein product		602733		ALDH7, ALDH4, ALDH9		8112751, 8786138	Standard	NM_000696		Approved	E3	uc001gdh.1	P49189	OTTHUMG00000034677	ENST00000354775.4:c.254C>T	1.37:g.165664562G>A	ENSP00000346827:p.Ala85Val	100.0	0.0	0		99.0	23.0	0.232323	NM_000696	B2R6X1|B4DXY7|Q5VV90|Q6LCL1|Q9NZT7	Missense_Mutation	SNP	ENST00000354775.4	37	CCDS1250.2	.	.	.	.	.	.	.	.	.	.	G	22.0	4.232550	0.79688	.	.	ENSG00000143149	ENST00000354775	D	0.94330	-3.4	5.44	5.44	0.79542	.	0.000000	0.85682	D	0.000000	D	0.96318	0.8799	M	0.81179	2.53	0.52099	D	0.999942	D;D	0.76494	0.999;0.999	D;D	0.72625	0.978;0.978	D	0.96736	0.9543	9	0.87932	D	0	.	16.7765	0.85552	0.0:0.0:1.0:0.0	.	75;85	B4DX14;B9EKV4	.;.	V	85	ENSP00000346827:A85V	ENSP00000346827:A85V	A	-	2	0	ALDH9A1	163931186	1.000000	0.71417	1.000000	0.80357	0.478000	0.33099	7.115000	0.77110	2.545000	0.85829	0.655000	0.94253	GCT	.	.	none		0.398	ALDH9A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000083899.1		
PTPRO	5800	hgsc.bcm.edu	37	12	15661564	15661564	+	Missense_Mutation	SNP	G	G	A	rs71459181	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr12:15661564G>A	ENST00000281171.4	+	7	1657	c.1327G>A	c.(1327-1329)Gtt>Att	p.V443I	PTPRO_ENST00000543886.1_Missense_Mutation_p.V443I|PTPRO_ENST00000348962.2_Missense_Mutation_p.V443I	NM_030667.2	NP_109592.1	Q16827	PTPRO_HUMAN	protein tyrosine phosphatase, receptor type, O	443	Fibronectin type-III 5. {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)				GAGTGTCCACGTTTTAAGCTC	0.502													G|||	18	0.00359425	0.0008	0.0072	5008	,	,		18994	0.0		0.0089	False		,,,				2504	0.0031				p.V443I		Atlas-SNP	.											.	PTPRO	148	.	0			c.G1327A						PASS	.	G	ILE/VAL,ILE/VAL	14,4392	22.3+/-47.3	0,14,2189	100.0	93.0	95.0		1327,1327	4.6	0.2	12	dbSNP_130	95	121,8479	62.8+/-124.8	2,117,4181	yes	missense,missense	PTPRO	NM_002848.3,NM_030667.2	29,29	2,131,6370	AA,AG,GG		1.407,0.3177,1.038	benign,benign	443/1189,443/1217	15661564	135,12871	2203	4300	6503	SO:0001583	missense	5800	exon7			GTCCACGTTTTAA	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.1327G>A	12.37:g.15661564G>A	ENSP00000281171:p.Val443Ile	198.0	0.0	0		198.0	109.0	0.550505	NM_002848	A0AV39|Q13101|Q8IYG3|Q9UBF0|Q9UBT5	Missense_Mutation	SNP	ENST00000281171.4	37	CCDS8675.1	10	0.004578754578754579	1	0.0020325203252032522	2	0.0055248618784530384	0	0.0	7	0.009234828496042216	G	14.57	2.576090	0.45902	0.003177	0.01407	ENSG00000151490	ENST00000281171;ENST00000543886;ENST00000348962	T;T;T	0.57752	0.38;0.38;0.38	5.44	4.55	0.56014	Fibronectin, type III (4);Immunoglobulin-like fold (1);	0.000000	0.46442	D	0.000284	T	0.20941	0.0504	N	0.12182	0.205	0.80722	D	1	P;P;B	0.40398	0.669;0.716;0.233	B;B;B	0.28385	0.053;0.089;0.04	T	0.07751	-1.0756	10	0.28530	T	0.3	.	12.3796	0.55299	0.0767:0.0:0.9233:0.0	.	443;443;443	Q16827-2;Q16827;Q8IYG3	.;PTPRO_HUMAN;.	I	443	ENSP00000281171:V443I;ENSP00000444173:V443I;ENSP00000343434:V443I	ENSP00000281171:V443I	V	+	1	0	PTPRO	15552831	0.869000	0.29996	0.175000	0.22980	0.976000	0.68499	1.352000	0.34033	1.537000	0.49254	0.655000	0.94253	GTT	G|0.991;A|0.009	0.009	strong		0.502	PTPRO-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000401079.1		
KIAA0754	643314	hgsc.bcm.edu	37	1	39879435	39879435	+	Silent	SNP	C	C	A	rs112569629		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr1:39879435C>A	ENST00000530275.1	+	1	3285	c.3090C>A	c.(3088-3090)ccC>ccA	p.P1030P	MACF1_ENST00000564288.1_Intron|MACF1_ENST00000539005.1_Intron|MACF1_ENST00000317713.7_Intron|MACF1_ENST00000545844.1_Intron|MACF1_ENST00000567887.1_Intron|MACF1_ENST00000361689.2_Intron|MACF1_ENST00000289893.4_Intron|MACF1_ENST00000372915.3_Intron	NM_015038.1	NP_055853.1	O94854	K0754_HUMAN	KIAA0754	1030	Ala-rich.									central_nervous_system(1)|large_intestine(6)|skin(1)	8	Lung NSC(20;5.57e-06)|Ovarian(52;0.00769)|Acute lymphoblastic leukemia(166;0.074)	Myeloproliferative disorder(586;0.0393)	OV - Ovarian serous cystadenocarcinoma(33;7.78e-19)|Epithelial(16;1.73e-17)|all cancers(16;2.49e-16)|LUSC - Lung squamous cell carcinoma(16;0.00146)|Lung(16;0.00204)			TGCCCACCCCCGAGGAATCTG	0.672																																					p.P1166P		Atlas-SNP	.											.	KIAA0754	93	.	0			c.C3498A						PASS	.						21.0	24.0	23.0					1																	39879435		1962	4129	6091	SO:0001819	synonymous_variant	643314	exon1			CACCCCCGAGGAA			1p34.2	2009-07-09				ENSG00000255103			29111	protein-coding gene	gene with protein product						9872452	Standard	NM_015038		Approved		uc009vvt.1	O94854		ENST00000530275.1:c.3090C>A	1.37:g.39879435C>A		200.0	0.0	0		74.0	44.0	0.594595	NM_015038	E9PMC2|Q6ZSB2	Silent	SNP	ENST00000530275.1	37																																																																																				C|0.995;A|0.005	0.005	weak		0.672	KIAA0754-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000392100.1	NM_015038	
PBK	55872	hgsc.bcm.edu	37	8	27685663	27685663	+	Silent	SNP	C	C	T	rs55973425	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr8:27685663C>T	ENST00000301905.4	-	3	574	c.111G>A	c.(109-111)aaG>aaA	p.K37K	PBK_ENST00000522944.1_Silent_p.K37K	NM_018492.2	NP_060962.2	Q96KB5	TOPK_HUMAN	PDZ binding kinase	37	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				mitotic nuclear division (GO:0007067)		ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)			endometrium(1)|large_intestine(2)|lung(1)	4		Ovarian(32;0.000953)		UCEC - Uterine corpus endometrioid carcinoma (27;0.0213)|KIRC - Kidney renal clear cell carcinoma(542;0.101)|Kidney(114;0.121)|Colorectal(74;0.141)		CAAAGCCAAGCTTCTGCATAA	0.299													C|||	5	0.000998403	0.0008	0.0	5008	,	,		16110	0.0		0.004	False		,,,				2504	0.0				p.K37K		Atlas-SNP	.											.	PBK	29	.	0			c.G111A						PASS	.	C		7,4399	11.4+/-27.6	0,7,2196	64.0	70.0	68.0		111	4.9	1.0	8	dbSNP_129	68	27,8573	18.5+/-59.3	0,27,4273	no	coding-synonymous	PBK	NM_018492.2		0,34,6469	TT,TC,CC		0.314,0.1589,0.2614		37/323	27685663	34,12972	2203	4300	6503	SO:0001819	synonymous_variant	55872	exon3			GCCAAGCTTCTGC	AB027249	CCDS6063.1, CCDS64858.1	8p21.2	2009-08-06			ENSG00000168078	ENSG00000168078			18282	protein-coding gene	gene with protein product	"""T-LAK cell-originated protein kinase"", ""cancer/testis antigen 84"""	611210				10781613, 10779557	Standard	NM_018492		Approved	TOPK, FLJ14385, Nori-3, SPK, CT84	uc003xgi.3	Q96KB5	OTTHUMG00000102113	ENST00000301905.4:c.111G>A	8.37:g.27685663C>T		69.0	0.0	0		97.0	41.0	0.42268	NM_018492	B4DX68|D3DST2|Q9NPD9|Q9NYL7|Q9NZK6	Silent	SNP	ENST00000301905.4	37	CCDS6063.1																																																																																			C|0.998;T|0.002	0.002	strong		0.299	PBK-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000219952.2	NM_018492	
ATP9A	10079	hgsc.bcm.edu	37	20	50346491	50346491	+	Missense_Mutation	SNP	C	C	A	rs142435125	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr20:50346491C>A	ENST00000338821.5	-	2	359	c.95G>T	c.(94-96)gGt>gTt	p.G32V	ATP9A_ENST00000477492.1_5'UTR|ATP9A_ENST00000402822.1_Missense_Mutation_p.G32V|ATP9A_ENST00000311637.5_Missense_Mutation_p.G17V	NM_006045.1	NP_006036.1	O75110	ATP9A_HUMAN	ATPase, class II, type 9A	32					phospholipid translocation (GO:0045332)	early endosome (GO:0005769)|integral component of membrane (GO:0016021)|perinuclear region of cytoplasm (GO:0048471)|recycling endosome (GO:0055037)|trans-Golgi network (GO:0005802)	ATP binding (GO:0005524)|cation-transporting ATPase activity (GO:0019829)|magnesium ion binding (GO:0000287)|phospholipid-translocating ATPase activity (GO:0004012)			breast(2)|cervix(2)|endometrium(6)|kidney(1)|large_intestine(10)|lung(18)|ovary(5)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	48						CTCCCCTCCACCGCAGCATCT	0.597													C|||	30	0.00599042	0.0	0.0014	5008	,	,		17873	0.0		0.003	False		,,,				2504	0.0266				p.G32V		Atlas-SNP	.											.	ATP9A	135	.	0			c.G95T						PASS	.	C	VAL/GLY	3,4403	6.2+/-15.9	0,3,2200	90.0	85.0	87.0		95	5.3	1.0	20	dbSNP_134	87	36,8564	24.6+/-71.5	0,36,4264	yes	missense	ATP9A	NM_006045.1	109	0,39,6464	AA,AC,CC		0.4186,0.0681,0.2999	benign	32/1048	50346491	39,12967	2203	4300	6503	SO:0001583	missense	10079	exon2			CCTCCACCGCAGC	AB014511	CCDS33489.1	20q13.2	2010-04-20	2007-09-19		ENSG00000054793	ENSG00000054793		"""ATPases / P-type"""	13540	protein-coding gene	gene with protein product		609126	"""ATPase, Class II, type 9A"""			9734811, 11015572	Standard	NM_006045		Approved	KIAA0611, ATPIIA	uc002xwg.1	O75110	OTTHUMG00000032751	ENST00000338821.5:c.95G>T	20.37:g.50346491C>A	ENSP00000342481:p.Gly32Val	46.0	0.0	0		57.0	27.0	0.473684	NM_006045	E1P5Y3|E1P5Y4|Q5TFW5|Q5TFW6|Q5TFW9|Q6ZMF3|Q9NQK6|Q9NQK7	Missense_Mutation	SNP	ENST00000338821.5	37	CCDS33489.1	4	0.0018315018315018315	0	0.0	1	0.0027624309392265192	0	0.0	3	0.00395778364116095	C	18.40	3.615508	0.66672	6.81E-4	0.004186	ENSG00000054793	ENST00000311637;ENST00000338821;ENST00000402822	T;T;T	0.54071	0.59;0.59;0.59	5.27	5.27	0.74061	.	0.000000	0.85682	D	0.000000	T	0.52108	0.1714	L	0.43152	1.355	0.58432	D	0.999996	B;P	0.36789	0.073;0.57	B;B	0.39805	0.31;0.147	T	0.53995	-0.8359	10	0.51188	T	0.08	-14.3884	19.2362	0.93861	0.0:1.0:0.0:0.0	.	32;32	O75110-2;O75110	.;ATP9A_HUMAN	V	17;32;32	ENSP00000309086:G17V;ENSP00000342481:G32V;ENSP00000385875:G32V	ENSP00000309086:G17V	G	-	2	0	ATP9A	49779898	1.000000	0.71417	0.997000	0.53966	0.922000	0.55478	7.257000	0.78362	2.608000	0.88229	0.563000	0.77884	GGT	C|0.997;A|0.003	0.003	strong		0.597	ATP9A-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000106494.1	NM_006045	
COX5B	1329	hgsc.bcm.edu	37	2	98264478	98264478	+	Silent	SNP	C	C	T	rs142899936		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr2:98264478C>T	ENST00000258424.2	+	4	344	c.297C>T	c.(295-297)agC>agT	p.S99S	COX5B_ENST00000464949.1_3'UTR	NM_001862.2	NP_001853.2	P10606	COX5B_HUMAN	cytochrome c oxidase subunit Vb	99					cellular metabolic process (GO:0044237)|hydrogen ion transmembrane transport (GO:1902600)|respiratory electron transport chain (GO:0022904)|respiratory gaseous exchange (GO:0007585)|small molecule metabolic process (GO:0044281)	extracellular vesicular exosome (GO:0070062)|mitochondrial inner membrane (GO:0005743)|mitochondrion (GO:0005739)	cytochrome-c oxidase activity (GO:0004129)|metal ion binding (GO:0046872)			endometrium(1)|lung(1)|urinary_tract(1)	3						ACAATACCAGCGTCGTCTGGT	0.522																																					p.S99S		Atlas-SNP	.											.	COX5B	9	.	0			c.C297T						PASS	.	C		1,4405		0,1,2202	65.0	61.0	62.0		297	-3.5	0.1	2	dbSNP_134	62	1,8599		0,1,4299	no	coding-synonymous	COX5B	NM_001862.2		0,2,6501	TT,TC,CC		0.0116,0.0227,0.0154		99/130	98264478	2,13004	2203	4300	6503	SO:0001819	synonymous_variant	1329	exon4			TACCAGCGTCGTC	BC006229	CCDS2032.1	2q11.2	2011-07-04			ENSG00000135940	ENSG00000135940	1.9.3.1	"""Mitochondrial respiratory chain complex / Complex IV"""	2269	protein-coding gene	gene with protein product		123866					Standard	NM_001862		Approved		uc002sya.3	P10606	OTTHUMG00000130548	ENST00000258424.2:c.297C>T	2.37:g.98264478C>T		182.0	0.0	0		151.0	58.0	0.384106	NM_001862	Q53YB7|Q96J18|Q99610	Silent	SNP	ENST00000258424.2	37	CCDS2032.1																																																																																			C|1.000;T|0.000	0.000	weak		0.522	COX5B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252972.2	NM_001862	
CBX5	23468	hgsc.bcm.edu	37	12	54639963	54639963	+	Silent	SNP	G	G	A			TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr12:54639963G>A	ENST00000439541.2	-	4	486	c.361C>T	c.(361-363)Ctg>Ttg	p.L121L	CBX5_ENST00000209875.4_Silent_p.L121L|CBX5_ENST00000550411.1_Silent_p.L121L	NM_001127321.1	NP_001120793.1	P45973	CBX5_HUMAN	chromobox homolog 5	121	Chromo 2; shadow subtype. {ECO:0000255|PROSITE-ProRule:PRU00053}.|Interaction with ASXL1.				blood coagulation (GO:0007596)|negative regulation of transcription, DNA-templated (GO:0045892)|viral process (GO:0016032)	chromocenter (GO:0010369)|histone deacetylase complex (GO:0000118)|histone methyltransferase complex (GO:0035097)|kinetochore (GO:0000776)|nuclear envelope (GO:0005635)|nuclear heterochromatin (GO:0005720)|nuclear pericentric heterochromatin (GO:0031618)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|transcriptional repressor complex (GO:0017053)	chromatin binding (GO:0003682)|methylated histone binding (GO:0035064)|protein binding, bridging (GO:0030674)|repressing transcription factor binding (GO:0070491)			endometrium(1)|kidney(1)|large_intestine(2)|lung(1)|prostate(1)|skin(2)	8						TCTGGTTCCAGTCCTCTCTCA	0.403																																					p.L121L	Colon(153;588 2459 18334 48613)	Atlas-SNP	.											.	CBX5	24	.	0			c.C361T						PASS	.						196.0	176.0	183.0					12																	54639963		2203	4300	6503	SO:0001819	synonymous_variant	23468	exon4			GTTCCAGTCCTCT	U26311	CCDS8875.1	12q13.13	2010-07-06	2010-06-24		ENSG00000094916	ENSG00000094916			1555	protein-coding gene	gene with protein product	"""HP1 alpha homolog (Drosophila)"""	604478	"""chromobox homolog 5 (Drosophila HP1 alpha)"", ""chromobox homolog 5 (HP1 alpha homolog, Drosophila)"""			8663349	Standard	NM_012117		Approved	HP1Hs-alpha, HP1, HP1-ALPHA	uc001sfj.4	P45973		ENST00000439541.2:c.361C>T	12.37:g.54639963G>A		191.0	0.0	0		159.0	73.0	0.459119	NM_012117	B2R8T9	Silent	SNP	ENST00000439541.2	37	CCDS8875.1																																																																																			.	.	none		0.403	CBX5-004	NOVEL	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000405468.1	NM_012117	
ZNF679	168417	hgsc.bcm.edu	37	7	63727212	63727212	+	Missense_Mutation	SNP	A	A	T	rs571908143		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr7:63727212A>T	ENST00000421025.1	+	5	1470	c.1201A>T	c.(1201-1203)Atg>Ttg	p.M401L	ZNF679_ENST00000255746.4_Missense_Mutation_p.M401L	NM_001159524.1|NM_153363.2	NP_001152996.1|NP_699194.2	Q8IYX0	ZN679_HUMAN	zinc finger protein 679	401					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(3)|lung(11)|skin(1)|stomach(1)	18						TCATAAGAGTATGCATACTGG	0.333																																					p.M401L		Atlas-SNP	.											.	ZNF679	80	.	0			c.A1201T						PASS	.						25.0	25.0	25.0					7																	63727212		692	1591	2283	SO:0001583	missense	168417	exon5			AAGAGTATGCATA	BC033523	CCDS47592.1	7q11.21	2013-01-08			ENSG00000197123	ENSG00000197123		"""Zinc fingers, C2H2-type"", ""-"""	28650	protein-coding gene	gene with protein product	"""hypothetical protein MGC42415"""					12477932	Standard	NM_153363		Approved	MGC42415	uc003tsx.3	Q8IYX0	OTTHUMG00000156486	ENST00000421025.1:c.1201A>T	7.37:g.63727212A>T	ENSP00000416809:p.Met401Leu	46.0	0.0	0		43.0	33.0	0.767442	NM_153363		Missense_Mutation	SNP	ENST00000421025.1	37	CCDS47592.1	.	.	.	.	.	.	.	.	.	.	A	11.30	1.598500	0.28445	.	.	ENSG00000197123	ENST00000421025;ENST00000255746	T;T	0.00949	5.51;5.51	0.819	0.819	0.18785	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.00440	0.0014	N	0.00801	-1.175	0.20196	N	0.999922	B	0.06786	0.001	B	0.09377	0.004	T	0.46952	-0.9154	9	0.72032	D	0.01	.	5.4486	0.16550	1.0:0.0:0.0:0.0	.	401	Q8IYX0	ZN679_HUMAN	L	401	ENSP00000416809:M401L;ENSP00000255746:M401L	ENSP00000255746:M401L	M	+	1	0	ZNF679	63364647	0.000000	0.05858	0.487000	0.27428	0.488000	0.33401	0.021000	0.13489	0.165000	0.19558	0.163000	0.16589	ATG	.	.	none		0.333	ZNF679-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000344317.2	NM_153363	
GSAP	54103	hgsc.bcm.edu	37	7	76984961	76984961	+	Missense_Mutation	SNP	T	T	C	rs375426636		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr7:76984961T>C	ENST00000257626.7	-	15	1109	c.1031A>G	c.(1030-1032)tAt>tGt	p.Y344C		NM_017439.3	NP_059135.2	A4D1B5	GSAP_HUMAN	gamma-secretase activating protein	344					positive regulation of beta-amyloid formation (GO:1902004)|regulation of proteolysis (GO:0030162)	trans-Golgi network (GO:0005802)	beta-amyloid binding (GO:0001540)										AGCCACATAATAGTCTATAGA	0.393																																					p.Y344C		Atlas-SNP	.											.	PION	74	.	0			c.A1031G						PASS	.						95.0	98.0	97.0					7																	76984961		2203	4300	6503	SO:0001583	missense	54103	exon15			ACATAATAGTCTA		CCDS34672.2	7q11.23	2013-04-05	2013-04-05	2013-04-05	ENSG00000186088	ENSG00000186088			28042	protein-coding gene	gene with protein product		613552	"""pigeon homolog (Drosophila)"""	PION		20811458	Standard	NM_017439		Approved	LOC54103	uc003ugf.3	A4D1B5	OTTHUMG00000150504	ENST00000257626.7:c.1031A>G	7.37:g.76984961T>C	ENSP00000257626:p.Tyr344Cys	112.0	0.0	0		163.0	106.0	0.650307	NM_017439	A4D1B6|Q3MJC0|Q8ND73|Q9UMH3|Q9Y4L9	Missense_Mutation	SNP	ENST00000257626.7	37	CCDS34672.2	.	.	.	.	.	.	.	.	.	.	T	11.76	1.734928	0.30774	.	.	ENSG00000186088	ENST00000257626	T	0.19669	2.13	5.87	1.96	0.26148	.	0.000000	0.64402	U	0.000007	T	0.18964	0.0455	M	0.69823	2.125	0.80722	D	1	B;B	0.29508	0.246;0.119	B;B	0.28139	0.086;0.048	T	0.03739	-1.1008	9	.	.	.	.	4.7934	0.13259	0.1393:0.1571:0.0:0.7037	.	344;344	A4D1B5-3;A4D1B5	.;GSAP_HUMAN	C	344	ENSP00000257626:Y344C	.	Y	-	2	0	PION	76822897	0.986000	0.35501	0.774000	0.31636	0.613000	0.37349	0.377000	0.20552	1.056000	0.40484	0.533000	0.62120	TAT	.	.	weak		0.393	GSAP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318672.2	NM_017439	
COL6A6	131873	hgsc.bcm.edu	37	3	130282383	130282383	+	Missense_Mutation	SNP	C	C	A	rs114511272	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr3:130282383C>A	ENST00000358511.6	+	2	567	c.536C>A	c.(535-537)aCg>aAg	p.T179K	COL6A6_ENST00000453409.2_Missense_Mutation_p.T179K	NM_001102608.1	NP_001096078.1	A6NMZ7	CO6A6_HUMAN	collagen, type VI, alpha 6	179	Nonhelical region.|VWFA 1. {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)		p.T179M(1)		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						GCCATGGCCACGTCTCAGTTT	0.468													C|||	43	0.00858626	0.0008	0.0072	5008	,	,		19242	0.006		0.0189	False		,,,				2504	0.0123				p.T179K		Atlas-SNP	.											COL6A6_ENST00000358511,colon,carcinoma,-1,3	COL6A6	497	3	1	Substitution - Missense(1)	breast(1)	c.C536A						PASS	.	C	LYS/THR	13,3867		0,13,1927	72.0	72.0	72.0		536	5.3	0.9	3	dbSNP_132	72	129,8135		1,127,4004	yes	missense	COL6A6	NM_001102608.1	78	1,140,5931	AA,AC,CC		1.561,0.3351,1.1693	probably-damaging	179/2264	130282383	142,12002	1940	4132	6072	SO:0001583	missense	131873	exon2			TGGCCACGTCTCA	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.536C>A	3.37:g.130282383C>A	ENSP00000351310:p.Thr179Lys	232.0	1.0	0.00431034		207.0	91.0	0.439614	NM_001102608	A7DZQ0|A7DZQ1|A7DZQ2|Q69YT0	Missense_Mutation	SNP	ENST00000358511.6	37	CCDS46911.1	18	0.008241758241758242	0	0.0	2	0.0055248618784530384	2	0.0034965034965034965	14	0.018469656992084433	C	23.3	4.401156	0.83120	0.003351	0.01561	ENSG00000206384	ENST00000358511;ENST00000453409	T;T	0.78246	-1.16;-1.16	5.3	5.3	0.74995	von Willebrand factor, type A (3);	0.000000	0.64402	D	0.000008	T	0.79516	0.4459	M	0.71206	2.165	0.42732	D	0.993717	D	0.89917	1.0	D	0.97110	1.0	T	0.82671	-0.0342	10	0.39692	T	0.17	.	18.0868	0.89460	0.0:1.0:0.0:0.0	.	179	A6NMZ7	CO6A6_HUMAN	K	179	ENSP00000351310:T179K;ENSP00000399236:T179K	ENSP00000351310:T179K	T	+	2	0	COL6A6	131765073	0.889000	0.30405	0.859000	0.33776	0.964000	0.63967	1.641000	0.37197	2.652000	0.90054	0.561000	0.74099	ACG	C|0.992;A|0.008	0.008	strong		0.468	COL6A6-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000356705.5	NM_001102608	
CCDC169	728591	hgsc.bcm.edu	37	13	36871782	36871782	+	Silent	SNP	G	G	T	rs201215750	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr13:36871782G>T	ENST00000239859.7	-	1	106	c.75C>A	c.(73-75)gtC>gtA	p.V25V	CCDC169_ENST00000379864.2_5'UTR|SOHLH2_ENST00000554962.1_5'UTR|CCDC169_ENST00000477250.1_5'UTR|CCDC169_ENST00000379862.2_5'UTR|CCDC169-SOHLH2_ENST00000511166.1_5'UTR|CCDC169_ENST00000510088.1_5'UTR|CCDC169_ENST00000491049.2_5'UTR|CCDC169_ENST00000503173.1_Silent_p.V25V|CCDC169_ENST00000239860.6_5'UTR			A6NNP5	CC169_HUMAN	coiled-coil domain containing 169	25										breast(1)|endometrium(1)	2						ACTTCTTGCGGACTTCTTCCA	0.617																																					p.V25V		Atlas-SNP	.											.	CCDC169	20	.	0			c.C75A						PASS	.	G	,,,,,,,	0,1384		0,0,692	52.0	53.0	52.0		75,,,,,,75,	2.3	1.0	13		52	15,3167		1,13,1577	no	coding-synonymous,utr-5,utr-5,utr-5,utr-5,utr-5,coding-synonymous,utr-5	CCDC169,CCDC169-SOHLH2	NM_001144981.2,NM_001144982.2,NM_001144983.2,NM_001144984.2,NM_001144985.2,NM_001144986.2,NM_001198908.1,NM_001198910.1	,,,,,,,	1,13,2269	TT,TG,GG		0.4714,0.0,0.3285	,,,,,,,	25/215,,,,,,25/242,	36871782	15,4551	692	1591	2283	SO:0001819	synonymous_variant	728591	exon1			CTTGCGGACTTCT		CCDS45027.1, CCDS45028.1, CCDS45029.1, CCDS53863.1, CCDS55897.1	13q13.3	2011-08-09	2011-08-09	2011-08-09	ENSG00000242715	ENSG00000242715			34361	protein-coding gene	gene with protein product			"""chromosome 13 open reading frame 38"""	C13orf38			Standard	NM_001144981		Approved	RP11-251J8.1, LOC728591		A6NNP5	OTTHUMG00000016731	ENST00000239859.7:c.75C>A	13.37:g.36871782G>T		61.0	0.0	0		60.0	26.0	0.433333	NM_001144981	A6NC13|A6NCT2|B7ZW45|B7ZW49|B9EJF2|Q9H1T4|Q9H1T5	Silent	SNP	ENST00000239859.7	37	CCDS45028.1																																																																																			G|0.993;T|0.007	0.007	strong		0.617	CCDC169-014	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000368255.1	NM_001144981	
GCN1L1	10985	hgsc.bcm.edu	37	12	120602208	120602208	+	Missense_Mutation	SNP	A	A	G			TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr12:120602208A>G	ENST00000300648.6	-	18	1792	c.1780T>C	c.(1780-1782)Tct>Cct	p.S594P		NM_006836.1	NP_006827	Q92616	GCN1L_HUMAN	GCN1 general control of amino-acid synthesis 1-like 1 (yeast)	594					regulation of translation (GO:0006417)|translation (GO:0006412)	cytoplasm (GO:0005737)|membrane (GO:0016020)|ribosome (GO:0005840)	poly(A) RNA binding (GO:0044822)|translation factor activity, nucleic acid binding (GO:0008135)			NS(2)|breast(2)|cervix(2)|endometrium(12)|haematopoietic_and_lymphoid_tissue(2)|kidney(6)|large_intestine(13)|liver(1)|lung(36)|ovary(4)|prostate(7)|skin(3)|upper_aerodigestive_tract(2)|urinary_tract(2)	94	all_neural(191;0.0804)|Medulloblastoma(191;0.0922)					CCCCCAAGAGAGGACAGCAGC	0.622																																					p.S594P		Atlas-SNP	.											.	GCN1L1	207	.	0			c.T1780C						PASS	.						75.0	80.0	78.0					12																	120602208		1969	4161	6130	SO:0001583	missense	10985	exon18			CAAGAGAGGACAG	U77700	CCDS41847.1	12q24.2	2008-07-03	2001-11-28						4199	protein-coding gene	gene with protein product		605614	"""GCN1 (general control of amino-acid synthesis 1, yeast)-like 1"""			9234705	Standard	NM_006836		Approved	KIAA0219, GCN1, GCN1L	uc001txo.3	Q92616	OTTHUMG00000169338	ENST00000300648.6:c.1780T>C	12.37:g.120602208A>G	ENSP00000300648:p.Ser594Pro	107.0	0.0	0		94.0	4.0	0.0425532	NM_006836	A8KAY1|O95001|O95651|Q6P2S3|Q86X65|Q8N5I5|Q8WU80|Q99736|Q9UE60	Missense_Mutation	SNP	ENST00000300648.6	37	CCDS41847.1	.	.	.	.	.	.	.	.	.	.	A	16.79	3.220268	0.58560	.	.	ENSG00000089154	ENST00000300648	T	0.05199	3.48	5.83	4.67	0.58626	Armadillo-like helical (1);Domain of unknown function DUF3554 (1);Armadillo-type fold (1);	0.000000	0.85682	D	0.000000	T	0.17619	0.0423	M	0.74881	2.28	0.80722	D	1	D	0.54047	0.964	P	0.54590	0.756	T	0.01570	-1.1322	10	0.30854	T	0.27	.	13.3498	0.60595	0.8686:0.1314:0.0:0.0	.	594	Q92616	GCN1L_HUMAN	P	594	ENSP00000300648:S594P	ENSP00000300648:S594P	S	-	1	0	GCN1L1	119086591	1.000000	0.71417	1.000000	0.80357	0.886000	0.51366	5.545000	0.67237	1.022000	0.39626	0.533000	0.62120	TCT	.	.	none		0.622	GCN1L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000403592.1		
ZNF668	79759	hgsc.bcm.edu	37	16	31072912	31072912	+	Missense_Mutation	SNP	G	G	A			TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr16:31072912G>A	ENST00000538906.1	-	3	2121	c.1337C>T	c.(1336-1338)cCg>cTg	p.P446L	ZNF668_ENST00000417110.2_Missense_Mutation_p.G34R|ZNF668_ENST00000539836.3_Missense_Mutation_p.P469L|ZNF668_ENST00000394983.2_Missense_Mutation_p.P446L|ZNF668_ENST00000535577.1_Missense_Mutation_p.P446L|ZNF668_ENST00000426488.2_Missense_Mutation_p.P469L|ZNF668_ENST00000300849.4_Missense_Mutation_p.P446L	NM_001172668.1	NP_001166139	Q96K58	ZN668_HUMAN	zinc finger protein 668	446					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(6)|endometrium(3)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(3)|lung(9)|ovary(1)|prostate(1)|urinary_tract(1)	27						CCCTGCTGCCGGGGCGGCTGA	0.711																																					p.P469L	Colon(181;1111 1980 5060 10512 25785)	Atlas-SNP	.											.	ZNF668	121	.	0			c.C1406T						PASS	.						32.0	40.0	37.0					16																	31072912		2194	4298	6492	SO:0001583	missense	79759	exon4			GCTGCCGGGGCGG		CCDS10701.1, CCDS54003.1	16p11.2	2013-01-08			ENSG00000167394	ENSG00000167394		"""Zinc fingers, C2H2-type"""	25821	protein-coding gene	gene with protein product						12477932	Standard	NM_024706		Approved	FLJ13479	uc021tgt.1	Q96K58	OTTHUMG00000047357	ENST00000538906.1:c.1337C>T	16.37:g.31072912G>A	ENSP00000440149:p.Pro446Leu	20.0	0.0	0		20.0	9.0	0.45	NM_001172669	C9JHH8|F5H7E7|Q59EV1|Q8N669|Q9H8L4	Missense_Mutation	SNP	ENST00000538906.1	37	CCDS10701.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	11.02|11.02	1.515722|1.515722	0.27123|0.27123	.|.	.|.	ENSG00000232748|ENSG00000167394	ENST00000417110|ENST00000539836;ENST00000535577;ENST00000538906;ENST00000394983;ENST00000300849	.|T;T;T;T;T	.|0.08546	.|3.08;3.09;3.09;3.09;3.09	4.84|4.84	4.84|4.84	0.62591|0.62591	.|.	.|0.000000	.|0.40302	.|N	.|0.001138	T|T	0.07548|0.07548	0.0190|0.0190	N|N	0.08118|0.08118	0|0	0.80722|0.80722	D|D	1|1	.|D	.|0.69078	.|0.997	.|P	.|0.50708	.|0.648	T|T	0.51702|0.51702	-0.8672|-0.8672	6|10	0.87932|0.21540	D|T	0|0.41	-20.0419|-20.0419	14.9766|14.9766	0.71277|0.71277	0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0	.|.	.|446	.|Q96K58	.|ZN668_HUMAN	R|L	34|469;446;446;446;446	.|ENSP00000442573:P469L;ENSP00000441349:P446L;ENSP00000440149:P446L;ENSP00000378434:P446L;ENSP00000300849:P446L	ENSP00000391989:G34R|ENSP00000300849:P446L	G|P	+|-	1|2	0|0	AC135050.1|ZNF668	30980413|30980413	0.837000|0.837000	0.29446|0.29446	0.637000|0.637000	0.29366|0.29366	0.430000|0.430000	0.31655|0.31655	1.657000|1.657000	0.37366|0.37366	2.531000|2.531000	0.85337|0.85337	0.462000|0.462000	0.41574|0.41574	GGG|CCG	.	.	none		0.711	ZNF668-202	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000108516.2	NM_024706	
C1orf127	148345	hgsc.bcm.edu	37	1	11017141	11017141	+	Intron	SNP	G	G	A	rs75810903	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr1:11017141G>A	ENST00000377008.4	-	7	724				C1orf127_ENST00000377004.4_Silent_p.L239L			Q8N9H9	CA127_HUMAN	chromosome 1 open reading frame 127											NS(2)|breast(1)|central_nervous_system(1)|endometrium(2)|kidney(2)|large_intestine(7)|lung(9)|ovary(1)|prostate(2)|skin(5)	32	Ovarian(185;0.249)	Lung NSC(185;0.000226)|all_lung(284;0.000302)|Renal(390;0.000469)|Colorectal(325;0.0062)|Breast(348;0.0139)|Hepatocellular(190;0.0305)|Myeloproliferative disorder(586;0.0393)|Ovarian(437;0.0731)	STAD - Stomach adenocarcinoma(5;0.0224)	UCEC - Uterine corpus endometrioid carcinoma (279;0.0228)|Colorectal(212;3.71e-07)|COAD - Colon adenocarcinoma(227;7.79e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000305)|Kidney(185;0.000785)|KIRC - Kidney renal clear cell carcinoma(229;0.00262)|READ - Rectum adenocarcinoma(331;0.0509)		ATAGTGGCAGGAGCTCAGCAG	0.602													G|||	16	0.00319489	0.0008	0.0014	5008	,	,		15143	0.002		0.0099	False		,,,				2504	0.002				p.L239L		Atlas-SNP	.											.	C1orf127	134	.	0			c.C717T						PASS	.	G		3,1381		0,3,689	33.0	41.0	38.0		717	-4.9	0.0	1	dbSNP_132	38	36,3146		0,36,1555	yes	coding-synonymous	C1orf127	NM_001170754.1		0,39,2244	AA,AG,GG		1.1314,0.2168,0.8541		239/824	11017141	39,4527	692	1591	2283	SO:0001627	intron_variant	148345	exon8			TGGCAGGAGCTCA	AK094437	CCDS53267.1	1p36.22	2008-02-05			ENSG00000175262	ENSG00000175262			26730	protein-coding gene	gene with protein product						14702039	Standard	NM_001170754		Approved	FLJ37118	uc010oao.2	Q8N9H9	OTTHUMG00000002032	ENST00000377008.4:c.277+500C>T	1.37:g.11017141G>A		40.0	0.0	0		52.0	29.0	0.557692	NM_001170754	A0AVG8|A6NKM7|Q5VXJ2	Silent	SNP	ENST00000377008.4	37		8	0.003663003663003663	0	0.0	0	0.0	1	0.0017482517482517483	7	0.009234828496042216	G	3.484	-0.105372	0.06967	0.002168	0.011314	ENSG00000175262	ENST00000520253	.	.	.	5.39	-4.9	0.03094	.	.	.	.	.	T	0.19208	0.0461	.	.	.	0.09310	N	0.999999	.	.	.	.	.	.	T	0.32025	-0.9922	4	.	.	.	.	6.7834	0.23659	0.1109:0.62:0.1446:0.1245	.	.	.	.	F	217	.	.	S	-	2	0	C1orf127	10939728	0.067000	0.21026	0.024000	0.17045	0.510000	0.34073	-0.085000	0.11250	-0.691000	0.05135	0.561000	0.74099	TCC	G|0.996;A|0.004	0.004	strong		0.602	C1orf127-202	KNOWN	basic	protein_coding	protein_coding		NM_173507	
KRTAP13-3	337960	hgsc.bcm.edu	37	21	31797919	31797919	+	Silent	SNP	G	G	A	rs73356706	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr21:31797919G>A	ENST00000390690.2	-	1	367	c.312C>T	c.(310-312)tcC>tcT	p.S104S		NM_181622.1	NP_853653.1	Q3SY46	KR133_HUMAN	keratin associated protein 13-3	104						intermediate filament (GO:0005882)				endometrium(1)|large_intestine(1)|lung(10)|ovary(1)|upper_aerodigestive_tract(1)	14						AGCAGCTATTGGATCCAAAAC	0.532													-|||	210	0.0419329	0.1505	0.0144	5008	,	,		18568	0.0		0.001	False		,,,				2504	0.0				p.S104S		Atlas-SNP	.											.	KRTAP13-3	47	.	0			c.C312T						PASS	.	G		432,3908		23,386,1761	51.0	57.0	55.0		312	3.4	0.3	21	dbSNP_130	55	9,8569		0,9,4280	no	coding-synonymous	KRTAP13-3	NM_181622.1		23,395,6041	AA,AG,GG		0.1049,9.9539,3.4138		104/173	31797919	441,12477	2170	4289	6459	SO:0001819	synonymous_variant	337960	exon1			GCTATTGGATCCA	AP001708	CCDS13591.1	21q22.1	2006-03-13			ENSG00000240432	ENSG00000240432		"""Keratin associated proteins"""	18925	protein-coding gene	gene with protein product						12359730	Standard	NM_181622		Approved	KAP13.3	uc002yob.1	Q3SY46	OTTHUMG00000057776	ENST00000390690.2:c.312C>T	21.37:g.31797919G>A		108.0	0.0	0		171.0	61.0	0.356725	NM_181622	Q3LI78	Silent	SNP	ENST00000390690.2	37	CCDS13591.1																																																																																			G|0.975;A|0.025	0.025	strong		0.532	KRTAP13-3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000128228.2		
RTEL1	51750	hgsc.bcm.edu	37	20	62322290	62322290	+	Missense_Mutation	SNP	G	G	A	rs190887884	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr20:62322290G>A	ENST00000360203.5	+	27	2871	c.2546G>A	c.(2545-2547)gGc>gAc	p.G849D	RTEL1_ENST00000370018.3_Missense_Mutation_p.G849D|RTEL1_ENST00000508582.2_Missense_Mutation_p.G873D|RTEL1-TNFRSF6B_ENST00000482936.1_Missense_Mutation_p.G849D|RTEL1_ENST00000318100.4_Missense_Mutation_p.G849D|RTEL1_ENST00000370003.1_Missense_Mutation_p.G94D					regulator of telomere elongation helicase 1											NS(1)|central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(3)|lung(12)|prostate(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	24	all_cancers(38;6.47e-12)|all_epithelial(29;3.75e-13)		Epithelial(9;1.25e-09)|all cancers(9;5.13e-09)|BRCA - Breast invasive adenocarcinoma(10;7.26e-05)|OV - Ovarian serous cystadenocarcinoma(5;0.00223)|Colorectal(105;0.107)			GGGAGCCCTGGCGAGGAGCAG	0.687													G|||	23	0.00459265	0.0023	0.0058	5008	,	,		15022	0.0		0.0099	False		,,,				2504	0.0061				p.G873D		Atlas-SNP	.											.	RTEL1	114	.	0			c.G2618A						PASS	.	G	ASP/GLY,ASP/GLY	9,4167		0,9,2079	14.0	15.0	14.0		2546,2618	-0.1	0.0	20		14	113,8185		0,113,4036	yes	missense,missense	RTEL1	NM_016434.3,NM_032957.4	94,94	0,122,6115	AA,AG,GG		1.3618,0.2155,0.978	benign,benign	849/1220,873/1244	62322290	122,12352	2088	4149	6237	SO:0001583	missense	51750	exon27			GCCCTGGCGAGGA	AB029011	CCDS13530.2, CCDS13531.1, CCDS13530.3, CCDS63331.1, CCDS74751.1	20q13.3	2012-06-27	2004-10-29	2004-10-29	ENSG00000258366	ENSG00000258366			15888	protein-coding gene	gene with protein product		608833	"""chromosome 20 open reading frame 41"""	C20orf41		10655513, 15210109	Standard	NM_016434		Approved	bK3184A7.3, NHL, DKFZP434C013, KIAA1088, RTEL	uc011abd.2	Q9NZ71	OTTHUMG00000032992	ENST00000360203.5:c.2546G>A	20.37:g.62322290G>A	ENSP00000353332:p.Gly849Asp	53.0	0.0	0		34.0	13.0	0.382353	NM_032957		Missense_Mutation	SNP	ENST00000360203.5	37		13	0.005952380952380952	1	0.0020325203252032522	2	0.0055248618784530384	0	0.0	10	0.013192612137203167	G	11.51	1.659474	0.29515	0.002155	0.013618	ENSG00000258366	ENST00000370018;ENST00000318100;ENST00000508582;ENST00000360203;ENST00000370003	T;T;T;T;T	0.09255	3.0;3.0;3.0;3.0;3.0	4.77	-0.131	0.13494	.	0.888187	0.09800	N	0.754121	T	0.04679	0.0127	L	0.34521	1.04	0.09310	N	1	B;B;B;B	0.34290	0.052;0.447;0.003;0.008	B;B;B;B	0.35413	0.075;0.202;0.017;0.046	T	0.38972	-0.9636	10	0.23302	T	0.38	-13.4816	2.5812	0.04818	0.4374:0.0:0.343:0.2196	.	873;94;849;849	Q9NZ71-7;Q9NZ71-5;Q9NZ71;Q9NZ71-6	.;.;RTEL1_HUMAN;.	D	849;849;873;849;94	ENSP00000359035:G849D;ENSP00000322287:G849D;ENSP00000424307:G873D;ENSP00000353332:G849D;ENSP00000359020:G94D	ENSP00000353332:G849D	G	+	2	0	AL353715.1	61792734	0.001000	0.12720	0.005000	0.12908	0.006000	0.05464	0.096000	0.15147	0.093000	0.17368	-0.217000	0.12591	GGC	G|0.994;A|0.006	0.006	strong		0.687	RTEL1-011	NOVEL	not_organism_supported|basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000289781.1	NM_032957	
KIAA0754	643314	hgsc.bcm.edu	37	1	39879410	39879410	+	Missense_Mutation	SNP	C	C	T			TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr1:39879410C>T	ENST00000530275.1	+	1	3260	c.3065C>T	c.(3064-3066)tCc>tTc	p.S1022F	MACF1_ENST00000564288.1_Intron|MACF1_ENST00000539005.1_Intron|MACF1_ENST00000317713.7_Intron|MACF1_ENST00000545844.1_Intron|MACF1_ENST00000567887.1_Intron|MACF1_ENST00000361689.2_Intron|MACF1_ENST00000289893.4_Intron|MACF1_ENST00000372915.3_Intron	NM_015038.1	NP_055853.1	O94854	K0754_HUMAN	KIAA0754	1022	Ala-rich.									central_nervous_system(1)|large_intestine(6)|skin(1)	8	Lung NSC(20;5.57e-06)|Ovarian(52;0.00769)|Acute lymphoblastic leukemia(166;0.074)	Myeloproliferative disorder(586;0.0393)	OV - Ovarian serous cystadenocarcinoma(33;7.78e-19)|Epithelial(16;1.73e-17)|all cancers(16;2.49e-16)|LUSC - Lung squamous cell carcinoma(16;0.00146)|Lung(16;0.00204)			GAATCCGCCTCCGCAGCTGTT	0.687																																					p.S1158F		Atlas-SNP	.											KIAA0754_ENST00000530275,NS,carcinoma,-1,2	KIAA0754	93	2	0			c.C3473T						scavenged	.						18.0	22.0	21.0					1																	39879410		1946	4130	6076	SO:0001583	missense	643314	exon1			CCGCCTCCGCAGC			1p34.2	2009-07-09				ENSG00000255103			29111	protein-coding gene	gene with protein product						9872452	Standard	NM_015038		Approved		uc009vvt.1	O94854		ENST00000530275.1:c.3065C>T	1.37:g.39879410C>T	ENSP00000431179:p.Ser1022Phe	206.0	0.0	0		58.0	9.0	0.155172	NM_015038	E9PMC2|Q6ZSB2	Missense_Mutation	SNP	ENST00000530275.1	37		.	.	.	.	.	.	.	.	.	.	N	12.12	1.842527	0.32606	.	.	ENSG00000255103	ENST00000530275	T	0.24350	1.86	4.0	2.07	0.26955	.	.	.	.	.	T	0.15522	0.0374	N	0.08118	0	0.09310	N	1	P	0.42203	0.773	P	0.44422	0.449	T	0.11299	-1.0593	9	0.72032	D	0.01	.	6.6382	0.22895	0.1876:0.5829:0.2295:0.0	.	1022	O94854	K0754_HUMAN	F	1022	ENSP00000431179:S1022F	ENSP00000431179:S1022F	S	+	2	0	RP4-562N20.1	39651997	0.000000	0.05858	0.000000	0.03702	0.016000	0.09150	-1.547000	0.02186	0.468000	0.27243	0.391000	0.25812	TCC	.	.	none		0.687	KIAA0754-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000392100.1	NM_015038	
PCDHGA8	9708	hgsc.bcm.edu	37	5	140774076	140774076	+	Missense_Mutation	SNP	G	G	T	rs367855808		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr5:140774076G>T	ENST00000398604.2	+	1	1696	c.1696G>T	c.(1696-1698)Gcc>Tcc	p.A566S	PCDHGA2_ENST00000394576.2_Intron|PCDHGA3_ENST00000253812.6_Intron|PCDHGB1_ENST00000523390.1_Intron|PCDHGB2_ENST00000522605.1_Intron|PCDHGA6_ENST00000517434.1_Intron|PCDHGA1_ENST00000517417.1_Intron|PCDHGA5_ENST00000518069.1_Intron|PCDHGB4_ENST00000519479.1_Intron|PCDHGA4_ENST00000571252.1_Intron|PCDHGB3_ENST00000576222.1_Intron|PCDHGA7_ENST00000518325.1_Intron	NM_032088.1	NP_114477.1	Q9Y5G5	PCDG8_HUMAN	protocadherin gamma subfamily A, 8	566					homophilic cell adhesion (GO:0007156)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			endometrium(6)|kidney(6)|large_intestine(6)|lung(30)|ovary(1)|stomach(1)|upper_aerodigestive_tract(1)	51			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			CCTGTACCCCGCCCTCCCCAC	0.667																																					p.A566S		Atlas-SNP	.											.	PCDHGA8	146	.	0			c.G1696T						PASS	.	A	,SER/ALA,,,,,,,,,,,SER/ALA	0,4406		0,0,2203	91.0	106.0	101.0		,1696,,,,,,,,,,,1696	-10.1	0.0	5		101	1,8595		0,1,4297	no	intron,missense,intron,intron,intron,intron,intron,intron,intron,intron,intron,intron,missense	PCDHGB4,PCDHGA8,PCDHGB3,PCDHGB2,PCDHGB1,PCDHGA7,PCDHGA6,PCDHGA5,PCDHGA4,PCDHGA3,PCDHGA2,PCDHGA1	NM_003736.2,NM_014004.2,NM_018912.2,NM_018915.2,NM_018916.3,NM_018917.2,NM_018918.2,NM_018919.2,NM_018920.2,NM_018922.2,NM_018923.2,NM_018924.2,NM_032088.1	,99,,,,,,,,,,,99	0,1,6500	TT,TG,GG		0.0116,0.0,0.0077	,,,,,,,,,,,,	,566/821,,,,,,,,,,,566/933	140774076	1,13001	2203	4298	6501	SO:0001583	missense	9708	exon1			TACCCCGCCCTCC	AF152515	CCDS47291.1, CCDS75338.1	5q31	2010-01-26			ENSG00000253767	ENSG00000253767		"""Cadherins / Protocadherins : Clustered"""	8706	other	protocadherin		606295				10380929	Standard	NM_014004		Approved	KIAA0327, PCDH-GAMMA-A8		Q9Y5G5	OTTHUMG00000164053	ENST00000398604.2:c.1696G>T	5.37:g.140774076G>T	ENSP00000381605:p.Ala566Ser	172.0	0.0	0		182.0	83.0	0.456044	NM_014004	A7MCZ4|O15039	Missense_Mutation	SNP	ENST00000398604.2	37	CCDS47291.1	.	.	.	.	.	.	.	.	.	.	.	0.012	-1.677464	0.00751	0.0	1.16E-4	ENSG00000253767	ENST00000398604	T	0.46063	0.88	5.06	-10.1	0.00402	Cadherin-like (1);	1.441770	0.05974	N	0.642917	T	0.13329	0.0323	N	0.02379	-0.575	0.09310	N	1	B;B	0.21071	0.051;0.004	B;B	0.19391	0.025;0.006	T	0.11767	-1.0574	10	0.07813	T	0.8	.	9.2393	0.37486	0.6616:0.0594:0.0798:0.1992	.	566;566	Q9Y5G5;Q9Y5G5-2	PCDG8_HUMAN;.	S	566	ENSP00000381605:A566S	ENSP00000381605:A566S	A	+	1	0	PCDHGA8	140754260	0.000000	0.05858	0.000000	0.03702	0.625000	0.37756	-8.772000	0.00017	-3.686000	0.00121	-1.652000	0.00757	GCC	.	.	weak		0.667	PCDHGA8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000376972.1	NM_032088	
TG	7038	hgsc.bcm.edu	37	8	133899008	133899008	+	Missense_Mutation	SNP	C	C	A			TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr8:133899008C>A	ENST00000220616.4	+	9	1431	c.1391C>A	c.(1390-1392)cCa>cAa	p.P464Q	TG_ENST00000377869.1_Missense_Mutation_p.P464Q	NM_003235.4	NP_003226.4	P01266	THYG_HUMAN	thyroglobulin	464					hormone biosynthetic process (GO:0042446)|iodide transport (GO:0015705)|regulation of myelination (GO:0031641)|signal transduction (GO:0007165)|thyroid gland development (GO:0030878)|thyroid hormone generation (GO:0006590)	extracellular region (GO:0005576)|extracellular space (GO:0005615)				NS(1)|breast(11)|central_nervous_system(3)|endometrium(12)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(34)|liver(2)|lung(59)|ovary(9)|pancreas(2)|prostate(6)|skin(7)|stomach(4)|upper_aerodigestive_tract(4)|urinary_tract(8)	168	Ovarian(258;0.00438)|Acute lymphoblastic leukemia(118;0.155)	Myeloproliferative disorder(644;0.00878)|Acute lymphoblastic leukemia(644;0.0559)|Breast(495;0.0735)	BRCA - Breast invasive adenocarcinoma(115;0.000701)	KIRC - Kidney renal clear cell carcinoma(542;0.0546)		ACCACCAACCCAAAGAGACTC	0.463																																					p.P464Q		Atlas-SNP	.											.	TG	416	.	0			c.C1391A						PASS	.						57.0	63.0	61.0					8																	133899008		2203	4300	6503	SO:0001583	missense	7038	exon9			CCAACCCAAAGAG	AU141420	CCDS34944.1	8q24	2012-10-02			ENSG00000042832	ENSG00000042832			11764	protein-coding gene	gene with protein product		188450					Standard	NM_003235		Approved	TGN, AITD3	uc003ytw.3	P01266	OTTHUMG00000164649	ENST00000220616.4:c.1391C>A	8.37:g.133899008C>A	ENSP00000220616:p.Pro464Gln	76.0	0.0	0		170.0	72.0	0.423529	NM_003235	O15274|O43899|Q15593|Q15948|Q9NYR1|Q9NYR2|Q9UMZ0|Q9UNY3	Missense_Mutation	SNP	ENST00000220616.4	37	CCDS34944.1	.	.	.	.	.	.	.	.	.	.	C	21.5	4.164144	0.78339	.	.	ENSG00000042832	ENST00000377869;ENST00000220616;ENST00000535932	D;T	0.81499	-1.5;-1.43	5.8	5.8	0.92144	.	0.190696	0.37348	N	0.002135	D	0.88894	0.6561	M	0.72894	2.215	0.40203	D	0.977531	D	0.76494	0.999	D	0.66602	0.945	D	0.88843	0.3314	10	0.52906	T	0.07	.	19.0314	0.92959	0.0:1.0:0.0:0.0	.	464	P01266	THYG_HUMAN	Q	464	ENSP00000367100:P464Q;ENSP00000220616:P464Q	ENSP00000220616:P464Q	P	+	2	0	TG	133968190	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	5.334000	0.65923	2.740000	0.93945	0.650000	0.86243	CCA	.	.	none		0.463	TG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000379606.1	NM_003235	
MYBPC3	4607	hgsc.bcm.edu	37	11	47365164	47365164	+	Missense_Mutation	SNP	T	T	C			TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr11:47365164T>C	ENST00000545968.1	-	13	1156	c.1102A>G	c.(1102-1104)Aag>Gag	p.K368E	MYBPC3_ENST00000256993.4_Missense_Mutation_p.K368E|MYBPC3_ENST00000399249.2_Missense_Mutation_p.K368E	NM_000256.3	NP_000247.2	Q14896	MYPC3_HUMAN	myosin binding protein C, cardiac	368	Ig-like C2-type 2.				cardiac muscle contraction (GO:0060048)|cell adhesion (GO:0007155)|heart morphogenesis (GO:0003007)|muscle filament sliding (GO:0030049)|myosin filament assembly (GO:0031034)|positive regulation of ATPase activity (GO:0032781)|regulation of heart rate (GO:0002027)|regulation of muscle filament sliding (GO:0032971)|regulation of striated muscle contraction (GO:0006942)|sarcomere organization (GO:0045214)|ventricular cardiac muscle tissue morphogenesis (GO:0055010)	A band (GO:0031672)|C zone (GO:0014705)|cytosol (GO:0005829)|sarcomere (GO:0030017)|striated muscle myosin thick filament (GO:0005863)	ATPase activator activity (GO:0001671)|identical protein binding (GO:0042802)|metal ion binding (GO:0046872)|myosin binding (GO:0017022)|myosin heavy chain binding (GO:0032036)|structural constituent of muscle (GO:0008307)|titin binding (GO:0031432)			breast(2)|central_nervous_system(2)|endometrium(9)|kidney(1)|large_intestine(4)|lung(16)|ovary(3)|prostate(3)|urinary_tract(2)	42				Lung(87;0.176)		GGCTCCAGCTTCTTCTGAAAG	0.647																																					p.K368E		Atlas-SNP	.											.	MYBPC3	102	.	0			c.A1102G						PASS	.						52.0	50.0	51.0					11																	47365164		1941	4129	6070	SO:0001583	missense	4607	exon13			CCAGCTTCTTCTG	X84075	CCDS53621.1	11p11.2	2014-09-17	2001-11-28			ENSG00000134571		"""Myosin binding proteins"", ""Immunoglobulin superfamily / I-set domain containing"", ""Fibronectin type III domain containing"""	7551	protein-coding gene	gene with protein product		600958	"""myosin-binding protein C, cardiac"""	CMH4		7744002, 8358441	Standard	NM_000256		Approved	MYBP-C, FHC	uc021qis.1	Q14896		ENST00000545968.1:c.1102A>G	11.37:g.47365164T>C	ENSP00000442795:p.Lys368Glu	89.0	0.0	0		97.0	4.0	0.0412371	NM_000256	A5PL00|Q16410|Q6R2F7|Q9UE27|Q9UM53	Missense_Mutation	SNP	ENST00000545968.1	37	CCDS53621.1	.	.	.	.	.	.	.	.	.	.	t	25.9	4.686390	0.88639	.	.	ENSG00000134571	ENST00000545968;ENST00000399249;ENST00000256993	T;T;T	0.67865	-0.29;-0.29;-0.29	4.99	4.99	0.66335	Immunoglobulin I-set (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	.	.	.	.	T	0.79587	0.4471	M	0.77616	2.38	0.46396	D	0.999024	D	0.69078	0.997	D	0.68621	0.959	T	0.80899	-0.1176	9	0.51188	T	0.08	.	11.5285	0.50595	0.0:0.0:0.1496:0.8504	.	368	Q14896	MYPC3_HUMAN	E	368	ENSP00000442795:K368E;ENSP00000382193:K368E;ENSP00000256993:K368E	ENSP00000256993:K368E	K	-	1	0	MYBPC3	47321740	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	3.639000	0.54339	2.103000	0.63969	0.456000	0.33151	AAG	.	.	none		0.647	MYBPC3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000392271.3		
GANAB	23193	hgsc.bcm.edu	37	11	62397114	62397114	+	Missense_Mutation	SNP	T	T	C	rs76572368	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr11:62397114T>C	ENST00000356638.3	-	15	1796	c.1780A>G	c.(1780-1782)Atg>Gtg	p.M594V	GANAB_ENST00000534779.1_Missense_Mutation_p.M502V|GANAB_ENST00000346178.4_Missense_Mutation_p.M616V|GANAB_ENST00000540933.1_Missense_Mutation_p.M497V	NM_198334.1	NP_938148.1	Q14697	GANAB_HUMAN	glucosidase, alpha; neutral AB	594					cellular protein metabolic process (GO:0044267)|post-translational protein modification (GO:0043687)|protein folding (GO:0006457)|protein N-linked glycosylation via asparagine (GO:0018279)	endoplasmic reticulum lumen (GO:0005788)|extracellular vesicular exosome (GO:0070062)|glucosidase II complex (GO:0017177)|Golgi apparatus (GO:0005794)|membrane (GO:0016020)	carbohydrate binding (GO:0030246)|glucan 1,3-alpha-glucosidase activity (GO:0033919)|poly(A) RNA binding (GO:0044822)			central_nervous_system(1)|cervix(2)|endometrium(2)|kidney(2)|large_intestine(6)|lung(14)|ovary(3)|skin(2)|urinary_tract(3)	35					Miglitol(DB00491)	GGGCGTTCCATGCCCCCAGAG	0.597													T|||	89	0.0177716	0.0008	0.0389	5008	,	,		20960	0.001		0.0547	False		,,,				2504	0.0051				p.M616V	Melanoma(23;1005 1074 15747 18937)	Atlas-SNP	.											.	GANAB	110	.	0			c.A1846G						PASS	.	T	VAL/MET,VAL/MET	28,4376	31.7+/-61.6	0,28,2174	37.0	37.0	37.0		1780,1846	-4.7	0.1	11	dbSNP_131	37	362,8236	115.7+/-175.5	10,342,3947	yes	missense,missense	GANAB	NM_198334.1,NM_198335.2	21,21	10,370,6121	CC,CT,TT		4.2103,0.6358,2.9995	benign,benign	594/945,616/967	62397114	390,12612	2202	4299	6501	SO:0001583	missense	23193	exon16			GTTCCATGCCCCC	AF144074	CCDS8026.1, CCDS41656.1, CCDS60817.1, CCDS60818.1	11q12.3	2012-10-02			ENSG00000089597	ENSG00000089597	3.2.1.20		4138	protein-coding gene	gene with protein product		104160				10764838, 6342981	Standard	NM_198335		Approved	GluII, G2AN, KIAA0088	uc001nua.4	Q14697	OTTHUMG00000167696	ENST00000356638.3:c.1780A>G	11.37:g.62397114T>C	ENSP00000349053:p.Met594Val	205.0	0.0	0		228.0	92.0	0.403509	NM_198335	A6NC20|Q8WTS9|Q9P0X0	Missense_Mutation	SNP	ENST00000356638.3	37	CCDS8026.1	53	0.024267399267399268	0	0.0	14	0.03867403314917127	0	0.0	39	0.051451187335092345	T	7.943	0.743196	0.15642	0.006358	0.042103	ENSG00000089597	ENST00000346178;ENST00000356638;ENST00000534779;ENST00000540933	D;D;D;D	0.91068	-2.78;-2.78;-2.78;-2.78	5.31	-4.7	0.03288	Glycoside hydrolase, superfamily (1);	0.908173	0.09646	N	0.774318	T	0.25419	0.0618	N	0.00368	-1.59	0.09310	N	1	B;B;B;B	0.02656	0.0;0.0;0.0;0.0	B;B;B;B	0.01281	0.0;0.0;0.0;0.0	T	0.53961	-0.8364	10	0.29301	T	0.29	0.5168	8.9385	0.35715	0.0:0.4806:0.1198:0.3996	.	480;502;594;616	B4DIW2;E9PKU7;Q14697;Q14697-2	.;.;GANAB_HUMAN;.	V	616;594;502;497	ENSP00000340466:M616V;ENSP00000349053:M594V;ENSP00000435306:M502V;ENSP00000442962:M497V	ENSP00000340466:M616V	M	-	1	0	GANAB	62153690	0.000000	0.05858	0.133000	0.22050	0.980000	0.70556	-1.352000	0.02619	-0.731000	0.04862	0.533000	0.62120	ATG	T|0.974;C|0.026	0.026	strong		0.597	GANAB-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000395689.1	NM_198334	
SYTL5	94122	hgsc.bcm.edu	37	X	37935844	37935844	+	Silent	SNP	G	G	A	rs12558731	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chrX:37935844G>A	ENST00000357972.5	+	6	1125	c.579G>A	c.(577-579)tcG>tcA	p.S193S	TM4SF2_ENST00000465127.1_Intron|SYTL5_ENST00000297875.2_Silent_p.S193S|SYTL5_ENST00000456733.2_Silent_p.S193S			Q8TDW5	SYTL5_HUMAN	synaptotagmin-like 5	193					exocytosis (GO:0006887)|intracellular protein transport (GO:0006886)	membrane (GO:0016020)	metal ion binding (GO:0046872)			central_nervous_system(1)|endometrium(5)|kidney(2)|large_intestine(9)|lung(23)|prostate(1)|skin(2)|urinary_tract(1)	44						AGTTCAGATCGGCAACCAGAG	0.338													A|||	12	0.00317881	0.0015	0.013	3775	,	,		12229	0.0		0.001	False		,,,				2504	0.0				p.S193S		Atlas-SNP	.											.	SYTL5	72	.	0			c.G579A						PASS	.	A	,,	5,3828		0,4,1,1627,570	68.0	52.0	57.0		579,579,579	5.2	1.0	X	dbSNP_120	57	75,6653		0,55,20,2373,1852	no	coding-synonymous,coding-synonymous,coding-synonymous	SYTL5	NM_001163334.1,NM_001163335.1,NM_138780.2	,,	0,59,21,4000,2422	AA,AG,A,GG,G		1.1147,0.1304,0.7575	,,	193/753,193/731,193/731	37935844	80,10481	2202	4300	6502	SO:0001819	synonymous_variant	94122	exon5			CAGATCGGCAACC		CCDS14244.1, CCDS55399.1	Xp21.1	2008-02-05			ENSG00000147041	ENSG00000147041			15589	protein-coding gene	gene with protein product	"""exophilin 9"""						Standard	NM_138780		Approved		uc004ddx.3	Q8TDW5	OTTHUMG00000033176	ENST00000357972.5:c.579G>A	X.37:g.37935844G>A		146.0	0.0	0		41.0	40.0	0.97561	NM_001163334	A2RRF2	Silent	SNP	ENST00000357972.5	37	CCDS14244.1																																																																																			G|0.993;A|0.007	0.007	strong		0.338	SYTL5-201	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000080883.1	NM_138780	
TXNDC16	57544	hgsc.bcm.edu	37	14	52981664	52981664	+	Missense_Mutation	SNP	G	G	C	rs117463339	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr14:52981664G>C	ENST00000281741.4	-	8	910	c.539C>G	c.(538-540)gCt>gGt	p.A180G	TXNDC16_ENST00000554399.1_Intron	NM_001160047.1|NM_020784.2	NP_001153519.1|NP_065835.2	Q9P2K2	TXD16_HUMAN	thioredoxin domain containing 16	180				A -> G (in Ref. 1; BAA92582). {ECO:0000305}.	cell redox homeostasis (GO:0045454)	endoplasmic reticulum lumen (GO:0005788)|extracellular vesicular exosome (GO:0070062)				breast(1)|cervix(1)|endometrium(2)|kidney(1)|large_intestine(2)|lung(10)|prostate(3)|skin(1)	21	Breast(41;0.0716)					ATACACAAAAGCGGCTTCCAT	0.363													G|||	73	0.0145767	0.0061	0.0101	5008	,	,		18339	0.004		0.0258	False		,,,				2504	0.0286				p.A180G		Atlas-SNP	.											.	TXNDC16	59	.	0			c.C539G						PASS	.	G	GLY/ALA,GLY/ALA	36,4370	40.8+/-73.8	0,36,2167	130.0	133.0	132.0		524,539	5.7	1.0	14	dbSNP_132	132	264,8334	102.1+/-163.3	2,260,4037	yes	missense,missense	TXNDC16	NM_001160047.1,NM_020784.2	60,60	2,296,6204	CC,CG,GG		3.0705,0.8171,2.307	probably-damaging,probably-damaging	175/821,180/826	52981664	300,12704	2203	4299	6502	SO:0001583	missense	57544	exon8			ACAAAAGCGGCTT	AB037765	CCDS32083.1	14q22.1	2007-08-16	2007-08-16	2007-08-16		ENSG00000087301			19965	protein-coding gene	gene with protein product			"""KIAA1344"""	KIAA1344			Standard	NM_020784		Approved		uc001wzs.3	Q9P2K2		ENST00000281741.4:c.539C>G	14.37:g.52981664G>C	ENSP00000281741:p.Ala180Gly	67.0	0.0	0		100.0	37.0	0.37	NM_020784	A5PKW9|A7E260|A7MD07|B9EH67|Q9H9W7	Missense_Mutation	SNP	ENST00000281741.4	37	CCDS32083.1	33	0.01510989010989011	3	0.006097560975609756	7	0.019337016574585635	0	0.0	23	0.030343007915567283	G	25.2	4.612167	0.87258	0.008171	0.030705	ENSG00000087301	ENST00000281741	T	0.36157	1.27	5.65	5.65	0.86999	.	0.000000	0.85682	D	0.000000	T	0.36717	0.0977	M	0.72894	2.215	0.54753	D	0.999984	D;D	0.89917	1.0;1.0	D;D	0.87578	0.998;0.997	T	0.54510	-0.8283	10	0.87932	D	0	-44.0895	17.2216	0.86959	0.0:0.0:1.0:0.0	.	175;180	B7ZME4;Q9P2K2	.;TXD16_HUMAN	G	180	ENSP00000281741:A180G	ENSP00000281741:A180G	A	-	2	0	TXNDC16	52051414	1.000000	0.71417	1.000000	0.80357	0.972000	0.66771	5.007000	0.63984	2.681000	0.91329	0.563000	0.77884	GCT	G|0.979;C|0.021	0.021	strong		0.363	TXNDC16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000411681.1	XM_051699	
AVPR1B	553	hgsc.bcm.edu	37	1	206225260	206225260	+	Missense_Mutation	SNP	C	C	G			TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr1:206225260C>G	ENST00000367126.4	+	1	1285	c.820C>G	c.(820-822)Cgg>Ggg	p.R274G	RP11-38J22.3_ENST00000425896.1_RNA	NM_000707.3	NP_000698.1	P47901	V1BR_HUMAN	arginine vasopressin receptor 1B	274					activation of phospholipase C activity (GO:0007202)|G-protein coupled receptor signaling pathway (GO:0007186)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|regulation of systemic arterial blood pressure by vasopressin (GO:0001992)	endosome (GO:0005768)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	protein kinase C binding (GO:0005080)|vasopressin receptor activity (GO:0005000)			breast(1)|cervix(1)|endometrium(1)|large_intestine(5)|lung(6)|ovary(3)|prostate(1)|skin(2)	20			BRCA - Breast invasive adenocarcinoma(75;0.0312)		Desmopressin(DB00035)|Terlipressin(DB02638)|Vasopressin(DB00067)	CACCATCTCACGGGCCAAGAT	0.597																																					p.R274G		Atlas-SNP	.											.	AVPR1B	47	.	0			c.C820G						PASS	.						71.0	68.0	69.0					1																	206225260		2203	4300	6503	SO:0001583	missense	553	exon1			ATCTCACGGGCCA	D31833	CCDS73015.1	1q32	2014-05-06			ENSG00000198049	ENSG00000198049		"""GPCR / Class A : Vasopressin and oxytocin receptors"""	896	protein-coding gene	gene with protein product		600264		AVPR3		7929452, 8586456	Standard	NM_000707		Approved		uc001hds.2	P47901	OTTHUMG00000184377	ENST00000367126.4:c.820C>G	1.37:g.206225260C>G	ENSP00000356094:p.Arg274Gly	144.0	0.0	0		190.0	39.0	0.205263	NM_000707	B0M0J6|Q5TZ00	Missense_Mutation	SNP	ENST00000367126.4	37	CCDS30994.1	.	.	.	.	.	.	.	.	.	.	C	14.44	2.537242	0.45176	.	.	ENSG00000198049	ENST00000367126	T	0.40756	1.02	5.34	-0.645	0.11475	GPCR, rhodopsin-like superfamily (1);	0.081659	0.48767	D	0.000165	T	0.65974	0.2743	M	0.85777	2.775	0.25895	N	0.983424	D	0.89917	1.0	D	0.83275	0.996	T	0.67189	-0.5733	10	0.72032	D	0.01	-31.1727	16.7694	0.85533	0.7528:0.2472:0.0:0.0	.	274	P47901	V1BR_HUMAN	G	274	ENSP00000356094:R274G	ENSP00000356094:R274G	R	+	1	2	AVPR1B	204391883	0.001000	0.12720	0.110000	0.21437	0.836000	0.47400	0.017000	0.13399	-0.086000	0.12550	0.462000	0.41574	CGG	.	.	none		0.597	AVPR1B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000087996.1	NM_000707	
DISC1	27185	hgsc.bcm.edu	37	1	231902975	231902975	+	Missense_Mutation	SNP	C	C	T	rs28930675	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr1:231902975C>T	ENST00000602281.1	+	5	1411	c.1358C>T	c.(1357-1359)aCg>aTg	p.T453M	TSNAX-DISC1_ENST00000602962.1_3'UTR|DISC1_ENST00000539444.1_Missense_Mutation_p.T453M|DISC1_ENST00000366633.3_Missense_Mutation_p.T453M|DISC1_ENST00000366637.3_5'UTR|DISC1_ENST00000439617.2_Missense_Mutation_p.T453M|DISC1_ENST00000535983.1_Missense_Mutation_p.T453M|DISC1_ENST00000366636.4_Missense_Mutation_p.T453M|DISC1_ENST00000537876.1_Missense_Mutation_p.T453M|DISC1_ENST00000602873.1_Missense_Mutation_p.T103M	NM_001164542.1|NM_001164544.1	NP_001158014.1|NP_001158016.1	Q9NRI5	DISC1_HUMAN	disrupted in schizophrenia 1	453	Interaction with TRAF3IP1.|Necessary and sufficient for interaction with PCNT and localization at the centrosome.|Required for localization to punctate cytoplasmic foci.				canonical Wnt signaling pathway (GO:0060070)|cell proliferation in forebrain (GO:0021846)|cellular protein localization (GO:0034613)|cerebral cortex radially oriented cell migration (GO:0021799)|microtubule cytoskeleton organization (GO:0000226)|mitochondrial calcium ion homeostasis (GO:0051560)|neuron migration (GO:0001764)|positive regulation of neuroblast proliferation (GO:0002052)|positive regulation of protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:2000060)|positive regulation of Wnt signaling pathway (GO:0030177)|regulation of neuron projection development (GO:0010975)|regulation of synapse maturation (GO:0090128)|TOR signaling (GO:0031929)	cell junction (GO:0030054)|centrosome (GO:0005813)|ciliary basal body (GO:0036064)|microtubule (GO:0005874)|mitochondrion (GO:0005739)|postsynaptic membrane (GO:0045211)				breast(1)|cervix(1)|kidney(1)|large_intestine(1)|liver(2)|lung(6)|skin(2)|upper_aerodigestive_tract(1)	15		all_cancers(173;0.0208)|Prostate(94;0.0975)				GTGTCCATCACGAGACGAGAC	0.507													C|||	7	0.00139776	0.0008	0.0	5008	,	,		18597	0.0		0.001	False		,,,				2504	0.0051				p.T485M		Atlas-SNP	.											.	DISC1	207	.	0			c.C1454T						PASS	.	C	MET/THR,MET/THR,MET/THR,MET/THR,MET/THR,,MET/THR,MET/THR,MET/THR,MET/THR,MET/THR,MET/THR,MET/THR,MET/THR,MET/THR,MET/THR	1,4405	2.1+/-5.4	0,1,2202	111.0	98.0	102.0		1358,1358,1454,1358,1358,,1358,1358,1358,1358,1358,1358,1358,1358,308,1358	3.7	0.2	1	dbSNP_125	102	25,8575	18.5+/-59.3	0,25,4275	yes	missense,missense,missense,missense,missense,intron,missense,missense,missense,missense,missense,missense,missense,missense,missense,missense	DISC1	NM_001012957.1,NM_001012959.1,NM_001164537.1,NM_001164538.1,NM_001164539.1,NM_001164540.1,NM_001164541.1,NM_001164542.1,NM_001164544.1,NM_001164545.1,NM_001164546.1,NM_001164547.1,NM_001164548.1,NM_001164549.1,NM_001164556.1,NM_018662.2	81,81,81,81,81,,81,81,81,81,81,81,81,81,81,81	0,26,6477	TT,TC,CC		0.2907,0.0227,0.1999	probably-damaging,probably-damaging,probably-damaging,probably-damaging,probably-damaging,,probably-damaging,probably-damaging,probably-damaging,probably-damaging,probably-damaging,probably-damaging,probably-damaging,probably-damaging,probably-damaging,probably-damaging	453/833,453/679,485/887,453/804,453/756,,453/696,453/682,453/663,453/580,453/560,453/560,453/552,453/548,103/202,453/855	231902975	26,12980	2203	4300	6503	SO:0001583	missense	27185	exon6			CCATCACGAGACG	AF222980	CCDS31055.1, CCDS31056.1, CCDS53482.1, CCDS53483.1, CCDS53484.1, CCDS59205.1, CCDS59206.1, CCDS59207.1	1q42.1	2008-02-05			ENSG00000162946	ENSG00000162946			2888	protein-coding gene	gene with protein product		605210				10814723	Standard	NM_001164550		Approved		uc010pxh.2	Q9NRI5	OTTHUMG00000037835	ENST00000602281.1:c.1358C>T	1.37:g.231902975C>T	ENSP00000473425:p.Thr453Met	108.0	0.0	0		124.0	32.0	0.258065	NM_001164537	A6NLH2|C4P091|C4P095|C4P0A1|C4P0A3|C4P0B3|C4P0B6|C4P0C1|C9J6D0|O75045|Q5VT44|Q5VT45|Q8IXJ0|Q8IXJ1|Q9BX19|Q9NRI3|Q9NRI4	Missense_Mutation	SNP	ENST00000602281.1	37	CCDS59205.1	3	0.0013736263736263737	2	0.0040650406504065045	0	0.0	0	0.0	1	0.0013192612137203166	C	12.61	1.989191	0.35131	2.27E-4	0.002907	ENSG00000162946	ENST00000439617;ENST00000366637;ENST00000366636;ENST00000366638;ENST00000535983;ENST00000537876;ENST00000366633;ENST00000539444;ENST00000295051;ENST00000535944	T;T;T;T;T;T;T;T	0.13901	2.92;2.73;2.72;2.57;2.9;2.57;2.57;2.55	3.74	3.74	0.42951	.	0.423266	0.24527	N	0.037752	T	0.23572	0.0570	M	0.62723	1.935	0.20638	N	0.999871	D;D;D;D;D;D;D;P;D;D;P;D;D;D;D;D;D;P	0.64830	0.992;0.992;0.988;0.983;0.989;0.966;0.979;0.941;0.994;0.988;0.941;0.994;0.988;0.979;0.988;0.979;0.988;0.941	P;P;P;P;P;B;B;B;P;P;B;P;P;B;P;B;P;B	0.54346	0.731;0.749;0.504;0.516;0.512;0.367;0.434;0.407;0.663;0.663;0.236;0.663;0.59;0.434;0.59;0.434;0.663;0.236	T	0.03413	-1.1039	10	0.59425	D	0.04	-3.9113	9.0698	0.36486	0.0:0.8923:0.0:0.1077	rs28930675	485;485;453;453;453;453;453;103;453;453;453;453;453;453;453;453;453;453	C4P096;E2QRA4;C4P0A3;C4P098;C4P0A1;C4P0A4;A6NLH2;C4P0C1;C4P0A5;C4P095;C4P0B6;C4P0C4;C4P0B1;A7E2W8;Q5T409;Q9NRI5-2;Q9NRI5;Q9NRI5-3	.;.;.;.;.;.;.;.;.;.;.;.;.;.;.;.;DISC1_HUMAN;.	M	453;453;453;485;453;453;453;453;453;453	ENSP00000403888:T453M;ENSP00000355596:T453M;ENSP00000443996:T453M;ENSP00000440909:T453M;ENSP00000355593:T453M;ENSP00000440953:T453M;ENSP00000295051:T453M;ENSP00000441193:T453M	ENSP00000295051:T453M	T	+	2	0	DISC1	229969598	0.470000	0.25854	0.174000	0.22961	0.391000	0.30476	1.717000	0.37991	2.063000	0.61619	0.655000	0.94253	ACG	C|0.998;T|0.002	0.002	strong		0.507	DISC1-019	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000467451.1	NM_018662	
MUC17	140453	hgsc.bcm.edu	37	7	100681920	100681920	+	Missense_Mutation	SNP	C	C	T	rs200222893|rs140211048	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr7:100681920C>T	ENST00000306151.4	+	3	7287	c.7223C>T	c.(7222-7224)cCg>cTg	p.P2408L		NM_001040105.1	NP_001035194.1	Q685J3	MUC17_HUMAN	mucin 17, cell surface associated	2408	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)					AGCACCATGCCGGTGGTCAGT	0.512																																					p.P2408L		Atlas-SNP	.											MUC17,NS,carcinoma,-1,1	MUC17	804	1	0			c.C7223T						PASS	.	C	LEU/PRO	1,4405		0,1,2202	381.0	361.0	368.0		7223	-1.5	0.0	7	dbSNP_134	368	1,8599		0,1,4299	no	missense	MUC17	NM_001040105.1	98	0,2,6501	TT,TC,CC		0.0116,0.0227,0.0154	probably-damaging	2408/4494	100681920	2,13004	2203	4300	6503	SO:0001583	missense	140453	exon3			CCATGCCGGTGGT	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.7223C>T	7.37:g.100681920C>T	ENSP00000302716:p.Pro2408Leu	210.0	0.0	0		314.0	16.0	0.0509554	NM_001040105	O14761|Q685J2|Q8TDH7	Missense_Mutation	SNP	ENST00000306151.4	37	CCDS34711.1	.	.	.	.	.	.	.	.	.	.	N	2.505	-0.314307	0.05422	2.27E-4	1.16E-4	ENSG00000169876	ENST00000306151	T	0.03242	4.0	0.762	-1.52	0.08637	.	.	.	.	.	T	0.06005	0.0156	L	0.34521	1.04	0.09310	N	1	D	0.76494	0.999	D	0.63283	0.913	T	0.24764	-1.0151	9	0.23302	T	0.38	.	3.7422	0.08534	0.0:0.6508:0.0:0.3492	.	2408	Q685J3	MUC17_HUMAN	L	2408	ENSP00000302716:P2408L	ENSP00000302716:P2408L	P	+	2	0	MUC17	100468640	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-1.422000	0.02453	-1.381000	0.02112	-1.368000	0.01194	CCG	C|1.000;T|0.000	0.000	strong		0.512	MUC17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347161.1	NM_001040105	
C20orf85	128602	hgsc.bcm.edu	37	20	56735761	56735761	+	Silent	SNP	C	C	T	rs61749694	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr20:56735761C>T	ENST00000371168.3	+	4	358	c.297C>T	c.(295-297)atC>atT	p.I99I		NM_178456.2	NP_848551.1	Q9H1P6	CT085_HUMAN	chromosome 20 open reading frame 85	99			I -> V (in dbSNP:rs17440813).							kidney(1)|large_intestine(2)|lung(6)|ovary(1)|skin(2)|urinary_tract(1)	13	all_epithelial(3;5.99e-14)|Lung NSC(12;0.000152)|all_lung(29;0.000518)|Melanoma(10;0.118)		BRCA - Breast invasive adenocarcinoma(13;5.53e-12)|Epithelial(14;7.42e-08)|all cancers(14;7.19e-07)			AGGGCTTCATCGGCTGGAGAT	0.577													C|||	9	0.00179712	0.0	0.0029	5008	,	,		19067	0.0		0.007	False		,,,				2504	0.0				p.I99I		Atlas-SNP	.											.	C20orf85	35	.	0			c.C297T						PASS	.	C		6,4400	9.9+/-24.2	0,6,2197	46.0	40.0	42.0		297	1.3	1.0	20	dbSNP_129	42	43,8557	27.9+/-77.7	0,43,4257	no	coding-synonymous	C20orf85	NM_178456.2		0,49,6454	TT,TC,CC		0.5,0.1362,0.3767		99/138	56735761	49,12957	2203	4300	6503	SO:0001819	synonymous_variant	128602	exon4			CTTCATCGGCTGG	AL354776	CCDS13465.1	20q13.32	2012-10-29			ENSG00000124237	ENSG00000124237			16216	protein-coding gene	gene with protein product	"""Low in Lung Cancer 1"""						Standard	NM_178456		Approved	bA196N14.1, LLC1	uc002xyv.3	Q9H1P6	OTTHUMG00000032836	ENST00000371168.3:c.297C>T	20.37:g.56735761C>T		90.0	0.0	0		80.0	36.0	0.45	NM_178456		Silent	SNP	ENST00000371168.3	37	CCDS13465.1																																																																																			C|0.997;T|0.003	0.003	strong		0.577	C20orf85-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079866.2	NM_178456	
C1orf35	79169	hgsc.bcm.edu	37	1	228290223	228290223	+	Silent	SNP	G	G	C	rs377443672	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr1:228290223G>C	ENST00000272139.4	-	4	564	c.330C>G	c.(328-330)ccC>ccG	p.P110P	C1orf35_ENST00000472617.1_5'UTR	NM_024319.2	NP_077295.1	Q9BU76	MMTA2_HUMAN	chromosome 1 open reading frame 35	110							poly(A) RNA binding (GO:0044822)			large_intestine(1)|lung(1)|skin(1)	3		Prostate(94;0.0488)				CCTTCTCCTCGGGGTCGCCTC	0.721													G|||	5	0.000998403	0.0008	0.0014	5008	,	,		9295	0.0		0.003	False		,,,				2504	0.0				p.P110P		Atlas-SNP	.											.	C1orf35	17	.	0			c.C330G						PASS	.	G		0,4340		0,0,2170	10.0	13.0	12.0		330	-8.1	0.6	1		12	9,8471		0,9,4231	no	coding-synonymous	C1orf35	NM_024319.2		0,9,6401	CC,CG,GG		0.1061,0.0,0.0702		110/264	228290223	9,12811	2170	4240	6410	SO:0001819	synonymous_variant	79169	exon4			CTCCTCGGGGTCG	AY137773	CCDS1566.1	1q42.13	2012-06-25			ENSG00000143793	ENSG00000143793			19032	protein-coding gene	gene with protein product	"""multiple myeloma tumor-associated protein 2"""					12545221	Standard	NM_024319		Approved	MGC4174, MMTAG2	uc001hrx.3	Q9BU76	OTTHUMG00000037793	ENST00000272139.4:c.330C>G	1.37:g.228290223G>C		148.0	0.0	0		175.0	66.0	0.377143	NM_024319	Q6P5Y0|Q6ZTZ6|Q6ZWA6|Q8IZH3	Silent	SNP	ENST00000272139.4	37	CCDS1566.1																																																																																			.	.	none		0.721	C1orf35-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000092245.1	NM_024319	
ZNF556	80032	hgsc.bcm.edu	37	19	2877426	2877426	+	Missense_Mutation	SNP	C	C	T	rs34849844	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr19:2877426C>T	ENST00000307635.2	+	4	557	c.470C>T	c.(469-471)aCc>aTc	p.T157I	ZNF556_ENST00000586426.1_Missense_Mutation_p.T156I	NM_024967.1	NP_079243.1	Q9HAH1	ZN556_HUMAN	zinc finger protein 556	157					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			endometrium(2)|kidney(1)|large_intestine(7)|lung(10)|pancreas(1)|prostate(3)|skin(7)	31				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)		AAACTCTTCACCCATTCCTCA	0.423													C|||	33	0.00658946	0.0015	0.0101	5008	,	,		20726	0.001		0.0159	False		,,,				2504	0.0072				p.T157I		Atlas-SNP	.											.	ZNF556	73	.	0			c.C470T						PASS	.	C	ILE/THR	15,4391	22.3+/-47.3	0,15,2188	136.0	123.0	127.0		470	-0.3	0.0	19	dbSNP_126	127	157,8443	74.8+/-137.4	3,151,4146	yes	missense	ZNF556	NM_024967.1	89	3,166,6334	TT,TC,CC		1.8256,0.3404,1.3225	benign	157/457	2877426	172,12834	2203	4300	6503	SO:0001583	missense	80032	exon4			TCTTCACCCATTC	BC009374	CCDS12097.1, CCDS74254.1	19p13.3	2013-09-20			ENSG00000172000	ENSG00000172000		"""Zinc fingers, C2H2-type"", ""-"""	25669	protein-coding gene	gene with protein product						12477932	Standard	XM_005259647		Approved	FLJ11637	uc002lwp.1	Q9HAH1	OTTHUMG00000180501	ENST00000307635.2:c.470C>T	19.37:g.2877426C>T	ENSP00000302603:p.Thr157Ile	94.0	0.0	0		65.0	36.0	0.553846	NM_024967	Q96GM3	Missense_Mutation	SNP	ENST00000307635.2	37	CCDS12097.1	15	0.006868131868131868	1	0.0020325203252032522	5	0.013812154696132596	0	0.0	9	0.011873350923482849	C	8.841	0.942299	0.18281	0.003404	0.018256	ENSG00000172000	ENST00000307635	T	0.28666	1.6	2.27	-0.272	0.12919	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.09291	0.0229	L	0.35487	1.065	0.09310	N	1	B	0.30068	0.267	B	0.24541	0.054	T	0.14924	-1.0455	9	0.44086	T	0.13	.	5.1815	0.15161	0.1587:0.4899:0.3514:0.0	rs34849844;rs62126859	157	Q9HAH1	ZN556_HUMAN	I	157	ENSP00000302603:T157I	ENSP00000302603:T157I	T	+	2	0	ZNF556	2828426	0.000000	0.05858	0.004000	0.12327	0.205000	0.24178	-3.911000	0.00336	0.139000	0.18822	0.407000	0.27541	ACC	C|0.987;T|0.013	0.013	strong		0.423	ZNF556-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000451638.2	NM_024967	
IGLL5	100423062	hgsc.bcm.edu	37	22	23230408	23230408	+	Missense_Mutation	SNP	A	A	C	rs552295669		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr22:23230408A>C	ENST00000526893.1	+	1	449	c.175A>C	c.(175-177)Agc>Cgc	p.S59R	IGLL5_ENST00000532223.2_Missense_Mutation_p.S59R|IGLL5_ENST00000531372.1_Missense_Mutation_p.S59R|hsa-mir-5571_ENST00000577998.1_RNA	NM_001178126.1	NP_001171597.1	B9A064	IGLL5_HUMAN	immunoglobulin lambda-like polypeptide 5	59						extracellular vesicular exosome (GO:0070062)				breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|lung(3)|urinary_tract(1)	7						AGTTGGAAGCAGCCGATCCAG	0.657																																					p.S59R		Atlas-SNP	.											.	IGLL5	26	.	0			c.A175C						PASS	.																																			SO:0001583	missense	100423062	exon1			GGAAGCAGCCGAT	M34518, M34515	CCDS54506.1	22q11.22	2013-01-11			ENSG00000254709	ENSG00000254709		"""Immunoglobulin superfamily / C1-set domain containing"""	38476	protein-coding gene	gene with protein product							Standard	NM_001178126		Approved		uc010gtu.3	B9A064	OTTHUMG00000165670	ENST00000526893.1:c.175A>C	22.37:g.23230408A>C	ENSP00000431254:p.Ser59Arg	164.0	0.0	0		145.0	38.0	0.262069	NM_001178126		Missense_Mutation	SNP	ENST00000526893.1	37	CCDS54506.1	.	.	.	.	.	.	.	.	.	.	A	12.14	1.848880	0.32699	.	.	ENSG00000254709	ENST00000532223;ENST00000526893;ENST00000531372	T;T	0.00593	6.34;6.35	3.92	-0.722	0.11184	.	.	.	.	.	T	0.00496	0.0016	L	0.29908	0.895	0.09310	N	1	B	0.21821	0.061	B	0.15870	0.014	T	0.45175	-0.9279	9	0.72032	D	0.01	.	3.8729	0.09044	0.4764:0.1955:0.3281:0.0	.	59	B9A064	IGLL5_HUMAN	R	59	ENSP00000436353:S59R;ENSP00000431254:S59R	ENSP00000431254:S59R	S	+	1	0	IGLL5	21560408	0.001000	0.12720	0.000000	0.03702	0.007000	0.05969	0.203000	0.17315	-0.212000	0.10109	0.523000	0.50628	AGC	.	.	none		0.657	IGLL5-002	KNOWN	basic|appris_candidate|readthrough_transcript|CCDS	protein_coding	protein_coding	OTTHUMT00000385699.1	NM_001178126	
ABR	29	hgsc.bcm.edu	37	17	970419	970419	+	Silent	SNP	G	G	A	rs199545490		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr17:970419G>A	ENST00000302538.5	-	10	1226	c.1080C>T	c.(1078-1080)ccC>ccT	p.P360P	ABR_ENST00000536794.2_Silent_p.P142P|ABR_ENST00000574437.1_Silent_p.P314P|ABR_ENST00000291107.2_Silent_p.P323P|ABR_ENST00000544583.2_Silent_p.P314P	NM_001282149.1|NM_021962.3	NP_001269078.1|NP_068781.2	Q12979	ABR_HUMAN	active BCR-related	360	PH. {ECO:0000255|PROSITE- ProRule:PRU00145}.				actin cytoskeleton organization (GO:0030036)|apoptotic signaling pathway (GO:0097190)|brain development (GO:0007420)|inner ear morphogenesis (GO:0042472)|negative regulation of cell migration (GO:0030336)|negative regulation of inflammatory response (GO:0050728)|negative regulation of neutrophil degranulation (GO:0043314)|neuromuscular process controlling balance (GO:0050885)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of apoptotic process (GO:0043065)|positive regulation of phagocytosis (GO:0050766)|regulation of small GTPase mediated signal transduction (GO:0051056)|response to lipopolysaccharide (GO:0032496)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)|membrane (GO:0016020)|plasma membrane (GO:0005886)	GTPase activator activity (GO:0005096)|Rac GTPase activator activity (GO:0030675)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)			breast(2)|central_nervous_system(1)|cervix(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(6)|lung(12)|ovary(2)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	39				UCEC - Uterine corpus endometrioid carcinoma (25;0.0228)		CAGACTCCTCGGGGGATGGAA	0.582																																					p.P360P	Esophageal Squamous(197;2016 2115 4129 29033 46447)	Atlas-SNP	.											ABR,colon,carcinoma,0,1	ABR	119	1	0			c.C1080T						scavenged	.						35.0	33.0	34.0					17																	970419		2203	4300	6503	SO:0001819	synonymous_variant	29	exon10			CTCCTCGGGGGAT	L19704	CCDS10999.1, CCDS11000.1, CCDS54060.1, CCDS58497.1, CCDS73936.1	17p13	2013-01-10	2012-02-27		ENSG00000159842	ENSG00000159842		"""Rho guanine nucleotide exchange factors"", ""Pleckstrin homology (PH) domain containing"""	81	protein-coding gene	gene with protein product		600365	"""active BCR-related gene"""			2587217, 7479768	Standard	NM_001092		Approved	MDB	uc002fsd.4	Q12979	OTTHUMG00000090313	ENST00000302538.5:c.1080C>T	17.37:g.970419G>A		66.0	1.0	0.0151515		73.0	40.0	0.547945	NM_021962	B3KW89|B7Z6H7|D3DTH3|D3DTH4|F5H3S2|F5H8B3|Q13693|Q13694	Silent	SNP	ENST00000302538.5	37	CCDS10999.1																																																																																			G|0.999;A|0.001	0.001	weak		0.582	ABR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206675.4		
KIAA0754	643314	hgsc.bcm.edu	37	1	39879405	39879405	+	Silent	SNP	C	C	T	rs548996855|rs199726261		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr1:39879405C>T	ENST00000530275.1	+	1	3255	c.3060C>T	c.(3058-3060)tcC>tcT	p.S1020S	MACF1_ENST00000564288.1_Intron|MACF1_ENST00000539005.1_Intron|MACF1_ENST00000317713.7_Intron|MACF1_ENST00000545844.1_Intron|MACF1_ENST00000567887.1_Intron|MACF1_ENST00000361689.2_Intron|MACF1_ENST00000289893.4_Intron|MACF1_ENST00000372915.3_Intron	NM_015038.1	NP_055853.1	O94854	K0754_HUMAN	KIAA0754	1020	Ala-rich.									central_nervous_system(1)|large_intestine(6)|skin(1)	8	Lung NSC(20;5.57e-06)|Ovarian(52;0.00769)|Acute lymphoblastic leukemia(166;0.074)	Myeloproliferative disorder(586;0.0393)	OV - Ovarian serous cystadenocarcinoma(33;7.78e-19)|Epithelial(16;1.73e-17)|all cancers(16;2.49e-16)|LUSC - Lung squamous cell carcinoma(16;0.00146)|Lung(16;0.00204)			CAGAGGAATCCGCCTCCGCAG	0.682																																					p.S1156S		Atlas-SNP	.											.	KIAA0754	93	.	0			c.C3468T						PASS	.						18.0	21.0	20.0					1																	39879405		1939	4131	6070	SO:0001819	synonymous_variant	643314	exon1			GGAATCCGCCTCC			1p34.2	2009-07-09				ENSG00000255103			29111	protein-coding gene	gene with protein product						9872452	Standard	NM_015038		Approved		uc009vvt.1	O94854		ENST00000530275.1:c.3060C>T	1.37:g.39879405C>T		206.0	0.0	0		55.0	20.0	0.363636	NM_015038	E9PMC2|Q6ZSB2	Silent	SNP	ENST00000530275.1	37																																																																																				.	.	none		0.682	KIAA0754-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000392100.1	NM_015038	
MGAT4A	11320	hgsc.bcm.edu	37	2	99271976	99271976	+	Missense_Mutation	SNP	T	T	C	rs61748145	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr2:99271976T>C	ENST00000264968.3	-	7	1069	c.706A>G	c.(706-708)Aca>Gca	p.T236A	MGAT4A_ENST00000461884.1_5'Flank|MGAT4A_ENST00000414521.2_Missense_Mutation_p.T108A|MGAT4A_ENST00000393487.1_Missense_Mutation_p.T236A|MGAT4A_ENST00000409391.1_Missense_Mutation_p.T236A			Q9UM21	MGT4A_HUMAN	mannosyl (alpha-1,3-)-glycoprotein beta-1,4-N-acetylglucosaminyltransferase, isozyme A	236					cellular protein metabolic process (GO:0044267)|N-glycan processing (GO:0006491)|post-translational protein modification (GO:0043687)|protein N-linked glycosylation via asparagine (GO:0018279)	extracellular vesicular exosome (GO:0070062)|Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)	alpha-1,3-mannosylglycoprotein 4-beta-N-acetylglucosaminyltransferase activity (GO:0008454)|metal ion binding (GO:0046872)			NS(1)|breast(2)|endometrium(2)|kidney(2)|large_intestine(3)|lung(7)|skin(1)|stomach(1)	19						TTTTGCTTTGTTCTCCATCTG	0.279													T|||	17	0.00339457	0.0008	0.0043	5008	,	,		20215	0.0		0.0099	False		,,,				2504	0.0031				p.T236A		Atlas-SNP	.											.	MGAT4A	51	.	0			c.A706G						PASS	.	T	ALA/THR,ALA/THR	12,4394	21.2+/-45.6	0,12,2191	94.0	88.0	90.0		322,706	5.1	1.0	2	dbSNP_129	90	92,8506	51.9+/-112.3	0,92,4207	yes	missense,missense	MGAT4A	NM_001160154.1,NM_012214.2	58,58	0,104,6398	CC,CT,TT		1.07,0.2724,0.7998	possibly-damaging,possibly-damaging	108/424,236/536	99271976	104,12900	2203	4299	6502	SO:0001583	missense	11320	exon8			GCTTTGTTCTCCA	AB000616	CCDS2036.1, CCDS54380.1	2q12	2013-02-25	2005-11-16		ENSG00000071073	ENSG00000071073	2.4.1.145	"""Mannosyl-glycoprotein beta N-acetylglucosaminyltransferases"""	7047	protein-coding gene	gene with protein product		604623	"""mannosyl (alpha-1,3-)-glycoprotein beta-1,4-N-acetylglucosaminyltransferase, isoenzyme A"""			10024668	Standard	NM_001160154		Approved	GnT-Iva, GnT-4a	uc002sze.3	Q9UM21	OTTHUMG00000130563	ENST00000264968.3:c.706A>G	2.37:g.99271976T>C	ENSP00000264968:p.Thr236Ala	99.0	0.0	0		98.0	48.0	0.489796	NM_012214	B4E2R6|D3DVH6|E9PEN2|Q53S97|Q86Z15	Missense_Mutation	SNP	ENST00000264968.3	37	CCDS2036.1	8	0.003663003663003663	1	0.0020325203252032522	3	0.008287292817679558	0	0.0	4	0.005277044854881266	T	24.9	4.578058	0.86645	0.002724	0.0107	ENSG00000071073	ENST00000393487;ENST00000414521;ENST00000264968;ENST00000409391	T;T;T;T	0.44482	0.92;0.92;0.92;0.92	5.12	5.12	0.69794	.	0.093140	0.85682	D	0.000000	T	0.63046	0.2478	M	0.90082	3.085	0.80722	D	1	D;D	0.76494	0.999;0.997	D;D	0.83275	0.996;0.992	T	0.73883	-0.3842	10	0.52906	T	0.07	-3.5017	14.3832	0.66926	0.0:0.0:0.0:1.0	rs61748145	108;236	E9PEN2;Q9UM21	.;MGT4A_HUMAN	A	236;108;236;236	ENSP00000377127:T236A;ENSP00000404889:T108A;ENSP00000264968:T236A;ENSP00000386841:T236A	ENSP00000264968:T236A	T	-	1	0	MGAT4A	98638408	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	7.938000	0.87678	2.044000	0.60594	0.533000	0.62120	ACA	T|0.993;C|0.007	0.007	strong		0.279	MGAT4A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252988.2	NM_012214	
HOXA7	3204	hgsc.bcm.edu	37	7	27196116	27196116	+	Missense_Mutation	SNP	C	C	T	rs78410337	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr7:27196116C>T	ENST00000242159.3	-	1	182	c.49G>A	c.(49-51)Ggg>Agg	p.G17R	HOXA7_ENST00000523796.2_5'Flank|HOXA-AS3_ENST00000518947.2_RNA|RP1-170O19.21_ENST00000602610.1_lincRNA	NM_006896.3	NP_008827.2	P31268	HXA7_HUMAN	homeobox A7	17					angiogenesis (GO:0001525)|anterior/posterior pattern specification (GO:0009952)|embryonic skeletal system morphogenesis (GO:0048704)|negative regulation of cell-matrix adhesion (GO:0001953)|negative regulation of keratinocyte differentiation (GO:0045617)|negative regulation of leukocyte migration (GO:0002686)|negative regulation of monocyte differentiation (GO:0045656)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|stem cell differentiation (GO:0048863)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription factor binding (GO:0008134)			endometrium(3)|large_intestine(1)|lung(10)|prostate(1)|urinary_tract(1)	16						AGAGAAGCCCCCGCCGTATAT	0.532													C|||	13	0.00259585	0.0	0.0029	5008	,	,		12045	0.0		0.0109	False		,,,				2504	0.0				p.G17R		Atlas-SNP	.											.	HOXA7	34	.	0			c.G49A						PASS	.	C	ARG/GLY	18,4380		0,18,2181	64.0	81.0	75.0		49	5.2	1.0	7	dbSNP_131	75	98,8490		0,98,4196	yes	missense	HOXA7	NM_006896.3	125	0,116,6377	TT,TC,CC		1.1411,0.4093,0.8933	probably-damaging	17/231	27196116	116,12870	2199	4294	6493	SO:0001583	missense	3204	exon1			AAGCCCCCGCCGT		CCDS5408.1	7p15.2	2011-06-20	2005-12-22		ENSG00000122592	ENSG00000122592		"""Homeoboxes / ANTP class : HOXL subclass"""	5108	protein-coding gene	gene with protein product		142950	"""homeo box A7"""	HOX1A, HOX1		1973146, 1358459	Standard	NM_006896		Approved		uc003sys.3	P31268	OTTHUMG00000023217	ENST00000242159.3:c.49G>A	7.37:g.27196116C>T	ENSP00000242159:p.Gly17Arg	116.0	0.0	0		164.0	47.0	0.286585	NM_006896	A4D191|O43368|O43486|O95655|Q9NSC8|Q9UDM1	Missense_Mutation	SNP	ENST00000242159.3	37	CCDS5408.1	8	0.003663003663003663	0	0.0	1	0.0027624309392265192	0	0.0	7	0.009234828496042216	C	32	5.110578	0.94292	0.004093	0.011411	ENSG00000122592	ENST00000242159;ENST00000519842	T;D	0.82081	1.53;-1.57	5.21	5.21	0.72293	.	0.121540	0.52532	D	0.000067	T	0.79834	0.4514	M	0.84948	2.725	0.80722	D	1	P	0.40144	0.704	B	0.31390	0.129	D	0.86042	0.1520	10	0.87932	D	0	.	18.7386	0.91765	0.0:1.0:0.0:0.0	.	17	P31268	HXA7_HUMAN	R	17	ENSP00000242159:G17R;ENSP00000428563:G17R	ENSP00000242159:G17R	G	-	1	0	HOXA7	27162641	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	7.510000	0.81708	2.599000	0.87857	0.561000	0.74099	GGG	C|0.993;T|0.007	0.007	strong		0.532	HOXA7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000358695.1		
PARK2	5071	hgsc.bcm.edu	37	6	162864492	162864492	+	Missense_Mutation	SNP	G	G	C			TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr6:162864492G>C	ENST00000366898.1	-	2	123	c.21C>G	c.(19-21)ttC>ttG	p.F7L	PARK2_ENST00000366894.1_5'UTR|PARK2_ENST00000366897.1_Missense_Mutation_p.F7L|PARK2_ENST00000338468.3_5'UTR|PARK2_ENST00000366896.1_Missense_Mutation_p.F7L|PARK2_ENST00000366892.1_Missense_Mutation_p.F7L	NM_004562.2	NP_004553.2	O60260	PRKN2_HUMAN	parkin RBR E3 ubiquitin protein ligase	7	Ubiquitin-like. {ECO:0000255|PROSITE- ProRule:PRU00214}.				adult locomotory behavior (GO:0008344)|aggresome assembly (GO:0070842)|cell death (GO:0008219)|cellular protein catabolic process (GO:0044257)|cellular response to dopamine (GO:1903351)|cellular response to manganese ion (GO:0071287)|cellular response to toxic substance (GO:0097237)|cellular response to unfolded protein (GO:0034620)|central nervous system development (GO:0007417)|dopamine metabolic process (GO:0042417)|dopamine uptake involved in synaptic transmission (GO:0051583)|learning (GO:0007612)|mitochondrion degradation (GO:0000422)|negative regulation of actin filament bundle assembly (GO:0032232)|negative regulation of cell death (GO:0060548)|negative regulation of endoplasmic reticulum stress-induced intrinsic apoptotic signaling pathway (GO:1902236)|negative regulation of glucokinase activity (GO:0033132)|negative regulation of insulin secretion (GO:0046676)|negative regulation of neuron apoptotic process (GO:0043524)|negative regulation of neuron death (GO:1901215)|negative regulation of oxidative stress-induced cell death (GO:1903202)|negative regulation of oxidative stress-induced neuron intrinsic apoptotic signaling pathway (GO:1903377)|negative regulation of protein phosphorylation (GO:0001933)|negative regulation of reactive oxygen species metabolic process (GO:2000378)|negative regulation of release of cytochrome c from mitochondria (GO:0090201)|norepinephrine metabolic process (GO:0042415)|positive regulation of DNA binding (GO:0043388)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of mitochondrial fusion (GO:0010636)|positive regulation of proteasomal protein catabolic process (GO:1901800)|positive regulation of protein linear polyubiquitination (GO:1902530)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of tumor necrosis factor-mediated signaling pathway (GO:1903265)|proteasome-mediated ubiquitin-dependent protein catabolic process (GO:0043161)|protein autoubiquitination (GO:0051865)|protein K27-linked ubiquitination (GO:0044314)|protein K29-linked ubiquitination (GO:0035519)|protein K48-linked ubiquitination (GO:0070936)|protein K6-linked ubiquitination (GO:0085020)|protein K63-linked ubiquitination (GO:0070534)|protein monoubiquitination (GO:0006513)|protein polyubiquitination (GO:0000209)|protein ubiquitination (GO:0016567)|protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:0042787)|regulation of autophagy (GO:0010506)|regulation of dopamine secretion (GO:0014059)|regulation of glucose metabolic process (GO:0010906)|regulation of lipid transport (GO:0032368)|regulation of mitochondrion degradation (GO:1903146)|regulation of mitochondrion organization (GO:0010821)|regulation of neurotransmitter secretion (GO:0046928)|regulation of reactive oxygen species metabolic process (GO:2000377)|regulation of synaptic vesicle transport (GO:1902803)|response to endoplasmic reticulum stress (GO:0034976)|startle response (GO:0001964)|synaptic transmission, glutamatergic (GO:0035249)|transcription, DNA-templated (GO:0006351)	aggresome (GO:0016235)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|Lewy body (GO:0097413)|mitochondrion (GO:0005739)|neuron projection (GO:0043005)|nucleus (GO:0005634)|Parkin-FBXW7-Cul1 ubiquitin ligase complex (GO:1990452)|perinuclear region of cytoplasm (GO:0048471)|ubiquitin ligase complex (GO:0000151)	chaperone binding (GO:0051087)|cullin family protein binding (GO:0097602)|F-box domain binding (GO:1990444)|G-protein coupled receptor binding (GO:0001664)|heat shock protein binding (GO:0031072)|Hsp70 protein binding (GO:0030544)|identical protein binding (GO:0042802)|kinase binding (GO:0019900)|ligase activity (GO:0016874)|PDZ domain binding (GO:0030165)|protein kinase binding (GO:0019901)|SH3 domain binding (GO:0017124)|ubiquitin binding (GO:0043130)|ubiquitin conjugating enzyme binding (GO:0031624)|ubiquitin protein ligase activity (GO:0061630)|ubiquitin protein ligase binding (GO:0031625)|ubiquitin-protein transferase activity (GO:0004842)|ubiquitin-specific protease binding (GO:1990381)|zinc ion binding (GO:0008270)			breast(1)|cervix(1)|endometrium(3)|kidney(1)|large_intestine(7)|lung(21)|prostate(2)|skin(1)|upper_aerodigestive_tract(2)	39		all_cancers(1;8.13e-65)|all_epithelial(1;5.77e-64)|Colorectal(1;9.65e-15)|all_lung(1;1.66e-13)|Lung NSC(1;7.54e-11)|Melanoma(1;1.75e-09)|Breast(66;7.81e-05)|Ovarian(120;0.000981)|Prostate(117;0.0288)|Esophageal squamous(34;0.102)		UCEC - Uterine corpus endometrioid carcinoma (4;0.0663)|all cancers(1;1.9e-63)|Epithelial(1;1.5e-59)|Colorectal(1;2.16e-23)|OV - Ovarian serous cystadenocarcinoma(65;3.53e-20)|COAD - Colon adenocarcinoma(1;2.11e-15)|STAD - Stomach adenocarcinoma(1;4.64e-07)|BRCA - Breast invasive adenocarcinoma(81;1.49e-06)|READ - Rectum adenocarcinoma(1;2.95e-06)|GBM - Glioblastoma multiforme(2;7.23e-06)|Lung(1;0.00163)|KIRC - Kidney renal clear cell carcinoma(4;0.00371)|LUSC - Lung squamous cell carcinoma(1;0.00442)|Kidney(4;0.0046)		GGCTGGAGTTGAACCTGACAA	0.498																																					p.F7L		Atlas-SNP	.											.	PARK2	96	.	0			c.C21G						PASS	.						108.0	93.0	98.0					6																	162864492		2203	4300	6503	SO:0001583	missense	5071	exon2			GGAGTTGAACCTG		CCDS5281.1, CCDS5282.1, CCDS5283.1	6q25.2-q27	2013-10-03	2013-10-03		ENSG00000185345	ENSG00000185345		"""Parkinson disease"""	8607	protein-coding gene	gene with protein product	"""E3 ubiquitin ligase"""	602544	"""Parkinson disease (autosomal recessive, juvenile) 2, parkin"", ""parkinson protein 2, E3 ubiquitin protein ligase (parkin)"""			9560156, 9570960	Standard	NM_004562		Approved	PDJ, AR-JP, parkin	uc003qtx.4	O60260	OTTHUMG00000015970	ENST00000366898.1:c.21C>G	6.37:g.162864492G>C	ENSP00000355865:p.Phe7Leu	118.0	0.0	0		129.0	35.0	0.271318	NM_004562	A3FG77|A8K975|D3JZW7|D3K2X0|Q5TFV8|Q5VVX4|Q6Q2I6|Q8NI41|Q8NI43|Q8NI44|Q8WW07	Missense_Mutation	SNP	ENST00000366898.1	37	CCDS5281.1	.	.	.	.	.	.	.	.	.	.	G	18.43	3.621739	0.66787	.	.	ENSG00000185345	ENST00000366898;ENST00000366897;ENST00000366896;ENST00000366892;ENST00000542682	D;D;D;D	0.95885	-3.84;-3.84;-3.84;-3.84	5.63	5.63	0.86233	Ubiquitin supergroup (1);Ubiquitin (1);	0.058575	0.64402	D	0.000002	D	0.96367	0.8815	M	0.61703	1.905	0.33112	D	0.540611	D;P;D;D	0.76494	0.999;0.88;0.997;0.995	D;D;D;D	0.80764	0.994;0.946;0.958;0.958	D	0.95572	0.8639	10	0.44086	T	0.13	.	14.8348	0.70175	0.0:0.0:0.8561:0.1438	.	7;7;7;7	O60260-5;Q5VVX3;Q5VVX4;O60260	.;.;.;PRKN2_HUMAN	L	7;7;7;7;6	ENSP00000355865:F7L;ENSP00000355863:F7L;ENSP00000355862:F7L;ENSP00000355858:F7L	ENSP00000355858:F7L	F	-	3	2	PARK2	162784482	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	3.700000	0.54786	2.805000	0.96524	0.655000	0.94253	TTC	.	.	none		0.498	PARK2-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042995.1		
TCF3	6929	hgsc.bcm.edu	37	19	1615393	1615393	+	Silent	SNP	C	C	T	rs143212973	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr19:1615393C>T	ENST00000262965.5	-	18	2057	c.1713G>A	c.(1711-1713)gaG>gaA	p.E571E	TCF3_ENST00000395423.3_Silent_p.E575E|TCF3_ENST00000588136.1_Intron|TCF3_ENST00000344749.5_Intron|TCF3_ENST00000453954.2_Intron|RNU6-1223P_ENST00000517124.1_RNA	NM_003200.3	NP_003191.1	Q9HCS4	TF7L1_HUMAN	transcription factor 3	0					anterior/posterior axis specification, embryo (GO:0008595)|axial mesoderm morphogenesis (GO:0048319)|brain development (GO:0007420)|canonical Wnt signaling pathway (GO:0060070)|chromatin organization (GO:0006325)|generation of neurons (GO:0048699)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of transcription from RNA polymerase II promoter during mitosis (GO:0046022)|regulation of stem cell maintenance (GO:2000036)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|regulation of transcription, DNA-templated (GO:0006355)|regulation of Wnt signaling pathway (GO:0030111)|skin development (GO:0043588)|somatic stem cell maintenance (GO:0035019)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)|transcription factor complex (GO:0005667)	beta-catenin binding (GO:0008013)|chromatin binding (GO:0003682)|DNA binding (GO:0003677)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription regulatory region DNA binding (GO:0044212)			breast(2)|central_nervous_system(1)|kidney(2)|large_intestine(2)|lung(6)|ovary(1)|skin(2)	16		Acute lymphoblastic leukemia(61;5.94e-12)|all_hematologic(61;1.27e-07)		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)		TGCGCCCCAGCTCCTTAAAGG	0.637			T	"""PBX1, HLF, TFPT"""	pre B-ALL								C|||	6	0.00119808	0.0	0.0	5008	,	,		14615	0.0		0.006	False		,,,				2504	0.0				p.E571E		Atlas-SNP	.		Dom	yes		19	19p13.3	6929	transcription factor 3 (E2A immunoglobulin enhancer binding factors E12/E47)		L	.	TCF3	72	.	0			c.G1713A						PASS	.	C	,	12,4394	20.2+/-43.8	0,12,2191	98.0	97.0	97.0		,1713	3.4	1.0	19	dbSNP_134	97	52,8548	33.8+/-87.4	2,48,4250	no	intron,coding-synonymous	TCF3	NM_001136139.2,NM_003200.3	,	2,60,6441	TT,TC,CC		0.6047,0.2724,0.4921	,	,571/655	1615393	64,12942	2203	4300	6503	SO:0001819	synonymous_variant	6929	exon18			CCCCAGCTCCTTA	M65214	CCDS12074.1, CCDS45899.1	19p13.3	2014-02-13	2013-02-26		ENSG00000071564	ENSG00000071564		"""Basic helix-loop-helix proteins"""	11633	protein-coding gene	gene with protein product	"""transcription factor E2-alpha"", ""immunoglobulin transcription factor 1"", ""kappa-E2-binding factor"", ""E2A immunoglobulin enhancer-binding factor E12/E47"", ""VDR interacting repressor"""	147141				2308859, 1967983	Standard	NM_003200		Approved	E2A, ITF1, MGC129647, MGC129648, bHLHb21, VDIR, E47	uc002ltt.4	P15923	OTTHUMG00000180031	ENST00000262965.5:c.1713G>A	19.37:g.1615393C>T		99.0	0.0	0		74.0	37.0	0.5	NM_003200	Q53R97|Q6PD70|Q9NP00	Silent	SNP	ENST00000262965.5	37	CCDS12074.1																																																																																			C|0.997;T|0.003	0.003	strong		0.637	TCF3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000449367.1	NM_003200	
PBLD	64081	hgsc.bcm.edu	37	10	70066553	70066553	+	Missense_Mutation	SNP	G	G	A	rs12359690	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr10:70066553G>A	ENST00000358769.2	-	2	251	c.49C>T	c.(49-51)Cgt>Tgt	p.R17C	PBLD_ENST00000432941.1_Missense_Mutation_p.R17C|PBLD_ENST00000495025.2_Missense_Mutation_p.R17C|PBLD_ENST00000309049.4_Missense_Mutation_p.R17C	NM_022129.3	NP_071412.2	P30039	PBLD_HUMAN	phenazine biosynthesis-like protein domain containing	17			R -> C (in dbSNP:rs12359690). {ECO:0000269|PubMed:15806103}.		biosynthetic process (GO:0009058)|maintenance of gastrointestinal epithelium (GO:0030277)|negative regulation of epithelial cell migration (GO:0010633)|negative regulation of epithelial cell proliferation (GO:0050680)|negative regulation of epithelial to mesenchymal transition (GO:0010719)|negative regulation of pathway-restricted SMAD protein phosphorylation (GO:0060394)|negative regulation of SMAD protein import into nucleus (GO:0060392)|negative regulation of transforming growth factor beta receptor signaling pathway (GO:0030512)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)	isomerase activity (GO:0016853)			endometrium(4)|kidney(2)|large_intestine(2)|liver(1)|lung(8)|ovary(1)|skin(2)|upper_aerodigestive_tract(1)	21						GGATTCCCACGAAATGCTCTT	0.383													G|||	117	0.0233626	0.0461	0.0245	5008	,	,		18502	0.0		0.0318	False		,,,				2504	0.0072				p.R17C		Atlas-SNP	.											.	PBLD	53	.	0			c.C49T						PASS	.	G	CYS/ARG,CYS/ARG	186,4220	119.6+/-157.3	6,174,2023	89.0	82.0	85.0		49,49	0.5	0.9	10	dbSNP_120	85	399,8201	127.2+/-185.5	8,383,3909	yes	missense,missense	PBLD	NM_001033083.1,NM_022129.3	180,180	14,557,5932	AA,AG,GG		4.6395,4.2215,4.4979	benign,benign	17/281,17/289	70066553	585,12421	2203	4300	6503	SO:0001583	missense	64081	exon2			TCCCACGAAATGC	AK027673	CCDS7277.2, CCDS44413.1	10q21.3	2006-11-27			ENSG00000108187	ENSG00000108187			23301	protein-coding gene	gene with protein product	MAWD binding protein	612189				11355021	Standard	XM_005270028		Approved	MAWBP, MAWDBP, FLJ14767	uc001jns.1	P30039	OTTHUMG00000073949	ENST00000358769.2:c.49C>T	10.37:g.70066553G>A	ENSP00000351619:p.Arg17Cys	264.0	0.0	0		117.0	117.0	1	NM_022129	A8MZJ3|C9JIM0|Q9HCC2	Missense_Mutation	SNP	ENST00000358769.2	37	CCDS7277.2	53	0.024267399267399268	25	0.0508130081300813	8	0.022099447513812154	0	0.0	20	0.026385224274406333	G	11.72	1.723233	0.30503	0.042215	0.046395	ENSG00000108187	ENST00000358769;ENST00000309049;ENST00000432941;ENST00000277795	T;T;T;T	0.31510	1.49;1.49;1.49;1.49	5.51	0.525	0.17072	.	0.445102	0.24249	N	0.040187	T	0.04363	0.0120	L	0.55017	1.72	0.21416	N	0.999695	B;B;B	0.16802	0.002;0.019;0.008	B;B;B	0.16289	0.001;0.015;0.007	T	0.11641	-1.0579	10	0.56958	D	0.05	0.3367	8.8276	0.35065	0.4705:0.0:0.5295:0.0	rs12359690;rs52804292;rs12359690	17;17;17	F8W7D0;C9JIM0;P30039	.;.;PBLD_HUMAN	C	17	ENSP00000351619:R17C;ENSP00000308466:R17C;ENSP00000395534:R17C;ENSP00000277795:R17C	ENSP00000277795:R17C	R	-	1	0	PBLD	69736559	0.038000	0.19896	0.910000	0.35882	0.979000	0.70002	-0.107000	0.10873	-0.157000	0.11059	-1.002000	0.02502	CGT	G|0.961;A|0.039	0.039	strong		0.383	PBLD-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048314.1	NM_022129	
ANXA7	310	hgsc.bcm.edu	37	10	75139952	75139952	+	Missense_Mutation	SNP	C	C	T	rs10159690	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr10:75139952C>T	ENST00000372921.5	-	10	982	c.926G>A	c.(925-927)cGt>cAt	p.R309H	RP11-537A6.9_ENST00000427492.1_RNA|ANXA7_ENST00000535178.1_Missense_Mutation_p.R179H	NM_001156.3	NP_001147.1	P20073	ANXA7_HUMAN	annexin A7	331					autophagy (GO:0006914)|cell proliferation (GO:0008283)|cellular calcium ion homeostasis (GO:0006874)|cellular water homeostasis (GO:0009992)|epithelial cell differentiation (GO:0030855)|hemostasis (GO:0007599)|membrane fusion (GO:0061025)|negative regulation of gene expression (GO:0010629)|regulation of cell shape (GO:0008360)|response to calcium ion (GO:0051592)|response to organic cyclic compound (GO:0014070)|response to salt stress (GO:0009651)|social behavior (GO:0035176)	cytosol (GO:0005829)|endoplasmic reticulum membrane (GO:0005789)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|nuclear envelope (GO:0005635)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|calcium-dependent phospholipid binding (GO:0005544)|calcium-dependent protein binding (GO:0048306)|integrin binding (GO:0005178)|poly(A) RNA binding (GO:0044822)			breast(2)|central_nervous_system(1)|endometrium(4)|kidney(2)|large_intestine(4)|lung(7)|ovary(2)|prostate(1)|stomach(2)|upper_aerodigestive_tract(1)	26	Prostate(51;0.0119)					GTTCTCATCACGATTTCCCTG	0.388																																					p.R331H		Atlas-SNP	.											ANXA7,colon,carcinoma,-1,1	ANXA7	50	1	0			c.G992A						scavenged	.						159.0	156.0	157.0					10																	75139952		2203	4300	6503	SO:0001583	missense	310	exon11			TCATCACGATTTC	J04543	CCDS7325.1, CCDS7326.1	10q22.2	2005-11-09			ENSG00000138279	ENSG00000138279		"""Annexins"""	545	protein-coding gene	gene with protein product		186360		ANX7		7515686	Standard	NM_001156		Approved		uc001jtz.2	P20073	OTTHUMG00000018463	ENST00000372921.5:c.926G>A	10.37:g.75139952C>T	ENSP00000362012:p.Arg309His	89.0	0.0	0		62.0	3.0	0.0483871	NM_004034	Q5F2H3|Q5T0M6|Q5T0M7	Missense_Mutation	SNP	ENST00000372921.5	37	CCDS7325.1	.	.	.	.	.	.	.	.	.	.	C	23.4	4.416323	0.83449	.	.	ENSG00000138279	ENST00000372921;ENST00000372919;ENST00000535178	T;T;T	0.17370	2.28;2.28;2.28	6.17	4.27	0.50696	.	0.000000	0.85682	D	0.000000	T	0.55226	0.1907	H	0.98178	4.165	0.51767	D	0.999933	D;D;D;D;D	0.89917	1.0;1.0;1.0;1.0;1.0	D;D;D;D;D	0.87578	0.997;0.998;0.996;0.998;0.997	T	0.68469	-0.5400	10	0.87932	D	0	.	10.012	0.41992	0.1369:0.7898:0.0:0.0733	rs10159690;rs10159690	309;309;236;309;331	Q53HM8;B2R7L2;B4DWU2;P20073-2;P20073	.;.;.;.;ANXA7_HUMAN	H	309;331;179	ENSP00000362012:R309H;ENSP00000362010:R331H;ENSP00000442864:R179H	ENSP00000362010:R331H	R	-	2	0	ANXA7	74809958	1.000000	0.71417	0.999000	0.59377	0.985000	0.73830	4.762000	0.62250	1.575000	0.49775	0.655000	0.94253	CGT	C|0.994;T|0.006	0.006	strong		0.388	ANXA7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048646.2	NM_001156	
ACE	1636	hgsc.bcm.edu	37	17	61573777	61573777	+	Missense_Mutation	SNP	C	C	A			TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr17:61573777C>A	ENST00000290866.4	+	23	3427	c.3403C>A	c.(3403-3405)Cag>Aag	p.Q1135K	ACE_ENST00000421982.2_Intron|ACE_ENST00000413513.3_Intron|ACE_ENST00000490216.2_Missense_Mutation_p.Q561K|ACE_ENST00000290863.6_Missense_Mutation_p.Q561K|ACE_ENST00000428043.1_Missense_Mutation_p.Q1135K|ACE_ENST00000577647.1_Missense_Mutation_p.Q561K	NM_000789.3	NP_000780.1	P12821	ACE_HUMAN	angiotensin I converting enzyme	1135	Peptidase M2 2.				angiotensin catabolic process in blood (GO:0002005)|angiotensin maturation (GO:0002003)|arachidonic acid secretion (GO:0050482)|blood vessel remodeling (GO:0001974)|cellular protein metabolic process (GO:0044267)|hematopoietic stem cell differentiation (GO:0060218)|hormone catabolic process (GO:0042447)|kidney development (GO:0001822)|mononuclear cell proliferation (GO:0032943)|peptide catabolic process (GO:0043171)|regulation of blood pressure (GO:0008217)|regulation of renal output by angiotensin (GO:0002019)|regulation of smooth muscle cell migration (GO:0014910)|regulation of systemic arterial blood pressure by renin-angiotensin (GO:0003081)|regulation of vasoconstriction (GO:0019229)|regulation of vasodilation (GO:0042312)	endosome (GO:0005768)|external side of plasma membrane (GO:0009897)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	actin binding (GO:0003779)|bradykinin receptor binding (GO:0031711)|carboxypeptidase activity (GO:0004180)|chloride ion binding (GO:0031404)|drug binding (GO:0008144)|endopeptidase activity (GO:0004175)|metallopeptidase activity (GO:0008237)|peptidyl-dipeptidase activity (GO:0008241)|zinc ion binding (GO:0008270)			autonomic_ganglia(1)|breast(2)|endometrium(5)|kidney(3)|large_intestine(3)|lung(22)|ovary(6)|pancreas(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(2)	51					Benazepril(DB00542)|Candoxatril(DB00616)|Captopril(DB01197)|Cilazapril(DB01340)|Enalapril(DB00584)|Fosinopril(DB00492)|Lisinopril(DB00722)|Moexipril(DB00691)|Perindopril(DB00790)|Quinapril(DB00881)|Ramipril(DB00178)|Rescinnamine(DB01180)|Spirapril(DB01348)|Trandolapril(DB00519)	CTTCATCATCCAGTTCCAGTT	0.657																																					p.Q1135K		Atlas-SNP	.											.	ACE	187	.	0			c.C3403A						PASS	.						104.0	99.0	100.0					17																	61573777		2203	4300	6503	SO:0001583	missense	1636	exon23			ATCATCCAGTTCC	J04144	CCDS11637.1, CCDS45755.1, CCDS54155.1	17q23.3	2013-06-12	2013-06-12		ENSG00000159640	ENSG00000159640	3.4.15.1	"""CD molecules"""	2707	protein-coding gene	gene with protein product	"""peptidyl-dipeptidase A"""	106180	"""angiotensin I converting enzyme (peptidyl-dipeptidase A) 1"""	DCP1		2554286, 10319862	Standard	NM_001178057		Approved	ACE1, CD143	uc002jau.2	P12821	OTTHUMG00000154927	ENST00000290866.4:c.3403C>A	17.37:g.61573777C>A	ENSP00000290866:p.Gln1135Lys	245.0	1.0	0.00408163		248.0	124.0	0.5	NM_000789	B0LPF0|B4DXI3|E7EU16|P22966|Q53YX9|Q59GY8|Q7M4L4	Missense_Mutation	SNP	ENST00000290866.4	37	CCDS11637.1	.	.	.	.	.	.	.	.	.	.	C	13.51	2.258736	0.39896	.	.	ENSG00000159640	ENST00000290866;ENST00000428043;ENST00000290863	T;T;T	0.37584	1.19;1.19;1.19	5.17	5.17	0.71159	.	0.000000	0.85682	D	0.000000	T	0.73110	0.3545	H	0.95950	3.745	0.80722	D	1	D;D	0.89917	0.998;1.0	D;D	0.81914	0.922;0.995	T	0.83186	-0.0086	10	0.87932	D	0	-44.5904	18.2622	0.90039	0.0:1.0:0.0:0.0	.	561;1135	P12821-3;P12821	.;ACE_HUMAN	K	1135;1135;561	ENSP00000290866:Q1135K;ENSP00000397593:Q1135K;ENSP00000290863:Q561K	ENSP00000290863:Q561K	Q	+	1	0	ACE	58927509	1.000000	0.71417	1.000000	0.80357	0.328000	0.28507	7.726000	0.84824	2.393000	0.81446	0.484000	0.47621	CAG	.	.	none		0.657	ACE-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000337675.2		
SLC6A15	55117	hgsc.bcm.edu	37	12	85257230	85257230	+	Missense_Mutation	SNP	C	C	A			TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr12:85257230C>A	ENST00000266682.5	-	11	2347	c.1806G>T	c.(1804-1806)tgG>tgT	p.W602C	SLC6A15_ENST00000309283.7_Missense_Mutation_p.W310C|SLC6A15_ENST00000552192.1_Missense_Mutation_p.W495C	NM_182767.5	NP_877499.1	Q9H2J7	S6A15_HUMAN	solute carrier family 6 (neutral amino acid transporter), member 15	602					amino acid transport (GO:0006865)|ion transport (GO:0006811)|leucine transport (GO:0015820)|neurotransmitter transport (GO:0006836)|neutral amino acid transport (GO:0015804)|proline transport (GO:0015824)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	neurotransmitter transporter activity (GO:0005326)|neurotransmitter:sodium symporter activity (GO:0005328)|proline:sodium symporter activity (GO:0005298)			kidney(1)|large_intestine(18)|lung(15)|ovary(1)|pancreas(2)|prostate(4)|skin(2)|upper_aerodigestive_tract(1)	44						TATCTTCAATCCATGCGTTAT	0.303																																					p.W602C		Atlas-SNP	.											.	SLC6A15	159	.	0			c.G1806T						PASS	.						85.0	91.0	89.0					12																	85257230		2203	4296	6499	SO:0001583	missense	55117	exon11			TTCAATCCATGCG	AF265577	CCDS9026.1, CCDS9027.1, CCDS53816.1	12q21.31	2013-07-15	2008-09-02		ENSG00000072041	ENSG00000072041		"""Solute carriers"""	13621	protein-coding gene	gene with protein product	"""homolog of rat orphan transporter v7-3"", ""sodium/chloride dependent neurotransmitter transporter Homo sapiens orphan neurotransmitter transporter NTT7"""	607971	"""solute carrier family 6 (neurotransmitter transporter), member 15"""			10471414, 11112352, 16185194	Standard	NM_182767		Approved	hv7-3, NTT73, FLJ10316, V7-3, SBAT1	uc001szv.4	Q9H2J7	OTTHUMG00000169742	ENST00000266682.5:c.1806G>T	12.37:g.85257230C>A	ENSP00000266682:p.Trp602Cys	247.0	0.0	0		241.0	76.0	0.315353	NM_182767	A8K592|B7Z2P7|E7ESJ5|Q9H9F5	Missense_Mutation	SNP	ENST00000266682.5	37	CCDS9026.1	.	.	.	.	.	.	.	.	.	.	C	22.4	4.283503	0.80803	.	.	ENSG00000072041	ENST00000309283;ENST00000266682;ENST00000552192;ENST00000548267	T;T;T	0.75704	-0.96;-0.96;-0.96	5.71	5.71	0.89125	.	0.000000	0.85682	D	0.000000	D	0.90417	0.7000	M	0.93241	3.395	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;0.997	D	0.92239	0.5799	10	0.87932	D	0	.	19.8516	0.96743	0.0:1.0:0.0:0.0	.	310;602	F8WJN6;Q9H2J7	.;S6A15_HUMAN	C	310;602;495;80	ENSP00000311645:W310C;ENSP00000266682:W602C;ENSP00000450145:W495C	ENSP00000266682:W602C	W	-	3	0	SLC6A15	83781361	1.000000	0.71417	1.000000	0.80357	0.987000	0.75469	7.395000	0.79876	2.685000	0.91497	0.585000	0.79938	TGG	.	.	none		0.303	SLC6A15-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000405678.1	NM_018057, NM_182767	
ACOT4	122970	hgsc.bcm.edu	37	14	74060476	74060476	+	Missense_Mutation	SNP	C	C	A			TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr14:74060476C>A	ENST00000326303.4	+	2	782	c.528C>A	c.(526-528)agC>agA	p.S176R		NM_152331.3	NP_689544.3	Q8N9L9	ACOT4_HUMAN	acyl-CoA thioesterase 4	176					acyl-CoA metabolic process (GO:0006637)|dicarboxylic acid catabolic process (GO:0043649)|dicarboxylic acid metabolic process (GO:0043648)|long-chain fatty acid metabolic process (GO:0001676)|saturated monocarboxylic acid metabolic process (GO:0032788)|short-chain fatty acid metabolic process (GO:0046459)|succinyl-CoA metabolic process (GO:0006104)|unsaturated monocarboxylic acid metabolic process (GO:0032789)|very long-chain fatty acid metabolic process (GO:0000038)	peroxisome (GO:0005777)	acyl-CoA hydrolase activity (GO:0047617)|carboxylic ester hydrolase activity (GO:0052689)|palmitoyl-CoA hydrolase activity (GO:0016290)|receptor binding (GO:0005102)|succinyl-CoA hydrolase activity (GO:0004778)			endometrium(1)|large_intestine(3)|lung(4)	8				BRCA - Breast invasive adenocarcinoma(234;0.00331)		ATCGAGCCAGCCTCCTTGCTG	0.463																																					p.S176R		Atlas-SNP	.											.	ACOT4	25	.	0			c.C528A						PASS	.						102.0	96.0	98.0					14																	74060476		2203	4300	6503	SO:0001583	missense	122970	exon2			AGCCAGCCTCCTT	BC031799	CCDS9817.1	14q24.1	2011-02-16			ENSG00000177465	ENSG00000177465		"""Acyl CoA thioesterases"""	19748	protein-coding gene	gene with protein product		614314				16103133, 16940157	Standard	NM_152331		Approved	FLJ31235, PTE-Ib, PTE2B	uc001xoo.3	Q8N9L9	OTTHUMG00000169485	ENST00000326303.4:c.528C>A	14.37:g.74060476C>A	ENSP00000323071:p.Ser176Arg	98.0	0.0	0		181.0	85.0	0.469613	NM_152331	Q17RF4|Q5BKT6|Q86TX0|Q86TX1|Q96N88	Missense_Mutation	SNP	ENST00000326303.4	37	CCDS9817.1	.	.	.	.	.	.	.	.	.	.	C	18.69	3.677650	0.68042	.	.	ENSG00000177465	ENST00000326303	T	0.39592	1.07	5.25	2.34	0.29019	.	0.451951	0.27437	N	0.019371	T	0.64427	0.2597	M	0.91561	3.22	0.37397	D	0.912664	D	0.76494	0.999	D	0.66979	0.948	T	0.68573	-0.5373	10	0.87932	D	0	-1.9598	6.2571	0.20879	0.0:0.6343:0.1404:0.2253	.	176	Q8N9L9	ACOT4_HUMAN	R	176	ENSP00000323071:S176R	ENSP00000323071:S176R	S	+	3	2	ACOT4	73130229	0.523000	0.26274	1.000000	0.80357	0.995000	0.86356	-0.120000	0.10660	0.554000	0.29061	0.561000	0.74099	AGC	.	.	none		0.463	ACOT4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000404298.2	NM_152331	
EXOC4	60412	hgsc.bcm.edu	37	7	133689801	133689801	+	Missense_Mutation	SNP	A	A	G			TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr7:133689801A>G	ENST00000253861.4	+	16	2514	c.2485A>G	c.(2485-2487)Agc>Ggc	p.S829G	EXOC4_ENST00000539845.1_Missense_Mutation_p.S728G|EXOC4_ENST00000541309.1_Missense_Mutation_p.S117G|EXOC4_ENST00000545148.1_Missense_Mutation_p.S439G	NM_021807.3	NP_068579.3	Q96A65	EXOC4_HUMAN	exocyst complex component 4	829					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)				AGAGGCCATGAGCGCCAGCCT	0.493																																					p.S829G		Atlas-SNP	.											EXOC4_ENST00000545148,NS,carcinoma,0,2	EXOC4	118	2	0			c.A2485G						PASS	.						131.0	125.0	127.0					7																	133689801		2203	4300	6503	SO:0001583	missense	60412	exon16			GCCATGAGCGCCA	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.2485A>G	7.37:g.133689801A>G	ENSP00000253861:p.Ser829Gly	122.0	0.0	0		61.0	9.0	0.147541	NM_021807	E9PED2|Q541U8|Q9C0G4|Q9H9K0|Q9P102	Missense_Mutation	SNP	ENST00000253861.4	37	CCDS5829.1	.	.	.	.	.	.	.	.	.	.	A	15.04	2.714902	0.48622	.	.	ENSG00000131558	ENST00000253861;ENST00000546185;ENST00000539845;ENST00000545148;ENST00000541309	.	.	.	5.44	4.28	0.50868	.	0.052853	0.85682	D	0.000000	T	0.53867	0.1823	L	0.46819	1.47	0.45239	D	0.998246	B;B;B	0.17038	0.001;0.02;0.001	B;B;B	0.25759	0.003;0.063;0.001	T	0.50363	-0.8837	9	0.48119	T	0.1	.	8.4959	0.33127	0.8499:0.0:0.1501:0.0	.	361;439;829	B7Z689;F5GZT1;Q96A65	.;.;EXOC4_HUMAN	G	829;448;728;439;117	.	ENSP00000253861:S829G	S	+	1	0	EXOC4	133340341	1.000000	0.71417	0.997000	0.53966	0.966000	0.64601	4.678000	0.61641	0.903000	0.36546	0.402000	0.26972	AGC	.	.	none		0.493	EXOC4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000339182.1	NM_021807	
FNDC1	84624	hgsc.bcm.edu	37	6	159667972	159667972	+	Missense_Mutation	SNP	C	C	T	rs61746218	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr6:159667972C>T	ENST00000297267.9	+	15	4861	c.4661C>T	c.(4660-4662)aCg>aTg	p.T1554M	FNDC1_ENST00000340366.6_Missense_Mutation_p.T1491M	NM_032532.2	NP_115921.2	Q4ZHG4	FNDC1_HUMAN	fibronectin type III domain containing 1	1554					cellular response to hypoxia (GO:0071456)|positive regulation of cardiac muscle cell apoptotic process (GO:0010666)|positive regulation of protein phosphorylation (GO:0001934)|regulation of protein transport (GO:0051223)	cell-cell junction (GO:0005911)|extracellular region (GO:0005576)|mitochondrial membrane (GO:0031966)|nucleus (GO:0005634)|plasma membrane (GO:0005886)				NS(1)|autonomic_ganglia(1)|breast(2)|central_nervous_system(1)|endometrium(16)|haematopoietic_and_lymphoid_tissue(3)|kidney(2)|large_intestine(29)|liver(2)|lung(23)|ovary(3)|pancreas(1)|prostate(5)|skin(1)|upper_aerodigestive_tract(3)	93		Breast(66;0.000781)|Ovarian(120;0.0308)|Prostate(117;0.195)		OV - Ovarian serous cystadenocarcinoma(65;2.6e-16)|BRCA - Breast invasive adenocarcinoma(81;1.06e-05)		GCAGTACCTACGGAAGAGGCC	0.428													C|||	17	0.00339457	0.0008	0.0058	5008	,	,		18897	0.0		0.004	False		,,,				2504	0.0082				p.T1554M		Atlas-SNP	.											.	FNDC1	250	.	0			c.C4661T						PASS	.	C	MET/THR	6,3840		0,6,1917	133.0	128.0	129.0		4661	5.5	0.8	6	dbSNP_129	129	65,8205		0,65,4070	yes	missense	FNDC1	NM_032532.2	81	0,71,5987	TT,TC,CC		0.786,0.156,0.586	probably-damaging	1554/1895	159667972	71,12045	1923	4135	6058	SO:0001583	missense	84624	exon15			TACCTACGGAAGA	AB058769	CCDS47512.1	6q25	2013-02-11			ENSG00000164694	ENSG00000164694		"""Fibronectin type III domain containing"""	21184	protein-coding gene	gene with protein product		609991	"""fibronectin type III domain containing 2"""	FNDC2		11347906	Standard	NM_032532		Approved	bA243O10.1, KIAA1866, dJ322A24.1	uc010kjv.3	Q4ZHG4	OTTHUMG00000015927	ENST00000297267.9:c.4661C>T	6.37:g.159667972C>T	ENSP00000297267:p.Thr1554Met	136.0	0.0	0		104.0	42.0	0.403846	NM_032532	A6H8X2|B7ZBR4|B7ZBR5|B9EK49|Q5JPI0|Q5VU31|Q5VU32|Q5VXX4|Q70CQ6|Q96JG1	Missense_Mutation	SNP	ENST00000297267.9	37	CCDS47512.1	8	0.003663003663003663	0	0.0	5	0.013812154696132596	0	0.0	3	0.00395778364116095	C	14.60	2.584588	0.46110	0.00156	0.00786	ENSG00000164694	ENST00000297267;ENST00000340366	T;T	0.09817	2.94;3.75	5.54	5.54	0.83059	.	0.207947	0.41001	D	0.000969	T	0.10294	0.0252	M	0.64997	1.995	0.33849	D	0.632415	D	0.56746	0.977	P	0.45794	0.493	T	0.04796	-1.0926	9	.	.	.	-21.4287	17.2366	0.87000	0.0:1.0:0.0:0.0	rs61746218	1554	Q4ZHG4	FNDC1_HUMAN	M	1554;1491	ENSP00000297267:T1554M;ENSP00000342460:T1491M	.	T	+	2	0	FNDC1	159587962	0.988000	0.35896	0.765000	0.31456	0.577000	0.36160	2.989000	0.49393	2.588000	0.87417	0.591000	0.81541	ACG	C|0.995;T|0.005	0.005	strong		0.428	FNDC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042897.3	NM_032532	
PCDHGB4	8641	hgsc.bcm.edu	37	5	140768442	140768442	+	Missense_Mutation	SNP	G	G	T	rs201053346		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr5:140768442G>T	ENST00000519479.1	+	1	991	c.991G>T	c.(991-993)Gtg>Ttg	p.V331L	PCDHGA2_ENST00000394576.2_Intron|PCDHGA3_ENST00000253812.6_Intron|PCDHGB1_ENST00000523390.1_Intron|PCDHGB2_ENST00000522605.1_Intron|PCDHGA6_ENST00000517434.1_Intron|PCDHGA1_ENST00000517417.1_Intron|PCDHGA5_ENST00000518069.1_Intron|PCDHGA4_ENST00000571252.1_Intron|PCDHGB3_ENST00000576222.1_Intron|PCDHGA7_ENST00000518325.1_Intron	NM_003736.2|NM_018925.2|NM_032098.1	NP_003727.1|NP_061748.1|NP_115269.1	Q9UN71	PCDGG_HUMAN	protocadherin gamma subfamily B, 4	331	Cadherin 3. {ECO:0000255|PROSITE- ProRule:PRU00043}.				calcium-dependent cell-cell adhesion (GO:0016339)|cell adhesion (GO:0007155)|homophilic cell adhesion (GO:0007156)	integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			endometrium(9)|kidney(3)|large_intestine(4)|lung(14)|ovary(1)|prostate(1)|stomach(3)|urinary_tract(2)	37			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			GCAATGCACAGTGGAGGTAGA	0.413																																					p.V331L		Atlas-SNP	.											.	PCDHGB4	125	.	0			c.G991T						PASS	.	G	LEU/VAL,,,,,,,,,,,LEU/VAL	0,3830		0,0,1915	86.0	80.0	82.0		991,,,,,,,,,,,991	4.2	0.1	5		82	3,8283		0,3,4140	yes	missense,intron,intron,intron,intron,intron,intron,intron,intron,intron,intron,missense	PCDHGB4,PCDHGB3,PCDHGB2,PCDHGB1,PCDHGA7,PCDHGA6,PCDHGA5,PCDHGA4,PCDHGA3,PCDHGA2,PCDHGA1	NM_003736.2,NM_018912.2,NM_018915.2,NM_018916.3,NM_018917.2,NM_018918.2,NM_018919.2,NM_018920.2,NM_018922.2,NM_018923.2,NM_018924.2,NM_032098.1	32,,,,,,,,,,,32	0,3,6055	TT,TG,GG		0.0362,0.0,0.0248	,,,,,,,,,,,	331/924,,,,,,,,,,,331/804	140768442	3,12113	1915	4143	6058	SO:0001583	missense	8641	exon1			TGCACAGTGGAGG	AF152520	CCDS54928.1, CCDS75337.1	5q31	2010-01-26				ENSG00000253953		"""Cadherins / Protocadherins : Clustered"""	8711	other	protocadherin	"""fibroblast cadherin FIB2"", ""cadherin 20"""	603058				10380929	Standard	NM_003736		Approved	FIB2, CDH20, PCDH-GAMMA-B4		Q9UN71		ENST00000519479.1:c.991G>T	5.37:g.140768442G>T	ENSP00000428288:p.Val331Leu	64.0	0.0	0		77.0	33.0	0.428571	NM_032098	O15099|Q2M267|Q9UN64	Missense_Mutation	SNP	ENST00000519479.1	37	CCDS54928.1	.	.	.	.	.	.	.	.	.	.	.	13.67	2.306759	0.40795	0.0	3.62E-4	ENSG00000253953	ENST00000519479	T	0.01787	4.64	5.09	4.2	0.49525	Cadherin (4);Cadherin-like (1);	.	.	.	.	T	0.06781	0.0173	M	0.74389	2.26	0.25118	N	0.990664	P;D	0.55385	0.918;0.971	P;P	0.53102	0.596;0.718	T	0.09552	-1.0669	9	0.49607	T	0.09	.	14.1498	0.65375	0.0773:0.0:0.9227:0.0	.	331;331	Q9UN71-2;Q9UN71	.;PCDGG_HUMAN	L	331	ENSP00000428288:V331L	ENSP00000428288:V331L	V	+	1	0	PCDHGB4	140748626	0.998000	0.40836	0.109000	0.21407	0.063000	0.16089	2.244000	0.43124	2.525000	0.85131	0.655000	0.94253	GTG	.	.	weak		0.413	PCDHGB4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000374745.1	NM_003736	
OXNAD1	92106	hgsc.bcm.edu	37	3	16336381	16336381	+	Silent	SNP	A	A	G			TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr3:16336381A>G	ENST00000285083.5	+	6	774	c.309A>G	c.(307-309)ccA>ccG	p.P103P	OXNAD1_ENST00000606098.1_Silent_p.P103P|OXNAD1_ENST00000544043.1_Silent_p.P121P|OXNAD1_ENST00000605932.1_Silent_p.P103P|OXNAD1_ENST00000435829.2_Silent_p.P121P	NM_138381.3	NP_612390.1	Q96HP4	OXND1_HUMAN	oxidoreductase NAD-binding domain containing 1	103	FAD-binding FR-type. {ECO:0000255|PROSITE-ProRule:PRU00716}.					mitochondrion (GO:0005739)	oxidoreductase activity (GO:0016491)			endometrium(3)|kidney(1)|large_intestine(2)|lung(5)|skin(2)	13						TCTTTATTCCAGGAGTCTCTG	0.363																																					p.P103P		Atlas-SNP	.											.	OXNAD1	31	.	0			c.A309G						PASS	.						140.0	143.0	142.0					3																	16336381		2203	4300	6503	SO:0001819	synonymous_variant	92106	exon6			TATTCCAGGAGTC	AL832787	CCDS2630.1	3p25-p24	2010-03-19			ENSG00000154814	ENSG00000154814			25128	protein-coding gene	gene with protein product						12477932	Standard	NM_138381		Approved	MGC15763	uc003caw.3	Q96HP4	OTTHUMG00000129867	ENST00000285083.5:c.309A>G	3.37:g.16336381A>G		216.0	0.0	0		214.0	94.0	0.439252	NM_138381	Q2HYC7|Q59FA4	Silent	SNP	ENST00000285083.5	37	CCDS2630.1																																																																																			.	.	none		0.363	OXNAD1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000252109.1	NM_138381	
SZT2	23334	hgsc.bcm.edu	37	1	43870071	43870071	+	Silent	SNP	C	C	A	rs41312024	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr1:43870071C>A	ENST00000562955.1	+	4	348	c.348C>A	c.(346-348)atC>atA	p.I116I	SZT2_ENST00000310739.4_Silent_p.I116I|SZT2_ENST00000372450.4_Silent_p.I114I	NM_015284.3	NP_056099.3	Q5T011	SZT2_HUMAN	seizure threshold 2 homolog (mouse)	116					central nervous system development (GO:0007417)|corpus callosum morphogenesis (GO:0021540)|embryo development (GO:0009790)|pigmentation (GO:0043473)|post-embryonic development (GO:0009791)|regulation of superoxide dismutase activity (GO:1901668)	extracellular vesicular exosome (GO:0070062)|peroxisome (GO:0005777)				NS(2)|breast(9)|central_nervous_system(1)|endometrium(17)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(19)|lung(39)|ovary(4)|pancreas(3)|prostate(4)|skin(2)|stomach(1)|upper_aerodigestive_tract(4)|urinary_tract(3)	113						CAGGGGAGATCTTGTTTGATG	0.562													C|||	18	0.00359425	0.0	0.0058	5008	,	,		18752	0.0		0.0139	False		,,,				2504	0.0				p.I116I		Atlas-SNP	.											.	SZT2	383	.	0			c.C348A						PASS	.	C		15,4391	22.3+/-47.3	0,15,2188	95.0	91.0	93.0		348	1.4	1.0	1	dbSNP_127	93	147,8453	71.0+/-133.6	0,147,4153	no	coding-synonymous	SZT2	NM_015284.3		0,162,6341	AA,AC,CC		1.7093,0.3404,1.2456		116/3376	43870071	162,12844	2203	4300	6503	SO:0001819	synonymous_variant	23334	exon4			GGAGATCTTGTTT	AB007936	CCDS30694.1, CCDS30694.2	1p34.2	2012-11-19	2011-06-10	2011-06-10	ENSG00000198198	ENSG00000198198			29040	protein-coding gene	gene with protein product	"""seizure threshold 2 homolog A (mouse)"", ""seizure threshold 2 homolog B (mouse)"""	615463	"""chromosome 1 open reading frame 84"", ""KIAA0467"""	C1orf84, KIAA0467		9455484	Standard	NM_015284		Approved	FLJ10387, SZT2B, RP11-506B15.1, FLJ34502, SZT2A	uc001cjk.3	Q5T011	OTTHUMG00000007423	ENST00000562955.1:c.348C>A	1.37:g.43870071C>A		147.0	0.0	0		83.0	68.0	0.819277	NM_015284	A0PJK5|A7E2X4|O75055|Q5JUY7|Q5T012|Q5XKC7|Q6ZNI8|Q6ZT24|Q7Z636|Q8NAY9|Q9H5H7|Q9UFQ8	Silent	SNP	ENST00000562955.1	37	CCDS30694.2																																																																																			C|0.990;A|0.010	0.010	strong		0.562	SZT2-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000019517.3	NM_015284	
PLEC	5339	hgsc.bcm.edu	37	8	144991925	144991925	+	Missense_Mutation	SNP	G	G	A	rs189061273	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr8:144991925G>A	ENST00000322810.4	-	32	12644	c.12475C>T	c.(12475-12477)Ctc>Ttc	p.L4159F	PLEC_ENST00000345136.3_Missense_Mutation_p.L4022F|PLEC_ENST00000357649.2_Missense_Mutation_p.L4026F|PLEC_ENST00000354589.3_Missense_Mutation_p.L4022F|PLEC_ENST00000436759.2_Missense_Mutation_p.L4049F|PLEC_ENST00000354958.2_Missense_Mutation_p.L4000F|PLEC_ENST00000356346.3_Missense_Mutation_p.L4008F|PLEC_ENST00000398774.2_Missense_Mutation_p.L3990F|PLEC_ENST00000527096.1_Missense_Mutation_p.L4045F	NM_201380.2	NP_958782.1	Q15149	PLEC_HUMAN	plectin	4159	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						AGGGAGATGAGCTTCCCAGAG	0.637													G|||	14	0.00279553	0.0	0.0	5008	,	,		18649	0.0139		0.0	False		,,,				2504	0.0				p.L4159F		Atlas-SNP	.											PLEC_ENST00000436759,bladder,carcinoma,+2,3	PLEC	1144	3	0			c.C12475T						PASS	.						49.0	57.0	54.0					8																	144991925		2110	4197	6307	SO:0001583	missense	5339	exon32			AGATGAGCTTCCC	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.12475C>T	8.37:g.144991925G>A	ENSP00000323856:p.Leu4159Phe	96.0	0.0	0		102.0	63.0	0.617647	NM_201380	Q15148|Q16640|Q6S376|Q6S377|Q6S378|Q6S379|Q6S380|Q6S381|Q6S382|Q6S383	Missense_Mutation	SNP	ENST00000322810.4	37	CCDS43772.1	10	0.004578754578754579	0	0.0	0	0.0	10	0.017482517482517484	0	0.0	G	8.561	0.877675	0.17395	.	.	ENSG00000178209	ENST00000345136;ENST00000357649;ENST00000354589;ENST00000398774;ENST00000322810;ENST00000354958;ENST00000356346;ENST00000436759;ENST00000527096	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	4.98	4.98	0.66077	.	0.420113	0.19781	U	0.106211	T	0.37758	0.1015	N	0.14661	0.345	0.34450	D	0.700616	P;P;P;P;P;P;P;P	0.49090	0.919;0.919;0.919;0.868;0.919;0.919;0.919;0.919	P;P;P;B;P;P;P;P	0.45506	0.483;0.483;0.483;0.289;0.483;0.483;0.483;0.483	T	0.63637	-0.6592	10	0.54805	T	0.06	.	13.0686	0.59048	0.0:0.0:0.8393:0.1607	.	4049;4008;4000;4159;3990;4022;4026;4022	Q15149-2;Q15149-9;Q15149-8;Q15149;Q15149-7;Q15149-5;Q15149-6;Q15149-4	.;.;.;PLEC_HUMAN;.;.;.;.	F	4022;4026;4022;3990;4159;4000;4008;4049;4045	ENSP00000344848:L4022F;ENSP00000350277:L4026F;ENSP00000346602:L4022F;ENSP00000381756:L3990F;ENSP00000323856:L4159F;ENSP00000347044:L4000F;ENSP00000348702:L4008F;ENSP00000388180:L4049F;ENSP00000434583:L4045F	ENSP00000323856:L4159F	L	-	1	0	PLEC	145063913	1.000000	0.71417	1.000000	0.80357	0.985000	0.73830	1.222000	0.32515	2.597000	0.87782	0.549000	0.68633	CTC	G|0.995;A|0.005	0.005	strong		0.637	PLEC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000383281.1	NM_000445	
CFAP53	220136	hgsc.bcm.edu	37	18	47788544	47788544	+	Silent	SNP	T	T	G	rs112087763	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr18:47788544T>G	ENST00000398545.4	-	2	232	c.115A>C	c.(115-117)Aga>Cga	p.R39R		NM_145020.3	NP_659457.2														endometrium(1)|kidney(4)|large_intestine(6)|lung(6)|ovary(1)|pancreas(1)|skin(1)	20				STAD - Stomach adenocarcinoma(97;2.66e-05)|Colorectal(21;7.57e-05)|Lung(128;0.00932)|READ - Rectum adenocarcinoma(32;0.164)		CGTCGGATTCTTTCTAGATGG	0.438													T|||	6	0.00119808	0.0	0.0014	5008	,	,		19087	0.0		0.004	False		,,,				2504	0.001				p.R39R		Atlas-SNP	.											.	CCDC11	59	.	0			c.A115C						PASS	.	T		1,3831		0,1,1915	113.0	108.0	109.0		115	4.0	0.2	18	dbSNP_132	109	24,8220		0,24,4098	no	coding-synonymous	CCDC11	NM_145020.3		0,25,6013	GG,GT,TT		0.2911,0.0261,0.207		39/515	47788544	25,12051	1916	4122	6038	SO:0001819	synonymous_variant	220136	exon2			GGATTCTTTCTAG																												ENST00000398545.4:c.115A>C	18.37:g.47788544T>G		100.0	0.0	0		121.0	53.0	0.438017	NM_145020		Silent	SNP	ENST00000398545.4	37	CCDS11940.2																																																																																			T|0.997;G|0.003	0.003	strong		0.438	CCDC11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255922.3		
KLHL7	55975	hgsc.bcm.edu	37	7	23212627	23212627	+	Silent	SNP	A	A	G	rs118185564	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr7:23212627A>G	ENST00000339077.5	+	10	1683	c.1440A>G	c.(1438-1440)aaA>aaG	p.K480K	KLHL7_ENST00000545443.1_Silent_p.K458K|AC005082.1_ENST00000366347.4_Intron|KLHL7_ENST00000322231.7_Silent_p.K458K|KLHL7_ENST00000542558.1_Silent_p.K255K|KLHL7_ENST00000409689.1_Silent_p.K432K|KLHL7_ENST00000539124.1_Silent_p.K404K	NM_001031710.2	NP_001026880.2	Q8IXQ5	KLHL7_HUMAN	kelch-like family member 7	480					protein ubiquitination (GO:0016567)	Cul3-RING ubiquitin ligase complex (GO:0031463)|cytoplasm (GO:0005737)|nucleolus (GO:0005730)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	protein homodimerization activity (GO:0042803)			breast(1)|central_nervous_system(1)|kidney(2)|large_intestine(6)|lung(11)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	25						TATTTGTAAAAGACAAGATAT	0.368													A|||	17	0.00339457	0.0008	0.0	5008	,	,		17141	0.0		0.0139	False		,,,				2504	0.002				p.K480K		Atlas-SNP	.											.	KLHL7	102	.	0			c.A1440G						PASS	.	A	,	8,4398	14.3+/-33.2	0,8,2195	283.0	269.0	273.0		1440,1296	2.2	1.0	7	dbSNP_132	273	53,8547	33.8+/-87.4	0,53,4247	no	coding-synonymous,coding-synonymous	KLHL7	NM_001031710.2,NM_018846.4	,	0,61,6442	GG,GA,AA		0.6163,0.1816,0.469	,	480/587,432/539	23212627	61,12945	2203	4300	6503	SO:0001819	synonymous_variant	55975	exon10			TGTAAAAGACAAG		CCDS5378.1, CCDS34609.1, CCDS5378.2, CCDS55095.1	7p15.3	2013-01-30	2013-01-30		ENSG00000122550	ENSG00000122550		"""Kelch-like"", ""BTB/POZ domain containing"""	15646	protein-coding gene	gene with protein product	"""retinitis pigmentosa 42"""	611119	"""kelch-like 7 (Drosophila)"""			19520207	Standard	NM_001031710		Approved	KLHL6, SBBI26, RP42	uc003svs.4	Q8IXQ5	OTTHUMG00000094813	ENST00000339077.5:c.1440A>G	7.37:g.23212627A>G		297.0	0.0	0		437.0	278.0	0.636156	NM_001031710	A4D144|B7Z5I9|G5E9G3|Q7Z765|Q96MV2|Q9BQF8|Q9UDQ9	Silent	SNP	ENST00000339077.5	37	CCDS34609.1																																																																																			A|0.994;G|0.006	0.006	strong		0.368	KLHL7-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000326860.3	NM_018846	
GPR133	283383	hgsc.bcm.edu	37	12	131620650	131620650	+	Missense_Mutation	SNP	C	C	T	rs61746588	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr12:131620650C>T	ENST00000261654.5	+	22	2895	c.2336C>T	c.(2335-2337)gCt>gTt	p.A779V	GPR133_ENST00000376682.4_Missense_Mutation_p.A465V|GPR133_ENST00000540207.1_3'UTR|GPR133_ENST00000535015.1_Missense_Mutation_p.A811V|GPR133_ENST00000543617.1_Missense_Mutation_p.A298V	NM_198827.3	NP_942122.2	Q6QNK2	GP133_HUMAN	G protein-coupled receptor 133	779					G-protein coupled receptor signaling pathway (GO:0007186)|neuropeptide signaling pathway (GO:0007218)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)			NS(2)|breast(2)|endometrium(6)|kidney(1)|large_intestine(12)|lung(20)|ovary(3)|pancreas(6)|prostate(6)|skin(4)|upper_aerodigestive_tract(1)|urinary_tract(4)	67	all_neural(191;0.0982)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;1.68e-06)|all cancers(50;2.71e-06)|Epithelial(86;6.75e-06)		GGCGTGCTTGCTGTCAACGGT	0.622													C|||	11	0.00219649	0.0	0.0086	5008	,	,		20891	0.0		0.003	False		,,,				2504	0.002				p.A779V		Atlas-SNP	.											.	GPR133	136	.	0			c.C2336T						PASS	.	C	VAL/ALA	7,4399	12.9+/-30.5	0,7,2196	288.0	182.0	218.0		2336	3.7	0.0	12	dbSNP_129	218	49,8551	31.7+/-84.0	0,49,4251	yes	missense	GPR133	NM_198827.3	64	0,56,6447	TT,TC,CC		0.5698,0.1589,0.4306	probably-damaging	779/875	131620650	56,12950	2203	4300	6503	SO:0001583	missense	283383	exon22			TGCTTGCTGTCAA	AY278561	CCDS9272.1	12q24.33	2014-08-08			ENSG00000111452	ENSG00000111452		"""-"", ""GPCR / Class B : Orphans"""	19893	protein-coding gene	gene with protein product		613639					Standard	NM_198827		Approved	DKFZp434B1272, PGR25	uc001uit.4	Q6QNK2	OTTHUMG00000168339	ENST00000261654.5:c.2336C>T	12.37:g.131620650C>T	ENSP00000261654:p.Ala779Val	238.0	0.0	0		197.0	82.0	0.416244	NM_198827	B2CKK9|B7ZLF7|Q2M1L3|Q6ZMQ1|Q7Z7M2|Q86SM4	Missense_Mutation	SNP	ENST00000261654.5	37	CCDS9272.1	6	0.0027472527472527475	1	0.0020325203252032522	2	0.0055248618784530384	0	0.0	3	0.00395778364116095	C	12.69	2.013191	0.35511	0.001589	0.005698	ENSG00000111452	ENST00000261654;ENST00000535015;ENST00000376682;ENST00000543617	T;T;T;T	0.42900	1.32;1.31;0.96;0.96	4.6	3.71	0.42584	GPCR, family 2-like (1);	0.000000	0.85682	D	0.000000	T	0.36991	0.0987	M	0.63428	1.95	0.58432	D	0.999998	P;P;B	0.42123	0.586;0.771;0.333	P;B;B	0.48089	0.566;0.444;0.348	T	0.18713	-1.0328	10	0.17369	T	0.5	.	10.3596	0.43984	0.0:0.902:0.0:0.098	rs61746588	811;132;779	B7ZLF7;Q9NSM3;Q6QNK2	.;.;GP133_HUMAN	V	779;811;465;298	ENSP00000261654:A779V;ENSP00000444425:A811V;ENSP00000365872:A465V;ENSP00000438021:A298V	ENSP00000261654:A779V	A	+	2	0	GPR133	130186603	1.000000	0.71417	0.036000	0.18154	0.315000	0.28087	4.744000	0.62118	0.913000	0.36797	0.491000	0.48974	GCT	C|0.997;T|0.003	0.003	strong		0.622	GPR133-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000399356.1	NM_198827	
ZNF676	163223	hgsc.bcm.edu	37	19	22364230	22364230	+	Missense_Mutation	SNP	C	C	A			TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr19:22364230C>A	ENST00000397121.2	-	3	606	c.289G>T	c.(289-291)Ggt>Tgt	p.G97C		NM_001001411.2	NP_001001411.2	Q8N7Q3	ZN676_HUMAN	zinc finger protein 676	97					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)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(9)|lung(49)|pancreas(1)|prostate(2)|upper_aerodigestive_tract(2)	67		Lung NSC(12;0.0207)|all_lung(12;0.0214)|all_epithelial(12;0.114)				TTATTATAACCTTCTTTGTGC	0.313																																					p.G97C		Atlas-SNP	.											ZNF676,NS,carcinoma,+1,2	ZNF676	146	2	0			c.G289T						PASS	.						131.0	121.0	124.0					19																	22364230		1971	4181	6152	SO:0001583	missense	163223	exon3			TATAACCTTCTTT	AK097798	CCDS42539.1	19p12	2013-01-08				ENSG00000196109		"""Zinc fingers, C2H2-type"""	20429	protein-coding gene	gene with protein product							Standard	NM_001001411		Approved		uc002nqs.1	Q8N7Q3		ENST00000397121.2:c.289G>T	19.37:g.22364230C>A	ENSP00000380310:p.Gly97Cys	292.0	1.0	0.00342466		282.0	100.0	0.35461	NM_001001411	A8MVX5	Missense_Mutation	SNP	ENST00000397121.2	37	CCDS42539.1	.	.	.	.	.	.	.	.	.	.	.	0.866	-0.733679	0.03111	.	.	ENSG00000196109	ENST00000397121	T	0.07688	3.17	0.398	-0.797	0.10909	.	.	.	.	.	T	0.09247	0.0228	M	0.70842	2.15	0.09310	N	1	B	0.16396	0.017	B	0.16289	0.015	T	0.33650	-0.9860	9	0.37606	T	0.19	.	4.101	0.10014	0.6355:0.3645:0.0:0.0	.	97	Q8N7Q3	ZN676_HUMAN	C	97	ENSP00000380310:G97C	ENSP00000380310:G97C	G	-	1	0	ZNF676	22156070	0.000000	0.05858	0.011000	0.14972	0.153000	0.21895	-0.155000	0.10115	-0.683000	0.05190	0.186000	0.17326	GGT	.	.	none		0.313	ZNF676-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000464392.1	NM_001001411	
NUP54	53371	hgsc.bcm.edu	37	4	77038912	77038912	+	Missense_Mutation	SNP	A	A	T	rs144785979	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr4:77038912A>T	ENST00000264883.3	-	11	1440	c.1300T>A	c.(1300-1302)Ttg>Atg	p.L434M	NUP54_ENST00000514987.1_Missense_Mutation_p.L386M|NUP54_ENST00000342467.6_Missense_Mutation_p.L218M|NUP54_ENST00000458189.2_Missense_Mutation_p.L254M	NM_017426.2	NP_059122.2	Q7Z3B4	NUP54_HUMAN	nucleoporin 54kDa	434	9 X 2 AA repeats of F-G.				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 transport (GO:0051028)|protein targeting (GO:0006605)|regulation of glucose transport (GO:0010827)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)|viral process (GO:0016032)	cytoplasm (GO:0005737)|nuclear envelope (GO:0005635)|nuclear pore (GO:0005643)|nucleoplasm (GO:0005654)	nucleocytoplasmic transporter activity (GO:0005487)			cervix(1)|endometrium(1)|kidney(2)|large_intestine(4)|lung(5)|ovary(1)|prostate(3)|skin(1)|stomach(1)	19						TGAGACATCAATTCATTTAGT	0.373													A|||	2	0.000399361	0.0	0.0	5008	,	,		20100	0.0		0.002	False		,,,				2504	0.0				p.L434M		Atlas-SNP	.											.	NUP54	48	.	0			c.T1300A						PASS	.	A	MET/LEU	1,4405	2.1+/-5.4	0,1,2202	116.0	109.0	111.0		1300	-1.2	1.0	4	dbSNP_134	111	4,8594	3.7+/-12.6	0,4,4295	yes	missense	NUP54	NM_017426.2	15	0,5,6497	TT,TA,AA		0.0465,0.0227,0.0384	possibly-damaging	434/508	77038912	5,12999	2203	4299	6502	SO:0001583	missense	53371	exon11			ACATCAATTCATT	AF157322	CCDS3576.1, CCDS63998.1	4q21.1	2008-07-03	2002-08-29		ENSG00000138750	ENSG00000138750			17359	protein-coding gene	gene with protein product		607607	"""nucleoporin 54kD"""			8707840	Standard	NM_017426		Approved		uc003hjs.3	Q7Z3B4	OTTHUMG00000130098	ENST00000264883.3:c.1300T>A	4.37:g.77038912A>T	ENSP00000264883:p.Leu434Met	251.0	0.0	0		256.0	115.0	0.449219	NM_017426	B2RCK7|B4DT35|Q96EA7|Q9NVL5|Q9P0I1	Missense_Mutation	SNP	ENST00000264883.3	37	CCDS3576.1	2	9.157509157509158E-4	0	0.0	0	0.0	0	0.0	2	0.002638522427440633	A	13.35	2.209809	0.39003	2.27E-4	4.65E-4	ENSG00000138750	ENST00000264883;ENST00000342467;ENST00000514987;ENST00000458189	.	.	.	5.88	-1.16	0.09678	.	0.000000	0.64402	D	0.000001	T	0.64757	0.2627	M	0.75615	2.305	0.47905	D	0.999546	P;P;D	0.52996	0.926;0.918;0.957	P;B;P	0.56612	0.802;0.436;0.802	T	0.64419	-0.6412	9	0.49607	T	0.09	-7.8541	9.651	0.39897	0.1989:0.1983:0.6027:0.0	.	386;218;434	B4DT35;Q7Z3B4-2;Q7Z3B4	.;.;NUP54_HUMAN	M	434;218;386;254	.	ENSP00000264883:L434M	L	-	1	2	NUP54	77257936	0.991000	0.36638	0.980000	0.43619	0.416000	0.31233	0.731000	0.26058	-0.151000	0.11176	-2.917000	0.00090	TTG	A|0.999;T|0.001	0.001	strong		0.373	NUP54-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252402.3		
AHNAK2	113146	hgsc.bcm.edu	37	14	105413220	105413220	+	Silent	SNP	A	A	C	rs151173659	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr14:105413220A>C	ENST00000333244.5	-	7	8687	c.8568T>G	c.(8566-8568)ctT>ctG	p.L2856L	AHNAK2_ENST00000557457.1_Intron	NM_138420.2	NP_612429.2	Q8IVF2	AHNK2_HUMAN	AHNAK nucleoprotein 2	2856						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)			CAGTGGTCTTAAGATCCCCTT	0.637													.|||	57	0.0113818	0.0386	0.0029	5008	,	,		17917	0.0		0.0	False		,,,				2504	0.0041				p.L2856L		Atlas-SNP	.											.	AHNAK2	719	.	0			c.T8568G						PASS	.	G		157,3765		7,143,1811	126.0	144.0	138.0		8568	-0.0	0.0	14	dbSNP_134	138	6,8298		0,6,4146	no	coding-synonymous	AHNAK2	NM_138420.2		7,149,5957	CC,CA,AA		0.0723,4.0031,1.3332		2856/5796	105413220	163,12063	1961	4152	6113	SO:0001819	synonymous_variant	113146	exon7			GGTCTTAAGATCC	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.8568T>G	14.37:g.105413220A>C		205.0	1.0	0.00487805		249.0	167.0	0.670683	NM_138420	Q5BKX7|Q7Z343|Q7Z358|Q7Z394|Q7Z3G0|Q86WQ6|Q8IYY1|Q8N3G4|Q96EX9	Silent	SNP	ENST00000333244.5	37	CCDS45177.1																																																																																			A|0.994;C|0.006	0.006	strong		0.637	AHNAK2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000410300.1	NM_138420	
Unknown	0	hgsc.bcm.edu	37	11	89819431	89819431	+	IGR	SNP	C	C	T			TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr11:89819431C>T								TRIM49C (12873 upstream) : SNORD56 (32127 downstream)																							AGGCCCCTTACTGCTTACAAT	0.428																																					p.T105I		Atlas-SNP	.											.	.	.	.	0			c.C314T						PASS	.						97.0	72.0	80.0					11																	89819431		682	1559	2241	SO:0001628	intergenic_variant	642623	exon1			CCCTTACTGCTTA																													11.37:g.89819431C>T		321.0	1.0	0.00311526		411.0	270.0	0.656934	NM_001143975		Missense_Mutation	SNP		37																																																																																				.	.	none	0	0.428								
NAP1L3	4675	hgsc.bcm.edu	37	X	92927728	92927728	+	Silent	SNP	T	T	C			TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chrX:92927728T>C	ENST00000373079.3	-	1	839	c.576A>G	c.(574-576)gaA>gaG	p.E192E	FAM133A_ENST00000538690.1_5'Flank|FAM133A_ENST00000355813.5_5'Flank|NAP1L3_ENST00000475430.2_Silent_p.E185E|FAM133A_ENST00000332647.4_5'Flank|FAM133A_ENST00000322139.4_5'Flank	NM_004538.5	NP_004529.2	Q99457	NP1L3_HUMAN	nucleosome assembly protein 1-like 3	192	Glu-rich.				nucleosome assembly (GO:0006334)	nucleus (GO:0005634)				haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(9)|lung(16)|ovary(2)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)	34						GGTTTTCTTCTTCCTCACCCT	0.438																																					p.E192E		Atlas-SNP	.											.	NAP1L3	81	.	0			c.A576G						PASS	.						80.0	79.0	79.0					X																	92927728		2203	4300	6503	SO:0001819	synonymous_variant	4675	exon1			TTCTTCTTCCTCA		CCDS14465.1	Xq21.3-q22	2008-08-01			ENSG00000186310	ENSG00000186310			7639	protein-coding gene	gene with protein product		300117				8976385	Standard	NM_004538		Approved	MB20, NPL3, MGC26312	uc004efq.3	Q99457	OTTHUMG00000021974	ENST00000373079.3:c.576A>G	X.37:g.92927728T>C		159.0	0.0	0		78.0	5.0	0.0641026	NM_004538	B2RCM0|O60788	Silent	SNP	ENST00000373079.3	37	CCDS14465.1																																																																																			.	.	none		0.438	NAP1L3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057449.1	NM_004538	
BOD1L1	259282	hgsc.bcm.edu	37	4	13602793	13602793	+	Missense_Mutation	SNP	C	C	G	rs199927242		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr4:13602793C>G	ENST00000040738.5	-	10	5866	c.5731G>C	c.(5731-5733)Gtg>Ctg	p.V1911L		NM_148894.2	NP_683692.2	Q8NFC6	BD1L1_HUMAN	biorientation of chromosomes in cell division 1-like 1	1911						nucleus (GO:0005634)	DNA binding (GO:0003677)										TGCTCTACCACAGTACCAATC	0.443													C|||	1	0.000199681	0.0008	0.0	5008	,	,		23179	0.0		0.0	False		,,,				2504	0.0				p.V1911L		Atlas-SNP	.											.	.	.	.	0			c.G5731C						PASS	.	C	LEU/VAL	1,4405	2.1+/-5.4	0,1,2202	119.0	118.0	118.0		5731	2.8	0.0	4		118	1,8599	1.2+/-3.3	0,1,4299	yes	missense	BOD1L	NM_148894.2	32	0,2,6501	GG,GC,CC		0.0116,0.0227,0.0154	benign	1911/3052	13602793	2,13004	2203	4300	6503	SO:0001583	missense	259282	exon10			CTACCACAGTACC	AF528529	CCDS3411.2	4p16.1	2012-04-10	2012-04-10	2012-04-10	ENSG00000038219	ENSG00000038219			31792	protein-coding gene	gene with protein product			"""family with sequence similarity 44, member A"", ""biorientation of chromosomes in cell division 1-like"""	FAM44A, BOD1L			Standard	XM_005248150		Approved	FLJ33215, KIAA1327	uc003gmz.1	Q8NFC6	OTTHUMG00000090659	ENST00000040738.5:c.5731G>C	4.37:g.13602793C>G	ENSP00000040738:p.Val1911Leu	160.0	0.0	0		147.0	68.0	0.462585	NM_148894	Q6P0M8|Q96AL1|Q9H6G0|Q9NTD6|Q9P2L9	Missense_Mutation	SNP	ENST00000040738.5	37	CCDS3411.2	.	.	.	.	.	.	.	.	.	.	C	5.583	0.292461	0.10567	2.27E-4	1.16E-4	ENSG00000038219	ENST00000040738	T	0.08807	3.05	4.79	2.8	0.32819	.	0.896444	0.09441	N	0.801789	T	0.06050	0.0157	N	0.19112	0.55	0.09310	N	1	B	0.22003	0.063	B	0.19148	0.024	T	0.40232	-0.9574	10	0.33940	T	0.23	0.4353	7.6976	0.28604	0.0:0.7633:0.0:0.2367	.	1911	Q8NFC6	BOD1L_HUMAN	L	1911	ENSP00000040738:V1911L	ENSP00000040738:V1911L	V	-	1	0	BOD1L	13211891	0.000000	0.05858	0.001000	0.08648	0.053000	0.15095	0.762000	0.26503	0.812000	0.34326	0.561000	0.74099	GTG	.	.	weak		0.443	BOD1L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207321.1	NM_148894	
NBPF14	25832	hgsc.bcm.edu	37	1	148004783	148004783	+	Missense_Mutation	SNP	C	C	A	rs147480284	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr1:148004783C>A	ENST00000369219.1	-	22	2547	c.2531G>T	c.(2530-2532)aGc>aTc	p.S844I				Q5TI25	NBPFE_HUMAN	neuroblastoma breakpoint family, member 14	844	NBPF 10. {ECO:0000255|PROSITE- ProRule:PRU00647}.					cytoplasm (GO:0005737)		p.S844I(1)		NS(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(1)|lung(23)|ovary(2)|pancreas(2)|prostate(2)|skin(1)|stomach(2)|urinary_tract(1)	42	all_hematologic(923;0.032)					CATCAGCATGCTGTTGAGCCT	0.453													-|||	73	0.0145767	0.0008	0.0187	5008	,	,		15184	0.001		0.0537	False		,,,				2504	0.0041				p.S844I		Atlas-SNP	.											NBPF14,NS,adenoma,0,2	NBPF14	107	2	1	Substitution - Missense(1)	haematopoietic_and_lymphoid_tissue(1)	c.G2531T						scavenged	.	C	ILE/SER	84,3292		31,22,1635	72.0	122.0	108.0		2531	0.5	0.0	1	dbSNP_134	108	565,7627		134,297,3665	no	missense	NBPF14	NM_015383.1	142	165,319,5300	AA,AC,CC		6.897,2.4882,5.6103	possibly-damaging	844/922	148004783	649,10919	1688	4096	5784	SO:0001583	missense	25832	exon22			AGCATGCTGTTGA	AK092351		1q21.1	2013-01-17			ENSG00000122497			"""neuroblastoma breakpoint family"""	25232	protein-coding gene	gene with protein product		614003				8619474, 9110174, 16079250	Standard	NM_015383		Approved	DJ328E19.C1.1	uc021owp.2	Q5TI25	OTTHUMG00000013900	ENST00000369219.1:c.2531G>T	1.37:g.148004783C>A	ENSP00000358221:p.Ser844Ile	529.0	2.0	0.00378072		412.0	393.0	0.953883	NM_015383	Q5TI23|Q8IX76|Q9UJI9	Missense_Mutation	SNP	ENST00000369219.1	37		61|61	0.027930402930402932|0.027930402930402932	1|1	0.0020325203252032522|0.0020325203252032522	6|6	0.016574585635359115|0.016574585635359115	0|0	0.0|0.0	54|54	0.0712401055408971|0.0712401055408971	c|c	9.996|9.996	1.232277|1.232277	0.22626|0.22626	0.024882|0.024882	0.06897|0.06897	ENSG00000122497|ENSG00000122497	ENST00000310701|ENST00000369219;ENST00000369368	.|T	.|0.06608	.|3.28	0.464|0.464	0.464|0.464	0.16706|0.16706	.|DUF1220 (2);	.|.	.|.	.|.	.|.	T|T	0.02571|0.02571	0.0078|0.0078	N|N	0.22421|0.22421	0.69|0.69	0.09310|0.09310	N|N	1|1	.|B;P;P	.|0.51653	.|0.228;0.947;0.858	.|B;P;P	.|0.54026	.|0.215;0.699;0.74	T|T	0.48068|0.48068	-0.9067|-0.9067	4|8	.|0.21014	.|T	.|0.42	.|.	.|.	.|.	.|.	.|.	.|192;825;844	.|F8WEX8;B4DH59;Q5TI25	.|.;.;NBPFE_HUMAN	S|I	850|844;192	.|ENSP00000358221:S844I	.|ENSP00000358221:S844I	A|S	-|-	1|2	0|0	NBPF14|NBPF14	146471407|146471407	0.009000|0.009000	0.17119|0.17119	0.004000|0.004000	0.12327|0.12327	0.011000|0.011000	0.07611|0.07611	0.685000|0.685000	0.25378|0.25378	0.550000|0.550000	0.28991|0.28991	0.388000|0.388000	0.25769|0.25769	GCA|AGC	C|0.960;A|0.040	0.040	strong		0.453	NBPF14-201	KNOWN	basic|appris_principal	protein_coding	protein_coding		NM_015383	
VNN2	8875	hgsc.bcm.edu	37	6	133073844	133073844	+	Silent	SNP	C	C	T	rs33980664	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr6:133073844C>T	ENST00000326499.6	-	4	706	c.582G>A	c.(580-582)ccG>ccA	p.P194P	RP1-55C23.7_ENST00000430895.1_RNA|VNN2_ENST00000526192.1_5'Flank|VNN2_ENST00000525289.1_Intron|VNN2_ENST00000525270.1_Silent_p.P141P	NM_004665.2	NP_004656	O95498	VNN2_HUMAN	vanin 2	194	CN hydrolase. {ECO:0000255|PROSITE- ProRule:PRU00054}.				cellular component movement (GO:0006928)|pantothenate metabolic process (GO:0015939)	anchored component of membrane (GO:0031225)|plasma membrane (GO:0005886)	pantetheine hydrolase activity (GO:0017159)			breast(1)|central_nervous_system(1)|cervix(1)|endometrium(3)|kidney(4)|large_intestine(7)|lung(14)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	36				OV - Ovarian serous cystadenocarcinoma(155;0.00237)|GBM - Glioblastoma multiforme(226;0.0267)		TCACCAACTCCGGCTTTTCAG	0.408													C|||	85	0.0169728	0.0023	0.049	5008	,	,		19553	0.004		0.0278	False		,,,				2504	0.0164				p.P194P		Atlas-SNP	.											.	VNN2	83	.	0			c.G582A						PASS	.	C	,,	24,4382	29.0+/-57.7	0,24,2179	119.0	115.0	116.0		,582,423	-10.8	0.0	6	dbSNP_126	116	294,8306	108.0+/-168.7	6,282,4012	no	intron,coding-synonymous,coding-synonymous	VNN2	NM_001242350.1,NM_004665.2,NM_078488.1	,,	6,306,6191	TT,TC,CC		3.4186,0.5447,2.445	,,	,194/521,141/468	133073844	318,12688	2203	4300	6503	SO:0001819	synonymous_variant	8875	exon4			CAACTCCGGCTTT	AB026705	CCDS5161.1, CCDS5162.1, CCDS56451.1	6q23-q24	2013-02-13			ENSG00000112303	ENSG00000112303	3.5.1.92	"""Vanins"""	12706	protein-coding gene	gene with protein product	"""pantetheinase"""	603571				9790769, 11491533	Standard	NM_078488		Approved	FOAP-4, GPI-80	uc003qdt.3	O95498	OTTHUMG00000015588	ENST00000326499.6:c.582G>A	6.37:g.133073844C>T		84.0	0.0	0		95.0	45.0	0.473684	NM_004665	A0AUZ3|A6NDY1|A8K4E3|A8K7W0|B2DFZ0|B2DFZ1|B2DFZ2|B2DFZ3|F6XL73|Q2XUN1|Q9UJF3|Q9UMW2	Silent	SNP	ENST00000326499.6	37	CCDS5161.1																																																																																			C|0.976;T|0.024	0.024	strong		0.408	VNN2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000042264.2		
MET	4233	hgsc.bcm.edu	37	7	116397572	116397572	+	Silent	SNP	A	A	G	rs13223756	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr7:116397572A>G	ENST00000318493.6	+	7	2131	c.1944A>G	c.(1942-1944)caA>caG	p.Q648Q	MET_ENST00000397752.3_Silent_p.Q648Q|MET_ENST00000436117.2_Silent_p.Q648Q			Q9NWH9	SLTM_HUMAN	MET proto-oncogene, receptor tyrosine kinase	0	Arg/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)			GGACAACACAATACAGTACAT	0.318			Mis		"""papillary renal, head-neck squamous cell """	papillary renal			Hereditary Papillary Renal Carcinoma (type 1)				A|||	941	0.187899	0.1089	0.1254	5008	,	,		17860	0.2728		0.2048	False		,,,				2504	0.2342				p.Q648Q		Atlas-SNP	.		Dom	yes	Familial Papillary Renal Cancer	7	7q31	4233	met proto-oncogene (hepatocyte growth factor receptor)		E	.	MET	412	.	0			c.A1944G						PASS	.	A	,	486,3224		27,432,1396	93.0	92.0	92.0		1944,1944	-6.5	0.0	7	dbSNP_121	92	1521,6665		129,1263,2701	no	coding-synonymous,coding-synonymous	MET	NM_000245.2,NM_001127500.1	,	156,1695,4097	GG,GA,AA		18.5805,13.0997,16.8712	,	648/1391,648/1409	116397572	2007,9889	1855	4093	5948	SO:0001819	synonymous_variant	4233	exon7	Familial Cancer Database	HPRC, Hereditary Papillary Renal Cell Cancer	AACACAATACAGT	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.1944A>G	7.37:g.116397572A>G		98.0	0.0	0		159.0	103.0	0.647799	NM_000245	A8K5V8|B2RTX3|Q2VPK7|Q52MB3|Q658J7|Q6ZNF2|Q86TK6|Q9H7C3|Q9H8U9	Silent	SNP	ENST00000318493.6	37	CCDS47689.1																																																																																			A|0.817;G|0.183	0.183	strong		0.318	MET-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000059620.3		
PCDHA13	56136	hgsc.bcm.edu	37	5	140262582	140262582	+	Nonsense_Mutation	SNP	C	C	G			TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr5:140262582C>G	ENST00000289272.2	+	1	729	c.729C>G	c.(727-729)taC>taG	p.Y243*	PCDHA1_ENST00000394633.3_Intron|PCDHA2_ENST00000526136.1_Intron|PCDHA10_ENST00000307360.5_Intron|PCDHA5_ENST00000529859.1_Intron|PCDHA1_ENST00000504120.2_Intron|PCDHA4_ENST00000512229.2_Intron|PCDHA5_ENST00000529619.1_Intron|PCDHA13_ENST00000409494.1_Nonsense_Mutation_p.Y243*|PCDHA10_ENST00000506939.2_Intron|PCDHA11_ENST00000398640.2_Intron|PCDHA7_ENST00000525929.1_Intron|PCDHA6_ENST00000527624.1_Intron|PCDHA6_ENST00000529310.1_Intron|PCDHA3_ENST00000522353.2_Intron|PCDHA8_ENST00000531613.1_Intron|PCDHA9_ENST00000532602.1_Intron|PCDHA12_ENST00000398631.2_Intron|PCDHA4_ENST00000530339.1_Intron	NM_018904.2|NM_031865.1	NP_061727.1|NP_114071.1	Q9Y5I0	PCDAD_HUMAN	protocadherin alpha 13	243	Cadherin 3. {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)|biliary_tract(2)|breast(3)|central_nervous_system(2)|cervix(2)|endometrium(11)|haematopoietic_and_lymphoid_tissue(7)|kidney(2)|large_intestine(18)|liver(3)|lung(23)|ovary(4)|prostate(6)|skin(7)|upper_aerodigestive_tract(2)|urinary_tract(2)	95			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			CGGAATTTTACCAATCCGTTT	0.453																																					p.Y243X	Melanoma(147;1739 1852 5500 27947 37288)	Atlas-SNP	.											.	PCDHA13	213	.	0			c.C729G						PASS	.						72.0	71.0	71.0					5																	140262582		2203	4300	6503	SO:0001587	stop_gained	56136	exon1			ATTTTACCAATCC	AF152478	CCDS4240.1	5q31	2010-11-26			ENSG00000239389	ENSG00000239389		"""Cadherins / Protocadherins : Clustered"""	8667	other	complex locus constituent	"""KIAA0345-like 1"", ""ortholog of mouse CNR5"""	606319		CNRS5		10380929, 10662547	Standard	NM_018904		Approved	CNR5, CRNR5, CNRN5, PCDH-ALPHA13		Q9Y5I0	OTTHUMG00000129614	ENST00000289272.2:c.729C>G	5.37:g.140262582C>G	ENSP00000289272:p.Tyr243*	133.0	0.0	0		141.0	49.0	0.347518	NM_031865	O75277	Nonsense_Mutation	SNP	ENST00000289272.2	37	CCDS4240.1	.	.	.	.	.	.	.	.	.	.	C	16.00	2.998714	0.54147	.	.	ENSG00000239389	ENST00000409494;ENST00000289272	.	.	.	5.58	-0.292	0.12839	.	.	.	.	.	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.66056	D	0.02	.	1.8341	0.03136	0.1235:0.1792:0.3522:0.345	.	.	.	.	X	243	.	ENSP00000289272:Y243X	Y	+	3	2	PCDHA13	140242766	0.000000	0.05858	0.101000	0.21167	0.535000	0.34838	-1.244000	0.02902	-0.053000	0.13289	0.561000	0.74099	TAC	.	.	none		0.453	PCDHA13-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000335000.1	NM_018904	
ST20	400410	hgsc.bcm.edu	37	15	80191280	80191280	+	Missense_Mutation	SNP	T	T	A	rs184575290	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr15:80191280T>A	ENST00000478497.1	-	3	912	c.233A>T	c.(232-234)tAc>tTc	p.Y78F	ST20-MTHFS_ENST00000494999.1_Intron|MTHFS_ENST00000258874.3_5'Flank|ST20-MTHFS_ENST00000479961.1_Intron|ST20_ENST00000485386.1_Missense_Mutation_p.Y78F|ST20_ENST00000562759.1_Missense_Mutation_p.Y78F|MTHFS_ENST00000559722.1_5'Flank	NM_001100879.1	NP_001094349.1	Q9HBF5	ST20_HUMAN	suppressor of tumorigenicity 20	78					extrinsic apoptotic signaling pathway in absence of ligand (GO:0097192)|intrinsic apoptotic signaling pathway in response to DNA damage (GO:0008630)|negative regulation of apoptotic process (GO:0043066)|negative regulation of intrinsic apoptotic signaling pathway (GO:2001243)	mitochondrial outer membrane (GO:0005741)	protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)			kidney(1)|large_intestine(1)|lung(1)|urinary_tract(1)	4						TATTTAAAAGTAGAAGTATGT	0.333													T|||	3	0.000599042	0.0	0.0	5008	,	,		18184	0.0		0.003	False		,,,				2504	0.0				p.Y78F		Atlas-SNP	.											ST20,NS,carcinoma,+1,1	ST20	9	1	0			c.A233T						PASS	.	T	PHE/TYR,PHE/TYR,PHE/TYR,	3,4391	6.2+/-15.9	0,3,2194	74.0	78.0	77.0		233,233,233,	-1.1	0.0	15		77	29,8561	17.9+/-57.8	0,29,4266	yes	missense,missense,missense,intron	ST20,ST20-MTHFS	NM_001100879.1,NM_001100880.2,NM_001199757.1,NM_001199760.1	22,22,22,	0,32,6460	AA,AT,TT		0.3376,0.0683,0.2465	possibly-damaging,possibly-damaging,possibly-damaging,	78/80,78/80,78/80,	80191280	32,12952	2197	4295	6492	SO:0001583	missense	400410	exon3			TAAAAGTAGAAGT	AF249277	CCDS42067.1	15q25.1	2007-07-16				ENSG00000180953			33520	protein-coding gene	gene with protein product							Standard	NM_001100879		Approved	HCCS-1		Q9HBF5		ENST00000478497.1:c.233A>T	15.37:g.80191280T>A	ENSP00000453502:p.Tyr78Phe	285.0	1.0	0.00350877		129.0	87.0	0.674419	NM_001199757		Missense_Mutation	SNP	ENST00000478497.1	37	CCDS42067.1	2	9.157509157509158E-4	0	0.0	0	0.0	0	0.0	2	0.002638522427440633	T	12.63	1.994958	0.35226	6.83E-4	0.003376	ENSG00000180953	ENST00000322484;ENST00000417278	.	.	.	1.78	-1.14	0.09741	.	.	.	.	.	T	0.16854	0.0405	.	.	.	0.09310	N	1	P	0.46020	0.871	B	0.31812	0.136	T	0.13150	-1.0520	7	0.87932	D	0	.	5.9491	0.19235	0.0:0.0:0.5632:0.4368	.	78	Q9HBF5	ST20_HUMAN	F	78	.	ENSP00000319125:Y78F	Y	-	2	0	ST20	77978335	0.002000	0.14202	0.000000	0.03702	0.446000	0.32137	-0.513000	0.06305	-0.277000	0.09193	0.172000	0.16884	TAC	T|0.998;A|0.002	0.002	strong		0.333	ST20-001	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000416728.2		
TMPRSS13	84000	hgsc.bcm.edu	37	11	117789317	117789317	+	Silent	SNP	T	T	C	rs201746372|rs58754377|rs201369736		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr11:117789317T>C	ENST00000430170.2	-	2	345	c.258A>G	c.(256-258)ccA>ccG	p.P86P	TMPRSS13_ENST00000445164.2_Silent_p.P86P|TMPRSS13_ENST00000526090.1_Silent_p.P86P|TMPRSS13_ENST00000524993.1_Silent_p.P86P|TMPRSS13_ENST00000528626.1_Silent_p.P86P	NM_001244995.1	NP_001231924.1	Q9BYE2	TMPSD_HUMAN	transmembrane protease, serine 13	86	13 X 5 AA repeats of A-S-P-A-[GLQR].|Ala-rich.					blood microparticle (GO:0072562)|integral component of membrane (GO:0016021)	scavenger receptor activity (GO:0005044)|serine-type endopeptidase activity (GO:0004252)	p.Q83_A87delQASPA(1)		endometrium(1)|kidney(3)|large_intestine(6)|lung(7)|pancreas(1)|prostate(1)|urinary_tract(1)	20	all_hematologic(175;0.0487)	Medulloblastoma(222;0.0425)|all_hematologic(192;0.196)|all_neural(223;0.234)		BRCA - Breast invasive adenocarcinoma(274;1.78e-05)|Epithelial(105;0.00106)		ATGCCCGGGCTGGAGATGCCT	0.652																																					p.P86P		Atlas-SNP	.											TMPRSS13,caecum,carcinoma,0,1	TMPRSS13	75	1	1	Deletion - In frame(1)	urinary_tract(1)	c.A258G						PASS	.						34.0	41.0	38.0					11																	117789317		1955	4135	6090	SO:0001819	synonymous_variant	84000	exon2			CCGGGCTGGAGAT	AB048796	CCDS41721.1, CCDS55788.1, CCDS55789.1, CCDS58185.1	11q23	2010-04-13	2005-03-11	2005-03-12	ENSG00000137747	ENSG00000137747		"""Serine peptidases / Transmembrane"""	29808	protein-coding gene	gene with protein product		610050	"""transmembrane protease, serine 11"""	TMPRSS11		11267681	Standard	NM_001077263		Approved	MSPL	uc001prs.2	Q9BYE2	OTTHUMG00000166992	ENST00000430170.2:c.258A>G	11.37:g.117789317T>C		118.0	0.0	0		268.0	13.0	0.0485075	NM_001206790	B4DTM9|E9PIJ5|F8WAJ3|Q86YM4|Q96JY8|Q9BYE1	Silent	SNP	ENST00000430170.2	37	CCDS58185.1																																																																																			.	.	weak		0.652	TMPRSS13-006	PUTATIVE	basic|appris_candidate|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000392318.1	NM_032046	
PRF1	5551	hgsc.bcm.edu	37	10	72360224	72360224	+	Silent	SNP	C	C	T	rs115281140	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr10:72360224C>T	ENST00000441259.1	-	2	595	c.435G>A	c.(433-435)gtG>gtA	p.V145V	PRF1_ENST00000373209.2_Silent_p.V145V	NM_001083116.1|NM_005041.4	NP_001076585.1|NP_005032.2	P14222	PERF_HUMAN	perforin 1 (pore forming protein)	145	MACPF. {ECO:0000255|PROSITE- ProRule:PRU00745}.				apoptotic process (GO:0006915)|cellular defense response (GO:0006968)|cytolysis (GO:0019835)|defense response to tumor cell (GO:0002357)|defense response to virus (GO:0051607)|immune response to tumor cell (GO:0002418)|protein homooligomerization (GO:0051260)|transmembrane transport (GO:0055085)	cytolytic granule (GO:0044194)|cytoplasmic membrane-bounded vesicle (GO:0016023)|endosome (GO:0005768)|extracellular region (GO:0005576)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|wide pore channel activity (GO:0022829)			breast(1)|central_nervous_system(1)|endometrium(1)|large_intestine(2)|lung(11)|ovary(1)|prostate(3)|urinary_tract(3)	23						CGGCCACAGACACATGCACAT	0.612			M			"""various leukaemia, lymphoma"""	Type 2 familial hemophagocytic lymphohistiocytosis		Familial Hemophagocytic Lymphohistiocytosis				C|||	64	0.0127796	0.0287	0.0086	5008	,	,		16983	0.0		0.0109	False		,,,				2504	0.0092				p.V145V		Atlas-SNP	.	yes	Rec			10	10q22	5551	perforin 1 (pore forming protein)		L	PRF1,NS,carcinoma,-2,1	PRF1	64	1	0			c.G435A						scavenged	.	C	,	88,4318	73.6+/-111.7	1,86,2116	88.0	76.0	80.0		435,435	2.8	0.0	10	dbSNP_132	80	71,8529	41.7+/-99.0	0,71,4229	no	coding-synonymous,coding-synonymous	PRF1	NM_001083116.1,NM_005041.4	,	1,157,6345	TT,TC,CC		0.8256,1.9973,1.2225	,	145/556,145/556	72360224	159,12847	2203	4300	6503	SO:0001819	synonymous_variant	5551	exon2	Familial Cancer Database	FHLH, FHL, Familial Hemophagocytic Reticulosis, FHR	CACAGACACATGC	BC047695	CCDS7305.1	10q22	2014-09-17			ENSG00000180644	ENSG00000180644			9360	protein-coding gene	gene with protein product	"""Perforin"", ""perforin 1 (preforming protein)"""	170280				1505959, 2592021	Standard	NM_005041		Approved	PFP, P1, HPLH2	uc001jrf.4	P14222	OTTHUMG00000018412	ENST00000441259.1:c.435G>A	10.37:g.72360224C>T		226.0	2.0	0.00884956		119.0	87.0	0.731092	NM_001083116	B2R6X4|Q59F57|Q86WX7	Silent	SNP	ENST00000441259.1	37	CCDS7305.1																																																																																			C|0.990;T|0.010	0.010	strong		0.612	PRF1-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048517.2	NM_005041	
TRAF3	7187	hgsc.bcm.edu	37	14	103336727	103336727	+	Silent	SNP	G	G	A	rs142350527	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr14:103336727G>A	ENST00000560371.1	+	2	406	c.189G>A	c.(187-189)ccG>ccA	p.P63P	TRAF3_ENST00000392745.2_Silent_p.P63P|TRAF3_ENST00000539721.1_Silent_p.P63P|TRAF3_ENST00000347662.4_Silent_p.P63P|TRAF3_ENST00000351691.5_Silent_p.P63P	NM_003300.3|NM_145725.2	NP_003291.2|NP_663777.1	Q13114	TRAF3_HUMAN	TNF receptor-associated factor 3	63					apoptotic process (GO:0006915)|innate immune response (GO:0045087)|MyD88-independent toll-like receptor signaling pathway (GO:0002756)|negative regulation of NF-kappaB transcription factor activity (GO:0032088)|negative regulation of type I interferon production (GO:0032480)|regulation of apoptotic process (GO:0042981)|regulation of cytokine production (GO:0001817)|regulation of defense response to virus (GO:0050688)|regulation of interferon-beta production (GO:0032648)|regulation of proteolysis (GO:0030162)|signal transduction (GO:0007165)|Toll signaling pathway (GO:0008063)|toll-like receptor 3 signaling pathway (GO:0034138)|toll-like receptor 4 signaling pathway (GO:0034142)|toll-like receptor signaling pathway (GO:0002224)|TRIF-dependent toll-like receptor signaling pathway (GO:0035666)|tumor necrosis factor-mediated signaling pathway (GO:0033209)	CD40 receptor complex (GO:0035631)|cytoplasmic side of plasma membrane (GO:0009898)|cytosol (GO:0005829)|endosome (GO:0005768)|mitochondrion (GO:0005739)	ligase activity (GO:0016874)|signal transducer activity (GO:0004871)|thioesterase binding (GO:0031996)|tumor necrosis factor receptor binding (GO:0005164)|ubiquitin protein ligase binding (GO:0031625)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			breast(4)|endometrium(2)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(10)|liver(2)|lung(7)|ovary(1)|prostate(2)	30		all_cancers(154;7.87e-06)|all_epithelial(191;0.0024)		Epithelial(152;9.92e-24)|all cancers(159;2.23e-21)|OV - Ovarian serous cystadenocarcinoma(161;7.85e-12)|Colorectal(3;0.0971)		TGTGCAGCCCGAAGCAGACCG	0.617													G|||	23	0.00459265	0.0	0.0159	5008	,	,		16014	0.0		0.0119	False		,,,				2504	0.0				p.P63P		Atlas-SNP	.											.	TRAF3	60	.	0			c.G189A						PASS	.	G	,,,	8,4398	14.3+/-33.2	0,8,2195	76.0	65.0	68.0		189,189,189,189	-10.9	0.4	14	dbSNP_134	68	28,8572	19.8+/-62.0	0,28,4272	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	TRAF3	NM_001199427.1,NM_003300.3,NM_145725.2,NM_145726.2	,,,	0,36,6467	AA,AG,GG		0.3256,0.1816,0.2768	,,,	63/486,63/569,63/569,63/544	103336727	36,12970	2203	4300	6503	SO:0001819	synonymous_variant	7187	exon3			CAGCCCGAAGCAG	U21092	CCDS9975.1, CCDS9976.1, CCDS55946.1	14q32.32	2014-09-17				ENSG00000131323			12033	protein-coding gene	gene with protein product		601896				7530216, 7859281	Standard	NM_145725		Approved	CAP-1, CD40bp, CRAF1, LAP1	uc001ymd.2	Q13114		ENST00000560371.1:c.189G>A	14.37:g.103336727G>A		82.0	0.0	0		93.0	37.0	0.397849	NM_145726	B7Z8C4|Q12990|Q13076|Q13947|Q6AZX1|Q9UNL1	Silent	SNP	ENST00000560371.1	37	CCDS9975.1																																																																																			G|0.996;A|0.004	0.004	strong		0.617	TRAF3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000415735.1	NM_145725	
DNA2	1763	hgsc.bcm.edu	37	10	70178965	70178965	+	Silent	SNP	T	T	C			TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr10:70178965T>C	ENST00000358410.3	-	19	2843	c.2793A>G	c.(2791-2793)ggA>ggG	p.G931G	DNA2_ENST00000399180.2_Silent_p.G1017G|DNA2_ENST00000399179.2_Silent_p.G693G	NM_001080449.2	NP_001073918.2	P51530	DNA2_HUMAN	DNA replication helicase/nuclease 2	931	Helicase activity. {ECO:0000250}.				ATP catabolic process (GO:0006200)|base-excision repair (GO:0006284)|DNA catabolic process, endonucleolytic (GO:0000737)|DNA double-strand break processing (GO:0000729)|DNA duplex unwinding (GO:0032508)|DNA replication (GO:0006260)|DNA replication checkpoint (GO:0000076)|DNA replication, Okazaki fragment processing (GO:0033567)|DNA replication, removal of RNA primer (GO:0043137)|DNA strand elongation involved in DNA replication (GO:0006271)|mitochondrial DNA repair (GO:0043504)|mitochondrial DNA replication (GO:0006264)|mitotic cell cycle (GO:0000278)|positive regulation of DNA replication (GO:0045740)|telomere maintenance (GO:0000723)|telomere maintenance via recombination (GO:0000722)|telomere maintenance via semi-conservative replication (GO:0032201)	mitochondrial nucleoid (GO:0042645)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	4 iron, 4 sulfur cluster binding (GO:0051539)|5'-3' DNA helicase activity (GO:0043139)|5'-flap endonuclease activity (GO:0017108)|ATP binding (GO:0005524)|ATPase activity (GO:0016887)|DNA binding (GO:0003677)|DNA helicase activity (GO:0003678)|helicase activity (GO:0004386)|metal ion binding (GO:0046872)|nuclease activity (GO:0004518)|single-stranded DNA-dependent ATPase activity (GO:0043142)|site-specific endodeoxyribonuclease activity, specific for altered base (GO:0016890)			breast(1)|endometrium(3)|kidney(1)|large_intestine(7)|lung(7)|prostate(1)	20						AGGGACTGCATCCAGCCTAAA	0.323																																					p.G931G		Atlas-SNP	.											.	DNA2	76	.	0			c.A2793G						PASS	.						54.0	46.0	49.0					10																	70178965		1838	4091	5929	SO:0001819	synonymous_variant	1763	exon19			ACTGCATCCAGCC	D42046	CCDS44415.1, CCDS44415.2	10q21.3-q22.1	2013-05-13	2013-05-13	2008-01-08	ENSG00000138346	ENSG00000138346			2939	protein-coding gene	gene with protein product		601810	"""DNA2 DNA replication helicase 2-like (yeast)"", ""DNA replication helicase 2 homolog (yeast)"""	DNA2L		8938459, 17032657, 23352259	Standard	NM_001080449		Approved	KIAA0083	uc031pvh.1	P51530	OTTHUMG00000018352	ENST00000358410.3:c.2793A>G	10.37:g.70178965T>C		49.0	0.0	0		38.0	19.0	0.5	NM_001080449	Q2NKM1|Q5TC49|Q5TC50|Q6P455|Q6PI80|Q7Z6H9|Q8N346	Silent	SNP	ENST00000358410.3	37		.	.	.	.	.	.	.	.	.	.	T	8.699	0.909289	0.17833	.	.	ENSG00000138346	ENST00000440722	.	.	.	5.39	-0.794	0.10918	.	.	.	.	.	T	0.50990	0.1648	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.40997	-0.9533	4	.	.	.	.	5.9261	0.19112	0.3798:0.0:0.2894:0.3308	.	.	.	.	V	253	.	.	M	-	1	0	DNA2	69848971	1.000000	0.71417	0.989000	0.46669	0.871000	0.50021	0.478000	0.22212	0.009000	0.14813	0.482000	0.46254	ATG	.	.	none		0.323	DNA2-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000048334.2		
PRPF4B	8899	hgsc.bcm.edu	37	6	4044109	4044109	+	Silent	SNP	G	G	A	rs12195092	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr6:4044109G>A	ENST00000337659.6	+	6	1813	c.1713G>A	c.(1711-1713)caG>caA	p.Q571Q	PRPF4B_ENST00000538861.1_Silent_p.Q557Q	NM_003913.4	NP_003904.3	Q13523	PRP4B_HUMAN	pre-mRNA processing factor 4B	571					mRNA splicing, via spliceosome (GO:0000398)|protein phosphorylation (GO:0006468)|RNA splicing (GO:0008380)	catalytic step 2 spliceosome (GO:0071013)|chromosome (GO:0005694)|nucleus (GO:0005634)	ATP binding (GO:0005524)|poly(A) RNA binding (GO:0044822)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)			breast(6)|endometrium(3)|large_intestine(5)|lung(4)|upper_aerodigestive_tract(3)|urinary_tract(1)	22	Ovarian(93;0.0925)	all_hematologic(90;0.0895)				GCAGCCCCCAGAGCAGTACGA	0.398													G|||	30	0.00599042	0.0015	0.0058	5008	,	,		18977	0.0		0.0219	False		,,,				2504	0.002				p.Q571Q		Atlas-SNP	.											.	PRPF4B	140	.	0			c.G1713A						PASS	.	G		15,4391	22.3+/-47.3	0,15,2188	90.0	85.0	87.0		1713	4.5	1.0	6	dbSNP_120	87	218,8382	91.4+/-153.5	1,216,4083	no	coding-synonymous	PRPF4B	NM_003913.4		1,231,6271	AA,AG,GG		2.5349,0.3404,1.7915		571/1008	4044109	233,12773	2203	4300	6503	SO:0001819	synonymous_variant	8899	exon6			CCCCCAGAGCAGT	U48736	CCDS4488.1	6p24.2	2013-10-03	2013-10-03		ENSG00000112739	ENSG00000112739			17346	protein-coding gene	gene with protein product		602338	"""PRP4 pre-mRNA processing factor 4 homolog B (yeast)"""			9628581, 11418604	Standard	XR_241936		Approved	Prp4, PR4H, KIAA0536	uc003mvv.3	Q13523	OTTHUMG00000014157	ENST00000337659.6:c.1713G>A	6.37:g.4044109G>A		163.0	0.0	0		119.0	56.0	0.470588	NM_003913	A8K5C9|Q5D0F6|Q5TAY8|Q8IVC3|Q8TDP2|Q96QT7|Q9UEE6	Silent	SNP	ENST00000337659.6	37	CCDS4488.1																																																																																			G|0.982;A|0.018	0.018	strong		0.398	PRPF4B-011	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000314018.2		
TAT	6898	hgsc.bcm.edu	37	16	71602660	71602660	+	Missense_Mutation	SNP	G	G	A	rs142634310	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr16:71602660G>A	ENST00000355962.4	-	11	1311	c.1178C>T	c.(1177-1179)aCg>aTg	p.T393M	RP11-432I5.1_ENST00000561529.1_RNA	NM_000353.2	NP_000344.1	P17735	ATTY_HUMAN	tyrosine aminotransferase	393					2-oxoglutarate metabolic process (GO:0006103)|biosynthetic process (GO:0009058)|cellular nitrogen compound metabolic process (GO:0034641)|glutamate metabolic process (GO:0006536)|L-phenylalanine catabolic process (GO:0006559)|response to glucocorticoid (GO:0051384)|response to mercury ion (GO:0046689)|response to oxidative stress (GO:0006979)|small molecule metabolic process (GO:0044281)|tyrosine catabolic process (GO:0006572)	cytosol (GO:0005829)|mitochondrion (GO:0005739)	amino acid binding (GO:0016597)|L-phenylalanine:2-oxoglutarate aminotransferase activity (GO:0080130)|L-tyrosine:2-oxoglutarate aminotransferase activity (GO:0004838)|pyridoxal phosphate binding (GO:0030170)			breast(1)|central_nervous_system(1)|cervix(1)|endometrium(3)|kidney(1)|large_intestine(7)|lung(9)|ovary(2)|prostate(1)|skin(3)	29		Ovarian(137;0.125)		Kidney(780;0.0157)	L-Phenylalanine(DB00120)|L-Tyrosine(DB00135)	TAACCGCTCCGTGAACTCCAC	0.517																																					p.T393M	Melanoma(198;542 2142 10292 21661 50033)|Esophageal Squamous(48;487 1013 5572 44395 52594)	Atlas-SNP	.											.	TAT	80	.	0			c.C1178T						PASS	.	G	MET/THR	0,4396		0,0,2198	82.0	69.0	73.0		1178	4.9	1.0	16	dbSNP_134	73	3,8597	3.0+/-9.4	0,3,4297	yes	missense	TAT	NM_000353.2	81	0,3,6495	AA,AG,GG		0.0349,0.0,0.0231	probably-damaging	393/455	71602660	3,12993	2198	4300	6498	SO:0001583	missense	6898	exon11			CGCTCCGTGAACT		CCDS10903.1	16q22.1	2012-10-02			ENSG00000198650	ENSG00000198650	2.6.1.5		11573	protein-coding gene	gene with protein product		613018					Standard	NM_000353		Approved		uc002fap.2	P17735	OTTHUMG00000137590	ENST00000355962.4:c.1178C>T	16.37:g.71602660G>A	ENSP00000348234:p.Thr393Met	148.0	0.0	0		156.0	32.0	0.205128	NM_000353	B2R8I1|D3DWS2	Missense_Mutation	SNP	ENST00000355962.4	37	CCDS10903.1	.	.	.	.	.	.	.	.	.	.	G	22.9	4.353229	0.82132	0.0	3.49E-4	ENSG00000198650	ENST00000355962	D	0.90676	-2.71	5.93	4.93	0.64822	Tyrosine aminotransferase (1);Aminotransferase, class I/classII (1);Tyrosine/nicotianamine aminotransferase (1);Pyridoxal phosphate-dependent transferase, major region, subdomain 2 (1);Pyridoxal phosphate-dependent transferase, major domain (1);	0.000000	0.85682	D	0.000000	D	0.94089	0.8105	L	0.55103	1.725	0.80722	D	1	D	0.89917	1.0	D	0.87578	0.998	D	0.93537	0.6874	10	0.49607	T	0.09	-17.5761	18.7826	0.91941	0.0:0.1252:0.8748:0.0	.	393	P17735	ATTY_HUMAN	M	393	ENSP00000348234:T393M	ENSP00000348234:T393M	T	-	2	0	TAT	70160161	1.000000	0.71417	0.970000	0.41538	0.977000	0.68977	7.610000	0.82949	2.826000	0.97356	0.655000	0.94253	ACG	G|0.999;A|0.001	0.001	strong		0.517	TAT-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000268989.1		
PCDHA10	56139	hgsc.bcm.edu	37	5	140237158	140237158	+	Missense_Mutation	SNP	G	G	A	rs142356019	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr5:140237158G>A	ENST00000307360.5	+	1	1525	c.1525G>A	c.(1525-1527)Gtg>Atg	p.V509M	PCDHA5_ENST00000529619.1_Intron|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_ENST00000527624.1_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	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	211.0	0.0	0		139.0	62.0	0.446043	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	
GAD2	2572	hgsc.bcm.edu	37	10	26575277	26575277	+	Silent	SNP	T	T	C	rs531559223		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr10:26575277T>C	ENST00000376261.3	+	13	1743	c.1240T>C	c.(1240-1242)Ttg>Ctg	p.L414L	GAD2_ENST00000259271.3_Silent_p.L414L	NM_001134366.1	NP_001127838.1	Q05329	DCE2_HUMAN	glutamate decarboxylase 2 (pancreatic islets and brain, 65kDa)	414					glutamate decarboxylation to succinate (GO:0006540)|neurotransmitter biosynthetic process (GO:0042136)|neurotransmitter secretion (GO:0007269)|response to drug (GO:0042493)|synaptic transmission (GO:0007268)	anchored component of membrane (GO:0031225)|axon (GO:0030424)|cell junction (GO:0030054)|clathrin-sculpted gamma-aminobutyric acid transport vesicle membrane (GO:0061202)|cytosol (GO:0005829)|Golgi apparatus (GO:0005794)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|synaptic vesicle membrane (GO:0030672)	glutamate binding (GO:0016595)|glutamate decarboxylase activity (GO:0004351)|pyridoxal phosphate binding (GO:0030170)			central_nervous_system(1)|endometrium(2)|large_intestine(8)|lung(26)|ovary(1)|pancreas(1)|prostate(3)|skin(4)|upper_aerodigestive_tract(1)|urinary_tract(1)	48						CTTGTAGGGATTGATGCAGAA	0.363													T|||	1	0.000199681	0.0	0.0	5008	,	,		18191	0.0		0.0	False		,,,				2504	0.001				p.L414L		Atlas-SNP	.											.	GAD2	116	.	0			c.T1240C						PASS	.						102.0	91.0	95.0					10																	26575277		2203	4300	6503	SO:0001819	synonymous_variant	2572	exon13			TAGGGATTGATGC	AJ251501	CCDS7149.1	10p13-p11.2	2003-11-11	2002-08-29		ENSG00000136750	ENSG00000136750	4.1.1.15		4093	protein-coding gene	gene with protein product		138275	"""glutamate decarboxylase 2 (pancreatic islets and brain, 65kD)"""			2039509	Standard	NM_000818		Approved	GAD65	uc001isp.2	Q05329	OTTHUMG00000017836	ENST00000376261.3:c.1240T>C	10.37:g.26575277T>C		84.0	0.0	0		56.0	15.0	0.267857	NM_000818	Q9UD87	Silent	SNP	ENST00000376261.3	37	CCDS7149.1																																																																																			.	.	none		0.363	GAD2-001	KNOWN	alternative_3_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047255.1	NM_000818	
ZNF300	91975	hgsc.bcm.edu	37	5	150275835	150275835	+	Missense_Mutation	SNP	C	C	A			TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr5:150275835C>A	ENST00000274599.5	-	6	1386	c.966G>T	c.(964-966)gaG>gaT	p.E322D	ZNF300_ENST00000446148.2_Missense_Mutation_p.E338D|ZNF300_ENST00000418587.2_Missense_Mutation_p.E286D|ZNF300_ENST00000394226.2_Missense_Mutation_p.E322D|ZNF300_ENST00000427179.1_3'UTR	NM_052860.2	NP_443092.1	Q96RE9	ZN300_HUMAN	zinc finger protein 300	322					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(4)|kidney(3)|large_intestine(3)|lung(13)|ovary(1)|prostate(1)|skin(2)	27		Medulloblastoma(196;0.109)|all_hematologic(541;0.131)	KIRC - Kidney renal clear cell carcinoma(527;0.000785)|Kidney(363;0.00101)			CATAAGGTTTCTCCCCAGTAT	0.398																																					p.E338D		Atlas-SNP	.											.	ZNF300	69	.	0			c.G1014T						PASS	.						84.0	89.0	87.0					5																	150275835		2202	4299	6501	SO:0001583	missense	91975	exon7			AGGTTTCTCCCCA	AF395541	CCDS4311.2, CCDS54939.1, CCDS54940.1	5q33.1	2013-01-08			ENSG00000145908	ENSG00000145908		"""Zinc fingers, C2H2-type"", ""-"""	13091	protein-coding gene	gene with protein product		612429				14746915	Standard	NM_052860		Approved		uc021yfx.1	Q96RE9	OTTHUMG00000130076	ENST00000274599.5:c.966G>T	5.37:g.150275835C>A	ENSP00000274599:p.Glu322Asp	126.0	0.0	0		102.0	26.0	0.254902	NM_001172831	A8MY91|B3KU35|B4DU78|F5GWS1|Q06DQ3|Q17RP3|Q5H9N5	Missense_Mutation	SNP	ENST00000274599.5	37	CCDS4311.2	.	.	.	.	.	.	.	.	.	.	C	17.05	3.289152	0.59976	.	.	ENSG00000145908	ENST00000446148;ENST00000274599;ENST00000418587;ENST00000394226	T;T;T;T	0.26810	1.71;1.71;1.71;1.71	3.59	2.71	0.32032	Zinc finger, C2H2 (1);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.29817	0.0745	L	0.41961	1.31	0.26287	N	0.97818	P	0.47484	0.896	P	0.50136	0.632	T	0.08432	-1.0722	9	0.72032	D	0.01	.	8.7303	0.34494	0.0:0.8839:0.0:0.1161	.	322	Q96RE9	ZN300_HUMAN	D	338;322;286;322	ENSP00000397178:E338D;ENSP00000274599:E322D;ENSP00000392593:E286D;ENSP00000377773:E322D	ENSP00000274599:E322D	E	-	3	2	ZNF300	150256028	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	1.994000	0.40757	0.846000	0.35142	0.563000	0.77884	GAG	.	.	none		0.398	ZNF300-201	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding		NM_052860	
HERC2	8924	hgsc.bcm.edu	37	15	28459393	28459393	+	Silent	SNP	C	C	T			TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr15:28459393C>T	ENST00000261609.7	-	41	6492	c.6384G>A	c.(6382-6384)gtG>gtA	p.V2128V		NM_004667.5	NP_004658.3			HECT and RLD domain containing E3 ubiquitin protein ligase 2											NS(1)|autonomic_ganglia(1)|breast(3)|central_nervous_system(3)|cervix(3)|endometrium(20)|kidney(11)|large_intestine(33)|lung(95)|ovary(7)|prostate(8)|skin(7)|upper_aerodigestive_tract(8)|urinary_tract(4)	204		all_lung(180;1.3e-11)|Breast(32;0.000194)|Colorectal(260;0.227)		all cancers(64;3.93e-09)|Epithelial(43;9.99e-08)|BRCA - Breast invasive adenocarcinoma(123;0.0271)|GBM - Glioblastoma multiforme(186;0.0497)|Lung(196;0.199)		CCTGCGGGCGCACCCTGCGCC	0.672																																					p.V2128V		Atlas-SNP	.											.	HERC2	501	.	0			c.G6384A						PASS	.						24.0	25.0	25.0					15																	28459393		2195	4293	6488	SO:0001819	synonymous_variant	8924	exon41			CGGGCGCACCCTG	AF071172	CCDS10021.1	15q13	2012-02-23	2012-02-23		ENSG00000128731	ENSG00000128731			4868	protein-coding gene	gene with protein product		605837	"""hect domain and RLD 2"""			9949213	Standard	NM_004667		Approved	jdf2, p528, D15F37S1	uc001zbj.4	O95714	OTTHUMG00000129251	ENST00000261609.7:c.6384G>A	15.37:g.28459393C>T		82.0	0.0	0		53.0	45.0	0.849057	NM_004667		Silent	SNP	ENST00000261609.7	37	CCDS10021.1																																																																																			.	.	none		0.672	HERC2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251358.2	NM_004667	
SPNS2	124976	hgsc.bcm.edu	37	17	4434031	4434031	+	Silent	SNP	G	G	A			TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr17:4434031G>A	ENST00000329078.3	+	4	888	c.678G>A	c.(676-678)acG>acA	p.T226T		NM_001124758.1	NP_001118230.1	Q8IVW8	SPNS2_HUMAN	spinster homolog 2 (Drosophila)	226					B cell homeostasis (GO:0001782)|bone development (GO:0060348)|lymph node development (GO:0048535)|lymphocyte migration (GO:0072676)|regulation of eye pigmentation (GO:0048073)|regulation of humoral immune response (GO:0002920)|sphingolipid metabolic process (GO:0006665)|sphingosine-1-phosphate signaling pathway (GO:0003376)|T cell homeostasis (GO:0043029)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)	sphingolipid transporter activity (GO:0046624)			large_intestine(3)|lung(1)|prostate(1)|skin(1)	6						CCAAGAACACGCGTACGCTCA	0.627																																					p.T226T		Atlas-SNP	.											SPNS2,colon,carcinoma,+1,1	SPNS2	24	1	0			c.G678A						PASS	.						69.0	61.0	63.0					17																	4434031		1568	3582	5150	SO:0001819	synonymous_variant	124976	exon4			GAACACGCGTACG	BC041772	CCDS42237.1	17p13.2	2008-12-15				ENSG00000183018			26992	protein-coding gene	gene with protein product		612584				12815463	Standard	NM_001124758		Approved		uc002fxx.2	Q8IVW8		ENST00000329078.3:c.678G>A	17.37:g.4434031G>A		201.0	0.0	0		205.0	103.0	0.502439	NM_001124758	B9A1T3	Silent	SNP	ENST00000329078.3	37	CCDS42237.1																																																																																			.	.	none		0.627	SPNS2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000438802.1		
CCDC108	255101	hgsc.bcm.edu	37	2	219890814	219890814	+	Missense_Mutation	SNP	C	C	T	rs114017706	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr2:219890814C>T	ENST00000341552.5	-	14	2362	c.2279G>A	c.(2278-2280)cGg>cAg	p.R760Q	CCDC108_ENST00000453220.1_Missense_Mutation_p.R760Q|CCDC108_ENST00000441968.1_Missense_Mutation_p.R760Q	NM_194302.2	NP_919278.2	Q6ZU64	CC108_HUMAN	coiled-coil domain containing 108	760						integral component of membrane (GO:0016021)	poly(A) RNA binding (GO:0044822)|structural molecule activity (GO:0005198)			autonomic_ganglia(1)|breast(1)|cervix(1)|endometrium(4)|kidney(2)|large_intestine(18)|liver(1)|lung(34)|ovary(2)|pancreas(1)|prostate(6)|skin(5)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	80		Renal(207;0.0915)		Epithelial(149;1.12e-06)|all cancers(144;0.000196)|LUSC - Lung squamous cell carcinoma(224;0.008)|Lung(261;0.00942)		GCCTCGTGCCCGCACCGTCAG	0.597													C|||	75	0.014976	0.0499	0.0086	5008	,	,		20085	0.0		0.002	False		,,,				2504	0.001				p.R760Q		Atlas-SNP	.											CCDC108,right_upper_lobe,carcinoma,+1,1	CCDC108	208	1	0			c.G2279A						PASS	.	C	GLN/ARG	149,4257	103.8+/-142.4	1,147,2055	80.0	71.0	74.0		2279	-1.5	0.0	2	dbSNP_132	74	5,8595	4.3+/-15.6	0,5,4295	yes	missense	CCDC108	NM_194302.2	43	1,152,6350	TT,TC,CC		0.0581,3.3818,1.1841	possibly-damaging	760/1926	219890814	154,12852	2203	4300	6503	SO:0001583	missense	255101	exon14			CGTGCCCGCACCG	NM_194302, AL833882, AK127189	CCDS2430.2, CCDS2431.2, CCDS63125.1, CCDS63126.1	2q35	2008-02-05			ENSG00000181378	ENSG00000181378			25325	protein-coding gene	gene with protein product		614270				12477932	Standard	NM_194302		Approved	DKFZp434O0527, MGC35338	uc002vjl.2	Q6ZU64	OTTHUMG00000133013	ENST00000341552.5:c.2279G>A	2.37:g.219890814C>T	ENSP00000340776:p.Arg760Gln	230.0	0.0	0		164.0	47.0	0.286585	NM_194302	A2BDD8|E9PCR1|E9PG25|E9PG72|Q6ZSR8|Q8N0T4|Q8NDJ3	Missense_Mutation	SNP	ENST00000341552.5	37	CCDS2430.2	21	0.009615384615384616	16	0.032520325203252036	4	0.011049723756906077	0	0.0	1	0.0013192612137203166	C	12.23	1.874254	0.33069	0.033818	5.81E-4	ENSG00000181378	ENST00000341552;ENST00000441968;ENST00000453220	T;T;T	0.06068	3.35;3.35;3.35	4.87	-1.46	0.08800	.	0.698236	0.11855	N	0.522902	T	0.01454	0.0047	L	0.55103	1.725	0.09310	N	1	P	0.39404	0.672	B	0.28139	0.086	T	0.34428	-0.9829	10	0.35671	T	0.21	-7.944	6.1253	0.20176	0.0:0.4501:0.1226:0.4273	.	760	Q6ZU64	CC108_HUMAN	Q	760	ENSP00000340776:R760Q;ENSP00000413377:R760Q;ENSP00000409117:R760Q	ENSP00000340776:R760Q	R	-	2	0	CCDC108	219599058	0.000000	0.05858	0.003000	0.11579	0.588000	0.36517	-0.972000	0.03802	-0.213000	0.10094	0.561000	0.74099	CGG	C|0.989;T|0.011	0.011	strong		0.597	CCDC108-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000256598.4	NM_194302	
DMBT1	1755	hgsc.bcm.edu	37	10	124351974	124351974	+	Missense_Mutation	SNP	T	T	G			TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr10:124351974T>G	ENST00000338354.3	+	20	2469	c.2363T>G	c.(2362-2364)tTt>tGt	p.F788C	DMBT1_ENST00000368955.3_Missense_Mutation_p.F778C|DMBT1_ENST00000368956.2_Intron|DMBT1_ENST00000368909.3_Missense_Mutation_p.F788C|DMBT1_ENST00000344338.3_Missense_Mutation_p.F778C|DMBT1_ENST00000330163.4_Intron|DMBT1_ENST00000359586.6_Intron			Q9UGM3	DMBT1_HUMAN	deleted in malignant brain tumors 1	788	SRCR 6. {ECO:0000255|PROSITE- ProRule:PRU00196}.				defense response to virus (GO:0051607)|epithelial cell differentiation (GO:0030855)|induction of bacterial agglutination (GO:0043152)|innate immune response (GO:0045087)|inner cell mass cell proliferation (GO:0001833)|pattern recognition receptor signaling pathway (GO:0002221)|positive regulation of epithelial cell differentiation (GO:0030858)|protein transport (GO:0015031)|receptor-mediated endocytosis (GO:0006898)|viral process (GO:0016032)	cytoplasm (GO:0005737)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|extrinsic component of membrane (GO:0019898)|phagocytic vesicle membrane (GO:0030670)|proteinaceous extracellular matrix (GO:0005578)|zymogen granule membrane (GO:0042589)	calcium-dependent protein binding (GO:0048306)|scavenger receptor activity (GO:0005044)|signaling pattern recognition receptor activity (GO:0008329)|zymogen binding (GO:0035375)			breast(2)|central_nervous_system(7)|cervix(3)|endometrium(8)|kidney(1)|large_intestine(1)|lung(46)|prostate(1)|urinary_tract(3)	72		all_neural(114;0.0765)|Lung NSC(174;0.132)|all_lung(145;0.163)|Breast(234;0.238)				AATGCCCGGTTTGGCCAGGGC	0.617																																					p.F788C	Ovarian(182;93 2026 18125 22222 38972)	Atlas-SNP	.											.	DMBT1	677	.	0			c.T2363G						PASS	.						172.0	135.0	147.0					10																	124351974		1994	4114	6108	SO:0001583	missense	1755	exon20			CCCGGTTTGGCCA		CCDS44490.1, CCDS44491.1, CCDS44492.1	10q25.3-q26.1	2008-08-01			ENSG00000187908	ENSG00000187908			2926	protein-coding gene	gene with protein product		601969				9288095, 17548659	Standard	NM_004406		Approved	GP340, muclin	uc001lgk.1	Q9UGM3	OTTHUMG00000019185	ENST00000338354.3:c.2363T>G	10.37:g.124351974T>G	ENSP00000342210:p.Phe788Cys	90.0	0.0	0		78.0	26.0	0.333333	NM_007329	A6NDG4|A6NDJ5|A8E4R5|B1ARE7|B1ARE8|B1ARE9|B1ARF0|B7Z8Y2|F8WEF7|Q59EX0|Q5JR26|Q6MZN4|Q96DU4|Q9UGM2|Q9UJ57|Q9UKJ4|Q9Y211|Q9Y4V9	Missense_Mutation	SNP	ENST00000338354.3	37		.	.	.	.	.	.	.	.	.	.	T	8.174	0.792281	0.16258	.	.	ENSG00000187908	ENST00000338354;ENST00000368915;ENST00000341278;ENST00000368953;ENST00000339871;ENST00000368942;ENST00000344338;ENST00000368909;ENST00000368955	T;T;T;T	0.64991	-0.13;-0.13;-0.13;-0.13	3.86	3.86	0.44501	Speract/scavenger receptor (2);Speract/scavenger receptor-related (2);	.	.	.	.	D	0.84547	0.5496	H	0.97962	4.115	0.80722	D	1	D;D;D;D	0.89917	1.0;1.0;1.0;1.0	D;D;D;D	0.97110	1.0;0.998;0.998;0.999	D	0.86955	0.2088	9	0.87932	D	0	.	8.6056	0.33771	0.1713:0.0:0.0:0.8286	.	549;788;778;788	Q9UGM3-4;Q9UGM3-6;Q9UGM3-3;Q9UGM3	.;.;.;DMBT1_HUMAN	C	788;788;788;788;788;788;778;788;778	ENSP00000342210:F788C;ENSP00000343175:F778C;ENSP00000357905:F788C;ENSP00000357951:F778C	ENSP00000342210:F788C	F	+	2	0	DMBT1	124341964	1.000000	0.71417	0.015000	0.15790	0.070000	0.16714	3.795000	0.55499	1.525000	0.49052	0.456000	0.33151	TTT	.	.	none		0.617	DMBT1-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000050792.2	NM_004406	
PKM	5315	hgsc.bcm.edu	37	15	72501072	72501072	+	Silent	SNP	C	C	T	rs11558376	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr15:72501072C>T	ENST00000335181.5	-	6	829	c.726G>A	c.(724-726)gcG>gcA	p.A242A	PKM_ENST00000389093.3_Silent_p.A242A|PKM_ENST00000568459.1_Silent_p.A242A|PKM_ENST00000568883.1_Silent_p.A77A|PKM_ENST00000565184.1_Silent_p.A242A|PKM_ENST00000319622.6_Silent_p.A242A|PKM_ENST00000565154.1_Silent_p.A242A|PKM_ENST00000449901.2_Silent_p.A227A	NM_002654.4	NP_002645.3	P14618	KPYM_HUMAN	pyruvate kinase, muscle	242					carbohydrate metabolic process (GO:0005975)|glucose metabolic process (GO:0006006)|glycolytic process (GO:0006096)|programmed cell death (GO:0012501)|small molecule metabolic process (GO:0044281)	cilium (GO:0005929)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular matrix (GO:0031012)|extracellular vesicular exosome (GO:0070062)|mitochondrion (GO:0005739)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|vesicle (GO:0031982)	ATP binding (GO:0005524)|magnesium ion binding (GO:0000287)|MHC class II protein complex binding (GO:0023026)|poly(A) RNA binding (GO:0044822)|potassium ion binding (GO:0030955)|pyruvate kinase activity (GO:0004743)			endometrium(1)|lung(7)	8					Pyruvic acid(DB00119)	GGATGAATGACGCAAACACCA	0.493													C|||	4	0.000798722	0.0	0.0	5008	,	,		21170	0.0		0.004	False		,,,				2504	0.0				p.A316A		Atlas-SNP	.											PKM2,NS,neuroblastoma,-1,2	PKM	25	2	0			c.G948A						PASS	.	C	,,,,,,	1,4397	2.1+/-5.4	0,1,2198	203.0	180.0	188.0		948,504,681,741,726,726,726	-10.5	0.5	15	dbSNP_120	188	15,8579	11.2+/-40.8	0,15,4282	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	PKM2	NM_001206796.1,NM_001206797.1,NM_001206798.1,NM_001206799.1,NM_002654.4,NM_182470.2,NM_182471.2	,,,,,,	0,16,6480	TT,TC,CC		0.1745,0.0227,0.1232	,,,,,,	316/606,168/458,227/517,247/537,242/532,242/532,242/532	72501072	16,12976	2199	4297	6496	SO:0001819	synonymous_variant	5315	exon7			GAATGACGCAAAC	M23725	CCDS32284.1, CCDS32285.1, CCDS55972.1, CCDS73752.1	15q23	2012-10-02		2012-05-23	ENSG00000067225	ENSG00000067225	2.7.1.40		9021	protein-coding gene	gene with protein product		179050		PKM2		2040271	Standard	NM_002654		Approved	THBP1, OIP3, PK3	uc002atr.1	P14618	OTTHUMG00000172709	ENST00000335181.5:c.726G>A	15.37:g.72501072C>T		140.0	1.0	0.00714286		85.0	64.0	0.752941	NM_001206796	A6NFK3|B2R5N8|B3KRY0|B4DFX8|B4DUU6|P14786|Q53GK4|Q96E76|Q9BWB5|Q9UCV6|Q9UPF2	Silent	SNP	ENST00000335181.5	37	CCDS32284.1																																																																																			C|0.999;T|0.001	0.001	strong		0.493	PKM-004	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000420056.1		
KIAA1324	57535	hgsc.bcm.edu	37	1	109714593	109714593	+	Silent	SNP	C	C	T	rs112023388	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr1:109714593C>T	ENST00000369939.3	+	4	756	c.573C>T	c.(571-573)ttC>ttT	p.F191F	KIAA1324_ENST00000529753.1_Silent_p.F191F	NM_020775.4	NP_065826	Q6UXG2	K1324_HUMAN	KIAA1324	191					cellular response to starvation (GO:0009267)|macroautophagy (GO:0016236)|negative regulation of extrinsic apoptotic signaling pathway in absence of ligand (GO:2001240)|positive regulation of autophagic vacuole assembly (GO:2000786)|positive regulation of vacuole organization (GO:0044090)	endosome (GO:0005768)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|integral component of plasma membrane (GO:0005887)|lysosome (GO:0005764)	poly(A) RNA binding (GO:0044822)			NS(1)|breast(4)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(10)|lung(9)|ovary(2)|skin(3)|upper_aerodigestive_tract(1)	34		all_epithelial(167;0.000102)|all_lung(203;0.000323)|Lung NSC(277;0.00063)		Colorectal(144;0.0188)|Lung(183;0.0527)|COAD - Colon adenocarcinoma(174;0.14)|Epithelial(280;0.21)|all cancers(265;0.249)		CCGTTAACTTCGAATACTACT	0.537																																					p.F191F		Atlas-SNP	.											.	KIAA1324	77	.	0			c.C573T						PASS	.	C		1,4405	2.1+/-5.4	0,1,2202	156.0	133.0	141.0		573	-3.8	1.0	1	dbSNP_132	141	3,8597	3.0+/-9.4	0,3,4297	no	coding-synonymous	KIAA1324	NM_020775.3		0,4,6499	TT,TC,CC		0.0349,0.0227,0.0308		191/1014	109714593	4,13002	2203	4300	6503	SO:0001819	synonymous_variant	57535	exon4			TAACTTCGAATAC	AK057647	CCDS794.1, CCDS58015.1	1p13.3	2008-09-18			ENSG00000116299	ENSG00000116299			29618	protein-coding gene	gene with protein product	"""estrogen induced gene 121"""	611298				10718198, 16322283	Standard	NM_020775		Approved	maba1, EIG121	uc021orb.1	Q6UXG2	OTTHUMG00000011725	ENST00000369939.3:c.573C>T	1.37:g.109714593C>T		267.0	0.0	0		160.0	122.0	0.7625	NM_020775	Q08AE6|Q5T5C9|Q5T5D0|Q5T5D1|Q9P2M2	Silent	SNP	ENST00000369939.3	37	CCDS794.1																																																																																			C|0.999;T|0.001	0.001	strong		0.537	KIAA1324-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000032389.2	NM_020775	
SLC35F1	222553	hgsc.bcm.edu	37	6	118588185	118588185	+	Missense_Mutation	SNP	G	G	A			TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr6:118588185G>A	ENST00000360388.4	+	4	706	c.505G>A	c.(505-507)Gtg>Atg	p.V169M		NM_001029858.3	NP_001025029.2	Q5T1Q4	S35F1_HUMAN	solute carrier family 35, member F1	169					transport (GO:0006810)	integral component of membrane (GO:0016021)				breast(3)|kidney(1)|large_intestine(7)|lung(21)|prostate(1)|skin(1)|upper_aerodigestive_tract(2)	36				GBM - Glioblastoma multiforme(226;0.217)		GATCCCAGTCGTGATTTTGCT	0.498																																					p.V169M		Atlas-SNP	.											SLC35F1,bladder,carcinoma,-2,2	SLC35F1	65	2	0			c.G505A						scavenged	.						387.0	354.0	365.0					6																	118588185		2203	4300	6503	SO:0001583	missense	222553	exon4			CCAGTCGTGATTT	BC028615	CCDS34524.1	6q22.31	2013-05-22			ENSG00000196376	ENSG00000196376		"""Solute carriers"""	21483	protein-coding gene	gene with protein product			"""chromosome 6 open reading frame 169"""	C6orf169			Standard	NM_001029858		Approved	dJ230I3.1	uc003pxx.4	Q5T1Q4	OTTHUMG00000015460	ENST00000360388.4:c.505G>A	6.37:g.118588185G>A	ENSP00000353557:p.Val169Met	366.0	2.0	0.00546448		379.0	117.0	0.308707	NM_001029858	E1P564|Q1RMG1|Q4G0U9|Q4G167|Q6N007	Missense_Mutation	SNP	ENST00000360388.4	37	CCDS34524.1	.	.	.	.	.	.	.	.	.	.	G	20.3	3.974196	0.74246	.	.	ENSG00000196376	ENST00000360388	T	0.71341	-0.56	4.99	4.99	0.66335	.	0.143231	0.46442	D	0.000299	T	0.80788	0.4690	M	0.84433	2.695	0.58432	D	0.999996	D	0.53312	0.959	P	0.55713	0.782	D	0.83597	0.0126	10	0.72032	D	0.01	-26.7614	18.8278	0.92125	0.0:0.0:1.0:0.0	.	169	Q5T1Q4	S35F1_HUMAN	M	169	ENSP00000353557:V169M	ENSP00000353557:V169M	V	+	1	0	SLC35F1	118694878	1.000000	0.71417	0.998000	0.56505	0.991000	0.79684	3.849000	0.55910	2.756000	0.94617	0.561000	0.74099	GTG	.	.	none		0.498	SLC35F1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041991.2	XM_167044	
CCDC57	284001	hgsc.bcm.edu	37	17	80059690	80059690	+	Silent	SNP	G	G	A	rs61735692	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr17:80059690G>A	ENST00000389641.4	-	18	2655	c.2619C>T	c.(2617-2619)ggC>ggT	p.G873G	CCDC57_ENST00000392347.1_Silent_p.G873G			Q2TAC2	CCD57_HUMAN	coiled-coil domain containing 57	873										endometrium(1)|kidney(1)|large_intestine(1)|lung(9)|ovary(2)|prostate(1)|urinary_tract(1)	16	Breast(20;0.00285)|all_neural(118;0.0878)|all_lung(278;0.0949)|Lung NSC(278;0.128)|Ovarian(332;0.227)		BRCA - Breast invasive adenocarcinoma(99;0.0232)|OV - Ovarian serous cystadenocarcinoma(97;0.0253)			GGGTGGCAATGCCTGCCTGCA	0.602													G|||	69	0.013778	0.0038	0.0288	5008	,	,		17944	0.0		0.0398	False		,,,				2504	0.0041				p.G872G		Atlas-SNP	.											.	CCDC57	102	.	0			c.C2616T						PASS	.	G		46,4056		0,46,2005	64.0	71.0	69.0		2616	0.4	0.0	17	dbSNP_129	69	420,7976		15,390,3793	no	coding-synonymous	CCDC57	NM_198082.2		15,436,5798	AA,AG,GG		5.0024,1.1214,3.7286		872/916	80059690	466,12032	2051	4198	6249	SO:0001819	synonymous_variant	284001	exon17			GGCAATGCCTGCC	BC040264		17q25.3	2006-03-08			ENSG00000176155	ENSG00000176155			27564	protein-coding gene	gene with protein product						12477932	Standard	XM_006722279		Approved	FLJ00130, FLJ23754	uc002kdx.1	Q2TAC2	OTTHUMG00000140396	ENST00000389641.4:c.2619C>T	17.37:g.80059690G>A		121.0	0.0	0		101.0	49.0	0.485149	NM_198082	A6NP51|A8MQC7|Q8IWG2|Q8TER3	Silent	SNP	ENST00000389641.4	37		46	0.021062271062271064	5	0.01016260162601626	7	0.019337016574585635	0	0.0	34	0.044854881266490766	G	3.247	-0.154002	0.06585	0.011214	0.050024	ENSG00000176155	ENST00000392345	.	.	.	2.53	0.444	0.16592	.	.	.	.	.	T	0.03871	0.0109	.	.	.	0.09310	N	0.999995	.	.	.	.	.	.	T	0.15896	-1.0421	4	.	.	.	.	4.2507	0.10693	0.4561:0.0:0.5439:0.0	.	.	.	.	V	185	.	.	A	-	2	0	CCDC57	77652979	0.001000	0.12720	0.001000	0.08648	0.000000	0.00434	0.849000	0.27723	0.392000	0.25172	-0.224000	0.12420	GCA	G|0.975;A|0.025	0.025	strong		0.602	CCDC57-001	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000277182.3	NM_198082	
XRCC3	7517	hgsc.bcm.edu	37	14	104174950	104174950	+	Missense_Mutation	SNP	G	G	T			TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr14:104174950G>T	ENST00000553264.1	-	3	898	c.102C>A	c.(100-102)gaC>gaA	p.D34E	XRCC3_ENST00000554974.1_Intron|XRCC3_ENST00000352127.7_Missense_Mutation_p.D34E|XRCC3_ENST00000555055.1_Missense_Mutation_p.D34E|XRCC3_ENST00000554913.1_Missense_Mutation_p.D34E|AL049840.1_ENST00000429169.1_5'Flank|XRCC3_ENST00000445556.1_Missense_Mutation_p.D34E			O43542	XRCC3_HUMAN	X-ray repair complementing defective repair in Chinese hamster cells 3	34					cellular response to DNA damage stimulus (GO:0006974)|DNA catabolic process, endonucleolytic (GO:0000737)|DNA recombination (GO:0006310)|DNA repair (GO:0006281)|double-strand break repair via homologous recombination (GO:0000724)|positive regulation of mitotic cell cycle spindle assembly checkpoint (GO:0090267)|regulation of centrosome duplication (GO:0010824)|resolution of mitotic recombination intermediates (GO:0071140)|response to organic substance (GO:0010033)	cytoplasm (GO:0005737)|mitochondrion (GO:0005739)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|Rad51C-XRCC3 complex (GO:0033065)|replication fork (GO:0005657)	ATP binding (GO:0005524)|DNA binding (GO:0003677)|DNA-dependent ATPase activity (GO:0008094)			endometrium(1)|large_intestine(1)|ovary(1)|prostate(1)	4		Melanoma(154;0.155)|all_epithelial(191;0.19)		Epithelial(152;0.239)		GTCTCTTCAAGTCTGGTCCAG	0.498								Direct reversal of damage;Homologous recombination																													p.D34E		Atlas-SNP	.											.	XRCC3	16	.	0			c.C102A						PASS	.						119.0	104.0	109.0					14																	104174950		2203	4300	6503	SO:0001583	missense	7517	exon5			CTTCAAGTCTGGT	AF035586	CCDS9984.1	14q32.3	2006-05-04				ENSG00000126215			12830	protein-coding gene	gene with protein product	"""RAD51-like"""	600675				7603995	Standard	NM_001100118		Approved		uc001ynz.4	O43542		ENST00000553264.1:c.102C>A	14.37:g.104174950G>T	ENSP00000451974:p.Asp34Glu	83.0	0.0	0		144.0	46.0	0.319444	NM_005432	O43568|Q9BU18	Missense_Mutation	SNP	ENST00000553264.1	37	CCDS9984.1	.	.	.	.	.	.	.	.	.	.	G	7.232	0.599455	0.13939	.	.	ENSG00000126215	ENST00000554913;ENST00000352127;ENST00000553264;ENST00000555055;ENST00000445556;ENST00000553361;ENST00000556980;ENST00000555964;ENST00000556682;ENST00000553332;ENST00000554170	T;T;T;T;T;T;T;T	0.60299	1.06;1.06;1.06;1.06;1.06;0.2;0.68;0.59	5.44	-0.127	0.13510	.	0.095213	0.64402	D	0.000001	T	0.35038	0.0918	L	0.45228	1.405	0.23754	N	0.996937	P	0.39535	0.677	B	0.31686	0.134	T	0.36335	-0.9752	10	0.10377	T	0.69	-0.0139	6.7499	0.23482	0.4232:0.0:0.4621:0.1147	.	34	O43542	XRCC3_HUMAN	E	34	ENSP00000451362:D34E;ENSP00000343392:D34E;ENSP00000451974:D34E;ENSP00000452598:D34E;ENSP00000412990:D34E;ENSP00000451118:D34E;ENSP00000451252:D34E;ENSP00000451173:D34E	ENSP00000343392:D34E	D	-	3	2	XRCC3	103244703	0.756000	0.28383	0.283000	0.24790	0.039000	0.13416	0.177000	0.16801	0.039000	0.15632	-0.918000	0.02743	GAC	.	.	none		0.498	XRCC3-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000414631.1	NM_005432	
HIST1H1A	3024	hgsc.bcm.edu	37	6	26017397	26017397	+	Missense_Mutation	SNP	C	C	G			TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr6:26017397C>G	ENST00000244573.3	-	1	643	c.564G>C	c.(562-564)aaG>aaC	p.K188N		NM_005325.3	NP_005316.1	Q02539	H11_HUMAN	histone cluster 1, H1a	188					nucleosome assembly (GO:0006334)|spermatogenesis (GO:0007283)	nuclear chromatin (GO:0000790)|nuclear euchromatin (GO:0005719)|nucleosome (GO:0000786)	chromatin DNA binding (GO:0031490)			cervix(1)|endometrium(4)|kidney(1)|large_intestine(3)|ovary(3)|prostate(1)	13						GTTTTACAGCCTTAGCTTTAG	0.453																																					p.K188N		Atlas-SNP	.											.	HIST1H1A	25	.	0			c.G564C						PASS	.						151.0	159.0	156.0					6																	26017397		2203	4300	6503	SO:0001583	missense	3024	exon1			TACAGCCTTAGCT	AF531299	CCDS4569.1	6p22.1	2012-11-16	2006-10-11	2003-02-21	ENSG00000124610	ENSG00000124610		"""Histones / Replication-dependent"""	4715	protein-coding gene	gene with protein product		142709	"""H1 histone family, member 1"", ""histone 1, H1a"""	H1F1		2759094, 12408966	Standard	NM_005325		Approved	H1.1, H1a	uc003nfo.3	Q02539	OTTHUMG00000016413	ENST00000244573.3:c.564G>C	6.37:g.26017397C>G	ENSP00000244573:p.Lys188Asn	292.0	1.0	0.00342466		251.0	125.0	0.498008	NM_005325	Q3MJ34	Missense_Mutation	SNP	ENST00000244573.3	37	CCDS4569.1	.	.	.	.	.	.	.	.	.	.	N	10.43	1.346702	0.24426	.	.	ENSG00000124610	ENST00000244573	T	0.20463	2.07	4.31	4.31	0.51392	.	0.070517	0.56097	D	0.000038	T	0.09949	0.0244	L	0.45352	1.415	0.51482	D	0.99992	P	0.37636	0.603	B	0.28385	0.089	T	0.08269	-1.0730	10	0.56958	D	0.05	-13.3791	16.683	0.85297	0.0:1.0:0.0:0.0	.	188	Q02539	H11_HUMAN	N	188	ENSP00000244573:K188N	ENSP00000244573:K188N	K	-	3	2	HIST1H1A	26125376	0.881000	0.30235	0.884000	0.34674	0.057000	0.15508	0.342000	0.19926	2.320000	0.78422	0.609000	0.83330	AAG	.	.	none		0.453	HIST1H1A-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000043884.1	NM_005325	
CDK12	51755	hgsc.bcm.edu	37	17	37627387	37627387	+	Silent	SNP	A	A	G	rs56158954	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr17:37627387A>G	ENST00000447079.4	+	2	1335	c.1302A>G	c.(1300-1302)tcA>tcG	p.S434S	CDK12_ENST00000430627.2_Silent_p.S434S	NM_015083.1|NM_016507.2	NP_055898.1|NP_057591.2	Q9NYV4	CDK12_HUMAN	cyclin-dependent kinase 12	434					mRNA processing (GO:0006397)|phosphorylation of RNA polymerase II C-terminal domain (GO:0070816)|protein autophosphorylation (GO:0046777)|regulation of MAP kinase activity (GO:0043405)|RNA splicing (GO:0008380)	cyclin K-CDK12 complex (GO:0002944)|nuclear cyclin-dependent protein kinase holoenzyme complex (GO:0019908)|nuclear speck (GO:0016607)|nucleolus (GO:0005730)|nucleus (GO:0005634)	ATP binding (GO:0005524)|cyclin binding (GO:0030332)|cyclin-dependent protein serine/threonine kinase activity (GO:0004693)|protein kinase activity (GO:0004672)|RNA polymerase II carboxy-terminal domain kinase activity (GO:0008353)			NS(4)|breast(3)|endometrium(5)|kidney(4)|large_intestine(11)|lung(23)|ovary(11)|prostate(4)|skin(2)|urinary_tract(3)	70						AGAACAGTTCAGTAGAGGCTA	0.428			"""Mis, N, F"""		serous ovarian					TCGA Ovarian(9;0.13)			A|||	28	0.00559105	0.0	0.0115	5008	,	,		17944	0.0		0.0179	False		,,,				2504	0.002				p.S434S		Atlas-SNP	.		Rec	yes		17	17q12	51755	cyclin-dependent kinase 12		E	CDK12,NS,carcinoma,0,1	CDK12	161	1	0			c.A1302G						PASS	.	A	,	21,4385	28.1+/-56.4	0,21,2182	68.0	69.0	69.0		1302,1302	2.7	1.0	17	dbSNP_129	69	170,8430	77.8+/-140.4	1,168,4131	no	coding-synonymous,coding-synonymous	CDK12	NM_015083.1,NM_016507.2	,	1,189,6313	GG,GA,AA		1.9767,0.4766,1.4686	,	434/1482,434/1491	37627387	191,12815	2203	4300	6503	SO:0001819	synonymous_variant	51755	exon2			CAGTTCAGTAGAG	AF227198	CCDS11337.1, CCDS45666.1	17q12	2011-10-25	2009-12-16	2009-12-16	ENSG00000167258	ENSG00000167258		"""Cyclin-dependent kinases"""	24224	protein-coding gene	gene with protein product	"""CDC2 related protein kinase 7"""	615514	"""Cdc2-related kinase, arginine/serine-rich"""	CRKRS		10048485, 11683387, 19884882	Standard	XM_005257456		Approved	CRK7, CRKR, KIAA0904	uc010cvv.3	Q9NYV4	OTTHUMG00000133214	ENST00000447079.4:c.1302A>G	17.37:g.37627387A>G		68.0	0.0	0		59.0	33.0	0.559322	NM_016507	A7E2B2|B4DYX4|B9EIQ6|O94978	Silent	SNP	ENST00000447079.4	37	CCDS11337.1																																																																																			A|0.987;G|0.013	0.013	strong		0.428	CDK12-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000256941.4	NM_016507	
CRYBB3	1417	hgsc.bcm.edu	37	22	25603052	25603052	+	Missense_Mutation	SNP	A	A	G			TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr22:25603052A>G	ENST00000215855.2	+	6	589	c.509A>G	c.(508-510)cAg>cGg	p.Q170R	CRYBB3_ENST00000404334.1_3'UTR	NM_004076.3	NP_004067.1	P26998	CRBB3_HUMAN	crystallin, beta B3	170	Beta/gamma crystallin 'Greek key' 4. {ECO:0000255|PROSITE-ProRule:PRU00028}.				visual perception (GO:0007601)		structural constituent of eye lens (GO:0005212)			large_intestine(2)|lung(2)|prostate(1)	5						CGTGGGCGCCAGTACGTGTTT	0.647																																					p.V170G		Atlas-SNP	.											.	CRYBB3	13	.	0			c.T509G						PASS	.						57.0	52.0	54.0					22																	25603052		2201	4300	6501	SO:0001583	missense	1417	exon6			GGCGCCAGTACGT		CCDS13830.1	22q11.23	2008-06-10			ENSG00000100053	ENSG00000100053			2400	protein-coding gene	gene with protein product		123630		CRYB3		8999933	Standard	NM_004076		Approved		uc003abo.2	P26998	OTTHUMG00000150869	ENST00000215855.2:c.509A>G	22.37:g.25603052A>G	ENSP00000215855:p.Gln170Arg	150.0	0.0	0		127.0	51.0	0.401575	NM_004076	Q3B7S9|Q3T1B7|Q6ISK6|Q92965|Q9UH09	Missense_Mutation	SNP	ENST00000215855.2	37	CCDS13830.1	.	.	.	.	.	.	.	.	.	.	A	27.3	4.816949	0.90790	.	.	ENSG00000100053	ENST00000215855	T	0.80123	-1.34	4.87	4.87	0.63330	Beta/gamma crystallin (4);Gamma-crystallin-related (1);	0.000000	0.85682	D	0.000000	D	0.92001	0.7466	H	0.94222	3.51	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.93900	0.7187	10	0.87932	D	0	.	13.2896	0.60264	1.0:0.0:0.0:0.0	.	170	P26998	CRBB3_HUMAN	R	170	ENSP00000215855:Q170R	ENSP00000215855:Q170R	Q	+	2	0	CRYBB3	23933052	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	8.664000	0.91139	1.804000	0.52760	0.459000	0.35465	CAG	.	.	none		0.647	CRYBB3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000320352.1	NM_004076	
CCDC129	223075	hgsc.bcm.edu	37	7	31682829	31682829	+	Missense_Mutation	SNP	G	G	C			TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr7:31682829G>C	ENST00000407970.3	+	11	1883	c.1845G>C	c.(1843-1845)gaG>gaC	p.E615D	CCDC129_ENST00000409210.1_Missense_Mutation_p.E523D|CCDC129_ENST00000319386.3_Missense_Mutation_p.E467D|CCDC129_ENST00000451887.2_Missense_Mutation_p.E641D	NM_001257967.1|NM_194300.3	NP_001244896.1|NP_919276.2	Q6ZRS4	CC129_HUMAN	coiled-coil domain containing 129	615										cervix(1)|endometrium(3)|kidney(3)|large_intestine(6)|lung(31)	44						TTGACTCTGAGGCCCCACGAG	0.498																																					p.E641D		Atlas-SNP	.											.	CCDC129	127	.	0			c.G1923C						PASS	.						119.0	112.0	114.0					7																	31682829		2203	4300	6503	SO:0001583	missense	223075	exon11			CTCTGAGGCCCCA	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.1845G>C	7.37:g.31682829G>C	ENSP00000384416:p.Glu615Asp	68.0	0.0	0		91.0	26.0	0.285714	NM_001257968	A2RU17|B3KTI9|B4DHB0|B4E2R1|F5H3V5	Missense_Mutation	SNP	ENST00000407970.3	37	CCDS5435.2	.	.	.	.	.	.	.	.	.	.	G	12.14	1.847181	0.32606	.	.	ENSG00000180347	ENST00000319386;ENST00000407970;ENST00000451887;ENST00000538406;ENST00000409210	T;T;T;T	0.19394	2.15;2.42;2.41;2.16	6.02	1.06	0.20224	.	0.998383	0.08108	N	0.996656	T	0.18509	0.0444	L	0.55103	1.725	0.09310	N	1	B;B;B;B	0.24186	0.025;0.099;0.099;0.099	B;B;B;B	0.26202	0.022;0.067;0.067;0.067	T	0.38373	-0.9664	10	0.22706	T	0.39	-6.6287	3.9948	0.09553	0.2297:0.0:0.4889:0.2814	.	641;625;615;467	F5H3V5;F5H2J8;Q6ZRS4;Q6ZRS4-2	.;.;CC129_HUMAN;.	D	467;615;641;625;523	ENSP00000313062:E467D;ENSP00000384416:E615D;ENSP00000395835:E641D;ENSP00000387214:E523D	ENSP00000313062:E467D	E	+	3	2	CCDC129	31649354	0.017000	0.18338	0.000000	0.03702	0.307000	0.27823	0.200000	0.17257	-0.075000	0.12798	0.655000	0.94253	GAG	.	.	none		0.498	CCDC129-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000318975.1	NM_194300	
HS6ST1	9394	hgsc.bcm.edu	37	2	129025800	129025800	+	Missense_Mutation	SNP	T	T	C			TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr2:129025800T>C	ENST00000259241.6	-	2	1185	c.1172A>G	c.(1171-1173)gAt>gGt	p.D391G		NM_004807.2	NP_004798.3	O60243	H6ST1_HUMAN	heparan sulfate 6-O-sulfotransferase 1	391					angiogenesis (GO:0001525)|carbohydrate metabolic process (GO:0005975)|glycosaminoglycan biosynthetic process (GO:0006024)|glycosaminoglycan metabolic process (GO:0030203)|heparan sulfate proteoglycan biosynthetic process, enzymatic modification (GO:0015015)|labyrinthine layer blood vessel development (GO:0060716)|lung alveolus development (GO:0048286)|neuron development (GO:0048666)|small molecule metabolic process (GO:0044281)	Golgi membrane (GO:0000139)|integral component of plasma membrane (GO:0005887)	heparan sulfate 6-O-sulfotransferase activity (GO:0017095)|sulfotransferase activity (GO:0008146)			endometrium(3)|liver(1)|lung(7)|pancreas(1)|prostate(2)|skin(1)	15	Colorectal(110;0.1)			BRCA - Breast invasive adenocarcinoma(221;0.117)		CTCGTCGGCATCCTCCCGCGG	0.692																																					p.D391G		Atlas-SNP	.											.	HS6ST1	31	.	0			c.A1172G						PASS	.						21.0	23.0	22.0					2																	129025800		2013	4161	6174	SO:0001583	missense	9394	exon2			TCGGCATCCTCCC	AB006179	CCDS42748.1	2q21	2010-03-19		2002-08-23	ENSG00000136720	ENSG00000136720		"""Sulfotransferases, membrane-bound"""	5201	protein-coding gene	gene with protein product		604846		HS6ST		9535912	Standard	NM_004807		Approved		uc002tpt.4	O60243	OTTHUMG00000153542	ENST00000259241.6:c.1172A>G	2.37:g.129025800T>C	ENSP00000259241:p.Asp391Gly	140.0	0.0	0		96.0	5.0	0.0520833	NM_004807	B4DEP2|B4DJ29|Q53SL2|Q9BVI1	Missense_Mutation	SNP	ENST00000259241.6	37	CCDS42748.1	.	.	.	.	.	.	.	.	.	.	T	6.511	0.462424	0.12342	.	.	ENSG00000136720	ENST00000259241	D	0.82893	-1.66	4.19	2.98	0.34508	.	0.419922	0.27622	N	0.018544	T	0.70710	0.3255	L	0.29908	0.895	0.32984	D	0.524007	B	0.02656	0.0	B	0.01281	0.0	T	0.65726	-0.6098	9	.	.	.	-2.5669	9.8137	0.40840	0.0:0.0842:0.0:0.9158	.	391	O60243	H6ST1_HUMAN	G	391	ENSP00000259241:D391G	.	D	-	2	0	HS6ST1	128742270	0.994000	0.37717	0.051000	0.19133	0.159000	0.22180	2.428000	0.44749	0.558000	0.29135	0.260000	0.18958	GAT	.	.	none		0.692	HS6ST1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000331572.1	NM_004807	
NPAT	4863	hgsc.bcm.edu	37	11	108044204	108044204	+	Missense_Mutation	SNP	C	C	G			TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr11:108044204C>G	ENST00000278612.8	-	13	1612	c.1507G>C	c.(1507-1509)Gat>Cat	p.D503H	NPAT_ENST00000610253.1_5'UTR	NM_002519.2	NP_002510.2	Q14207	NPAT_HUMAN	nuclear protein, ataxia-telangiectasia locus	503					positive regulation of transcription, DNA-templated (GO:0045893)|regulation of gene expression (GO:0010468)|regulation of transcription involved in G1/S transition of mitotic cell cycle (GO:0000083)|transcription, DNA-templated (GO:0006351)	Cajal body (GO:0015030)|cytoplasm (GO:0005737)|Gemini of coiled bodies (GO:0097504)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	protein C-terminus binding (GO:0008022)|protein N-terminus binding (GO:0047485)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription coactivator activity (GO:0003713)|transcription corepressor activity (GO:0003714)			breast(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(6)|lung(21)|ovary(2)|prostate(2)|skin(5)	46		all_cancers(61;2.31e-10)|all_epithelial(67;1.11e-06)|Melanoma(852;2.55e-06)|Acute lymphoblastic leukemia(157;3.95e-05)|all_hematologic(158;0.00014)|Breast(348;0.0258)|all_neural(303;0.072)		BRCA - Breast invasive adenocarcinoma(274;1.05e-05)|Epithelial(105;3.01e-05)|all cancers(92;0.000816)|Colorectal(284;0.116)		TCAGGCTGATCAGGCTGTAAC	0.368																																					p.D503H		Atlas-SNP	.											.	NPAT	124	.	0			c.G1507C						PASS	.						127.0	122.0	123.0					11																	108044204		1867	4096	5963	SO:0001583	missense	4863	exon13			GCTGATCAGGCTG	X97186	CCDS41710.1	11q22-q23	2008-02-01			ENSG00000149308	ENSG00000149308			7896	protein-coding gene	gene with protein product		601448				9205109	Standard	NM_002519		Approved	E14	uc001pjz.4	Q14207	OTTHUMG00000166385	ENST00000278612.8:c.1507G>C	11.37:g.108044204C>G	ENSP00000278612:p.Asp503His	207.0	0.0	0		386.0	99.0	0.256477	NM_002519	A8K1V5|A8K6M2|Q13632|Q14967|Q16580|Q86W55|Q8IWE9	Missense_Mutation	SNP	ENST00000278612.8	37	CCDS41710.1	.	.	.	.	.	.	.	.	.	.	C	4.278	0.050716	0.08243	.	.	ENSG00000149308	ENST00000278612	T	0.28069	1.63	6.08	4.21	0.49690	.	0.380295	0.29493	N	0.011997	T	0.44265	0.1285	M	0.62723	1.935	0.29803	N	0.832279	D;P	0.56287	0.975;0.956	P;P	0.56960	0.81;0.551	T	0.46289	-0.9202	10	0.62326	D	0.03	-4.1581	9.7917	0.40710	0.1397:0.7908:0.0:0.0695	.	503;503	B9EG70;Q14207	.;NPAT_HUMAN	H	503	ENSP00000278612:D503H	ENSP00000278612:D503H	D	-	1	0	NPAT	107549414	0.946000	0.32159	0.671000	0.29857	0.037000	0.13140	0.380000	0.20602	0.897000	0.36392	-0.181000	0.13052	GAT	.	.	none		0.368	NPAT-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000389506.2	NM_002519	
NPAS3	64067	hgsc.bcm.edu	37	14	34247747	34247747	+	Silent	SNP	C	C	T	rs147070037	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr14:34247747C>T	ENST00000356141.4	+	9	1122	c.1122C>T	c.(1120-1122)gaC>gaT	p.D374D	NPAS3_ENST00000551492.1_Silent_p.D379D|NPAS3_ENST00000346562.2_Silent_p.D342D|NPAS3_ENST00000548645.1_Silent_p.D344D|NPAS3_ENST00000357798.5_Silent_p.D361D			Q8IXF0	NPAS3_HUMAN	neuronal PAS domain protein 3	374	PAC.|PAS 2. {ECO:0000255|PROSITE- ProRule:PRU00140}.				locomotory behavior (GO:0007626)|maternal behavior (GO:0042711)|positive regulation of transcription, DNA-templated (GO:0045893)|startle response (GO:0001964)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	DNA binding (GO:0003677)|signal transducer activity (GO:0004871)			breast(4)|endometrium(3)|kidney(1)|large_intestine(6)|liver(2)|lung(14)|ovary(1)|prostate(2)|skin(3)|upper_aerodigestive_tract(3)|urinary_tract(1)	40	Breast(36;0.0102)|Hepatocellular(127;0.133)		LUAD - Lung adenocarcinoma(48;0.00169)|Lung(238;0.00968)	GBM - Glioblastoma multiforme(1;1.31e-09)|all cancers(1;0.000112)|OV - Ovarian serous cystadenocarcinoma(311;0.115)		ATGCTGAAGACGTGGAGGGCA	0.493													C|||	3	0.000599042	0.0	0.0	5008	,	,		19225	0.0		0.003	False		,,,				2504	0.0				p.D374D		Atlas-SNP	.											.	NPAS3	266	.	0			c.C1122T						PASS	.	C	,,,	1,4405	2.1+/-5.4	0,1,2202	117.0	102.0	107.0		1122,1032,1026,1083	-6.6	0.2	14	dbSNP_134	107	20,8580	14.6+/-50.1	0,20,4280	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	NPAS3	NM_001164749.1,NM_001165893.1,NM_022123.2,NM_173159.2	,,,	0,21,6482	TT,TC,CC		0.2326,0.0227,0.1615	,,,	374/934,344/904,342/902,361/921	34247747	21,12985	2203	4300	6503	SO:0001819	synonymous_variant	64067	exon9			TGAAGACGTGGAG	AF164438	CCDS9645.1, CCDS53891.1, CCDS53892.1, CCDS55912.1	14q13.1	2013-08-23			ENSG00000151322	ENSG00000151322		"""Basic helix-loop-helix proteins"""	19311	protein-coding gene	gene with protein product		609430					Standard	NM_022123		Approved	MOP6, PASD6, bHLHe12	uc001wru.3	Q8IXF0	OTTHUMG00000140215	ENST00000356141.4:c.1122C>T	14.37:g.34247747C>T		133.0	0.0	0		166.0	108.0	0.650602	NM_001164749	Q86US6|Q86US7|Q8IXF2|Q9BY81|Q9H323|Q9Y4L8	Silent	SNP	ENST00000356141.4	37	CCDS53891.1	2	9.157509157509158E-4	0	0.0	0	0.0	0	0.0	2	0.002638522427440633	C	8.823	0.937989	0.18206	2.27E-4	0.002326	ENSG00000151322	ENST00000552874	.	.	.	6.03	-6.63	0.01807	.	.	.	.	.	T	0.67552	0.2905	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.70385	-0.4886	4	.	.	.	.	19.2046	0.93724	0.0:0.2337:0.0:0.7663	.	.	.	.	M	121	.	.	T	+	2	0	NPAS3	33317498	0.002000	0.14202	0.183000	0.23137	0.952000	0.60782	-1.517000	0.02248	-1.491000	0.01840	-0.226000	0.12346	ACG	C|0.999;T|0.001	0.001	strong		0.493	NPAS3-004	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000276645.1		
ADCK1	57143	hgsc.bcm.edu	37	14	78399654	78399654	+	Missense_Mutation	SNP	C	C	T			TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr14:78399654C>T	ENST00000238561.5	+	11	1591	c.1492C>T	c.(1492-1494)Ctc>Ttc	p.L498F	ADCK1_ENST00000556560.1_3'UTR|ADCK1_ENST00000341211.5_Missense_Mutation_p.L430F	NM_020421.3	NP_065154.2	Q86TW2	ADCK1_HUMAN	aarF domain containing kinase 1	505						extracellular region (GO:0005576)|mitochondrion (GO:0005739)	ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)			breast(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(5)|lung(6)|ovary(1)|prostate(2)|skin(2)|stomach(2)	25			Kidney(204;0.164)	BRCA - Breast invasive adenocarcinoma(234;0.0376)		CCTCCATGAGCTCATCCTGCG	0.517																																					p.L498F		Atlas-SNP	.											.	ADCK1	81	.	0			c.C1492T						PASS	.						130.0	122.0	124.0					14																	78399654		2203	4300	6503	SO:0001583	missense	57143	exon11			CATGAGCTCATCC	AK096919	CCDS9869.1, CCDS45144.1	14q24	2005-10-30							19038	protein-coding gene	gene with protein product						12471243	Standard	NM_020421		Approved	FLJ39600	uc001xui.3	Q86TW2		ENST00000238561.5:c.1492C>T	14.37:g.78399654C>T	ENSP00000238561:p.Leu498Phe	217.0	0.0	0		268.0	122.0	0.455224	NM_020421	B3KUD5|Q6PD65|Q9UIE6	Missense_Mutation	SNP	ENST00000238561.5	37	CCDS9869.1	.	.	.	.	.	.	.	.	.	.	C	8.266	0.812185	0.16537	.	.	ENSG00000063761	ENST00000238561;ENST00000341211	T;T	0.68479	-0.33;1.07	5.58	4.66	0.58398	.	0.194806	0.45126	N	0.000398	T	0.58104	0.2099	L	0.50333	1.59	0.80722	D	1	B;B;B	0.09022	0.001;0.002;0.001	B;B;B	0.12837	0.003;0.008;0.007	T	0.52555	-0.8560	10	0.23302	T	0.38	-20.9933	10.9445	0.47294	0.0:0.9076:0.0:0.0924	.	505;430;498	Q86TW2;Q9UIE6;Q86TW2-2	ADCK1_HUMAN;.;.	F	498;430	ENSP00000238561:L498F;ENSP00000339663:L430F	ENSP00000238561:L498F	L	+	1	0	ADCK1	77469407	1.000000	0.71417	0.458000	0.27068	0.072000	0.16883	2.926000	0.48892	1.298000	0.44778	0.655000	0.94253	CTC	.	.	none		0.517	ADCK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000413864.1	NM_020421	
GPR108	56927	hgsc.bcm.edu	37	19	6733582	6733582	+	Splice_Site	SNP	G	G	A	rs201134279	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr19:6733582G>A	ENST00000264080.7	-	8	748	c.722C>T	c.(721-723)aCg>aTg	p.T241M	GPR108_ENST00000598626.1_5'Flank|GPR108_ENST00000430424.4_De_novo_Start_InFrame	NM_001080452.1	NP_001073921.1	Q9NPR9	GP108_HUMAN	G protein-coupled receptor 108	241						integral component of membrane (GO:0016021)				breast(2)|cervix(1)|large_intestine(4)|lung(4)|skin(1)|urinary_tract(1)	13						TCCGCTCACCGTGATGTCGAA	0.632													G|||	21	0.00419329	0.0	0.0	5008	,	,		16071	0.0		0.005	False		,,,				2504	0.0164				p.T241M		Atlas-SNP	.											.	GPR108	35	.	0			c.C722T						PASS	.	G	MET/THR	11,4095		0,11,2042	81.0	79.0	80.0		722	3.9	1.0	19		80	45,8347		0,45,4151	yes	missense-near-splice	GPR108	NM_001080452.1	81	0,56,6193	AA,AG,GG		0.5362,0.2679,0.4481	probably-damaging	241/544	6733582	56,12442	2053	4196	6249	SO:0001630	splice_region_variant	56927	exon8			CTCACCGTGATGT		CCDS42479.1	19p13.3	2014-01-30				ENSG00000125734		"""GPCR / Unclassified : 7TM orphan receptors"""	17829	protein-coding gene	gene with protein product							Standard	NM_001080452		Approved	LUSTR2	uc002mfp.3	Q9NPR9	OTTHUMG00000170129	ENST00000264080.7:c.723+1C>T	19.37:g.6733582G>A		159.0	1.0	0.00628931		129.0	129.0	1	NM_001080452	B9EJD7	Missense_Mutation	SNP	ENST00000264080.7	37	CCDS42479.1	5	0.0022893772893772895	0	0.0	0	0.0	0	0.0	5	0.006596306068601583	G	32	5.147240	0.94603	0.002679	0.005362	ENSG00000125734	ENST00000264080	T	0.26373	1.74	3.92	3.92	0.45320	.	0.198041	0.28600	U	0.014764	T	0.38665	0.1049	M	0.70595	2.14	0.80722	D	1	D	0.89917	1.0	D	0.77557	0.99	T	0.34700	-0.9818	10	0.48119	T	0.1	-26.584	11.595	0.50968	0.0:0.0:1.0:0.0	.	241	Q9NPR9	GP108_HUMAN	M	241	ENSP00000264080:T241M	ENSP00000264080:T241M	T	-	2	0	GPR108	6684582	0.981000	0.34729	0.999000	0.59377	0.813000	0.45954	1.961000	0.40432	2.172000	0.68678	0.555000	0.69702	ACG	G|0.995;A|0.005	0.005	strong		0.632	GPR108-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000407508.2		Missense_Mutation
NFKBIB	4793	hgsc.bcm.edu	37	19	39399416	39399416	+	Missense_Mutation	SNP	C	C	T	rs17886215		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr19:39399416C>T	ENST00000313582.5	+	6	1049	c.1015C>T	c.(1015-1017)Cgg>Tgg	p.R339W	NFKBIB_ENST00000392079.3_3'UTR	NM_002503.4	NP_002494.2	Q15653	IKBB_HUMAN	nuclear factor of kappa light polypeptide gene enhancer in B-cells inhibitor, beta	339			R -> W (in dbSNP:rs17886215). {ECO:0000269|Ref.3}.		innate immune response (GO:0045087)|MyD88-dependent toll-like receptor signaling pathway (GO:0002755)|MyD88-independent toll-like receptor signaling pathway (GO:0002756)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of type I interferon production (GO:0032481)|signal transduction (GO:0007165)|toll-like receptor 10 signaling pathway (GO:0034166)|toll-like receptor 2 signaling pathway (GO:0034134)|toll-like receptor 3 signaling pathway (GO:0034138)|toll-like receptor 4 signaling pathway (GO:0034142)|toll-like receptor 5 signaling pathway (GO:0034146)|toll-like receptor 9 signaling pathway (GO:0034162)|toll-like receptor signaling pathway (GO:0002224)|toll-like receptor TLR1:TLR2 signaling pathway (GO:0038123)|toll-like receptor TLR6:TLR2 signaling pathway (GO:0038124)|transcription, DNA-templated (GO:0006351)|TRIF-dependent toll-like receptor signaling pathway (GO:0035666)	cytosol (GO:0005829)|nucleus (GO:0005634)	signal transducer activity (GO:0004871)|transcription coactivator activity (GO:0003713)			endometrium(1)|kidney(1)|large_intestine(1)|lung(4)|ovary(1)	8	all_cancers(60;4.39e-06)|Ovarian(47;0.0454)		Lung(45;0.000419)|LUSC - Lung squamous cell carcinoma(53;0.000554)			CAGCCAAACCCGGCTGCCTCC	0.547																																					p.R339W	Pancreas(165;1492 2005 6979 7739 34483)	Atlas-SNP	.											.	NFKBIB	23	.	0			c.C1015T						PASS	.	C	,TRP/ARG	0,4406		0,0,2203	81.0	89.0	87.0		,1015	0.3	0.0	19	dbSNP_124	87	3,8597	3.0+/-9.4	0,3,4297	yes	utr-3,missense	NFKBIB	NM_001001716.1,NM_002503.4	,101	0,3,6500	TT,TC,CC		0.0349,0.0,0.0231	,possibly-damaging	,339/357	39399416	3,13003	2203	4300	6503	SO:0001583	missense	4793	exon6			CAAACCCGGCTGC	L40407	CCDS12524.1, CCDS74362.1	19q13.1	2013-01-10				ENSG00000104825		"""Ankyrin repeat domain containing"""	7798	protein-coding gene	gene with protein product		604495				9763672	Standard	NM_002503		Approved	IKBB, TRIP9	uc002ojw.3	Q15653		ENST00000313582.5:c.1015C>T	19.37:g.39399416C>T	ENSP00000312988:p.Arg339Trp	109.0	0.0	0		127.0	58.0	0.456693	NM_002503	A8K3F4|Q96BJ7	Missense_Mutation	SNP	ENST00000313582.5	37	CCDS12524.1	.	.	.	.	.	.	.	.	.	.	C	11.78	1.739866	0.30865	0.0	3.49E-4	ENSG00000104825	ENST00000313582	T	0.54675	0.56	5.08	0.314	0.15847	.	1.956000	0.02482	N	0.088598	T	0.36690	0.0976	N	0.19112	0.55	0.09310	N	1	B	0.06786	0.001	B	0.01281	0.0	T	0.28650	-1.0037	10	0.56958	D	0.05	1.3469	2.9887	0.05977	0.1946:0.4876:0.0:0.3178	rs17886215;rs17886215	339	Q15653	IKBB_HUMAN	W	339	ENSP00000312988:R339W	ENSP00000312988:R339W	R	+	1	2	NFKBIB	44091256	0.000000	0.05858	0.000000	0.03702	0.058000	0.15608	-0.182000	0.09726	0.293000	0.22520	0.655000	0.94253	CGG	C|0.998;T|0.002	0.002	strong		0.547	NFKBIB-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000438155.1	NM_002503	
AKAP6	9472	hgsc.bcm.edu	37	14	33014876	33014876	+	Silent	SNP	C	C	T	rs375820695		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr14:33014876C>T	ENST00000280979.4	+	4	1187	c.1017C>T	c.(1015-1017)ccC>ccT	p.P339P	AKAP6_ENST00000557354.1_Silent_p.P339P|AKAP6_ENST00000557272.1_Silent_p.P339P	NM_004274.4	NP_004265.3	Q13023	AKAP6_HUMAN	A kinase (PRKA) anchor protein 6	339					action potential (GO:0001508)|cAMP-mediated signaling (GO:0019933)|cellular response to cAMP (GO:0071320)|cellular response to cytokine stimulus (GO:0071345)|negative regulation of cAMP biosynthetic process (GO:0030818)|positive regulation of calcineurin-NFAT signaling cascade (GO:0070886)|positive regulation of cell growth (GO:0030307)|positive regulation of cell growth involved in cardiac muscle cell development (GO:0061051)|positive regulation of delayed rectifier potassium channel activity (GO:1902261)|positive regulation of NFAT protein import into nucleus (GO:0051533)|positive regulation of potassium ion transmembrane transport (GO:1901381)|positive regulation of protein phosphatase type 2B activity (GO:0032514)|positive regulation of release of sequestered calcium ion into cytosol (GO:0051281)|positive regulation of ryanodine-sensitive calcium-release channel activity (GO:0060316)|protein targeting (GO:0006605)|regulation of membrane repolarization (GO:0060306)|regulation of protein kinase A signaling (GO:0010738)|regulation of release of sequestered calcium ion into cytosol by sarcoplasmic reticulum (GO:0010880)	calcium channel complex (GO:0034704)|caveola (GO:0005901)|cytoplasm (GO:0005737)|intercalated disc (GO:0014704)|junctional sarcoplasmic reticulum membrane (GO:0014701)|nuclear envelope (GO:0005635)|perinuclear region of cytoplasm (GO:0048471)|sarcoplasmic reticulum (GO:0016529)|T-tubule (GO:0030315)	adenylate cyclase binding (GO:0008179)|ion channel binding (GO:0044325)|protein anchor (GO:0043495)|protein complex scaffold (GO:0032947)|protein kinase A binding (GO:0051018)|protein kinase A regulatory subunit binding (GO:0034237)			NS(2)|breast(10)|cervix(1)|endometrium(11)|haematopoietic_and_lymphoid_tissue(2)|kidney(8)|large_intestine(25)|lung(42)|ovary(5)|pancreas(2)|prostate(3)|skin(9)|urinary_tract(2)	122	Breast(36;0.0388)|Prostate(35;0.15)		LUAD - Lung adenocarcinoma(48;0.00107)|Lung(238;0.00677)|STAD - Stomach adenocarcinoma(7;0.116)	GBM - Glioblastoma multiforme(265;0.019)		CTGCTCAACCCTCCTCTGAGA	0.498																																					p.P339P	Melanoma(49;821 1200 7288 13647 42351)	Atlas-SNP	.											.	AKAP6	308	.	0			c.C1017T						PASS	.	C		0,4406		0,0,2203	71.0	62.0	65.0		1017	0.4	0.0	14		65	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous	AKAP6	NM_004274.4		0,1,6502	TT,TC,CC		0.0116,0.0,0.0077		339/2320	33014876	1,13005	2203	4300	6503	SO:0001819	synonymous_variant	9472	exon4			TCAACCCTCCTCT	AB002309	CCDS9644.1	14q12	2008-08-11			ENSG00000151320	ENSG00000151320		"""A-kinase anchor proteins"""	376	protein-coding gene	gene with protein product	"""protein kinase A anchoring protein 6"""	604691				7721854, 9205841	Standard	NM_004274		Approved	KIAA0311, mAKAP, AKAP100, PRKA6, ADAP6	uc001wrq.3	Q13023	OTTHUMG00000140207	ENST00000280979.4:c.1017C>T	14.37:g.33014876C>T		89.0	0.0	0		123.0	51.0	0.414634	NM_004274	A7E242|A7E2D4|O15028	Silent	SNP	ENST00000280979.4	37	CCDS9644.1																																																																																			.	.	weak		0.498	AKAP6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276617.2	NM_004274	
CACNA1B	774	hgsc.bcm.edu	37	9	140773613	140773613	+	Splice_Site	SNP	T	T	A	rs201604190		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr9:140773613T>A	ENST00000371372.1	+	2	535		c.e2+2		CACNA1B_ENST00000371355.4_Splice_Site|CACNA1B_ENST00000371357.1_Splice_Site|CACNA1B_ENST00000277549.5_Splice_Site|CACNA1B_ENST00000277551.2_Splice_Site|CACNA1B_ENST00000371363.1_Splice_Site|RP11-188C12.3_ENST00000371390.1_RNA	NM_000718.3|NM_001243812.1	NP_000709.1|NP_001230741.1	Q00975	CAC1B_HUMAN	calcium channel, voltage-dependent, N type, alpha 1B subunit						calcium ion import (GO:0070509)|locomotory behavior (GO:0007626)|membrane depolarization (GO:0051899)|membrane depolarization during action potential (GO:0086010)|neurotransmitter secretion (GO:0007269)|regulation of blood pressure (GO:0008217)|regulation of calcium ion transport (GO:0051924)|regulation of heart contraction (GO:0008016)|response to pain (GO:0048265)|synaptic transmission (GO:0007268)|transport (GO:0006810)	dendrite (GO:0030425)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)|voltage-gated calcium channel complex (GO:0005891)	ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|high voltage-gated calcium channel activity (GO:0008331)|protein C-terminus binding (GO:0008022)|voltage-gated calcium channel activity (GO:0005245)	p.?(2)		NS(3)|autonomic_ganglia(1)|breast(7)|central_nervous_system(1)|endometrium(10)|kidney(2)|large_intestine(17)|lung(31)|ovary(1)|prostate(1)|skin(2)|stomach(2)|urinary_tract(2)	80	all_cancers(76;0.166)			OV - Ovarian serous cystadenocarcinoma(145;1.16e-05)|Epithelial(140;0.000476)	Amlodipine(DB00381)|Gabapentin(DB00996)|Levetiracetam(DB01202)|Spironolactone(DB00421)|Verapamil(DB00661)	GAGCGGCTGGTGAGTGCCCGG	0.632																																					.		Atlas-SNP	.											CACNA1B,colon,carcinoma,0,8	CACNA1B	266	8	2	Unknown(2)	lung(1)|breast(1)	c.390+2T>A						scavenged	.						25.0	29.0	28.0					9																	140773613		2104	4235	6339	SO:0001630	splice_region_variant	774	exon2			GGCTGGTGAGTGC	AB209467	CCDS59522.1, CCDS59523.1	9q34	2013-01-10	2007-02-16		ENSG00000148408	ENSG00000148408		"""Calcium channel subunits"", ""Voltage-gated ion channels / Calcium channels"", ""EF-hand domain containing"""	1389	protein-coding gene	gene with protein product		601012		CACNL1A5		8825650, 16382099	Standard	NM_000718		Approved	Cav2.2, CACNN	uc004cog.3	Q00975	OTTHUMG00000021002	ENST00000371372.1:c.390+2T>A	9.37:g.140773613T>A		59.0	2.0	0.0338983		68.0	10.0	0.147059	NM_001243812	B1AQK5	Splice_Site	SNP	ENST00000371372.1	37	CCDS59522.1	.	.	.	.	.	.	.	.	.	.	T	20.3	3.975539	0.74360	.	.	ENSG00000148408	ENST00000371372;ENST00000277551;ENST00000371363;ENST00000371357;ENST00000371355	.	.	.	4.73	3.57	0.40892	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	11.6445	0.51253	0.0:0.0:0.1485:0.8515	.	.	.	.	.	-1	.	.	.	+	.	.	CACNA1B	139893434	1.000000	0.71417	1.000000	0.80357	0.962000	0.63368	7.830000	0.86741	0.644000	0.30656	0.459000	0.35465	.	.	.	weak		0.632	CACNA1B-001	KNOWN	non_canonical_conserved|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000055380.1	NM_000718	Intron
COG3	83548	hgsc.bcm.edu	37	13	46104849	46104849	+	Silent	SNP	C	C	T	rs62637564	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr13:46104849C>T	ENST00000349995.5	+	22	2503	c.2391C>T	c.(2389-2391)caC>caT	p.H797H		NM_031431.3	NP_113619	Q96JB2	COG3_HUMAN	component of oligomeric golgi complex 3	797					ER to Golgi vesicle-mediated transport (GO:0006888)|intra-Golgi vesicle-mediated transport (GO:0006891)|intracellular protein transport (GO:0006886)|protein glycosylation (GO:0006486)|protein localization to organelle (GO:0033365)|protein stabilization (GO:0050821)|retrograde vesicle-mediated transport, Golgi to ER (GO:0006890)	cis-Golgi network (GO:0005801)|cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|Golgi transport complex (GO:0017119)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	protein transporter activity (GO:0008565)			breast(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(4)|lung(8)|prostate(2)|skin(2)|stomach(1)	24		Lung NSC(96;0.000145)|Breast(56;0.000596)|Prostate(109;0.00438)|Hepatocellular(98;0.0207)|Lung SC(185;0.0262)	KIRC - Kidney renal clear cell carcinoma(16;0.234)	GBM - Glioblastoma multiforme(144;0.000124)		AGAAGTTCCACGCTCTGTTAA	0.393													T|||	189	0.0377396	0.115	0.0144	5008	,	,		16886	0.0		0.0169	False		,,,				2504	0.0102				p.H797H	Ovarian(150;1048 1859 18083 21577 42700)	Atlas-SNP	.											.	COG3	52	.	0			c.C2391T						PASS	.	T		363,4043		11,341,1851	114.0	109.0	111.0		2391	-3.4	0.3	13	dbSNP_129	111	174,8426		4,166,4130	no	coding-synonymous	COG3	NM_031431.3		15,507,5981	TT,TC,CC		2.0233,8.2388,4.1289		797/829	46104849	537,12469	2203	4300	6503	SO:0001819	synonymous_variant	83548	exon22			GTTCCACGCTCTG	AF131829	CCDS9398.1	13q14.11	2008-02-05			ENSG00000136152	ENSG00000136152		"""Components of oligomeric golgi complex"""	18619	protein-coding gene	gene with protein product		606975				11980916	Standard	NM_031431		Approved	SEC34	uc001vak.3	Q96JB2	OTTHUMG00000016855	ENST00000349995.5:c.2391C>T	13.37:g.46104849C>T		106.0	0.0	0		122.0	61.0	0.5	NM_031431	B2RAW5|Q5VT70|Q8IXX4|Q9BZ92	Silent	SNP	ENST00000349995.5	37	CCDS9398.1																																																																																			C|0.964;T|0.036	0.036	strong		0.393	COG3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044777.2		
HDAC9	9734	hgsc.bcm.edu	37	7	18687542	18687542	+	Silent	SNP	A	A	T	rs35614472	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr7:18687542A>T	ENST00000432645.2	+	9	1161	c.1161A>T	c.(1159-1161)ccA>ccT	p.P387P	HDAC9_ENST00000406451.4_Silent_p.P387P|HDAC9_ENST00000524023.1_Silent_p.P310P|HDAC9_ENST00000405010.3_Silent_p.P387P|HDAC9_ENST00000406072.1_Silent_p.P374P|HDAC9_ENST00000417496.2_Silent_p.P385P|HDAC9_ENST00000401921.1_Silent_p.P346P|HDAC9_ENST00000441542.2_Silent_p.P390P|HDAC9_ENST00000456174.2_Silent_p.P359P|HDAC9_ENST00000428307.2_Silent_p.P343P	NM_058176.2	NP_478056.1	Q9UKV0	HDAC9_HUMAN	histone deacetylase 9	387					B cell activation (GO:0042113)|B cell differentiation (GO:0030183)|cellular response to insulin stimulus (GO:0032869)|heart development (GO:0007507)|histone deacetylation (GO:0016575)|histone H3 deacetylation (GO:0070932)|histone H4 deacetylation (GO:0070933)|inflammatory response (GO:0006954)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|Notch signaling pathway (GO:0007219)|peptidyl-lysine deacetylation (GO:0034983)|positive regulation of cell migration involved in sprouting angiogenesis (GO:0090050)|regulation of skeletal muscle fiber development (GO:0048742)|regulation of striated muscle cell differentiation (GO:0051153)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|histone deacetylase complex (GO:0000118)|histone methyltransferase complex (GO:0035097)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	histone deacetylase activity (GO:0004407)|histone deacetylase binding (GO:0042826)|metal ion binding (GO:0046872)|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)|protein deacetylase activity (GO:0033558)|protein kinase C binding (GO:0005080)|repressing transcription factor binding (GO:0070491)|transcription corepressor activity (GO:0003714)|transcription factor binding (GO:0008134)			breast(3)|central_nervous_system(4)|cervix(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(18)|liver(2)|lung(37)|ovary(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(2)	82	all_lung(11;0.187)				Valproic Acid(DB00313)	AGGGAAAGCCACCCAACAGCA	0.502													A|||	19	0.00379393	0.0015	0.0043	5008	,	,		17684	0.0		0.0139	False		,,,				2504	0.0				p.P390P		Atlas-SNP	.											.	HDAC9	560	.	0			c.A1170T						PASS	.	A	,,,,,,,,	7,4069		0,7,2031	39.0	40.0	39.0		1155,1029,1038,930,1077,1161,1161,1161,1170	-5.0	0.7	7	dbSNP_126	39	115,8287		0,115,4086	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	HDAC9	NM_001204144.1,NM_001204145.1,NM_001204146.1,NM_001204147.1,NM_001204148.1,NM_014707.1,NM_058176.2,NM_178423.1,NM_178425.2	,,,,,,,,	0,122,6117	TT,TA,AA		1.3687,0.1717,0.9777	,,,,,,,,	385/589,343/547,346/550,310/514,359/563,387/591,387/1012,387/1067,390/1070	18687542	122,12356	2038	4201	6239	SO:0001819	synonymous_variant	9734	exon9			AAAGCCACCCAAC	AF124924	CCDS47553.1, CCDS47554.1, CCDS47555.1, CCDS47557.1, CCDS56465.1, CCDS56466.1, CCDS56467.1, CCDS56468.1, CCDS75565.1	7p21.1	2008-05-15			ENSG00000048052	ENSG00000048052			14065	protein-coding gene	gene with protein product		606543				10523670, 10487760	Standard	NM_178425		Approved	KIAA0744, HDAC, MITR, HD7, HDAC7B	uc003sui.3	Q9UKV0	OTTHUMG00000152487	ENST00000432645.2:c.1161A>T	7.37:g.18687542A>T		90.0	0.0	0		88.0	34.0	0.386364	NM_178425	A7E2F3|B7Z4I4|B7Z917|B7Z928|B7Z940|C9JS87|E7EX34|F8W9E0|O94845|O95028|Q2M2R6|Q86SL1|Q86US3	Silent	SNP	ENST00000432645.2	37	CCDS47555.1																																																																																			A|0.992;T|0.008	0.008	strong		0.502	HDAC9-023	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000376176.1		
ALKBH8	91801	hgsc.bcm.edu	37	11	107375703	107375703	+	Missense_Mutation	SNP	C	C	T	rs139390837	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr11:107375703C>T	ENST00000428149.2	-	12	1827	c.1676G>A	c.(1675-1677)cGc>cAc	p.R559H	ALKBH8_ENST00000429370.1_Intron|ALKBH8_ENST00000417449.2_Missense_Mutation_p.R562H|ALKBH8_ENST00000389568.3_Missense_Mutation_p.R559H	NM_138775.2	NP_620130.2	Q96BT7	ALKB8_HUMAN	alkB, alkylation repair homolog 8 (E. coli)	559	Methyltransferase domain.				cellular response to DNA damage stimulus (GO:0006974)|tRNA methylation (GO:0030488)	cytosol (GO:0005829)|nucleus (GO:0005634)	metal ion binding (GO:0046872)|oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, 2-oxoglutarate as one donor, and incorporation of one atom each of oxygen into both donors (GO:0016706)|RNA binding (GO:0003723)|tRNA (uracil) methyltransferase activity (GO:0016300)			breast(2)|large_intestine(2)|lung(5)	9		Melanoma(852;0.000288)|Acute lymphoblastic leukemia(157;0.000966)|all_hematologic(158;0.00301)|all_epithelial(67;0.00512)|Breast(348;0.104)		BRCA - Breast invasive adenocarcinoma(274;3.53e-05)|Epithelial(105;0.00029)|all cancers(92;0.00518)		GTCATTAATGCGGGGGACAGA	0.453													C|||	7	0.00139776	0.0038	0.0014	5008	,	,		20733	0.0		0.001	False		,,,				2504	0.0				p.R559H		Atlas-SNP	.											.	ALKBH8	88	.	0			c.G1676A						PASS	.	C	HIS/ARG	1,1383		0,1,691	118.0	98.0	104.0		1676	2.1	0.0	11	dbSNP_134	104	0,3182		0,0,1591	yes	missense	ALKBH8	NM_138775.2	29	0,1,2282	TT,TC,CC		0.0,0.0723,0.0219	benign	559/665	107375703	1,4565	692	1591	2283	SO:0001583	missense	91801	exon12			TTAATGCGGGGGA	AF086489	CCDS8337.2, CCDS73376.1	11q22.3	2013-10-04			ENSG00000137760	ENSG00000137760	2.1.1.229	"""Alkylation repair homologs"", ""RNA binding motif (RRM) containing"""	25189	protein-coding gene	gene with protein product		613306				20123966	Standard	NM_138775		Approved	MGC10235	uc009yxp.3	Q96BT7	OTTHUMG00000157008	ENST00000428149.2:c.1676G>A	11.37:g.107375703C>T	ENSP00000415885:p.Arg559His	91.0	0.0	0		133.0	36.0	0.270677	NM_138775	B1Q2M0|B4DEF6|Q8N989	Missense_Mutation	SNP	ENST00000428149.2	37	CCDS8337.2	4	0.0018315018315018315	2	0.0040650406504065045	1	0.0027624309392265192	0	0.0	1	0.0013192612137203166	C	4.450	0.083419	0.08533	7.23E-4	0.0	ENSG00000137760	ENST00000428149;ENST00000389568;ENST00000417449	T;T;T	0.45668	0.89;0.89;0.89	5.07	2.13	0.27403	.	0.956250	0.08831	N	0.887349	T	0.20251	0.0487	N	0.08118	0	0.09310	N	1	B;B	0.25351	0.124;0.001	B;B	0.08055	0.003;0.0	T	0.18272	-1.0342	10	0.42905	T	0.14	-2.6235	4.1101	0.10055	0.0872:0.3134:0.4508:0.1486	.	559;562	Q96BT7;Q96BT7-4	ALKB8_HUMAN;.	H	559;559;562	ENSP00000415885:R559H;ENSP00000374219:R559H;ENSP00000397673:R562H	ENSP00000374219:R559H	R	-	2	0	ALKBH8	106880913	0.000000	0.05858	0.000000	0.03702	0.036000	0.12997	-0.511000	0.06321	0.241000	0.21283	-0.865000	0.03005	CGC	C|0.998;T|0.002	0.002	strong		0.453	ALKBH8-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000347071.2	NM_138775	
CPT2	1376	hgsc.bcm.edu	37	1	53668099	53668099	+	Missense_Mutation	SNP	C	C	T	rs74315294	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr1:53668099C>T	ENST00000371486.3	+	3	853	c.338C>T	c.(337-339)tCg>tTg	p.S113L	CPT2_ENST00000468572.1_3'UTR	NM_000098.2	NP_000089.1	P23786	CPT2_HUMAN	carnitine palmitoyltransferase 2	113			S -> L (in CPT2D; muscular form; frequent mutation; dbSNP:rs74315294). {ECO:0000269|PubMed:15489334, ECO:0000269|PubMed:15622536, ECO:0000269|PubMed:8358442, ECO:0000269|PubMed:9758712}.		carnitine shuttle (GO:0006853)|cellular lipid metabolic process (GO:0044255)|fatty acid beta-oxidation (GO:0006635)|small molecule metabolic process (GO:0044281)	mitochondrial inner membrane (GO:0005743)|mitochondrion (GO:0005739)|nucleolus (GO:0005730)|nucleus (GO:0005634)	carnitine O-palmitoyltransferase activity (GO:0004095)			breast(1)|central_nervous_system(1)|endometrium(2)|large_intestine(2)|lung(7)|skin(1)|upper_aerodigestive_tract(1)	15					L-Carnitine(DB00583)|Perhexiline(DB01074)	AGCTACATTTCGGGTAGGTAG	0.418													C|||	3	0.000599042	0.0008	0.0014	5008	,	,		20386	0.0		0.001	False		,,,				2504	0.0				p.S113L		Atlas-SNP	.											CPT2,right_upper_lobe,carcinoma,0,1	CPT2	34	1	0			c.C338T	GRCh37	CM930171	CPT2	M	rs74315294	PASS	.	C	LEU/SER	2,4404	4.2+/-10.8	0,2,2201	92.0	89.0	90.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	338	5.9	1.0	1	dbSNP_131	90	16,8584	11.9+/-42.8	0,16,4284	yes	missense	CPT2	NM_000098.2	145	0,18,6485	TT,TC,CC		0.186,0.0454,0.1384	probably-damaging	113/659	53668099	18,12988	2203	4300	6503	SO:0001583	missense	1376	exon3			ACATTTCGGGTAG	BC002445	CCDS575.1	1p32.3	2014-01-09	2009-03-04		ENSG00000157184	ENSG00000157184	2.3.1.21		2330	protein-coding gene	gene with protein product		600650	"""carnitine palmitoyltransferase II"""	CPT1		1339389	Standard	NM_000098		Approved	CPTASE	uc001cvb.4	P23786	OTTHUMG00000008942	ENST00000371486.3:c.338C>T	1.37:g.53668099C>T	ENSP00000360541:p.Ser113Leu	162.0	0.0	0		123.0	78.0	0.634146	NM_000098	B2R6S0|Q5SW68|Q9BQ26	Missense_Mutation	SNP	ENST00000371486.3	37	CCDS575.1	2	9.157509157509158E-4	0	0.0	1	0.0027624309392265192	0	0.0	1	0.0013192612137203166	C	33	5.265643	0.95399	4.54E-4	0.00186	ENSG00000157184	ENST00000371486	D	0.90676	-2.71	5.88	5.88	0.94601	.	0.064942	0.64402	D	0.000004	D	0.96889	0.8984	H	0.94306	3.52	0.80722	A	1	D	0.76494	0.999	D	0.73708	0.981	D	0.97157	0.9835	9	0.66056	D	0.02	-1.9784	19.8509	0.96740	0.0:1.0:0.0:0.0	.	113	P23786	CPT2_HUMAN	L	113	ENSP00000360541:S113L	ENSP00000360541:S113L	S	+	2	0	CPT2	53440687	1.000000	0.71417	1.000000	0.80357	0.773000	0.43773	6.952000	0.75989	2.797000	0.96272	0.561000	0.74099	TCG	C|0.999;T|0.001	0.001	strong		0.418	CPT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000024757.1	NM_000098	
RFWD3	55159	hgsc.bcm.edu	37	16	74664698	74664698	+	Silent	SNP	A	A	G	rs78796563	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr16:74664698A>G	ENST00000361070.4	-	10	1832	c.1735T>C	c.(1735-1737)Tta>Cta	p.L579L	RFWD3_ENST00000571750.1_Silent_p.L579L	NM_018124.3	NP_060594.3	Q6PCD5	RFWD3_HUMAN	ring finger and WD repeat domain 3	579					DNA repair (GO:0006281)|mitotic G1 DNA damage checkpoint (GO:0031571)|protein ubiquitination (GO:0016567)|regulation of DNA damage checkpoint (GO:2000001)|response to ionizing radiation (GO:0010212)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	ligase activity (GO:0016874)|MDM2/MDM4 family protein binding (GO:0097371)|p53 binding (GO:0002039)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)	p.L579L(1)		NS(1)|breast(1)|endometrium(3)|kidney(1)|large_intestine(3)|lung(12)|ovary(1)|skin(2)|stomach(1)|urinary_tract(1)	26						TGAGCTACTAACTCCTGCACA	0.473													A|||	67	0.0133786	0.0023	0.0259	5008	,	,		18719	0.0		0.0288	False		,,,				2504	0.0174				p.L579L		Atlas-SNP	.											RFWD3,NS,carcinoma,0,1	RFWD3	49	1	1	Substitution - coding silent(1)	lung(1)	c.T1735C						PASS	.	A		28,4368	32.6+/-62.9	1,26,2171	94.0	70.0	78.0		1735	3.5	0.3	16	dbSNP_132	78	267,8333	102.3+/-163.5	4,259,4037	no	coding-synonymous	RFWD3	NM_018124.3		5,285,6208	GG,GA,AA		3.1047,0.6369,2.2699		579/775	74664698	295,12701	2198	4300	6498	SO:0001819	synonymous_variant	55159	exon10			CTACTAACTCCTG	AK001382	CCDS32486.1	16q22.3	2013-01-09						"""WD repeat domain containing"", ""RING-type (C3HC4) zinc fingers"""	25539	protein-coding gene	gene with protein product		614151				21504906	Standard	XM_005256021		Approved	FLJ10520, RNF201	uc002fda.3	Q6PCD5		ENST00000361070.4:c.1735T>C	16.37:g.74664698A>G		91.0	0.0	0		87.0	16.0	0.183908	NM_018124	A8K585|B2RE35|D3DUJ8|Q5XKR3|Q9H9Q3|Q9NVT4	Silent	SNP	ENST00000361070.4	37	CCDS32486.1																																																																																			A|0.981;G|0.019	0.019	strong		0.473	RFWD3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000436506.2	NM_018124	
SCRIB	23513	hgsc.bcm.edu	37	8	144885669	144885669	+	Missense_Mutation	SNP	G	G	C	rs138257744	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr8:144885669G>C	ENST00000320476.3	-	24	3493	c.3487C>G	c.(3487-3489)Cag>Gag	p.Q1163E	SCRIB_ENST00000356994.2_Missense_Mutation_p.Q1163E|SCRIB_ENST00000377533.3_Missense_Mutation_p.Q1082E	NM_015356.4	NP_056171	Q14160	SCRIB_HUMAN	scribbled planar cell polarity protein	1163	Interaction with ARHGEF7.|PDZ 4. {ECO:0000255|PROSITE- ProRule:PRU00143}.				activation of Rac GTPase activity (GO:0032863)|apoptotic process involved in morphogenesis (GO:0060561)|astrocyte cell migration (GO:0043615)|asymmetric protein localization (GO:0008105)|auditory receptor cell stereocilium organization (GO:0060088)|cell migration (GO:0016477)|cell proliferation (GO:0008283)|cochlear nucleus development (GO:0021747)|establishment of apical/basal cell polarity (GO:0035089)|mammary gland duct morphogenesis (GO:0060603)|negative regulation of mitotic cell cycle (GO:0045930)|neural tube closure (GO:0001843)|positive chemotaxis (GO:0050918)|positive regulation of apoptotic process (GO:0043065)|positive regulation of receptor recycling (GO:0001921)|protein localization to adherens junction (GO:0071896)|single organismal cell-cell adhesion (GO:0016337)|synaptic vesicle endocytosis (GO:0048488)|synaptic vesicle targeting (GO:0016080)|viral process (GO:0016032)|wound healing (GO:0042060)	basolateral plasma membrane (GO:0016323)|cell projection (GO:0042995)|cell-cell adherens junction (GO:0005913)|cell-cell junction (GO:0005911)|extracellular vesicular exosome (GO:0070062)|myelin sheath abaxonal region (GO:0035748)|plasma membrane (GO:0005886)|Scrib-APC-beta-catenin complex (GO:0034750)				NS(1)|autonomic_ganglia(1)|central_nervous_system(2)|endometrium(3)|kidney(3)|large_intestine(3)|lung(20)|ovary(2)|pancreas(1)|skin(1)|upper_aerodigestive_tract(4)|urinary_tract(1)	42	all_cancers(97;2.31e-11)|all_epithelial(106;1.58e-09)|Lung NSC(106;0.00013)|all_lung(105;0.000374)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155)		OV - Ovarian serous cystadenocarcinoma(54;2.46e-41)|Epithelial(56;1.23e-39)|all cancers(56;1.12e-34)|Colorectal(110;0.055)|BRCA - Breast invasive adenocarcinoma(115;0.18)			AGCAGGCTCTGCTGGTTCACC	0.692													G|||	17	0.00339457	0.0	0.0	5008	,	,		11201	0.0169		0.0	False		,,,				2504	0.0				p.Q1163E	Pancreas(51;966 1133 10533 14576 29674)	Atlas-SNP	.											.	SCRIB	192	.	0			c.C3487G						PASS	.	G	GLU/GLN,GLU/GLN	2,4362		0,2,2180	20.0	20.0	20.0		3487,3487	4.8	1.0	8	dbSNP_134	20	0,8554		0,0,4277	yes	missense,missense	SCRIB	NM_015356.3,NM_182706.3	29,29	0,2,6457	CC,CG,GG		0.0,0.0458,0.0155	possibly-damaging,possibly-damaging	1163/1631,1163/1656	144885669	2,12916	2182	4277	6459	SO:0001583	missense	23513	exon24			GGCTCTGCTGGTT	AY062238	CCDS6411.1, CCDS6412.1	8q24.3	2013-03-05	2013-03-05		ENSG00000180900	ENSG00000180900			30377	protein-coding gene	gene with protein product		607733	"""scribbled homolog (Drosophila)"""			11027293, 14681682	Standard	NM_182706		Approved	KIAA0147, SCRB1, Vartul	uc003yzo.1	Q14160	OTTHUMG00000165154	ENST00000320476.3:c.3487C>G	8.37:g.144885669G>C	ENSP00000322938:p.Gln1163Glu	21.0	0.0	0		15.0	9.0	0.6	NM_015356	Q6P496|Q7Z5D1|Q8WWV8|Q96C69|Q96GG1	Missense_Mutation	SNP	ENST00000320476.3	37	CCDS6411.1	7|7	0.003205128205128205|0.003205128205128205	0|0	0.0|0.0	0|0	0.0|0.0	7|7	0.012237762237762238|0.012237762237762238	0|0	0.0|0.0	G|G	17.95|17.95	3.514052|3.514052	0.64522|0.64522	4.58E-4|4.58E-4	0.0|0.0	ENSG00000180900|ENSG00000180900	ENST00000526832|ENST00000356994;ENST00000320476;ENST00000377533;ENST00000377539	.|T;T;T	.|0.27256	.|1.68;1.68;1.68	4.82|4.82	4.82|4.82	0.62117|0.62117	.|PDZ/DHR/GLGF (4);	.|.	.|.	.|.	.|.	T|T	0.16085|0.16085	0.0387|0.0387	N|N	0.10618|0.10618	0.005|0.005	0.24765|0.24765	N|N	0.99291|0.99291	.|P;P	.|0.48089	.|0.855;0.905	.|P;P	.|0.50860	.|0.634;0.652	T|T	0.13629|0.13629	-1.0502|-1.0502	5|9	.|0.30854	.|T	.|0.27	.|.	15.1122|15.1122	0.72368|0.72368	0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0	.|.	.|1163;1163	.|Q14160;Q14160-3	.|SCRIB_HUMAN;.	G|E	158|1163;1163;1082;532	.|ENSP00000349486:Q1163E;ENSP00000322938:Q1163E;ENSP00000366756:Q1082E	.|ENSP00000322938:Q1163E	A|Q	-|-	2|1	0|0	SCRIB|SCRIB	144957657|144957657	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.913000|0.913000	0.54294|0.54294	5.594000|5.594000	0.67557|0.67557	2.222000|2.222000	0.72286|0.72286	0.456000|0.456000	0.33151|0.33151	GCA|CAG	G|0.999;C|0.001	0.001	strong		0.692	SCRIB-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000382215.1	NM_015356	
FPR3	2359	hgsc.bcm.edu	37	19	52327479	52327479	+	Missense_Mutation	SNP	A	A	T			TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr19:52327479A>T	ENST00000339223.4	+	2	657	c.478A>T	c.(478-480)Aat>Tat	p.N160Y	FPR3_ENST00000595991.1_Missense_Mutation_p.N160Y	NM_002030.3	NP_002021.3	P25089	FPR3_HUMAN	formyl peptide receptor 3	160					cellular component movement (GO:0006928)|chemotaxis (GO:0006935)|signal transduction (GO:0007165)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	N-formyl peptide receptor activity (GO:0004982)			NS(1)|breast(3)|endometrium(3)|kidney(1)|large_intestine(5)|lung(17)|ovary(1)|prostate(1)|skin(3)	35						TACCTTACCAAATTTCATCTT	0.478																																					p.N160Y		Atlas-SNP	.											.	FPR3	66	.	0			c.A478T						PASS	.						134.0	122.0	126.0					19																	52327479		2203	4300	6503	SO:0001583	missense	2359	exon2			TTACCAAATTTCA		CCDS12841.1	19q13.3-q13.4	2012-08-08	2008-04-17	2008-04-17		ENSG00000187474		"""GPCR / Class A : Formyl peptide receptors"""	3828	protein-coding gene	gene with protein product		136539	"""formyl peptide receptor-like 2"""	FPRL2		1612600, 8198572	Standard	NM_002030		Approved	FPRH1, FMLPY, RMLP-R-I	uc002pxt.1	P25089		ENST00000339223.4:c.478A>T	19.37:g.52327479A>T	ENSP00000341821:p.Asn160Tyr	258.0	0.0	0		243.0	97.0	0.399177	NM_002030		Missense_Mutation	SNP	ENST00000339223.4	37	CCDS12841.1	.	.	.	.	.	.	.	.	.	.	.	0	-2.601169	0.00123	.	.	ENSG00000187474	ENST00000339223	T	0.36520	1.25	2.34	-4.67	0.03319	GPCR, rhodopsin-like superfamily (1);	0.726121	0.12818	N	0.436647	T	0.08268	0.0206	N	0.00926	-1.1	0.09310	N	1	B	0.06786	0.001	B	0.16722	0.016	T	0.19712	-1.0297	10	0.02654	T	1	.	6.9341	0.24457	0.6963:0.0:0.1696:0.1341	.	160	P25089	FPR3_HUMAN	Y	160	ENSP00000341821:N160Y	ENSP00000341821:N160Y	N	+	1	0	FPR3	57019291	0.000000	0.05858	0.000000	0.03702	0.006000	0.05464	-0.708000	0.05035	-1.822000	0.01211	-1.486000	0.00981	AAT	.	.	none		0.478	FPR3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466914.1	NM_002030	
MLKL	197259	hgsc.bcm.edu	37	16	74709233	74709233	+	Missense_Mutation	SNP	C	C	A	rs144526386	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr16:74709233C>A	ENST00000306247.7	-	4	944	c.605G>T	c.(604-606)gGc>gTc	p.G202V	MLKL_ENST00000308807.7_Intron	NM_001142497.1	NP_001135969.1			mixed lineage kinase domain-like											breast(1)|endometrium(2)|kidney(2)|large_intestine(3)|liver(2)|lung(6)|skin(1)|stomach(2)	19						ACTGGCTGAGCCAGTCTTCAC	0.493													C|||	51	0.0101837	0.0023	0.0144	5008	,	,		19105	0.0		0.0209	False		,,,				2504	0.0174				p.G202V		Atlas-SNP	.											.	MLKL	51	.	0			c.G605T						PASS	.	C	VAL/GLY,	17,4379	23.3+/-48.9	0,17,2181	113.0	108.0	110.0		605,	-1.0	0.0	16	dbSNP_134	110	162,8438	76.3+/-139.0	2,158,4140	yes	missense,intron	MLKL	NM_001142497.1,NM_152649.2	109,	2,175,6321	AA,AC,CC		1.8837,0.3867,1.3773	,	202/264,	74709233	179,12817	2198	4300	6498	SO:0001583	missense	197259	exon4			GCTGAGCCAGTCT	AK091708	CCDS32487.1, CCDS45528.1	16q22.3	2008-02-05				ENSG00000168404			26617	protein-coding gene	gene with protein product		615153				12477932	Standard	NM_152649		Approved	FLJ34389	uc002fdb.2	Q8NB16		ENST00000306247.7:c.605G>T	16.37:g.74709233C>A	ENSP00000303118:p.Gly202Val	126.0	0.0	0		122.0	25.0	0.204918	NM_001142497		Missense_Mutation	SNP	ENST00000306247.7	37	CCDS45528.1	23	0.010531135531135532	1	0.0020325203252032522	7	0.019337016574585635	0	0.0	15	0.01978891820580475	C	8.923	0.961462	0.18583	0.003867	0.018837	ENSG00000168404	ENST00000306247	T	0.12147	2.71	4.96	-1.05	0.10036	.	.	.	.	.	T	0.14313	0.0346	.	.	.	0.09310	N	1	D	0.67145	0.996	D	0.65573	0.936	T	0.07501	-1.0769	8	0.48119	T	0.1	.	8.2986	0.32001	0.0:0.4852:0.0:0.5148	.	202	Q8NB16-2	.	V	202	ENSP00000303118:G202V	ENSP00000303118:G202V	G	-	2	0	MLKL	73266734	0.000000	0.05858	0.001000	0.08648	0.016000	0.09150	-0.620000	0.05565	-0.228000	0.09869	-0.374000	0.07098	GGC	C|0.986;A|0.014	0.014	strong		0.493	MLKL-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000436402.1	NM_152649	
PCMTD1	115294	hgsc.bcm.edu	37	8	52733127	52733127	+	Silent	SNP	G	G	A			TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr8:52733127G>A	ENST00000360540.5	-	7	1264	c.858C>T	c.(856-858)aaC>aaT	p.N286N	PCMTD1_ENST00000544451.1_Silent_p.N210N|PCMTD1_ENST00000519559.1_5'UTR|PCMTD1_ENST00000522514.1_Silent_p.N286N	NM_052937.2	NP_443169.2	Q96MG8	PCMD1_HUMAN	protein-L-isoaspartate (D-aspartate) O-methyltransferase domain containing 1	286						cytoplasm (GO:0005737)	protein-L-isoaspartate (D-aspartate) O-methyltransferase activity (GO:0004719)			NS(2)|endometrium(1)|kidney(3)|large_intestine(3)|lung(17)|prostate(2)|skin(8)|soft_tissue(1)	37		Lung NSC(129;0.0795)|all_lung(136;0.144)				ATACGTAAGTGTTAATTCTCT	0.398																																					p.N286N		Atlas-SNP	.											.	PCMTD1	73	.	0			c.C858T						PASS	.						189.0	188.0	188.0					8																	52733127		2203	4300	6503	SO:0001819	synonymous_variant	115294	exon6			GTAAGTGTTAATT		CCDS6148.1, CCDS69480.1	8q11.23	2010-08-05			ENSG00000168300	ENSG00000168300			30483	protein-coding gene	gene with protein product							Standard	XM_005251146		Approved	FLJ10883	uc003xqx.4	Q96MG8	OTTHUMG00000164246	ENST00000360540.5:c.858C>T	8.37:g.52733127G>A		400.0	0.0	0		518.0	28.0	0.0540541	NM_052937	Q96FK9	Silent	SNP	ENST00000360540.5	37	CCDS6148.1																																																																																			.	.	none		0.398	PCMTD1-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000377909.2	NM_052937	
COL12A1	1303	hgsc.bcm.edu	37	6	75836079	75836079	+	Missense_Mutation	SNP	A	A	G	rs200450866		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr6:75836079A>G	ENST00000322507.8	-	39	6757	c.6448T>C	c.(6448-6450)Tat>Cat	p.Y2150H	COL12A1_ENST00000416123.2_Missense_Mutation_p.Y2150H|COL12A1_ENST00000345356.6_Missense_Mutation_p.Y986H|COL12A1_ENST00000483888.2_Missense_Mutation_p.Y2150H	NM_004370.5	NP_004361.3	Q99715	COCA1_HUMAN	collagen, type XII, alpha 1	2150	Fibronectin type-III 17. {ECO:0000255|PROSITE-ProRule:PRU00316}.				cell adhesion (GO:0007155)|collagen catabolic process (GO:0030574)|collagen fibril organization (GO:0030199)|endodermal cell differentiation (GO:0035987)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|skeletal system development (GO:0001501)	collagen type XII trimer (GO:0005595)|endoplasmic reticulum lumen (GO:0005788)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|vesicle (GO:0031982)	extracellular matrix structural constituent conferring tensile strength (GO:0030020)			breast(7)|central_nervous_system(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(5)|kidney(5)|large_intestine(44)|liver(1)|lung(77)|ovary(7)|prostate(3)|skin(4)|stomach(2)|upper_aerodigestive_tract(4)|urinary_tract(2)	169						ACTGGCTTATATACTATTTTA	0.428																																					p.Y2150H		Atlas-SNP	.											.	COL12A1	385	.	0			c.T6448C						PASS	.	A	HIS/TYR,HIS/TYR	0,3684		0,0,1842	108.0	103.0	105.0		6448,2956	5.7	1.0	6		105	3,8163		0,3,4080	yes	missense,missense	COL12A1	NM_004370.5,NM_080645.2	83,83	0,3,5922	GG,GA,AA		0.0367,0.0,0.0253	probably-damaging,probably-damaging	2150/3064,986/1900	75836079	3,11847	1842	4083	5925	SO:0001583	missense	1303	exon39			GCTTATATACTAT	U73779	CCDS43481.1, CCDS43482.1	6q12-q13	2013-02-11	2003-07-24		ENSG00000111799	ENSG00000111799		"""Proteoglycans / Extracellular Matrix : Collagen proteoglycans"", ""Collagens"", ""Fibronectin type III domain containing"""	2188	protein-coding gene	gene with protein product	"""collagen type XII proteoglycan"""	120320	"""collagen, type XII, alpha 1-like"""	COL12A1L		9143499	Standard	XM_006715334		Approved		uc003phs.3	Q99715	OTTHUMG00000015051	ENST00000322507.8:c.6448T>C	6.37:g.75836079A>G	ENSP00000325146:p.Tyr2150His	100.0	0.0	0		84.0	40.0	0.47619	NM_004370	O43853|Q15955|Q5VYK1|Q5VYK2|Q71UR3|Q99716	Missense_Mutation	SNP	ENST00000322507.8	37	CCDS43482.1	.	.	.	.	.	.	.	.	.	.	A	24.1	4.498898	0.85069	0.0	3.67E-4	ENSG00000111799	ENST00000322507;ENST00000432784;ENST00000345356;ENST00000416123;ENST00000483888	T;T;T;T	0.62639	0.01;0.01;0.01;0.01	5.7	5.7	0.88788	Fibronectin, type III (4);Immunoglobulin-like fold (1);	0.000000	0.85682	D	0.000000	T	0.78786	0.4338	M	0.86805	2.84	0.58432	D	0.999998	D;D	0.89917	1.0;1.0	D;D	0.97110	0.999;1.0	D	0.83385	0.0014	10	0.87932	D	0	.	15.9743	0.80049	1.0:0.0:0.0:0.0	.	986;2150	Q99715-2;Q99715	.;COCA1_HUMAN	H	2150;2150;986;2150;2150	ENSP00000325146:Y2150H;ENSP00000305147:Y986H;ENSP00000412864:Y2150H;ENSP00000421216:Y2150H	ENSP00000325146:Y2150H	Y	-	1	0	COL12A1	75892799	1.000000	0.71417	1.000000	0.80357	0.916000	0.54674	8.905000	0.92613	2.173000	0.68751	0.528000	0.53228	TAT	.	.	weak		0.428	COL12A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041249.3	NM_004370	
FBXW5	54461	hgsc.bcm.edu	37	9	139836694	139836694	+	Silent	SNP	C	C	T	rs34391108	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr9:139836694C>T	ENST00000325285.3	-	6	979	c.900G>A	c.(898-900)gaG>gaA	p.E300E	FBXW5_ENST00000483559.1_5'UTR	NM_018998.3	NP_061871.1	Q969U6	FBXW5_HUMAN	F-box and WD repeat domain containing 5	300					centrosome duplication (GO:0051298)|mitotic nuclear division (GO:0007067)|proteasome-mediated ubiquitin-dependent protein catabolic process (GO:0043161)|protein ubiquitination (GO:0016567)|SCF-dependent proteasomal ubiquitin-dependent protein catabolic process (GO:0031146)	Cul4-RING E3 ubiquitin ligase complex (GO:0080008)|cytoplasm (GO:0005737)|SCF ubiquitin ligase complex (GO:0019005)	protein kinase binding (GO:0019901)			breast(1)|endometrium(2)|large_intestine(2)|lung(3)|prostate(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	12	all_cancers(76;0.11)	Myeloproliferative disorder(178;0.0511)	STAD - Stomach adenocarcinoma(284;0.19)	OV - Ovarian serous cystadenocarcinoma(145;7.8e-06)|Epithelial(140;0.000106)		GCCGCAAGCCCTCCTTGGCGT	0.711													C|||	176	0.0351438	0.0023	0.0259	5008	,	,		15047	0.004		0.0477	False		,,,				2504	0.1053				p.E300E		Atlas-SNP	.											.	FBXW5	36	.	0			c.G900A						PASS	.	C		38,4292		1,36,2128	11.0	14.0	13.0		900	0.9	0.9	9	dbSNP_126	13	318,8216		4,310,3953	no	coding-synonymous	FBXW5	NM_018998.2		5,346,6081	TT,TC,CC		3.7263,0.8776,2.7674		300/567	139836694	356,12508	2165	4267	6432	SO:0001819	synonymous_variant	54461	exon6			CAAGCCCTCCTTG	BC014130	CCDS7014.1	9q34.3	2013-01-09	2007-02-08		ENSG00000159069	ENSG00000159069		"""F-boxes / WD-40 domains"", ""WD repeat domain containing"""	13613	protein-coding gene	gene with protein product		609072	"""F-box and WD-40 domain protein 5"""				Standard	NM_018998		Approved	DKFZP434B205, MGC20962, Fbw5	uc004cjx.3	Q969U6	OTTHUMG00000020967	ENST00000325285.3:c.900G>A	9.37:g.139836694C>T		40.0	0.0	0		7.0	6.0	0.857143	NM_018998	B2RDZ6|Q59ET5|Q5SPZ8|Q5SPZ9|Q5SQ00|Q5SQ02|Q5SQ03|Q5SQ04|Q8WY79|Q96GJ6|Q9BSU8|Q9H6A8|Q9HBQ6|Q9NSZ3	Silent	SNP	ENST00000325285.3	37	CCDS7014.1																																																																																			C|0.975;T|0.025	0.025	strong		0.711	FBXW5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055227.1	NM_018998	
SLC1A6	6511	hgsc.bcm.edu	37	19	15083555	15083555	+	Silent	SNP	G	G	A	rs115001292	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr19:15083555G>A	ENST00000221742.3	-	1	175	c.168C>T	c.(166-168)aaC>aaT	p.N56N	SLC1A6_ENST00000600144.1_Silent_p.N56N|SLC1A6_ENST00000430939.2_Missense_Mutation_p.R61C|SLC1A6_ENST00000598504.1_Silent_p.N56N|SLC1A6_ENST00000544886.2_Silent_p.N56N	NM_005071.1	NP_005062.1	P48664	EAA4_HUMAN	solute carrier family 1 (high affinity aspartate/glutamate transporter), member 6	56					aspartate transport (GO:0015810)|ion transport (GO:0006811)|L-glutamate transport (GO:0015813)|regulation of membrane potential (GO:0042391)|synaptic transmission (GO:0007268)|transmembrane transport (GO:0055085)	Golgi apparatus (GO:0005794)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)	L-aspartate transmembrane transporter activity (GO:0015183)|L-glutamate transmembrane transporter activity (GO:0005313)|sodium:dicarboxylate symporter activity (GO:0017153)			breast(1)|central_nervous_system(2)|endometrium(6)|large_intestine(8)|liver(1)|lung(12)|ovary(3)|pancreas(3)|prostate(3)|skin(2)|upper_aerodigestive_tract(1)	42						GAATGAAGGCGTTTCGGCGCA	0.637													G|||	44	0.00878594	0.0	0.0245	5008	,	,		19459	0.0		0.0239	False		,,,				2504	0.0031				p.N56N		Atlas-SNP	.											.	SLC1A6	111	.	0			c.C168T						PASS	.	G		7,4393		0,7,2193	29.0	29.0	29.0		168	-4.8	0.9	19	dbSNP_132	29	53,8547		1,51,4248	no	coding-synonymous	SLC1A6	NM_005071.1		1,58,6441	AA,AG,GG		0.6163,0.1591,0.4615		56/565	15083555	60,12940	2200	4300	6500	SO:0001819	synonymous_variant	6511	exon4			GAAGGCGTTTCGG		CCDS12321.1, CCDS62578.1	19p13.12	2013-07-15			ENSG00000105143	ENSG00000105143		"""Solute carriers"""	10944	protein-coding gene	gene with protein product		600637				7791878	Standard	NM_005071		Approved	EAAT4	uc002naa.2	P48664	OTTHUMG00000183351	ENST00000221742.3:c.168C>T	19.37:g.15083555G>A		133.0	0.0	0		110.0	57.0	0.518182	NM_001272087	Q8N753	Silent	SNP	ENST00000221742.3	37	CCDS12321.1	26	0.011904761904761904	0	0.0	6	0.016574585635359115	0	0.0	20	0.026385224274406333	G	10.63	1.404119	0.25291	0.001591	0.006163	ENSG00000105143	ENST00000430939	T	0.75260	-0.92	4.46	-4.79	0.03200	.	.	.	.	.	T	0.37865	0.1019	.	.	.	0.80722	D	1	B	0.06786	0.001	B	0.04013	0.001	T	0.32771	-0.9894	8	0.87932	D	0	-17.863	10.8289	0.46649	0.7382:0.0:0.2618:0.0	.	61	E7EV13	.	C	61	ENSP00000409386:R61C	ENSP00000409386:R61C	R	-	1	0	SLC1A6	14944555	0.036000	0.19791	0.931000	0.37212	0.642000	0.38348	-0.826000	0.04429	-0.758000	0.04690	0.313000	0.20887	CGC	G|0.993;A|0.007	0.007	strong		0.637	SLC1A6-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466283.1	NM_005071	
MLLT6	4302	hgsc.bcm.edu	37	17	36868976	36868976	+	Silent	SNP	G	G	A			TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr17:36868976G>A	ENST00000325718.7	+	8	844	c.753G>A	c.(751-753)aaG>aaA	p.K251K	CTB-58E17.9_ENST00000579499.1_RNA|MLLT6_ENST00000378137.5_Silent_p.K251K	NM_005937.3	NP_005928	P55198	AF17_HUMAN	myeloid/lymphoid or mixed-lineage leukemia (trithorax homolog, Drosophila); translocated to, 6	251					regulation of transcription, DNA-templated (GO:0006355)	nucleus (GO:0005634)	zinc ion binding (GO:0008270)			breast(3)|lung(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)	8	Breast(7;4.43e-21)					TTAAGCAGAAGCACAAGAAGC	0.587			T	MLL	AL																																p.K251K		Atlas-SNP	.		Dom	yes		17	17q21	4302	"""myeloid/lymphoid or mixed-lineage leukemia (trithorax homolog, Drosophila); translocated to, 6 (AF17)"""		L	.	MLLT6	80	.	0			c.G753A						PASS	.						108.0	104.0	105.0					17																	36868976		2203	4300	6503	SO:0001819	synonymous_variant	4302	exon8			GCAGAAGCACAAG		CCDS11327.1	17q21	2014-04-10	2001-11-28		ENSG00000108292	ENSG00000275023		"""Zinc fingers, PHD-type"""	7138	protein-coding gene	gene with protein product	"""Myeloid/lymphoid or mixed-lineage leukemia, translocated to, 6"", ""trithorax homolog"""	600328	"""myeloid/lymphoid or mixed-lineage leukemia (trithorax (Drosophila) homolog); translocated to, 6"""			8058765	Standard	NM_005937		Approved	AF17, FLJ23480	uc002hqi.4	P55198	OTTHUMG00000188498	ENST00000325718.7:c.753G>A	17.37:g.36868976G>A		107.0	0.0	0		123.0	34.0	0.276423	NM_005937	Q59F28|Q96IU3|Q9H5F6|Q9UF49	Silent	SNP	ENST00000325718.7	37	CCDS11327.1																																																																																			.	.	none		0.587	MLLT6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256799.1	NM_005937	
TCP10L2	401285	hgsc.bcm.edu	37	6	167592571	167592571	+	Missense_Mutation	SNP	G	G	A	rs28690444	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr6:167592571G>A	ENST00000366832.2	+	6	861	c.730G>A	c.(730-732)Gcc>Acc	p.A244T		NM_001145121.1	NP_001138593.1	B9ZVM9	TCP2L_HUMAN	t-complex 10-like 2	244										endometrium(1)|kidney(2)|lung(3)	6						TTCCCAGGCCGCCACGCTGCA	0.592																																					p.A244T		Atlas-SNP	.											.	TCP10L2	41	.	0			c.G730A						PASS	.						23.0	28.0	27.0					6																	167592571		692	1591	2283	SO:0001583	missense	401285	exon6			CAGGCCGCCACGC		CCDS47514.1	6q27	2012-09-20	2012-09-20		ENSG00000166984	ENSG00000166984			21254	protein-coding gene	gene with protein product			"""t-complex 10-like 2 (mouse)"""				Standard	NM_001145121		Approved	bA517H2.3	uc010kkp.3	B9ZVM9	OTTHUMG00000016014	ENST00000366832.2:c.730G>A	6.37:g.167592571G>A	ENSP00000355797:p.Ala244Thr	82.0	0.0	0		130.0	31.0	0.238462	NM_001145121		Missense_Mutation	SNP	ENST00000366832.2	37	CCDS47514.1	87	0.03983516483516483	17	0.034552845528455285	12	0.03314917127071823	14	0.024475524475524476	44	0.05804749340369393	c	8.486	0.860926	0.17178	.	.	ENSG00000166984	ENST00000366832	T	0.13901	2.55	1.87	-1.19	0.09585	.	.	.	.	.	T	0.00906	0.0030	N	0.11560	0.145	0.09310	N	1	B	0.32968	0.392	B	0.17433	0.018	T	0.43718	-0.9374	9	0.02654	T	1	.	2.6095	0.04887	0.3443:0.2689:0.3868:0.0	rs28690444	244	B9ZVM9	TCP2L_HUMAN	T	244	ENSP00000355797:A244T	ENSP00000283507:A244T	A	+	1	0	TCP10L2	167512561	0.000000	0.05858	0.000000	0.03702	0.115000	0.19883	-0.863000	0.04259	-0.321000	0.08627	-1.962000	0.00476	GCC	G|0.965;A|0.035	0.035	strong		0.592	TCP10L2-001	NOVEL	not_best_in_genome_evidence|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000043112.5	XR_040749	
GAK	2580	hgsc.bcm.edu	37	4	843536	843536	+	Silent	SNP	G	G	A	rs55904229	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr4:843536G>A	ENST00000314167.4	-	28	3971	c.3861C>T	c.(3859-3861)caC>caT	p.H1287H	GAK_ENST00000511163.1_Silent_p.H1208H|GAK_ENST00000509566.1_5'UTR	NM_005255.2	NP_005246.2	O14976	GAK_HUMAN	cyclin G associated kinase	1287	J. {ECO:0000255|PROSITE- ProRule:PRU00286}.				cell cycle (GO:0007049)|cell development (GO:0048468)|clathrin coat disassembly (GO:0072318)|clathrin-mediated endocytosis (GO:0072583)|endoplasmic reticulum organization (GO:0007029)|epidermal cell differentiation (GO:0009913)|establishment of skin barrier (GO:0061436)|forebrain morphogenesis (GO:0048853)|Golgi organization (GO:0007030)|intrahepatic bile duct development (GO:0035622)|positive regulation of neural precursor cell proliferation (GO:2000179)	cell junction (GO:0030054)|Golgi apparatus (GO:0005794)|intracellular membrane-bounded organelle (GO:0043231)|membrane (GO:0016020)	ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)			autonomic_ganglia(1)|central_nervous_system(1)|endometrium(4)|kidney(1)|large_intestine(7)|lung(16)|skin(7)|urinary_tract(2)	39				Colorectal(103;0.219)		TCATCTTGGCGTGCTGCTCGT	0.672													G|||	9	0.00179712	0.0008	0.0	5008	,	,		14022	0.0		0.006	False		,,,				2504	0.002				p.H1287H		Atlas-SNP	.											.	GAK	104	.	0			c.C3861T						PASS	.	G		7,4399	12.9+/-30.5	0,7,2196	51.0	49.0	50.0		3861	-7.5	0.0	4	dbSNP_129	50	55,8545	34.3+/-88.2	0,55,4245	no	coding-synonymous	GAK	NM_005255.2		0,62,6441	AA,AG,GG		0.6395,0.1589,0.4767		1287/1312	843536	62,12944	2203	4300	6503	SO:0001819	synonymous_variant	2580	exon28			CTTGGCGTGCTGC	D88435	CCDS3340.1	4p16	2011-09-07			ENSG00000178950	ENSG00000178950		"""Heat shock proteins / DNAJ (HSP40)"""	4113	protein-coding gene	gene with protein product	"""auxilin-2"""	602052				9299234	Standard	NM_005255		Approved	DNAJC26	uc003gbm.4	O14976	OTTHUMG00000088301	ENST00000314167.4:c.3861C>T	4.37:g.843536G>A		279.0	0.0	0		268.0	132.0	0.492537	NM_005255	Q5U4P5|Q9BVY6	Silent	SNP	ENST00000314167.4	37	CCDS3340.1	2	9.157509157509158E-4	0	0.0	0	0.0	0	0.0	2	0.002638522427440633	G	1.270	-0.613465	0.03690	0.001589	0.006395	ENSG00000178950	ENST00000511980	.	.	.	4.76	-7.48	0.01360	.	.	.	.	.	T	0.45458	0.1343	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.59005	-0.7535	4	.	.	.	-0.8575	11.9205	0.52789	0.7915:0.1057:0.1028:0.0	rs55904229	.	.	.	M	443	.	.	T	-	2	0	GAK	833536	0.555000	0.26530	0.003000	0.11579	0.228000	0.25075	-0.100000	0.10990	-1.556000	0.01695	-0.796000	0.03273	ACG	G|0.997;A|0.003	0.003	strong		0.672	GAK-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000239188.1	NM_005255	
SDK2	54549	hgsc.bcm.edu	37	17	71344769	71344769	+	Missense_Mutation	SNP	G	G	A	rs199591952		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr17:71344769G>A	ENST00000392650.3	-	44	6134	c.6134C>T	c.(6133-6135)aCg>aTg	p.T2045M	SDK2_ENST00000410094.1_5'UTR|SDK2_ENST00000388726.3_Missense_Mutation_p.T2026M	NM_001144952.1	NP_001138424.1	Q58EX2	SDK2_HUMAN	sidekick cell adhesion molecule 2	2045					cell adhesion (GO:0007155)	integral component of membrane (GO:0016021)				breast(4)|central_nervous_system(2)|cervix(1)|endometrium(10)|haematopoietic_and_lymphoid_tissue(3)|kidney(8)|large_intestine(15)|lung(31)|ovary(3)|prostate(2)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(3)	86						GGGCTTCTCCGTCAGGCTGCT	0.637													G|||	1	0.000199681	0.0	0.0	5008	,	,		16899	0.001		0.0	False		,,,				2504	0.0				p.T2045M		Atlas-SNP	.											.	SDK2	219	.	0			c.C6134T						PASS	.						61.0	54.0	56.0					17																	71344769		2203	4299	6502	SO:0001583	missense	54549	exon44			TTCTCCGTCAGGC	AB040947	CCDS45769.1	17q21.31	2013-02-11	2011-12-09		ENSG00000069188	ENSG00000069188		"""Immunoglobulin superfamily / I-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"", ""Fibronectin type III domain containing"""	19308	protein-coding gene	gene with protein product		607217	"""sidekick homolog 2 (chicken)"""			12230981, 15213259	Standard	NM_001144952		Approved	FLJ10832, KIAA1514	uc010dfm.3	Q58EX2	OTTHUMG00000152726	ENST00000392650.3:c.6134C>T	17.37:g.71344769G>A	ENSP00000376421:p.Thr2045Met	88.0	0.0	0		67.0	34.0	0.507463	NM_001144952	A6NMR8|C9JA57|Q86VY3|Q9NTD2|Q9NVB3|Q9P214	Missense_Mutation	SNP	ENST00000392650.3	37	CCDS45769.1	0	0.0	0	0.0	0	0.0	0	0.0	0	0.0	G	23.3	4.399737	0.83120	.	.	ENSG00000069188	ENST00000409227;ENST00000392650;ENST00000388726;ENST00000424778;ENST00000316893;ENST00000410094	T;T;T	0.62941	-0.01;0.03;1.29	4.81	4.81	0.61882	.	0.000000	0.85682	D	0.000000	T	0.76905	0.4053	M	0.62723	1.935	0.58432	D	0.999999	D;D	0.89917	1.0;1.0	D;D	0.76575	0.983;0.988	T	0.80042	-0.1548	10	0.87932	D	0	.	16.6634	0.85247	0.0:0.0:1.0:0.0	.	2045;2026	Q58EX2;Q58EX2-3	SDK2_HUMAN;.	M	1669;2045;2026;1202;2045;386	ENSP00000376421:T2045M;ENSP00000373378:T2026M;ENSP00000407098:T1202M	ENSP00000324967:T2045M	T	-	2	0	SDK2	68856364	1.000000	0.71417	0.919000	0.36401	0.935000	0.57460	7.721000	0.84768	2.204000	0.70986	0.563000	0.77884	ACG	A|0.000;G|1.000	0.000	strong		0.637	SDK2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000327598.2	NM_019064	
PRPF4	9128	hgsc.bcm.edu	37	9	116045007	116045007	+	Missense_Mutation	SNP	A	A	C	rs148684386	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr9:116045007A>C	ENST00000374198.4	+	4	579	c.477A>C	c.(475-477)aaA>aaC	p.K159N	PRPF4_ENST00000488937.1_3'UTR|PRPF4_ENST00000374199.4_Missense_Mutation_p.K158N	NM_001244926.1|NM_004697.4	NP_001231855.1|NP_004688.2	O43172	PRP4_HUMAN	pre-mRNA processing factor 4	159					gene expression (GO:0010467)|mRNA splicing, via spliceosome (GO:0000398)|RNA processing (GO:0006396)|RNA splicing (GO:0008380)|RNA splicing, via transesterification reactions (GO:0000375)	Cajal body (GO:0015030)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|spliceosomal complex (GO:0005681)|U4/U6 snRNP (GO:0071001)				NS(1)|breast(2)|endometrium(3)|large_intestine(6)|lung(6)|ovary(2)|pancreas(1)|prostate(2)	23						AAAAGTCCAAAGAAGAGGTAG	0.348																																					p.K159N		Atlas-SNP	.											.	PRPF4	56	.	0			c.A477C						PASS	.	A	ASN/LYS	1,4405	2.1+/-5.4	0,1,2202	78.0	76.0	77.0		477	3.5	1.0	9	dbSNP_134	77	3,8597	2.2+/-6.3	0,3,4297	yes	missense	PRPF4	NM_004697.3	94	0,4,6499	CC,CA,AA		0.0349,0.0227,0.0308	benign	159/523	116045007	4,13002	2203	4300	6503	SO:0001583	missense	9128	exon4			GTCCAAAGAAGAG	AF001687	CCDS6791.1, CCDS59142.1	9q31-q33	2013-10-03	2013-10-03		ENSG00000136875	ENSG00000136875		"""WD repeat domain containing"""	17349	protein-coding gene	gene with protein product	"""PRP4/STK/WD splicing factor"", ""U4/U6 small nuclear ribonucleoprotein Prp4"""	607795	"""PRP4 pre-mRNA processing factor 4 homolog (yeast)"""			9257651, 9404889	Standard	NM_004697		Approved	Prp4p, HPRP4, HPRP4P, PRP4, SNRNP60	uc004bgx.3	O43172	OTTHUMG00000020517	ENST00000374198.4:c.477A>C	9.37:g.116045007A>C	ENSP00000363313:p.Lys159Asn	162.0	0.0	0		127.0	61.0	0.480315	NM_004697	O43445|O43864|Q5T1M8|Q96DG2|Q96IK4	Missense_Mutation	SNP	ENST00000374198.4	37	CCDS6791.1	.	.	.	.	.	.	.	.	.	.	A	12.32	1.901787	0.33535	2.27E-4	3.49E-4	ENSG00000136875	ENST00000374199;ENST00000374198	T;T	0.63417	-0.04;0.01	5.9	3.5	0.40072	.	0.381275	0.33005	N	0.005394	T	0.45054	0.1323	L	0.29908	0.895	0.44012	D	0.996725	B;B	0.06786	0.001;0.001	B;B	0.06405	0.002;0.002	T	0.22521	-1.0214	10	0.35671	T	0.21	.	6.3671	0.21461	0.7403:0.1367:0.123:0.0	.	174;159	Q59EL4;O43172	.;PRP4_HUMAN	N	158;159	ENSP00000363315:K158N;ENSP00000363313:K159N	ENSP00000363313:K159N	K	+	3	2	PRPF4	115084828	1.000000	0.71417	1.000000	0.80357	0.977000	0.68977	1.947000	0.40293	0.462000	0.27095	0.460000	0.39030	AAA	A|0.999;C|0.001	0.001	strong		0.348	PRPF4-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000053708.2	NM_004697	
CDON	50937	hgsc.bcm.edu	37	11	125873796	125873796	+	Splice_Site	SNP	C	C	T			TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr11:125873796C>T	ENST00000392693.3	-	10	2154		c.e10+1		CDON_ENST00000531738.1_Splice_Site|CDON_ENST00000263577.7_Splice_Site	NM_001243597.1|NM_016952.4	NP_001230526.1|NP_058648.4	Q4KMG0	CDON_HUMAN	cell adhesion associated, oncogene regulated						anterior/posterior pattern specification (GO:0009952)|cell adhesion (GO:0007155)|cell fate specification (GO:0001708)|cerebral cortex development (GO:0021987)|embryonic body morphogenesis (GO:0010172)|embryonic retina morphogenesis in camera-type eye (GO:0060059)|lens development in camera-type eye (GO:0002088)|muscle cell differentiation (GO:0042692)|myoblast fusion (GO:0007520)|positive regulation of MAPK cascade (GO:0043410)|positive regulation of muscle cell differentiation (GO:0051149)|positive regulation of neural precursor cell proliferation (GO:2000179)|positive regulation of neuron differentiation (GO:0045666)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of skeletal muscle tissue development (GO:0048643)|positive regulation of small GTPase mediated signal transduction (GO:0051057)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of protein heterodimerization activity (GO:0043497)|skeletal muscle satellite cell differentiation (GO:0014816)|smoothened signaling pathway (GO:0007224)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				breast(2)|central_nervous_system(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(22)|lung(9)|ovary(3)|prostate(2)|skin(4)|stomach(5)|upper_aerodigestive_tract(2)|urinary_tract(1)	61	all_hematologic(175;0.177)	Breast(109;0.00157)|Lung NSC(97;0.0127)|all_lung(97;0.0133)|Medulloblastoma(222;0.0425)|all_neural(223;0.112)		BRCA - Breast invasive adenocarcinoma(274;1.51e-06)|OV - Ovarian serous cystadenocarcinoma(99;0.0604)		CCCTCACTCACCTTTGCTGGT	0.458																																					.		Atlas-SNP	.											.	CDON	137	.	0			c.2026+1G>A						PASS	.						83.0	75.0	78.0					11																	125873796		2201	4299	6500	SO:0001630	splice_region_variant	50937	exon11			CACTCACCTTTGC	AF004841	CCDS8468.1, CCDS58192.1	11q24.2	2013-02-11	2012-12-07		ENSG00000064309	ENSG00000064309		"""Immunoglobulin superfamily / I-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"", ""Fibronectin type III domain containing"""	17104	protein-coding gene	gene with protein product	"""cell adhesion molecule-related/down-regulated by oncogenes"""	608707	"""Cdon homolog (mouse)"""			9214393	Standard	NM_016952		Approved	ORCAM, CDO, CDON1	uc009zbw.3	Q4KMG0	OTTHUMG00000165862	ENST00000392693.3:c.2026+1G>A	11.37:g.125873796C>T		60.0	0.0	0		97.0	5.0	0.0515464	NM_001243597	O14631	Splice_Site	SNP	ENST00000392693.3	37	CCDS58192.1	.	.	.	.	.	.	.	.	.	.	C	14.26	2.483812	0.44147	.	.	ENSG00000064309	ENST00000392693;ENST00000531738;ENST00000263577	.	.	.	6.08	6.08	0.98989	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	20.6634	0.99662	0.0:1.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	-	.	.	CDON	125379006	1.000000	0.71417	1.000000	0.80357	0.161000	0.22273	7.440000	0.80464	2.894000	0.99253	0.655000	0.94253	.	.	.	none		0.458	CDON-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000386749.2	NM_016952	Intron
ZNF560	147741	hgsc.bcm.edu	37	19	9579809	9579809	+	Missense_Mutation	SNP	C	C	A	rs61737643	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr19:9579809C>A	ENST00000301480.4	-	9	797	c.584G>T	c.(583-585)tGt>tTt	p.C195F		NM_152476.2	NP_689689.2	Q96MR9	ZN560_HUMAN	zinc finger protein 560	195					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						TGTTTTTAAACAAAAATTATC	0.313													C|||	5	0.000998403	0.0	0.0029	5008	,	,		18821	0.0		0.003	False		,,,				2504	0.0				p.C195F		Atlas-SNP	.											.	ZNF560	162	.	0			c.G584T						PASS	.	C	PHE/CYS	6,4398		0,6,2196	29.0	30.0	30.0		584	0.9	0.0	19	dbSNP_129	30	23,8571		0,23,4274	yes	missense	ZNF560	NM_152476.2	205	0,29,6470	AA,AC,CC		0.2676,0.1362,0.2231	possibly-damaging	195/791	9579809	29,12969	2202	4297	6499	SO:0001583	missense	147741	exon9			TTTAAACAAAAAT	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.584G>T	19.37:g.9579809C>A	ENSP00000301480:p.Cys195Phe	251.0	0.0	0		194.0	85.0	0.438144	NM_152476	Q495S9|Q495T1	Missense_Mutation	SNP	ENST00000301480.4	37	CCDS12214.1	5	0.0022893772893772895	0	0.0	1	0.0027624309392265192	0	0.0	4	0.005277044854881266	C	4.197	0.035323	0.08148	0.001362	0.002676	ENSG00000198028	ENST00000301480	T	0.05258	3.47	1.99	0.933	0.19471	.	.	.	.	.	T	0.01940	0.0061	N	0.13098	0.295	0.09310	N	1	B	0.32010	0.351	B	0.19148	0.024	T	0.43637	-0.9379	9	0.38643	T	0.18	.	3.29	0.06945	0.0:0.5484:0.2782:0.1734	.	195	Q96MR9	ZN560_HUMAN	F	195	ENSP00000301480:C195F	ENSP00000301480:C195F	C	-	2	0	ZNF560	9440809	0.000000	0.05858	0.000000	0.03702	0.084000	0.17831	-0.516000	0.06282	0.386000	0.24997	0.555000	0.69702	TGT	C|0.997;A|0.003	0.003	strong		0.313	ZNF560-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000449901.1	NM_152476	
ALDH4A1	8659	hgsc.bcm.edu	37	1	19212007	19212007	+	Missense_Mutation	SNP	G	G	A	rs139640415	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr1:19212007G>A	ENST00000375341.3	-	5	670	c.413C>T	c.(412-414)cCg>cTg	p.P138L	ALDH4A1_ENST00000538839.1_Missense_Mutation_p.P138L|MIR4695_ENST00000577305.1_RNA|RP13-279N23.2_ENST00000494072.3_3'UTR|ALDH4A1_ENST00000290597.5_Missense_Mutation_p.P138L|ALDH4A1_ENST00000454547.1_5'UTR|ALDH4A1_ENST00000538309.1_Missense_Mutation_p.P78L	NM_003748.3	NP_003739.2	P30038	AL4A1_HUMAN	aldehyde dehydrogenase 4 family, member A1	138					4-hydroxyproline catabolic process (GO:0019470)|cellular nitrogen compound metabolic process (GO:0034641)|glutamate biosynthetic process (GO:0006537)|proline biosynthetic process (GO:0006561)|proline catabolic process (GO:0006562)|proline catabolic process to glutamate (GO:0010133)|proline metabolic process (GO:0006560)|small molecule metabolic process (GO:0044281)	mitochondrial matrix (GO:0005759)	1-pyrroline-5-carboxylate dehydrogenase activity (GO:0003842)|aldehyde dehydrogenase (NAD) activity (GO:0004029)|electron carrier activity (GO:0009055)|identical protein binding (GO:0042802)			cervix(2)|endometrium(1)|large_intestine(3)|lung(8)|prostate(1)	15		Colorectal(325;3.46e-05)|all_lung(284;0.000321)|Lung NSC(340;0.000398)|Renal(390;0.000518)|Breast(348;0.000812)|Ovarian(437;0.00764)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.00479)|BRCA - Breast invasive adenocarcinoma(304;3.67e-05)|Kidney(64;0.000182)|KIRC - Kidney renal clear cell carcinoma(64;0.00269)|STAD - Stomach adenocarcinoma(196;0.00644)|READ - Rectum adenocarcinoma(331;0.0649)		AGCCCTGCGCGGCCCACTCAG	0.672													G|||	6	0.00119808	0.0008	0.0014	5008	,	,		10477	0.0		0.004	False		,,,				2504	0.0				p.P138L		Atlas-SNP	.											ALDH4A1_ENST00000375341,NS,carcinoma,+1,2	ALDH4A1	72	2	0			c.C413T						PASS	.	G	LEU/PRO,LEU/PRO,LEU/PRO	12,4392		0,12,2190	27.0	25.0	26.0		233,413,413	3.5	0.7	1	dbSNP_134	26	12,8588		0,12,4288	yes	missense,missense,missense	ALDH4A1	NM_001161504.1,NM_003748.3,NM_170726.2	98,98,98	0,24,6478	AA,AG,GG		0.1395,0.2725,0.1846	possibly-damaging,possibly-damaging,possibly-damaging	78/504,138/564,138/564	19212007	24,12980	2202	4300	6502	SO:0001583	missense	8659	exon5			CTGCGCGGCCCAC	U24266	CCDS188.1, CCDS53272.1	1p36	2008-02-05			ENSG00000159423	ENSG00000159423	1.5.1.12	"""Aldehyde dehydrogenases"""	406	protein-coding gene	gene with protein product		606811		ALDH4		8621661	Standard	NM_003748		Approved	P5CDh	uc001bbc.3	P30038	OTTHUMG00000002443	ENST00000375341.3:c.413C>T	1.37:g.19212007G>A	ENSP00000364490:p.Pro138Leu	98.0	0.0	0		44.0	32.0	0.727273	NM_003748	A8K1Q7|B4DGE4|D2D4A3|Q16882|Q53HU4|Q5JNV6|Q8IZ38|Q96IF0|Q9UDI6	Missense_Mutation	SNP	ENST00000375341.3	37	CCDS188.1	3	0.0013736263736263737	0	0.0	0	0.0	0	0.0	3	0.00395778364116095	G	14.66	2.601317	0.46423	0.002725	0.001395	ENSG00000159423	ENST00000290597;ENST00000375341;ENST00000538839;ENST00000538309;ENST00000375335;ENST00000454547;ENST00000375334;ENST00000432718	T;T;T;T;T	0.29397	1.57;1.57;1.57;1.57;1.57	5.41	3.54	0.40534	Aldehyde dehydrogenase domain (1);Aldehyde dehydrogenase, N-terminal (1);Aldehyde/histidinol dehydrogenase (1);	0.237912	0.43416	D	0.000562	T	0.42177	0.1191	M	0.83852	2.665	0.80722	D	1	D	0.53151	0.958	P	0.47864	0.559	T	0.40553	-0.9557	10	0.48119	T	0.1	-36.7716	10.2054	0.43109	0.0751:0.1365:0.7884:0.0	.	138	P30038	AL4A1_HUMAN	L	138;138;138;78;122;36;78;122	ENSP00000290597:P138L;ENSP00000364490:P138L;ENSP00000446071:P138L;ENSP00000442988:P78L;ENSP00000393209:P122L	ENSP00000290597:P138L	P	-	2	0	ALDH4A1	19084594	1.000000	0.71417	0.671000	0.29857	0.115000	0.19883	6.100000	0.71473	0.667000	0.31107	-0.264000	0.10439	CCG	G|0.999;A|0.001	0.001	strong		0.672	ALDH4A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000006954.1		
DDX54	79039	hgsc.bcm.edu	37	12	113596866	113596866	+	Missense_Mutation	SNP	G	G	A	rs1048889	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr12:113596866G>A	ENST00000306014.5	-	20	2489	c.2462C>T	c.(2461-2463)cCg>cTg	p.P821L	DDX54_ENST00000314045.7_Missense_Mutation_p.P822L|Y_RNA_ENST00000363029.1_RNA|CCDC42B_ENST00000335621.6_3'UTR|DDX54_ENST00000549271.1_5'UTR	NM_024072.3	NP_076977.3	Q8TDD1	DDX54_HUMAN	DEAD (Asp-Glu-Ala-Asp) box polypeptide 54	821			P -> L (in dbSNP:rs1048889).		ATP catabolic process (GO:0006200)|intracellular estrogen receptor signaling pathway (GO:0030520)|regulation of transcription, DNA-templated (GO:0006355)|RNA metabolic process (GO:0016070)|RNA processing (GO:0006396)|transcription, DNA-templated (GO:0006351)	membrane (GO:0016020)|nucleolus (GO:0005730)|nucleus (GO:0005634)	ATP binding (GO:0005524)|ATP-dependent RNA helicase activity (GO:0004004)|estrogen receptor binding (GO:0030331)|poly(A) RNA binding (GO:0044822)|receptor binding (GO:0005102)|transcription corepressor activity (GO:0003714)			breast(1)|central_nervous_system(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(8)|lung(8)|ovary(2)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)	31						CTTGAGTTCCGGGCGGACTCG	0.662													G|||	124	0.0247604	0.0023	0.0432	5008	,	,		15410	0.0		0.0805	False		,,,				2504	0.0102				p.P822L		Atlas-SNP	.											.	DDX54	73	.	0			c.C2465T						PASS	.	G	LEU/PRO,,LEU/PRO	56,4350		1,54,2148	17.0	19.0	18.0		2465,,2462	5.1	0.9	12	dbSNP_86	18	498,8102		16,466,3818	yes	missense,utr-3,missense	DDX54,CCDC42B	NM_001111322.1,NM_001144872.1,NM_024072.3	98,,98	17,520,5966	AA,AG,GG		5.7907,1.271,4.2596	benign,,benign	822/883,,821/882	113596866	554,12452	2203	4300	6503	SO:0001583	missense	79039	exon20			AGTTCCGGGCGGA	AF144056	CCDS31907.1, CCDS44984.1	12q24.11	2006-01-30				ENSG00000123064		"""DEAD-boxes"""	20084	protein-coding gene	gene with protein product		611665				12466272	Standard	NM_001111322		Approved	MGC2835, APR-5, DP97	uc001tuq.4	Q8TDD1	OTTHUMG00000169676	ENST00000306014.5:c.2462C>T	12.37:g.113596866G>A	ENSP00000304072:p.Pro821Leu	117.0	0.0	0		86.0	36.0	0.418605	NM_001111322	Q86YT8|Q9BRZ1	Missense_Mutation	SNP	ENST00000306014.5	37	CCDS31907.1	80	0.03663003663003663	3	0.006097560975609756	16	0.04419889502762431	0	0.0	61	0.08047493403693931	G	14.61	2.587399	0.46110	0.01271	0.057907	ENSG00000123064	ENST00000314045;ENST00000306014	T;T	0.09350	2.99;2.99	5.06	5.06	0.68205	.	0.218861	0.40908	D	0.000994	T	0.00496	0.0016	L	0.29908	0.895	0.20074	P	0.9999367728	B;B	0.17667	0.009;0.023	B;B	0.15870	0.013;0.014	T	0.23797	-1.0178	9	0.33141	T	0.24	.	16.5805	0.84713	0.0:0.0:1.0:0.0	rs1048889;rs1048889	822;821	Q8TDD1-2;Q8TDD1	.;DDX54_HUMAN	L	822;821	ENSP00000323858:P822L;ENSP00000304072:P821L	ENSP00000304072:P821L	P	-	2	0	DDX54	112081249	1.000000	0.71417	0.886000	0.34754	0.404000	0.30871	8.858000	0.92256	2.509000	0.84616	0.561000	0.74099	CCG	G|0.963;A|0.037	0.037	strong		0.662	DDX54-002	KNOWN	NAGNAG_splice_site|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000405435.1	NM_024072	
PCM1	5108	hgsc.bcm.edu	37	8	17824674	17824674	+	Missense_Mutation	SNP	C	C	T	rs565676613		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr8:17824674C>T	ENST00000519253.1	+	21	3658	c.3407C>T	c.(3406-3408)gCa>gTa	p.A1136V	PCM1_ENST00000325083.8_Missense_Mutation_p.A1136V|PCM1_ENST00000524226.1_Missense_Mutation_p.A1137V			Q15154	PCM1_HUMAN	pericentriolar material 1	1136					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)	p.A1136V(1)	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)		TCATCATTTGCACCAGGTAGG	0.353			T	"""RET, JAK2"""	"""papillary thyroid, CML, MPD"""																																p.A1136V		Atlas-SNP	.		Dom	yes		8	8p22-p21.3	5108	pericentriolar material 1  (PTC4)		"""E, L"""	PCM1,colon,carcinoma,0,1	PCM1	120	1	1	Substitution - Missense(1)	large_intestine(1)	c.C3407T						PASS	.						43.0	42.0	42.0					8																	17824674		1826	4087	5913	SO:0001583	missense	5108	exon21			CATTTGCACCAGG		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.3407C>T	8.37:g.17824674C>T	ENSP00000431099:p.Ala1136Val	144.0	0.0	0		134.0	82.0	0.61194	NM_006197	Q58F13|Q6P1K7|Q8NB85|Q9BWC1|Q9H4A2	Missense_Mutation	SNP	ENST00000519253.1	37		.	.	.	.	.	.	.	.	.	.	C	15.01	2.707472	0.48412	.	.	ENSG00000078674	ENST00000325083;ENST00000519253;ENST00000524226	T;T;T	0.56776	0.44;0.44;0.44	5.7	4.83	0.62350	.	0.317735	0.40302	N	0.001125	T	0.32882	0.0844	N	0.14661	0.345	0.80722	D	1	P;B;P	0.35575	0.51;0.001;0.51	B;B;B	0.31442	0.13;0.004;0.13	T	0.19976	-1.0289	10	0.40728	T	0.16	-3.1369	11.1977	0.48722	0.0:0.8595:0.0:0.1405	.	1136;1137;1136	E7ETA6;E7EV56;Q15154	.;.;PCM1_HUMAN	V	1136;1136;1137	ENSP00000327077:A1136V;ENSP00000431099:A1136V;ENSP00000430521:A1137V	ENSP00000327077:A1136V	A	+	2	0	PCM1	17868954	1.000000	0.71417	1.000000	0.80357	0.938000	0.57974	2.612000	0.46343	1.584000	0.49913	-0.151000	0.13558	GCA	.	.	none		0.353	PCM1-003	NOVEL	basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000374800.1	NM_006197	
HSD3B1	3283	hgsc.bcm.edu	37	1	120056849	120056849	+	Silent	SNP	C	C	T	rs141977722	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr1:120056849C>T	ENST00000369413.3	+	4	848	c.703C>T	c.(703-705)Ctg>Ttg	p.L235L	HSD3B1_ENST00000528909.1_Silent_p.L235L|HSD3B1_ENST00000235547.6_Silent_p.L237L			P14060	3BHS1_HUMAN	hydroxy-delta-5-steroid dehydrogenase, 3 beta- and steroid delta-isomerase 1	235					androgen biosynthetic process (GO:0006702)|estrogen biosynthetic process (GO:0006703)|glucocorticoid biosynthetic process (GO:0006704)|mineralocorticoid biosynthetic process (GO:0006705)|small molecule metabolic process (GO:0044281)|steroid biosynthetic process (GO:0006694)|steroid metabolic process (GO:0008202)	endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|mitochondrial inner membrane (GO:0005743)|mitochondrial intermembrane space (GO:0005758)|smooth endoplasmic reticulum membrane (GO:0030868)	3-beta-hydroxy-delta5-steroid dehydrogenase activity (GO:0003854)|steroid delta-isomerase activity (GO:0004769)			central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(5)|lung(18)|ovary(2)|prostate(1)|skin(1)	32	all_neural(166;0.219)	all_lung(203;3.16e-06)|Lung NSC(69;2.19e-05)|all_epithelial(167;0.000624)		Lung(183;0.0106)|LUSC - Lung squamous cell carcinoma(189;0.0554)	Trilostane(DB01108)	GGCCCACATTCTGGCCTTGAG	0.512													C|||	2	0.000399361	0.0	0.0	5008	,	,		18576	0.0		0.002	False		,,,				2504	0.0				p.L235L		Atlas-SNP	.											.	HSD3B1	53	.	0			c.C703T						PASS	.	C		0,4406		0,0,2203	64.0	69.0	68.0		703	1.2	1.0	1	dbSNP_134	68	20,8580	11.2+/-40.8	0,20,4280	no	coding-synonymous	HSD3B1	NM_000862.2		0,20,6483	TT,TC,CC		0.2326,0.0,0.1538		235/374	120056849	20,12986	2203	4300	6503	SO:0001819	synonymous_variant	3283	exon4			CACATTCTGGCCT	S45679	CCDS903.1	1p12	2014-06-03			ENSG00000203857	ENSG00000203857	1.1.1.145, 5.3.3.1	"""Short chain dehydrogenase/reductase superfamily / Extended SDR fold"""	5217	protein-coding gene	gene with protein product	"""short chain dehydrogenase/reductase family 11E, member 1"""	109715		HSDB3, HSD3B		2779585, 19027726	Standard	NM_000862		Approved	SDR11E1	uc001ehv.1	P14060	OTTHUMG00000012525	ENST00000369413.3:c.703C>T	1.37:g.120056849C>T		128.0	0.0	0		175.0	65.0	0.371429	NM_000862	A8K691|Q14545|Q8IV65	Silent	SNP	ENST00000369413.3	37	CCDS903.1																																																																																			C|0.998;T|0.002	0.002	strong		0.512	HSD3B1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000034993.3	NM_000862	
CDRT1	374286	hgsc.bcm.edu	37	17	15519029	15519029	+	Silent	SNP	A	A	C			TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr17:15519029A>C	ENST00000395906.3	-	2	599	c.600T>G	c.(598-600)acT>acG	p.T200T	RP11-385D13.1_ENST00000455584.2_Silent_p.T510T	NM_006382.3	NP_006373.2	O95170	CDRT1_HUMAN	CMT1A duplicated region transcript 1	200										endometrium(2)|kidney(1)|large_intestine(4)|lung(1)|stomach(1)|upper_aerodigestive_tract(1)	10				UCEC - Uterine corpus endometrioid carcinoma (92;0.0822)|READ - Rectum adenocarcinoma(2;1.36e-05)|BRCA - Breast invasive adenocarcinoma(8;0.0541)		ATGTGTGCTGAGTTTTGGCTG	0.468																																					p.T200T		Atlas-SNP	.											.	CDRT1	83	.	0			c.T600G						PASS	.						58.0	62.0	61.0					17																	15519029		2202	4297	6499	SO:0001819	synonymous_variant	374286	exon2			GTGCTGAGTTTTG	U65652	CCDS45619.1, CCDS73996.1	17p11	2013-01-10			ENSG00000241322	ENSG00000241322		"""F-boxes / WD-40 domains"", ""WD repeat domain containing"""	14379	protein-coding gene	gene with protein product		604596	"""F-box and WD repeat domain containing 10 pseudogene 1"", ""F-box and WD-40 domain protein 10 pseudogene 1"""	FBXW10P1		9787083, 11381029	Standard	NM_006382		Approved	HREP, SM25H2, FBXW10B		O95170	OTTHUMG00000059074	ENST00000395906.3:c.600T>G	17.37:g.15519029A>C		295.0	0.0	0		272.0	32.0	0.117647	NM_006382	O43848|O95611	Silent	SNP	ENST00000395906.3	37	CCDS45619.1	.	.	.	.	.	.	.	.	.	.	A	3.489	-0.104310	0.06967	.	.	ENSG00000251537	ENST00000455584	.	.	.	3.68	2.66	0.31614	.	.	.	.	.	T	0.27349	0.0671	.	.	.	0.09310	N	0.999996	.	.	.	.	.	.	T	0.18085	-1.0348	4	.	.	.	.	5.4733	0.16682	0.1721:0.0:0.8279:0.0	.	.	.	.	R	525	.	.	L	-	2	0	RP11-385D13.1	15459754	0.007000	0.16637	0.004000	0.12327	0.024000	0.10985	1.274000	0.33132	1.021000	0.39600	0.454000	0.30748	CTC	.	.	none		0.468	CDRT1-007	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000448127.1	NM_006382	
CLEC16A	23274	hgsc.bcm.edu	37	16	11272330	11272330	+	Missense_Mutation	SNP	G	G	A	rs72650689	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr16:11272330G>A	ENST00000409790.1	+	24	3175	c.2945G>A	c.(2944-2946)aGc>aAc	p.S982N	CLEC16A_ENST00000381822.2_Missense_Mutation_p.S69N	NM_015226.2	NP_056041.1			C-type lectin domain family 16, member A									p.0?(1)		breast(1)|central_nervous_system(2)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(10)|lung(12)|ovary(2)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	37						CTGTCCCCCAGCCTCGTCCCT	0.637													G|||	14	0.00279553	0.0008	0.0	5008	,	,		18303	0.0		0.0089	False		,,,				2504	0.0041				p.S982N		Atlas-SNP	.											.	CLEC16A	101	.	1	Whole gene deletion(1)	haematopoietic_and_lymphoid_tissue(1)	c.G2945A						PASS	.	G	ASN/SER	6,4296		0,6,2145	63.0	77.0	72.0		2945	4.6	1.0	16	dbSNP_130	72	64,8436		0,64,4186	yes	missense	CLEC16A	NM_015226.2	46	0,70,6331	AA,AG,GG		0.7529,0.1395,0.5468	possibly-damaging	982/1054	11272330	70,12732	2151	4250	6401	SO:0001583	missense	23274	exon23			CCCCCAGCCTCGT	AB002348	CCDS45409.1, CCDS58423.1	16p13.13	2010-04-27	2007-07-17	2007-07-17	ENSG00000038532	ENSG00000038532		"""C-type lectin domain containing"""	29013	protein-coding gene	gene with protein product		611303	"""KIAA0350"""	KIAA0350		9205841, 17632545	Standard	NM_015226		Approved	Gop-1	uc002dao.3	Q2KHT3	OTTHUMG00000152915	ENST00000409790.1:c.2945G>A	16.37:g.11272330G>A	ENSP00000387122:p.Ser982Asn	106.0	0.0	0		96.0	44.0	0.458333	NM_015226		Missense_Mutation	SNP	ENST00000409790.1	37	CCDS45409.1	9	0.004120879120879121	0	0.0	0	0.0	0	0.0	9	0.011873350923482849	G	26.8	4.771612	0.90108	0.001395	0.007529	ENSG00000038532	ENST00000409790;ENST00000542102;ENST00000381822	T	0.55930	0.49	4.64	4.64	0.57946	.	0.000000	0.85682	D	0.000000	T	0.52058	0.1711	L	0.27053	0.805	0.38000	D	0.934194	D;D	0.67145	0.996;0.967	D;P	0.75484	0.986;0.878	T	0.65878	-0.6061	10	0.72032	D	0.01	-25.0792	15.032	0.71713	0.0:0.0:1.0:0.0	.	69;982	Q2KHT3-3;Q2KHT3	.;CL16A_HUMAN	N	982;982;69	ENSP00000387122:S982N	ENSP00000371244:S69N	S	+	2	0	CLEC16A	11179831	1.000000	0.71417	1.000000	0.80357	0.949000	0.60115	6.910000	0.75741	2.304000	0.77564	0.655000	0.94253	AGC	A|0.006;G|0.994	0.006	strong		0.637	CLEC16A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000328540.2	NM_015226	
HEATR6	63897	hgsc.bcm.edu	37	17	58153586	58153586	+	Missense_Mutation	SNP	G	G	C	rs552733926		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr17:58153586G>C	ENST00000184956.6	-	2	248	c.232C>G	c.(232-234)Ctt>Gtt	p.L78V	HEATR6_ENST00000585712.1_5'Flank|HEATR6_ENST00000585976.1_Missense_Mutation_p.L78V	NM_022070.4	NP_071353.4	Q6AI08	HEAT6_HUMAN	HEAT repeat containing 6	78							poly(A) RNA binding (GO:0044822)			NS(1)|breast(4)|endometrium(5)|kidney(2)|large_intestine(4)|lung(7)|ovary(2)|pancreas(1)|prostate(4)|skin(10)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	44	all_cancers(5;2.25e-13)|Breast(5;4.84e-25)|all_neural(34;0.0878)|Medulloblastoma(34;0.0922)		BRCA - Breast invasive adenocarcinoma(1;5.93e-19)|Epithelial(12;7.59e-12)|all cancers(12;1.26e-10)			TGGACAAGAAGAGCACTAACG	0.368																																					p.L78V		Atlas-SNP	.											.	HEATR6	98	.	0			c.C232G						PASS	.						62.0	55.0	57.0					17																	58153586		2203	4300	6503	SO:0001583	missense	63897	exon2			CAAGAAGAGCACT	BX640819	CCDS11623.1	17q23.2	2007-05-01				ENSG00000068097			24076	protein-coding gene	gene with protein product	"""amplified in breast cancer 1"""					12755490	Standard	NM_022070		Approved	ABC1, FLJ22087	uc002iyk.1	Q6AI08		ENST00000184956.6:c.232C>G	17.37:g.58153586G>C	ENSP00000184956:p.Leu78Val	15.0	0.0	0		24.0	12.0	0.5	NM_022070	B3KXP3|Q6MZX1|Q6MZY2|Q8TDM9|Q9H6B3|Q9H6M7	Missense_Mutation	SNP	ENST00000184956.6	37	CCDS11623.1	.	.	.	.	.	.	.	.	.	.	G	13.22	2.171512	0.38315	.	.	ENSG00000068097	ENST00000184956	T	0.44083	0.93	5.1	3.9	0.45041	Armadillo-like helical (1);	0.069197	0.56097	D	0.000024	T	0.32852	0.0843	M	0.64997	1.995	0.35789	D	0.822271	B	0.31077	0.307	B	0.24701	0.055	T	0.50423	-0.8830	10	0.62326	D	0.03	-11.8567	3.2759	0.06898	0.166:0.0:0.5802:0.2538	.	78	Q6AI08	HEAT6_HUMAN	V	78	ENSP00000184956:L78V	ENSP00000184956:L78V	L	-	1	0	HEATR6	55508368	0.992000	0.36948	1.000000	0.80357	0.989000	0.77384	0.478000	0.22212	2.557000	0.86248	0.644000	0.83932	CTT	.	.	none		0.368	HEATR6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000449165.1	NM_022070	
LINC00283	100874057	hgsc.bcm.edu	37	13	103395769	103395769	+	RNA	SNP	G	G	C	rs117896704	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr13:103395769G>C	ENST00000430111.1	+	0	430									long intergenic non-protein coding RNA 283																		CTTTCAGTTTGGTTTTTAAAT	0.353													G|||	46	0.0091853	0.0	0.0086	5008	,	,		21584	0.0		0.0338	False		,,,				2504	0.0061				p.T2426T		Atlas-SNP	.											.	.	.	.	0			c.C7278G						PASS	.	G		8,1376		0,8,684	87.0	64.0	71.0		7278	2.8	0.0	13	dbSNP_132	71	108,3072		0,108,1482	no	coding-synonymous	CCDC168	NM_001146197.1		0,116,2166	CC,CG,GG		3.3962,0.578,2.5416		2426/7082	103395769	116,4448	692	1590	2282			643677	exon4			CAGTTTGGTTTTT			13q33.1	2012-10-12	2011-08-10	2011-08-10	ENSG00000231633	ENSG00000231633		"""Long non-coding RNAs"""	38809	non-coding RNA	RNA, long non-coding			"""non-protein coding RNA 283"""	NCRNA00283			Standard			Approved				OTTHUMG00000017311		13.37:g.103395769G>C		241.0	0.0	0		203.0	103.0	0.507389	NM_001146197		Silent	SNP	ENST00000430111.1	37																																																																																				G|0.986;C|0.014	0.014	strong		0.353	LINC00283-001	KNOWN	not_organism_supported|basic	antisense	antisense	OTTHUMT00000045714.1		
SEMA3C	10512	hgsc.bcm.edu	37	7	80380645	80380645	+	Silent	SNP	G	G	T	rs138526129		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr7:80380645G>T	ENST00000265361.3	-	16	2212	c.1651C>A	c.(1651-1653)Cga>Aga	p.R551R	SEMA3C_ENST00000544525.1_Silent_p.R569R|SEMA3C_ENST00000419255.2_Silent_p.R551R	NM_006379.3	NP_006370.1	Q99985	SEM3C_HUMAN	sema domain, immunoglobulin domain (Ig), short basic domain, secreted, (semaphorin) 3C	551					axon guidance (GO:0007411)|blood vessel remodeling (GO:0001974)|cardiac right ventricle morphogenesis (GO:0003215)|dichotomous subdivision of terminal units involved in salivary gland branching (GO:0060666)|immune response (GO:0006955)|limb bud formation (GO:0060174)|neural crest cell migration (GO:0001755)|neural tube development (GO:0021915)|outflow tract morphogenesis (GO:0003151)|post-embryonic development (GO:0009791)|pulmonary myocardium development (GO:0003350)|response to drug (GO:0042493)|somitogenesis (GO:0001756)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)	receptor activity (GO:0004872)			NS(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(4)|lung(17)|ovary(1)|skin(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	34						TCTTGTCTTCGGCTCCTCCTG	0.388																																					p.R551R		Atlas-SNP	.											.	SEMA3C	106	.	0			c.C1651A						PASS	.	G		0,4406		0,0,2203	155.0	137.0	143.0		1651	4.7	1.0	7	dbSNP_134	143	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous	SEMA3C	NM_006379.3		0,1,6502	TT,TG,GG		0.0116,0.0,0.0077		551/752	80380645	1,13005	2203	4300	6503	SO:0001819	synonymous_variant	10512	exon16			GTCTTCGGCTCCT	AB000220	CCDS5596.1	7q21-q31	2013-01-11			ENSG00000075223	ENSG00000075223		"""Semaphorins"", ""Immunoglobulin superfamily / I-set domain containing"""	10725	protein-coding gene	gene with protein product		602645		SEMAE		7748561, 9168980	Standard	NM_006379		Approved	SemE	uc003uhj.3	Q99985	OTTHUMG00000023447	ENST00000265361.3:c.1651C>A	7.37:g.80380645G>T		210.0	0.0	0		251.0	151.0	0.601594	NM_006379	B4DRL8	Silent	SNP	ENST00000265361.3	37	CCDS5596.1																																																																																			G|1.000;T|0.000	0.000	weak		0.388	SEMA3C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253279.1	NM_006379	
TJP2	9414	hgsc.bcm.edu	37	9	71851969	71851969	+	Missense_Mutation	SNP	T	T	C			TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr9:71851969T>C	ENST00000377245.4	+	14	2304	c.2096T>C	c.(2095-2097)cTg>cCg	p.L699P	TJP2_ENST00000539225.1_Missense_Mutation_p.L730P|TJP2_ENST00000453658.2_Missense_Mutation_p.L676P|TJP2_ENST00000348208.4_Missense_Mutation_p.L699P|TJP2_ENST00000535702.1_Missense_Mutation_p.L703P|TJP2_ENST00000265384.7_Missense_Mutation_p.L699P	NM_004817.3	NP_004808.2	Q9UDY2	ZO2_HUMAN	tight junction protein 2	699	Guanylate kinase-like. {ECO:0000255|PROSITE-ProRule:PRU00100}.				apoptotic process (GO:0006915)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|hippo signaling (GO:0035329)|nucleotide phosphorylation (GO:0046939)|response to organic substance (GO:0010033)	cell junction (GO:0030054)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleoplasm (GO:0005654)|plasma membrane (GO:0005886)|tight junction (GO:0005923)	guanylate kinase activity (GO:0004385)			NS(1)|breast(1)|central_nervous_system(1)|endometrium(8)|kidney(2)|large_intestine(5)|lung(9)|prostate(3)|skin(3)|soft_tissue(1)|upper_aerodigestive_tract(1)	35						AAGAAGAACCTGAGGAAAAGT	0.532																																					p.L730P		Atlas-SNP	.											.	TJP2	120	.	0			c.T2189C						PASS	.						155.0	165.0	162.0					9																	71851969		2203	4300	6503	SO:0001583	missense	9414	exon14			AGAACCTGAGGAA	L27476	CCDS6627.1, CCDS6628.1, CCDS55314.1, CCDS55315.1, CCDS55316.1, CCDS55317.1	9q13-q21	2012-07-12	2012-07-12		ENSG00000119139	ENSG00000119139			11828	protein-coding gene	gene with protein product	"""Friedreich ataxia region gene X104 (tight junction protein ZO-2)"", ""zona occludens 2"""	607709	"""deafness, autosomal dominant 51"""	DFNA51		7951235, 20602916	Standard	NM_001170630		Approved	ZO-2, X104, ZO2	uc011lrv.2	Q9UDY2	OTTHUMG00000019978	ENST00000377245.4:c.2096T>C	9.37:g.71851969T>C	ENSP00000366453:p.Leu699Pro	155.0	0.0	0		148.0	68.0	0.459459	NM_001170416	A2A3H9|B7Z2R8|B7Z7T6|F5H301|F5H886|Q15883|Q5VXL0|Q5VXL1|Q8N756|Q8NI14|Q99839|Q9UDY0|Q9UDY1	Missense_Mutation	SNP	ENST00000377245.4	37	CCDS6627.1	.	.	.	.	.	.	.	.	.	.	T	16.54	3.152156	0.57259	.	.	ENSG00000119139	ENST00000453658;ENST00000377245;ENST00000348208;ENST00000265384;ENST00000535702;ENST00000539225	T;T;T;T;T;T	0.12361	2.72;2.69;2.72;2.71;2.7;2.74	5.77	5.77	0.91146	Src homology-3 domain (1);Guanylate kinase/L-type calcium channel (1);Guanylate kinase (1);	0.374098	0.27927	N	0.017282	T	0.36853	0.0982	M	0.82056	2.57	0.58432	D	0.999998	P;P;D;D;D	0.67145	0.853;0.919;0.963;0.996;0.995	P;P;P;D;D	0.68943	0.502;0.888;0.679;0.95;0.961	T	0.19386	-1.0307	10	0.87932	D	0	.	10.6932	0.45884	0.0:0.0712:0.0:0.9288	.	730;703;699;699;699	F5H301;F5H886;Q9UDY2-2;Q9UDY2;Q9UDY2-5	.;.;.;ZO2_HUMAN;.	P	676;699;699;699;703;730	ENSP00000392178:L676P;ENSP00000366453:L699P;ENSP00000345893:L699P;ENSP00000265384:L699P;ENSP00000442090:L703P;ENSP00000438262:L730P	ENSP00000265384:L699P	L	+	2	0	TJP2	71041789	0.994000	0.37717	0.014000	0.15608	0.620000	0.37586	6.251000	0.72441	2.330000	0.79161	0.528000	0.53228	CTG	.	.	none		0.532	TJP2-003	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000052572.2	NM_201629	
CIDEB	27141	hgsc.bcm.edu	37	14	24775287	24775287	+	Silent	SNP	G	G	A	rs139893717	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr14:24775287G>A	ENST00000336557.5	-	7	1695	c.393C>T	c.(391-393)atC>atT	p.I131I	CIDEB_ENST00000554411.1_Silent_p.I131I|LTB4R2_ENST00000528054.1_5'Flank|NOP9_ENST00000267425.3_3'UTR|CIDEB_ENST00000258807.5_Silent_p.I131I			Q9UHD4	CIDEB_HUMAN	cell death-inducing DFFA-like effector b	131					apoptotic process (GO:0006915)|execution phase of apoptosis (GO:0097194)|intrinsic apoptotic signaling pathway in response to DNA damage (GO:0008630)|regulation of apoptotic process (GO:0042981)	cytosol (GO:0005829)|lipid particle (GO:0005811)	identical protein binding (GO:0042802)			NS(1)|endometrium(1)|kidney(1)|large_intestine(3)|urinary_tract(1)	7				GBM - Glioblastoma multiforme(265;0.0181)		TGAATCGGGCGATGTCCTTGC	0.527													G|||	8	0.00159744	0.0	0.0072	5008	,	,		21522	0.0		0.002	False		,,,				2504	0.001				p.I131I		Atlas-SNP	.											.	CIDEB	17	.	0			c.C393T						PASS	.	G		9,4397	15.5+/-35.6	0,9,2194	196.0	166.0	176.0		393	0.1	1.0	14	dbSNP_134	176	72,8528	43.1+/-100.9	1,70,4229	no	coding-synonymous	CIDEB	NM_014430.2		1,79,6423	AA,AG,GG		0.8372,0.2043,0.6228		131/220	24775287	81,12925	2203	4300	6503	SO:0001819	synonymous_variant	27141	exon6			TCGGGCGATGTCC	AF190901	CCDS32056.1	14q12	2012-09-20			ENSG00000136305	ENSG00000136305			1977	protein-coding gene	gene with protein product		604441				10619428, 10837461	Standard	XM_005267540		Approved		uc001woo.3	Q9UHD4	OTTHUMG00000171555	ENST00000336557.5:c.393C>T	14.37:g.24775287G>A		53.0	0.0	0		83.0	53.0	0.638554	NM_014430	D3DS73|Q546V8|Q9NNW9	Silent	SNP	ENST00000336557.5	37	CCDS32056.1																																																																																			G|0.995;A|0.005	0.005	strong		0.527	CIDEB-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000414120.1		
KL	9365	hgsc.bcm.edu	37	13	33635910	33635910	+	Silent	SNP	T	T	C			TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr13:33635910T>C	ENST00000380099.3	+	4	2702	c.2694T>C	c.(2692-2694)gcT>gcC	p.A898A	KL_ENST00000487852.1_3'UTR	NM_004795.3	NP_004786.2	Q9UEF7	KLOT_HUMAN	klotho	898	Glycosyl hydrolase-1 2.				acute inflammatory response (GO:0002526)|aging (GO:0007568)|calcium ion homeostasis (GO:0055074)|carbohydrate metabolic process (GO:0005975)|energy reserve metabolic process (GO:0006112)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|innate immune response (GO:0045087)|insulin receptor signaling pathway (GO:0008286)|neurotrophin TRK receptor signaling pathway (GO:0048011)|phosphatidylinositol-mediated signaling (GO:0048015)|positive regulation of bone mineralization (GO:0030501)|positive regulation of MAPKKK cascade by fibroblast growth factor receptor signaling pathway (GO:0090080)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	beta-glucosidase activity (GO:0008422)|beta-glucuronidase activity (GO:0004566)|fibroblast growth factor binding (GO:0017134)|signal transducer activity (GO:0004871)|vitamin D binding (GO:0005499)			breast(2)|endometrium(5)|kidney(3)|large_intestine(10)|lung(14)|ovary(2)|skin(5)	41	all_epithelial(80;0.133)	Ovarian(182;1.78e-06)|Breast(139;4.08e-05)|Hepatocellular(188;0.00886)|Lung SC(185;0.0262)		GBM - Glioblastoma multiforme(144;7.13e-230)|all cancers(112;1.33e-165)|OV - Ovarian serous cystadenocarcinoma(117;1.09e-113)|Epithelial(112;3.79e-112)|Lung(94;8.52e-27)|LUSC - Lung squamous cell carcinoma(192;1.4e-13)|Kidney(163;3.04e-09)|KIRC - Kidney renal clear cell carcinoma(186;5.63e-08)|BRCA - Breast invasive adenocarcinoma(63;1.41e-05)		TAAACGAAGCTCTCAAAGGTA	0.473																																					p.A898A		Atlas-SNP	.											.	KL	106	.	0			c.T2694C						PASS	.						77.0	81.0	79.0					13																	33635910		2203	4300	6503	SO:0001819	synonymous_variant	9365	exon4			CGAAGCTCTCAAA	AB005142	CCDS9347.1	13q12	2008-02-05			ENSG00000133116	ENSG00000133116			6344	protein-coding gene	gene with protein product		604824				9464267	Standard	NM_004795		Approved		uc001uus.3	Q9UEF7	OTTHUMG00000017408	ENST00000380099.3:c.2694T>C	13.37:g.33635910T>C		17.0	0.0	0		18.0	11.0	0.611111	NM_004795	Q5VZ95|Q96KV5|Q96KW5|Q9UEI9|Q9Y4F0	Silent	SNP	ENST00000380099.3	37	CCDS9347.1																																																																																			.	.	none		0.473	KL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045987.1		
ANKS3	124401	hgsc.bcm.edu	37	16	4776685	4776685	+	Missense_Mutation	SNP	C	C	T			TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr16:4776685C>T	ENST00000304283.4	-	5	760	c.466G>A	c.(466-468)Gac>Aac	p.D156N	ANKS3_ENST00000585773.1_Missense_Mutation_p.D83N|ANKS3_ENST00000450067.2_Intron|ANKS3_ENST00000592711.1_Intron|ANKS3_ENST00000446014.2_Missense_Mutation_p.D27N	NM_133450.3	NP_597707.1	Q6ZW76	ANKS3_HUMAN	ankyrin repeat and sterile alpha motif domain containing 3	156										endometrium(5)|kidney(4)|large_intestine(3)|lung(5)|prostate(1)|stomach(1)	19						GCTCCACTGTCCAAGAGGAAC	0.567																																					p.D156N		Atlas-SNP	.											.	ANKS3	44	.	0			c.G466A						PASS	.						95.0	78.0	84.0					16																	4776685		2197	4300	6497	SO:0001583	missense	124401	exon5			CACTGTCCAAGAG	AK057329	CCDS10520.1, CCDS73820.1	16p13.3	2013-01-10			ENSG00000168096	ENSG00000168096		"""Sterile alpha motif (SAM) domain containing"", ""Ankyrin repeat domain containing"""	29422	protein-coding gene	gene with protein product						11853319	Standard	NM_133450		Approved	KIAA1977, FLJ32345, FLJ32767	uc002cxj.2	Q6ZW76	OTTHUMG00000129478	ENST00000304283.4:c.466G>A	16.37:g.4776685C>T	ENSP00000304586:p.Asp156Asn	91.0	0.0	0		102.0	5.0	0.0490196	NM_133450	B4DWU4|D3DUE2|Q8TF25	Missense_Mutation	SNP	ENST00000304283.4	37	CCDS10520.1	.	.	.	.	.	.	.	.	.	.	C	24.1	4.496348	0.85069	.	.	ENSG00000168096	ENST00000304283;ENST00000446014	T;T	0.65732	-0.12;-0.17	5.35	5.35	0.76521	Ankyrin repeat-containing domain (4);	0.136125	0.64402	D	0.000003	T	0.66317	0.2777	L	0.41573	1.285	0.80722	D	1	P	0.47253	0.892	P	0.51055	0.657	T	0.68416	-0.5414	10	0.62326	D	0.03	-17.1943	18.4258	0.90608	0.0:1.0:0.0:0.0	.	156	Q6ZW76	ANKS3_HUMAN	N	156;27	ENSP00000304586:D156N;ENSP00000406796:D27N	ENSP00000304586:D156N	D	-	1	0	ANKS3	4716686	1.000000	0.71417	1.000000	0.80357	0.975000	0.68041	7.445000	0.80570	2.675000	0.91044	0.555000	0.69702	GAC	.	.	none		0.567	ANKS3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251642.3	NM_133450	
NDUFA13	51079	hgsc.bcm.edu	37	19	19627083	19627083	+	Silent	SNP	G	G	C	rs11552886		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr19:19627083G>C	ENST00000507754.4	+	1	520	c.36G>C	c.(34-36)ccG>ccC	p.P12P	NDUFA13_ENST00000512771.3_Silent_p.P12P|TSSK6_ENST00000360913.3_5'Flank|CTC-260F20.3_ENST00000555938.1_Silent_p.P12P|NDUFA13_ENST00000428459.2_Silent_p.P12P|TSSK6_ENST00000585580.3_5'Flank|YJEFN3_ENST00000608404.1_Silent_p.P12P|NDUFA13_ENST00000503283.1_Silent_p.P12P|NDUFA13_ENST00000252576.5_Silent_p.P95P|CTC-260F20.3_ENST00000586674.1_3'UTR			Q9P0J0	NDUAD_HUMAN	NADH dehydrogenase (ubiquinone) 1 alpha subcomplex, 13	12					apoptotic signaling pathway (GO:0097190)|cellular metabolic process (GO:0044237)|cellular response to interferon-beta (GO:0035458)|cellular response to retinoic acid (GO:0071300)|negative regulation of cell growth (GO:0030308)|negative regulation of intrinsic apoptotic signaling pathway (GO:2001243)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043280)|positive regulation of peptidase activity (GO:0010952)|positive regulation of protein catabolic process (GO:0045732)|protein import into mitochondrial inner membrane (GO:0045039)|reactive oxygen species metabolic process (GO:0072593)|respiratory electron transport chain (GO:0022904)|small molecule metabolic process (GO:0044281)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|mitochondrial inner membrane (GO:0005743)|mitochondrial membrane (GO:0031966)|mitochondrial respiratory chain (GO:0005746)|mitochondrial respiratory chain complex I (GO:0005747)|mitochondrion (GO:0005739)|nucleoplasm (GO:0005654)	ATP binding (GO:0005524)|NADH dehydrogenase (ubiquinone) activity (GO:0008137)|NADH dehydrogenase activity (GO:0003954)	p.P95P(1)		endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(1)|lung(4)|ovary(1)	12						ACATGCCTCCGCCGGGGGGCT	0.622																																					p.P12P		Atlas-SNP	.											NDUFA13,NS,carcinoma,0,1	NDUFA13	17	1	1	Substitution - coding silent(1)	ovary(1)	c.G36C						scavenged	.						38.0	43.0	41.0					19																	19627083		2203	4300	6503	SO:0001819	synonymous_variant	51079	exon1			GCCTCCGCCGGGG	AF261134	CCDS12404.1, CCDS12404.2	19p13.11	2011-07-04			ENSG00000186010	ENSG00000186010		"""Mitochondrial respiratory chain complex / Complex I"""	17194	protein-coding gene	gene with protein product	"""complex I B16.6 subunit"""	609435				12837546, 10924506, 15367666	Standard	NM_015965		Approved	CGI-39, CDA016, GRIM-19, GRIM19, B16.6		Q9P0J0	OTTHUMG00000162211	ENST00000507754.4:c.36G>C	19.37:g.19627083G>C		262.0	2.0	0.00763359		243.0	112.0	0.460905	NM_015965	B4DF76|K7EK58|Q6PKI0|Q9H2L3|Q9Y327	Silent	SNP	ENST00000507754.4	37	CCDS12404.2																																																																																			.	.	alt		0.622	NDUFA13-001	KNOWN	upstream_ATG|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000367916.6	NM_015965	
FRMPD4	9758	hgsc.bcm.edu	37	X	12720127	12720127	+	Silent	SNP	C	C	T			TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chrX:12720127C>T	ENST00000380682.1	+	10	1574	c.1068C>T	c.(1066-1068)atC>atT	p.I356I		NM_014728.3	NP_055543.2	Q14CM0	FRPD4_HUMAN	FERM and PDZ domain containing 4	356	FERM. {ECO:0000255|PROSITE- ProRule:PRU00084}.				positive regulation of synapse structural plasticity (GO:0051835)	cytoskeleton (GO:0005856)|dendritic spine (GO:0043197)	phosphatidylinositol-4,5-bisphosphate binding (GO:0005546)	p.I346I(1)		breast(1)|central_nervous_system(5)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(7)|lung(1)|ovary(3)|pancreas(1)|skin(3)	22						TCAAATACATCGAGTAAGTGT	0.468											OREG0019670	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.I356I		Atlas-SNP	.											.	FRMPD4	214	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C1068T						PASS	.						124.0	103.0	110.0					X																	12720127		2203	4300	6503	SO:0001819	synonymous_variant	9758	exon10			ATACATCGAGTAA	AB002314	CCDS35201.1	Xp22.31	2006-02-09	2006-02-09	2006-02-09	ENSG00000169933	ENSG00000169933			29007	protein-coding gene	gene with protein product		300838	"""PDZ domain containing 10"""	PDZK10, PDZD10		9205841	Standard	NM_014728		Approved	KIAA0316	uc004cuz.2	Q14CM0	OTTHUMG00000021138	ENST00000380682.1:c.1068C>T	X.37:g.12720127C>T		101.0	0.0	0	682	39.0	39.0	1	NM_014728	A8K0X9|O15032	Silent	SNP	ENST00000380682.1	37	CCDS35201.1																																																																																			.	.	none		0.468	FRMPD4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055771.1	XM_045712	
TSNAX	7257	hgsc.bcm.edu	37	1	231665038	231665038	+	Silent	SNP	C	C	T	rs138421350	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr1:231665038C>T	ENST00000366639.4	+	2	212	c.54C>T	c.(52-54)ttC>ttT	p.F18F	RP11-295G20.2_ENST00000450783.1_RNA|TSNAX-DISC1_ENST00000602962.1_Silent_p.F18F|RP11-295G20.2_ENST00000440665.1_RNA|RP11-295G20.2_ENST00000425412.1_RNA|RP11-295G20.2_ENST00000416221.1_RNA|TSNAX_ENST00000602825.1_3'UTR|RP11-295G20.2_ENST00000454631.1_RNA	NM_005999.2	NP_005990.1	Q99598	TSNAX_HUMAN	translin-associated factor X	18					cell differentiation (GO:0030154)|multicellular organismal development (GO:0007275)|protein transport (GO:0015031)|spermatogenesis (GO:0007283)	Golgi apparatus (GO:0005794)|nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|poly(A) RNA binding (GO:0044822)|protein transporter activity (GO:0008565)|sequence-specific DNA binding (GO:0043565)			endometrium(1)|kidney(1)|large_intestine(2)|lung(5)	9		all_cancers(173;0.0395)|Acute lymphoblastic leukemia(190;3.76e-06)|Prostate(94;0.116)				ATGACAATTTCCCACATAACC	0.398													C|||	3	0.000599042	0.0	0.0014	5008	,	,		18625	0.0		0.0	False		,,,				2504	0.002				p.F18F		Atlas-SNP	.											.	TSNAX	14	.	0			c.C54T						PASS	.	C		2,4404	4.2+/-10.8	0,2,2201	174.0	158.0	163.0		54	2.5	1.0	1	dbSNP_134	163	8,8592	7.1+/-27.0	0,8,4292	no	coding-synonymous	TSNAX	NM_005999.2		0,10,6493	TT,TC,CC		0.093,0.0454,0.0769		18/291	231665038	10,12996	2203	4300	6503	SO:0001819	synonymous_variant	7257	exon2			CAATTTCCCACAT	X95073	CCDS1596.1	1q42.2	2008-02-05			ENSG00000116918	ENSG00000116918			12380	protein-coding gene	gene with protein product		602964				9013868	Standard	NM_005999		Approved	TRAX	uc001huw.3	Q99598	OTTHUMG00000039486	ENST00000366639.4:c.54C>T	1.37:g.231665038C>T		143.0	0.0	0		190.0	67.0	0.352632	NM_005999	B1APC6	Silent	SNP	ENST00000366639.4	37	CCDS1596.1																																																																																			C|0.999;T|0.001	0.001	strong		0.398	TSNAX-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000095267.2	NM_005999	
CLTCL1	8218	hgsc.bcm.edu	37	22	19175133	19175133	+	Silent	SNP	C	C	A	rs187075533	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr22:19175133C>A	ENST00000263200.10	-	29	4614	c.4542G>T	c.(4540-4542)ctG>ctT	p.L1514L	CLTCL1_ENST00000427926.1_Silent_p.L1514L|CLTCL1_ENST00000353891.5_Intron|CLTCL1_ENST00000442042.2_Intron	NM_007098.3	NP_009029.3	P53675	CLH2_HUMAN	clathrin, heavy chain-like 1	1514	Heavy chain arm.|Involved in binding clathrin light chain. {ECO:0000250}.|Proximal segment.				anatomical structure morphogenesis (GO:0009653)|intracellular protein transport (GO:0006886)|mitotic nuclear division (GO:0007067)|positive regulation of glucose import (GO:0046326)|receptor-mediated endocytosis (GO:0006898)|signal transduction (GO:0007165)	clathrin coat of coated pit (GO:0030132)|clathrin coat of trans-Golgi network vesicle (GO:0030130)|clathrin-coated vesicle (GO:0030136)|coated pit (GO:0005905)|coated vesicle (GO:0030135)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|spindle (GO:0005819)|trans-Golgi network (GO:0005802)	signal transducer activity (GO:0004871)|structural molecule activity (GO:0005198)			breast(2)|central_nervous_system(3)|cervix(2)|endometrium(9)|kidney(3)|large_intestine(11)|lung(9)|ovary(5)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	49	Colorectal(54;0.0993)					TGCCCTTGTACAGATAGGCCG	0.552			T	?	ALCL								C|||	5	0.000998403	0.0038	0.0	5008	,	,		22029	0.0		0.0	False		,,,				2504	0.0				p.L1514L		Atlas-SNP	.		Dom	yes		22	22q11.21	8218	"""clathrin, heavy polypeptide-like 1"""		L	.	CLTCL1	115	.	0			c.G4542T						PASS	.	C	,	6,4122		0,6,2058	103.0	106.0	105.0		,4542	0.4	0.8	22		105	2,8402		0,2,4200	no	intron,coding-synonymous	CLTCL1	NM_001835.3,NM_007098.3	,	0,8,6258	AA,AC,CC		0.0238,0.1453,0.0638	,	,1514/1641	19175133	8,12524	2064	4202	6266	SO:0001819	synonymous_variant	8218	exon29			CTTGTACAGATAG		CCDS46662.1, CCDS54497.1, CCDS46662.2, CCDS54497.2	22q11.2	2008-06-10	2006-09-29		ENSG00000070371	ENSG00000070371			2093	protein-coding gene	gene with protein product		601273	"""clathrin, heavy polypeptide-like 1"""	CLTCL		8844170, 15133132	Standard	NM_007098		Approved	CLTD, CLH22, CHC22	uc021wle.1	P53675	OTTHUMG00000150109	ENST00000263200.10:c.4542G>T	22.37:g.19175133C>A		278.0	0.0	0		215.0	108.0	0.502326	NM_007098	B7Z7U5|Q14017|Q15808|Q15809	Silent	SNP	ENST00000263200.10	37	CCDS46662.1																																																																																			C|0.999;A|0.001	0.001	strong		0.552	CLTCL1-001	KNOWN	non_canonical_genome_sequence_error|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000316397.5	NM_007098	
KRTAP6-1	337966	hgsc.bcm.edu	37	21	31986163	31986163	+	Missense_Mutation	SNP	C	C	T	rs138494765		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr21:31986163C>T	ENST00000329122.2	-	1	86	c.61G>A	c.(61-63)Gga>Aga	p.G21R	KRTAP20-1_ENST00000334664.2_5'Flank	NM_181602.1	NP_853633.1	Q3LI64	KRA61_HUMAN	keratin associated protein 6-1	21						cytosol (GO:0005829)|intermediate filament (GO:0005882)				breast(2)|endometrium(1)|lung(7)	10						CCCAGGCCTCCATAGCCACAG	0.592																																					p.G21R		Atlas-SNP	.											.	KRTAP6-1	21	.	0			c.G61A						PASS	.	C	ARG/GLY	0,4406		0,0,2203	181.0	178.0	179.0		61	3.1	1.0	21	dbSNP_134	179	2,8598	2.2+/-6.3	0,2,4298	yes	missense	KRTAP6-1	NM_181602.1	125	0,2,6501	TT,TC,CC		0.0233,0.0,0.0154	benign	21/72	31986163	2,13004	2203	4300	6503	SO:0001583	missense	337966	exon1			GGCCTCCATAGCC	AP001708	CCDS13602.1	21q22.1	2006-03-13			ENSG00000184724	ENSG00000184724		"""Keratin associated proteins"""	18931	protein-coding gene	gene with protein product						12359730	Standard	NM_181602		Approved	KAP6.1, C21orf103	uc002yop.3	Q3LI64	OTTHUMG00000057788	ENST00000329122.2:c.61G>A	21.37:g.31986163C>T	ENSP00000332690:p.Gly21Arg	267.0	0.0	0		383.0	158.0	0.412533	NM_181602		Missense_Mutation	SNP	ENST00000329122.2	37	CCDS13602.1	.	.	.	.	.	.	.	.	.	.	C	11.99	1.802250	0.31869	0.0	2.33E-4	ENSG00000184724	ENST00000329122	T	0.23552	1.9	4.91	3.08	0.35506	.	0.237368	0.21800	U	0.068932	T	0.20740	0.0499	.	.	.	0.26580	N	0.973391	B	0.28552	0.215	B	0.28991	0.097	T	0.17899	-1.0354	9	0.87932	D	0	.	8.6058	0.33773	0.0:0.7606:0.1541:0.0853	.	21	Q3LI64	KRA61_HUMAN	R	21	ENSP00000332690:G21R	ENSP00000332690:G21R	G	-	1	0	KRTAP6-1	30908034	0.000000	0.05858	0.982000	0.44146	0.940000	0.58332	-1.080000	0.03407	0.786000	0.33708	0.643000	0.83706	GGA	C|1.000;T|0.000	0.000	weak		0.592	KRTAP6-1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000128240.2	NM_181602	
RELN	5649	hgsc.bcm.edu	37	7	103292201	103292201	+	Missense_Mutation	SNP	G	G	A	rs78008536	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr7:103292201G>A	ENST00000428762.1	-	15	1958	c.1799C>T	c.(1798-1800)tCc>tTc	p.S600F	RELN_ENST00000424685.2_Missense_Mutation_p.S600F|RELN_ENST00000343529.5_Missense_Mutation_p.S600F	NM_005045.3	NP_005036.2	P78509	RELN_HUMAN	reelin	600					associative learning (GO:0008306)|axon guidance (GO:0007411)|brain development (GO:0007420)|cell adhesion (GO:0007155)|cell morphogenesis involved in differentiation (GO:0000904)|central nervous system development (GO:0007417)|cerebral cortex tangential migration (GO:0021800)|dendrite development (GO:0016358)|glial cell differentiation (GO:0010001)|hippocampus development (GO:0021766)|lateral motor column neuron migration (GO:0097477)|layer formation in cerebral cortex (GO:0021819)|long-term memory (GO:0007616)|N-methyl-D-aspartate receptor clustering (GO:0097114)|neuron migration (GO:0001764)|peptidyl-tyrosine phosphorylation (GO:0018108)|positive regulation of alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity (GO:2000969)|positive regulation of CREB transcription factor activity (GO:0032793)|positive regulation of dendritic spine morphogenesis (GO:0061003)|positive regulation of excitatory postsynaptic membrane potential (GO:2000463)|positive regulation of lateral motor column neuron migration (GO:1902078)|positive regulation of long-term synaptic potentiation (GO:1900273)|positive regulation of neuron projection development (GO:0010976)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|positive regulation of phosphatidylinositol 3-kinase signaling (GO:0014068)|positive regulation of protein kinase activity (GO:0045860)|positive regulation of protein tyrosine kinase activity (GO:0061098)|positive regulation of small GTPase mediated signal transduction (GO:0051057)|positive regulation of synapse maturation (GO:0090129)|positive regulation of synaptic transmission, glutamatergic (GO:0051968)|positive regulation of TOR signaling (GO:0032008)|postsynaptic density protein 95 clustering (GO:0097119)|receptor localization to synapse (GO:0097120)|reelin-mediated signaling pathway (GO:0038026)|regulation of behavior (GO:0050795)|regulation of N-methyl-D-aspartate selective glutamate receptor activity (GO:2000310)|regulation of synaptic transmission (GO:0050804)|response to pain (GO:0048265)|spinal cord patterning (GO:0021511)|ventral spinal cord development (GO:0021517)	cytoplasm (GO:0005737)|dendrite (GO:0030425)|extracellular space (GO:0005615)|proteinaceous extracellular matrix (GO:0005578)	lipoprotein particle receptor binding (GO:0070325)|metal ion binding (GO:0046872)|protein serine/threonine/tyrosine kinase activity (GO:0004712)|serine-type peptidase activity (GO:0008236)|very-low-density lipoprotein particle receptor binding (GO:0070326)			NS(3)|breast(8)|central_nervous_system(3)|cervix(1)|endometrium(13)|haematopoietic_and_lymphoid_tissue(4)|kidney(6)|large_intestine(43)|lung(101)|ovary(9)|pancreas(2)|prostate(4)|skin(14)|stomach(2)|upper_aerodigestive_tract(12)|urinary_tract(2)	227				COAD - Colon adenocarcinoma(1;8.98e-05)|Colorectal(1;0.00184)		GAGGGACCAGGAGCGCCCATG	0.473													G|||	30	0.00599042	0.0008	0.013	5008	,	,		15954	0.0		0.0169	False		,,,				2504	0.0031				p.S600F	NSCLC(146;835 1944 15585 22231 52158)	Atlas-SNP	.											.	RELN	593	.	0			c.C1799T						PASS	.	G	PHE/SER,PHE/SER	12,4394	19.1+/-41.9	0,12,2191	72.0	58.0	63.0		1799,1799	5.8	1.0	7	dbSNP_131	63	130,8470	66.3+/-128.7	1,128,4171	yes	missense,missense	RELN	NM_005045.3,NM_173054.2	155,155	1,140,6362	AA,AG,GG		1.5116,0.2724,1.0918	probably-damaging,probably-damaging	600/3461,600/3459	103292201	142,12864	2203	4300	6503	SO:0001583	missense	5649	exon15			GACCAGGAGCGCC		CCDS34722.1, CCDS47680.1	7q22	2008-07-18			ENSG00000189056	ENSG00000189056			9957	protein-coding gene	gene with protein product		600514				9049633	Standard	NM_005045		Approved	RL, PRO1598	uc010liz.3	P78509	OTTHUMG00000157247	ENST00000428762.1:c.1799C>T	7.37:g.103292201G>A	ENSP00000392423:p.Ser600Phe	102.0	0.0	0		163.0	71.0	0.435583	NM_173054	A4D0P9|A4D0Q0|Q86UJ0|Q86UJ8|Q8NDV0|Q9UDQ2	Missense_Mutation	SNP	ENST00000428762.1	37	CCDS47680.1	19	0.0086996336996337	1	0.0020325203252032522	5	0.013812154696132596	0	0.0	13	0.017150395778364115	G	26.8	4.768385	0.90020	0.002724	0.015116	ENSG00000189056	ENST00000428762;ENST00000343529;ENST00000424685;ENST00000448171	T;T;T	0.34072	1.38;1.38;1.38	5.8	5.8	0.92144	.	0.055760	0.85682	D	0.000000	T	0.30947	0.0781	L	0.47016	1.485	0.51767	D	0.999932	P;P	0.52061	0.95;0.612	P;B	0.54238	0.746;0.424	T	0.20907	-1.0261	10	0.87932	D	0	.	15.5384	0.76021	0.0:0.1373:0.8627:0.0	.	600;600	P78509-2;P78509	.;RELN_HUMAN	F	600	ENSP00000392423:S600F;ENSP00000345694:S600F;ENSP00000388446:S600F	ENSP00000345694:S600F	S	-	2	0	RELN	103079437	1.000000	0.71417	1.000000	0.80357	0.975000	0.68041	7.513000	0.81739	2.758000	0.94735	0.563000	0.77884	TCC	G|0.990;A|0.010	0.010	strong		0.473	RELN-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000348148.1	NM_005045	
OR8K5	219453	hgsc.bcm.edu	37	11	55927584	55927584	+	Missense_Mutation	SNP	A	A	T	rs141612231	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr11:55927584A>T	ENST00000313447.1	-	1	209	c.210T>A	c.(208-210)gaT>gaA	p.D70E		NM_001004058.2	NP_001004058.2	Q8NH50	OR8K5_HUMAN	olfactory receptor, family 8, subfamily K, member 5	70						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			large_intestine(3)|lung(24)|ovary(2)|pancreas(2)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	34	Esophageal squamous(21;0.00693)	Lung NSC(402;0.197)|all_epithelial(135;0.236)				AATTACCAAGATCAACAAAAG	0.403													A|||	5	0.000998403	0.0015	0.0	5008	,	,		21723	0.0		0.003	False		,,,				2504	0.0				p.D70E		Atlas-SNP	.											.	OR8K5	82	.	0			c.T210A						PASS	.	A	GLU/ASP	4,4398	8.1+/-20.4	0,4,2197	109.0	108.0	109.0		210	-1.8	1.0	11	dbSNP_134	109	44,8548	29.6+/-80.5	0,44,4252	yes	missense	OR8K5	NM_001004058.2	45	0,48,6449	TT,TA,AA		0.5121,0.0909,0.3694	probably-damaging	70/308	55927584	48,12946	2201	4296	6497	SO:0001583	missense	219453	exon1			ACCAAGATCAACA	BK004347	CCDS31521.1	11q11	2012-08-09			ENSG00000181752	ENSG00000181752		"""GPCR / Class A : Olfactory receptors"""	15315	protein-coding gene	gene with protein product							Standard	NM_001004058		Approved		uc010rja.2	Q8NH50	OTTHUMG00000166820	ENST00000313447.1:c.210T>A	11.37:g.55927584A>T	ENSP00000323853:p.Asp70Glu	177.0	0.0	0		193.0	99.0	0.512953	NM_001004058	Q6IFB5	Missense_Mutation	SNP	ENST00000313447.1	37	CCDS31521.1	3	0.0013736263736263737	0	0.0	0	0.0	0	0.0	3	0.00395778364116095	A	15.04	2.715189	0.48622	9.09E-4	0.005121	ENSG00000181752	ENST00000313447	T	0.01152	5.26	3.87	-1.8	0.07907	GPCR, rhodopsin-like superfamily (1);	.	.	.	.	T	0.01976	0.0062	L	0.43701	1.375	0.23260	N	0.998023	D	0.89917	1.0	D	0.83275	0.996	T	0.45381	-0.9265	9	0.87932	D	0	.	4.7748	0.13173	0.4794:0.0:0.3737:0.1469	.	70	Q8NH50	OR8K5_HUMAN	E	70	ENSP00000323853:D70E	ENSP00000323853:D70E	D	-	3	2	OR8K5	55684160	0.000000	0.05858	0.991000	0.47740	0.512000	0.34134	-1.621000	0.02044	-0.081000	0.12662	-0.377000	0.06932	GAT	A|0.998;T|0.002	0.002	strong		0.403	OR8K5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391543.1	NM_001004058	
MUC7	4589	hgsc.bcm.edu	37	4	71347333	71347333	+	Missense_Mutation	SNP	C	C	T	rs72655156	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr4:71347333C>T	ENST00000304887.5	+	3	1062	c.872C>T	c.(871-873)aCa>aTa	p.T291I	MUC7_ENST00000413702.1_Missense_Mutation_p.T291I|MUC7_ENST00000456088.1_Missense_Mutation_p.T291I	NM_152291.2	NP_689504.2	Q8TAX7	MUC7_HUMAN	mucin 7, secreted	291	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)			TCTGCAACTACACCAGCTCCA	0.562													-|||	28	0.00559105	0.0	0.0086	5008	,	,		22130	0.0		0.0199	False		,,,				2504	0.002				p.T291I		Atlas-SNP	.											.	MUC7	91	.	0			c.C872T						PASS	.	C	ILE/THR,ILE/THR,ILE/THR	16,4390		0,16,2187	389.0	355.0	367.0		872,872,872	1.5	0.0	4	dbSNP_131	367	195,8405		1,193,4106	yes	missense,missense,missense	MUC7	NM_001145006.1,NM_001145007.1,NM_152291.2	89,89,89	1,209,6293	TT,TC,CC		2.2674,0.3631,1.6223	probably-damaging,probably-damaging,probably-damaging	291/378,291/378,291/378	71347333	211,12795	2203	4300	6503	SO:0001583	missense	4589	exon4			CAACTACACCAGC	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.872C>T	4.37:g.71347333C>T	ENSP00000302021:p.Thr291Ile	398.0	1.0	0.00251256		409.0	185.0	0.452323	NM_001145007	Q9UCD7|Q9UCD8	Missense_Mutation	SNP	ENST00000304887.5	37	CCDS3541.1	24	0.01098901098901099	0	0.0	6	0.016574585635359115	0	0.0	18	0.023746701846965697	-	9.647	1.140465	0.21205	0.003631	0.022674	ENSG00000171195	ENST00000413702;ENST00000456088;ENST00000304887	T;T;T	0.58210	0.35;0.35;0.35	1.52	1.52	0.23074	.	.	.	.	.	T	0.36276	0.0961	N	0.19112	0.55	0.09310	N	1	D	0.71674	0.998	D	0.74023	0.982	T	0.28713	-1.0035	8	.	.	.	.	8.9663	0.35879	0.0:1.0:0.0:0.0	.	291	Q8TAX7	MUC7_HUMAN	I	291	ENSP00000407422:T291I;ENSP00000400585:T291I;ENSP00000302021:T291I	.	T	+	2	0	MUC7	71381922	0.384000	0.25164	0.002000	0.10522	0.002000	0.02628	3.421000	0.52742	1.122000	0.41944	0.505000	0.49811	ACA	C|0.985;T|0.015	0.015	strong		0.562	MUC7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252168.2	NM_152291	
NOL8	55035	hgsc.bcm.edu	37	9	95076771	95076771	+	Silent	SNP	A	A	C			TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr9:95076771A>C	ENST00000535387.1	-	6	2135	c.2136T>G	c.(2134-2136)tcT>tcG	p.S712S	NOL8_ENST00000358855.4_Silent_p.S644S|NOL8_ENST00000442668.2_Silent_p.S712S|NOL8_ENST00000545558.1_Silent_p.S712S|NOL8_ENST00000542053.1_Silent_p.S644S					nucleolar protein 8											endometrium(3)|kidney(2)|large_intestine(5)|lung(5)|ovary(1)	16						CGCTTGAATCAGACCGCTCTT	0.428																																					p.S712S		Atlas-SNP	.											.	NOL8	118	.	0			c.T2136G						PASS	.						57.0	51.0	53.0					9																	95076771		1899	4115	6014	SO:0001819	synonymous_variant	55035	exon7			TGAATCAGACCGC	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.2136T>G	9.37:g.95076771A>C		98.0	0.0	0		90.0	24.0	0.266667	NM_017948		Silent	SNP	ENST00000535387.1	37	CCDS47993.1																																																																																			.	.	none		0.428	NOL8-010	NOVEL	basic|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000053082.2	NM_017948	
ANKAR	150709	hgsc.bcm.edu	37	2	190569908	190569908	+	Missense_Mutation	SNP	G	G	A	rs116660656	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr2:190569908G>A	ENST00000520309.1	+	8	1956	c.1868G>A	c.(1867-1869)tGt>tAt	p.C623Y	ANKAR_ENST00000431575.2_Missense_Mutation_p.C552Y|ANKAR_ENST00000281412.6_Missense_Mutation_p.C387Y|ANKAR_ENST00000438402.2_Missense_Mutation_p.C623Y|ANKAR_ENST00000313581.4_Missense_Mutation_p.C623Y	NM_144708.3	NP_653309.3	Q7Z5J8	ANKAR_HUMAN	ankyrin and armadillo repeat containing	623				C -> Y (in Ref. 3; AAH47413). {ECO:0000305}.		integral component of membrane (GO:0016021)				breast(3)|central_nervous_system(2)|endometrium(5)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(7)|liver(2)|lung(16)|ovary(2)|pancreas(1)|skin(1)|urinary_tract(2)	46			OV - Ovarian serous cystadenocarcinoma(117;0.00156)|Epithelial(96;0.0256)|all cancers(119;0.0744)			ATTGCTCTCTGTAGGAAGGAT	0.403													G|||	40	0.00798722	0.0008	0.0058	5008	,	,		17427	0.0		0.0258	False		,,,				2504	0.0092				p.C623Y		Atlas-SNP	.											.	ANKAR	184	.	0			c.G1868A						PASS	.	G	TYR/CYS	15,4391	21.2+/-45.6	0,15,2188	145.0	141.0	142.0		1868	3.0	1.0	2	dbSNP_132	142	236,8364	95.9+/-157.7	3,230,4067	yes	missense	ANKAR	NM_144708.3	194	3,245,6255	AA,AG,GG		2.7442,0.3404,1.9299	benign	623/1435	190569908	251,12755	2203	4300	6503	SO:0001583	missense	150709	exon8			CTCTCTGTAGGAA	AJ549812	CCDS33351.1, CCDS33351.2	2q32.2	2013-02-14			ENSG00000151687	ENSG00000151687		"""Ankyrin repeat domain containing"", ""Armadillo repeat containing"""	26350	protein-coding gene	gene with protein product		609803				15110750	Standard	NM_144708		Approved	FLJ25415	uc002uqw.2	Q7Z5J8	OTTHUMG00000154398	ENST00000520309.1:c.1868G>A	2.37:g.190569908G>A	ENSP00000427882:p.Cys623Tyr	306.0	0.0	0		235.0	110.0	0.468085	NM_144708	Q3ZCS6|Q4G0M2|Q6ZU02	Missense_Mutation	SNP	ENST00000520309.1	37	CCDS33351.2	23	0.010531135531135532	1	0.0020325203252032522	2	0.0055248618784530384	0	0.0	20	0.026385224274406333	G	15.26	2.781995	0.49891	0.003404	0.027442	ENSG00000151687	ENST00000520309;ENST00000313581;ENST00000438402;ENST00000431575;ENST00000281412	T;T;T;T;T	0.64260	-0.09;-0.09;-0.09;-0.09;-0.09	5.84	2.97	0.34412	.	0.580099	0.16803	N	0.198888	T	0.30039	0.0752	L	0.33792	1.035	0.40694	D	0.982421	.	.	.	.	.	.	T	0.23762	-1.0179	8	0.35671	T	0.21	-1.9537	7.6426	0.28303	0.4252:0.0:0.5748:0.0	.	.	.	.	Y	623;623;623;552;387	ENSP00000427882:C623Y;ENSP00000313513:C623Y;ENSP00000397243:C623Y;ENSP00000393043:C552Y;ENSP00000281412:C387Y	ENSP00000281412:C387Y	C	+	2	0	ANKAR	190278153	0.095000	0.21747	0.981000	0.43875	0.973000	0.67179	0.169000	0.16641	0.332000	0.23536	-0.345000	0.07892	TGT	G|0.983;A|0.017	0.017	strong		0.403	ANKAR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000335045.3	NM_144708	
GLIS3	169792	hgsc.bcm.edu	37	9	4286248	4286248	+	Missense_Mutation	SNP	G	G	T			TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr9:4286248G>T	ENST00000381971.3	-	2	771	c.178C>A	c.(178-180)Ctc>Atc	p.L60I		NM_001042413.1	NP_001035878.1	Q8NEA6	GLIS3_HUMAN	GLIS family zinc finger 3	0	Ser-rich.				negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|transcription from RNA polymerase II promoter (GO:0006366)	Golgi apparatus (GO:0005794)|nucleus (GO:0005634)	metal ion binding (GO:0046872)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in 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)			NS(1)|breast(1)|central_nervous_system(1)|endometrium(3)|large_intestine(12)|lung(4)|ovary(2)|prostate(1)|skin(1)	26		Acute lymphoblastic leukemia(2;0.00464)|Breast(48;0.148)		Lung(2;0.00163)|GBM - Glioblastoma multiforme(50;0.00301)|LUSC - Lung squamous cell carcinoma(2;0.0148)		GGCATCTTGAGATGGAGGTTG	0.592																																					p.L60I		Atlas-SNP	.											.	GLIS3	152	.	0			c.C178A						PASS	.						64.0	70.0	68.0					9																	4286248		2088	4214	6302	SO:0001583	missense	169792	exon2			TCTTGAGATGGAG	BC033899	CCDS6451.1, CCDS43784.1	9p24.2	2008-05-02	2004-07-16	2004-07-16	ENSG00000107249	ENSG00000107249		"""Zinc fingers, C2H2-type"""	28510	protein-coding gene	gene with protein product		610192	"""zinc finger protein 515"""	ZNF515		14500813	Standard	NM_152629		Approved	MGC33662	uc003zhx.1	Q8NEA6	OTTHUMG00000019463	ENST00000381971.3:c.178C>A	9.37:g.4286248G>T	ENSP00000371398:p.Leu60Ile	149.0	0.0	0		145.0	55.0	0.37931	NM_001042413	B1AL19|Q1PHK5	Missense_Mutation	SNP	ENST00000381971.3	37	CCDS43784.1	.	.	.	.	.	.	.	.	.	.	G	15.26	2.781727	0.49891	.	.	ENSG00000107249	ENST00000381971;ENST00000477901;ENST00000481827	T	0.12361	2.69	5.75	5.75	0.90469	.	.	.	.	.	T	0.19765	0.0475	N	0.24115	0.695	0.29128	N	0.879822	D;P	0.63880	0.993;0.882	P;P	0.61397	0.888;0.477	T	0.06409	-1.0828	9	0.62326	D	0.03	.	8.9189	0.35599	0.1588:0.0:0.8412:0.0	.	60;60	F8WEV9;Q8NEA6-2	.;.	I	60	ENSP00000371398:L60I	ENSP00000371398:L60I	L	-	1	0	GLIS3	4276248	1.000000	0.71417	1.000000	0.80357	0.968000	0.65278	3.698000	0.54771	2.711000	0.92665	0.655000	0.94253	CTC	.	.	none		0.592	GLIS3-008	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000354776.1	NM_152629	
DNAH17	8632	hgsc.bcm.edu	37	17	76488794	76488794	+	Silent	SNP	G	G	A	rs76641546	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr17:76488794G>A	ENST00000585328.1	-	42	6571	c.6447C>T	c.(6445-6447)gcC>gcT	p.A2149A	DNAH17_ENST00000586052.1_5'Flank|RP11-559N14.5_ENST00000591373.1_RNA|RP11-559N14.5_ENST00000585969.1_RNA|RP11-559N14.5_ENST00000588565.1_RNA|DNAH17_ENST00000389840.5_Silent_p.A2140A	NM_173628.3	NP_775899.3	Q9UFH2	DYH17_HUMAN	dynein, axonemal, heavy chain 17	2140	AAA 2. {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)			CCAGGTCCACGGCGACCGGCT	0.587													G|||	17	0.00339457	0.0	0.0043	5008	,	,		16651	0.0		0.0139	False		,,,				2504	0.0				p.A2154A		Atlas-SNP	.											.	DNAH17	347	.	0			c.C6462T						PASS	.	G		7,3935		0,7,1964	63.0	67.0	66.0		6462	-9.5	0.0	17	dbSNP_133	66	78,8248		1,76,4086	no	coding-synonymous	DNAH17	NM_173628.3		1,83,6050	AA,AG,GG		0.9368,0.1776,0.6929		2154/4463	76488794	85,12183	1971	4163	6134	SO:0001819	synonymous_variant	8632	exon42			GTCCACGGCGACC	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.6447C>T	17.37:g.76488794G>A		137.0	0.0	0		129.0	68.0	0.527132	NM_173628	O00431|O15206|Q2M2Y1|Q6ZRQ2|Q8N7Q7	Silent	SNP	ENST00000585328.1	37																																																																																				G|0.994;A|0.006	0.006	strong		0.587	DNAH17-001	PUTATIVE	not_organism_supported|basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000318962.2	NM_173628	
RASL12	51285	hgsc.bcm.edu	37	15	65357558	65357558	+	Silent	SNP	A	A	G	rs36045000	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr15:65357558A>G	ENST00000220062.4	-	2	433	c.157T>C	c.(157-159)Ttg>Ctg	p.L53L	RASL12_ENST00000434605.2_Silent_p.L42L|RASL12_ENST00000421977.3_Intron	NM_016563.2	NP_057647.1	Q9NYN1	RASLC_HUMAN	RAS-like, family 12	53					GTP catabolic process (GO:0006184)|small GTPase mediated signal transduction (GO:0007264)	membrane (GO:0016020)	GTP binding (GO:0005525)			lung(1)|ovary(1)|skin(1)|urinary_tract(1)	4						TTCTTACCCAAGTTGGGGTCA	0.562													A|||	47	0.00938498	0.0227	0.0029	5008	,	,		17164	0.0		0.0129	False		,,,				2504	0.002				p.L53L		Atlas-SNP	.											.	RASL12	32	.	0			c.T157C						PASS	.	A		83,4321	68.7+/-106.4	0,83,2119	133.0	97.0	110.0		157	3.4	1.0	15	dbSNP_126	110	115,8481	59.8+/-121.6	2,111,4185	no	coding-synonymous	RASL12	NM_016563.2		2,194,6304	GG,GA,AA		1.3378,1.8847,1.5231		53/267	65357558	198,12802	2202	4298	6500	SO:0001819	synonymous_variant	51285	exon2			TACCCAAGTTGGG	AF233588	CCDS10200.1	15q11.2-q22.33	2014-05-09			ENSG00000103710	ENSG00000103710			30289	protein-coding gene	gene with protein product	"""Ras family member Ris"""					12107412	Standard	NM_016563		Approved	RIS	uc002aoi.1	Q9NYN1	OTTHUMG00000133115	ENST00000220062.4:c.157T>C	15.37:g.65357558A>G		144.0	0.0	0		101.0	18.0	0.178218	NM_016563	B2RC29|B4DJW2|B4DU82	Silent	SNP	ENST00000220062.4	37	CCDS10200.1																																																																																			A|0.987;G|0.013	0.013	strong		0.562	RASL12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256782.2	NM_016563	
ZNF345	25850	hgsc.bcm.edu	37	19	37368535	37368535	+	Missense_Mutation	SNP	G	G	C	rs112729744	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr19:37368535G>C	ENST00000529555.1	+	2	1591	c.803G>C	c.(802-804)aGt>aCt	p.S268T	ZNF345_ENST00000420450.1_Missense_Mutation_p.S268T|ZNF345_ENST00000432005.2_Intron|ZNF345_ENST00000589046.1_Missense_Mutation_p.S268T|ZNF345_ENST00000526123.1_Intron			Q14585	ZN345_HUMAN	zinc finger protein 345	268					negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|regulation of transcription from RNA polymerase III promoter (GO:0006359)|regulation of transcription, DNA-templated (GO:0006355)|transcription from RNA polymerase II promoter (GO:0006366)|transcription from RNA polymerase III promoter (GO:0006383)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(1)|endometrium(1)|kidney(1)|large_intestine(13)|lung(5)|ovary(2)|prostate(1)	24	Esophageal squamous(110;0.183)		COAD - Colon adenocarcinoma(19;0.114)|Colorectal(19;0.177)			AAGGCCTTTAGTTTTGGATCA	0.418													G|||	10	0.00199681	0.0	0.0058	5008	,	,		21427	0.0		0.006	False		,,,				2504	0.0				p.S268T		Atlas-SNP	.											.	ZNF345	68	.	0			c.G803C						PASS	.	G	THR/SER,THR/SER,THR/SER,THR/SER,THR/SER	11,4395	16.8+/-37.8	0,11,2192	84.0	87.0	86.0		803,803,803,803,803	1.6	1.0	19	dbSNP_132	86	106,8494	57.2+/-118.5	1,104,4195	no	missense,missense,missense,missense,missense	ZNF345	NM_001242472.1,NM_001242474.1,NM_001242475.1,NM_001242476.1,NM_003419.4	58,58,58,58,58	1,115,6387	CC,CG,GG		1.2326,0.2497,0.8996	benign,benign,benign,benign,benign	268/489,268/489,268/489,268/489,268/489	37368535	117,12889	2203	4300	6503	SO:0001583	missense	25850	exon4			CCTTTAGTTTTGG	X78933	CCDS12497.1	19q13.12	2013-01-08			ENSG00000251247	ENSG00000251247		"""Zinc fingers, C2H2-type"""	16367	protein-coding gene	gene with protein product						7865130	Standard	NM_003419		Approved	HZF10	uc002oey.4	Q14585	OTTHUMG00000048162	ENST00000529555.1:c.803G>C	19.37:g.37368535G>C	ENSP00000431202:p.Ser268Thr	123.0	0.0	0		131.0	70.0	0.534351	NM_001242476		Missense_Mutation	SNP	ENST00000529555.1	37	CCDS12497.1	7	0.003205128205128205	0	0.0	3	0.008287292817679558	0	0.0	4	0.005277044854881266	G	4.013	-0.000126	0.07819	0.002497	0.012326	ENSG00000251247	ENST00000420450;ENST00000529555;ENST00000344705	T;T	0.07567	3.18;3.18	3.96	1.58	0.23477	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.04815	0.0130	L	0.31371	0.925	0.09310	N	1	B	0.02656	0.0	B	0.04013	0.001	T	0.33929	-0.9849	9	0.35671	T	0.21	.	11.5634	0.50792	0.0:0.5461:0.4539:0.0	.	268	Q14585	ZN345_HUMAN	T	268;268;32	ENSP00000431216:S268T;ENSP00000431202:S268T	ENSP00000442320:S32T	S	+	2	0	ZNF345	42060375	0.000000	0.05858	1.000000	0.80357	0.994000	0.84299	-0.912000	0.04046	0.347000	0.23924	0.561000	0.74099	AGT	G|0.993;C|0.007	0.007	strong		0.418	ZNF345-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000388258.1		
CDH1	999	hgsc.bcm.edu	37	16	68855966	68855966	+	Missense_Mutation	SNP	G	G	A	rs35187787	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr16:68855966G>A	ENST00000261769.5	+	12	1965	c.1774G>A	c.(1774-1776)Gcc>Acc	p.A592T	CDH1_ENST00000562836.1_3'UTR|CDH1_ENST00000422392.2_Missense_Mutation_p.A531T|RP11-354M1.2_ENST00000563916.1_RNA	NM_004360.3	NP_004351.1	P12830	CADH1_HUMAN	cadherin 1, type 1, E-cadherin (epithelial)	592	Cadherin 4. {ECO:0000255|PROSITE- ProRule:PRU00043}.		A -> T (in a thyroid cancer sample; may play a role in colorectal carcinogenesis; dbSNP:rs35187787). {ECO:0000269|PubMed:11562785, ECO:0000269|PubMed:8985087}.		adherens junction organization (GO:0034332)|apoptotic process (GO:0006915)|calcium-dependent cell-cell adhesion (GO:0016339)|cell junction assembly (GO:0034329)|cell-cell junction organization (GO:0045216)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|cellular response to amino acid stimulus (GO:0071230)|cellular response to indole-3-methanol (GO:0071681)|cellular response to lithium ion (GO:0071285)|cochlea development (GO:0090102)|epithelial cell morphogenesis (GO:0003382)|establishment of protein localization to plasma membrane (GO:0090002)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|homophilic cell adhesion (GO:0007156)|intestinal epithelial cell development (GO:0060576)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of cell-cell adhesion (GO:0022408)|negative regulation of epithelial cell proliferation (GO:0050680)|neuron projection development (GO:0031175)|pituitary gland development (GO:0021983)|positive regulation of transcription factor import into nucleus (GO:0042993)|positive regulation of transcription, DNA-templated (GO:0045893)|protein homooligomerization (GO:0051260)|protein localization to plasma membrane (GO:0072659)|protein metabolic process (GO:0019538)|regulation of branching involved in salivary gland morphogenesis (GO:0060693)|regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043281)|regulation of immune response (GO:0050776)|regulation of neuron migration (GO:2001222)|regulation of protein localization to cell surface (GO:2000008)|regulation of water loss via skin (GO:0033561)|response to drug (GO:0042493)|response to toxic substance (GO:0009636)|salivary gland cavitation (GO:0060662)|sensory perception of sound (GO:0007605)|single organismal cell-cell adhesion (GO:0016337)|synapse assembly (GO:0007416)|tight junction assembly (GO:0070830)|trophectodermal cell differentiation (GO:0001829)	actin cytoskeleton (GO:0015629)|aggresome (GO:0016235)|apical junction complex (GO:0043296)|apical part of cell (GO:0045177)|axon terminus (GO:0043679)|basolateral plasma membrane (GO:0016323)|catenin complex (GO:0016342)|cell junction (GO:0030054)|cell surface (GO:0009986)|cell-cell adherens junction (GO:0005913)|cytoplasm (GO:0005737)|cytoplasmic side of plasma membrane (GO:0009898)|endosome (GO:0005768)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|integral component of membrane (GO:0016021)|lateral loop (GO:0043219)|lateral plasma membrane (GO:0016328)|node of Ranvier (GO:0033268)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|Schmidt-Lanterman incisure (GO:0043220)|trans-Golgi network (GO:0005802)	ankyrin binding (GO:0030506)|beta-catenin binding (GO:0008013)|calcium ion binding (GO:0005509)|cell adhesion molecule binding (GO:0050839)|gamma-catenin binding (GO:0045295)|glycoprotein binding (GO:0001948)|GTPase activating protein binding (GO:0032794)	p.A592T(4)		NS(6)|biliary_tract(8)|breast(161)|central_nervous_system(4)|endometrium(9)|kidney(4)|large_intestine(13)|lung(13)|oesophagus(3)|ovary(2)|prostate(3)|soft_tissue(2)|stomach(76)|thyroid(1)|upper_aerodigestive_tract(3)|urinary_tract(3)	311		all_neural(199;0.0189)|Ovarian(137;0.0563)		Epithelial(162;8.44e-05)|all cancers(182;0.000404)|OV - Ovarian serous cystadenocarcinoma(108;0.000426)|BRCA - Breast invasive adenocarcinoma(181;0.0261)		GAATGACAACGCCCCCATACC	0.458			"""Mis, N, F, S"""		"""lobular breast, gastric"""	gastric			Hereditary Diffuse Gastric Cancer				G|||	6	0.00119808	0.0008	0.0029	5008	,	,		21048	0.0		0.002	False		,,,				2504	0.001				p.A592T		Atlas-SNP	.	yes	Rec	yes	Familial gastric carcinoma	16	16q22.1	999	"""cadherin 1, type 1, E-cadherin (epithelial) (ECAD)"""		E	CDH1,NS,carcinoma,0,4	CDH1	535	4	4	Substitution - Missense(4)	breast(2)|thyroid(1)|stomach(1)	c.G1774A	GRCh37	CM994192	CDH1	M	rs35187787	PASS	.	G	THR/ALA	5,4391	9.9+/-24.2	0,5,2193	133.0	121.0	125.0		1774	5.6	0.1	16	dbSNP_126	125	54,8546	34.3+/-88.2	0,54,4246	yes	missense	CDH1	NM_004360.3	58	0,59,6439	AA,AG,GG		0.6279,0.1137,0.454	possibly-damaging	592/883	68855966	59,12937	2198	4300	6498	SO:0001583	missense	999	exon12	Familial Cancer Database	HDGC	GACAACGCCCCCA	L08599	CCDS10869.1	16q22.1	2014-09-17			ENSG00000039068	ENSG00000039068		"""CD molecules"", ""Cadherins / Major cadherins"""	1748	protein-coding gene	gene with protein product	"""E-Cadherin"""	192090		UVO		9925936	Standard	NM_004360		Approved	uvomorulin, CD324	uc002ewg.1	P12830	OTTHUMG00000137561	ENST00000261769.5:c.1774G>A	16.37:g.68855966G>A	ENSP00000261769:p.Ala592Thr	171.0	0.0	0		161.0	21.0	0.130435	NM_004360	A8K1U7|Q13799|Q14216|Q15855|Q16194|Q4PJ14|Q9UII8	Missense_Mutation	SNP	ENST00000261769.5	37	CCDS10869.1	3	0.0013736263736263737	1	0.0020325203252032522	1	0.0027624309392265192	0	0.0	1	0.0013192612137203166	G	15.26	2.781583	0.49891	0.001137	0.006279	ENSG00000039068	ENST00000261769;ENST00000379120;ENST00000268794;ENST00000422392	T;T	0.61627	0.09;0.09	5.56	5.56	0.83823	Cadherin (4);Cadherin conserved site (1);Cadherin-like (2);	0.595783	0.14702	N	0.303477	T	0.45816	0.1361	L	0.45744	1.44	0.34229	D	0.676292	P;P	0.51791	0.948;0.492	B;B	0.38156	0.266;0.092	T	0.68153	-0.5484	10	0.87932	D	0	.	19.1853	0.93641	0.0:0.0:1.0:0.0	rs35187787	531;592	Q9UII8;P12830	.;CADH1_HUMAN	T	592;610;592;531	ENSP00000261769:A592T;ENSP00000414946:A531T	ENSP00000261769:A592T	A	+	1	0	CDH1	67413467	1.000000	0.71417	0.149000	0.22428	0.254000	0.26022	8.900000	0.92551	2.641000	0.89580	0.536000	0.68110	GCC	A|0.003;G|0.997	0.003	strong		0.458	CDH1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000268897.2	NM_004360	
TYK2	7297	hgsc.bcm.edu	37	19	10463118	10463118	+	Missense_Mutation	SNP	G	G	C	rs34536443	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr19:10463118G>C	ENST00000525621.1	-	23	3791	c.3310C>G	c.(3310-3312)Ccc>Gcc	p.P1104A	TYK2_ENST00000524462.1_Missense_Mutation_p.P919A|TYK2_ENST00000529422.1_Intron|TYK2_ENST00000264818.6_Missense_Mutation_p.P1104A	NM_003331.4	NP_003322.3	P29597	TYK2_HUMAN	tyrosine kinase 2	1104	Protein kinase 2. {ECO:0000255|PROSITE- ProRule:PRU00159}.		P -> A (in dbSNP:rs34536443). {ECO:0000269|PubMed:17344846}.		cytokine-mediated signaling pathway (GO:0019221)|intracellular signal transduction (GO:0035556)|peptidyl-tyrosine phosphorylation (GO:0018108)|protein phosphorylation (GO:0006468)|regulation of type I interferon-mediated signaling pathway (GO:0060338)|type I interferon signaling pathway (GO:0060337)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|nucleus (GO:0005634)	ATP binding (GO:0005524)|growth hormone receptor binding (GO:0005131)|non-membrane spanning protein tyrosine kinase activity (GO:0004715)|protein tyrosine kinase activity (GO:0004713)			breast(1)|central_nervous_system(1)|endometrium(12)|haematopoietic_and_lymphoid_tissue(11)|kidney(6)|large_intestine(3)|lung(19)|ovary(4)|prostate(3)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	64			OV - Ovarian serous cystadenocarcinoma(20;1.77e-09)|Epithelial(33;3.92e-06)|all cancers(31;8.95e-06)			ACCGTGGGGGGGCTCTGGCTG	0.592													g|||	51	0.0101837	0.0015	0.0202	5008	,	,		14995	0.0		0.0288	False		,,,				2504	0.0061				p.P1104A		Atlas-SNP	.											.	TYK2	126	.	0			c.C3310G	GRCh37	CM070300	TYK2	M	rs34536443	PASS	.	G	ALA/PRO	30,4376	36.0+/-67.5	0,30,2173	69.0	76.0	73.0		3310	4.3	1.0	19	dbSNP_126	73	347,8253	117.0+/-176.6	4,339,3957	yes	missense	TYK2	NM_003331.4	27	4,369,6130	CC,CG,GG		4.0349,0.6809,2.8987	probably-damaging	1104/1188	10463118	377,12629	2203	4300	6503	SO:0001583	missense	7297	exon23			TGGGGGGGCTCTG		CCDS12236.1	19p13.2	2014-09-17			ENSG00000105397	ENSG00000105397	2.7.10.1		12440	protein-coding gene	gene with protein product		176941				2156206	Standard	NM_003331		Approved	JTK1	uc002moc.4	P29597	OTTHUMG00000166373	ENST00000525621.1:c.3310C>G	19.37:g.10463118G>C	ENSP00000431885:p.Pro1104Ala	213.0	1.0	0.00469484		260.0	160.0	0.615385	NM_003331	Q6QB10|Q96CH0	Missense_Mutation	SNP	ENST00000525621.1	37	CCDS12236.1	31	0.014194139194139194	1	0.0020325203252032522	7	0.019337016574585635	0	0.0	23	0.030343007915567283	G	24.3	4.511294	0.85389	0.006809	0.040349	ENSG00000105397	ENST00000524462;ENST00000525621;ENST00000264818;ENST00000543792;ENST00000529739	T;T;T;D	0.82344	-1.32;-1.32;-1.32;-1.6	5.35	4.32	0.51571	Serine-threonine/tyrosine-protein kinase (2);Protein kinase-like domain (1);Tyrosine-protein kinase, catalytic domain (1);Protein kinase, catalytic domain (1);	0.273195	0.25750	N	0.028545	T	0.71617	0.3361	M	0.72118	2.19	0.80722	D	1	D	0.89917	1.0	D	0.72982	0.979	T	0.82143	-0.0603	10	0.87932	D	0	-42.3966	11.8328	0.52305	0.0853:0.0:0.9147:0.0	rs34536443	1104	P29597	TYK2_HUMAN	A	919;1104;1104;851;127	ENSP00000433203:P919A;ENSP00000431885:P1104A;ENSP00000264818:P1104A;ENSP00000436155:P127A	ENSP00000264818:P1104A	P	-	1	0	TYK2	10324118	1.000000	0.71417	0.978000	0.43139	0.888000	0.51559	7.317000	0.79018	1.283000	0.44513	0.549000	0.68633	CCC	G|0.975;C|0.025	0.025	strong		0.592	TYK2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000389443.1		
VPS53	55275	hgsc.bcm.edu	37	17	534812	534812	+	Missense_Mutation	SNP	G	G	A	rs138639431		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr17:534812G>A	ENST00000571805.1	-	8	801	c.665C>T	c.(664-666)gCg>gTg	p.A222V	VPS53_ENST00000576149.1_5'UTR|VPS53_ENST00000291074.5_Missense_Mutation_p.A193V|VPS53_ENST00000437048.2_Missense_Mutation_p.A222V|VPS53_ENST00000446250.2_Missense_Mutation_p.A24V|VPS53_ENST00000401468.3_Intron|VPS53_ENST00000574029.1_Intron			Q5VIR6	VPS53_HUMAN	vacuolar protein sorting 53 homolog (S. cerevisiae)	222					protein transport (GO:0015031)	endosome (GO:0005768)|GARP complex (GO:0000938)|membrane (GO:0016020)				breast(1)|endometrium(4)|large_intestine(5)|lung(8)|prostate(1)	19				UCEC - Uterine corpus endometrioid carcinoma (25;0.0265)		GGAAGGAAACGCTTCTTCAAA	0.502													G|||	1	0.000199681	0.0	0.0	5008	,	,		21279	0.0		0.001	False		,,,				2504	0.0				p.A222V		Atlas-SNP	.											.	VPS53	109	.	0			c.C665T						PASS	.	G	VAL/ALA,VAL/ALA	0,4406		0,0,2203	153.0	117.0	129.0		665,578	5.8	1.0	17	dbSNP_134	129	1,8599	1.2+/-3.3	0,1,4299	no	missense,missense	VPS53	NM_001128159.2,NM_018289.3	64,64	0,1,6502	AA,AG,GG		0.0116,0.0,0.0077	benign,benign	222/833,193/671	534812	1,13005	2203	4300	6503	SO:0001583	missense	55275	exon8			GGAAACGCTTCTT		CCDS10995.1, CCDS45558.1	17p13.3	2007-07-13	2006-12-19			ENSG00000141252			25608	protein-coding gene	gene with protein product		615850	"""vacuolar protein sorting 53 (yeast)"""			15878329	Standard	NM_018289		Approved	FLJ10979, HCCS1	uc010cjo.2	Q5VIR6		ENST00000571805.1:c.665C>T	17.37:g.534812G>A	ENSP00000459312:p.Ala222Val	98.0	0.0	0		109.0	47.0	0.431193	NM_001128159	A8K2S8|B3FH42|Q8WYW3|Q9BRR2|Q9BY02|Q9NV25	Missense_Mutation	SNP	ENST00000571805.1	37		1	4.578754578754579E-4	0	0.0	0	0.0	0	0.0	1	0.0013192612137203166	G	24.9	4.586261	0.86851	0.0	1.16E-4	ENSG00000141252	ENST00000437048;ENST00000446250;ENST00000291074;ENST00000389040	T;T;T;T	0.32988	1.43;1.43;1.43;1.43	5.82	5.82	0.92795	Vps53-like, N-terminal (1);	0.212444	0.49305	D	0.000142	T	0.42899	0.1223	M	0.61703	1.905	0.80722	D	1	P;P;P;P	0.51537	0.946;0.786;0.821;0.786	P;B;B;B	0.47402	0.546;0.286;0.409;0.286	T	0.33548	-0.9864	10	0.62326	D	0.03	-8.2413	19.0968	0.93255	0.0:0.0:1.0:0.0	.	222;24;222;193	Q5VIR6-4;G3V0H8;Q5VIR6;Q5VIR6-2	.;.;VPS53_HUMAN;.	V	222;24;193;222	ENSP00000401435:A222V;ENSP00000394386:A24V;ENSP00000291074:A193V;ENSP00000373692:A222V	ENSP00000291074:A193V	A	-	2	0	VPS53	481562	1.000000	0.71417	0.995000	0.50966	0.981000	0.71138	9.199000	0.95003	2.756000	0.94617	0.563000	0.77884	GCG	G|1.000;A|0.000	0.000	strong		0.502	VPS53-006	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000436940.2	NM_018289	
SLC16A8	23539	hgsc.bcm.edu	37	22	38477275	38477275	+	Missense_Mutation	SNP	G	G	A	rs75640043	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr22:38477275G>A	ENST00000320521.5	-	4	878	c.770C>T	c.(769-771)gCc>gTc	p.A257V	SLC16A8_ENST00000469516.1_Intron	NM_013356.2	NP_037488.2	O95907	MOT3_HUMAN	solute carrier family 16 (monocarboxylate transporter), member 8	257					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)	CTTGGTGACGGCGTACACGGC	0.721													G|||	140	0.0279553	0.0053	0.0533	5008	,	,		11403	0.003		0.0785	False		,,,				2504	0.0143				p.A257V		Atlas-SNP	.											SLC16A8,NS,carcinoma,0,1	SLC16A8	13	1	0			c.C770T						PASS	.	G	VAL/ALA	70,4292		2,66,2113	18.0	17.0	17.0		770	-0.7	0.9	22	dbSNP_131	17	783,7775		28,727,3524	yes	missense	SLC16A8	NM_013356.2	64	30,793,5637	AA,AG,GG		9.1493,1.6048,6.6022	benign	257/505	38477275	853,12067	2181	4279	6460	SO:0001583	missense	23539	exon4			GTGACGGCGTACA	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.770C>T	22.37:g.38477275G>A	ENSP00000321735:p.Ala257Val	94.0	0.0	0		46.0	44.0	0.956522	NM_013356	Q9UBE2	Missense_Mutation	SNP	ENST00000320521.5	37	CCDS13966.1	82	0.037545787545787544	5	0.01016260162601626	13	0.03591160220994475	2	0.0034965034965034965	62	0.08179419525065963	G	13.23	2.173754	0.38413	0.016048	0.091493	ENSG00000100156	ENST00000320521	T	0.55930	0.49	3.34	-0.715	0.11215	Major facilitator superfamily domain, general substrate transporter (1);Major facilitator superfamily domain (1);	1.106640	0.06977	N	0.819091	T	0.01870	0.0059	L	0.41124	1.26	0.22975	N	0.998482	B	0.19583	0.037	B	0.24974	0.057	T	0.10428	-1.0630	10	0.20046	T	0.44	.	7.5375	0.27719	0.4057:0.0:0.5943:0.0	.	257	O95907	MOT3_HUMAN	V	257	ENSP00000321735:A257V	ENSP00000321735:A257V	A	-	2	0	SLC16A8	36807221	0.995000	0.38212	0.948000	0.38648	0.931000	0.56810	2.753000	0.47524	-0.042000	0.13535	0.313000	0.20887	GCC	G|0.951;A|0.049	0.049	strong		0.721	SLC16A8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000321724.1	NM_013356	
ST6GALNAC5	81849	hgsc.bcm.edu	37	1	77510008	77510008	+	Silent	SNP	C	C	A	rs35763299	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr1:77510008C>A	ENST00000477717.1	+	3	616	c.381C>A	c.(379-381)ccC>ccA	p.P127P		NM_030965.1	NP_112227.1	Q9BVH7	SIA7E_HUMAN	ST6 (alpha-N-acetyl-neuraminyl-2,3-beta-galactosyl-1,3)-N-acetylgalactosaminide alpha-2,6-sialyltransferase 5	127					glycosphingolipid biosynthetic process (GO:0006688)|oligosaccharide biosynthetic process (GO:0009312)|protein glycosylation (GO:0006486)|sialylation (GO:0097503)	integral component of Golgi membrane (GO:0030173)	alpha-N-acetylgalactosaminide alpha-2,6-sialyltransferase activity (GO:0001665)|sialyltransferase activity (GO:0008373)			endometrium(2)|kidney(1)|large_intestine(6)|lung(5)|pancreas(2)|skin(1)|upper_aerodigestive_tract(1)	18						ATGACGCCCCCACACGCGGCT	0.622													C|||	75	0.014976	0.0015	0.0331	5008	,	,		20009	0.0		0.0398	False		,,,				2504	0.0102				p.P127P		Atlas-SNP	.											.	ST6GALNAC5	59	.	0			c.C381A						PASS	.	C		17,4389	22.3+/-47.3	1,15,2187	65.0	59.0	61.0		381	1.6	1.0	1	dbSNP_126	61	232,8368	94.0+/-155.9	5,222,4073	no	coding-synonymous	ST6GALNAC5	NM_030965.1		6,237,6260	AA,AC,CC		2.6977,0.3858,1.9145		127/337	77510008	249,12757	2203	4300	6503	SO:0001819	synonymous_variant	81849	exon3			CGCCCCCACACGC		CCDS673.1	1p31.1	2013-03-01	2005-02-07	2005-02-07	ENSG00000117069	ENSG00000117069		"""Sialyltransferases"""	19342	protein-coding gene	gene with protein product		610134	"""sialyltransferase 7 ((alpha-N-acetylneuraminyl-2,3-beta-galactosyl-1,3)-N-acetyl galactosaminide alpha-2,6-sialyltransferase) E"""	SIAT7E		10521438, 10601645	Standard	NM_030965		Approved	MGC3184, ST6GalNAcV	uc001dhi.3	Q9BVH7	OTTHUMG00000009687	ENST00000477717.1:c.381C>A	1.37:g.77510008C>A		111.0	0.0	0		65.0	19.0	0.292308	NM_030965	B1AK82	Silent	SNP	ENST00000477717.1	37	CCDS673.1																																																																																			T|0.009;C|0.980;A|0.010	0.010	strong		0.622	ST6GALNAC5-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000026692.2	NM_030965	
ZNF493	284443	hgsc.bcm.edu	37	19	21607253	21607253	+	Missense_Mutation	SNP	A	A	G	rs150159158	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr19:21607253A>G	ENST00000355504.4	+	2	1674	c.1408A>G	c.(1408-1410)Aag>Gag	p.K470E	ZNF493_ENST00000392288.2_Missense_Mutation_p.K598E|CTD-2561J22.3_ENST00000600810.1_Intron	NM_175910.6	NP_787106.4	Q6ZR52	ZN493_HUMAN	zinc finger protein 493	470					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)			central_nervous_system(2)|cervix(1)|endometrium(1)|kidney(1)|large_intestine(6)|lung(10)|ovary(1)|prostate(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	30						TCATACTGATAAGAAACCCTA	0.338													.|||	3	0.000599042	0.0	0.0	5008	,	,		19874	0.0		0.003	False		,,,				2504	0.0				p.K598E		Atlas-SNP	.											.	ZNF493	178	.	0			c.A1792G						PASS	.						33.0	33.0	33.0					19																	21607253		2201	4298	6499	SO:0001583	missense	284443	exon4			ACTGATAAGAAAC	AK093823, BC006408, BC022394	CCDS12412.1, CCDS42536.1, CCDS12411.1	19p12	2013-01-08			ENSG00000196268	ENSG00000196268		"""Zinc fingers, C2H2-type"", ""-"""	23708	protein-coding gene	gene with protein product							Standard	NM_001076678		Approved	FLJ36504	uc002npw.3	Q6ZR52	OTTHUMG00000141297	ENST00000355504.4:c.1408A>G	19.37:g.21607253A>G	ENSP00000347691:p.Lys470Glu	75.0	0.0	0		65.0	11.0	0.169231	NM_001076678	G5E974|Q59GM3|Q6ZSF6|Q8N1Z6|Q8N965|Q9BR99	Missense_Mutation	SNP	ENST00000355504.4	37	CCDS12412.1	.	.	.	.	.	.	.	.	.	.	N	0.006	-2.049581	0.00394	.	.	ENSG00000196268	ENST00000392288;ENST00000355504	T;T	0.12672	2.66;2.66	1.06	-2.12	0.07165	Zinc finger, C2H2 (1);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.01940	0.0061	N	0.00191	-1.88	0.38843	D	0.956104	B;B	0.06786	0.001;0.0	B;B	0.04013	0.001;0.0	T	0.50575	-0.8812	9	0.02654	T	1	.	4.9183	0.13856	0.3932:0.1603:0.4464:0.0	.	470;598	Q6ZR52;Q6ZR52-2	ZN493_HUMAN;.	E	598;470	ENSP00000376110:K598E;ENSP00000347691:K470E	ENSP00000347691:K470E	K	+	1	0	ZNF493	21399093	0.015000	0.18098	0.000000	0.03702	0.000000	0.00434	0.849000	0.27723	-2.911000	0.00308	-2.864000	0.00100	AAG	.	.	weak		0.338	ZNF493-003	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000280563.1	NM_175910	
SIGLEC15	284266	hgsc.bcm.edu	37	18	43422149	43422149	+	Silent	SNP	G	G	A	rs143689799	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr18:43422149G>A	ENST00000389474.3	+	6	1201	c.984G>A	c.(982-984)ccG>ccA	p.P328P	SIGLEC15_ENST00000546268.1_Silent_p.P174P|SIGLEC15_ENST00000602118.2_3'UTR	NM_213602.2	NP_998767.1	Q6ZMC9	SIG15_HUMAN	sialic acid binding Ig-like lectin 15	328					cellular response to lipoprotein particle stimulus (GO:0071402)|innate immune response (GO:0045087)|regulation of actin cytoskeleton organization (GO:0032956)|regulation of bone resorption (GO:0045124)|regulation of osteoclast development (GO:2001204)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|protein complex (GO:0043234)				endometrium(1)|large_intestine(1)|lung(1)|upper_aerodigestive_tract(1)	4						TGTGCTCACCGTGAGGAGTCC	0.562													G|||	8	0.00159744	0.0015	0.0	5008	,	,		18230	0.0		0.006	False		,,,				2504	0.0				p.P328P		Atlas-SNP	.											.	SIGLEC15	10	.	0			c.G984A						PASS	.	G		2,4404	4.2+/-10.8	0,2,2201	73.0	69.0	70.0		984	-8.6	0.0	18	dbSNP_134	70	27,8573	19.2+/-60.6	0,27,4273	no	coding-synonymous	SIGLEC15	NM_213602.2		0,29,6474	AA,AG,GG		0.314,0.0454,0.223		328/329	43422149	29,12977	2203	4300	6503	SO:0001819	synonymous_variant	284266	exon6			CTCACCGTGAGGA	AK095432	CCDS32819.1	18q21.1	2014-01-28	2007-05-31	2007-05-31	ENSG00000197046	ENSG00000197046		"""Sialic acid binding Ig-like lectins"", ""Immunoglobulin superfamily / V-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	27596	protein-coding gene	gene with protein product			"""CD33 antigen-like 3"", ""CD33 molecule-like 3"""	CD33L3		17483134	Standard	NM_213602		Approved	HsT1361	uc002lbl.1	Q6ZMC9		ENST00000389474.3:c.984G>A	18.37:g.43422149G>A		131.0	0.0	0		115.0	61.0	0.530435	NM_213602	A8K2Y5|B4DVQ9	Silent	SNP	ENST00000389474.3	37	CCDS32819.1																																																																																			G|0.997;A|0.003	0.003	strong		0.562	SIGLEC15-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000410768.2	NM_213602	
PTCH1	5727	hgsc.bcm.edu	37	9	98244242	98244242	+	Silent	SNP	T	T	C	rs1805154	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr9:98244242T>C	ENST00000331920.6	-	5	1034	c.735A>G	c.(733-735)acA>acG	p.T245T	PTCH1_ENST00000437951.1_Silent_p.T179T|PTCH1_ENST00000429896.2_Silent_p.T94T|PTCH1_ENST00000418258.1_Silent_p.T94T|PTCH1_ENST00000468211.2_Silent_p.T179T|PTCH1_ENST00000375274.2_Silent_p.T244T|PTCH1_ENST00000548379.1_5'UTR|PTCH1_ENST00000421141.1_Silent_p.T94T|PTCH1_ENST00000430669.2_Silent_p.T179T	NM_000264.3	NP_000255.2	Q13635	PTC1_HUMAN	patched 1	245					brain development (GO:0007420)|branching involved in ureteric bud morphogenesis (GO:0001658)|cell differentiation involved in kidney development (GO:0061005)|cell proliferation involved in metanephros development (GO:0072203)|cellular response to cholesterol (GO:0071397)|dorsal/ventral pattern formation (GO:0009953)|embryonic limb morphogenesis (GO:0030326)|embryonic organ development (GO:0048568)|epidermis development (GO:0008544)|glucose homeostasis (GO:0042593)|heart morphogenesis (GO:0003007)|hindlimb morphogenesis (GO:0035137)|in utero embryonic development (GO:0001701)|keratinocyte proliferation (GO:0043616)|limb morphogenesis (GO:0035108)|mammary gland duct morphogenesis (GO:0060603)|mammary gland epithelial cell differentiation (GO:0060644)|negative regulation of cell division (GO:0051782)|negative regulation of epithelial cell proliferation (GO:0050680)|negative regulation of multicellular organism growth (GO:0040015)|negative regulation of osteoblast differentiation (GO:0045668)|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 (GO:0000122)|neural plate axis specification (GO:0021997)|neural tube closure (GO:0001843)|neural tube patterning (GO:0021532)|organ morphogenesis (GO:0009887)|pharyngeal system development (GO:0060037)|positive regulation of cholesterol efflux (GO:0010875)|protein processing (GO:0016485)|protein targeting to plasma membrane (GO:0072661)|regulation of mitotic cell cycle (GO:0007346)|regulation of protein localization (GO:0032880)|regulation of smoothened signaling pathway (GO:0008589)|renal system development (GO:0072001)|response to chlorate (GO:0010157)|response to drug (GO:0042493)|response to estradiol (GO:0032355)|response to mechanical stimulus (GO:0009612)|response to retinoic acid (GO:0032526)|smoothened signaling pathway (GO:0007224)|smoothened signaling pathway involved in dorsal/ventral neural tube patterning (GO:0060831)|somite development (GO:0061053)|spinal cord motor neuron differentiation (GO:0021522)	axonal growth cone (GO:0044295)|caveola (GO:0005901)|dendritic growth cone (GO:0044294)|integral component of membrane (GO:0016021)|intracellular membrane-bounded organelle (GO:0043231)|midbody (GO:0030496)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|postsynaptic density (GO:0014069)|primary cilium (GO:0072372)	cholesterol binding (GO:0015485)|cyclin binding (GO:0030332)|hedgehog family protein binding (GO:0097108)|hedgehog receptor activity (GO:0008158)|heparin binding (GO:0008201)|smoothened binding (GO:0005119)			NS(8)|bone(33)|breast(10)|central_nervous_system(95)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(8)|kidney(2)|large_intestine(18)|lung(22)|meninges(1)|oesophagus(3)|ovary(6)|prostate(2)|skin(262)|upper_aerodigestive_tract(11)|urinary_tract(2)|vulva(1)	490		Medulloblastoma(1;7.87e-06)|all_neural(1;0.000555)|Acute lymphoblastic leukemia(62;0.136)				GGAGGTATGCTGTCCCAGACT	0.388													T|||	47	0.00938498	0.0023	0.0202	5008	,	,		17942	0.0		0.0249	False		,,,				2504	0.0051				p.T245T		Atlas-SNP	.											.	PTCH1	1850	.	0			c.A735G						PASS	.	T	,,,,,,	30,4376	34.3+/-65.2	0,30,2173	84.0	70.0	75.0		735,537,732,282,282,282,282	-2.5	1.0	9	dbSNP_89	75	329,8271	115.2+/-175.0	4,321,3975	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	PTCH1	NM_000264.3,NM_001083602.1,NM_001083603.1,NM_001083604.1,NM_001083605.1,NM_001083606.1,NM_001083607.1	,,,,,,	4,351,6148	CC,CT,TT		3.8256,0.6809,2.7603	,,,,,,	245/1448,179/1382,244/1447,94/1297,94/1297,94/1297,94/1297	98244242	359,12647	2203	4300	6503	SO:0001819	synonymous_variant	5727	exon5			GTATGCTGTCCCA	AI494442	CCDS6714.1, CCDS43851.1, CCDS47995.1, CCDS47996.1	9q22.1-q31	2014-09-17	2010-06-24	2006-09-26	ENSG00000185920	ENSG00000185920			9585	protein-coding gene	gene with protein product		601309	"""patched (Drosophila) homolog"", ""patched homolog (Drosophila)"", ""patched homolog 1 (Drosophila)"""	NBCCS, PTCH		8658145	Standard	NM_001083603		Approved	BCNS	uc004avk.4	Q13635	OTTHUMG00000020280	ENST00000331920.6:c.735A>G	9.37:g.98244242T>C		106.0	0.0	0		95.0	45.0	0.473684	NM_000264	A3KBI9|E9PEJ8|Q13463|Q5R1U7|Q5R1U9|Q5R1V0|Q5VZC0|Q5VZC2|Q86XG7	Silent	SNP	ENST00000331920.6	37	CCDS6714.1																																																																																			T|0.976;C|0.024	0.024	strong		0.388	PTCH1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053229.2	NM_000264	
TACC3	10460	hgsc.bcm.edu	37	4	1729958	1729958	+	Missense_Mutation	SNP	G	G	T			TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr4:1729958G>T	ENST00000313288.4	+	4	935	c.829G>T	c.(829-831)Gcg>Tcg	p.A277S		NM_006342.2	NP_006333.1	Q9Y6A5	TACC3_HUMAN	transforming, acidic coiled-coil containing protein 3	277					astral microtubule organization (GO:0030953)|cerebral cortex development (GO:0021987)|cytoplasmic sequestering of transcription factor (GO:0042994)|hemopoiesis (GO:0030097)|interkinetic nuclear migration (GO:0022027)|neurogenesis (GO:0022008)|regulation of cell cycle (GO:0051726)|regulation of microtubule-based process (GO:0032886)|response to hypoxia (GO:0001666)	centrosome (GO:0005813)|cytoplasm (GO:0005737)				central_nervous_system(1)|endometrium(4)|large_intestine(1)|lung(10)|ovary(4)|prostate(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	25		Breast(71;0.212)|all_epithelial(65;0.241)	OV - Ovarian serous cystadenocarcinoma(23;0.00765)|Epithelial(3;0.0126)			GGGCTGCCCTGCGGGTGTGGG	0.667																																					p.A277S	Ovarian(120;482 2294 11894 35824)	Atlas-SNP	.											.	TACC3	69	.	0			c.G829T						PASS	.						15.0	17.0	16.0					4																	1729958		2193	4293	6486	SO:0001583	missense	10460	exon4			TGCCCTGCGGGTG	AF093543	CCDS3352.1	4p16.3	2008-07-29			ENSG00000013810	ENSG00000013810			11524	protein-coding gene	gene with protein product		605303				17675670	Standard	NM_006342		Approved	ERIC1	uc003gdo.3	Q9Y6A5	OTTHUMG00000089535	ENST00000313288.4:c.829G>T	4.37:g.1729958G>T	ENSP00000326550:p.Ala277Ser	67.0	0.0	0		95.0	59.0	0.621053	NM_006342	Q2NKK4|Q3KQS5|Q9UMQ1	Missense_Mutation	SNP	ENST00000313288.4	37	CCDS3352.1	.	.	.	.	.	.	.	.	.	.	G	3.044	-0.196772	0.06259	.	.	ENSG00000013810	ENST00000313288	T	0.10477	2.87	3.55	-3.23	0.05109	.	10.642000	0.00481	U	0.000126	T	0.04907	0.0132	N	0.08118	0	0.09310	N	1	B;B	0.16396	0.017;0.004	B;B	0.12837	0.008;0.004	T	0.30736	-0.9968	10	0.10636	T	0.68	0.0017	4.8773	0.13662	0.3038:0.2546:0.4416:0.0	.	277;277	B4DYJ1;Q9Y6A5	.;TACC3_HUMAN	S	277	ENSP00000326550:A277S	ENSP00000326550:A277S	A	+	1	0	TACC3	1699756	0.000000	0.05858	0.000000	0.03702	0.004000	0.04260	-0.169000	0.09911	-0.955000	0.03636	0.563000	0.77884	GCG	.	.	none		0.667	TACC3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000203730.2		
LTA4H	4048	hgsc.bcm.edu	37	12	96408716	96408716	+	Missense_Mutation	SNP	T	T	C			TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr12:96408716T>C	ENST00000228740.2	-	12	1262	c.1121A>G	c.(1120-1122)gAc>gGc	p.D374G	LTA4H_ENST00000548375.1_5'UTR|LTA4H_ENST00000413268.2_Missense_Mutation_p.D350G|LTA4H_ENST00000552789.1_Missense_Mutation_p.D350G	NM_000895.2	NP_000886.1	P09960	LKHA4_HUMAN	leukotriene A4 hydrolase	374					arachidonic acid metabolic process (GO:0019369)|inflammatory response (GO:0006954)|leukotriene biosynthetic process (GO:0019370)|leukotriene metabolic process (GO:0006691)|peptide catabolic process (GO:0043171)|small molecule metabolic process (GO:0044281)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)	aminopeptidase activity (GO:0004177)|epoxide hydrolase activity (GO:0004301)|leukotriene-A4 hydrolase activity (GO:0004463)|metallopeptidase activity (GO:0008237)|peptidase activity (GO:0008233)|poly(A) RNA binding (GO:0044822)|zinc ion binding (GO:0008270)			haematopoietic_and_lymphoid_tissue(2)|kidney(3)|lung(4)|skin(2)|stomach(1)	12					Captopril(DB01197)	TACATCAGGGTCTATATCTGT	0.393																																					p.D374G		Atlas-SNP	.											.	LTA4H	38	.	0			c.A1121G						PASS	.						172.0	157.0	162.0					12																	96408716		2203	4300	6503	SO:0001583	missense	4048	exon12			TCAGGGTCTATAT	BC032528	CCDS9059.1, CCDS58266.1, CCDS58267.1	12q22	2005-10-06				ENSG00000111144	3.3.2.6		6710	protein-coding gene	gene with protein product		151570				7628486	Standard	NM_000895		Approved		uc001ten.2	P09960	OTTHUMG00000170355	ENST00000228740.2:c.1121A>G	12.37:g.96408716T>C	ENSP00000228740:p.Asp374Gly	148.0	0.0	0		185.0	8.0	0.0432432	NM_000895	B4DNQ9|F8VV40|Q6IAT6|Q9UCT7	Missense_Mutation	SNP	ENST00000228740.2	37	CCDS9059.1	.	.	.	.	.	.	.	.	.	.	T	17.73	3.461791	0.63513	.	.	ENSG00000111144	ENST00000228740;ENST00000552789;ENST00000413268	T;T;T	0.02944	4.1;4.1;4.1	6.07	6.07	0.98685	Peptidase M1, membrane alanine aminopeptidase, N-terminal (1);	0.000000	0.85682	D	0.000000	T	0.16599	0.0399	M	0.88512	2.96	0.80722	D	1	P;P;D	0.53312	0.502;0.698;0.959	P;P;P	0.57846	0.499;0.736;0.828	T	0.00350	-1.1797	10	0.52906	T	0.07	-23.543	16.6277	0.84984	0.0:0.0:0.0:1.0	.	350;350;374	P09960-3;F8VV40;P09960	.;.;LKHA4_HUMAN	G	374;350;350	ENSP00000228740:D374G;ENSP00000449958:D350G;ENSP00000395051:D350G	ENSP00000228740:D374G	D	-	2	0	LTA4H	94932847	1.000000	0.71417	0.996000	0.52242	0.627000	0.37826	5.728000	0.68531	2.330000	0.79161	0.528000	0.53228	GAC	.	.	none		0.393	LTA4H-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000408655.1	NM_000895	
TENM3	55714	hgsc.bcm.edu	37	4	183721088	183721088	+	Silent	SNP	C	C	T			TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr4:183721088C>T	ENST00000511685.1	+	28	7807	c.7684C>T	c.(7684-7686)Ctg>Ttg	p.L2562L	TENM3_ENST00000406950.2_Silent_p.L2562L			Q9P273	TEN3_HUMAN	teneurin transmembrane protein 3	2562					camera-type eye morphogenesis (GO:0048593)|homophilic cell adhesion (GO:0007156)|positive regulation of neuron projection development (GO:0010976)|self proteolysis (GO:0097264)|signal transduction (GO:0007165)	cell projection (GO:0042995)|integral component of membrane (GO:0016021)|membrane (GO:0016020)	protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)										CCTGGGCACGCTGCGGTTGAC	0.632																																					p.L2562L		Atlas-SNP	.											.	.	.	.	0			c.C7684T						PASS	.						23.0	30.0	28.0					4																	183721088		2175	4263	6438	SO:0001819	synonymous_variant	55714	exon27			GGCACGCTGCGGT	AF195420	CCDS47165.1	4q35	2012-10-02	2012-10-02	2012-10-02	ENSG00000218336	ENSG00000218336			29944	protein-coding gene	gene with protein product		610083	"""odz, odd Oz/ten-m homolog 3 (Drosophila)"""	ODZ3		10331952, 10625539	Standard	NM_001080477		Approved	Ten-M3, KIAA1455	uc003ivd.1	Q9P273	OTTHUMG00000160682	ENST00000511685.1:c.7684C>T	4.37:g.183721088C>T		198.0	0.0	0		101.0	5.0	0.049505	NM_001080477	Q5XUL9|Q96SY2|Q9NV77|Q9NVW1|Q9NZJ2	Silent	SNP	ENST00000511685.1	37	CCDS47165.1																																																																																			.	.	none		0.632	TENM3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000361734.1		
MDN1	23195	hgsc.bcm.edu	37	6	90500067	90500067	+	Silent	SNP	C	C	T			TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr6:90500067C>T	ENST00000369393.3	-	6	1024	c.909G>A	c.(907-909)gtG>gtA	p.V303V	MDN1_ENST00000428876.1_Silent_p.V303V			Q9NU22	MDN1_HUMAN	MDN1, midasin homolog (yeast)	303					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)		ACTCAACCAGCACATAAGACC	0.478																																					p.V303V		Atlas-SNP	.											.	MDN1	478	.	0			c.G909A						PASS	.						164.0	169.0	167.0					6																	90500067		2203	4300	6503	SO:0001819	synonymous_variant	23195	exon6			AACCAGCACATAA	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.909G>A	6.37:g.90500067C>T		114.0	0.0	0		130.0	6.0	0.0461538	NM_014611	O15019|Q5T794	Silent	SNP	ENST00000369393.3	37	CCDS5024.1																																																																																			.	.	none		0.478	MDN1-005	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041514.2		
ITIH2	3698	hgsc.bcm.edu	37	10	7759736	7759736	+	Silent	SNP	G	G	A	rs370987991		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr10:7759736G>A	ENST00000358415.4	+	6	781	c.615G>A	c.(613-615)ctG>ctA	p.L205L	ITIH2_ENST00000480387.1_3'UTR|ITIH2_ENST00000379587.4_Silent_p.L194L	NM_002216.2	NP_002207.2	P19823	ITIH2_HUMAN	inter-alpha-trypsin inhibitor heavy chain 2	205					hyaluronan metabolic process (GO:0030212)|negative regulation of endopeptidase activity (GO:0010951)	blood microparticle (GO:0072562)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)	endopeptidase inhibitor activity (GO:0004866)|serine-type endopeptidase inhibitor activity (GO:0004867)			NS(2)|breast(1)|endometrium(8)|kidney(1)|large_intestine(17)|lung(25)|ovary(1)|pancreas(1)|prostate(2)|skin(2)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	64						CTGGACGGCTGGCCAAACACT	0.507																																					p.L205L		Atlas-SNP	.											.	ITIH2	144	.	0			c.G615A						PASS	.	G		0,4406		0,0,2203	129.0	125.0	126.0		615	3.3	1.0	10		126	4,8596	3.7+/-12.6	0,4,4296	no	coding-synonymous	ITIH2	NM_002216.2		0,4,6499	AA,AG,GG		0.0465,0.0,0.0308		205/947	7759736	4,13002	2203	4300	6503	SO:0001819	synonymous_variant	3698	exon6			ACGGCTGGCCAAA	X07173	CCDS31141.1	10p14	2011-10-26	2011-10-26		ENSG00000151655	ENSG00000151655			6167	protein-coding gene	gene with protein product		146640	"""inter-alpha (globulin) inhibitor, H2 polypeptide"""			1385302, 10100603	Standard	NM_002216		Approved	H2P	uc001ijs.3	P19823	OTTHUMG00000017633	ENST00000358415.4:c.615G>A	10.37:g.7759736G>A		154.0	0.0	0		122.0	86.0	0.704918	NM_002216	Q14659|Q15484|Q5T986	Silent	SNP	ENST00000358415.4	37	CCDS31141.1																																																																																			.	.	none		0.507	ITIH2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000046678.2	NM_002216	
DDX54	79039	hgsc.bcm.edu	37	12	113600940	113600940	+	Missense_Mutation	SNP	C	C	T	rs11564	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr12:113600940C>T	ENST00000306014.5	-	16	2105	c.2078G>A	c.(2077-2079)cGg>cAg	p.R693Q	DDX54_ENST00000314045.7_Missense_Mutation_p.R693Q|DDX54_ENST00000549271.1_5'Flank	NM_024072.3	NP_076977.3	Q8TDD1	DDX54_HUMAN	DEAD (Asp-Glu-Ala-Asp) box polypeptide 54	693			R -> Q (in dbSNP:rs11564).		ATP catabolic process (GO:0006200)|intracellular estrogen receptor signaling pathway (GO:0030520)|regulation of transcription, DNA-templated (GO:0006355)|RNA metabolic process (GO:0016070)|RNA processing (GO:0006396)|transcription, DNA-templated (GO:0006351)	membrane (GO:0016020)|nucleolus (GO:0005730)|nucleus (GO:0005634)	ATP binding (GO:0005524)|ATP-dependent RNA helicase activity (GO:0004004)|estrogen receptor binding (GO:0030331)|poly(A) RNA binding (GO:0044822)|receptor binding (GO:0005102)|transcription corepressor activity (GO:0003714)			breast(1)|central_nervous_system(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(8)|lung(8)|ovary(2)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)	31						CACTCACCCCCGCTCGCTGTC	0.637													C|||	155	0.0309505	0.025	0.0447	5008	,	,		15348	0.0		0.0805	False		,,,				2504	0.0102				p.R693Q		Atlas-SNP	.											.	DDX54	73	.	0			c.G2078A						PASS	.	C	GLN/ARG,GLN/ARG	115,4291	85.8+/-124.5	1,113,2089	47.0	54.0	52.0		2078,2078	4.2	1.0	12	dbSNP_52	52	501,8099	142.3+/-198.5	14,473,3813	yes	missense,missense	DDX54	NM_001111322.1,NM_024072.3	43,43	15,586,5902	TT,TC,CC		5.8256,2.6101,4.7363	possibly-damaging,possibly-damaging	693/883,693/882	113600940	616,12390	2203	4300	6503	SO:0001583	missense	79039	exon16			CACCCCCGCTCGC	AF144056	CCDS31907.1, CCDS44984.1	12q24.11	2006-01-30				ENSG00000123064		"""DEAD-boxes"""	20084	protein-coding gene	gene with protein product		611665				12466272	Standard	NM_001111322		Approved	MGC2835, APR-5, DP97	uc001tuq.4	Q8TDD1	OTTHUMG00000169676	ENST00000306014.5:c.2078G>A	12.37:g.113600940C>T	ENSP00000304072:p.Arg693Gln	101.0	0.0	0		103.0	45.0	0.436893	NM_024072	Q86YT8|Q9BRZ1	Missense_Mutation	SNP	ENST00000306014.5	37	CCDS31907.1	86	0.039377289377289376	8	0.016260162601626018	16	0.04419889502762431	0	0.0	62	0.08179419525065963	C	17.30	3.355570	0.61293	0.026101	0.058256	ENSG00000123064	ENST00000314045;ENST00000306014	T;T	0.11277	2.79;2.8	5.1	4.21	0.49690	.	0.112829	0.56097	D	0.000030	T	0.00666	0.0022	M	0.73598	2.24	0.19575	P	0.9999672619	B;B	0.25486	0.127;0.078	B;B	0.18561	0.022;0.01	T	0.10359	-1.0633	9	0.21014	T	0.42	.	13.0042	0.58694	0.0:0.9213:0.0:0.0787	rs11564;rs1130231;rs3188910;rs17296035;rs17354493;rs34797478	693;693	Q8TDD1-2;Q8TDD1	.;DDX54_HUMAN	Q	693	ENSP00000323858:R693Q;ENSP00000304072:R693Q	ENSP00000304072:R693Q	R	-	2	0	DDX54	112085323	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	4.529000	0.60588	1.146000	0.42352	0.643000	0.83706	CGG	C|0.954;T|0.046	0.046	strong		0.637	DDX54-002	KNOWN	NAGNAG_splice_site|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000405435.1	NM_024072	
C14orf79	122616	hgsc.bcm.edu	37	14	105457923	105457923	+	Missense_Mutation	SNP	T	T	A	rs61745867	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr14:105457923T>A	ENST00000547315.1	+	3	1304	c.665T>A	c.(664-666)tTc>tAc	p.F222Y	C14orf79_ENST00000549584.1_3'UTR|C14orf79_ENST00000550614.1_5'UTR|C14orf79_ENST00000549240.1_5'UTR	NM_174891.3	NP_777551.2	Q96F83	CN079_HUMAN	chromosome 14 open reading frame 79	222										breast(1)|endometrium(1)|lung(1)	3		all_cancers(154;0.0798)|Melanoma(154;0.155)|all_epithelial(191;0.183)	all cancers(16;0.00326)|OV - Ovarian serous cystadenocarcinoma(23;0.00659)|Epithelial(46;0.0181)			CAGGAGAACTTCTTTCTTGTT	0.542													T|||	24	0.00479233	0.0015	0.0072	5008	,	,		18114	0.0		0.0099	False		,,,				2504	0.0072				p.F222Y		Atlas-SNP	.											.	C14orf79	13	.	0			c.T665A						PASS	.	T	TYR/PHE	9,3843		0,9,1917	132.0	123.0	126.0		665	2.4	0.0	14	dbSNP_129	126	169,8123		4,161,3981	yes	missense	C14orf79	NM_174891.3	22	4,170,5898	AA,AT,TT		2.0381,0.2336,1.4657	benign	222/326	105457923	178,11966	1926	4146	6072	SO:0001583	missense	122616	exon3			AGAACTTCTTTCT		CCDS42000.1	14q32.33	2012-09-25			ENSG00000140104	ENSG00000140104			20126	protein-coding gene	gene with protein product							Standard	NM_174891		Approved		uc001ypy.1	Q96F83	OTTHUMG00000170474	ENST00000547315.1:c.665T>A	14.37:g.105457923T>A	ENSP00000450114:p.Phe222Tyr	116.0	0.0	0		159.0	69.0	0.433962	NM_174891	B2RPK9|Q9BTP4	Missense_Mutation	SNP	ENST00000547315.1	37	CCDS42000.1	11|11	0.005036630036630037|0.005036630036630037	1|1	0.0020325203252032522|0.0020325203252032522	2|2	0.0055248618784530384|0.0055248618784530384	0|0	0.0|0.0	8|8	0.010554089709762533|0.010554089709762533	T|T	3.056|3.056	-0.194267|-0.194267	0.06259|0.06259	0.002336|0.002336	0.020381|0.020381	ENSG00000140104|ENSG00000140104	ENST00000547315|ENST00000551606	.|.	.|.	.|.	3.62|3.62	2.43|2.43	0.29744|0.29744	.|.	1.254200|.	0.06177|.	N|.	0.678664|.	T|T	0.21103|0.21103	0.0508|0.0508	N|N	0.19112|0.19112	0.55|0.55	0.39067|0.39067	D|D	0.960632|0.960632	B|.	0.14805|.	0.011|.	B|.	0.08055|.	0.003|.	T|T	0.05241|0.05241	-1.0897|-1.0897	9|5	0.29301|.	T|.	0.29|.	-3.7825|-3.7825	6.0924|6.0924	0.20001|0.20001	0.2279:0.0:0.0:0.7721|0.2279:0.0:0.0:0.7721	rs61745867|rs61745867	222|.	Q96F83|.	CN079_HUMAN|.	Y|T	222|116	.|.	ENSP00000450114:F222Y|.	F|S	+|+	2|1	0|0	C14orf79|C14orf79	104528968|104528968	0.021000|0.021000	0.18746|0.18746	0.010000|0.010000	0.14722|0.14722	0.012000|0.012000	0.07955|0.07955	2.128000|2.128000	0.42045|0.42045	0.298000|0.298000	0.22638|0.22638	0.378000|0.378000	0.23410|0.23410	TTC|TCT	T|0.990;A|0.010	0.010	strong		0.542	C14orf79-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000409318.1	NM_174891	
TRIP6	7205	hgsc.bcm.edu	37	7	100465747	100465747	+	Missense_Mutation	SNP	G	G	T	rs139351872	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr7:100465747G>T	ENST00000200457.4	+	3	615	c.255G>T	c.(253-255)agG>agT	p.R85S		NM_003302.2	NP_003293.2	Q15654	TRIP6_HUMAN	thyroid hormone receptor interactor 6	85					focal adhesion assembly (GO:0048041)|positive regulation of cell migration (GO:0030335)|regulation of transcription, DNA-templated (GO:0006355)|release of cytoplasmic sequestered NF-kappaB (GO:0008588)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|focal adhesion (GO:0005925)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	interleukin-1 receptor binding (GO:0005149)|kinase binding (GO:0019900)|poly(A) RNA binding (GO:0044822)|thyroid hormone receptor binding (GO:0046966)|zinc ion binding (GO:0008270)			breast(1)|central_nervous_system(3)|endometrium(2)|large_intestine(2)|liver(1)|lung(5)	14	Lung NSC(181;0.041)|all_lung(186;0.0581)					CTGCAGACAGGGGGGGCCTTC	0.647													G|||	4	0.000798722	0.0015	0.0014	5008	,	,		15814	0.0		0.001	False		,,,				2504	0.0				p.R85S		Atlas-SNP	.											.	TRIP6	45	.	0			c.G255T						PASS	.	G	SER/ARG	2,4404	4.2+/-10.8	0,2,2201	40.0	45.0	43.0		255	-0.6	0.0	7	dbSNP_134	43	6,8594	4.3+/-15.6	0,6,4294	yes	missense	TRIP6	NM_003302.2	110	0,8,6495	TT,TG,GG		0.0698,0.0454,0.0615	probably-damaging	85/477	100465747	8,12998	2203	4300	6503	SO:0001583	missense	7205	exon3			AGACAGGGGGGGC	L40374, AF000974	CCDS5708.1	7q22	2006-09-05			ENSG00000087077	ENSG00000087077			12311	protein-coding gene	gene with protein product		602933				9598321, 7776974	Standard	NM_003302		Approved	ZRP-1, OIP1, MGC10556, MGC10558, MGC29959, MGC3837, MGC4423	uc003uww.3	Q15654	OTTHUMG00000157029	ENST00000200457.4:c.255G>T	7.37:g.100465747G>T	ENSP00000200457:p.Arg85Ser	180.0	0.0	0		212.0	71.0	0.334906	NM_003302	A4D2E7|F2ZC07|F2ZC08|O15170|O15275|Q9BTB2|Q9BUE5|Q9BXP3|Q9UNT4	Missense_Mutation	SNP	ENST00000200457.4	37	CCDS5708.1	3	0.0013736263736263737	1	0.0020325203252032522	1	0.0027624309392265192	0	0.0	1	0.0013192612137203166	G	7.094	0.572692	0.13623	4.54E-4	6.98E-4	ENSG00000087077	ENST00000200457	T	0.62364	0.03	4.67	-0.581	0.11713	.	0.120807	0.53938	D	0.000055	T	0.51210	0.1661	L	0.47716	1.5	0.23101	N	0.998297	P	0.47762	0.9	P	0.44518	0.452	T	0.49113	-0.8973	10	0.35671	T	0.21	.	7.89	0.29672	0.5076:0.0:0.4924:0.0	.	85	Q15654	TRIP6_HUMAN	S	85	ENSP00000200457:R85S	ENSP00000200457:R85S	R	+	3	2	TRIP6	100303683	0.884000	0.30299	0.018000	0.16275	0.003000	0.03518	0.211000	0.17474	-0.471000	0.06891	-1.022000	0.02435	AGG	C|0.000;G|0.999;T|0.001	0.001	strong		0.647	TRIP6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347151.2	NM_003302	
CPSF1	29894	hgsc.bcm.edu	37	8	145624559	145624559	+	Missense_Mutation	SNP	C	C	T			TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr8:145624559C>T	ENST00000349769.3	-	15	1520	c.1426G>A	c.(1426-1428)Gcc>Acc	p.A476T	MIR1234_ENST00000408875.1_RNA	NM_013291.2	NP_037423.2	Q10570	CPSF1_HUMAN	cleavage and polyadenylation specific factor 1, 160kDa	476					gene expression (GO:0010467)|mRNA 3'-end processing (GO:0031124)|mRNA cleavage (GO:0006379)|mRNA export from nucleus (GO:0006406)|mRNA polyadenylation (GO:0006378)|mRNA splicing, via spliceosome (GO:0000398)|RNA splicing (GO:0008380)|termination of RNA polymerase II transcription (GO:0006369)|transcription from RNA polymerase II promoter (GO:0006366)	mRNA cleavage and polyadenylation specificity factor complex (GO:0005847)|nucleoplasm (GO:0005654)	mRNA 3'-UTR binding (GO:0003730)			NS(1)|autonomic_ganglia(1)|breast(2)|central_nervous_system(2)|cervix(1)|endometrium(4)|kidney(3)|large_intestine(5)|lung(15)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	38	all_cancers(97;6.64e-12)|all_epithelial(106;2.89e-10)|Lung NSC(106;5.7e-05)|all_lung(105;0.000174)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155)		OV - Ovarian serous cystadenocarcinoma(54;2.88e-41)|Epithelial(56;1.67e-40)|all cancers(56;1.2e-35)|BRCA - Breast invasive adenocarcinoma(115;0.0323)|Colorectal(110;0.055)			GCGGCATTGGCACAGGGTCCA	0.701																																					p.A476T	NSCLC(133;1088 1848 27708 34777 35269)	Atlas-SNP	.											.	CPSF1	92	.	0			c.G1426A						PASS	.						8.0	9.0	9.0					8																	145624559		2182	4242	6424	SO:0001583	missense	29894	exon15			CATTGGCACAGGG	U37012	CCDS34966.1	8q24	2014-05-06	2002-08-29		ENSG00000071894	ENSG00000071894			2324	protein-coding gene	gene with protein product		606027	"""cleavage and polyadenylation specific factor 1, 160kD subunit"""			7651824, 7590244	Standard	NM_013291		Approved		uc003zcj.3	Q10570	OTTHUMG00000174612	ENST00000349769.3:c.1426G>A	8.37:g.145624559C>T	ENSP00000339353:p.Ala476Thr	103.0	0.0	0		153.0	36.0	0.235294	NM_013291	Q96AF0	Missense_Mutation	SNP	ENST00000349769.3	37	CCDS34966.1	.	.	.	.	.	.	.	.	.	.	C	15.45	2.836638	0.50951	.	.	ENSG00000071894	ENST00000349769	T	0.39406	1.08	5.62	5.62	0.85841	.	0.054386	0.64402	D	0.000001	T	0.34308	0.0893	L	0.32530	0.975	0.58432	D	0.999999	B	0.18310	0.027	B	0.19666	0.026	T	0.09292	-1.0681	10	0.17832	T	0.49	-17.6509	17.1693	0.86825	0.0:1.0:0.0:0.0	.	476	Q10570	CPSF1_HUMAN	T	476	ENSP00000339353:A476T	ENSP00000339353:A476T	A	-	1	0	CPSF1	145595367	1.000000	0.71417	0.995000	0.50966	0.082000	0.17680	5.468000	0.66743	2.658000	0.90341	0.561000	0.74099	GCC	.	.	none		0.701	CPSF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000382422.2	NM_013291	
UBE4A	9354	hgsc.bcm.edu	37	11	118253436	118253436	+	Silent	SNP	T	T	C	rs567105943		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr11:118253436T>C	ENST00000431736.2	+	13	2235	c.2163T>C	c.(2161-2163)taT>taC	p.Y721Y	UBE4A_ENST00000545354.1_Silent_p.Y186Y|UBE4A_ENST00000252108.3_Silent_p.Y714Y					ubiquitination factor E4A											autonomic_ganglia(1)|breast(2)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(17)|large_intestine(7)|liver(2)|lung(14)|ovary(3)|prostate(1)|upper_aerodigestive_tract(5)|urinary_tract(2)	56	all_hematologic(175;0.046)	Medulloblastoma(222;0.0425)|Breast(348;0.181)|all_hematologic(192;0.196)|all_neural(223;0.234)		BRCA - Breast invasive adenocarcinoma(274;3.28e-05)		ACTTTCAGTATGCACCCCAAC	0.498																																					p.Y721Y		Atlas-SNP	.											.	UBE4A	97	.	0			c.T2163C						PASS	.						180.0	167.0	172.0					11																	118253436		2200	4296	6496	SO:0001819	synonymous_variant	9354	exon13			TCAGTATGCACCC	D50916	CCDS8396.1, CCDS55790.1	11q23.3	2013-01-28	2011-05-19					"""U-box domain containing"""	12499	protein-coding gene	gene with protein product		603753	"""ubiquitination factor E4A (homologous to yeast UFD2)"", ""ubiquitination factor E4A (UFD2 homolog, yeast)"""			10089879	Standard	NM_004788		Approved	UBOX2, UFD2, KIAA0126, E4	uc001psv.3	Q14139	OTTHUMG00000168100	ENST00000431736.2:c.2163T>C	11.37:g.118253436T>C		85.0	0.0	0		110.0	76.0	0.690909	NM_004788		Silent	SNP	ENST00000431736.2	37	CCDS8396.1																																																																																			.	.	none		0.498	UBE4A-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000398143.1	NM_004788	
SLC22A16	85413	hgsc.bcm.edu	37	6	110763935	110763935	+	Missense_Mutation	SNP	T	T	C	rs41288594	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr6:110763935T>C	ENST00000368919.3	-	4	761	c.695A>G	c.(694-696)gAa>gGa	p.E232G	RN7SL617P_ENST00000485298.2_RNA|SLC22A16_ENST00000456137.2_3'UTR|SLC22A16_ENST00000439654.1_Missense_Mutation_p.E232G|SLC22A16_ENST00000330550.4_Missense_Mutation_p.E198G	NM_033125.3	NP_149116.2	Q86VW1	S22AG_HUMAN	solute carrier family 22 (organic cation/carnitine transporter), member 16	232					acid secretion (GO:0046717)|amine transport (GO:0015837)|carnitine transmembrane transport (GO:1902603)|carnitine transport (GO:0015879)|cell differentiation (GO:0030154)|multicellular organismal development (GO:0007275)|organic cation transport (GO:0015695)|single fertilization (GO:0007338)|sperm motility (GO:0030317)|spermatogenesis (GO:0007283)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	amine transmembrane transporter activity (GO:0005275)|carnitine transmembrane transporter activity (GO:0015226)|organic cation transmembrane transporter activity (GO:0015101)			breast(1)|endometrium(1)|kidney(3)|large_intestine(6)|lung(16)|ovary(1)|prostate(1)|skin(4)|upper_aerodigestive_tract(1)	34		all_cancers(87;0.00221)|Acute lymphoblastic leukemia(125;2.27e-07)|all_hematologic(75;1.38e-05)|all_epithelial(87;0.0485)|Colorectal(196;0.101)		OV - Ovarian serous cystadenocarcinoma(136;0.0513)|Epithelial(106;0.0921)|all cancers(137;0.115)	Doxorubicin(DB00997)|L-Carnitine(DB00583)	GCCAATGAATTCCATCACATA	0.428													T|||	33	0.00658946	0.003	0.0144	5008	,	,		19307	0.0		0.0099	False		,,,				2504	0.0092				p.E232G		Atlas-SNP	.											.	SLC22A16	81	.	0			c.A695G						PASS	.	T	GLY/GLU	28,4378	31.7+/-61.6	0,28,2175	71.0	69.0	69.0		695	4.7	0.2	6	dbSNP_127	69	186,8414	80.4+/-143.0	1,184,4115	yes	missense	SLC22A16	NM_033125.2	98	1,212,6290	CC,CT,TT		2.1628,0.6355,1.6454	probably-damaging	232/578	110763935	214,12792	2203	4300	6503	SO:0001583	missense	85413	exon4			ATGAATTCCATCA		CCDS5084.1	6q21	2013-05-22	2008-01-11		ENSG00000004809	ENSG00000004809		"""Solute carriers"""	20302	protein-coding gene	gene with protein product		608276	"""solute carrier family 22 (organic cation transporter), member 16"""			12372408, 12089149, 17473959	Standard	NM_033125		Approved	FLIPT2, CT2, OKB1, OAT6	uc003puf.3	Q86VW1	OTTHUMG00000016171	ENST00000368919.3:c.695A>G	6.37:g.110763935T>C	ENSP00000357915:p.Glu232Gly	91.0	0.0	0		107.0	52.0	0.485981	NM_033125	O14567|Q5JXM1|Q8IUG8|Q8IZD5|Q96M90|Q96RU0	Missense_Mutation	SNP	ENST00000368919.3	37	CCDS5084.1	15	0.006868131868131868	4	0.008130081300813009	6	0.016574585635359115	0	0.0	5	0.006596306068601583	T	16.01	3.001806	0.54254	0.006355	0.021628	ENSG00000004809	ENST00000368919;ENST00000451557;ENST00000330550;ENST00000439654;ENST00000434949;ENST00000437378	D;D;D;D;D;D	0.86694	-2.16;-2.16;-2.16;-2.16;-2.16;-2.16	4.74	4.74	0.60224	Major facilitator superfamily domain, general substrate transporter (1);Major facilitator superfamily domain (1);	0.000000	0.85682	D	0.000000	D	0.95053	0.8398	H	0.97023	3.925	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.83275	0.996;0.993	D	0.96626	0.9463	10	0.87932	D	0	.	14.2102	0.65759	0.0:0.0:0.0:1.0	rs41288594	232;198	Q86VW1;Q86VW1-2	S22AG_HUMAN;.	G	232;149;198;232;62;189	ENSP00000357915:E232G;ENSP00000395642:E149G;ENSP00000328583:E198G;ENSP00000408799:E232G;ENSP00000409306:E62G;ENSP00000416310:E189G	ENSP00000328583:E198G	E	-	2	0	SLC22A16	110870628	1.000000	0.71417	0.215000	0.23724	0.120000	0.20174	7.301000	0.78850	1.762000	0.52044	0.533000	0.62120	GAA	T|0.985;C|0.015	0.015	strong		0.428	SLC22A16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000043428.1	NM_033125	
RPE65	6121	hgsc.bcm.edu	37	1	68914353	68914353	+	Silent	SNP	A	A	G	rs62642581		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr1:68914353A>G	ENST00000262340.5	-	2	101	c.48T>C	c.(46-48)ttT>ttC	p.F16F		NM_000329.2	NP_000320.1	Q16518	RPE65_HUMAN	retinal pigment epithelium-specific protein 65kDa	16					cellular response to electrical stimulus (GO:0071257)|detection of light stimulus involved in visual perception (GO:0050908)|insulin receptor signaling pathway (GO:0008286)|phototransduction, visible light (GO:0007603)|regulation of rhodopsin gene expression (GO:0007468)|retina homeostasis (GO:0001895)|retina morphogenesis in camera-type eye (GO:0060042)|retinal metabolic process (GO:0042574)|retinoid metabolic process (GO:0001523)|visual perception (GO:0007601)|vitamin A metabolic process (GO:0006776)	endoplasmic reticulum (GO:0005783)|plasma membrane (GO:0005886)	all-trans-retinyl-ester hydrolase, 11-cis retinol forming activity (GO:0052885)|all-trans-retinyl-palmitate hydrolase, 11-cis retinol forming activity (GO:0052884)|metal ion binding (GO:0046872)|retinal isomerase activity (GO:0004744)			central_nervous_system(1)|kidney(3)|large_intestine(12)|lung(15)|ovary(1)|prostate(2)|upper_aerodigestive_tract(1)	35						CCACAGTTTCAAACAGTTTCT	0.488													A|||	1	0.000199681	0.0	0.0	5008	,	,		14614	0.0		0.001	False		,,,				2504	0.0				p.F16F		Atlas-SNP	.											.	RPE65	87	.	0			c.T48C						PASS	.	A		1,4405	2.1+/-5.4	0,1,2202	116.0	100.0	106.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	48	-4.9	0.9	1	dbSNP_129	106	5,8595	4.3+/-15.6	0,5,4295	no	coding-synonymous	RPE65	NM_000329.2		0,6,6497	GG,GA,AA		0.0581,0.0227,0.0461		16/534	68914353	6,13000	2203	4300	6503	SO:0001819	synonymous_variant	6121	exon2			AGTTTCAAACAGT	U18991	CCDS643.1	1p31	2014-05-13	2002-08-29		ENSG00000116745	ENSG00000116745	3.1.1.64		10294	protein-coding gene	gene with protein product	"""retinol isomerase"", ""all-trans-retinyl-palmitate hydrolase"", ""retinoid isomerohydrolase"", ""BCO family, member 3"""	180069	"""retinal pigment epithelium-specific protein (65kD)"""	RP20		8340400	Standard	XM_006710811		Approved	LCA2, rd12, BCO3	uc001dei.1	Q16518	OTTHUMG00000009208	ENST00000262340.5:c.48T>C	1.37:g.68914353A>G		158.0	0.0	0		97.0	25.0	0.257732	NM_000329	A8K1L0|Q5T9U3	Silent	SNP	ENST00000262340.5	37	CCDS643.1																																																																																			A|1.000;G|0.000	0.000	strong		0.488	RPE65-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000025509.1	NM_000329	
EXOC1	55763	hgsc.bcm.edu	37	4	56737278	56737278	+	Missense_Mutation	SNP	C	C	G			TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr4:56737278C>G	ENST00000381295.2	+	7	1191	c.843C>G	c.(841-843)gaC>gaG	p.D281E	EXOC1_ENST00000349598.6_Missense_Mutation_p.D281E|EXOC1_ENST00000346134.7_Missense_Mutation_p.D281E	NM_001024924.1	NP_001020095.1	Q9NV70	EXOC1_HUMAN	exocyst complex component 1	281					cellular protein metabolic process (GO:0044267)|exocytosis (GO:0006887)|membrane organization (GO:0061024)|protein transport (GO:0015031)	exocyst (GO:0000145)|membrane (GO:0016020)|plasma membrane (GO:0005886)				breast(2)|central_nervous_system(1)|cervix(1)|endometrium(6)|kidney(1)|large_intestine(3)|lung(14)|ovary(2)|skin(4)|upper_aerodigestive_tract(1)	35	Glioma(25;0.08)|all_neural(26;0.101)					ACCACATGGACTTGGCCAAAG	0.448																																					p.D281E		Atlas-SNP	.											.	EXOC1	103	.	0			c.C843G						PASS	.						98.0	86.0	90.0					4																	56737278		2203	4300	6503	SO:0001583	missense	55763	exon7			CATGGACTTGGCC	AK027047	CCDS3502.1, CCDS3503.1	4q12	2013-01-22	2005-11-01	2005-11-01	ENSG00000090989	ENSG00000090989			30380	protein-coding gene	gene with protein product		607879	"""SEC3-like 1 (S. cerevisiae)"""	SEC3L1		11042152, 11406615	Standard	XM_005265747		Approved	SEC3, FLJ10893, BM-102, Sec3p	uc003hbf.1	Q9NV70	OTTHUMG00000102165	ENST00000381295.2:c.843C>G	4.37:g.56737278C>G	ENSP00000370695:p.Asp281Glu	198.0	0.0	0		158.0	77.0	0.487342	NM_018261	Q504V4|Q8WUE7|Q96T15|Q9NZE4	Missense_Mutation	SNP	ENST00000381295.2	37	CCDS3502.1	.	.	.	.	.	.	.	.	.	.	C	20.7	4.040304	0.75732	.	.	ENSG00000090989	ENST00000381295;ENST00000346134;ENST00000349598	.	.	.	5.97	4.23	0.50019	.	0.043036	0.85682	D	0.000000	T	0.63510	0.2517	L	0.58669	1.825	0.58432	D	0.999993	D;P	0.76494	0.999;0.95	D;P	0.80764	0.994;0.836	T	0.59669	-0.7411	9	0.11182	T	0.66	.	6.0347	0.19699	0.0:0.7065:0.0:0.2935	.	281;281	Q9NV70-2;Q9NV70	.;EXOC1_HUMAN	E	281	.	ENSP00000326514:D281E	D	+	3	2	EXOC1	56432035	1.000000	0.71417	1.000000	0.80357	0.951000	0.60555	1.604000	0.36804	2.833000	0.97629	0.585000	0.79938	GAC	.	.	none		0.448	EXOC1-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000361799.1	NM_018261	
PLEKHO2	80301	hgsc.bcm.edu	37	15	65158047	65158047	+	Missense_Mutation	SNP	G	G	A	rs77456635	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr15:65158047G>A	ENST00000323544.4	+	6	1561	c.1433G>A	c.(1432-1434)cGg>cAg	p.R478Q	AC069368.3_ENST00000437723.1_Intron	NM_001195059.1|NM_025201.4	NP_001181988.1|NP_079477.2	Q8TD55	PKHO2_HUMAN	pleckstrin homology domain containing, family O member 2	478										NS(1)|breast(1)|cervix(3)|endometrium(1)|kidney(2)|large_intestine(5)|lung(9)|ovary(1)|skin(1)|upper_aerodigestive_tract(1)	25						AGGGAGAAGCGGAAGGAGCTG	0.607													G|||	49	0.00978435	0.0008	0.0115	5008	,	,		19769	0.0		0.0239	False		,,,				2504	0.0164				p.R478Q		Atlas-SNP	.											.	PLEKHO2	50	.	0			c.G1433A						PASS	.	G	GLN/ARG,GLN/ARG	33,4371	36.0+/-67.5	0,33,2169	30.0	31.0	31.0		1283,1433	-0.6	1.0	15	dbSNP_132	31	242,8356	95.2+/-157.0	5,232,4062	yes	missense,missense	PLEKHO2	NM_001195059.1,NM_025201.4	43,43	5,265,6231	AA,AG,GG		2.8146,0.7493,2.1151	benign,benign	428/441,478/491	65158047	275,12727	2202	4299	6501	SO:0001583	missense	80301	exon6			AGAAGCGGAAGGA	AF318373	CCDS10196.1, CCDS73739.1	15q22.31	2013-01-10	2007-12-14	2007-12-14	ENSG00000241839	ENSG00000241839		"""Pleckstrin homology (PH) domain containing"""	30026	protein-coding gene	gene with protein product			"""pleckstrin homology domain containing, family Q member 1"""	PLEKHQ1		12477932	Standard	NM_025201		Approved	DKFZp761K2312, PP1628, pp9099	uc002anv.3	Q8TD55	OTTHUMG00000133050	ENST00000323544.4:c.1433G>A	15.37:g.65158047G>A	ENSP00000326706:p.Arg478Gln	24.0	0.0	0		17.0	13.0	0.764706	NM_025201	Q7L4H4|Q8WYS8	Missense_Mutation	SNP	ENST00000323544.4	37	CCDS10196.1	27	0.012362637362637362	1	0.0020325203252032522	5	0.013812154696132596	0	0.0	21	0.027704485488126648	G	12.58	1.980799	0.34942	0.007493	0.028146	ENSG00000241839	ENST00000323544	T	0.31510	1.49	5.13	-0.638	0.11500	.	0.335637	0.24633	N	0.036878	T	0.04907	0.0132	N	0.19112	0.55	0.28088	N	0.931902	B;B	0.23490	0.086;0.026	B;B	0.16722	0.016;0.004	T	0.22068	-1.0227	10	0.17832	T	0.49	.	8.772	0.34737	0.5539:0.0:0.4461:0.0	.	428;478	Q8TD55-2;Q8TD55	.;PKHO2_HUMAN	Q	478	ENSP00000326706:R478Q	ENSP00000326706:R478Q	R	+	2	0	PLEKHO2	62945100	0.998000	0.40836	0.993000	0.49108	0.988000	0.76386	0.377000	0.20552	-0.025000	0.13918	-0.275000	0.10095	CGG	G|0.982;A|0.018	0.018	strong		0.607	PLEKHO2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256659.1	NM_025201	
EFEMP1	2202	hgsc.bcm.edu	37	2	56144930	56144930	+	Silent	SNP	T	T	C	rs14282	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr2:56144930T>C	ENST00000394555.2	-	4	822	c.387A>G	c.(385-387)gaA>gaG	p.E129E	EFEMP1_ENST00000424836.2_Silent_p.E71E|EFEMP1_ENST00000355426.3_Silent_p.E129E|EFEMP1_ENST00000394554.1_Silent_p.E129E	NM_001039348.2|NM_001039349.2	NP_001034437.1|NP_001034438.1	Q12805	FBLN3_HUMAN	EGF containing fibulin-like extracellular matrix protein 1	129					epidermal growth factor receptor signaling pathway (GO:0007173)|extracellular matrix organization (GO:0030198)|negative regulation of chondrocyte differentiation (GO:0032331)|peptidyl-tyrosine phosphorylation (GO:0018108)|regulation of transcription, DNA-templated (GO:0006355)|visual perception (GO:0007601)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|proteinaceous extracellular matrix (GO:0005578)	calcium ion binding (GO:0005509)|epidermal growth factor receptor binding (GO:0005154)|epidermal growth factor-activated receptor activity (GO:0005006)			NS(1)|breast(2)|endometrium(4)|large_intestine(6)|lung(5)|ovary(5)|pancreas(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	28			LUSC - Lung squamous cell carcinoma(58;0.127)|Lung(47;0.132)			CAGTCTGCATTTCAGGGCCTG	0.612													T|||	97	0.019369	0.0008	0.0216	5008	,	,		16856	0.001		0.0239	False		,,,				2504	0.0573				p.E129E	GBM(92;934 1319 7714 28760 40110)	Atlas-SNP	.											.	EFEMP1	81	.	0			c.A387G						PASS	.	T	,	33,4373	37.6+/-69.7	0,33,2170	56.0	55.0	55.0		387,387	2.2	1.0	2	dbSNP_52	55	231,8369	95.2+/-157.0	3,225,4072	yes	coding-synonymous,coding-synonymous	EFEMP1	NM_001039348.2,NM_001039349.2	,	3,258,6242	CC,CT,TT		2.686,0.749,2.0298	,	129/494,129/494	56144930	264,12742	2203	4300	6503	SO:0001819	synonymous_variant	2202	exon4			CTGCATTTCAGGG	U03877	CCDS1857.1	2p16	2013-01-08	2011-01-25		ENSG00000115380	ENSG00000115380		"""Fibulins"""	3218	protein-coding gene	gene with protein product	"""fibulin 3"""	601548	"""fibrillin-like"", ""EGF-containing fibulin-like extracellular matrix protein 1"""	DHRD, FBNL		8812496, 7799918	Standard	NM_001039348		Approved	S1-5, FBLN3, MTLV	uc002rzi.3	Q12805	OTTHUMG00000129343	ENST00000394555.2:c.387A>G	2.37:g.56144930T>C		97.0	0.0	0		101.0	48.0	0.475248	NM_001039349	A8K3I4|B4DW75|D6W5D2|Q541U7	Silent	SNP	ENST00000394555.2	37	CCDS1857.1																																																																																			T|0.979;C|0.021	0.021	strong		0.612	EFEMP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251491.2		
TTLL6	284076	hgsc.bcm.edu	37	17	46877017	46877017	+	Silent	SNP	C	C	T	rs201225285	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr17:46877017C>T	ENST00000393382.3	-	6	858	c.717G>A	c.(715-717)gtG>gtA	p.V239V		NM_001130918.1	NP_001124390.1			tubulin tyrosine ligase-like family, member 6											endometrium(1)|large_intestine(5)|lung(9)|prostate(1)|skin(2)	18						TGATTTCTTTCACTGTCCGGG	0.428																																					p.V239V		Atlas-SNP	.											.	TTLL6	113	.	0			c.G717A						PASS	.						173.0	141.0	151.0					17																	46877017		692	1591	2283	SO:0001819	synonymous_variant	284076	exon6			TTCTTTCACTGTC	AK093127	CCDS11537.2, CCDS45724.1	17q21.32	2013-02-14			ENSG00000170703	ENSG00000170703		"""Tubulin tyrosine ligase-like family"""	26664	protein-coding gene	gene with protein product		610849				15890843	Standard	NM_173623		Approved	FLJ35808	uc021tzm.1	Q8N841	OTTHUMG00000156978	ENST00000393382.3:c.717G>A	17.37:g.46877017C>T		189.0	0.0	0		148.0	63.0	0.425676	NM_001130918		Silent	SNP	ENST00000393382.3	37	CCDS45724.1																																																																																			C|0.996;T|0.004	0.004	strong		0.428	TTLL6-003	KNOWN	downstream_ATG|non_canonical_conserved|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000346939.3	NM_173623	
CYP2A6	1548	hgsc.bcm.edu	37	19	41356246	41356246	+	Missense_Mutation	SNP	C	C	T	rs28399435	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr19:41356246C>T	ENST00000301141.5	-	1	106	c.86G>A	c.(85-87)aGc>aAc	p.S29N	CTC-490E21.12_ENST00000601627.1_Intron	NM_000762.5	NP_000753	P11509	CP2A6_HUMAN	cytochrome P450, family 2, subfamily A, polypeptide 6	29			S -> N (in allele CYP2A6*14; dbSNP:rs28399435). {ECO:0000269|PubMed:15469410, ECO:0000269|PubMed:15618701, ECO:0000269|PubMed:2726448}.		coumarin catabolic process (GO:0046226)|coumarin metabolic process (GO:0009804)|drug metabolic process (GO:0017144)|exogenous drug catabolic process (GO:0042738)|small molecule metabolic process (GO:0044281)|steroid metabolic process (GO:0008202)|xenobiotic metabolic process (GO:0006805)	cytoplasmic microtubule (GO:0005881)|endoplasmic reticulum membrane (GO:0005789)	coumarin 7-hydroxylase activity (GO:0008389)|enzyme binding (GO:0019899)|heme binding (GO:0020037)|iron ion binding (GO:0005506)|oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, reduced flavin or flavoprotein as one donor, and incorporation of one atom of oxygen (GO:0016712)			breast(1)|central_nervous_system(1)|endometrium(4)|kidney(3)|large_intestine(7)|lung(9)|ovary(3)|prostate(5)|skin(2)|upper_aerodigestive_tract(2)	37			LUSC - Lung squamous cell carcinoma(20;0.000219)|Lung(22;0.000959)		Acetaminophen(DB00316)|Amiodarone(DB01118)|Amlodipine(DB00381)|Amobarbital(DB01351)|Amphetamine(DB00182)|Antipyrine(DB01435)|Arformoterol(DB01274)|Azelastine(DB00972)|Azithromycin(DB00207)|Buprenorphine(DB00921)|Bupropion(DB01156)|Chlorzoxazone(DB00356)|Cinnarizine(DB00568)|Cisapride(DB00604)|Clofibrate(DB00636)|Clomifene(DB00882)|Clotrimazole(DB00257)|Clozapine(DB00363)|Cyclophosphamide(DB00531)|Dapagliflozin(DB06292)|Desipramine(DB01151)|Dexamethasone(DB01234)|Dexfenfluramine(DB01191)|Diethylstilbestrol(DB00255)|Dronabinol(DB00470)|Eletriptan(DB00216)|Ezogabine(DB04953)|Flunarizine(DB04841)|Flunitrazepam(DB01544)|Fluorouracil(DB00544)|Flurazepam(DB00690)|Fomepizole(DB01213)|Formoterol(DB00983)|Halothane(DB01159)|Ifosfamide(DB01181)|Isoniazid(DB00951)|Ketoconazole(DB01026)|Letrozole(DB01006)|Lidocaine(DB00281)|Lorcaserin(DB04871)|Memantine(DB01043)|Menadione(DB00170)|Methimazole(DB00763)|Methoxsalen(DB00553)|Methoxyflurane(DB01028)|Metyrapone(DB01011)|Miconazole(DB01110)|Montelukast(DB00471)|Nevirapine(DB00238)|Nicotine(DB00184)|Nifedipine(DB01115)|Nilvadipine(DB06712)|Norfloxacin(DB01059)|Pentobarbital(DB00312)|Phenobarbital(DB01174)|Pilocarpine(DB01085)|Prednisolone(DB00860)|Progesterone(DB00396)|Propofol(DB00818)|Rifampicin(DB01045)|Rosiglitazone(DB00412)|Selegiline(DB01037)|Sevoflurane(DB01236)|Sulfaphenazole(DB06729)|Tamoxifen(DB00675)|Tranylcypromine(DB00752)|Tretinoin(DB00755)|Troleandomycin(DB01361)|Valproic Acid(DB00313)|Zidovudine(DB00495)	CTTCCCCTTGCTCTTCCTCTG	0.557													.|||	70	0.0139776	0.0023	0.0173	5008	,	,		17142	0.0		0.0328	False		,,,				2504	0.0225				p.S29N		Atlas-SNP	.											.	CYP2A6	69	.	0			c.G86A						PASS	.	C	ASN/SER	45,4361		2,41,2160	108.0	92.0	98.0		86	-3.7	0.0	19	dbSNP_125	98	350,8248		12,326,3961	no	missense	CYP2A6	NM_000762.5	46	14,367,6121	TT,TC,CC		4.0707,1.0213,3.0375	benign	29/495	41356246	395,12609	2203	4299	6502	SO:0001583	missense	1548	exon1			CCCTTGCTCTTCC	AF182275	CCDS12568.1	19q13.2	2013-11-11	2003-01-14		ENSG00000255974	ENSG00000255974		"""Cytochrome P450s"""	2610	protein-coding gene	gene with protein product		122720	"""cytochrome P450, subfamily IIA (phenobarbital-inducible), polypeptide 6"""	CYP2A3		7668294, 2748347	Standard	NM_000762		Approved	CPA6, CYP2A	uc002opl.4	P11509	OTTHUMG00000182713	ENST00000301141.5:c.86G>A	19.37:g.41356246C>T	ENSP00000301141:p.Ser29Asn	341.0	1.0	0.00293255		330.0	166.0	0.50303	NM_000762	A7YAE5|B2R7F6|P00190|P10890|Q16803|Q4VAT9|Q4VAU0|Q4VAU1|Q9H1Z7|Q9UCU0|Q9UK48	Missense_Mutation	SNP	ENST00000301141.5	37	CCDS12568.1	34	0.015567765567765568	0	0.0	6	0.016574585635359115	0	0.0	28	0.036939313984168866	-	5.795	0.330971	0.10956	0.010213	0.040707	ENSG00000255974	ENST00000301141	T	0.69435	-0.4	2.86	-3.66	0.04489	.	1.227710	0.05870	U	0.624444	T	0.21427	0.0516	L	0.40543	1.245	0.09310	N	1	B	0.20671	0.047	B	0.27262	0.078	T	0.26677	-1.0096	10	0.22706	T	0.39	.	6.2921	0.21065	0.5064:0.3714:0.1222:0.0	rs28399435;rs57299031	29	P11509	CP2A6_HUMAN	N	29	ENSP00000301141:S29N	ENSP00000301141:S29N	S	-	2	0	CYP2A6	46048086	0.000000	0.05858	0.001000	0.08648	0.019000	0.09904	-2.019000	0.01442	-0.197000	0.10350	0.173000	0.16961	AGC	C|0.975;T|0.025	0.025	strong		0.557	CYP2A6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000463259.1	NM_000762	
ERBB2IP	55914	hgsc.bcm.edu	37	5	65350044	65350044	+	Silent	SNP	A	A	G	rs35278406	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr5:65350044A>G	ENST00000284037.5	+	21	3287	c.2898A>G	c.(2896-2898)caA>caG	p.Q966Q	ERBB2IP_ENST00000380939.2_Silent_p.Q966Q|ERBB2IP_ENST00000380943.2_Silent_p.Q966Q|ERBB2IP_ENST00000380938.2_Silent_p.Q966Q|ERBB2IP_ENST00000380935.1_Silent_p.Q966Q|ERBB2IP_ENST00000506030.1_Silent_p.Q966Q|ERBB2IP_ENST00000511297.1_Silent_p.Q962Q|ERBB2IP_ENST00000380936.1_Silent_p.Q966Q|ERBB2IP_ENST00000508515.1_Silent_p.Q966Q|ERBB2IP_ENST00000416865.2_Intron	NM_001253697.1	NP_001240626.1	Q96RT1	LAP2_HUMAN	erbb2 interacting protein	966					basal protein localization (GO:0045175)|cell adhesion (GO:0007155)|cell cycle (GO:0007049)|cell growth (GO:0016049)|epidermal growth factor receptor signaling pathway (GO:0007173)|establishment or maintenance of epithelial cell apical/basal polarity (GO:0045197)|integrin-mediated signaling pathway (GO:0007229)|intermediate filament cytoskeleton organization (GO:0045104)|signal transduction (GO:0007165)	basal plasma membrane (GO:0009925)|basement membrane (GO:0005604)|cytoplasm (GO:0005737)|hemidesmosome (GO:0030056)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	ErbB-2 class receptor binding (GO:0005176)|integrin binding (GO:0005178)|structural constituent of cytoskeleton (GO:0005200)			breast(2)|central_nervous_system(2)|endometrium(3)|kidney(5)|large_intestine(8)|lung(11)|ovary(3)|skin(2)	36		Lung NSC(167;9.45e-06)|Prostate(74;0.0139)|Ovarian(174;0.0547)|Breast(144;0.093)|Colorectal(97;0.234)		UCEC - Uterine corpus endometrioid carcinoma (4;0.0767)|Lung(70;0.00191)		GTGGCCCACAATCTGCACCTC	0.398													A|||	87	0.0173722	0.0008	0.0159	5008	,	,		17609	0.0		0.0388	False		,,,				2504	0.0368				p.Q966Q		Atlas-SNP	.											.	ERBB2IP	120	.	0			c.A2898G						PASS	.	A	,	33,4363		0,33,2165	71.0	79.0	76.0		2898,2898	-5.2	0.5	5	dbSNP_126	76	343,8255		5,333,3961	no	coding-synonymous,coding-synonymous	ERBB2IP	NM_001006600.1,NM_018695.2	,	5,366,6126	GG,GA,AA		3.9893,0.7507,2.8936	,	966/1303,966/1372	65350044	376,12618	2198	4299	6497	SO:0001819	synonymous_variant	55914	exon21			CCCACAATCTGCA		CCDS3990.1, CCDS34172.1, CCDS58951.1, CCDS58952.1, CCDS58953.1, CCDS58954.1	5p14.3-q12.3	2008-07-18	2001-11-29		ENSG00000112851	ENSG00000112851			15842	protein-coding gene	gene with protein product	"""densin-180-like protein"", ""ERBB2-interacting protein"""	606944	"""erbb2-interacting protein"""			10574462, 10878805	Standard	NM_001253697		Approved	ERBIN, LAP2	uc011cqx.2	Q96RT1	OTTHUMG00000097808	ENST00000284037.5:c.2898A>G	5.37:g.65350044A>G		97.0	0.0	0		94.0	33.0	0.351064	NM_001253699	A0AVR1|B4E3F1|B7ZLV9|E7EQW9|E9PCR8|Q1RMD0|Q86W38|Q9NR18|Q9NW48|Q9ULJ5	Silent	SNP	ENST00000284037.5	37	CCDS58953.1																																																																																			A|0.974;G|0.026	0.026	strong		0.398	ERBB2IP-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000215070.1	NM_018695	
OR9G1	390174	hgsc.bcm.edu	37	11	56468225	56468225	+	Missense_Mutation	SNP	G	G	A	rs148651508	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr11:56468225G>A	ENST00000312153.1	+	1	362	c.362G>A	c.(361-363)cGc>cAc	p.R121H		NM_001005213.1	NP_001005213.1	Q8NH87	OR9G1_HUMAN	olfactory receptor, family 9, subfamily G, member 1	121						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)	p.R121P(1)		breast(2)|kidney(1)|lung(25)|stomach(2)|upper_aerodigestive_tract(1)	31						GCTTATGACCGCTACGTGGCC	0.527													G|||	5	0.000998403	0.0	0.0	5008	,	,		17980	0.0		0.0	False		,,,				2504	0.0051				p.R121H		Atlas-SNP	.											OR9G1,NS,carcinoma,0,1	.	.	1	1	Substitution - Missense(1)	lung(1)	c.G362A						scavenged	.	G	HIS/ARG	6,4396	4.2+/-10.8	0,6,2195	134.0	124.0	127.0		362	0.5	0.7	11	dbSNP_134	127	5,8587	4.3+/-15.6	0,5,4291	yes	missense	OR9G1	NM_001005213.1	29	0,11,6486	AA,AG,GG		0.0582,0.1363,0.0847	benign	121/306	56468225	11,12983	2201	4296	6497	SO:0001583	missense	504191	exon1			ATGACCGCTACGT	AB065500	CCDS31536.1	11q11	2012-08-09			ENSG00000174914	ENSG00000174914		"""GPCR / Class A : Olfactory receptors"""	15319	protein-coding gene	gene with protein product				OR9G5			Standard	NM_001005213		Approved			Q8NH87	OTTHUMG00000167112	ENST00000312153.1:c.362G>A	11.37:g.56468225G>A	ENSP00000309012:p.Arg121His	289.0	2.0	0.00692042		298.0	76.0	0.255034	NM_001013358	Q6IEU9|Q8NGQ0	Missense_Mutation	SNP	ENST00000312153.1	37	CCDS31536.1	.	.	.	.	.	.	.	.	.	.	G	9.545	1.114336	0.20795	0.001363	5.82E-4	ENSG00000174914	ENST00000312153	T	0.77489	-1.1	4.54	0.508	0.16972	GPCR, rhodopsin-like superfamily (1);	0.000000	0.56097	D	0.000040	T	0.76147	0.3947	M	0.88842	2.985	0.33993	D	0.649336	B	0.28026	0.198	B	0.26969	0.075	T	0.74272	-0.3719	10	0.72032	D	0.01	-11.8484	5.9681	0.19336	0.2233:0.0:0.6439:0.1329	.	121	Q8NH87	OR9G1_HUMAN	H	121	ENSP00000309012:R121H	ENSP00000309012:R121H	R	+	2	0	OR9G1	56224801	0.996000	0.38824	0.684000	0.30055	0.041000	0.13682	2.226000	0.42963	0.004000	0.14682	-0.203000	0.12734	CGC	G|1.000;A|0.000	0.000	weak		0.527	OR9G1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000393253.1	NM_001005213	
TMPRSS13	84000	hgsc.bcm.edu	37	11	117789327	117789327	+	Missense_Mutation	SNP	T	T	C	rs201746372|rs58754377|rs61900346	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr11:117789327T>C	ENST00000430170.2	-	2	335	c.248A>G	c.(247-249)cAg>cGg	p.Q83R	TMPRSS13_ENST00000445164.2_Missense_Mutation_p.Q83R|TMPRSS13_ENST00000526090.1_Missense_Mutation_p.Q83R|TMPRSS13_ENST00000524993.1_Missense_Mutation_p.Q83R|TMPRSS13_ENST00000528626.1_Missense_Mutation_p.Q83R	NM_001244995.1	NP_001231924.1	Q9BYE2	TMPSD_HUMAN	transmembrane protease, serine 13	83	13 X 5 AA repeats of A-S-P-A-[GLQR].|Ala-rich.					blood microparticle (GO:0072562)|integral component of membrane (GO:0016021)	scavenger receptor activity (GO:0005044)|serine-type endopeptidase activity (GO:0004252)	p.Q83_A87delQASPA(1)		endometrium(1)|kidney(3)|large_intestine(6)|lung(7)|pancreas(1)|prostate(1)|urinary_tract(1)	20	all_hematologic(175;0.0487)	Medulloblastoma(222;0.0425)|all_hematologic(192;0.196)|all_neural(223;0.234)		BRCA - Breast invasive adenocarcinoma(274;1.78e-05)|Epithelial(105;0.00106)		TGGAGATGCCTGGGCTGGAGA	0.672													t|||	6	0.00119808	0.0038	0.0	5008	,	,		14227	0.001		0.0	False		,,,				2504	0.0				p.Q83R		Atlas-SNP	.											TMPRSS13_ENST00000445164,NS,carcinoma,0,4	TMPRSS13	75	4	1	Deletion - In frame(1)	urinary_tract(1)	c.A248G						scavenged	.						30.0	37.0	35.0					11																	117789327		1948	4128	6076	SO:0001583	missense	84000	exon2			GATGCCTGGGCTG	AB048796	CCDS41721.1, CCDS55788.1, CCDS55789.1, CCDS58185.1	11q23	2010-04-13	2005-03-11	2005-03-12	ENSG00000137747	ENSG00000137747		"""Serine peptidases / Transmembrane"""	29808	protein-coding gene	gene with protein product		610050	"""transmembrane protease, serine 11"""	TMPRSS11		11267681	Standard	NM_001077263		Approved	MSPL	uc001prs.2	Q9BYE2	OTTHUMG00000166992	ENST00000430170.2:c.248A>G	11.37:g.117789327T>C	ENSP00000387702:p.Gln83Arg	108.0	1.0	0.00925926		266.0	25.0	0.093985	NM_001206790	B4DTM9|E9PIJ5|F8WAJ3|Q86YM4|Q96JY8|Q9BYE1	Missense_Mutation	SNP	ENST00000430170.2	37	CCDS58185.1	408|408	0.18681318681318682|0.18681318681318682	89|89	0.18089430894308944|0.18089430894308944	74|74	0.20441988950276244|0.20441988950276244	90|90	0.15734265734265734|0.15734265734265734	155|155	0.20448548812664907|0.20448548812664907	T|t	0.044|0.044	-1.272742|-1.272742	0.01421|0.01421	.|.	.|.	ENSG00000137747|ENSG00000137747	ENST00000336500|ENST00000528626;ENST00000524993;ENST00000430170;ENST00000445164;ENST00000526090	.|D;D;D;D;D	.|0.87729	.|-2.27;-2.29;-2.29;-2.27;-2.17	3.98|3.98	0.663|0.663	0.17885|0.17885	.|.	.|0.679012	.|0.12584	.|N	.|0.456148	.|T	.|0.00144	.|0.0004	.|.	.|.	.|.	0.80722|0.80722	P|P	0.0|0.0	.|B;B	.|0.02656	.|0.0;0.0	.|B;B	.|0.01281	.|0.0;0.0	.|T	.|0.10917	.|-1.0609	.|8	.|0.02654	.|T	.|1	.|.	6.985|6.985	0.24723|0.24723	0.0:0.7178:0.1731:0.1091|0.0:0.7178:0.1731:0.1091	rs61900346|rs61900346	.|78;83	.|Q9BYE2-4;E9PRA0	.|.;.	.|R	-1|83	.|ENSP00000435813:Q83R;ENSP00000434279:Q83R;ENSP00000387702:Q83R;ENSP00000394114:Q83R;ENSP00000436502:Q83R	.|ENSP00000387702:Q83R	.|Q	-|-	.|2	.|0	TMPRSS13|TMPRSS13	117294537|117294537	0.000000|0.000000	0.05858|0.05858	0.014000|0.014000	0.15608|0.15608	0.022000|0.022000	0.10575|0.10575	-1.912000|-1.912000	0.01582|0.01582	0.897000|0.897000	0.36392|0.36392	-0.390000|-0.390000	0.06520|0.06520	.|CAG	T|0.814;C|0.186	0.186	strong		0.672	TMPRSS13-006	PUTATIVE	basic|appris_candidate|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000392318.1	NM_032046	
PLAT	5327	hgsc.bcm.edu	37	8	42044965	42044965	+	Missense_Mutation	SNP	G	G	A	rs2020921	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr8:42044965G>A	ENST00000220809.4	-	6	746	c.490C>T	c.(490-492)Cgg>Tgg	p.R164W	PLAT_ENST00000429089.2_Missense_Mutation_p.R164W|PLAT_ENST00000352041.3_Missense_Mutation_p.R118W|PLAT_ENST00000519510.1_Intron|PLAT_ENST00000429710.2_Intron|PLAT_ENST00000524009.1_Intron|PLAT_ENST00000270189.6_Missense_Mutation_p.R164W	NM_000930.3	NP_000921.1	P00750	TPA_HUMAN	plasminogen activator, tissue	164	Kringle 1. {ECO:0000255|PROSITE- ProRule:PRU00121}.		R -> W (in dbSNP:rs2020921). {ECO:0000269|Ref.12}.		blood coagulation (GO:0007596)|cellular protein modification process (GO:0006464)|fibrinolysis (GO:0042730)|negative regulation of proteolysis (GO:0045861)|plasminogen activation (GO:0031639)|platelet-derived growth factor receptor signaling pathway (GO:0048008)|positive regulation of ovulation (GO:0060279)|proteolysis (GO:0006508)|regulation of synaptic plasticity (GO:0048167)|response to cAMP (GO:0051591)|response to glucocorticoid (GO:0051384)|response to hypoxia (GO:0001666)|response to peptide hormone (GO:0043434)|smooth muscle cell migration (GO:0014909)|synaptic transmission, glutamatergic (GO:0035249)	apical part of cell (GO:0045177)|cell surface (GO:0009986)|cytoplasm (GO:0005737)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|secretory granule (GO:0030141)|synapse (GO:0045202)	serine-type endopeptidase activity (GO:0004252)			breast(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(7)|lung(10)|skin(1)|soft_tissue(1)|urinary_tract(1)	27	all_cancers(6;3.84e-26)|all_epithelial(6;9.61e-28)|all_lung(13;7.2e-13)|Lung NSC(13;1.18e-11)|Ovarian(28;0.00438)|Prostate(17;0.0119)|Colorectal(14;0.0468)|Lung SC(25;0.211)	all_lung(54;0.000378)|Lung NSC(58;0.00145)|Hepatocellular(245;0.0524)|Renal(179;0.0822)|Esophageal squamous(32;0.0954)	BRCA - Breast invasive adenocarcinoma(8;5.23e-10)|OV - Ovarian serous cystadenocarcinoma(14;0.00135)|Colorectal(10;0.00165)|Lung(22;0.00467)|COAD - Colon adenocarcinoma(11;0.0171)|LUSC - Lung squamous cell carcinoma(45;0.024)		Aminocaproic Acid(DB00513)|Ibuprofen(DB01050)|Iloprost(DB01088)|Urokinase(DB00013)	TCTGGCCTCCGCCCGCTGTAG	0.652													G|||	34	0.00678914	0.0038	0.0029	5008	,	,		20354	0.0		0.0229	False		,,,				2504	0.0041				p.R164W		Atlas-SNP	.											PLAT,NS,carcinoma,+1,1	PLAT	62	1	0			c.C490T						PASS	.	G	TRP/ARG,TRP/ARG	22,4384	29.0+/-57.7	0,22,2181	43.0	42.0	43.0		490,352	1.9	0.3	8	dbSNP_94	43	191,8409	83.4+/-145.9	2,187,4111	yes	missense,missense	PLAT	NM_000930.3,NM_033011.2	101,101	2,209,6292	AA,AG,GG		2.2209,0.4993,1.6377	benign,benign	164/563,118/517	42044965	213,12793	2203	4300	6503	SO:0001583	missense	5327	exon6			GCCTCCGCCCGCT		CCDS6126.1, CCDS6127.1	8p11.21	2012-10-02			ENSG00000104368	ENSG00000104368			9051	protein-coding gene	gene with protein product		173370					Standard	NM_033011		Approved		uc003xos.2	P00750	OTTHUMG00000164072	ENST00000220809.4:c.490C>T	8.37:g.42044965G>A	ENSP00000220809:p.Arg164Trp	37.0	0.0	0		60.0	35.0	0.583333	NM_000930	A8K022|B2R8E8|Q15103|Q503B0|Q6PJA5|Q7Z7N2|Q86YK8|Q9BU99|Q9BZW1	Missense_Mutation	SNP	ENST00000220809.4	37	CCDS6126.1	20	0.009157509157509158	3	0.006097560975609756	2	0.0055248618784530384	0	0.0	15	0.01978891820580475	G	11.06	1.529003	0.27387	0.004993	0.022209	ENSG00000104368	ENST00000270189;ENST00000429089;ENST00000220809;ENST00000352041;ENST00000520523	T;T;T;T;T	0.67865	-0.29;-0.29;-0.29;-0.29;-0.29	5.95	1.92	0.25849	Kringle (4);Kringle-like fold (1);	0.147675	0.64402	N	0.000015	T	0.33614	0.0869	L	0.35288	1.05	0.34497	D	0.705653	B;B;B	0.24920	0.114;0.036;0.037	B;B;B	0.24848	0.035;0.021;0.056	T	0.47169	-0.9138	10	0.51188	T	0.08	.	5.6142	0.17422	0.0641:0.1146:0.4484:0.3729	rs2020921;rs2020921	164;118;164	B8ZX62;P00750-3;P00750	.;.;TPA_HUMAN	W	164;164;164;118;164	ENSP00000270189:R164W;ENSP00000392045:R164W;ENSP00000220809:R164W;ENSP00000270188:R118W;ENSP00000428797:R164W	ENSP00000220809:R164W	R	-	1	2	PLAT	42164122	0.009000	0.17119	0.283000	0.24790	0.227000	0.25037	1.460000	0.35244	0.376000	0.24707	0.655000	0.94253	CGG	G|0.987;A|0.013	0.013	strong		0.652	PLAT-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000377100.1	NM_000930	
KIAA0922	23240	hgsc.bcm.edu	37	4	154388363	154388363	+	Splice_Site	SNP	C	C	T	rs78441178	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	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		218.0	0.0	0		137.0	93.0	0.678832	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
PRX	57716	hgsc.bcm.edu	37	19	40909695	40909695	+	Silent	SNP	T	T	G			TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr19:40909695T>G	ENST00000324001.7	-	5	372	c.102A>C	c.(100-102)gtA>gtC	p.V34V	PRX_ENST00000291825.7_Silent_p.V34V	NM_181882.2	NP_870998.2	Q9BXM0	PRAX_HUMAN	periaxin	34	PDZ. {ECO:0000255|PROSITE- ProRule:PRU00143}.				axon ensheathment (GO:0008366)|cell death (GO:0008219)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|plasma membrane (GO:0005886)				breast(1)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(7)|lung(12)|ovary(2)|prostate(3)|skin(1)|urinary_tract(9)	47			Lung(22;6.24e-05)|LUSC - Lung squamous cell carcinoma(20;0.000384)			CGCCGCCCGCTACGTTGATGC	0.692																																					p.V34V		Atlas-SNP	.											.	PRX	151	.	0			c.A102C						PASS	.						15.0	14.0	14.0					19																	40909695		2193	4294	6487	SO:0001819	synonymous_variant	57716	exon5			GCCCGCTACGTTG	AB046840	CCDS12556.1, CCDS33028.1	19q13.2	2014-09-17				ENSG00000105227			13797	protein-coding gene	gene with protein product		605725				10839370, 9143514	Standard	NM_181882		Approved	KIAA1620	uc002onr.3	Q9BXM0		ENST00000324001.7:c.102A>C	19.37:g.40909695T>G		159.0	0.0	0		116.0	56.0	0.482759	NM_181882	Q9BXL9|Q9HCF2	Silent	SNP	ENST00000324001.7	37	CCDS33028.1																																																																																			.	.	none		0.692	PRX-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000462582.1	NM_020956	
BRWD1	54014	hgsc.bcm.edu	37	21	40574434	40574434	+	Missense_Mutation	SNP	T	T	C	rs144295288	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr21:40574434T>C	ENST00000333229.2	-	38	4729	c.4402A>G	c.(4402-4404)Ata>Gta	p.I1468V	BRWD1_ENST00000380800.3_Missense_Mutation_p.I1468V|BRWD1_ENST00000342449.3_Missense_Mutation_p.I1468V	NM_018963.4	NP_061836.2	Q9NSI6	BRWD1_HUMAN	bromodomain and WD repeat domain containing 1	1468					cytoskeleton organization (GO:0007010)|regulation of cell shape (GO:0008360)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)				cervix(2)|endometrium(6)|kidney(8)|large_intestine(14)|liver(2)|lung(13)|ovary(1)|pancreas(1)|prostate(2)|skin(7)|urinary_tract(2)	58		Prostate(19;8.44e-08)|all_epithelial(19;0.223)				TCAGGAATTATTTTTGTCTGA	0.398													T|||	7	0.00139776	0.0	0.0	5008	,	,		18729	0.0		0.007	False		,,,				2504	0.0				p.I1468V	Melanoma(170;988 1986 4794 16843 39731)	Atlas-SNP	.											.	BRWD1	325	.	0			c.A4402G						PASS	.	T	VAL/ILE,VAL/ILE	6,4400	9.9+/-24.2	0,6,2197	72.0	67.0	69.0		4402,4402	3.4	0.7	21	dbSNP_134	69	46,8554	29.0+/-79.6	2,42,4256	yes	missense,missense	BRWD1	NM_018963.4,NM_033656.3	29,29	2,48,6453	CC,CT,TT		0.5349,0.1362,0.3998	benign,benign	1468/2321,1468/2270	40574434	52,12954	2203	4300	6503	SO:0001583	missense	54014	exon38			GAATTATTTTTGT	AJ002572	CCDS13662.1, CCDS13663.1, CCDS33557.1	21q22.2	2013-05-21	2005-05-13	2005-05-13	ENSG00000185658	ENSG00000185658		"""WD repeat domain containing"""	12760	protein-coding gene	gene with protein product			"""chromosome 21 open reading frame 107"", ""WD repeat domain 9"""	C21orf107, WDR9			Standard	NM_033656		Approved	FLJ11315, N143	uc002yxk.2	Q9NSI6	OTTHUMG00000066030	ENST00000333229.2:c.4402A>G	21.37:g.40574434T>C	ENSP00000330753:p.Ile1468Val	115.0	0.0	0		151.0	55.0	0.364238	NM_018963	C9JK25|O43721|Q5R2V0|Q5R2V1|Q6P2D1|Q8TCV3|Q96QG9|Q96QH0|Q9NUK1	Missense_Mutation	SNP	ENST00000333229.2	37	CCDS13662.1	6|6	0.0027472527472527475|0.0027472527472527475	0|0	0.0|0.0	0|0	0.0|0.0	0|0	0.0|0.0	6|6	0.0079155672823219|0.0079155672823219	T|T	0.007|0.007	-1.938401|-1.938401	0.00484|0.00484	0.001362|0.001362	0.005349|0.005349	ENSG00000185658|ENSG00000185658	ENST00000333229;ENST00000342449;ENST00000380800;ENST00000380783|ENST00000424441	T;T;T|.	0.52983|.	0.64;0.66;0.73|.	5.27|5.27	3.39|3.39	0.38822|0.38822	.|.	0.692467|.	0.13487|.	N|.	0.384267|.	T|T	0.04815|0.04815	0.0130|0.0130	N|N	0.00436|0.00436	-1.5|-1.5	0.09310|0.09310	N|N	1|1	B;B;B|.	0.02656|.	0.0;0.0;0.0|.	B;B;B|.	0.04013|.	0.001;0.001;0.0|.	T|T	0.33727|0.33727	-0.9857|-0.9857	10|5	0.24483|.	T|.	0.36|.	-2.138|-2.138	4.6929|4.6929	0.12790|0.12790	0.0:0.5271:0.151:0.3219|0.0:0.5271:0.151:0.3219	.|.	1468;1468;1468|.	Q9NSI6-3;Q9NSI6-2;Q9NSI6|.	.;.;BRWD1_HUMAN|.	V|S	1468;1468;1468;424|405	ENSP00000330753:I1468V;ENSP00000344333:I1468V;ENSP00000370178:I1468V|.	ENSP00000330753:I1468V|.	I|N	-|-	1|2	0|0	BRWD1|BRWD1	39496304|39496304	0.054000|0.054000	0.20591|0.20591	0.729000|0.729000	0.30791|0.30791	0.351000|0.351000	0.29236|0.29236	0.360000|0.360000	0.20250|0.20250	0.608000|0.608000	0.30000|0.30000	-0.177000|-0.177000	0.13119|0.13119	ATA|AAT	T|0.997;C|0.003	0.003	strong		0.398	BRWD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000141398.3	NM_033656	
PVR	5817	hgsc.bcm.edu	37	19	45153113	45153113	+	Missense_Mutation	SNP	G	G	C	rs35959395	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr19:45153113G>C	ENST00000425690.3	+	3	759	c.460G>C	c.(460-462)Gtc>Ctc	p.V154L	PVR_ENST00000403059.4_Missense_Mutation_p.V154L|PVR_ENST00000406449.4_Missense_Mutation_p.V154L|CTB-171A8.1_ENST00000590796.1_RNA|PVR_ENST00000344956.4_Missense_Mutation_p.V154L	NM_006505.3	NP_006496.3	P15151	PVR_HUMAN	poliovirus receptor	154	Ig-like C2-type 1.				adherens junction organization (GO:0034332)|cell adhesion (GO:0007155)|cell junction assembly (GO:0034329)|cell-cell junction organization (GO:0045216)|positive regulation of natural killer cell mediated cytotoxicity (GO:0045954)|positive regulation of natural killer cell mediated cytotoxicity directed against tumor cell target (GO:0002860)|regulation of immune response (GO:0050776)|susceptibility to natural killer cell mediated cytotoxicity (GO:0042271)|susceptibility to T cell mediated cytotoxicity (GO:0060370)|viral process (GO:0016032)	cell surface (GO:0009986)|cytoplasm (GO:0005737)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	cell adhesion molecule binding (GO:0050839)|receptor activity (GO:0004872)			large_intestine(2)|lung(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	6	Lung NSC(12;0.00608)|all_lung(12;0.0148)	Medulloblastoma(540;0.0425)|Ovarian(192;0.0728)|Prostate(69;0.081)|all_neural(266;0.112)		Epithelial(262;0.000601)		GGTTCAGAAGGTCCAGCTCAC	0.602													G|||	6	0.00119808	0.0	0.0	5008	,	,		16803	0.0		0.006	False		,,,				2504	0.0				p.V154L		Atlas-SNP	.											.	PVR	23	.	0			c.G460C						PASS	.	G	LEU/VAL,LEU/VAL,LEU/VAL,LEU/VAL	2,4404	4.2+/-10.8	0,2,2201	121.0	129.0	126.0		460,460,460,460	-0.5	0.0	19	dbSNP_126	126	19,8581	11.9+/-42.8	0,19,4281	yes	missense,missense,missense,missense	PVR	NM_001135768.1,NM_001135769.1,NM_001135770.1,NM_006505.3	32,32,32,32	0,21,6482	CC,CG,GG		0.2209,0.0454,0.1615	probably-damaging,probably-damaging,probably-damaging,probably-damaging	154/373,154/365,154/393,154/418	45153113	21,12985	2203	4300	6503	SO:0001583	missense	5817	exon3			CAGAAGGTCCAGC	BC015542	CCDS12640.1, CCDS46105.1, CCDS46106.1, CCDS46107.1	19q13.2	2013-01-29			ENSG00000073008	ENSG00000073008		"""CD molecules"", ""Immunoglobulin superfamily / V-set domain containing"", ""Immunoglobulin superfamily / C2-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	9705	protein-coding gene	gene with protein product	"""nectin-like 5"""	173850		PVS		2170108	Standard	XM_005259120		Approved	CD155, HVED, Necl-5, NECL5, Tage4	uc002ozm.3	P15151	OTTHUMG00000151527	ENST00000425690.3:c.460G>C	19.37:g.45153113G>C	ENSP00000402060:p.Val154Leu	155.0	0.0	0		133.0	60.0	0.451128	NM_001135769	B4DTS9|P15152|Q15267|Q15268|Q96BJ1	Missense_Mutation	SNP	ENST00000425690.3	37	CCDS12640.1	3	0.0013736263736263737	0	0.0	0	0.0	0	0.0	3	0.00395778364116095	G	15.03	2.712862	0.48517	4.54E-4	0.002209	ENSG00000073008	ENST00000344956;ENST00000425690;ENST00000406449;ENST00000403059	T;T;T;T	0.76316	-1.01;-1.01;-1.01;-1.01	4.35	-0.515	0.11954	CD80-like, immunoglobulin C2-set (1);Immunoglobulin-like (1);	1.055660	0.07497	N	0.906707	D	0.86493	0.5946	M	0.90309	3.105	0.09310	N	1	P;D;D;D	0.59767	0.842;0.983;0.983;0.986	P;D;D;D	0.74023	0.698;0.957;0.969;0.982	T	0.70328	-0.4902	10	0.20046	T	0.44	.	4.0615	0.09841	0.3186:0.1848:0.4966:0.0	rs35959395	154;154;154;154	P15151-2;P15151-3;P15151-4;P15151	.;.;.;PVR_HUMAN	L	154	ENSP00000340870:V154L;ENSP00000402060:V154L;ENSP00000383907:V154L;ENSP00000385344:V154L	ENSP00000340870:V154L	V	+	1	0	PVR	49844953	0.005000	0.15991	0.000000	0.03702	0.020000	0.10135	0.802000	0.27069	-0.290000	0.09025	-0.339000	0.08088	GTC	G|0.999;C|0.001	0.001	strong		0.602	PVR-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000323017.2	NM_006505	
KRTAP13-4	284827	hgsc.bcm.edu	37	21	31802629	31802629	+	Silent	SNP	C	C	T	rs73356729	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr21:31802629C>T	ENST00000334068.2	+	1	58	c.36C>T	c.(34-36)tcC>tcT	p.S12S		NM_181600.1	NP_853631.1	Q3LI77	KR134_HUMAN	keratin associated protein 13-4	12						intermediate filament (GO:0005882)				NS(1)|breast(1)|kidney(1)|large_intestine(2)|lung(9)|skin(1)	15						ACTTCTCCTCCCGCTCCTTTG	0.547													-|||	220	0.0439297	0.1581	0.0144	5008	,	,		18637	0.0		0.001	False		,,,				2504	0.0				p.S12S	NSCLC(196;2401 3038 18004 35753)	Atlas-SNP	.											.	KRTAP13-4	46	.	0			c.C36T						PASS	.	C		473,3933		25,423,1755	109.0	111.0	110.0		36	0.1	0.1	21	dbSNP_130	110	10,8590		0,10,4290	no	coding-synonymous	KRTAP13-4	NM_181600.1		25,433,6045	TT,TC,CC		0.1163,10.7354,3.7137		12/161	31802629	483,12523	2203	4300	6503	SO:0001819	synonymous_variant	284827	exon1			CTCCTCCCGCTCC	AP001708	CCDS13592.1	21q22.1	2006-03-13			ENSG00000186971	ENSG00000186971		"""Keratin associated proteins"""	18926	protein-coding gene	gene with protein product						12359730	Standard	NM_181600		Approved	KAP13.4	uc011acw.2	Q3LI77	OTTHUMG00000057770	ENST00000334068.2:c.36C>T	21.37:g.31802629C>T		181.0	0.0	0		240.0	79.0	0.329167	NM_181600	A2RRL3	Silent	SNP	ENST00000334068.2	37	CCDS13592.1																																																																																			C|0.963;T|0.037	0.037	strong		0.547	KRTAP13-4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000128222.1		
RTTN	25914	hgsc.bcm.edu	37	18	67755252	67755252	+	Missense_Mutation	SNP	C	C	G	rs376382612		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr18:67755252C>G	ENST00000255674.6	-	31	4561	c.4275G>C	c.(4273-4275)caG>caC	p.Q1425H	RTTN_ENST00000454359.1_3'UTR|RTTN_ENST00000437017.1_Missense_Mutation_p.Q1425H	NM_173630.3	NP_775901.3	Q86VV8	RTTN_HUMAN	rotatin	1425					determination of left/right symmetry (GO:0007368)	ciliary basal body (GO:0036064)|cytoplasm (GO:0005737)				NS(1)|breast(3)|central_nervous_system(2)|endometrium(11)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(9)|lung(35)|ovary(4)|pancreas(2)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	80		Esophageal squamous(42;0.129)				TACATTCTGACTGGTCCAGAA	0.483																																					p.Q1425H		Atlas-SNP	.											.	RTTN	184	.	0			c.G4275C						PASS	.	C	HIS/GLN	0,3862		0,0,1931	100.0	98.0	98.0		4275	-1.0	1.0	18		98	1,8241		0,1,4120	no	missense	RTTN	NM_173630.3	24	0,1,6051	GG,GC,CC		0.0121,0.0,0.0083	benign	1425/2227	67755252	1,12103	1931	4121	6052	SO:0001583	missense	25914	exon31			TTCTGACTGGTCC	AL117635	CCDS42443.1	18q22.1	2008-08-01				ENSG00000176225			18654	protein-coding gene	gene with protein product		610436				11900971	Standard	NM_173630		Approved	DKFZP434G145	uc002lkp.2	Q86VV8		ENST00000255674.6:c.4275G>C	18.37:g.67755252C>G	ENSP00000255674:p.Gln1425His	70.0	0.0	0		59.0	26.0	0.440678	NM_173630	Q68CS9|Q6ZRL8|Q6ZTK3|Q86TG4|Q8N8N8|Q8TBQ4|Q96IN9|Q9UFJ4	Missense_Mutation	SNP	ENST00000255674.6	37	CCDS42443.1	.	.	.	.	.	.	.	.	.	.	C	12.24	1.878046	0.33162	0.0	1.21E-4	ENSG00000176225	ENST00000255674;ENST00000437017	T;T	0.68331	-0.32;-0.32	5.45	-0.961	0.10337	Armadillo-like helical (1);	0.110450	0.64402	D	0.000007	T	0.43389	0.1245	L	0.35414	1.06	0.80722	D	1	P	0.34934	0.476	B	0.26094	0.066	T	0.10428	-1.0630	10	0.40728	T	0.16	.	5.2259	0.15393	0.2225:0.4534:0.0:0.3242	.	1425	Q86VV8	RTTN_HUMAN	H	1425	ENSP00000255674:Q1425H;ENSP00000399520:Q1425H	ENSP00000255674:Q1425H	Q	-	3	2	RTTN	65906232	0.988000	0.35896	0.987000	0.45799	0.968000	0.65278	0.302000	0.19192	0.074000	0.16767	0.484000	0.47621	CAG	.	.	weak		0.483	RTTN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000442988.1	NM_173630	
MSI2	124540	hgsc.bcm.edu	37	17	55752389	55752389	+	Missense_Mutation	SNP	G	G	A	rs116924898	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr17:55752389G>A	ENST00000284073.2	+	12	1056	c.847G>A	c.(847-849)Gcc>Acc	p.A283T	MSI2_ENST00000579505.1_3'UTR|MSI2_ENST00000442934.2_Missense_Mutation_p.A222T|MSI2_ENST00000416426.2_Missense_Mutation_p.A279T	NM_138962.2	NP_620412.1	Q96DH6	MSI2H_HUMAN	musashi RNA-binding protein 2	283						cytoplasm (GO:0005737)|polysome (GO:0005844)	nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)|poly(U) RNA binding (GO:0008266)			central_nervous_system(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(2)|ovary(1)|pancreas(1)|skin(1)	7	Breast(9;1.78e-08)			GBM - Glioblastoma multiforme(1;0.0025)		AGGACCTGTCGCCGATCTCTA	0.687			T	HOXA9	CML								G|||	15	0.00299521	0.0008	0.0043	5008	,	,		15149	0.0		0.0099	False		,,,				2504	0.001				p.A283T		Atlas-SNP	.		Dom	yes		17	17q23.2	124540	musashi homolog 2 (Drosophila)		L	.	MSI2	52	.	0			c.G847A						PASS	.	G	THR/ALA	7,4399	11.4+/-27.6	0,7,2196	47.0	58.0	55.0		847	4.5	1.0	17	dbSNP_132	55	94,8500	49.8+/-109.6	0,94,4203	yes	missense	MSI2	NM_138962.2	58	0,101,6399	AA,AG,GG		1.0938,0.1589,0.7769	probably-damaging	283/329	55752389	101,12899	2203	4297	6500	SO:0001583	missense	124540	exon12			CCTGTCGCCGATC	BC001526	CCDS11596.1, CCDS11597.1	17q23.2	2013-07-16	2012-12-13					"""RNA binding motif (RRM) containing"""	18585	protein-coding gene	gene with protein product		607897	"""musashi homolog 2 (Drosophila)"""			11588182	Standard	NM_138962		Approved		uc002iuz.1	Q96DH6		ENST00000284073.2:c.847G>A	17.37:g.55752389G>A	ENSP00000284073:p.Ala283Thr	142.0	0.0	0		120.0	57.0	0.475	NM_138962	Q7Z6M7|Q8N9T4	Missense_Mutation	SNP	ENST00000284073.2	37	CCDS11596.1	12	0.005494505494505495	1	0.0020325203252032522	2	0.0055248618784530384	0	0.0	9	0.011873350923482849	G	25.8	4.674614	0.88445	0.001589	0.010938	ENSG00000153944	ENST00000416426;ENST00000284073;ENST00000442934	D;D;D	0.85773	-2.03;-2.03;-2.03	4.48	4.48	0.54585	.	0.000000	0.85682	D	0.000000	D	0.87014	0.6072	M	0.63428	1.95	0.80722	D	1	D;D	0.89917	0.999;1.0	D;D	0.71656	0.959;0.974	D	0.85771	0.1355	10	0.15952	T	0.53	.	17.1487	0.86773	0.0:0.0:1.0:0.0	.	279;283	B4DHE8;Q96DH6	.;MSI2H_HUMAN	T	279;283;222	ENSP00000414671:A279T;ENSP00000284073:A283T;ENSP00000392607:A222T	ENSP00000284073:A283T	A	+	1	0	MSI2	53107388	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	9.418000	0.97395	2.038000	0.60285	0.491000	0.48974	GCC	A|0.007;C|0.000;G|0.992	0.007	strong		0.687	MSI2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000441813.1		
GBP1	2633	hgsc.bcm.edu	37	1	89523911	89523911	+	Missense_Mutation	SNP	C	C	T	rs75161612	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr1:89523911C>T	ENST00000370473.4	-	6	857	c.638G>A	c.(637-639)aGt>aAt	p.S213N	GBP1_ENST00000484970.1_5'Flank	NM_002053.2	NP_002044.2	P32455	GBP1_HUMAN	guanylate binding protein 1, interferon-inducible	213	GB1/RHD3-type G.|GTPase domain (Globular).				cytokine-mediated signaling pathway (GO:0019221)|defense response to virus (GO:0051607)|interferon-gamma-mediated signaling pathway (GO:0060333)	cytosol (GO:0005829)|extracellular region (GO:0005576)|Golgi apparatus (GO:0005794)|membrane (GO:0016020)	GTP binding (GO:0005525)|GTPase activity (GO:0003924)|identical protein binding (GO:0042802)			endometrium(7)|kidney(4)|large_intestine(8)|lung(6)|ovary(1)|prostate(1)|skin(2)|urinary_tract(1)	30		Lung NSC(277;0.123)		all cancers(265;0.0156)|Epithelial(280;0.0291)		ATCTTTTTGACTGGTACCTAG	0.368													.|||	91	0.0181709	0.0053	0.0159	5008	,	,		16962	0.0		0.0298	False		,,,				2504	0.044				p.S213N		Atlas-SNP	.											.	GBP1	68	.	0			c.G638A						PASS	.	C	ASN/SER	30,4374	31.7+/-61.6	0,30,2172	97.0	109.0	105.0		638	-2.4	0.0	1	dbSNP_131	105	220,8380	88.4+/-150.7	1,218,4081	yes	missense	GBP1	NM_002053.2	46	1,248,6253	TT,TC,CC		2.5581,0.6812,1.9225	benign	213/593	89523911	250,12754	2202	4300	6502	SO:0001583	missense	2633	exon6			TTTTGACTGGTAC	BC002666	CCDS718.1	1p22.2	2011-03-09	2011-03-09		ENSG00000117228	ENSG00000117228			4182	protein-coding gene	gene with protein product		600411	"""guanylate binding protein 1, interferon-inducible, 67kDa"""			7518790	Standard	NM_002053		Approved		uc001dmx.2	P32455	OTTHUMG00000010614	ENST00000370473.4:c.638G>A	1.37:g.89523911C>T	ENSP00000359504:p.Ser213Asn	55.0	0.0	0		27.0	27.0	1	NM_002053	D3DT26|Q5T8M1	Missense_Mutation	SNP	ENST00000370473.4	37	CCDS718.1	27	0.012362637362637362	4	0.008130081300813009	6	0.016574585635359115	0	0.0	17	0.022427440633245383	C	0.084	-1.178538	0.01633	0.006812	0.025581	ENSG00000117228	ENST00000370473;ENST00000542693	T	0.73789	-0.78	4.48	-2.37	0.06643	Guanylate-binding protein, N-terminal (1);	1.837820	0.02201	N	0.062280	T	0.24928	0.0605	N	0.11845	0.185	0.09310	N	1	B	0.02656	0.0	B	0.04013	0.001	T	0.15925	-1.0420	10	0.06757	T	0.87	.	5.8264	0.18556	0.0:0.432:0.1405:0.4275	.	213	P32455	GBP1_HUMAN	N	213;176	ENSP00000359504:S213N	ENSP00000359504:S213N	S	-	2	0	GBP1	89296499	0.000000	0.05858	0.000000	0.03702	0.013000	0.08279	-2.686000	0.00834	-0.598000	0.05806	0.313000	0.20887	AGT	C|0.981;T|0.019	0.019	strong		0.368	GBP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000029289.3	NM_002053	
CKM	1158	hgsc.bcm.edu	37	19	45815163	45815163	+	Missense_Mutation	SNP	G	G	A	rs17357122	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr19:45815163G>A	ENST00000221476.3	-	5	671	c.497C>T	c.(496-498)aCg>aTg	p.T166M		NM_001824.4	NP_001815.2	P06732	KCRM_HUMAN	creatine kinase, muscle	166	Phosphagen kinase C-terminal. {ECO:0000255|PROSITE-ProRule:PRU00843}.		T -> M (in dbSNP:rs17357122).		cellular nitrogen compound metabolic process (GO:0034641)|creatine metabolic process (GO:0006600)|phosphocreatine biosynthetic process (GO:0046314)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)	ATP binding (GO:0005524)|creatine kinase activity (GO:0004111)			cervix(1)|endometrium(1)|large_intestine(8)|lung(3)|prostate(2)|skin(2)	17		Ovarian(192;0.0336)|all_neural(266;0.112)		OV - Ovarian serous cystadenocarcinoma(262;2.29e-44)|Epithelial(262;1.05e-38)|GBM - Glioblastoma multiforme(486;3.56e-07)	Creatine(DB00148)	GAACTCGCCCGTCAGGCTGTT	0.597													G|||	14	0.00279553	0.0015	0.0043	5008	,	,		15490	0.0		0.007	False		,,,				2504	0.002				p.T166M		Atlas-SNP	.											.	CKM	40	.	0			c.C497T						PASS	.	G	MET/THR	12,4394	19.1+/-41.9	0,12,2191	77.0	61.0	67.0		497	4.6	1.0	19	dbSNP_123	67	66,8534	40.8+/-97.7	0,66,4234	yes	missense	CKM	NM_001824.3	81	0,78,6425	AA,AG,GG		0.7674,0.2724,0.5997	possibly-damaging	166/382	45815163	78,12928	2203	4300	6503	SO:0001583	missense	1158	exon5			TCGCCCGTCAGGC	M14780	CCDS12659.1	19q13.32	2012-10-02			ENSG00000104879	ENSG00000104879	2.7.3.2		1994	protein-coding gene	gene with protein product		123310		CKMM			Standard	NM_001824		Approved		uc002pbd.4	P06732		ENST00000221476.3:c.497C>T	19.37:g.45815163G>A	ENSP00000221476:p.Thr166Met	189.0	0.0	0		152.0	58.0	0.381579	NM_001824	Q96QL9	Missense_Mutation	SNP	ENST00000221476.3	37	CCDS12659.1	9	0.004120879120879121	1	0.0020325203252032522	2	0.0055248618784530384	0	0.0	6	0.0079155672823219	g	17.70	3.454039	0.63290	0.002724	0.007674	ENSG00000104879	ENST00000221476	T	0.24151	1.87	4.64	4.64	0.57946	ATP:guanido phosphotransferase, catalytic domain (2);Glutamine synthetase/guanido kinase, catalytic domain (1);	0.255179	0.38959	N	0.001515	T	0.32734	0.0839	M	0.84683	2.71	0.42644	D	0.99342	P	0.49185	0.92	P	0.45998	0.5	T	0.51164	-0.8740	10	0.72032	D	0.01	-36.3443	15.0589	0.71936	0.0:0.0:1.0:0.0	rs17357122;rs52824783;rs17357122	166	P06732	KCRM_HUMAN	M	166	ENSP00000221476:T166M	ENSP00000221476:T166M	T	-	2	0	CKM	50507003	0.984000	0.35163	0.997000	0.53966	0.892000	0.51952	2.104000	0.41815	2.421000	0.82119	0.556000	0.70494	ACG	G|0.995;A|0.005	0.005	strong		0.597	CKM-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000457569.1		
APOD	347	hgsc.bcm.edu	37	3	195306289	195306289	+	Missense_Mutation	SNP	A	A	G	rs5952	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr3:195306289A>G	ENST00000343267.3	-	2	405	c.44T>C	c.(43-45)tTc>tCc	p.F15S		NM_001647.3	NP_001638.1	P05090	APOD_HUMAN	apolipoprotein D	15			F -> S (in dbSNP:rs5952). {ECO:0000269|PubMed:10391209}.		aging (GO:0007568)|angiogenesis (GO:0001525)|brain development (GO:0007420)|glucose metabolic process (GO:0006006)|lipid metabolic process (GO:0006629)|lipid transport (GO:0006869)|negative regulation of cytokine production involved in inflammatory response (GO:1900016)|negative regulation of focal adhesion assembly (GO:0051895)|negative regulation of lipoprotein lipid oxidation (GO:0060588)|negative regulation of monocyte chemotactic protein-1 production (GO:0071638)|negative regulation of platelet-derived growth factor receptor signaling pathway (GO:0010642)|negative regulation of protein import into nucleus (GO:0042308)|negative regulation of smooth muscle cell proliferation (GO:0048662)|negative regulation of smooth muscle cell-matrix adhesion (GO:2000098)|negative regulation of T cell migration (GO:2000405)|peripheral nervous system axon regeneration (GO:0014012)|response to axon injury (GO:0048678)|response to drug (GO:0042493)|response to reactive oxygen species (GO:0000302)|tissue regeneration (GO:0042246)	cytosolic ribosome (GO:0022626)|dendrite (GO:0030425)|endoplasmic reticulum (GO:0005783)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|neuronal cell body (GO:0043025)|perinuclear region of cytoplasm (GO:0048471)	cholesterol binding (GO:0015485)|lipid transporter activity (GO:0005319)			breast(1)|endometrium(1)|large_intestine(1)|lung(1)|ovary(3)|skin(1)|upper_aerodigestive_tract(1)	9	all_cancers(143;1.8e-08)|Ovarian(172;0.0634)	Lung NSC(153;0.191)	Epithelial(36;1e-21)|all cancers(36;9.02e-20)|OV - Ovarian serous cystadenocarcinoma(49;1.6e-18)|Lung(62;0.000104)|LUSC - Lung squamous cell carcinoma(58;0.000128)	GBM - Glioblastoma multiforme(46;1.66e-05)		TGCCGCACCGAAGAGGCCAGC	0.582													A|||	7	0.00139776	0.0	0.0043	5008	,	,		18597	0.0		0.004	False		,,,				2504	0.0				p.F15S		Atlas-SNP	.											.	APOD	28	.	0			c.T44C						PASS	.	A	SER/PHE	6,4400	9.9+/-24.2	0,6,2197	41.0	44.0	43.0		44	1.6	0.0	3	dbSNP_52	43	54,8546	30.1+/-81.4	0,54,4246	yes	missense	APOD	NM_001647.3	155	0,60,6443	GG,GA,AA		0.6279,0.1362,0.4613	benign	15/190	195306289	60,12946	2203	4300	6503	SO:0001583	missense	347	exon2			GCACCGAAGAGGC		CCDS33925.1	3q29	2013-09-19			ENSG00000189058	ENSG00000189058		"""Lipocalins"", ""Apolipoproteins"""	612	protein-coding gene	gene with protein product		107740				2439269, 3453108	Standard	NM_001647		Approved		uc003fur.2	P05090	OTTHUMG00000155854	ENST00000343267.3:c.44T>C	3.37:g.195306289A>G	ENSP00000345179:p.Phe15Ser	50.0	0.0	0		53.0	24.0	0.45283	NM_001647	B2R579|D3DNW6|Q6IBG6	Missense_Mutation	SNP	ENST00000343267.3	37	CCDS33925.1	7	0.003205128205128205	0	0.0	3	0.008287292817679558	0	0.0	4	0.005277044854881266	A	12.13	1.844610	0.32606	0.001362	0.006279	ENSG00000189058	ENST00000343267;ENST00000421243;ENST00000453131	T;T;T	0.21031	2.03;2.03;2.03	5.68	1.61	0.23674	Calycin (1);	0.701798	0.13384	N	0.391946	T	0.11196	0.0273	L	0.38175	1.15	0.09310	N	1	B;B	0.09022	0.001;0.002	B;B	0.06405	0.002;0.002	T	0.19976	-1.0289	10	0.62326	D	0.03	-0.2464	7.3764	0.26831	0.7035:0.0:0.2965:0.0	rs5952	15;15	B4DGC3;P05090	.;APOD_HUMAN	S	15;43;15	ENSP00000345179:F15S;ENSP00000415235:F43S;ENSP00000393076:F15S	ENSP00000345179:F15S	F	-	2	0	APOD	196787578	0.127000	0.22367	0.000000	0.03702	0.009000	0.06853	1.338000	0.33873	0.434000	0.26340	0.533000	0.62120	TTC	A|0.996;G|0.004	0.004	strong		0.582	APOD-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000342004.1	NM_001647	
ZNF33A	7581	hgsc.bcm.edu	37	10	38345455	38345455	+	Silent	SNP	A	A	G	rs12242343	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr10:38345455A>G	ENST00000458705.2	+	5	2558	c.2400A>G	c.(2398-2400)ggA>ggG	p.G800G	ZNF33A_ENST00000469037.2_Intron|ZNF33A_ENST00000432900.2_Silent_p.G807G|ZNF33A_ENST00000374618.3_Silent_p.G801G|ZNF33A_ENST00000307441.9_Silent_p.G800G			Q06730	ZN33A_HUMAN	zinc finger protein 33A	800					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)			cervix(2)|endometrium(2)|large_intestine(8)|liver(2)|lung(27)|ovary(2)|prostate(1)|skin(2)	46						CACACTGTGGAGAAAGCCCTG	0.388													A|||	140	0.0279553	0.0915	0.013	5008	,	,		18836	0.0		0.0099	False		,,,				2504	0.0				p.G801G		Atlas-SNP	.											.	ZNF33A	103	.	0			c.A2403G						PASS	.	A	,	359,4047	175.9+/-205.1	19,321,1863	61.0	59.0	60.0		2403,2400	1.9	0.1	10	dbSNP_120	60	53,8547	32.3+/-84.9	0,53,4247	no	coding-synonymous,coding-synonymous	ZNF33A	NM_006954.1,NM_006974.2	,	19,374,6110	GG,GA,AA		0.6163,8.148,3.1678	,	801/812,800/811	38345455	412,12594	2203	4300	6503	SO:0001819	synonymous_variant	7581	exon5			CTGTGGAGAAAGC	D31763	CCDS31182.1, CCDS60514.1, CCDS73088.1, CCDS73089.1	10p11.2	2013-01-08	2005-03-18		ENSG00000189180	ENSG00000189180		"""Zinc fingers, C2H2-type"", ""-"""	13096	protein-coding gene	gene with protein product	"""zinc finger and ZAK associated protein with KRAB domain"""	194521	"""zinc finger protein 33a (KOX 31)"", ""zinc finger protein 11A"""	ZNF33, ZNF11A		2014798, 8464732	Standard	NM_006974		Approved	KOX5, KOX31, KIAA0065, FLJ23404, ZZAPK	uc031pui.1	Q06730	OTTHUMG00000017983	ENST00000458705.2:c.2400A>G	10.37:g.38345455A>G		102.0	0.0	0		66.0	17.0	0.257576	NM_006954	A8K9X9|B4E0M8|F6TH33|F8WAJ5|P17013|Q5VZ86	Silent	SNP	ENST00000458705.2	37	CCDS31182.1																																																																																			A|0.968;G|0.032	0.032	strong		0.388	ZNF33A-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000047614.1	NM_006974	
FAM118A	55007	hgsc.bcm.edu	37	22	45719125	45719125	+	Silent	SNP	C	C	T	rs138980075	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr22:45719125C>T	ENST00000216214.3	+	4	951	c.117C>T	c.(115-117)agC>agT	p.S39S	FAM118A_ENST00000405673.1_Silent_p.S39S|FAM118A_ENST00000441876.2_Silent_p.S39S	NM_001104595.1	NP_001098065.1	Q9NWS6	F118A_HUMAN	family with sequence similarity 118, member A	39						integral component of membrane (GO:0016021)				endometrium(2)|kidney(2)|large_intestine(2)|lung(3)|stomach(1)|upper_aerodigestive_tract(1)	11		Ovarian(80;0.00965)|all_neural(38;0.0416)		UCEC - Uterine corpus endometrioid carcinoma (28;0.0178)		CTGGCGTCAGCGCAGCAGTGG	0.572													C|||	10	0.00199681	0.0	0.0014	5008	,	,		17209	0.0		0.006	False		,,,				2504	0.0031				p.S39S		Atlas-SNP	.											.	FAM118A	32	.	0			c.C117T						PASS	.	C	,	2,4404	4.2+/-10.8	0,2,2201	44.0	49.0	47.0		117,117	-11.3	0.0	22	dbSNP_134	47	36,8564	23.4+/-69.3	0,36,4264	no	coding-synonymous,coding-synonymous	FAM118A	NM_001104595.1,NM_017911.2	,	0,38,6465	TT,TC,CC		0.4186,0.0454,0.2922	,	39/358,39/358	45719125	38,12968	2203	4300	6503	SO:0001819	synonymous_variant	55007	exon3			CGTCAGCGCAGCA	BC013696	CCDS14065.1	22q13.3	2006-04-26	2006-04-26	2006-04-26	ENSG00000100376	ENSG00000100376			1313	protein-coding gene	gene with protein product			"""chromosome 22 open reading frame 8"""	C22orf8		12477932	Standard	NM_001104595		Approved	FLJ20635, bK268H5.C22.4	uc003bga.4	Q9NWS6	OTTHUMG00000151338	ENST00000216214.3:c.117C>T	22.37:g.45719125C>T		165.0	0.0	0		175.0	83.0	0.474286	NM_017911	B3KWG4|B4DY02|Q5TII5|Q96CY3	Silent	SNP	ENST00000216214.3	37	CCDS14065.1																																																																																			C|0.997;T|0.003	0.003	strong		0.572	FAM118A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000322260.1	NM_017911	
LRRIQ1	84125	hgsc.bcm.edu	37	12	85450426	85450426	+	Missense_Mutation	SNP	G	G	A	rs74720621	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr12:85450426G>A	ENST00000393217.2	+	8	1916	c.1855G>A	c.(1855-1857)Gaa>Aaa	p.E619K		NM_001079910.1	NP_001073379.1	Q96JM4	LRIQ1_HUMAN	leucine-rich repeats and IQ motif containing 1	619										breast(1)|central_nervous_system(1)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(2)|kidney(4)|large_intestine(21)|liver(1)|lung(28)|ovary(5)|prostate(1)|skin(8)|stomach(2)|upper_aerodigestive_tract(2)	83				GBM - Glioblastoma multiforme(134;0.212)		ACTAACATCAGAAAATTCCAA	0.284													G|||	17	0.00339457	0.0	0.0029	5008	,	,		17719	0.0		0.0149	False		,,,				2504	0.0				p.E619K		Atlas-SNP	.											.	LRRIQ1	512	.	0			c.G1855A						PASS	.	G	LYS/GLU	5,4371		0,5,2183	24.0	25.0	24.0		1855	5.3	0.2	12	dbSNP_132	24	96,8474		0,96,4189	yes	missense	LRRIQ1	NM_001079910.1	56	0,101,6372	AA,AG,GG		1.1202,0.1143,0.7802	possibly-damaging	619/1723	85450426	101,12845	2188	4285	6473	SO:0001583	missense	84125	exon8			ACATCAGAAAATT	AK022365	CCDS41816.1	12q21	2008-02-05			ENSG00000133640	ENSG00000133640			25708	protein-coding gene	gene with protein product						11347906	Standard	NM_001079910		Approved	FLJ12303, KIAA1801	uc001tac.3	Q96JM4	OTTHUMG00000166185	ENST00000393217.2:c.1855G>A	12.37:g.85450426G>A	ENSP00000376910:p.Glu619Lys	118.0	0.0	0		99.0	46.0	0.464646	NM_001079910	Q567P4|Q9BS17|Q9HA36	Missense_Mutation	SNP	ENST00000393217.2	37	CCDS41816.1	13	0.005952380952380952	0	0.0	1	0.0027624309392265192	0	0.0	12	0.0158311345646438	G	18.93	3.728055	0.69074	0.001143	0.011202	ENSG00000133640	ENST00000256007;ENST00000378580;ENST00000393217	T	0.53423	0.62	5.32	5.32	0.75619	.	0.664291	0.13539	N	0.380378	T	0.25606	0.0623	L	0.29908	0.895	0.29964	N	0.819151	P;P	0.47350	0.807;0.894	B;B	0.43950	0.294;0.437	T	0.20571	-1.0271	10	0.41790	T	0.15	.	13.6724	0.62434	0.0767:0.0:0.9233:0.0	.	619;594	Q96JM4;C9JI57	LRIQ1_HUMAN;.	K	619;594;619	ENSP00000376910:E619K	ENSP00000256007:E619K	E	+	1	0	LRRIQ1	83974557	1.000000	0.71417	0.163000	0.22734	0.028000	0.11728	3.334000	0.52097	2.640000	0.89533	0.591000	0.81541	GAA	G|0.992;A|0.008	0.008	strong		0.284	LRRIQ1-004	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000388249.2	NM_032165	
OSMR	9180	hgsc.bcm.edu	37	5	38904082	38904082	+	Missense_Mutation	SNP	T	T	C	rs35117676	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr5:38904082T>C	ENST00000274276.3	+	8	1492	c.1090T>C	c.(1090-1092)Tat>Cat	p.Y364H		NM_003999.2	NP_003990.1	Q99650	OSMR_HUMAN	oncostatin M receptor	364	Fibronectin type-III 1. {ECO:0000255|PROSITE-ProRule:PRU00316}.				cell proliferation (GO:0008283)|cell surface receptor signaling pathway (GO:0007166)|oncostatin-M-mediated signaling pathway (GO:0038165)|positive regulation of acute inflammatory response (GO:0002675)|positive regulation of cell proliferation (GO:0008284)|response to cytokine (GO:0034097)	oncostatin-M receptor complex (GO:0005900)	growth factor binding (GO:0019838)|oncostatin-M receptor activity (GO:0004924)			NS(1)|breast(3)|central_nervous_system(2)|endometrium(1)|kidney(1)|large_intestine(8)|lung(20)|ovary(2)|pancreas(2)|prostate(1)|skin(3)|upper_aerodigestive_tract(2)	46	all_lung(31;0.000365)					TAATTTCACATATTTGTGTCA	0.328													T|||	18	0.00359425	0.0	0.0072	5008	,	,		18317	0.0		0.0109	False		,,,				2504	0.002				p.Y364H		Atlas-SNP	.											.	OSMR	133	.	0			c.T1090C						PASS	.	T	HIS/TYR	16,4390	24.3+/-50.5	0,16,2187	61.0	63.0	62.0		1090	-1.3	0.0	5	dbSNP_126	62	124,8474	64.9+/-127.2	1,122,4176	yes	missense	OSMR	NM_003999.2	83	1,138,6363	CC,CT,TT		1.4422,0.3631,1.0766	benign	364/980	38904082	140,12864	2203	4299	6502	SO:0001583	missense	9180	exon8			TTCACATATTTGT	U60805	CCDS3928.1, CCDS54847.1	5p13.2	2013-02-11			ENSG00000145623	ENSG00000145623		"""Fibronectin type III domain containing"""	8507	protein-coding gene	gene with protein product		601743				8999038	Standard	NM_001168355		Approved	OSMRB	uc003jln.2	Q99650	OTTHUMG00000090811	ENST00000274276.3:c.1090T>C	5.37:g.38904082T>C	ENSP00000274276:p.Tyr364His	387.0	1.0	0.00258398		365.0	171.0	0.468493	NM_003999	Q6P4E8|Q96QJ6	Missense_Mutation	SNP	ENST00000274276.3	37	CCDS3928.1	13	0.005952380952380952	0	0.0	3	0.008287292817679558	0	0.0	10	0.013192612137203167	T	12.79	2.044954	0.36085	0.003631	0.014422	ENSG00000145623	ENST00000274276	T	0.53640	0.61	5.75	-1.26	0.09376	Fibronectin, type III (3);Immunoglobulin-like fold (1);	0.457709	0.22766	N	0.055885	T	0.19644	0.0472	N	0.22421	0.69	0.09310	N	1	P	0.48640	0.913	B	0.37601	0.254	T	0.25222	-1.0138	10	0.87932	D	0	.	9.3318	0.38027	0.0:0.32:0.0:0.68	rs35117676	364	Q99650	OSMR_HUMAN	H	364	ENSP00000274276:Y364H	ENSP00000274276:Y364H	Y	+	1	0	OSMR	38939839	0.001000	0.12720	0.002000	0.10522	0.020000	0.10135	-0.039000	0.12124	-0.126000	0.11682	-0.408000	0.06270	TAT	T|0.991;C|0.009	0.009	strong		0.328	OSMR-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000207609.2	NM_003999	
PIKFYVE	200576	hgsc.bcm.edu	37	2	209168942	209168942	+	Silent	SNP	C	C	T			TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr2:209168942C>T	ENST00000264380.4	+	11	1526	c.1368C>T	c.(1366-1368)aaC>aaT	p.N456N	PIKFYVE_ENST00000392202.3_Silent_p.N359N|PIKFYVE_ENST00000407449.1_Silent_p.N456N|PIKFYVE_ENST00000308862.6_Silent_p.N370N	NM_015040.3	NP_055855.2	Q9Y2I7	FYV1_HUMAN	phosphoinositide kinase, FYVE finger containing	456					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						ACTCAGTGAACTCCGTGGAAG	0.443																																					p.N456N		Atlas-SNP	.											.	PIKFYVE	223	.	0			c.C1368T						PASS	.						125.0	120.0	122.0					2																	209168942		2203	4300	6503	SO:0001819	synonymous_variant	200576	exon11			AGTGAACTCCGTG	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.1368C>T	2.37:g.209168942C>T		93.0	0.0	0		59.0	42.0	0.711864	NM_015040	Q08AR7|Q08AR8|Q53ST3|Q53T36|Q8N5H0|Q8NB67	Silent	SNP	ENST00000264380.4	37	CCDS2382.1																																																																																			.	.	none		0.443	PIKFYVE-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256477.2	NM_015040	
CNOT4	4850	hgsc.bcm.edu	37	7	135098310	135098310	+	Missense_Mutation	SNP	C	C	T			TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr7:135098310C>T	ENST00000315544.5	-	6	893	c.614G>A	c.(613-615)tGt>tAt	p.C205Y	CNOT4_ENST00000361528.4_Missense_Mutation_p.C205Y|CNOT4_ENST00000356162.4_Missense_Mutation_p.C205Y|CNOT4_ENST00000541284.1_Missense_Mutation_p.C205Y|CNOT4_ENST00000414802.1_Missense_Mutation_p.C205Y|CNOT4_ENST00000451834.1_Missense_Mutation_p.C205Y|CNOT4_ENST00000428680.2_Missense_Mutation_p.C205Y|CNOT4_ENST00000423368.2_Missense_Mutation_p.C205Y	NM_001190848.1	NP_001177777.1	O95628	CNOT4_HUMAN	CCR4-NOT transcription complex, subunit 4	205					gene expression (GO:0010467)|mRNA metabolic process (GO:0016071)|nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay (GO:0000288)|nuclear-transcribed mRNA poly(A) tail shortening (GO:0000289)|protein autoubiquitination (GO:0051865)|RNA metabolic process (GO:0016070)	cytosol (GO:0005829)|nucleus (GO:0005634)	ligase activity (GO:0016874)|nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			autonomic_ganglia(1)|endometrium(3)|kidney(1)|large_intestine(5)|lung(10)|prostate(1)|skin(1)	22						AGGTTTTGGACACTGCATATT	0.418																																					p.C205Y	Ovarian(51;766 1130 5502 35047 50875)	Atlas-SNP	.											.	CNOT4	146	.	0			c.G614A						PASS	.						130.0	118.0	122.0					7																	135098310		1876	4110	5986	SO:0001583	missense	4850	exon6			TTTGGACACTGCA	AF180475	CCDS43650.1, CCDS47719.1, CCDS55164.1, CCDS55165.1, CCDS55166.1, CCDS55167.1	7q33	2013-09-19			ENSG00000080802	ENSG00000080802		"""RNA binding motif (RRM) containing"""	7880	protein-coding gene	gene with protein product		604911		NOT4		10637334	Standard	NM_013316		Approved	CLONE243, NOT4H	uc011kpy.2	O95628	OTTHUMG00000155568	ENST00000315544.5:c.614G>A	7.37:g.135098310C>T	ENSP00000326731:p.Cys205Tyr	242.0	0.0	0		133.0	72.0	0.541353	NM_001190850	B7Z6I4|E7ET38|F8VQP3|O95339|O95627|Q8IYM7|Q8NCL0|Q9NPQ1|Q9NZN6	Missense_Mutation	SNP	ENST00000315544.5	37	CCDS55166.1	.	.	.	.	.	.	.	.	.	.	C	20.8	4.043251	0.75732	.	.	ENSG00000080802	ENST00000541284;ENST00000451834;ENST00000423368;ENST00000262563;ENST00000361528;ENST00000414802;ENST00000356162;ENST00000428680;ENST00000315544	D;D;T;D;T;T;D;D	0.82619	-1.52;-1.57;-1.44;-1.51;-1.38;-1.38;-1.63;-1.56	5.95	5.07	0.68467	Zinc finger, CCCH-type (1);	0.000000	0.85682	D	0.000000	D	0.92756	0.7697	M	0.91612	3.225	0.80722	D	1	D;D;D;D;B;D	0.89917	1.0;1.0;1.0;1.0;0.16;0.997	D;D;D;D;B;D	0.97110	0.999;1.0;0.999;1.0;0.051;0.991	D	0.94292	0.7529	10	0.87932	D	0	-12.3216	15.3196	0.74112	0.0:0.9329:0.0:0.0671	.	205;205;205;205;205;205	E7ET38;F8VQP3;O95628;O95628-2;O95628-4;O95628-8	.;.;CNOT4_HUMAN;.;.;.	Y	205	ENSP00000445508:C205Y;ENSP00000388491:C205Y;ENSP00000406777:C205Y;ENSP00000354673:C205Y;ENSP00000416532:C205Y;ENSP00000348485:C205Y;ENSP00000399108:C205Y;ENSP00000326731:C205Y	ENSP00000262563:C205Y	C	-	2	0	CNOT4	134748850	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	7.506000	0.81665	1.527000	0.49086	0.563000	0.77884	TGT	.	.	none		0.418	CNOT4-201	KNOWN	basic|CCDS	protein_coding	protein_coding		NM_013316	
LAMC1	3915	hgsc.bcm.edu	37	1	183079729	183079729	+	Missense_Mutation	SNP	C	C	T	rs142614579	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr1:183079729C>T	ENST00000258341.4	+	4	1218	c.961C>T	c.(961-963)Cct>Tct	p.P321S		NM_002293.3	NP_002284.3	P11047	LAMC1_HUMAN	laminin, gamma 1 (formerly LAMB2)	321	Laminin EGF-like 1. {ECO:0000255|PROSITE- ProRule:PRU00460}.				axon guidance (GO:0007411)|cell adhesion (GO:0007155)|cell migration (GO:0016477)|endoderm development (GO:0007492)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|hemidesmosome assembly (GO:0031581)|positive regulation of epithelial cell proliferation (GO:0050679)|protein complex assembly (GO:0006461)|substrate adhesion-dependent cell spreading (GO:0034446)	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)	extracellular matrix structural constituent (GO:0005201)|glycosphingolipid binding (GO:0043208)			NS(2)|breast(5)|central_nervous_system(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(17)|lung(27)|ovary(3)|prostate(2)|skin(3)|upper_aerodigestive_tract(3)	76						AAAGTGTCTTCCTTTCTTCAA	0.473																																					p.P321S		Atlas-SNP	.											.	LAMC1	176	.	0			c.C961T						PASS	.	C	SER/PRO	3,4403	6.2+/-15.9	0,3,2200	188.0	184.0	186.0		961	4.9	0.3	1	dbSNP_134	186	4,8596	3.7+/-12.6	0,4,4296	yes	missense	LAMC1	NM_002293.3	74	0,7,6496	TT,TC,CC		0.0465,0.0681,0.0538	probably-damaging	321/1610	183079729	7,12999	2203	4300	6503	SO:0001583	missense	3915	exon4			TGTCTTCCTTTCT	J03202	CCDS1351.1	1q31	2013-03-01			ENSG00000135862	ENSG00000135862		"""Laminins"""	6492	protein-coding gene	gene with protein product		150290		LAMB2		3234037	Standard	NM_002293		Approved		uc001gpy.4	P11047	OTTHUMG00000035418	ENST00000258341.4:c.961C>T	1.37:g.183079729C>T	ENSP00000258341:p.Pro321Ser	162.0	0.0	0		203.0	122.0	0.600985	NM_002293	Q5VYE7	Missense_Mutation	SNP	ENST00000258341.4	37	CCDS1351.1	.	.	.	.	.	.	.	.	.	.	C	23.2	4.382348	0.82792	6.81E-4	4.65E-4	ENSG00000135862	ENST00000258341	T	0.62498	0.02	4.87	4.87	0.63330	EGF-like, laminin (4);	0.054481	0.85682	D	0.000000	T	0.76026	0.3930	M	0.79475	2.455	0.80722	D	1	P	0.46142	0.873	P	0.54026	0.74	T	0.80443	-0.1380	10	0.87932	D	0	.	17.9961	0.89184	0.0:1.0:0.0:0.0	.	321	P11047	LAMC1_HUMAN	S	321	ENSP00000258341:P321S	ENSP00000258341:P321S	P	+	1	0	LAMC1	181346352	0.998000	0.40836	0.254000	0.24359	0.975000	0.68041	3.714000	0.54889	2.239000	0.73571	0.305000	0.20034	CCT	C|0.999;T|0.001	0.001	strong		0.473	LAMC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000085954.2	NM_002293	
MYO5A	4644	hgsc.bcm.edu	37	15	52635394	52635394	+	Splice_Site	SNP	T	T	A	rs61731219	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr15:52635394T>A	ENST00000399231.3	-	31	4203	c.3960A>T	c.(3958-3960)agA>agT	p.R1320S	MYO5A_ENST00000553916.1_Intron|MYO5A_ENST00000358212.6_Splice_Site_p.R1320S|MYO5A_ENST00000356338.6_Intron|MYO5A_ENST00000399233.2_Splice_Site_p.R1317S	NM_000259.3	NP_000250	Q9Y4I1	MYO5A_HUMAN	myosin VA (heavy chain 12, myoxin)	1320					actin filament-based movement (GO:0030048)|anagen (GO:0042640)|cellular protein metabolic process (GO:0044267)|cellular response to insulin stimulus (GO:0032869)|endoplasmic reticulum localization (GO:0051643)|exocytosis (GO:0006887)|insulin secretion (GO:0030073)|locomotion involved in locomotory behavior (GO:0031987)|long-chain fatty acid biosynthetic process (GO:0042759)|melanin biosynthetic process (GO:0042438)|melanocyte differentiation (GO:0030318)|melanosome transport (GO:0032402)|membrane organization (GO:0061024)|myelination (GO:0042552)|odontogenesis (GO:0042476)|post-Golgi vesicle-mediated transport (GO:0006892)|protein localization to plasma membrane (GO:0072659)|protein transport (GO:0015031)|regulation of inositol 1,4,5-trisphosphate-sensitive calcium-release channel activity (GO:0031585)|secretory granule localization (GO:0032252)|synapse organization (GO:0050808)|synaptic transmission (GO:0007268)|transport (GO:0006810)|vesicle transport along actin filament (GO:0030050)|vesicle-mediated transport (GO:0016192)|visual perception (GO:0007601)	actomyosin (GO:0042641)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|filopodium tip (GO:0032433)|Golgi apparatus (GO:0005794)|growth cone (GO:0030426)|insulin-responsive compartment (GO:0032593)|intermediate filament (GO:0005882)|melanosome (GO:0042470)|membrane (GO:0016020)|microtubule plus-end (GO:0035371)|myosin complex (GO:0016459)|neuron projection (GO:0043005)|neuronal cell body (GO:0043025)|photoreceptor outer segment (GO:0001750)|ruffle (GO:0001726)	ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|microfilament motor activity (GO:0000146)|poly(A) RNA binding (GO:0044822)|Rab GTPase binding (GO:0017137)			breast(4)|central_nervous_system(1)|cervix(2)|endometrium(5)|kidney(7)|large_intestine(12)|lung(19)|ovary(3)|skin(3)|stomach(1)	57				all cancers(107;0.0085)|Colorectal(133;0.077)|READ - Rectum adenocarcinoma(133;0.196)		GAGCAGATGATCTTCCATGCA	0.408													T|||	58	0.0115815	0.0023	0.0072	5008	,	,		19797	0.0		0.0437	False		,,,				2504	0.0061				p.R1320S		Atlas-SNP	.											.	MYO5A	145	.	0			c.A3960T						PASS	.	T	SER/ARG,	24,3884		0,24,1930	92.0	85.0	87.0		3960,	5.9	1.0	15	dbSNP_129	87	339,7997		6,327,3835	yes	missense-near-splice,intron	MYO5A	NM_000259.3,NM_001142495.1	110,	6,351,5765	AA,AT,TT		4.0667,0.6141,2.9647	benign,	1320/1856,	52635394	363,11881	1954	4168	6122	SO:0001630	splice_region_variant	4644	exon31			AGATGATCTTCCA		CCDS42037.1, CCDS45262.1	15q21	2014-09-17	2006-09-29		ENSG00000197535	ENSG00000197535		"""Myosins / Myosin superfamily : Class V"""	7602	protein-coding gene	gene with protein product	"""myosin, heavy polypeptide kinase"", ""myosin heavy chain 12"", ""myoxin"", ""myosin V"""	160777	"""myosin VA (heavy polypeptide 12, myoxin)"""	MYH12		8188282, 8022818	Standard	NM_000259		Approved	MYO5, GS1, MYR12	uc002aby.2	Q9Y4I1	OTTHUMG00000137383	ENST00000399231.3:c.3960-1A>T	15.37:g.52635394T>A		152.0	0.0	0		56.0	48.0	0.857143	NM_000259	A8MZC5|O60653|Q07902|Q16249|Q9UE30|Q9UE31	Missense_Mutation	SNP	ENST00000399231.3	37	CCDS42037.1	37	0.01694139194139194	0	0.0	4	0.011049723756906077	0	0.0	33	0.04353562005277045	T	15.01	2.706322	0.48412	0.006141	0.040667	ENSG00000197535	ENST00000399231;ENST00000399233;ENST00000358212;ENST00000399228	T;T;T;T	0.04454	3.62;3.62;3.62;3.62	5.87	5.87	0.94306	.	0.059846	0.64402	D	0.000003	T	0.02807	0.0084	L	0.43152	1.355	0.80722	D	1	D;D;P	0.61080	0.989;0.989;0.495	D;D;B	0.75020	0.985;0.985;0.034	T	0.05566	-1.0877	10	0.38643	T	0.18	.	10.8931	0.47006	0.0:0.0783:0.0:0.9217	rs61731219	110;113;1320	Q9UES5;O95317;Q9Y4I1	.;.;MYO5A_HUMAN	S	1320;1317;1320;110	ENSP00000382177:R1320S;ENSP00000382179:R1317S;ENSP00000350945:R1320S;ENSP00000382174:R110S	ENSP00000350945:R1320S	R	-	3	2	MYO5A	50422686	1.000000	0.71417	1.000000	0.80357	0.989000	0.77384	3.751000	0.55165	2.236000	0.73375	0.528000	0.53228	AGA	T|0.955;A|0.045	0.045	strong		0.408	MYO5A-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000268102.1	NM_000259	Missense_Mutation
MUC17	140453	hgsc.bcm.edu	37	7	100681917	100681917	+	Missense_Mutation	SNP	T	T	G	rs111633703	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr7:100681917T>G	ENST00000306151.4	+	3	7284	c.7220T>G	c.(7219-7221)aTg>aGg	p.M2407R		NM_001040105.1	NP_001035194.1	Q685J3	MUC17_HUMAN	mucin 17, cell surface associated	2407	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)					GTCAGCACCATGCCGGTGGTC	0.507																																					p.M2407R		Atlas-SNP	.											.	MUC17	804	.	0			c.T7220G						PASS	.						383.0	363.0	370.0					7																	100681917		2203	4300	6503	SO:0001583	missense	140453	exon3			GCACCATGCCGGT	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.7220T>G	7.37:g.100681917T>G	ENSP00000302716:p.Met2407Arg	217.0	0.0	0		326.0	16.0	0.0490798	NM_001040105	O14761|Q685J2|Q8TDH7	Missense_Mutation	SNP	ENST00000306151.4	37	CCDS34711.1	.	.	.	.	.	.	.	.	.	.	N	0.009	-1.819708	0.00595	.	.	ENSG00000169876	ENST00000306151	T	0.02216	4.39	0.679	-1.36	0.09085	.	.	.	.	.	T	0.01156	0.0038	N	0.14661	0.345	0.09310	N	1	P	0.35139	0.486	B	0.22601	0.04	T	0.50311	-0.8843	9	0.17832	T	0.49	.	7.4277	0.27109	0.0:0.7775:0.0:0.2225	.	2407	Q685J3	MUC17_HUMAN	R	2407	ENSP00000302716:M2407R	ENSP00000302716:M2407R	M	+	2	0	MUC17	100468637	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-0.128000	0.10531	-1.293000	0.02362	-1.602000	0.00811	ATG	T|0.996;C|0.004	.	alt		0.507	MUC17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347161.1	NM_001040105	
MUC2	4583	hgsc.bcm.edu	37	11	1093344	1093344	+	Silent	SNP	G	G	T			TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr11:1093344G>T	ENST00000441003.2	+	30	5190	c.5163G>T	c.(5161-5163)ccG>ccT	p.P1721P	MUC2_ENST00000333592.6_Silent_p.P9P|MUC2_ENST00000361558.6_Intron|MUC2_ENST00000359061.5_Silent_p.P1688P	NM_002457.2	NP_002448.2	Q02817	MUC2_HUMAN	mucin 2, oligomeric mucus/gel-forming	0	Approximate repeats.				cellular protein metabolic process (GO:0044267)|maintenance of gastrointestinal epithelium (GO:0030277)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	Golgi lumen (GO:0005796)|inner mucus layer (GO:0070702)|outer mucus layer (GO:0070703)		p.P1688P(1)|p.P1721P(1)		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)	ccccaaccccgacacccatct	0.642																																					p.P1721P		Atlas-SNP	.											MUC2_ENST00000441003,NS,carcinoma,0,2	MUC2	614	2	2	Substitution - coding silent(2)	lung(2)	c.G5163T						PASS	.						231.0	269.0	256.0					11																	1093344		1975	3757	5732	SO:0001819	synonymous_variant	4583	exon30			AACCCCGACACCC	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.5163G>T	11.37:g.1093344G>T		88.0	0.0	0		77.0	7.0	0.0909091	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	
DMKN	93099	hgsc.bcm.edu	37	19	36002421	36002421	+	Silent	SNP	A	A	G	rs72334573	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr19:36002421A>G	ENST00000339686.3	-	5	986	c.810T>C	c.(808-810)ggT>ggC	p.G270G	DMKN_ENST00000492341.2_5'Flank|DMKN_ENST00000429837.1_Intron|DMKN_ENST00000488892.1_5'Flank|DMKN_ENST00000474928.1_5'Flank|DMKN_ENST00000440396.1_Silent_p.G270G|DMKN_ENST00000424570.2_Silent_p.G270G|DMKN_ENST00000392206.2_5'Flank|DMKN_ENST00000467637.1_5'Flank|DMKN_ENST00000402589.2_5'Flank|DMKN_ENST00000451297.2_Silent_p.G270G|DMKN_ENST00000602781.1_5'Flank|DMKN_ENST00000419602.1_Intron|DMKN_ENST00000436012.1_5'Flank|DMKN_ENST00000458071.1_5'Flank|DMKN_ENST00000480502.1_5'Flank|DMKN_ENST00000447113.2_Silent_p.G270G|DMKN_ENST00000472252.2_5'Flank|DMKN_ENST00000461300.1_5'Flank|DMKN_ENST00000414866.2_5'Flank|DMKN_ENST00000443640.1_5'Flank|DMKN_ENST00000418261.1_Silent_p.G270G|DMKN_ENST00000462126.1_5'Flank	NM_033317.4	NP_201574	Q6E0U4	DMKN_HUMAN	dermokine	270	Gly-rich.					extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)				NS(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(8)|lung(7)|ovary(1)|prostate(1)|skin(2)	27	all_lung(56;1.89e-08)|Lung NSC(56;2.9e-08)|Esophageal squamous(110;0.162)		LUSC - Lung squamous cell carcinoma(66;0.0724)			tgctgctgccaccactgctgc	0.652																																					p.G270G		Atlas-SNP	.											DMKN,colon,carcinoma,0,1	DMKN	116	1	0			c.T810C						PASS	.						30.0	23.0	25.0					19																	36002421		2166	4245	6411	SO:0001819	synonymous_variant	93099	exon5			GCTGCCACCACTG	BC035311	CCDS12463.1, CCDS42549.1, CCDS46051.1, CCDS46052.1, CCDS46053.1, CCDS46054.1, CCDS46054.2, CCDS54250.1, CCDS54251.1, CCDS54252.1	19q13.12	2008-10-27			ENSG00000161249	ENSG00000161249			25063	protein-coding gene	gene with protein product						16374476	Standard	NM_001035516		Approved	ZD52F10	uc002nzm.4	Q6E0U4	OTTHUMG00000048101	ENST00000339686.3:c.810T>C	19.37:g.36002421A>G		35.0	0.0	0		72.0	6.0	0.0833333	NM_001126058	A3EZ79|A3EZ80|A3EZ81|A3EZ82|A3EZ83|C9J4P6|C9J5N8|C9JAL3|Q32W58|Q32W62|Q32W63|Q32W64|Q32W65|Q32W66|Q32W67|Q6E0U5|Q6UXC7|Q96EW8|Q9BSY6	Silent	SNP	ENST00000339686.3	37	CCDS12463.1																																																																																			.	.	none		0.652	DMKN-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000109461.2	NM_033317	
ITSN2	50618	hgsc.bcm.edu	37	2	24426581	24426581	+	Missense_Mutation	SNP	G	G	A	rs140804905	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr2:24426581G>A	ENST00000355123.4	-	40	5451	c.5008C>T	c.(5008-5010)Cgc>Tgc	p.R1670C	AC008073.9_ENST00000429717.1_RNA|ITSN2_ENST00000361999.3_Missense_Mutation_p.R1643C	NM_006277.2	NP_006268.2	Q9NZM3	ITSN2_HUMAN	intersectin 2	1670					endocytosis (GO:0006897)|positive regulation of signal transduction (GO:0009967)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)	calcium ion binding (GO:0005509)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)|SH3/SH2 adaptor activity (GO:0005070)			breast(1)|central_nervous_system(1)|cervix(1)|endometrium(5)|kidney(8)|large_intestine(11)|liver(3)|lung(28)|ovary(2)|stomach(1)	61	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)					AGCAGTCGGCGGGTCATAGGG	0.507													G|||	4	0.000798722	0.0023	0.0	5008	,	,		16966	0.0		0.001	False		,,,				2504	0.0				p.R1670C		Atlas-SNP	.											.	ITSN2	224	.	0			c.C5008T						PASS	.	G	CYS/ARG,CYS/ARG	2,4404	4.2+/-10.8	0,2,2201	82.0	83.0	83.0		5008,4927	4.5	1.0	2	dbSNP_134	83	4,8596	3.7+/-12.6	0,4,4296	yes	missense,missense	ITSN2	NM_006277.2,NM_019595.3	180,180	0,6,6497	AA,AG,GG		0.0465,0.0454,0.0461	probably-damaging,probably-damaging	1670/1698,1643/1671	24426581	6,13000	2203	4300	6503	SO:0001583	missense	50618	exon40			GTCGGCGGGTCAT	AB033082	CCDS1710.2, CCDS1711.2, CCDS46230.1	2p23.3	2013-09-19	2002-10-30		ENSG00000198399	ENSG00000198399		"""Rho guanine nucleotide exchange factors"", ""EF-hand domain containing"""	6184	protein-coding gene	gene with protein product	"""SH3 domain protein 1B"", ""SH3P18-like WASP associated protein"""	604464	"""SH3 domain protein 1B"""	SH3D1B		10922467, 11748279	Standard	NM_006277		Approved	KIAA1256, SWAP, SH3P18, SWA, PRO2015	uc002rfe.2	Q9NZM3	OTTHUMG00000090818	ENST00000355123.4:c.5008C>T	2.37:g.24426581G>A	ENSP00000347244:p.Arg1670Cys	82.0	0.0	0		77.0	32.0	0.415584	NM_006277	O95062|Q15812|Q9HAK4|Q9NXE6|Q9NYG0|Q9NZM2|Q9ULG4	Missense_Mutation	SNP	ENST00000355123.4	37	CCDS1710.2	5	0.0022893772893772895	4	0.008130081300813009	0	0.0	0	0.0	1	0.0013192612137203166	G	16.42	3.118003	0.56505	4.54E-4	4.65E-4	ENSG00000198399	ENST00000361999;ENST00000355123;ENST00000380868	T;T;T	0.67523	-0.27;-0.27;-0.27	5.46	4.52	0.55395	C2 calcium/lipid-binding domain, CaLB (1);	0.412335	0.15639	U	0.251972	T	0.69611	0.3130	L	0.54323	1.7	0.53005	D	0.999968	D;D	0.89917	1.0;1.0	D;P	0.65773	0.938;0.869	T	0.73877	-0.3844	10	0.87932	D	0	.	11.956	0.52981	0.0:0.0:0.6677:0.3323	.	1643;1670	Q9NZM3-2;Q9NZM3	.;ITSN2_HUMAN	C	1643;1670;1643	ENSP00000354561:R1643C;ENSP00000347244:R1670C;ENSP00000370250:R1643C	ENSP00000347244:R1670C	R	-	1	0	ITSN2	24280085	1.000000	0.71417	1.000000	0.80357	0.911000	0.54048	4.498000	0.60373	2.735000	0.93741	0.561000	0.74099	CGC	G|0.999;A|0.001	0.001	strong		0.507	ITSN2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000207620.2	NM_006277	
CCND1	595	hgsc.bcm.edu	37	11	69457987	69457987	+	Silent	SNP	C	C	T	rs371689281		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr11:69457987C>T	ENST00000227507.2	+	2	614	c.387C>T	c.(385-387)gaC>gaT	p.D129D	CCND1_ENST00000536559.1_Intron	NM_053056.2	NP_444284.1	P24385	CCND1_HUMAN	cyclin D1	129	Cyclin N-terminal.				canonical Wnt signaling pathway (GO:0060070)|cell division (GO:0051301)|cellular response to DNA damage stimulus (GO:0006974)|endoplasmic reticulum unfolded protein response (GO:0030968)|fat cell differentiation (GO:0045444)|G1/S transition of mitotic cell cycle (GO:0000082)|lactation (GO:0007595)|Leydig cell differentiation (GO:0033327)|liver development (GO:0001889)|mammary gland alveolus development (GO:0060749)|mammary gland epithelial cell proliferation (GO:0033598)|mitotic cell cycle (GO:0000278)|mitotic G1 DNA damage checkpoint (GO:0031571)|negative regulation of cell cycle arrest (GO:0071157)|negative regulation of epithelial cell differentiation (GO:0030857)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of Wnt signaling pathway (GO:0030178)|Notch signaling pathway (GO:0007219)|organ regeneration (GO:0031100)|positive regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0045737)|positive regulation of G2/M transition of mitotic cell cycle (GO:0010971)|positive regulation of mammary gland epithelial cell proliferation (GO:0033601)|positive regulation of protein phosphorylation (GO:0001934)|re-entry into mitotic cell cycle (GO:0000320)|response to calcium ion (GO:0051592)|response to corticosterone (GO:0051412)|response to drug (GO:0042493)|response to estrogen (GO:0043627)|response to ethanol (GO:0045471)|response to iron ion (GO:0010039)|response to magnesium ion (GO:0032026)|response to organonitrogen compound (GO:0010243)|response to UV-A (GO:0070141)|response to vitamin E (GO:0033197)|response to X-ray (GO:0010165)|transcription, DNA-templated (GO:0006351)	cyclin-dependent protein kinase holoenzyme complex (GO:0000307)|cytosol (GO:0005829)|intracellular (GO:0005622)|membrane (GO:0016020)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|tight junction (GO:0005923)|transcriptional repressor complex (GO:0017053)	cyclin-dependent protein serine/threonine kinase regulator activity (GO:0016538)|enzyme binding (GO:0019899)|histone deacetylase binding (GO:0042826)|proline-rich region binding (GO:0070064)|protein kinase activity (GO:0004672)|protein kinase binding (GO:0019901)|transcription corepressor activity (GO:0003714)|transcription factor binding (GO:0008134)			NS(2)|endometrium(11)|haematopoietic_and_lymphoid_tissue(1)|lung(7)|ovary(1)|urinary_tract(1)	23	all_cancers(3;2.01e-114)|all_epithelial(3;3.59e-122)|Breast(3;5.4e-34)|all_lung(4;1.99e-21)|Lung NSC(4;4.65e-21)|Hepatocellular(3;8.22e-16)|Melanoma(5;1.89e-05)|Ovarian(3;0.0348)		Epithelial(3;7.2e-57)|all cancers(3;7.75e-51)|BRCA - Breast invasive adenocarcinoma(2;4.9e-48)|Lung(3;1.13e-16)|LUSC - Lung squamous cell carcinoma(11;3.74e-15)|STAD - Stomach adenocarcinoma(18;0.0278)|LUAD - Lung adenocarcinoma(13;0.0537)		Arsenic trioxide(DB01169)	TCTACACCGACAACTCCATCC	0.687			T	"""IGH@, FSTL3"""	"""CLL, B-ALL, breast"""					Multiple Myeloma(6;0.086)																											p.D129D	Pancreas(65;393 884 2788 21700 24360 27795 36895)	Atlas-SNP	.		Dom	yes		11	11q13	595	cyclin D1		"""L, E"""	.	CCND1	107	.	0			c.C387T						PASS	.	C		0,4378		0,0,2189	38.0	36.0	37.0		387	3.7	1.0	11		37	2,8578		0,2,4288	no	coding-synonymous	CCND1	NM_053056.2		0,2,6477	TT,TC,CC		0.0233,0.0,0.0154		129/296	69457987	2,12956	2189	4290	6479	SO:0001819	synonymous_variant	595	exon2			CACCGACAACTCC	Z23022	CCDS8191.1	11q13	2008-07-18	2005-09-12		ENSG00000110092	ENSG00000110092			1582	protein-coding gene	gene with protein product	"""parathyroid adenomatosis 1"", ""B-cell CLL/lymphoma 1"", ""G1/S-specific cyclin D1"""	168461	"""cyclin D1 (PRAD1: parathyroid adenomatosis 1)"""	BCL1, D11S287E, PRAD1		1826542, 1833066	Standard	XM_006718653		Approved	U21B31	uc001opa.3	P24385	OTTHUMG00000167877	ENST00000227507.2:c.387C>T	11.37:g.69457987C>T		47.0	0.0	0		42.0	18.0	0.428571	NM_053056	Q6LEF0	Silent	SNP	ENST00000227507.2	37	CCDS8191.1																																																																																			.	.	weak		0.687	CCND1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000396775.2	NM_053056	
LEPRE1	64175	hgsc.bcm.edu	37	1	43212926	43212926	+	Intron	SNP	G	G	A	rs67014447	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr1:43212926G>A	ENST00000296388.5	-	14	2107				LEPRE1_ENST00000397054.3_Missense_Mutation_p.A691V|LEPRE1_ENST00000236040.4_Missense_Mutation_p.A691V|LEPRE1_ENST00000462474.1_5'UTR			Q32P28	P3H1_HUMAN	leucine proline-enriched proteoglycan (leprecan) 1						bone development (GO:0060348)|cell growth (GO:0016049)|chaperone-mediated protein folding (GO:0061077)|collagen fibril organization (GO:0030199)|collagen metabolic process (GO:0032963)|extracellular matrix organization (GO:0030198)|negative regulation of cell proliferation (GO:0008285)|negative regulation of post-translational protein modification (GO:1901874)|peptidyl-proline hydroxylation (GO:0019511)|protein folding (GO:0006457)|protein hydroxylation (GO:0018126)|protein stabilization (GO:0050821)|regulation of ossification (GO:0030278)|regulation of protein secretion (GO:0050708)	endoplasmic reticulum (GO:0005783)|endoplasmic reticulum lumen (GO:0005788)|extracellular vesicular exosome (GO:0070062)|macromolecular complex (GO:0032991)|membrane (GO:0016020)|nucleus (GO:0005634)|proteinaceous extracellular matrix (GO:0005578)	iron ion binding (GO:0005506)|L-ascorbic acid binding (GO:0031418)|procollagen-proline 3-dioxygenase activity (GO:0019797)|protein complex binding (GO:0032403)			large_intestine(2)|lung(15)|ovary(5)|prostate(1)|urinary_tract(3)	26	Ovarian(52;0.00744)|all_hematologic(146;0.0977)|Acute lymphoblastic leukemia(166;0.155)	Myeloproliferative disorder(586;0.0505)			L-Proline(DB00172)|Succinic acid(DB00139)|Vitamin C(DB00126)	GCTCTCACCCGCTCGAGCTGC	0.627											OREG0013422	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	-|||	310	0.061901	0.1384	0.0389	5008	,	,		19053	0.001		0.0398	False		,,,				2504	0.0603				p.A691V		Atlas-SNP	.											.	LEPRE1	130	.	0			c.C2072T						PASS	.	-	VAL/ALA,	584,3822		33,518,1652	61.0	61.0	61.0		2072,		0.0	1	dbSNP_130	61	378,8222		7,364,3929	yes	missense,intron	LEPRE1	NM_001146289.1,NM_022356.3	64,	40,882,5581	AA,AG,GG		4.3953,13.2547,7.3966	,	691/698,	43212926	962,12044	2203	4300	6503	SO:0001627	intron_variant	64175	exon14			TCACCCGCTCGAG	AK027648	CCDS472.2, CCDS53307.1, CCDS57986.1	1p34.1	2014-09-17			ENSG00000117385	ENSG00000117385			19316	protein-coding gene	gene with protein product	"""prolyl 3-hydroxylase 1"", ""growth suppressor 1"""	610339				10951563	Standard	NM_022356		Approved	GROS1, P3H1, LEPRECAN, MGC117314	uc001chx.4	Q32P28	OTTHUMG00000007525	ENST00000296388.5:c.2055+16C>T	1.37:g.43212926G>A		65.0	0.0	0	914	45.0	11.0	0.244444	NM_001146289	Q7KZR4|Q96BR8|Q96SK8|Q96SL5|Q96SN3|Q9H6K3|Q9HC86|Q9HC87	Missense_Mutation	SNP	ENST00000296388.5	37	CCDS472.2	112	0.05128205128205128	61	0.12398373983739837	19	0.052486187845303865	0	0.0	32	0.04221635883905013	-	0.009	-1.803442	0.00611	0.132547	0.043953	ENSG00000117385	ENST00000397054;ENST00000236040	T;T	0.37411	1.2;1.28	.	.	.	.	.	.	.	.	T	0.00241	0.0007	.	.	.	0.09310	N	1	.	.	.	.	.	.	T	0.19224	-1.0312	4	0.21540	T	0.41	.	.	.	.	.	691	Q32P28-3	.	V	691	ENSP00000380245:A691V;ENSP00000236040:A691V	ENSP00000236040:A691V	A	-	2	0	LEPRE1	42985513	0.009000	0.17119	0.014000	0.15608	0.025000	0.11179	-0.234000	0.09028	0.000000	0.14550	0.000000	0.15137	GCG	G|0.936;A|0.064	0.064	strong		0.627	LEPRE1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000019790.2	NM_022356	
MED12L	116931	hgsc.bcm.edu	37	3	151150568	151150568	+	Silent	SNP	G	G	A	rs142871635	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr3:151150568G>A	ENST00000474524.1	+	43	6452	c.6414G>A	c.(6412-6414)ccG>ccA	p.P2138P	MED12L_ENST00000273432.4_Silent_p.P1802P	NM_053002.4	NP_443728.3	Q86YW9	MD12L_HUMAN	mediator complex subunit 12-like	2138						mediator complex (GO:0016592)	RNA polymerase II transcription cofactor activity (GO:0001104)			NS(1)|breast(3)|central_nervous_system(3)|cervix(2)|endometrium(9)|haematopoietic_and_lymphoid_tissue(2)|kidney(9)|large_intestine(27)|lung(50)|ovary(6)|prostate(3)|skin(4)|stomach(3)|upper_aerodigestive_tract(5)|urinary_tract(1)	128			LUSC - Lung squamous cell carcinoma(72;0.0394)|Lung(72;0.0517)			GAGTGACTCCGTATGGGCATC	0.393													G|||	4	0.000798722	0.0	0.0029	5008	,	,		20900	0.0		0.002	False		,,,				2504	0.0				p.P2138P		Atlas-SNP	.											.	MED12L	271	.	0			c.G6414A						PASS	.	G		3,4403	6.2+/-15.9	0,3,2200	111.0	98.0	102.0		6414	-3.0	1.0	3	dbSNP_134	102	37,8563	24.6+/-71.5	0,37,4263	no	coding-synonymous	MED12L	NM_053002.4		0,40,6463	AA,AG,GG		0.4302,0.0681,0.3076		2138/2146	151150568	40,12966	2203	4300	6503	SO:0001819	synonymous_variant	116931	exon43			GACTCCGTATGGG	AB046855, AF388364	CCDS33876.1	3q25.1	2007-07-30	2007-07-30		ENSG00000144893	ENSG00000144893			16050	protein-coding gene	gene with protein product		611318	"""mediator of RNA polymerase II transcription, subunit 12 homolog (S. cerevisiae)-like"""			11524702	Standard	XM_006713487		Approved	KIAA1635, TNRC11L, TRALPUSH, TRALP	uc003eyp.3	Q86YW9	OTTHUMG00000159844	ENST00000474524.1:c.6414G>A	3.37:g.151150568G>A		173.0	0.0	0		166.0	90.0	0.542169	NM_053002	Q96PC7|Q96PC8|Q9H9M5|Q9HCD7|Q9UI69	Silent	SNP	ENST00000474524.1	37	CCDS33876.1																																																																																			G|0.997;A|0.003	0.003	strong		0.393	MED12L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000357707.2	NM_053002	
POLE	5426	hgsc.bcm.edu	37	12	133253180	133253180	+	Missense_Mutation	SNP	A	A	T	rs139075637	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr12:133253180A>T	ENST00000320574.5	-	9	904	c.861T>A	c.(859-861)gaT>gaA	p.D287E	POLE_ENST00000535270.1_Missense_Mutation_p.D260E	NM_006231.2	NP_006222.2	Q07864	DPOE1_HUMAN	polymerase (DNA directed), epsilon, catalytic subunit	287					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)	CTGTCTCAGCATCAGGAAACT	0.498								DNA polymerases (catalytic subunits)					A|||	2	0.000399361	0.0	0.0	5008	,	,		20902	0.0		0.002	False		,,,				2504	0.0				p.D287E		Atlas-SNP	.											.	POLE	416	.	0			c.T861A						PASS	.	A	GLU/ASP	1,4405	2.1+/-5.4	0,1,2202	115.0	99.0	105.0		861	1.9	1.0	12	dbSNP_134	105	11,8589	8.4+/-32.0	0,11,4289	yes	missense	POLE	NM_006231.2	45	0,12,6491	TT,TA,AA		0.1279,0.0227,0.0923	probably-damaging	287/2287	133253180	12,12994	2203	4300	6503	SO:0001583	missense	5426	exon9			CTCAGCATCAGGA		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.861T>A	12.37:g.133253180A>T	ENSP00000322570:p.Asp287Glu	223.0	0.0	0		167.0	91.0	0.54491	NM_006231	Q13533|Q86VH9	Missense_Mutation	SNP	ENST00000320574.5	37	CCDS9278.1	2	9.157509157509158E-4	0	0.0	0	0.0	0	0.0	2	0.002638522427440633	A	22.2	4.257395	0.80246	2.27E-4	0.001279	ENSG00000177084	ENST00000320574;ENST00000455752;ENST00000535270;ENST00000539006;ENST00000376577	T;T;T;T	0.48201	3.07;3.07;3.07;0.82	5.49	1.9	0.25705	DNA-directed DNA polymerase, family B, exonuclease domain (1);Ribonuclease H-like (1);	0.000000	0.85682	D	0.000000	T	0.62841	0.2461	M	0.71206	2.165	0.51233	D	0.999917	D;D	0.89917	1.0;1.0	D;D	0.83275	0.992;0.996	T	0.62469	-0.6848	10	0.87932	D	0	.	8.9216	0.35615	0.718:0.0:0.282:0.0	.	260;287	F5H1D6;Q07864	.;DPOE1_HUMAN	E	287;298;260;67;222	ENSP00000322570:D287E;ENSP00000406383:D298E;ENSP00000445753:D260E;ENSP00000442519:D67E	ENSP00000322570:D287E	D	-	3	2	POLE	131763253	1.000000	0.71417	1.000000	0.80357	0.952000	0.60782	1.156000	0.31712	0.376000	0.24707	-0.441000	0.05720	GAT	A|0.999;T|0.001	0.001	strong		0.498	POLE-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000397689.2	NM_006231	
DNAH14	127602	hgsc.bcm.edu	37	1	225393787	225393787	+	Missense_Mutation	SNP	T	T	G			TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr1:225393787T>G	ENST00000445597.2	+	27	4811	c.4811T>G	c.(4810-4812)aTa>aGa	p.I1604R	DNAH14_ENST00000430092.1_Missense_Mutation_p.I2009R|DNAH14_ENST00000439375.2_Missense_Mutation_p.I2009R			Q0VDD8	DYH14_HUMAN	dynein, axonemal, heavy chain 14	1604					microtubule-based movement (GO:0007018)	cilium (GO:0005929)|cytoplasm (GO:0005737)|dynein complex (GO:0030286)|microtubule (GO:0005874)	ATP binding (GO:0005524)|microtubule motor activity (GO:0003777)			NS(2)|breast(3)|central_nervous_system(3)|endometrium(8)|kidney(4)|large_intestine(2)|lung(2)|skin(2)|stomach(1)	27						AGTGAGAGAATAGCTTTAACT	0.423																																					p.I2009R		Atlas-SNP	.											.	DNAH14	300	.	0			c.T6026G						PASS	.						96.0	84.0	87.0					1																	225393787		692	1591	2283	SO:0001583	missense	127602	exon39			AGAGAATAGCTTT	U61741	CCDS41472.1, CCDS44322.1	1q42.13	2009-02-12	2006-09-04		ENSG00000185842	ENSG00000185842		"""Axonemal dyneins"""	2945	protein-coding gene	gene with protein product		603341	"""dynein, axonemal, heavy polypeptide 14"", ""chromosome 1 open reading frame 67"""	C1orf67		8812413	Standard	NM_144989		Approved	Dnahc14, HL-18, HL18, DKFZp781B1548, MGC27277	uc001how.2	Q0VDD8	OTTHUMG00000037447	ENST00000445597.2:c.4811T>G	1.37:g.225393787T>G	ENSP00000409472:p.Ile1604Arg	79.0	0.0	0		103.0	34.0	0.330097	NM_001373	A6NG62|A6NNL2|Q0VDD9|Q4VXC7|Q4VXG4|Q4VXG5|Q5VU33|Q5VU34	Missense_Mutation	SNP	ENST00000445597.2	37		.	.	.	.	.	.	.	.	.	.	T	23.2	4.387882	0.82902	.	.	ENSG00000185842	ENST00000445597;ENST00000430092;ENST00000439375	D;D;D	0.94280	-3.39;-3.39;-3.39	5.44	5.44	0.79542	.	.	.	.	.	D	0.97920	0.9316	H	0.97758	4.07	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	D	0.99250	1.0887	9	0.87932	D	0	.	14.4654	0.67480	0.0:0.0:0.0:1.0	.	2009	Q0VDD8-4	.	R	1604;2009;2009	ENSP00000409472:I1604R;ENSP00000414402:I2009R;ENSP00000392061:I2009R	ENSP00000414402:I2009R	I	+	2	0	DNAH14	223460410	1.000000	0.71417	0.908000	0.35775	0.995000	0.86356	6.910000	0.75741	2.063000	0.61619	0.481000	0.45027	ATA	.	.	none		0.423	DNAH14-007	PUTATIVE	basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000331217.3	XM_059166	
UTP6	55813	hgsc.bcm.edu	37	17	30200750	30200750	+	Missense_Mutation	SNP	G	G	A	rs267604797		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr17:30200750G>A	ENST00000261708.4	-	15	1465	c.1328C>T	c.(1327-1329)tCc>tTc	p.S443F	CTC-542B22.2_ENST00000583236.1_lincRNA	NM_018428.2	NP_060898.2	Q9NYH9	UTP6_HUMAN	UTP6, small subunit (SSU) processome component, homolog (yeast)	443					rRNA processing (GO:0006364)	nucleolus (GO:0005730)				breast(1)|endometrium(3)|kidney(1)|large_intestine(6)|lung(8)|ovary(1)|skin(1)	21		all_hematologic(16;0.0149)|Ovarian(249;0.021)|Myeloproliferative disorder(56;0.0255)|Acute lymphoblastic leukemia(14;0.0257)|Breast(31;0.231)				CTCTGCCCAGGAAATCCACAA	0.428																																					p.S443F		Atlas-SNP	.											.	UTP6	46	.	0			c.C1328T						PASS	.						199.0	189.0	192.0					17																	30200750		2203	4300	6503	SO:0001583	missense	55813	exon15			GCCCAGGAAATCC	AF116631	CCDS11269.1	17q11.2	2010-06-24	2006-05-16	2006-05-16	ENSG00000108651	ENSG00000108651			18279	protein-coding gene	gene with protein product	"""hepatocellular carcinoma associated antigen 66"""		"""chromosome 17 open reading frame 40"""	C17orf40		10843809, 16138909	Standard	NM_018428		Approved	HCA66	uc002hgr.3	Q9NYH9	OTTHUMG00000132815	ENST00000261708.4:c.1328C>T	17.37:g.30200750G>A	ENSP00000261708:p.Ser443Phe	69.0	0.0	0		51.0	4.0	0.0784314	NM_018428	Q8IX96|Q96BL2|Q9NQ91	Missense_Mutation	SNP	ENST00000261708.4	37	CCDS11269.1	.	.	.	.	.	.	.	.	.	.	G	11.40	1.626443	0.28978	.	.	ENSG00000108651	ENST00000261708	T	0.34859	1.34	5.1	2.71	0.32032	Tetratricopeptide-like helical (1);	0.326861	0.31301	N	0.007891	T	0.18841	0.0452	L	0.29908	0.895	0.29239	N	0.872766	B;B	0.06786	0.001;0.001	B;B	0.04013	0.001;0.001	T	0.15636	-1.0430	10	0.08837	T	0.75	-7.7125	4.5063	0.11889	0.3816:0.0:0.6184:0.0	.	443;443	B3KQ21;Q9NYH9	.;UTP6_HUMAN	F	443	ENSP00000261708:S443F	ENSP00000261708:S443F	S	-	2	0	UTP6	27224863	1.000000	0.71417	1.000000	0.80357	0.919000	0.55068	4.107000	0.57811	1.291000	0.44653	0.650000	0.86243	TCC	.	.	none		0.428	UTP6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256265.2	NM_018428	
PAK2	5062	hgsc.bcm.edu	37	3	196529917	196529917	+	Silent	SNP	A	A	G	rs183020057	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr3:196529917A>G	ENST00000327134.3	+	4	640	c.318A>G	c.(316-318)ctA>ctG	p.L106L		NM_002577.4	NP_002568.2	Q13177	PAK2_HUMAN	p21 protein (Cdc42/Rac)-activated kinase 2	106	Autoregulatory region. {ECO:0000250}.|GTPase-binding. {ECO:0000250}.				apoptotic process (GO:0006915)|axon guidance (GO:0007411)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|Fc-epsilon receptor signaling pathway (GO:0038095)|innate immune response (GO:0045087)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cysteine-type endopeptidase activity involved in execution phase of apoptosis (GO:2001271)|negative regulation of protein kinase activity (GO:0006469)|peptidyl-serine phosphorylation (GO:0018105)|phosphorylation (GO:0016310)|positive regulation of extrinsic apoptotic signaling pathway (GO:2001238)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|positive regulation of protein tyrosine kinase activity (GO:0061098)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|regulation of apoptotic process (GO:0042981)|regulation of defense response to virus by virus (GO:0050690)|regulation of growth (GO:0040008)|signal transduction (GO:0007165)|T cell costimulation (GO:0031295)|T cell receptor signaling pathway (GO:0050852)|viral process (GO:0016032)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|identical protein binding (GO:0042802)|protein kinase activity (GO:0004672)|protein kinase binding (GO:0019901)|protein serine/threonine kinase activity (GO:0004674)|protein tyrosine kinase activator activity (GO:0030296)			breast(1)|cervix(1)|kidney(2)|large_intestine(1)|lung(4)|ovary(1)|prostate(2)	12	all_cancers(143;1.8e-08)|Ovarian(172;0.0634)|Breast(254;0.135)		Epithelial(36;1.07e-23)|all cancers(36;6.38e-22)|OV - Ovarian serous cystadenocarcinoma(49;1.5e-18)|LUSC - Lung squamous cell carcinoma(58;1.51e-06)|Lung(62;1.95e-06)	GBM - Glioblastoma multiforme(46;0.00405)		CTCGATTACTACAGACCTCCA	0.378													A|||	5	0.000998403	0.0008	0.0	5008	,	,		19631	0.001		0.001	False		,,,				2504	0.002				p.L106L		Atlas-SNP	.											.	PAK2	113	.	0			c.A318G						PASS	.						93.0	81.0	85.0					3																	196529917		2203	4300	6503	SO:0001819	synonymous_variant	5062	exon4			ATTACTACAGACC	U24153	CCDS3321.1	3q29	2008-06-17	2008-06-17			ENSG00000180370	2.7.11.1		8591	protein-coding gene	gene with protein product	"""S6/H4 kinase"""	605022	"""p21 (CDKN1A)-activated kinase 2"""			7744004, 7618083	Standard	NM_002577		Approved	PAK65, PAKgamma	uc003fwy.4	Q13177		ENST00000327134.3:c.318A>G	3.37:g.196529917A>G		180.0	0.0	0		214.0	10.0	0.046729	NM_002577	Q13154|Q6ISC3	Silent	SNP	ENST00000327134.3	37	CCDS3321.1																																																																																			A|1.000;G|0.000	0.000	strong		0.378	PAK2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000340548.1	NM_002577	
FAT3	120114	hgsc.bcm.edu	37	11	92257991	92257991	+	Missense_Mutation	SNP	C	C	A			TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr11:92257991C>A	ENST00000298047.6	+	2	3501	c.3484C>A	c.(3484-3486)Cca>Aca	p.P1162T	FAT3_ENST00000409404.2_Missense_Mutation_p.P1162T|FAT3_ENST00000541502.1_Missense_Mutation_p.P1162T|FAT3_ENST00000525166.1_Missense_Mutation_p.P1012T			Q8TDW7	FAT3_HUMAN	FAT atypical cadherin 3	1162	Cadherin 11. {ECO:0000255|PROSITE- ProRule:PRU00043}.				homophilic cell adhesion (GO:0007156)|multicellular organismal development (GO:0007275)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			NS(1)|breast(2)|endometrium(10)|kidney(4)|large_intestine(11)|liver(2)|lung(37)|ovary(5)|pancreas(1)|prostate(4)|skin(2)|stomach(1)|upper_aerodigestive_tract(5)	85		Acute lymphoblastic leukemia(157;3.01e-05)|all_hematologic(158;0.00858)				GGAAAACTCTCCAAAGGACGT	0.418										TCGA Ovarian(4;0.039)																											p.P1162T		Atlas-SNP	.											.	FAT3	1822	.	0			c.C3484A						PASS	.						58.0	58.0	58.0					11																	92257991		1968	4167	6135	SO:0001583	missense	120114	exon2			AACTCTCCAAAGG	AB076400		11q14.3	2013-05-31	2013-05-31		ENSG00000165323	ENSG00000165323		"""Cadherins / Cadherin-related"""	23112	protein-coding gene	gene with protein product	"""cadherin-related family member 10"""	612483	"""FAT tumor suppressor homolog 3 (Drosophila)"""			11811999	Standard	NM_001008781		Approved	KIAA1989, CDHF15, CDHR10	uc001pdj.4	Q8TDW7	OTTHUMG00000154468	ENST00000298047.6:c.3484C>A	11.37:g.92257991C>A	ENSP00000298047:p.Pro1162Thr	134.0	0.0	0		200.0	123.0	0.615	NM_001008781	B5MDB0|Q96AU6	Missense_Mutation	SNP	ENST00000298047.6	37		.	.	.	.	.	.	.	.	.	.	C	21.8	4.197532	0.79015	.	.	ENSG00000165323	ENST00000298047;ENST00000409404;ENST00000541502;ENST00000525166	T;T;T;T	0.54675	0.56;0.56;0.56;0.56	5.66	5.66	0.87406	.	.	.	.	.	T	0.68933	0.3055	L	0.58925	1.835	0.51482	D	0.999922	D	0.89917	1.0	D	0.91635	0.999	T	0.68969	-0.5269	9	0.54805	T	0.06	.	15.2581	0.73601	0.0:0.8603:0.1397:0.0	.	1162	Q8TDW7-3	.	T	1162;1162;1162;1012	ENSP00000298047:P1162T;ENSP00000387040:P1162T;ENSP00000443786:P1162T;ENSP00000432586:P1012T	ENSP00000298047:P1162T	P	+	1	0	FAT3	91897639	1.000000	0.71417	0.998000	0.56505	0.955000	0.61496	5.946000	0.70234	2.682000	0.91365	0.650000	0.86243	CCA	.	.	none		0.418	FAT3-201	KNOWN	basic	protein_coding	protein_coding		NM_001008781	
SCAMP5	192683	hgsc.bcm.edu	37	15	75308976	75308976	+	Missense_Mutation	SNP	C	C	T			TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr15:75308976C>T	ENST00000361900.6	+	5	386	c.179C>T	c.(178-180)gCg>gTg	p.A60V	SCAMP5_ENST00000562212.1_Missense_Mutation_p.A60V|SCAMP5_ENST00000568081.1_5'Flank|SCAMP5_ENST00000545456.1_Intron|SCAMP5_ENST00000565923.1_3'UTR|SCAMP5_ENST00000425597.3_Missense_Mutation_p.A60V	NM_001178111.1	NP_001171582.1	Q8TAC9	SCAM5_HUMAN	secretory carrier membrane protein 5	60					exocytosis (GO:0006887)|negative regulation of endocytosis (GO:0045806)|positive regulation of calcium ion-dependent exocytosis (GO:0045956)|positive regulation of cytokine secretion (GO:0050715)|protein transport (GO:0015031)|response to endoplasmic reticulum stress (GO:0034976)	cell junction (GO:0030054)|cytoplasmic vesicle (GO:0031410)|Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|recycling endosome membrane (GO:0055038)|synapse (GO:0045202)|trans-Golgi network membrane (GO:0032588)				large_intestine(1)|lung(1)|ovary(1)|urinary_tract(2)	5						GGCTGTCTCGCGTGGCTGATC	0.612																																					p.A60V		Atlas-SNP	.											.	SCAMP5	34	.	0			c.C179T						PASS	.						107.0	111.0	109.0					15																	75308976		2165	4255	6420	SO:0001583	missense	192683	exon5			GTCTCGCGTGGCT	AL833230	CCDS45306.1	15q24.2	2014-05-20			ENSG00000198794	ENSG00000198794		"""Secretory carrier membrane proteins"""	30386	protein-coding gene	gene with protein product		613766				12477932	Standard	NM_001178111		Approved	MGC24969	uc002azk.2	Q8TAC9	OTTHUMG00000172704	ENST00000361900.6:c.179C>T	15.37:g.75308976C>T	ENSP00000355387:p.Ala60Val	118.0	0.0	0		67.0	33.0	0.492537	NM_001178111	B3KPJ7|B7Z762|D3DW71|Q8N3M4	Missense_Mutation	SNP	ENST00000361900.6	37	CCDS45306.1	.	.	.	.	.	.	.	.	.	.	C	31	5.087901	0.94100	.	.	ENSG00000198794	ENST00000361900;ENST00000425597	T;T	0.18016	2.24;2.24	4.84	4.84	0.62591	.	0.000000	0.85682	D	0.000000	T	0.33118	0.0852	L	0.45352	1.415	0.80722	D	1	P;D	0.71674	0.842;0.998	B;D	0.63793	0.214;0.918	T	0.03443	-1.1036	10	0.59425	D	0.04	-8.1334	17.2941	0.87166	0.0:1.0:0.0:0.0	.	60;60	Q8TAC9-2;Q8TAC9	.;SCAM5_HUMAN	V	60	ENSP00000355387:A60V;ENSP00000406547:A60V	ENSP00000355387:A60V	A	+	2	0	SCAMP5	73096029	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.681000	0.84073	2.391000	0.81399	0.561000	0.74099	GCG	.	.	none		0.612	SCAMP5-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000420015.2	NM_138967	
DRG2	1819	hgsc.bcm.edu	37	17	18003919	18003919	+	Missense_Mutation	SNP	G	G	A	rs143296623	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr17:18003919G>A	ENST00000225729.3	+	7	715	c.577G>A	c.(577-579)Gtc>Atc	p.V193I	DRG2_ENST00000583355.1_Intron|DRG2_ENST00000395726.4_Missense_Mutation_p.V193I	NM_001388.4	NP_001379.1	P55039	DRG2_HUMAN	developmentally regulated GTP binding protein 2	193	OBG-type G. {ECO:0000255|PROSITE- ProRule:PRU01047}.				signal transduction (GO:0007165)	cytoplasm (GO:0005737)|membrane (GO:0016020)|mitochondrion (GO:0005739)	GTP binding (GO:0005525)	p.V193fs*2(1)		endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(3)|lung(3)|ovary(1)|prostate(1)|skin(1)|urinary_tract(2)	14	all_neural(463;0.228)					TAACTCGACAGTCACGCTGAC	0.562													G|||	13	0.00259585	0.0	0.0086	5008	,	,		22449	0.0		0.006	False		,,,				2504	0.001				p.V193I		Atlas-SNP	.											.	DRG2	27	.	1	Deletion - Frameshift(1)	ovary(1)	c.G577A						PASS	.	G	ILE/VAL	4,4402	8.1+/-20.4	0,4,2199	91.0	78.0	82.0		577	5.3	1.0	17	dbSNP_134	82	47,8553	30.1+/-81.4	0,47,4253	yes	missense	DRG2	NM_001388.3	29	0,51,6452	AA,AG,GG		0.5465,0.0908,0.3921	benign	193/365	18003919	51,12955	2203	4300	6503	SO:0001583	missense	1819	exon7			TCGACAGTCACGC	X80754	CCDS11191.1	17p13-p12	2008-07-18	2001-11-28		ENSG00000108591	ENSG00000108591			3030	protein-coding gene	gene with protein product		602986	"""developmentally regulated GTP-binding protein 2"""			9605870, 7929244	Standard	NM_001388		Approved		uc002gsh.2	P55039	OTTHUMG00000059399	ENST00000225729.3:c.577G>A	17.37:g.18003919G>A	ENSP00000225729:p.Val193Ile	83.0	0.0	0		102.0	51.0	0.5	NM_001388	B2R8G5|Q53Y50|Q9BWB2	Missense_Mutation	SNP	ENST00000225729.3	37	CCDS11191.1	8	0.003663003663003663	0	0.0	3	0.008287292817679558	0	0.0	5	0.006596306068601583	G	14.49	2.551381	0.45383	9.08E-4	0.005465	ENSG00000108591	ENST00000395726;ENST00000225729	T;T	0.30182	1.54;1.54	5.29	5.29	0.74685	Small GTP-binding protein domain (1);	0.000000	0.85682	D	0.000000	T	0.29491	0.0735	M	0.66378	2.025	0.80722	D	1	B;B	0.18310	0.027;0.015	B;B	0.12837	0.008;0.008	T	0.16305	-1.0407	10	0.59425	D	0.04	-21.1669	18.9395	0.92600	0.0:0.0:1.0:0.0	.	193;193	A8MZF9;P55039	.;DRG2_HUMAN	I	193	ENSP00000379076:V193I;ENSP00000225729:V193I	ENSP00000225729:V193I	V	+	1	0	DRG2	17944644	1.000000	0.71417	0.952000	0.39060	0.257000	0.26127	7.764000	0.85297	2.484000	0.83849	0.462000	0.41574	GTC	G|0.996;A|0.004	0.004	strong		0.562	DRG2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000132075.3	NM_001388	
BRAT1	221927	hgsc.bcm.edu	37	7	2577809	2577809	+	Missense_Mutation	SNP	G	G	A	rs375916445		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr7:2577809G>A	ENST00000340611.4	-	14	2616	c.2360C>T	c.(2359-2361)aCg>aTg	p.T787M	BRAT1_ENST00000473879.1_5'Flank	NM_152743.3	NP_689956.2	Q6PJG6	BRAT1_HUMAN	BRCA1-associated ATM activator 1	787					response to ionizing radiation (GO:0010212)	membrane (GO:0016020)|nucleus (GO:0005634)				breast(1)|central_nervous_system(1)|endometrium(4)|kidney(2)|large_intestine(3)|lung(7)|ovary(1)|pancreas(1)|skin(2)|urinary_tract(1)	23						CTCGGCCAGCGTGCTCCGCAG	0.701																																					p.T787M		Atlas-SNP	.											.	BRAT1	57	.	0			c.C2360T						PASS	.						22.0	22.0	22.0					7																	2577809		2187	4272	6459	SO:0001583	missense	221927	exon14			GCCAGCGTGCTCC	BC015632	CCDS5334.1	7p22.3	2011-03-22	2011-02-28	2011-03-22	ENSG00000106009	ENSG00000106009			21701	protein-coding gene	gene with protein product	"""BRCA1-associated protein required for ATM activation protein 1"""	614506	"""chromosome 7 open reading frame 27"""	C7orf27, BAAT1		16452482	Standard	NM_152743		Approved	MGC22916	uc003smi.3	Q6PJG6	OTTHUMG00000119091	ENST00000340611.4:c.2360C>T	7.37:g.2577809G>A	ENSP00000339637:p.Thr787Met	65.0	0.0	0		72.0	53.0	0.736111	NM_152743	A4D200|C9JY24|Q8IW85|Q8IZ43|Q8WVR8|Q96IV9|Q9H7J8|Q9UFA3	Missense_Mutation	SNP	ENST00000340611.4	37	CCDS5334.1	.	.	.	.	.	.	.	.	.	.	G	9.550	1.115689	0.20795	.	.	ENSG00000106009	ENST00000340611	T	0.30981	1.51	5.42	4.53	0.55603	.	0.648485	0.17239	N	0.181608	T	0.24851	0.0603	N	0.14661	0.345	0.09310	N	1	D	0.76494	0.999	P	0.50490	0.642	T	0.05209	-1.0899	10	0.34782	T	0.22	-11.8434	10.0764	0.42362	0.0:0.189:0.6795:0.1314	.	787	Q6PJG6	BRAT1_HUMAN	M	787	ENSP00000339637:T787M	ENSP00000339637:T787M	T	-	2	0	BRAT1	2544335	0.005000	0.15991	0.006000	0.13384	0.041000	0.13682	1.359000	0.34113	1.239000	0.43787	0.561000	0.74099	ACG	.	.	weak		0.701	BRAT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000239305.2	NM_152743	
CUL4A	8451	hgsc.bcm.edu	37	13	113909008	113909008	+	Splice_Site	SNP	G	G	A			TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr13:113909008G>A	ENST00000375440.4	+	17	1838	c.1754G>A	c.(1753-1755)gGg>gAg	p.G585E	CUL4A_ENST00000451881.1_Splice_Site_p.G485E|CUL4A_ENST00000375441.3_Splice_Site_p.G485E|CUL4A_ENST00000326335.4_Splice_Site_p.G485E	NM_001008895.1	NP_001008895.1	Q13619	CUL4A_HUMAN	cullin 4A	585					cell cycle arrest (GO:0007050)|DNA repair (GO:0006281)|G1/S transition of mitotic cell cycle (GO:0000082)|hemopoiesis (GO:0030097)|intrinsic apoptotic signaling pathway (GO:0097193)|negative regulation of cell proliferation (GO:0008285)|negative regulation of granulocyte differentiation (GO:0030853)|positive regulation of cell proliferation (GO:0008284)|positive regulation of G1/S transition of mitotic cell cycle (GO:1900087)|proteasome-mediated ubiquitin-dependent protein catabolic process (GO:0043161)|protein ubiquitination (GO:0016567)|regulation of DNA damage checkpoint (GO:2000001)|regulation of nucleotide-excision repair (GO:2000819)|regulation of protein metabolic process (GO:0051246)|somatic stem cell maintenance (GO:0035019)|viral process (GO:0016032)	Cul4-RING E3 ubiquitin ligase complex (GO:0080008)|Cul4A-RING E3 ubiquitin ligase complex (GO:0031464)				NS(1)|breast(1)|central_nervous_system(2)|cervix(1)|endometrium(1)|large_intestine(5)|lung(5)|skin(1)	17	Lung NSC(43;0.0161)|all_neural(89;0.0804)|Hepatocellular(20;0.0877)|Medulloblastoma(90;0.163)|Lung SC(71;0.218)	all_cancers(25;0.0482)|all_epithelial(44;0.0148)|all_lung(25;0.0271)|Lung NSC(25;0.0977)|Breast(118;0.188)	all cancers(43;0.112)			CTCTTCCAGGGGAAGAAGGAA	0.443																																					p.G585E		Atlas-SNP	.											.	CUL4A	50	.	0			c.G1754A						PASS	.						138.0	130.0	133.0					13																	113909008		2203	4300	6503	SO:0001630	splice_region_variant	8451	exon17			TCCAGGGGAAGAA	U58090	CCDS9533.1, CCDS41908.1, CCDS73604.1	13q34	2011-05-24			ENSG00000139842	ENSG00000139842			2554	protein-coding gene	gene with protein product		603137				8681378	Standard	NM_001008895		Approved		uc021rmv.1	Q13619	OTTHUMG00000017384	ENST00000375440.4:c.1753-1G>A	13.37:g.113909008G>A		98.0	0.0	0		104.0	53.0	0.509615	NM_001008895	A2A2W2|O75834|Q589T6|Q5TC62|Q6UP08|Q9UP17	Missense_Mutation	SNP	ENST00000375440.4	37	CCDS41908.1	.	.	.	.	.	.	.	.	.	.	G	18.32	3.598067	0.66332	.	.	ENSG00000139842	ENST00000375441;ENST00000451881;ENST00000326335;ENST00000375440	T;T;T;T	0.74106	-0.81;-0.81;-0.81;-0.81	5.3	5.3	0.74995	Cullin, N-terminal (1);Cullin homology (2);	0.000000	0.85682	D	0.000000	T	0.72203	0.3431	M	0.61703	1.905	0.80722	D	1	P;P	0.42161	0.772;0.772	B;B	0.41036	0.346;0.346	T	0.74077	-0.3781	10	0.46703	T	0.11	-31.6571	12.6463	0.56735	0.0762:0.0:0.9238:0.0	.	585;585	Q13619;A8MSH7	CUL4A_HUMAN;.	E	485;485;485;585	ENSP00000364590:G485E;ENSP00000389118:G485E;ENSP00000322132:G485E;ENSP00000364589:G585E	ENSP00000322132:G485E	G	+	2	0	CUL4A	112957009	1.000000	0.71417	0.998000	0.56505	0.908000	0.53690	7.668000	0.83897	2.627000	0.88993	0.561000	0.74099	GGG	.	.	none		0.443	CUL4A-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045888.3	NM_003589	Missense_Mutation
FAM178A	55719	hgsc.bcm.edu	37	10	102716222	102716222	+	Silent	SNP	A	A	G			TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr10:102716222A>G	ENST00000238961.4	+	18	3887	c.3345A>G	c.(3343-3345)ctA>ctG	p.L1115L	FAM178A_ENST00000370269.3_Silent_p.L1115L	NM_018121.3	NP_060591.3	Q8IX21	F178A_HUMAN	family with sequence similarity 178, member A	1115						chromatin (GO:0000785)|extracellular space (GO:0005615)|nucleus (GO:0005634)											ACTTTGTGCTACTCTGTGGGG	0.328																																					p.L1115L		Atlas-SNP	.											.	FAM178A	9	.	0			c.A3345G						PASS	.						145.0	143.0	144.0					10																	102716222		2203	4300	6503	SO:0001819	synonymous_variant	55719	exon18			TGTGCTACTCTGT	AF460991	CCDS7500.1, CCDS44470.1, CCDS65918.1	10q24.31	2008-07-18	2008-07-18	2008-07-18	ENSG00000119906	ENSG00000119906			17814	protein-coding gene	gene with protein product		610348	"""chromosome 10 open reading frame 6"""	C10orf6		12459258	Standard	NM_018121		Approved	FLJ10512, FLJ25012	uc001krs.3	Q8IX21	OTTHUMG00000018919	ENST00000238961.4:c.3345A>G	10.37:g.102716222A>G		127.0	0.0	0		98.0	4.0	0.0408163	NM_001136123	A8K950|B1AL17|Q5W0L8|Q6GMU6|Q9NPE8	Silent	SNP	ENST00000238961.4	37	CCDS7500.1																																																																																			.	.	none		0.328	FAM178A-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000049897.3		
CAMKMT	79823	hgsc.bcm.edu	37	2	44942450	44942450	+	Missense_Mutation	SNP	A	A	G			TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr2:44942450A>G	ENST00000378494.3	+	7	625	c.581A>G	c.(580-582)aAt>aGt	p.N194S		NM_024766.4	NP_079042.1	Q7Z624	CMKMT_HUMAN	calmodulin-lysine N-methyltransferase	194						Golgi apparatus (GO:0005794)|nucleus (GO:0005634)	calmodulin-lysine N-methyltransferase activity (GO:0018025)			breast(2)|large_intestine(3)|lung(5)	10						ATCACAAGGAATCAGAAGGCT	0.363																																					p.N194S		Atlas-SNP	.											.	CAMKMT	20	.	0			c.A581G						PASS	.						87.0	92.0	90.0					2																	44942450		2203	4300	6503	SO:0001583	missense	79823	exon7			CAAGGAATCAGAA		CCDS1820.1	2p21	2011-06-22	2011-03-10	2011-03-10	ENSG00000143919	ENSG00000143919	2.1.1.60		26276	protein-coding gene	gene with protein product	"""CaM KMT"""	609559	"""chromosome 2 open reading frame 34"""	C2orf34		20975703	Standard	NM_024766		Approved	CLNMT	uc002rum.3	Q7Z624	OTTHUMG00000128761	ENST00000378494.3:c.581A>G	2.37:g.44942450A>G	ENSP00000367755:p.Asn194Ser	99.0	0.0	0		106.0	45.0	0.424528	NM_024766	Q4ZG15|Q53SS6|Q8N6P5|Q9H5G8	Missense_Mutation	SNP	ENST00000378494.3	37	CCDS1820.1	.	.	.	.	.	.	.	.	.	.	A	17.82	3.482904	0.63962	.	.	ENSG00000143919	ENST00000378494	T	0.12879	2.64	5.52	5.52	0.82312	.	0.086330	0.85682	D	0.000000	T	0.39279	0.1072	M	0.89478	3.035	0.80722	D	1	D	0.56746	0.977	P	0.61874	0.895	T	0.42050	-0.9474	10	0.72032	D	0.01	-12.628	10.9403	0.47270	0.8434:0.1566:0.0:0.0	.	194	Q7Z624	CMKMT_HUMAN	S	194	ENSP00000367755:N194S	ENSP00000367755:N194S	N	+	2	0	CAMKMT	44795954	1.000000	0.71417	1.000000	0.80357	0.922000	0.55478	5.066000	0.64351	2.104000	0.64026	0.528000	0.53228	AAT	.	.	none		0.363	CAMKMT-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250678.2	NM_024766	
ADAMTS6	11174	hgsc.bcm.edu	37	5	64756136	64756136	+	Silent	SNP	C	C	T			TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr5:64756136C>T	ENST00000536360.1	-	4	1305	c.492G>A	c.(490-492)gaG>gaA	p.E164E				Q9UKP5	ATS6_HUMAN	ADAM metallopeptidase with thrombospondin type 1 motif, 6	164						proteinaceous extracellular matrix (GO:0005578)	metalloendopeptidase activity (GO:0004222)|metallopeptidase activity (GO:0008237)|zinc ion binding (GO:0008270)			breast(2)|cervix(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(1)|lung(7)|pancreas(1)|prostate(1)|skin(3)	18		Lung NSC(167;2.44e-06)|Prostate(74;0.014)|Ovarian(174;0.0549)|Breast(144;0.111)|Colorectal(97;0.235)		Lung(70;0.00942)		CGATAAAATACTCTTCATCTT	0.308																																					p.E164E		Atlas-SNP	.											.	ADAMTS6	174	.	0			c.G492A						PASS	.						109.0	114.0	112.0					5																	64756136		2203	4300	6503	SO:0001819	synonymous_variant	11174	exon4			AAAATACTCTTCA	AF140674	CCDS3983.2	5q13	2008-07-18	2005-08-19		ENSG00000049192	ENSG00000049192		"""ADAM metallopeptidases with thrombospondin type 1 motif"""	222	protein-coding gene	gene with protein product	"""a disintegrin and metalloproteinase with thrombospondin motifs 6"""	605008	"""a disintegrin-like and metalloprotease (reprolysin type) with thrombospondin type 1 motif, 6"""			10464288	Standard	NM_197941		Approved	ADAM-TS6	uc003jtp.3	Q9UKP5	OTTHUMG00000074079	ENST00000536360.1:c.492G>A	5.37:g.64756136C>T		113.0	0.0	0		114.0	8.0	0.0701754	NM_197941	Q59EX6|Q5IR87|Q5IR88|Q5IR89|Q68DL1	Silent	SNP	ENST00000536360.1	37																																																																																				.	.	none		0.308	ADAMTS6-201	KNOWN	basic	protein_coding	protein_coding		NM_197941	
SAMD4A	23034	hgsc.bcm.edu	37	14	55226987	55226987	+	Missense_Mutation	SNP	C	C	T			TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr14:55226987C>T	ENST00000554335.1	+	7	1948	c.1285C>T	c.(1285-1287)Cgc>Tgc	p.R429C	SAMD4A_ENST00000357634.3_Missense_Mutation_p.R428C|SAMD4A_ENST00000555192.1_Missense_Mutation_p.R20C|SAMD4A_ENST00000251091.5_Missense_Mutation_p.R341C|SAMD4A_ENST00000392067.3_Missense_Mutation_p.R429C			Q9UPU9	SMAG1_HUMAN	sterile alpha motif domain containing 4A	429					negative regulation of translation (GO:0017148)|positive regulation of translation (GO:0045727)	cell junction (GO:0030054)|cytoplasm (GO:0005737)|neuron projection (GO:0043005)|synapse (GO:0045202)	poly(A) RNA binding (GO:0044822)|translation repressor activity (GO:0030371)			breast(2)|central_nervous_system(2)|cervix(1)|endometrium(1)|kidney(2)|large_intestine(9)|lung(10)|prostate(1)|skin(1)	29						CGAGGCTCGCCGCCGGGAGCC	0.716																																					p.R429C		Atlas-SNP	.											.	SAMD4A	68	.	0			c.C1285T						PASS	.																																			SO:0001583	missense	23034	exon6			GCTCGCCGCCGGG	AB028976	CCDS32084.1, CCDS55917.1, CCDS55918.1, CCDS32084.2, CCDS55917.2	14q22.2	2013-01-10	2006-01-27	2006-01-27	ENSG00000020577	ENSG00000020577		"""Sterile alpha motif (SAM) domain containing"""	23023	protein-coding gene	gene with protein product	"""smaug homolog (Drosophila)"""	610747	"""sterile alpha motif domain containing 4"""	SAMD4		16221671	Standard	NM_001161577		Approved	KIAA1053, DKFZP434H0350, Smaug, SMG, SMGA, hSmaug1	uc001xbb.4	Q9UPU9	OTTHUMG00000170999	ENST00000554335.1:c.1285C>T	14.37:g.55226987C>T	ENSP00000452535:p.Arg429Cys	45.0	0.0	0		46.0	32.0	0.695652	NM_015589	A8MPZ5|Q0VA96|Q6PEW4	Missense_Mutation	SNP	ENST00000554335.1	37	CCDS32084.2	.	.	.	.	.	.	.	.	.	.	C	13.96	2.391816	0.42410	.	.	ENSG00000020577	ENST00000554335;ENST00000392067;ENST00000305831;ENST00000251091;ENST00000357634;ENST00000555192	.	.	.	5.07	3.07	0.35406	.	0.889887	0.09934	N	0.736892	T	0.23451	0.0567	N	0.14661	0.345	0.24451	N	0.994482	B;D;P	0.53151	0.012;0.958;0.474	B;P;B	0.50617	0.002;0.646;0.093	T	0.09271	-1.0682	9	0.51188	T	0.08	-15.041	3.4091	0.07352	0.288:0.5045:0.1175:0.09	.	20;341;429	G3V2R1;Q9UPU9-3;Q9UPU9	.;.;SMAG1_HUMAN	C	429;429;341;340;428;20	.	ENSP00000251091:R58C	R	+	1	0	SAMD4A	54296737	0.921000	0.31238	0.318000	0.25279	0.343000	0.28985	1.821000	0.39041	1.331000	0.45412	0.609000	0.83330	CGC	.	.	none		0.716	SAMD4A-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000411186.1	NM_015589	
TACC2	10579	hgsc.bcm.edu	37	10	123846252	123846252	+	Missense_Mutation	SNP	G	G	A	rs201709460		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr10:123846252G>A	ENST00000369005.1	+	4	4577	c.4237G>A	c.(4237-4239)Gcc>Acc	p.A1413T	TACC2_ENST00000453444.2_Missense_Mutation_p.A1413T|TACC2_ENST00000334433.3_Missense_Mutation_p.A1413T|TACC2_ENST00000513429.1_Intron|TACC2_ENST00000515603.1_Missense_Mutation_p.A1413T|TACC2_ENST00000358010.1_Intron|TACC2_ENST00000515273.1_Missense_Mutation_p.A1413T	NM_206862.2	NP_996744.2	O95359	TACC2_HUMAN	transforming, acidic coiled-coil containing protein 2	1413					astral microtubule organization (GO:0030953)|cerebral cortex development (GO:0021987)|interkinetic nuclear migration (GO:0022027)|neurogenesis (GO:0022008)|regulation of microtubule-based process (GO:0032886)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|Golgi apparatus (GO:0005794)|nucleolus (GO:0005730)|nucleus (GO:0005634)	nuclear hormone receptor binding (GO:0035257)			NS(1)|breast(5)|central_nervous_system(1)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(3)|kidney(3)|large_intestine(15)|lung(27)|ovary(6)|prostate(3)|skin(8)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(3)	83		all_neural(114;0.0656)|Lung NSC(174;0.136)|all_lung(145;0.17)|Breast(234;0.197)				GGAGCACATCGCCAAGATCTT	0.592													G|||	0	0.0	0.0	0.0	5008	,	,		19162	0.0		0.0	False		,,,				2504	0.0				p.A1413T		Atlas-SNP	.											.	TACC2	271	.	0			c.G4237A						PASS	.	G	,THR/ALA	0,4406		0,0,2203	70.0	67.0	68.0		,4237	4.2	1.0	10		68	1,8599	1.2+/-3.3	0,1,4299	yes	intron,missense	TACC2	NM_206861.1,NM_206862.2	,58	0,1,6502	AA,AG,GG		0.0116,0.0,0.0077	,benign	,1413/2949	123846252	1,13005	2203	4300	6503	SO:0001583	missense	10579	exon4			CACATCGCCAAGA	AF095791	CCDS7625.1, CCDS7626.1, CCDS7627.1, CCDS7628.1	10q26	2008-07-29			ENSG00000138162	ENSG00000138162			11523	protein-coding gene	gene with protein product		605302				14767476	Standard	XM_005269388		Approved	AZU-1	uc001lfv.3	O95359	OTTHUMG00000019181	ENST00000369005.1:c.4237G>A	10.37:g.123846252G>A	ENSP00000358001:p.Ala1413Thr	106.0	0.0	0		119.0	51.0	0.428571	NM_206862	Q4VXL0|Q4VXL3|Q4VXL6|Q4VXL7|Q5U5T7|Q86WG6|Q86WG7|Q8TCK9|Q9BVQ1|Q9NZ41|Q9NZR5	Missense_Mutation	SNP	ENST00000369005.1	37	CCDS7626.1	0	0.0	0	0.0	0	0.0	0	0.0	0	0.0	G	3.835	-0.035002	0.07543	0.0	1.16E-4	ENSG00000138162	ENST00000369005;ENST00000515273;ENST00000515603;ENST00000334433;ENST00000453444;ENST00000340076	T;T;T;T;T	0.02301	4.35;4.46;4.37;4.35;4.46	5.27	4.15	0.48705	.	0.234704	0.22121	N	0.064340	T	0.00936	0.0031	N	0.02539	-0.55	0.22280	N	0.999238	B;B;B	0.10296	0.003;0.003;0.003	B;B;B	0.01281	0.0;0.0;0.0	T	0.47724	-0.9095	10	0.02654	T	1	-6.9253	7.1361	0.25529	0.8892:0.0:0.1108:0.0	.	1413;1413;1413	E9PBC6;E7EMZ9;O95359	.;.;TACC2_HUMAN	T	1413;1413;1413;1413;1413;1403	ENSP00000358001:A1413T;ENSP00000424467:A1413T;ENSP00000427618:A1413T;ENSP00000334280:A1413T;ENSP00000395048:A1413T	ENSP00000334280:A1413T	A	+	1	0	TACC2	123836242	1.000000	0.71417	1.000000	0.80357	0.731000	0.41821	3.191000	0.50981	0.855000	0.35359	0.549000	0.68633	GCC	G|0.999;A|0.001	0.001	strong		0.592	TACC2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000090004.1		
RBM6	10180	hgsc.bcm.edu	37	3	50005855	50005855	+	Missense_Mutation	SNP	G	G	A	rs143972186	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr3:50005855G>A	ENST00000266022.4	+	3	1256	c.997G>A	c.(997-999)Gaa>Aaa	p.E333K	RBM6_ENST00000422955.1_Intron|RBM6_ENST00000441115.1_Intron|RBM6_ENST00000443081.1_Missense_Mutation_p.E201K|RBM6_ENST00000539992.1_Intron|RBM6_ENST00000442092.1_Intron	NM_005777.2	NP_005768.1	P78332	RBM6_HUMAN	RNA binding motif protein 6	333					RNA processing (GO:0006396)	nucleus (GO:0005634)	DNA binding (GO:0003677)|nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)			breast(1)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(7)|lung(10)|ovary(3)|prostate(1)|skin(4)|urinary_tract(1)	33				BRCA - Breast invasive adenocarcinoma(193;6.81e-05)|KIRC - Kidney renal clear cell carcinoma(197;0.0084)|Kidney(197;0.00977)		TCAGAAGGGAGAATTTGAGCA	0.423													G|||	5	0.000998403	0.0	0.0014	5008	,	,		21143	0.0		0.003	False		,,,				2504	0.001				p.E333K		Atlas-SNP	.											.	RBM6	85	.	0			c.G997A						PASS	.	G	,LYS/GLU	7,4399	12.9+/-30.5	0,7,2196	81.0	72.0	75.0		,997	6.0	1.0	3	dbSNP_134	75	37,8563	25.1+/-72.6	0,37,4263	yes	intron,missense	RBM6	NM_001167582.1,NM_005777.2	,56	0,44,6459	AA,AG,GG		0.4302,0.1589,0.3383	,probably-damaging	,333/1124	50005855	44,12962	2203	4300	6503	SO:0001583	missense	10180	exon3			AAGGGAGAATTTG	AF069517	CCDS2809.1, CCDS54586.1	3p21.3	2013-01-28			ENSG00000004534	ENSG00000004534		"""RNA binding motif (RRM) containing"", ""G patch domain containing"""	9903	protein-coding gene	gene with protein product		606886				10352938	Standard	NM_001167582		Approved	DEF-3, 3G2, NY-LU-12, g16, DEF3	uc003cyc.3	P78332	OTTHUMG00000156736	ENST00000266022.4:c.997G>A	3.37:g.50005855G>A	ENSP00000266022:p.Glu333Lys	219.0	1.0	0.00456621		205.0	106.0	0.517073	NM_005777	O60549|O75524|Q86SS3	Missense_Mutation	SNP	ENST00000266022.4	37	CCDS2809.1	3	0.0013736263736263737	0	0.0	1	0.0027624309392265192	0	0.0	2	0.002638522427440633	G	16.90	3.249072	0.59103	0.001589	0.004302	ENSG00000004534	ENST00000266022;ENST00000443081	T;T	0.38887	1.11;1.15	6.04	6.04	0.98038	.	0.128334	0.51477	D	0.000098	T	0.49695	0.1572	L	0.27053	0.805	0.80722	D	1	D	0.69078	0.997	D	0.75020	0.985	T	0.35574	-0.9783	9	.	.	.	-13.7992	13.7331	0.62802	0.0698:0.0:0.9302:0.0	.	333	P78332	RBM6_HUMAN	K	333;201	ENSP00000266022:E333K;ENSP00000396466:E201K	.	E	+	1	0	RBM6	49980859	1.000000	0.71417	1.000000	0.80357	0.845000	0.48019	4.840000	0.62817	2.873000	0.98535	0.561000	0.74099	GAA	G|0.997;A|0.003	0.003	strong		0.423	RBM6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000345528.4	NM_005777	
ZNF215	7762	hgsc.bcm.edu	37	11	6962879	6962879	+	Missense_Mutation	SNP	C	C	T	rs141940336	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr11:6962879C>T	ENST00000278319.5	+	4	1066	c.478C>T	c.(478-480)Cca>Tca	p.P160S	ZNF215_ENST00000527171.1_3'UTR|ZNF215_ENST00000414517.2_Missense_Mutation_p.P160S|ZNF215_ENST00000529903.1_Missense_Mutation_p.P160S	NM_013250.2	NP_037382.2	Q9UL58	ZN215_HUMAN	zinc finger protein 215	160					regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription from RNA polymerase II promoter (GO:0006366)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0000981)|sequence-specific DNA binding transcription factor activity (GO:0003700)			NS(4)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(5)|lung(12)|ovary(1)|prostate(2)|skin(4)	32				Epithelial(150;6.33e-08)|BRCA - Breast invasive adenocarcinoma(625;0.134)		AACAGGCAAACCACAGGTGAA	0.413																																					p.P160S		Atlas-SNP	.											.	ZNF215	72	.	0			c.C478T						PASS	.	C	SER/PRO	0,4402		0,0,2201	90.0	86.0	87.0		478	1.1	0.0	11	dbSNP_134	87	2,8590	2.2+/-6.3	0,2,4294	yes	missense	ZNF215	NM_013250.2	74	0,2,6495	TT,TC,CC		0.0233,0.0,0.0154	benign	160/518	6962879	2,12992	2201	4296	6497	SO:0001583	missense	7762	exon4			GGCAAACCACAGG	AF056618	CCDS7775.1	11p15.4	2013-01-09			ENSG00000149054	ENSG00000149054		"""Zinc fingers, C2H2-type"", ""-"", ""-"", ""-"""	13007	protein-coding gene	gene with protein product		605016					Standard	XM_005253130		Approved	ZKSCAN11, ZSCAN43	uc001mey.3	Q9UL58	OTTHUMG00000165507	ENST00000278319.5:c.478C>T	11.37:g.6962879C>T	ENSP00000278319:p.Pro160Ser	83.0	0.0	0		87.0	40.0	0.45977	NM_013250	Q96C84	Missense_Mutation	SNP	ENST00000278319.5	37	CCDS7775.1	.	.	.	.	.	.	.	.	.	.	C	0.861	-0.735158	0.03111	0.0	2.33E-4	ENSG00000149054	ENST00000278319;ENST00000414517;ENST00000529903	T;T;T	0.00768	5.72;5.72;5.72	4.32	1.07	0.20283	Krueppel-associated box (1);	0.585459	0.14355	N	0.324834	T	0.00328	0.0010	N	0.01705	-0.755	0.34821	D	0.738729	B;B;B	0.06786	0.0;0.001;0.0	B;B;B	0.04013	0.0;0.001;0.0	T	0.31998	-0.9923	10	0.02654	T	1	4.8197	5.2224	0.15375	0.0:0.4366:0.0:0.5634	.	160;160;160	B4DYW9;Q96C84;Q9UL58	.;.;ZN215_HUMAN	S	160	ENSP00000278319:P160S;ENSP00000393202:P160S;ENSP00000432306:P160S	ENSP00000278319:P160S	P	+	1	0	ZNF215	6919455	0.000000	0.05858	0.000000	0.03702	0.091000	0.18340	0.273000	0.18662	0.419000	0.25927	0.591000	0.81541	CCA	C|1.000;T|0.000	0.000	strong		0.413	ZNF215-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000384550.1		
SYNGR4	23546	hgsc.bcm.edu	37	19	48879375	48879375	+	Nonsense_Mutation	SNP	C	C	T			TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr19:48879375C>T	ENST00000344846.2	+	5	755	c.505C>T	c.(505-507)Cga>Tga	p.R169*	SYNGR4_ENST00000601610.1_Missense_Mutation_p.P145L|SYNGR4_ENST00000595322.1_Missense_Mutation_p.P73L	NM_012451.3	NP_036583.2	O95473	SNG4_HUMAN	synaptogyrin 4	169	MARVEL. {ECO:0000255|PROSITE- ProRule:PRU00581}.					integral component of membrane (GO:0016021)				breast(1)|endometrium(2)|large_intestine(4)|lung(2)|skin(1)	10		all_epithelial(76;5.08e-07)|all_lung(116;5.76e-06)|Lung NSC(112;1.18e-05)|Prostate(7;0.0143)|all_neural(266;0.0189)|Ovarian(192;0.0261)|Breast(70;0.203)		OV - Ovarian serous cystadenocarcinoma(262;0.000138)|all cancers(93;0.00017)|Epithelial(262;0.0138)|GBM - Glioblastoma multiforme(486;0.0146)		CCAGGACCTCCGAAATGATGC	0.602																																					p.R169X		Atlas-SNP	.											SYNGR4,NS,carcinoma,-2,3	SYNGR4	31	3	0			c.C505T						PASS	.						104.0	98.0	100.0					19																	48879375		2203	4300	6503	SO:0001587	stop_gained	23546	exon5			GACCTCCGAAATG	AJ011733	CCDS12717.1	19q13.3	2008-07-04				ENSG00000105467			11502	protein-coding gene	gene with protein product		608373					Standard	NM_012451		Approved		uc002piz.3	O95473		ENST00000344846.2:c.505C>T	19.37:g.48879375C>T	ENSP00000344041:p.Arg169*	147.0	0.0	0		147.0	38.0	0.258503	NM_012451	Q3KP58	Nonsense_Mutation	SNP	ENST00000344846.2	37	CCDS12717.1	.	.	.	.	.	.	.	.	.	.	C	36	5.676643	0.96764	.	.	ENSG00000105467	ENST00000344846	.	.	.	5.61	4.55	0.56014	.	0.948152	0.08692	N	0.907770	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-2.6799	7.5531	0.27808	0.1663:0.7504:0.0:0.0833	.	.	.	.	X	169	.	ENSP00000344041:R169X	R	+	1	2	SYNGR4	53571187	0.522000	0.26266	0.855000	0.33649	0.846000	0.48090	0.827000	0.27421	1.480000	0.48289	0.555000	0.69702	CGA	.	.	none		0.602	SYNGR4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000465704.1		
PRKAA1	5562	hgsc.bcm.edu	37	5	40765280	40765280	+	Silent	SNP	A	A	G			TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr5:40765280A>G	ENST00000397128.2	-	7	890	c.882T>C	c.(880-882)taT>taC	p.Y294Y	PRKAA1_ENST00000354209.3_Silent_p.Y309Y	NM_006251.5|NM_206907.3	NP_006242.5|NP_996790.3	Q13131	AAPK1_HUMAN	protein kinase, AMP-activated, alpha 1 catalytic subunit	294					activation of MAPK activity (GO:0000187)|autophagy (GO:0006914)|cell cycle arrest (GO:0007050)|cellular response to ethanol (GO:0071361)|cellular response to glucose starvation (GO:0042149)|cellular response to hydrogen peroxide (GO:0070301)|cellular response to hypoxia (GO:0071456)|cellular response to nutrient levels (GO:0031669)|cholesterol biosynthetic process (GO:0006695)|cold acclimation (GO:0009631)|fatty acid biosynthetic process (GO:0006633)|fatty acid homeostasis (GO:0055089)|fatty acid oxidation (GO:0019395)|glucose homeostasis (GO:0042593)|glucose metabolic process (GO:0006006)|insulin receptor signaling pathway (GO:0008286)|lipid biosynthetic process (GO:0008610)|negative regulation of apoptotic process (GO:0043066)|negative regulation of glucose import in response to insulin stimulus (GO:2001274)|negative regulation of glucosylceramide biosynthetic process (GO:0046318)|negative regulation of lipid catabolic process (GO:0050995)|negative regulation of TOR signaling (GO:0032007)|positive regulation of autophagy (GO:0010508)|positive regulation of cell proliferation (GO:0008284)|positive regulation of cholesterol biosynthetic process (GO:0045542)|positive regulation of gene expression (GO:0010628)|positive regulation of glycolytic process (GO:0045821)|protein heterooligomerization (GO:0051291)|protein phosphorylation (GO:0006468)|regulation of circadian rhythm (GO:0042752)|regulation of energy homeostasis (GO:2000505)|regulation of transcription, DNA-templated (GO:0006355)|regulation of vesicle-mediated transport (GO:0060627)|response to activity (GO:0014823)|response to caffeine (GO:0031000)|response to camptothecin (GO:1901563)|response to gamma radiation (GO:0010332)|response to hypoxia (GO:0001666)|response to UV (GO:0009411)|rhythmic process (GO:0048511)|signal transduction (GO:0007165)|transcription, DNA-templated (GO:0006351)|Wnt signaling pathway (GO:0016055)	AMP-activated protein kinase complex (GO:0031588)|apical plasma membrane (GO:0016324)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|intracellular (GO:0005622)|nucleus (GO:0005634)	[acetyl-CoA carboxylase] kinase activity (GO:0050405)|[hydroxymethylglutaryl-CoA reductase (NADPH)] kinase activity (GO:0047322)|AMP-activated protein kinase activity (GO:0004679)|ATP binding (GO:0005524)|cAMP-dependent protein kinase activity (GO:0004691)|chromatin binding (GO:0003682)|histone serine kinase activity (GO:0035174)|metal ion binding (GO:0046872)|protein kinase activity (GO:0004672)|tau-protein kinase activity (GO:0050321)			breast(1)	1					Acetylsalicylic acid(DB00945)|Adenosine monophosphate(DB00131)|Adenosine triphosphate(DB00171)|Phenformin(DB00914)	TGGTTGAACTATATGATGGAT	0.388																																					p.Y309Y		Atlas-SNP	.											.	PRKAA1	27	.	0			c.T927C						PASS	.						126.0	115.0	118.0					5																	40765280		1838	4091	5929	SO:0001819	synonymous_variant	5562	exon8			TGAACTATATGAT		CCDS3932.2, CCDS3933.2	5p13.1	2012-10-03			ENSG00000132356	ENSG00000132356			9376	protein-coding gene	gene with protein product	"""AMPK, alpha, 1"""	602739				8557660	Standard	XM_006714481		Approved	AMPKa1	uc003jmb.3	Q13131	OTTHUMG00000162269	ENST00000397128.2:c.882T>C	5.37:g.40765280A>G		277.0	0.0	0		306.0	131.0	0.428105	NM_206907	A8MTQ6|B2R7E1|O00286|Q5D0E1|Q86VS1|Q9UNQ4	Silent	SNP	ENST00000397128.2	37	CCDS3932.2																																																																																			.	.	none		0.388	PRKAA1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253833.2	NM_006251	
JADE1	79960	hgsc.bcm.edu	37	4	129792787	129792787	+	Silent	SNP	A	A	G	rs6850940	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr4:129792787A>G	ENST00000226319.6	+	11	2179	c.1899A>G	c.(1897-1899)ttA>ttG	p.L633L	PHF17_ENST00000512960.1_Silent_p.L633L|PHF17_ENST00000452328.2_Silent_p.L621L	NM_199320.2	NP_955352.1														NS(1)|breast(2)|endometrium(1)|kidney(2)|large_intestine(10)|lung(10)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	29						TTTTGGGTTTAGAAAAGACCT	0.483													G|||	111	0.0221645	0.0734	0.0144	5008	,	,		18630	0.0		0.002	False		,,,				2504	0.002				p.L633L		Atlas-SNP	.											.	PHF17	63	.	0			c.A1899G						PASS	.	G		329,4077	793.1+/-415.2	13,303,1887	62.0	66.0	65.0		1899	-4.7	0.1	4	dbSNP_116	65	10,8590	817.4+/-406.9	0,10,4290	no	coding-synonymous	PHF17	NM_199320.2		13,313,6177	GG,GA,AA		0.1163,7.4671,2.6065		633/843	129792787	339,12667	2203	4300	6503	SO:0001819	synonymous_variant	79960	exon11			GGGTTTAGAAAAG																												ENST00000226319.6:c.1899A>G	4.37:g.129792787A>G		117.0	0.0	0		86.0	22.0	0.255814	NM_199320		Silent	SNP	ENST00000226319.6	37	CCDS34062.1																																																																																			A|0.972;G|0.028	0.028	strong		0.483	PHF17-201	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000364280.1		
OR4A5	81318	hgsc.bcm.edu	37	11	51411918	51411918	+	Missense_Mutation	SNP	C	C	T	rs150995059	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr11:51411918C>T	ENST00000319760.6	-	1	530	c.478G>A	c.(478-480)Gtg>Atg	p.V160M		NM_001005272.3	NP_001005272.3	Q8NH83	OR4A5_HUMAN	olfactory receptor, family 4, subfamily A, member 5	160						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)				AGACTGTACACAACAATTTGA	0.448													.|||	15	0.00299521	0.0008	0.0014	5008	,	,		21527	0.0		0.0089	False		,,,				2504	0.0041				p.V160M		Atlas-SNP	.											.	OR4A5	116	.	0			c.G478A						PASS	.	C	MET/VAL	10,4392		0,10,2191	79.0	71.0	74.0		478	1.0	0.1	11	dbSNP_134	74	109,8483		1,107,4188	no	missense	OR4A5	NM_001005272.3	21	1,117,6379	TT,TC,CC		1.2686,0.2272,0.9158	benign	160/316	51411918	119,12875	2201	4296	6497	SO:0001583	missense	81318	exon1			TGTACACAACAAT	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.478G>A	11.37:g.51411918C>T	ENSP00000367664:p.Val160Met	143.0	0.0	0		148.0	72.0	0.486486	NM_001005272	Q6IF84	Missense_Mutation	SNP	ENST00000319760.6	37	CCDS31497.1	7	0.003205128205128205	0	0.0	0	0.0	0	0.0	7	0.009234828496042216	.	2.005	-0.428430	0.04701	0.002272	0.012686	ENSG00000221840	ENST00000319760	T	0.00130	8.69	1.93	0.984	0.19773	GPCR, rhodopsin-like superfamily (1);	0.547041	0.15102	N	0.280442	T	0.00073	0.0002	N	0.11673	0.155	0.09310	N	0.999999	B	0.33739	0.422	B	0.41666	0.363	T	0.03493	-1.1031	10	0.33141	T	0.24	.	4.1454	0.10214	0.0:0.6238:0.0:0.3762	.	160	Q8NH83	OR4A5_HUMAN	M	160	ENSP00000367664:V160M	ENSP00000367664:V160M	V	-	1	0	OR4A5	51268494	0.000000	0.05858	0.070000	0.20053	0.214000	0.24535	-0.808000	0.04515	0.371000	0.24564	0.162000	0.16502	GTG	C|0.993;T|0.007	0.007	strong		0.448	OR4A5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391399.1	NM_001005272	
HIP1	3092	hgsc.bcm.edu	37	7	75171262	75171262	+	Silent	SNP	G	G	A			TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr7:75171262G>A	ENST00000336926.6	-	29	2954	c.2928C>T	c.(2926-2928)atC>atT	p.I976I	HIP1_ENST00000434438.2_Silent_p.I925I	NM_005338.5	NP_005329.3	O00291	HIP1_HUMAN	huntingtin interacting protein 1	976	I/LWEQ. {ECO:0000255|PROSITE- ProRule:PRU00292}.				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						CTTGGCGTTTGATCTGTGTCA	0.463			T	PDGFRB	CMML																																p.I976I		Atlas-SNP	.		Dom	yes		7	7q11.23	3092	huntingtin interacting protein 1		L	HIP1,NS,carcinoma,-2,1	HIP1	91	1	0			c.C2928T						PASS	.						180.0	162.0	168.0					7																	75171262		2203	4300	6503	SO:0001819	synonymous_variant	3092	exon29			GCGTTTGATCTGT	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.2928C>T	7.37:g.75171262G>A		256.0	0.0	0		317.0	72.0	0.227129	NM_005338	B4E3I7|E7ES17|O00328|Q2TB58|Q8TDL4	Silent	SNP	ENST00000336926.6	37	CCDS34669.1																																																																																			.	.	none		0.463	HIP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000342863.2	NM_005338	
FAM171A1	221061	hgsc.bcm.edu	37	10	15256368	15256368	+	Missense_Mutation	SNP	C	C	T	rs143772901	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr10:15256368C>T	ENST00000378116.4	-	8	1225	c.1219G>A	c.(1219-1221)Gaa>Aaa	p.E407K	FAM171A1_ENST00000477161.1_5'UTR	NM_001010924.1	NP_001010924.1	Q5VUB5	F1711_HUMAN	family with sequence similarity 171, member A1	407						extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)				breast(6)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(9)|lung(20)|ovary(3)|prostate(2)|skin(3)|stomach(1)|upper_aerodigestive_tract(2)	52						AGGTCCCCTTCGCCGCCCGGA	0.622													C|||	2	0.000399361	0.0	0.0	5008	,	,		16253	0.0		0.0	False		,,,				2504	0.002				p.E407K		Atlas-SNP	.											.	FAM171A1	252	.	0			c.G1219A						PASS	.	C	LYS/GLU	1,4405	2.1+/-5.4	0,1,2202	58.0	62.0	61.0		1219	5.1	0.1	10	dbSNP_134	61	5,8595	4.3+/-15.6	0,5,4295	yes	missense	FAM171A1	NM_001010924.1	56	0,6,6497	TT,TC,CC		0.0581,0.0227,0.0461	probably-damaging	407/891	15256368	6,13000	2203	4300	6503	SO:0001583	missense	221061	exon8			CCCCTTCGCCGCC	AK022946	CCDS31154.1	10p13	2008-06-16	2008-06-16	2008-06-16	ENSG00000148468	ENSG00000148468			23522	protein-coding gene	gene with protein product			"""chromosome 10 open reading frame 38"""	C10orf38			Standard	NM_001010924		Approved	FLJ12884	uc001iob.3	Q5VUB5	OTTHUMG00000017732	ENST00000378116.4:c.1219G>A	10.37:g.15256368C>T	ENSP00000367356:p.Glu407Lys	94.0	0.0	0		58.0	21.0	0.362069	NM_001010924	D3DRT9|Q32M49|Q8N4I0	Missense_Mutation	SNP	ENST00000378116.4	37	CCDS31154.1	.	.	.	.	.	.	.	.	.	.	C	16.76	3.213121	0.58452	2.27E-4	5.81E-4	ENSG00000148468	ENST00000378116;ENST00000396781	T	0.35421	1.31	5.14	5.14	0.70334	.	0.101232	0.64402	D	0.000003	T	0.51092	0.1654	M	0.72894	2.215	0.80722	D	1	D	0.54397	0.966	P	0.51101	0.659	T	0.51965	-0.8638	10	0.45353	T	0.12	-22.4632	18.8133	0.92068	0.0:1.0:0.0:0.0	.	407	Q5VUB5	F1711_HUMAN	K	407;408	ENSP00000367356:E407K	ENSP00000367356:E407K	E	-	1	0	FAM171A1	15296374	1.000000	0.71417	0.106000	0.21319	0.055000	0.15305	7.103000	0.77014	2.667000	0.90743	0.563000	0.77884	GAA	C|1.000;T|0.000	0.000	weak		0.622	FAM171A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000046984.1	XM_167709	
FRMPD1	22844	hgsc.bcm.edu	37	9	37733752	37733752	+	Missense_Mutation	SNP	G	G	A	rs140800271	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr9:37733752G>A	ENST00000539465.1	+	12	1741	c.1148G>A	c.(1147-1149)cGt>cAt	p.R383H	FRMPD1_ENST00000541302.1_Missense_Mutation_p.R252H|FRMPD1_ENST00000536622.1_Missense_Mutation_p.R205H|FRMPD1_ENST00000377765.3_Missense_Mutation_p.R383H|RP11-613M10.9_ENST00000540557.1_Intron			Q5SYB0	FRPD1_HUMAN	FERM and PDZ domain containing 1	383	FERM. {ECO:0000255|PROSITE- ProRule:PRU00084}.					cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|extracellular vesicular exosome (GO:0070062)|plasma membrane (GO:0005886)				NS(3)|breast(2)|central_nervous_system(2)|endometrium(5)|kidney(4)|large_intestine(22)|lung(34)|ovary(5)|prostate(3)|skin(8)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(3)	93				GBM - Glioblastoma multiforme(29;0.00655)		GCCCAGCTACGTTTAAATTAT	0.343													G|||	16	0.00319489	0.0015	0.0101	5008	,	,		20643	0.0		0.007	False		,,,				2504	0.0				p.R383H		Atlas-SNP	.											.	FRMPD1	237	.	0			c.G1148A						PASS	.	G	HIS/ARG	4,4402	8.1+/-20.4	0,4,2199	143.0	146.0	145.0		1148	5.2	1.0	9	dbSNP_134	145	29,8571	21.0+/-64.5	0,29,4271	yes	missense	FRMPD1	NM_014907.2	29	0,33,6470	AA,AG,GG		0.3372,0.0908,0.2537	probably-damaging	383/1579	37733752	33,12973	2203	4300	6503	SO:0001583	missense	22844	exon12			AGCTACGTTTAAA	AB023184	CCDS6612.1	9p13.1	2008-02-05			ENSG00000070601	ENSG00000070601			29159	protein-coding gene	gene with protein product						10231032	Standard	NM_014907		Approved	KIAA0967, FRMD2	uc004aag.1	Q5SYB0	OTTHUMG00000019927	ENST00000539465.1:c.1148G>A	9.37:g.37733752G>A	ENSP00000444411:p.Arg383His	109.0	0.0	0		126.0	64.0	0.507937	NM_014907	B4DZC8|B7Z807|D3DRQ3|Q14C73|Q5HY96|Q9Y2H3	Missense_Mutation	SNP	ENST00000539465.1	37	CCDS6612.1	11	0.005036630036630037	1	0.0020325203252032522	5	0.013812154696132596	0	0.0	5	0.006596306068601583	G	25.5	4.643088	0.87859	9.08E-4	0.003372	ENSG00000070601	ENST00000377765;ENST00000539465;ENST00000536622;ENST00000541302	T;T;T;T	0.78246	-1.16;-1.16;-1.16;-1.16	5.16	5.16	0.70880	Band 4.1 domain (1);FERM central domain (2);FERM domain (1);	0.000000	0.85682	D	0.000000	T	0.81049	0.4742	L	0.60455	1.87	0.80722	D	1	D;D	0.89917	0.998;1.0	D;D	0.64687	0.923;0.928	D	0.84554	0.0646	10	0.66056	D	0.02	-11.2075	16.1394	0.81513	0.0:0.0:1.0:0.0	.	252;383	B4DZC8;Q5SYB0	.;FRPD1_HUMAN	H	383;383;205;252	ENSP00000366995:R383H;ENSP00000444411:R383H;ENSP00000437762:R205H;ENSP00000444804:R252H	ENSP00000366995:R383H	R	+	2	0	FRMPD1	37723752	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	7.626000	0.83164	2.400000	0.81607	0.609000	0.83330	CGT	G|0.997;A|0.003	0.003	strong		0.343	FRMPD1-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402969.1	NM_014907	
ARID4B	51742	hgsc.bcm.edu	37	1	235383742	235383742	+	Missense_Mutation	SNP	C	C	G	rs148132837		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr1:235383742C>G	ENST00000264183.3	-	15	1779	c.1282G>C	c.(1282-1284)Gtt>Ctt	p.V428L	ARID4B_ENST00000366603.2_Missense_Mutation_p.V428L|ARID4B_ENST00000349213.3_Missense_Mutation_p.V428L	NM_016374.5	NP_057458.4	Q4LE39	ARI4B_HUMAN	AT rich interactive domain 4B (RBP1-like)	428	Glu-rich.				histone H3-K9 trimethylation (GO:0036124)|histone H4-K20 trimethylation (GO:0034773)|regulation of gene expression by genetic imprinting (GO:0006349)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	DNA binding (GO:0003677)			NS(1)|breast(2)|large_intestine(2)|lung(1)|ovary(2)	8	Ovarian(103;0.0473)|Breast(184;0.23)	all_cancers(173;0.000782)|Prostate(94;0.0132)|all_epithelial(177;0.0808)|Lung SC(1967;0.24)	OV - Ovarian serous cystadenocarcinoma(106;2.86e-05)			TCCTCCTTAACTTTTATTTCT	0.348													C|||	1	0.000199681	0.0	0.0	5008	,	,		14311	0.0		0.001	False		,,,				2504	0.0				p.V428L		Atlas-SNP	.											.	ARID4B	142	.	0			c.G1282C						PASS	.	C	LEU/VAL,LEU/VAL,LEU/VAL	0,4406		0,0,2203	128.0	118.0	121.0		1282,1282,1282	-0.5	1.0	1	dbSNP_134	121	9,8585	7.1+/-27.0	0,9,4288	yes	missense,missense,missense	ARID4B	NM_001206794.1,NM_016374.5,NM_031371.3	32,32,32	0,9,6491	GG,GC,CC		0.1047,0.0,0.0692	benign,benign,benign	428/1313,428/1313,428/1227	235383742	9,12991	2203	4297	6500	SO:0001583	missense	51742	exon15			CCTTAACTTTTAT	AF214114	CCDS31060.1, CCDS31061.1	1q42.1-q43	2013-02-07	2006-11-08	2004-01-30	ENSG00000054267	ENSG00000054267		"""-"""	15550	protein-coding gene	gene with protein product		609696	"""retinoblastoma binding protein 1-like 1"", ""AT rich interactive domain 4B (RBP1- like)"""	RBP1L1		11481388	Standard	NM_016374		Approved	BCAA, BRCAA1, SAP180	uc001hwq.3	Q4LE39	OTTHUMG00000039621	ENST00000264183.3:c.1282G>C	1.37:g.235383742C>G	ENSP00000264183:p.Val428Leu	405.0	0.0	0		487.0	158.0	0.324435	NM_016374	A1L465|Q3MHV4|Q5HY99|Q5T2C2|Q5T2C3|Q5T2C4|Q5T2C5|Q5T2C6|Q6P600|Q86UX1|Q86WR4|Q9H915|Q9NYU3|Q9NZB6|Q9NZG4|Q9P2W4|Q9UF62|Q9Y6E1	Missense_Mutation	SNP	ENST00000264183.3	37	CCDS31061.1	.	.	.	.	.	.	.	.	.	.	C	5.309	0.242397	0.10077	0.0	0.001047	ENSG00000054267	ENST00000391856;ENST00000349213;ENST00000366603;ENST00000264183;ENST00000439834;ENST00000418304	T;T;T;T	0.22945	1.95;1.93;1.93;1.97	5.29	-0.47	0.12131	.	0.806611	0.11942	N	0.514583	T	0.13586	0.0329	N	0.19112	0.55	0.25879	N	0.983618	B;B;B;B	0.12013	0.005;0.005;0.005;0.003	B;B;B;B	0.15052	0.007;0.012;0.007;0.003	T	0.36986	-0.9725	10	0.09084	T	0.74	-3.7761	10.6262	0.45508	0.0:0.4311:0.0:0.5689	.	109;428;428;428	Q4LE39-4;Q4LE39-3;Q4LE39-2;Q4LE39	.;.;.;ARI4B_HUMAN	L	428	ENSP00000264184:V428L;ENSP00000355562:V428L;ENSP00000264183:V428L;ENSP00000391497:V428L	ENSP00000264183:V428L	V	-	1	0	ARID4B	233450365	0.953000	0.32496	0.997000	0.53966	0.690000	0.40134	-0.041000	0.12084	-0.034000	0.13713	0.609000	0.83330	GTT	C|0.999;G|0.001	0.001	strong		0.348	ARID4B-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000095566.3	NM_016374	
NLRX1	79671	hgsc.bcm.edu	37	11	119050906	119050906	+	Missense_Mutation	SNP	G	G	A	rs45450295	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr11:119050906G>A	ENST00000409109.1	+	7	2763	c.2176G>A	c.(2176-2178)Gcc>Acc	p.A726T	NLRX1_ENST00000292199.2_Missense_Mutation_p.A726T|NLRX1_ENST00000525863.1_Missense_Mutation_p.A726T|NLRX1_ENST00000409265.4_Missense_Mutation_p.A726T|NLRX1_ENST00000409991.1_Missense_Mutation_p.A726T	NM_001282144.1	NP_001269073.1	Q86UT6	NLRX1_HUMAN	NLR family member X1	726	Required for the repression of MAVS- induced interferon signaling.				innate immune response (GO:0045087)|negative regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043124)|negative regulation of inflammatory response (GO:0050728)|negative regulation of innate immune response (GO:0045824)|negative regulation of interferon-beta production (GO:0032688)|negative regulation of interleukin-6 production (GO:0032715)|negative regulation of RIG-I signaling pathway (GO:0039536)|negative regulation of type I interferon production (GO:0032480)|viral process (GO:0016032)	mitochondrial outer membrane (GO:0005741)	ATP binding (GO:0005524)			cervix(1)|endometrium(2)|kidney(2)|lung(10)|ovary(1)|prostate(3)|skin(1)|upper_aerodigestive_tract(2)	22	all_hematologic(175;0.0977)	Medulloblastoma(222;0.0425)|Breast(348;0.052)|all_neural(223;0.112)		BRCA - Breast invasive adenocarcinoma(274;7.7e-05)		CGGAAGGCATGCCCTGGATGA	0.637													G|||	45	0.00898562	0.0295	0.0043	5008	,	,		18736	0.0		0.002	False		,,,				2504	0.001				p.A726T		Atlas-SNP	.											.	NLRX1	128	.	0			c.G2176A						PASS	.	G	THR/ALA,THR/ALA	162,4238	104.3+/-142.8	2,158,2040	51.0	47.0	49.0		2176,2176	-0.9	0.9	11	dbSNP_127	49	41,8549	26.3+/-74.7	0,41,4254	yes	missense,missense	NLRX1	NM_024618.2,NM_170722.1	58,58	2,199,6294	AA,AG,GG		0.4773,3.6818,1.5627	benign,benign	726/976,726/922	119050906	203,12787	2200	4295	6495	SO:0001583	missense	79671	exon7			AGGCATGCCCTGG	AB094095	CCDS8416.1	11q23.3	2007-02-07			ENSG00000160703	ENSG00000160703		"""Nucleotide-binding domain and leucine rich repeat containing"""	29890	protein-coding gene	gene with protein product	"""nucleotide-binding oligomerization domain, leucine rich repeat containing X1"", ""NOD-like receptor X1"", ""NLR family, X1"""	611947				12766759	Standard	XM_005271669		Approved	NOD9, CLR11.3	uc001pvw.3	Q86UT6	OTTHUMG00000154476	ENST00000409109.1:c.2176G>A	11.37:g.119050906G>A	ENSP00000387334:p.Ala726Thr	234.0	0.0	0		428.0	99.0	0.231308	NM_024618	A8K6Q1|B3KPK2|B3KTA2|Q7RTR3|Q96D51|Q9H724	Missense_Mutation	SNP	ENST00000409109.1	37	CCDS8416.1	13	0.005952380952380952	11	0.022357723577235773	0	0.0	0	0.0	2	0.002638522427440633	G	5.185	0.219615	0.09863	0.036818	0.004773	ENSG00000160703	ENST00000409991;ENST00000292199;ENST00000409265;ENST00000409109;ENST00000525863	T;T;T;T;T	0.50813	0.73;0.73;0.73;0.73;0.73	5.17	-0.941	0.10402	.	0.788838	0.11541	N	0.553714	T	0.04588	0.0125	N	0.08118	0	0.18873	N	0.999983	B;B	0.15473	0.013;0.0	B;B	0.12156	0.007;0.002	T	0.16867	-1.0388	10	0.13108	T	0.6	.	3.8077	0.08783	0.1544:0.3464:0.3861:0.1131	rs45450295	726;726	Q86UT6-2;Q86UT6	.;NLRX1_HUMAN	T	726	ENSP00000386851:A726T;ENSP00000292199:A726T;ENSP00000386858:A726T;ENSP00000387334:A726T;ENSP00000433442:A726T	ENSP00000292199:A726T	A	+	1	0	NLRX1	118556116	0.000000	0.05858	0.911000	0.35937	0.797000	0.45037	-0.202000	0.09451	0.162000	0.19483	0.313000	0.20887	GCC	G|0.988;A|0.012	0.012	strong		0.637	NLRX1-004	PUTATIVE	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000335403.1	NM_170722	
KIAA0319L	79932	hgsc.bcm.edu	37	1	35972375	35972375	+	Silent	SNP	A	A	T			TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr1:35972375A>T	ENST00000325722.3	-	3	738	c.504T>A	c.(502-504)gcT>gcA	p.A168A		NM_024874.4	NP_079150.3	Q8IZA0	K319L_HUMAN	KIAA0319-like	168						cytoplasmic vesicle (GO:0031410)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)				breast(1)|endometrium(2)|kidney(3)|large_intestine(7)|lung(12)|pancreas(1)|prostate(2)|skin(4)|stomach(1)|urinary_tract(1)	34		Myeloproliferative disorder(586;0.0255)|all_neural(195;0.0887)				GTCTGAGTGCAGCTCTGGGTG	0.502																																					p.A168A		Atlas-SNP	.											.	KIAA0319L	156	.	0			c.T504A						PASS	.						121.0	117.0	118.0					1																	35972375		2203	4300	6503	SO:0001819	synonymous_variant	79932	exon3			GAGTGCAGCTCTG	AY163234	CCDS390.1	1p34.3	2008-10-24			ENSG00000142687	ENSG00000142687			30071	protein-coding gene	gene with protein product		613535				11347906	Standard	NM_024874		Approved	KIAA1837	uc001byx.3	Q8IZA0	OTTHUMG00000004370	ENST00000325722.3:c.504T>A	1.37:g.35972375A>T		161.0	0.0	0		103.0	29.0	0.281553	NM_024874	B1AN13|D3DPR8|O95010|Q6PJJ7|Q7L1C9|Q8N2B3|Q8NDA0|Q8WY39|Q8WYZ5|Q96IC3|Q96JJ0|Q9BUW6|Q9H7V0	Silent	SNP	ENST00000325722.3	37	CCDS390.1	.	.	.	.	.	.	.	.	.	.	A	0.044	-1.271484	0.01421	.	.	ENSG00000142687	ENST00000431916	.	.	.	5.78	-1.12	0.09808	.	.	.	.	.	T	0.22166	0.0534	.	.	.	0.09310	N	0.999999	.	.	.	.	.	.	T	0.28459	-1.0043	4	.	.	.	-0.4253	4.2445	0.10665	0.5279:0.2944:0.0697:0.108	.	.	.	.	S	32	.	.	C	-	1	0	KIAA0319L	35744962	0.905000	0.30787	0.001000	0.08648	0.083000	0.17756	0.332000	0.19751	0.104000	0.17725	0.533000	0.62120	TGC	.	.	none		0.502	KIAA0319L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000012684.2	NM_024874	
MMP19	4327	hgsc.bcm.edu	37	12	56236136	56236136	+	Splice_Site	SNP	C	C	T	rs145293054		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr12:56236136C>T	ENST00000322569.4	-	2	265		c.e2+1		MMP19_ENST00000409200.3_Splice_Site|MMP19_ENST00000548629.1_Splice_Site|MMP19_ENST00000547487.1_Splice_Site	NM_002429.4	NP_002420.1	Q99542	MMP19_HUMAN	matrix metallopeptidase 19						angiogenesis (GO:0001525)|cell differentiation (GO:0030154)|collagen catabolic process (GO:0030574)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|luteolysis (GO:0001554)|ovarian follicle development (GO:0001541)|ovulation from ovarian follicle (GO:0001542)|proteolysis (GO:0006508)|response to cAMP (GO:0051591)|response to hormone (GO:0009725)	extracellular region (GO:0005576)|proteinaceous extracellular matrix (GO:0005578)	calcium ion binding (GO:0005509)|metalloendopeptidase activity (GO:0004222)|zinc ion binding (GO:0008270)			endometrium(1)|kidney(2)|large_intestine(7)|lung(12)|ovary(2)|skin(2)	26					Marimastat(DB00786)	TAGCTTCTCACCTCAGAGCCT	0.498													C|||	1	0.000199681	0.0	0.0	5008	,	,		19637	0.0		0.001	False		,,,				2504	0.0				.		Atlas-SNP	.											.	MMP19	61	.	0			c.173+1G>A						PASS	.	C		1,4405	2.1+/-5.4	0,1,2202	154.0	119.0	131.0			6.1	1.0	12	dbSNP_134	131	17,8583	12.6+/-44.7	0,17,4283	yes	splice-5	MMP19	NM_002429.4		0,18,6485	TT,TC,CC		0.1977,0.0227,0.1384			56236136	18,12988	2203	4300	6503	SO:0001630	splice_region_variant	4327	exon3			TTCTCACCTCAGA	X92521	CCDS8895.1, CCDS61146.1	12q14	2005-08-08	2005-08-08			ENSG00000123342			7165	protein-coding gene	gene with protein product		601807	"""matrix metalloproteinase 19"""	MMP18		9232430	Standard	NM_002429		Approved	RASI-1	uc001sib.4	Q99542	OTTHUMG00000170216	ENST00000322569.4:c.173+1G>A	12.37:g.56236136C>T		227.0	1.0	0.00440529		230.0	117.0	0.508696	NM_002429	B4E030|O15278|O95606|Q99580	Splice_Site	SNP	ENST00000322569.4	37	CCDS8895.1	2	9.157509157509158E-4	0	0.0	0	0.0	0	0.0	2	0.002638522427440633	C	24.7	4.564157	0.86335	2.27E-4	0.001977	ENSG00000123342	ENST00000322569;ENST00000548629;ENST00000409200	.	.	.	6.08	6.08	0.98989	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	19.4349	0.94788	0.0:1.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	-	.	.	MMP19	54522403	1.000000	0.71417	1.000000	0.80357	0.951000	0.60555	4.839000	0.62810	2.894000	0.99253	0.655000	0.94253	.	C|0.999;T|0.001	0.001	strong		0.498	MMP19-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000408023.1	NM_002429	Intron
MAD2L1BP	9587	hgsc.bcm.edu	37	6	43608220	43608220	+	Missense_Mutation	SNP	G	G	A			TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr6:43608220G>A	ENST00000372171.4	+	3	832	c.775G>A	c.(775-777)Gac>Aac	p.D259N	MAD2L1BP_ENST00000451025.2_Missense_Mutation_p.D291N	NM_014628.2	NP_055443.1	Q15013	MD2BP_HUMAN	MAD2L1 binding protein	259					mitotic cell cycle checkpoint (GO:0007093)|regulation of exit from mitosis (GO:0007096)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|intracellular membrane-bounded organelle (GO:0043231)|nucleolus (GO:0005730)|nucleus (GO:0005634)				breast(1)|large_intestine(1)|lung(3)	5	all_cancers(18;9.36e-06)|Lung NSC(15;0.00161)|all_lung(25;0.004)		all cancers(41;0.000351)|Colorectal(64;0.00245)|COAD - Colon adenocarcinoma(64;0.00536)|STAD - Stomach adenocarcinoma(11;0.0826)|OV - Ovarian serous cystadenocarcinoma(102;0.167)			GGCTTGGGAAGACTACATTTG	0.493																																					p.D291N		Atlas-SNP	.											.	MAD2L1BP	12	.	0			c.G871A						PASS	.						51.0	48.0	49.0					6																	43608220		2203	4300	6503	SO:0001583	missense	9587	exon4			TGGGAAGACTACA	BC002904	CCDS4904.1, CCDS47431.1	6p21.1	2003-06-23			ENSG00000124688	ENSG00000124688			21059	protein-coding gene	gene with protein product						7788527, 12456649	Standard	NM_014628		Approved	CMT2, KIAA0110, dJ261G23.1	uc003ovu.3	Q15013	OTTHUMG00000014747	ENST00000372171.4:c.775G>A	6.37:g.43608220G>A	ENSP00000361244:p.Asp259Asn	100.0	0.0	0		101.0	30.0	0.29703	NM_001003690	B4DLV3|E9PAT7|Q6IBB1	Missense_Mutation	SNP	ENST00000372171.4	37	CCDS4904.1	.	.	.	.	.	.	.	.	.	.	G	27.4	4.831484	0.91036	.	.	ENSG00000124688	ENST00000451025;ENST00000372171	T	0.57752	0.38	5.09	5.09	0.68999	.	0.000000	0.85682	D	0.000000	T	0.57227	0.2039	L	0.36672	1.1	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;1.0	T	0.62511	-0.6839	10	0.72032	D	0.01	-18.5445	16.7112	0.85386	0.0:0.0:1.0:0.0	.	259;291	Q15013;E9PAT7	MD2BP_HUMAN;.	N	291;259	ENSP00000410818:D291N	ENSP00000361244:D259N	D	+	1	0	MAD2L1BP	43716198	1.000000	0.71417	0.997000	0.53966	0.568000	0.35870	6.281000	0.72632	2.365000	0.80145	0.555000	0.69702	GAC	.	.	none		0.493	MAD2L1BP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040692.2	NM_014628	
ORC4	5000	hgsc.bcm.edu	37	2	148730367	148730367	+	Missense_Mutation	SNP	G	G	C	rs2307397	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr2:148730367G>C	ENST00000392857.5	-	4	273	c.166C>G	c.(166-168)Ctc>Gtc	p.L56V	ORC4_ENST00000542387.1_5'UTR|ORC4_ENST00000392858.1_Missense_Mutation_p.L56V|ORC4_ENST00000536575.1_Intron|ORC4_ENST00000535373.1_Missense_Mutation_p.L56V|ORC4_ENST00000264169.2_Missense_Mutation_p.L56V|ORC4_ENST00000540442.1_5'UTR	NM_001190879.2|NM_001190882.2|NM_002552.4|NM_181741.3	NP_001177808.1|NP_001177811.1|NP_002543.2|NP_859525.1	O43929	ORC4_HUMAN	origin recognition complex, subunit 4	56			L -> V (in dbSNP:rs2307397). {ECO:0000269|Ref.4}.		DNA replication (GO:0006260)|DNA replication initiation (GO:0006270)|G1/S transition of mitotic cell cycle (GO:0000082)|mitotic cell cycle (GO:0000278)	nuclear origin of replication recognition complex (GO:0005664)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|origin recognition complex (GO:0000808)	ATP binding (GO:0005524)|DNA replication origin binding (GO:0003688)|nucleotide binding (GO:0000166)			cervix(1)|endometrium(1)|kidney(2)|large_intestine(3)|lung(2)|ovary(2)|pancreas(1)|prostate(1)|urinary_tract(1)	14						TCTCCATGGAGAGCAGTTCTT	0.358													G|||	86	0.0171725	0.0045	0.0288	5008	,	,		13467	0.0		0.0447	False		,,,				2504	0.0153				p.L56V		Atlas-SNP	.											.	ORC4	40	.	0			c.C166G						PASS	.	G	VAL/LEU,,,VAL/LEU,VAL/LEU,VAL/LEU	51,4355	51.6+/-87.1	1,49,2153	73.0	75.0	74.0		166,,,166,166,166	2.3	1.0	2	dbSNP_100	74	464,8136	138.3+/-195.1	13,438,3849	yes	missense,intron,utr-5,missense,missense,missense	ORC4	NM_001190879.2,NM_001190881.2,NM_001190882.2,NM_002552.4,NM_181741.3,NM_181742.3	32,,,32,32,32	14,487,6002	CC,CG,GG		5.3953,1.1575,3.9597	benign,,,benign,benign,benign	56/437,,,56/437,56/437,56/437	148730367	515,12491	2203	4300	6503	SO:0001583	missense	5000	exon4			CATGGAGAGCAGT	AF022108	CCDS2187.1, CCDS54404.1, CCDS54405.1	2q22-q23	2010-10-12	2010-10-12	2010-10-12	ENSG00000115947	ENSG00000115947		"""ATPases / AAA-type"""	8490	protein-coding gene	gene with protein product		603056	"""origin recognition complex, subunit 4 (yeast homolog)-like"", ""origin recognition complex, subunit 4-like (yeast)"", ""origin recognition complex, subunit 4-like (S. cerevisiae)"", ""origin recognition complex, subunit 4 homolog (S. cerevisiae)"""	ORC4L		9353276, 9691185	Standard	NM_181742		Approved	HsORC4, Orc4p	uc002twk.3	O43929	OTTHUMG00000131849	ENST00000392857.5:c.166C>G	2.37:g.148730367G>C	ENSP00000376597:p.Leu56Val	223.0	0.0	0		206.0	122.0	0.592233	NM_002552	B7Z3D0|B7Z5F1|D3DP86|F5H069|Q96C42	Missense_Mutation	SNP	ENST00000392857.5	37	CCDS2187.1	56	0.02564102564102564	6	0.012195121951219513	14	0.03867403314917127	0	0.0	36	0.047493403693931395	G	9.786	1.176749	0.21704	0.011575	0.053953	ENSG00000115947	ENST00000264169;ENST00000535373;ENST00000392858;ENST00000392857;ENST00000416719;ENST00000457954;ENST00000440042	T;T;T;T;T;T;T	0.60920	0.15;0.15;0.15;0.15;0.15;0.15;0.15	5.88	2.28	0.28536	.	0.171869	0.51477	N	0.000088	T	0.03608	0.0103	N	0.01257	-0.925	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	0.01961	-1.1239	10	0.26408	T	0.33	-4.2923	4.915	0.13842	0.0:0.2245:0.1536:0.6219	rs2307397;rs17219015;rs56449945;rs2307397	56;56;56	B7Z2M4;A8K7H4;O43929	.;.;ORC4_HUMAN	V	56	ENSP00000264169:L56V;ENSP00000441953:L56V;ENSP00000376598:L56V;ENSP00000376597:L56V;ENSP00000413939:L56V;ENSP00000391484:L56V;ENSP00000403105:L56V	ENSP00000264169:L56V	L	-	1	0	ORC4	148446837	0.997000	0.39634	1.000000	0.80357	0.885000	0.51271	0.434000	0.21494	0.487000	0.27698	-0.266000	0.10368	CTC	G|0.964;C|0.036	0.036	strong		0.358	ORC4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254797.3	NM_181742	
EPHA4	2043	hgsc.bcm.edu	37	2	222301160	222301160	+	Silent	SNP	G	G	T	rs56159060		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr2:222301160G>T	ENST00000281821.2	-	13	2346	c.2305C>A	c.(2305-2307)Cga>Aga	p.R769R	EPHA4_ENST00000392071.4_Silent_p.R718R|EPHA4_ENST00000409854.1_Silent_p.R769R|EPHA4_ENST00000409938.1_Silent_p.R769R	NM_004438.3	NP_004429.1	P54764	EPHA4_HUMAN	EPH receptor A4	769	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				adult walking behavior (GO:0007628)|cell adhesion (GO:0007155)|corticospinal tract morphogenesis (GO:0021957)|fasciculation of motor neuron axon (GO:0097156)|fasciculation of sensory neuron axon (GO:0097155)|glial cell migration (GO:0008347)|motor neuron axon guidance (GO:0008045)|negative regulation of axon regeneration (GO:0048681)|peptidyl-tyrosine phosphorylation (GO:0018108)|positive regulation of dendrite morphogenesis (GO:0050775)|positive regulation of JUN kinase activity (GO:0043507)|positive regulation of Rho guanyl-nucleotide exchange factor activity (GO:2001108)|protein autophosphorylation (GO:0046777)|regulation of astrocyte differentiation (GO:0048710)|regulation of axonogenesis (GO:0050770)|regulation of dendritic spine morphogenesis (GO:0061001)|regulation of Rac GTPase activity (GO:0032314)|regulation of Rap GTPase activity (GO:0032317)	axon (GO:0030424)|axon terminus (GO:0043679)|axonal growth cone (GO:0044295)|cell junction (GO:0030054)|cell surface (GO:0009986)|cytoplasm (GO:0005737)|dendrite (GO:0030425)|dendritic spine (GO:0043197)|early endosome membrane (GO:0031901)|endoplasmic reticulum (GO:0005783)|filopodium (GO:0030175)|Golgi apparatus (GO:0005794)|integral component of plasma membrane (GO:0005887)|mitochondrial outer membrane (GO:0005741)|neuromuscular junction (GO:0031594)|perikaryon (GO:0043204)|postsynaptic density (GO:0014069)|postsynaptic membrane (GO:0045211)	ATP binding (GO:0005524)|DH domain binding (GO:0097161)|GPI-linked ephrin receptor activity (GO:0005004)|PH domain binding (GO:0042731)|protein kinase activity (GO:0004672)|transmembrane-ephrin receptor activity (GO:0005005)			NS(1)|breast(1)|central_nervous_system(2)|cervix(1)|endometrium(4)|kidney(1)|large_intestine(9)|liver(1)|lung(21)|prostate(3)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	49		Renal(207;0.0183)		Epithelial(121;5.38e-09)|all cancers(144;2.47e-06)|LUSC - Lung squamous cell carcinoma(224;0.0115)|Lung(261;0.0154)		TCAAGCACTCGGGACATGCCA	0.488																																					p.R769R		Atlas-SNP	.											.	EPHA4	263	.	0			c.C2305A						PASS	.						101.0	83.0	89.0					2																	222301160		2203	4300	6503	SO:0001819	synonymous_variant	2043	exon13			GCACTCGGGACAT	L36645	CCDS2447.1	2q36.3	2013-02-11	2004-10-28		ENSG00000116106	ENSG00000116106	2.7.10.1	"""EPH receptors"", ""Sterile alpha motif (SAM) domain containing"", ""Fibronectin type III domain containing"""	3388	protein-coding gene	gene with protein product		602188	"""EphA4"""	TYRO1		9267020	Standard	NM_004438		Approved	Hek8	uc002vmq.3	P54764	OTTHUMG00000133142	ENST00000281821.2:c.2305C>A	2.37:g.222301160G>T		106.0	0.0	0		71.0	16.0	0.225352	NM_004438	A8K2P1|B2R601|B7Z6Q8|Q2M380	Silent	SNP	ENST00000281821.2	37	CCDS2447.1																																																																																			.	.	weak		0.488	EPHA4-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256836.3		
LMNTD2	256329	hgsc.bcm.edu	37	11	556584	556584	+	Silent	SNP	G	G	A			TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr11:556584G>A	ENST00000329451.3	-	9	1043	c.981C>T	c.(979-981)ctC>ctT	p.L327L	RP11-496I9.1_ENST00000527620.1_RNA|RP11-496I9.1_ENST00000527113.1_RNA	NM_173573.2	NP_775844.2	Q8IXW0	LMTD2_HUMAN		327										NS(1)|breast(1)|central_nervous_system(1)|lung(4)|pancreas(1)	8		all_cancers(49;2.16e-06)|all_epithelial(84;0.000256)|Breast(177;0.00122)|Ovarian(85;0.0228)|Medulloblastoma(188;0.0321)|all_neural(188;0.0762)		all cancers(45;7.18e-28)|Epithelial(43;6.93e-27)|OV - Ovarian serous cystadenocarcinoma(40;6.97e-21)|BRCA - Breast invasive adenocarcinoma(625;3.56e-05)|Lung(200;0.0375)|LUSC - Lung squamous cell carcinoma(625;0.0703)		GGGTTTTCTGGAGATCTAGAG	0.657																																					p.L327L		Atlas-SNP	.											.	C11orf35	22	.	0			c.C981T						PASS	.						20.0	20.0	20.0					11																	556584		2172	4248	6420	SO:0001819	synonymous_variant	256329	exon9			TTTCTGGAGATCT																												ENST00000329451.3:c.981C>T	11.37:g.556584G>A		67.0	0.0	0		45.0	28.0	0.622222	NM_173573		Silent	SNP	ENST00000329451.3	37	CCDS7701.1																																																																																			.	.	none		0.657	C11orf35-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254973.2		
FAT3	120114	hgsc.bcm.edu	37	11	92568149	92568149	+	Missense_Mutation	SNP	A	A	G	rs75651194	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr11:92568149A>G	ENST00000298047.6	+	14	10002	c.9985A>G	c.(9985-9987)Atc>Gtc	p.I3329V	FAT3_ENST00000409404.2_Missense_Mutation_p.I3329V|FAT3_ENST00000525166.1_Missense_Mutation_p.I3179V			Q8TDW7	FAT3_HUMAN	FAT atypical cadherin 3	3329	Cadherin 30. {ECO:0000255|PROSITE- ProRule:PRU00043}.				homophilic cell adhesion (GO:0007156)|multicellular organismal development (GO:0007275)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			NS(1)|breast(2)|endometrium(10)|kidney(4)|large_intestine(11)|liver(2)|lung(37)|ovary(5)|pancreas(1)|prostate(4)|skin(2)|stomach(1)|upper_aerodigestive_tract(5)	85		Acute lymphoblastic leukemia(157;3.01e-05)|all_hematologic(158;0.00858)				CACTGTCAACATCAACCTCAC	0.498										TCGA Ovarian(4;0.039)			A|||	27	0.00539137	0.0008	0.0115	5008	,	,		16819	0.0		0.0119	False		,,,				2504	0.0061				p.I3329V		Atlas-SNP	.											.	FAT3	1822	.	0			c.A9985G						PASS	.	A	VAL/ILE	2,3912		0,2,1955	50.0	51.0	51.0		9985	3.2	1.0	11	dbSNP_133	51	113,8195		2,109,4043	yes	missense	FAT3	NM_001008781.2	29	2,111,5998	GG,GA,AA		1.3601,0.0511,0.9409	benign	3329/4558	92568149	115,12107	1957	4154	6111	SO:0001583	missense	120114	exon14			GTCAACATCAACC	AB076400		11q14.3	2013-05-31	2013-05-31		ENSG00000165323	ENSG00000165323		"""Cadherins / Cadherin-related"""	23112	protein-coding gene	gene with protein product	"""cadherin-related family member 10"""	612483	"""FAT tumor suppressor homolog 3 (Drosophila)"""			11811999	Standard	NM_001008781		Approved	KIAA1989, CDHF15, CDHR10	uc001pdj.4	Q8TDW7	OTTHUMG00000154468	ENST00000298047.6:c.9985A>G	11.37:g.92568149A>G	ENSP00000298047:p.Ile3329Val	118.0	0.0	0		183.0	50.0	0.273224	NM_001008781	B5MDB0|Q96AU6	Missense_Mutation	SNP	ENST00000298047.6	37		13	0.005952380952380952	0	0.0	5	0.013812154696132596	0	0.0	8	0.010554089709762533	A	3.371	-0.128480	0.06753	5.11E-4	0.013601	ENSG00000165323	ENST00000298047;ENST00000409404;ENST00000525166	T;T;T	0.35421	1.31;1.31;1.31	5.46	3.17	0.36434	.	.	.	.	.	T	0.15652	0.0377	N	0.20574	0.59	0.80722	D	1	B	0.13594	0.008	B	0.18263	0.021	T	0.04128	-1.0975	9	0.28530	T	0.3	.	8.4034	0.32601	0.7733:0.0:0.2267:0.0	.	3329	Q8TDW7-3	.	V	3329;3329;3179	ENSP00000298047:I3329V;ENSP00000387040:I3329V;ENSP00000432586:I3179V	ENSP00000298047:I3329V	I	+	1	0	FAT3	92207797	1.000000	0.71417	1.000000	0.80357	0.122000	0.20287	1.781000	0.38644	0.897000	0.36392	-0.256000	0.11100	ATC	A|0.991;G|0.009	0.009	strong		0.498	FAT3-201	KNOWN	basic	protein_coding	protein_coding		NM_001008781	
ZNF33B	7582	hgsc.bcm.edu	37	10	43089278	43089278	+	Missense_Mutation	SNP	T	T	C	rs71505624	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr10:43089278T>C	ENST00000359467.3	-	5	1234	c.1120A>G	c.(1120-1122)Aaa>Gaa	p.K374E	ZNF33B_ENST00000486187.1_RNA	NM_006955.1	NP_008886.1	Q06732	ZN33B_HUMAN	zinc finger protein 33B	374					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(1)|endometrium(4)|kidney(1)|large_intestine(6)|lung(15)|skin(1)|stomach(1)	29						CTCTGATGTTTAGTGAGGTTT	0.433													t|||	7	0.00139776	0.0	0.0014	5008	,	,		20809	0.0		0.004	False		,,,				2504	0.002				p.K374E	Melanoma(137;1247 1767 16772 25727 43810)	Atlas-SNP	.											.	ZNF33B	78	.	0			c.A1120G						PASS	.	T	GLU/LYS	2,4404	4.2+/-10.8	0,2,2201	117.0	117.0	117.0		1120	2.3	1.0	10	dbSNP_130	117	20,8580	14.6+/-50.1	0,20,4280	yes	missense	ZNF33B	NM_006955.1	56	0,22,6481	CC,CT,TT		0.2326,0.0454,0.1692	probably-damaging	374/779	43089278	22,12984	2203	4300	6503	SO:0001583	missense	7582	exon5			GATGTTTAGTGAG	X68688, AJ491697	CCDS7198.1	10q11.2	2013-01-08	2005-03-18		ENSG00000196693	ENSG00000196693		"""Zinc fingers, C2H2-type"", ""-"""	13097	protein-coding gene	gene with protein product		194522	"""zinc finger protein 33b (KOX 31)"", ""zinc finger protein 11B"""	ZNF11B		2014798	Standard	NM_006955		Approved	KOX31, KOX2	uc001jaf.1	Q06732	OTTHUMG00000018014	ENST00000359467.3:c.1120A>G	10.37:g.43089278T>C	ENSP00000352444:p.Lys374Glu	200.0	0.0	0		174.0	33.0	0.189655	NM_006955	Q06731|Q32MA2|Q86XY8|Q8NDW3	Missense_Mutation	SNP	ENST00000359467.3	37	CCDS7198.1	4	0.0018315018315018315	0	0.0	1	0.0027624309392265192	0	0.0	3	0.00395778364116095	T	5.009	0.187437	0.09547	4.54E-4	0.002326	ENSG00000196693	ENST00000359467;ENST00000395836	T	0.19394	2.15	2.28	2.28	0.28536	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	0.000000	0.38548	N	0.001658	T	0.17959	0.0431	N	0.12569	0.235	0.09310	N	1	D	0.76494	0.999	D	0.69479	0.964	T	0.13548	-1.0505	10	0.02654	T	1	.	8.5071	0.33195	0.0:0.0:0.0:1.0	.	374	Q06732	ZN33B_HUMAN	E	374;340	ENSP00000352444:K374E	ENSP00000352444:K374E	K	-	1	0	ZNF33B	42409284	0.000000	0.05858	1.000000	0.80357	0.981000	0.71138	-0.059000	0.11731	1.324000	0.45282	0.341000	0.21757	AAA	T|0.998;C|0.002	0.002	strong		0.433	ZNF33B-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_006955	
BTN2A2	10385	hgsc.bcm.edu	37	6	26384092	26384092	+	Missense_Mutation	SNP	C	C	T	rs546542545		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr6:26384092C>T	ENST00000356709.4	+	2	154	c.43C>T	c.(43-45)Ctc>Ttc	p.L15F	BTN2A2_ENST00000482536.1_Missense_Mutation_p.L15F|BTN2A2_ENST00000416795.2_Missense_Mutation_p.L15F|BTN2A2_ENST00000469230.1_Missense_Mutation_p.L15F|BTN2A2_ENST00000352867.2_Missense_Mutation_p.L15F|BTN2A2_ENST00000432533.2_Missense_Mutation_p.L15F	NM_001197240.1|NM_006995.4	NP_001184169.1|NP_008926.2	Q8WVV5	BT2A2_HUMAN	butyrophilin, subfamily 2, member A2	15					negative regulation of activated T cell proliferation (GO:0046007)|negative regulation of cellular metabolic process (GO:0031324)|negative regulation of cytokine secretion (GO:0050710)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)				breast(2)|endometrium(3)|large_intestine(5)|lung(13)	23						GCCAGCCTCcctcctcctcct	0.587																																					p.L15F		Atlas-SNP	.											BTN2A2_ENST00000432533,bladder,carcinoma,-1,2	BTN2A2	87	2	0			c.C43T						scavenged	.						191.0	138.0	156.0					6																	26384092		2203	4300	6503	SO:0001583	missense	10385	exon2			GCCTCCCTCCTCC	U90550	CCDS4606.1, CCDS4607.1, CCDS56401.1, CCDS56402.1, CCDS56403.1	6p22.1	2014-01-14			ENSG00000124508	ENSG00000124508		"""Immunoglobulin superfamily / V-set domain containing"", ""Immunoglobulin superfamily / C2-set domain containing"", ""Butyrophilins"""	1137	protein-coding gene	gene with protein product		613591				10354554, 9149941	Standard	NM_006995		Approved	BTF2, BT2.2, BTN2.2	uc003nhq.3	Q8WVV5	OTTHUMG00000014452	ENST00000356709.4:c.43C>T	6.37:g.26384092C>T	ENSP00000349143:p.Leu15Phe	125.0	0.0	0		125.0	6.0	0.048	NM_181531	A6NM84|B4DE97|B4DQ01|E9PH07|O00480	Missense_Mutation	SNP	ENST00000356709.4	37	CCDS4606.1	.	.	.	.	.	.	.	.	.	.	c	14.03	2.412871	0.42817	.	.	ENSG00000124508	ENST00000469230;ENST00000356709;ENST00000352867;ENST00000493275;ENST00000472507;ENST00000482536;ENST00000432533;ENST00000416795;ENST00000494184;ENST00000483410	T;T;T;T;T;T;D;T;T;T	0.90444	3.76;1.1;0.43;4.24;3.36;-0.21;-2.67;1.1;2.29;3.8	2.01	1.1	0.20463	.	0.656368	0.12607	N	0.454165	T	0.62085	0.2399	N	0.08118	0	0.21675	N	0.999591	B;B;B;B;B;B	0.24132	0.003;0.008;0.098;0.014;0.003;0.003	B;B;B;B;B;B	0.15052	0.002;0.003;0.012;0.006;0.002;0.002	T	0.57562	-0.7790	10	0.87932	D	0	.	4.8159	0.13367	0.0:0.8071:0.0:0.1929	.	15;15;15;15;15;15	E9PH07;B4DQ01;B4E3J1;Q8WVV5-2;A6NM84;Q8WVV5	.;.;.;.;.;BT2A2_HUMAN	F	15	ENSP00000417472:L15F;ENSP00000349143:L15F;ENSP00000337117:L15F;ENSP00000418857:L15F;ENSP00000419226:L15F;ENSP00000419451:L15F;ENSP00000394241:L15F;ENSP00000399308:L15F;ENSP00000417511:L15F;ENSP00000418176:L15F	ENSP00000337117:L15F	L	+	1	0	BTN2A2	26492071	0.000000	0.05858	0.368000	0.25939	0.580000	0.36256	-0.390000	0.07332	0.383000	0.24910	0.298000	0.19748	CTC	.	.	none		0.587	BTN2A2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040117.1		
MUC17	140453	hgsc.bcm.edu	37	7	100681345	100681345	+	Missense_Mutation	SNP	T	T	G	rs142097516		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr7:100681345T>G	ENST00000306151.4	+	3	6712	c.6648T>G	c.(6646-6648)agT>agG	p.S2216R		NM_001040105.1	NP_001035194.1	Q685J3	MUC17_HUMAN	mucin 17, cell surface associated	2216	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)					CAACTCCTAGTGAAGGAAGCA	0.507																																					p.S2216R		Atlas-SNP	.											.	MUC17	804	.	0			c.T6648G						PASS	.						343.0	338.0	340.0					7																	100681345		2203	4300	6503	SO:0001583	missense	140453	exon3			TCCTAGTGAAGGA	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.6648T>G	7.37:g.100681345T>G	ENSP00000302716:p.Ser2216Arg	177.0	0.0	0		249.0	23.0	0.0923695	NM_001040105	O14761|Q685J2|Q8TDH7	Missense_Mutation	SNP	ENST00000306151.4	37	CCDS34711.1	.	.	.	.	.	.	.	.	.	.	T	2.901	-0.227411	0.06022	.	.	ENSG00000169876	ENST00000306151	T	0.02606	4.23	1.11	-2.01	0.07410	.	.	.	.	.	T	0.01489	0.0048	N	0.14661	0.345	0.09310	N	1	B	0.24963	0.115	B	0.13407	0.009	T	0.49351	-0.8949	9	0.18710	T	0.47	.	4.0824	0.09932	0.3049:0.0:0.0:0.695	.	2216	Q685J3	MUC17_HUMAN	R	2216	ENSP00000302716:S2216R	ENSP00000302716:S2216R	S	+	3	2	MUC17	100468065	0.013000	0.17824	0.006000	0.13384	0.003000	0.03518	-0.741000	0.04855	0.459000	0.27016	0.113000	0.15668	AGT	.	.	weak		0.507	MUC17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347161.1	NM_001040105	
RRM1	6240	hgsc.bcm.edu	37	11	4154851	4154851	+	Missense_Mutation	SNP	T	T	C	rs145770432	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr11:4154851T>C	ENST00000300738.5	+	17	2168	c.1964T>C	c.(1963-1965)aTg>aCg	p.M655T	RRM1_ENST00000423050.2_Missense_Mutation_p.M558T|RRM1_ENST00000534285.1_Missense_Mutation_p.M433T|RRM1_ENST00000537197.1_Missense_Mutation_p.M317T	NM_001033.3	NP_001024.1	P23921	RIR1_HUMAN	ribonucleotide reductase M1	655					cell proliferation in forebrain (GO:0021846)|deoxyribonucleotide biosynthetic process (GO:0009263)|DNA replication (GO:0006260)|male gonad development (GO:0008584)|mitotic cell cycle (GO:0000278)|nucleobase-containing small molecule interconversion (GO:0015949)|nucleobase-containing small molecule metabolic process (GO:0055086)|protein heterotetramerization (GO:0051290)|pyrimidine nucleobase metabolic process (GO:0006206)|response to ionizing radiation (GO:0010212)|retina development in camera-type eye (GO:0060041)|small molecule metabolic process (GO:0044281)	cell projection (GO:0042995)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|neuronal cell body (GO:0043025)|nuclear envelope (GO:0005635)|nucleoplasm (GO:0005654)	ATP binding (GO:0005524)|ribonucleoside-diphosphate reductase activity, thioredoxin disulfide as acceptor (GO:0004748)			breast(2)|endometrium(1)|kidney(1)|large_intestine(1)|lung(7)|skin(2)	14		Medulloblastoma(188;0.0025)|Breast(177;0.00502)|all_neural(188;0.0227)		BRCA - Breast invasive adenocarcinoma(625;0.0848)|LUSC - Lung squamous cell carcinoma(625;0.205)	Cladribine(DB00242)|Clofarabine(DB00631)|Fludarabine(DB01073)|Gemcitabine(DB00441)|Hydroxyurea(DB01005)	CATGAAGAGATGAAAAACCAG	0.403													T|||	2	0.000399361	0.0	0.0	5008	,	,		20309	0.0		0.002	False		,,,				2504	0.0				p.M655T	NSCLC(45;1345 1376 6258 22925)|Ovarian(34;894 1053 6175 12768)	Atlas-SNP	.											.	RRM1	31	.	0			c.T1964C						PASS	.	T	THR/MET	1,4401	2.1+/-5.4	0,1,2200	111.0	103.0	106.0		1964	5.5	1.0	11	dbSNP_134	106	2,8594	2.2+/-6.3	0,2,4296	yes	missense	RRM1	NM_001033.3	81	0,3,6496	CC,CT,TT		0.0233,0.0227,0.0231	benign	655/793	4154851	3,12995	2201	4298	6499	SO:0001583	missense	6240	exon17			AAGAGATGAAAAA	X59543	CCDS7750.1	11p15.5	2009-07-10	2008-03-11		ENSG00000167325	ENSG00000167325	1.17.14.1		10451	protein-coding gene	gene with protein product		180410	"""ribonucleotide reductase M1 polypeptide"""			7557993	Standard	NM_001033		Approved		uc001lyw.4	P23921	OTTHUMG00000133361	ENST00000300738.5:c.1964T>C	11.37:g.4154851T>C	ENSP00000300738:p.Met655Thr	118.0	0.0	0		112.0	40.0	0.357143	NM_001033	Q9UNN2	Missense_Mutation	SNP	ENST00000300738.5	37	CCDS7750.1	2	9.157509157509158E-4	0	0.0	0	0.0	0	0.0	2	0.002638522427440633	T	17.36	3.368737	0.61624	2.27E-4	2.33E-4	ENSG00000167325	ENST00000300738;ENST00000423050;ENST00000536894;ENST00000534285;ENST00000543838;ENST00000537197	T;T;T;T	0.42131	0.98;0.98;0.98;0.98	5.52	5.52	0.82312	Ribonucleoside-diphosphate reductase, alpha subunit (1);Ribonucleotide reductase large subunit, C-terminal (1);	0.000000	0.85682	D	0.000000	T	0.45736	0.1357	M	0.75884	2.315	0.80722	D	1	P	0.42757	0.789	B	0.38264	0.269	T	0.55179	-0.8181	10	0.87932	D	0	-17.4615	14.8104	0.69992	0.0:0.0:0.0:1.0	.	655	P23921	RIR1_HUMAN	T	655;558;568;433;433;317	ENSP00000300738:M655T;ENSP00000390539:M558T;ENSP00000431464:M433T;ENSP00000442148:M317T	ENSP00000300738:M655T	M	+	2	0	RRM1	4111427	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	7.698000	0.84413	2.092000	0.63282	0.533000	0.62120	ATG	T|0.999;C|0.001	0.001	strong		0.403	RRM1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257197.1	NM_001033	
PAPD7	11044	hgsc.bcm.edu	37	5	6753013	6753013	+	Silent	SNP	C	C	T	rs28381429	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr5:6753013C>T	ENST00000230859.6	+	12	1426	c.1297C>T	c.(1297-1299)Cta>Tta	p.L433L		NM_001171805.1|NM_001171806.1|NM_006999.4	NP_001165276.1|NP_001165277.1|NP_008930.1	Q5XG87	PAPD7_HUMAN	PAP associated domain containing 7	663	PAP-associated.				double-strand break repair (GO:0006302)|mitotic chromosome condensation (GO:0007076)|response to drug (GO:0042493)|sister chromatid cohesion (GO:0007062)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	DNA binding (GO:0003677)|DNA-directed DNA polymerase activity (GO:0003887)|metal ion binding (GO:0046872)|polynucleotide adenylyltransferase activity (GO:0004652)|SMC family protein binding (GO:0043221)			cervix(1)|endometrium(2)|large_intestine(8)|lung(10)|ovary(2)|pancreas(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	27						TCCACCGACCCTAGGGGTTGC	0.532													C|||	74	0.0147764	0.0	0.0159	5008	,	,		17117	0.0		0.0288	False		,,,				2504	0.0348				p.L433L	NSCLC(7;212 333 5667 23379 46547)	Atlas-SNP	.											.	PAPD7	69	.	0			c.C1297T						PASS	.	C	,,	25,4381	32.6+/-62.9	0,25,2178	103.0	97.0	99.0		1297,757,1297	2.2	1.0	5	dbSNP_125	99	247,8353	97.0+/-158.7	3,241,4056	no	coding-synonymous,coding-synonymous,coding-synonymous	PAPD7	NM_001171805.1,NM_001171806.1,NM_006999.4	,,	3,266,6234	TT,TC,CC		2.8721,0.5674,2.0913	,,	433/542,253/363,433/543	6753013	272,12734	2203	4300	6503	SO:0001819	synonymous_variant	11044	exon12			CCGACCCTAGGGG	AF089896	CCDS3871.1	5p15	2010-11-18	2010-01-19	2010-01-19	ENSG00000112941	ENSG00000112941			16705	protein-coding gene	gene with protein product	"""topoisomerase-related function protein 4-1"", ""polymerase (DNA-directed) sigma"", ""DNA polymerase kappa"", ""TUTase5"""	605198	"""polymerase (DNA directed) sigma"""	POLS		10066793, 10926539	Standard	NM_006999		Approved	POLK, TRF4, LAK-1, TRF4-1	uc003jdx.1	Q5XG87	OTTHUMG00000090457	ENST00000230859.6:c.1297C>T	5.37:g.6753013C>T		219.0	0.0	0		210.0	89.0	0.42381	NM_001171805	A8K1E2|M1JCE6|O43289|Q17RZ1|Q9Y6C1	Silent	SNP	ENST00000230859.6	37	CCDS3871.1																																																																																			C|0.979;T|0.021	0.021	strong		0.532	PAPD7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206904.1	NM_006999	
TNS1	7145	hgsc.bcm.edu	37	2	218682757	218682757	+	Missense_Mutation	SNP	G	G	A	rs140104262	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr2:218682757G>A	ENST00000171887.4	-	24	4438	c.3986C>T	c.(3985-3987)cCg>cTg	p.P1329L	TNS1_ENST00000430930.1_Missense_Mutation_p.P1308L|TNS1_ENST00000419504.1_Missense_Mutation_p.P1316L	NM_022648.4	NP_072174.3	Q9HBL0	TENS1_HUMAN	tensin 1	1329					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)		CCGATCCTCCGGGGTAGAATA	0.662													G|||	4	0.000798722	0.0	0.0	5008	,	,		15504	0.0		0.003	False		,,,				2504	0.001				p.P1329L		Atlas-SNP	.											TNS1,NS,carcinoma,+1,1	TNS1	251	1	0			c.C3986T						PASS	.	G	LEU/PRO	1,4405		0,1,2202	22.0	23.0	23.0		3986	4.6	1.0	2	dbSNP_134	23	21,8577		0,21,4278	yes	missense	TNS1	NM_022648.4	98	0,22,6480	AA,AG,GG		0.2442,0.0227,0.1692	possibly-damaging	1329/1736	218682757	22,12982	2203	4299	6502	SO:0001583	missense	7145	exon24			TCCTCCGGGGTAG	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.3986C>T	2.37:g.218682757G>A	ENSP00000171887:p.Pro1329Leu	73.0	0.0	0		39.0	37.0	0.948718	NM_022648	Q4ZG71|Q6IPI5	Missense_Mutation	SNP	ENST00000171887.4	37	CCDS2407.1	2	9.157509157509158E-4	0	0.0	0	0.0	0	0.0	2	0.002638522427440633	G	18.68	3.675106	0.67928	2.27E-4	0.002442	ENSG00000079308	ENST00000171887;ENST00000446688;ENST00000419504;ENST00000430930	D;T;D;D	0.94138	-3.36;1.7;-3.36;-3.36	4.57	4.57	0.56435	.	0.605025	0.15502	N	0.258967	D	0.94853	0.8337	L	0.50333	1.59	0.80722	D	1	D;D;D	0.76494	0.999;0.998;0.998	P;P;P	0.58721	0.844;0.754;0.826	D	0.95184	0.8302	10	0.87932	D	0	.	17.5631	0.87912	0.0:0.0:1.0:0.0	.	1329;1308;1316	Q9HBL0;E9PGF5;E9PF55	TENS1_HUMAN;.;.	L	1329;467;1316;1308	ENSP00000171887:P1329L;ENSP00000394171:P467L;ENSP00000408724:P1316L;ENSP00000406016:P1308L	ENSP00000171887:P1329L	P	-	2	0	TNS1	218391002	1.000000	0.71417	0.989000	0.46669	0.311000	0.27955	6.993000	0.76245	2.368000	0.80403	0.563000	0.77884	CCG	G|0.999;A|0.001	0.001	strong		0.662	TNS1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000256672.2	NM_022648	
MAP3K10	4294	hgsc.bcm.edu	37	19	40712040	40712040	+	Missense_Mutation	SNP	G	G	A			TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr19:40712040G>A	ENST00000253055.3	+	5	1699	c.1411G>A	c.(1411-1413)Ggc>Agc	p.G471S	AC118344.1_ENST00000408124.1_RNA	NM_002446.3	NP_002437.2	Q02779	M3K10_HUMAN	mitogen-activated protein kinase kinase kinase 10	471				G -> S (in Ref. 2; CAA88531). {ECO:0000305}.|LKLREGGSHISLPSGF -> AQAAGRRQPHQPALWL (in Ref. 3). {ECO:0000305}.	activation of JNKK activity (GO:0007256)|activation of JUN kinase activity (GO:0007257)|apoptotic process (GO:0006915)|JNK cascade (GO:0007254)|negative regulation of sequence-specific DNA binding transcription factor activity (GO:0043433)|negative regulation of transcription, DNA-templated (GO:0045892)|peptidyl-serine phosphorylation (GO:0018105)|peptidyl-threonine phosphorylation (GO:0018107)|positive regulation of apoptotic process (GO:0043065)|positive regulation of JNK cascade (GO:0046330)|positive regulation of JUN kinase activity (GO:0043507)|protein autophosphorylation (GO:0046777)|signal transduction (GO:0007165)|smoothened signaling pathway (GO:0007224)	cytoplasm (GO:0005737)	ATP binding (GO:0005524)|bHLH transcription factor binding (GO:0043425)|JUN kinase kinase kinase activity (GO:0004706)|protein homodimerization activity (GO:0042803)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)|transcription corepressor activity (GO:0003714)	p.G471C(1)		NS(1)|breast(1)|endometrium(4)|kidney(3)|large_intestine(4)|lung(5)|ovary(2)|pancreas(1)|prostate(1)|skin(2)	24						GCGGGAAGGCGGCAGCCACAT	0.657																																					p.G471S		Atlas-SNP	.											.	MAP3K10	70	.	1	Substitution - Missense(1)	lung(1)	c.G1411A						PASS	.						16.0	19.0	18.0					19																	40712040		2094	4126	6220	SO:0001583	missense	4294	exon5			GAAGGCGGCAGCC	X90846	CCDS12549.1	19q13.2	2014-08-12			ENSG00000130758		2.7.11.1	"""Mitogen-activated protein kinase cascade / Kinase kinase kinases"""	6849	protein-coding gene	gene with protein product	"""MKN28 kinase"", ""mixed lineage kinase 2"", ""MKN28 derived nonreceptor_type serine/threonine kinase"""	600137		MLK2		8536694, 7731697	Standard	NM_002446		Approved	MST, MEKK10	uc002ona.3	Q02779	OTTHUMG00000182591	ENST00000253055.3:c.1411G>A	19.37:g.40712040G>A	ENSP00000253055:p.Gly471Ser	168.0	0.0	0		144.0	80.0	0.555556	NM_002446	Q12761|Q14871	Missense_Mutation	SNP	ENST00000253055.3	37	CCDS12549.1	.	.	.	.	.	.	.	.	.	.	G	14.82	2.649911	0.47362	.	.	ENSG00000130758	ENST00000253055	T	0.73469	-0.75	4.53	-1.14	0.09741	.	0.279022	0.41097	N	0.000942	T	0.56790	0.2009	L	0.28192	0.835	0.31735	N	0.636552	B	0.15930	0.015	B	0.21917	0.037	T	0.51568	-0.8689	10	0.41790	T	0.15	.	8.6882	0.34251	0.5148:0.0:0.4852:0.0	.	471	Q02779	M3K10_HUMAN	S	471	ENSP00000253055:G471S	ENSP00000253055:G471S	G	+	1	0	MAP3K10	45403880	0.376000	0.25098	0.585000	0.28666	0.988000	0.76386	-0.143000	0.10296	-0.078000	0.12730	0.491000	0.48974	GGC	.	.	none		0.657	MAP3K10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000462552.1	NM_002446	
AHNAK2	113146	hgsc.bcm.edu	37	14	105411619	105411619	+	Missense_Mutation	SNP	T	T	C	rs200461684		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr14:105411619T>C	ENST00000333244.5	-	7	10288	c.10169A>G	c.(10168-10170)cAc>cGc	p.H3390R	AHNAK2_ENST00000557457.1_Intron	NM_138420.2	NP_612429.2	Q8IVF2	AHNK2_HUMAN	AHNAK nucleoprotein 2	3390						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)			CTTGGGCAGGTGCCCTTTGAG	0.627													.|||	1	0.000199681	0.0	0.0	5008	,	,		17915	0.0		0.001	False		,,,				2504	0.0				p.H3390R		Atlas-SNP	.											.	AHNAK2	719	.	0			c.A10169G						PASS	.	T	ARG/HIS	1,3791		0,1,1895	149.0	161.0	157.0		10169	4.2	0.8	14		157	10,8194		0,10,4092	no	missense	AHNAK2	NM_138420.2	29	0,11,5987	CC,CT,TT		0.1219,0.0264,0.0917	probably-damaging	3390/5796	105411619	11,11985	1896	4102	5998	SO:0001583	missense	113146	exon7			GGCAGGTGCCCTT	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.10169A>G	14.37:g.105411619T>C	ENSP00000353114:p.His3390Arg	156.0	0.0	0		246.0	96.0	0.390244	NM_138420	Q5BKX7|Q7Z343|Q7Z358|Q7Z394|Q7Z3G0|Q86WQ6|Q8IYY1|Q8N3G4|Q96EX9	Missense_Mutation	SNP	ENST00000333244.5	37	CCDS45177.1	.	.	.	.	.	.	.	.	.	.	t	2.101	-0.406153	0.04832	2.64E-4	0.001219	ENSG00000185567	ENST00000333244	T	0.01902	4.57	4.22	4.22	0.49857	.	.	.	.	.	T	0.07007	0.0178	M	0.82923	2.615	0.09310	N	1	D	0.59357	0.985	P	0.52109	0.69	T	0.24977	-1.0145	9	0.17832	T	0.49	.	8.3292	0.32175	0.0:0.0:0.2686:0.7314	.	3390	Q8IVF2	AHNK2_HUMAN	R	3390	ENSP00000353114:H3390R	ENSP00000353114:H3390R	H	-	2	0	AHNAK2	104482664	0.865000	0.29922	0.833000	0.33012	0.077000	0.17291	3.174000	0.50847	1.792000	0.52537	0.402000	0.26972	CAC	T|0.999;C|0.001	0.001	weak		0.627	AHNAK2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000410300.1	NM_138420	
MT-ND1	4535	hgsc.bcm.edu	37	M	4153	4153	+	Missense_Mutation	SNP	G	G	A			TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chrM:4153G>A	ENST00000361390.2	+	1	847	c.847G>A	c.(847-849)Gac>Aac	p.D283N	MT-TA_ENST00000387392.1_RNA|MT-ND2_ENST00000361453.3_5'Flank|MT-TV_ENST00000387342.1_RNA|MT-TM_ENST00000387377.1_RNA|MT-CO1_ENST00000361624.2_5'Flank|MT-TC_ENST00000387405.1_RNA|MT-TI_ENST00000387365.1_RNA|MT-TY_ENST00000387409.1_RNA|MT-TW_ENST00000387382.1_RNA|MT-TN_ENST00000387400.1_RNA|MT-RNR1_ENST00000389680.2_RNA|MT-TL1_ENST00000386347.1_RNA|MT-TQ_ENST00000387372.1_RNA|MT-RNR2_ENST00000387347.2_RNA			P03886	NU1M_HUMAN	mitochondrially encoded NADH dehydrogenase 1	283					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 membrane (GO:0031966)|mitochondrial respiratory chain complex I (GO:0005747)	NADH dehydrogenase (ubiquinone) activity (GO:0008137)			breast(1)|endometrium(13)|kidney(17)|lung(2)|prostate(1)	34					Desflurane(DB01189)|Halothane(DB01159)|Isoflurane(DB00753)|Methoxyflurane(DB01028)|Sevoflurane(DB01236)	GATTCCGCTACGACCAACTCA	0.443																																					p.D283N		Atlas-SNP	.											.	.	.	.	0			c.G847A						PASS	.																																			SO:0001583	missense	10625	exon1			CGCTACGACCAAC			mitochondria	2011-07-04	2005-02-15	2005-02-16	ENSG00000198888	ENSG00000198888	1.6.5.3	"""Mitochondrial respiratory chain complex / Complex I"""	7455	protein-coding gene	gene with protein product	"""complex I ND1 subunit"", ""NADH-ubiquinone oxidoreductase chain 1"""	516000	"""NADH dehydrogenase 1"""	MTND1			Standard			Approved	ND1, NAD1		P03886		ENST00000361390.2:c.847G>A	M.37:g.4153G>A	ENSP00000354687:p.Asp283Asn	5.0	0.0	0		12.0	8.0	0.666667	ENST00000361390	C0JKH6|Q37523	Missense_Mutation	SNP	ENST00000361390.2	37																																																																																				.	.	none		0.443	MT-ND1-201	KNOWN	basic|appris_principal	protein_coding	protein_coding		YP_003024026	
RBM6	10180	hgsc.bcm.edu	37	3	50005373	50005373	+	Missense_Mutation	SNP	C	C	T	rs142246877	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr3:50005373C>T	ENST00000266022.4	+	3	774	c.515C>T	c.(514-516)cCa>cTa	p.P172L	RBM6_ENST00000422955.1_Intron|RBM6_ENST00000441115.1_Intron|RBM6_ENST00000443081.1_Missense_Mutation_p.P40L|RBM6_ENST00000539992.1_Intron|RBM6_ENST00000442092.1_Intron	NM_005777.2	NP_005768.1	P78332	RBM6_HUMAN	RNA binding motif protein 6	172					RNA processing (GO:0006396)	nucleus (GO:0005634)	DNA binding (GO:0003677)|nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)			breast(1)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(7)|lung(10)|ovary(3)|prostate(1)|skin(4)|urinary_tract(1)	33				BRCA - Breast invasive adenocarcinoma(193;6.81e-05)|KIRC - Kidney renal clear cell carcinoma(197;0.0084)|Kidney(197;0.00977)		GATGCTCCTCCATCTGACTTC	0.473													C|||	5	0.000998403	0.0	0.0014	5008	,	,		17453	0.0		0.003	False		,,,				2504	0.001				p.P172L		Atlas-SNP	.											.	RBM6	85	.	0			c.C515T						PASS	.	C	,LEU/PRO	7,4399	12.9+/-30.5	0,7,2196	61.0	63.0	62.0		,515	5.9	1.0	3	dbSNP_134	62	37,8563	25.7+/-73.6	0,37,4263	yes	intron,missense	RBM6	NM_001167582.1,NM_005777.2	,98	0,44,6459	TT,TC,CC		0.4302,0.1589,0.3383	,probably-damaging	,172/1124	50005373	44,12962	2203	4300	6503	SO:0001583	missense	10180	exon3			CTCCTCCATCTGA	AF069517	CCDS2809.1, CCDS54586.1	3p21.3	2013-01-28			ENSG00000004534	ENSG00000004534		"""RNA binding motif (RRM) containing"", ""G patch domain containing"""	9903	protein-coding gene	gene with protein product		606886				10352938	Standard	NM_001167582		Approved	DEF-3, 3G2, NY-LU-12, g16, DEF3	uc003cyc.3	P78332	OTTHUMG00000156736	ENST00000266022.4:c.515C>T	3.37:g.50005373C>T	ENSP00000266022:p.Pro172Leu	112.0	0.0	0		102.0	49.0	0.480392	NM_005777	O60549|O75524|Q86SS3	Missense_Mutation	SNP	ENST00000266022.4	37	CCDS2809.1	3	0.0013736263736263737	0	0.0	1	0.0027624309392265192	0	0.0	2	0.002638522427440633	C	14.30	2.493001	0.44352	0.001589	0.004302	ENSG00000004534	ENST00000266022;ENST00000443081	T;T	0.34472	1.43;1.36	5.88	5.88	0.94601	.	0.109289	0.41396	D	0.000894	T	0.32315	0.0825	L	0.40543	1.245	0.80722	D	1	B	0.31383	0.321	B	0.25614	0.062	T	0.03910	-1.0993	9	.	.	.	-3.6177	20.2405	0.98372	0.0:1.0:0.0:0.0	.	172	P78332	RBM6_HUMAN	L	172;40	ENSP00000266022:P172L;ENSP00000396466:P40L	.	P	+	2	0	RBM6	49980377	0.965000	0.33210	0.985000	0.45067	0.994000	0.84299	4.345000	0.59360	2.797000	0.96272	0.561000	0.74099	CCA	C|0.997;T|0.003	0.003	strong		0.473	RBM6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000345528.4	NM_005777	
ADGB	79747	hgsc.bcm.edu	37	6	147038089	147038089	+	Missense_Mutation	SNP	G	G	T	rs61748896	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr6:147038089G>T	ENST00000397944.3	+	15	1888	c.1812G>T	c.(1810-1812)gaG>gaT	p.E604D	ADGB_ENST00000367493.3_Missense_Mutation_p.E23D	NM_024694.3	NP_078970.3	Q8N7X0	ADGB_HUMAN	androglobin	604					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						TGGAAAGAGAGATAGTCAGCC	0.378													T|||	425	0.0848642	0.2995	0.0288	5008	,	,		15968	0.004		0.002	False		,,,				2504	0.0031				p.E604D		Atlas-SNP	.											.	ADGB	93	.	0			c.G1812T						PASS	.	T	ASP/GLU	344,1040		44,256,392	122.0	111.0	115.0		1812	-1.0	0.0	6	dbSNP_129	115	8,3174		0,8,1583	yes	missense	C6orf103	NM_024694.3	45	44,264,1975	TT,TG,GG		0.2514,24.8555,7.7092	benign	604/1668	147038089	352,4214	692	1591	2283	SO:0001583	missense	79747	exon15			AAGAGAGATAGTC	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.1812G>T	6.37:g.147038089G>T	ENSP00000381036:p.Glu604Asp	117.0	0.0	0		78.0	42.0	0.538462	NM_024694	Q5T402|Q5T904|Q5T905	Missense_Mutation	SNP	ENST00000397944.3	37		162	0.07417582417582418	146	0.2967479674796748	11	0.03038674033149171	4	0.006993006993006993	1	0.0013192612137203166	T	0.671	-0.801848	0.02841	0.248555	0.002514	ENSG00000118492	ENST00000397944;ENST00000367493	T	0.29917	1.55	4.87	-0.985	0.10256	Peptidase C2, calpain, catalytic domain (1);	0.461581	0.22279	N	0.062150	T	0.01124	0.0037	N	0.00237	-1.79	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.28902	-1.0029	9	0.08837	T	0.75	-15.0076	1.0124	0.01500	0.1439:0.1814:0.2969:0.3777	rs61748896	604	Q8N7X0	CAN7L_HUMAN	D	604;23	ENSP00000381036:E604D	ENSP00000356463:E23D	E	+	3	2	C6orf103	147079782	0.564000	0.26602	0.007000	0.13788	0.002000	0.02628	-0.080000	0.11339	-0.519000	0.06444	-0.525000	0.04345	GAG	G|0.941;T|0.059	0.059	strong		0.378	ADGB-009	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000376350.2	NM_024694	
CLGN	1047	hgsc.bcm.edu	37	4	141313500	141313500	+	Silent	SNP	G	G	A	rs34492995	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr4:141313500G>A	ENST00000325617.5	-	13	1964	c.1524C>T	c.(1522-1524)acC>acT	p.T508T	CLGN_ENST00000537281.1_Silent_p.T508T|CLGN_ENST00000414773.1_Silent_p.T508T	NM_004362.2	NP_004353.1	O14967	CLGN_HUMAN	calmegin	508					binding of sperm to zona pellucida (GO:0007339)|protein complex assembly (GO:0006461)|protein folding (GO:0006457)|single fertilization (GO:0007338)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|nuclear envelope (GO:0005635)	calcium ion binding (GO:0005509)|unfolded protein binding (GO:0051082)			breast(2)|endometrium(3)|kidney(1)|large_intestine(2)|liver(2)|lung(5)|ovary(2)|prostate(3)|skin(4)|urinary_tract(1)	25	all_hematologic(180;0.162)					TACATATGTCGGTTTTTTTAT	0.333													G|||	19	0.00379393	0.0008	0.0043	5008	,	,		16252	0.0		0.0139	False		,,,				2504	0.001				p.T508T		Atlas-SNP	.											.	CLGN	76	.	0			c.C1524T						PASS	.	G	,	10,4396	16.8+/-37.8	0,10,2193	129.0	123.0	125.0		1524,1524	-9.4	0.0	4	dbSNP_126	125	131,8469	66.7+/-129.0	3,125,4172	no	coding-synonymous,coding-synonymous	CLGN	NM_001130675.1,NM_004362.2	,	3,135,6365	AA,AG,GG		1.5233,0.227,1.0841	,	508/611,508/611	141313500	141,12865	2203	4300	6503	SO:0001819	synonymous_variant	1047	exon14			TATGTCGGTTTTT	D86322	CCDS3751.1	4q28.3-q31.1	2008-02-05			ENSG00000153132	ENSG00000153132			2060	protein-coding gene	gene with protein product		601858					Standard	NM_004362		Approved		uc003iii.3	O14967	OTTHUMG00000133414	ENST00000325617.5:c.1524C>T	4.37:g.141313500G>A		223.0	0.0	0		163.0	117.0	0.717791	NM_001130675	B3KS90|B4DXV8|D3DNY8	Silent	SNP	ENST00000325617.5	37	CCDS3751.1																																																																																			G|0.992;A|0.008	0.008	strong		0.333	CLGN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257272.2	NM_004362	
HIVEP1	3096	hgsc.bcm.edu	37	6	12164308	12164308	+	Missense_Mutation	SNP	G	G	A	rs181056704		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr6:12164308G>A	ENST00000379388.2	+	9	8103	c.7771G>A	c.(7771-7773)Gca>Aca	p.A2591T	HIVEP1_ENST00000541134.1_Missense_Mutation_p.A456T	NM_002114.2	NP_002105.2	P15822	ZEP1_HUMAN	human immunodeficiency virus type I enhancer binding protein 1	2591					negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|transcription, DNA-templated (GO:0006351)	mitochondrion (GO:0005739)|nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			NS(1)|breast(5)|central_nervous_system(1)|cervix(1)|endometrium(13)|haematopoietic_and_lymphoid_tissue(3)|kidney(8)|large_intestine(11)|liver(1)|lung(31)|ovary(4)|prostate(1)|skin(4)|upper_aerodigestive_tract(3)|urinary_tract(3)	90	Breast(50;0.0639)|Ovarian(93;0.0816)	all_hematologic(90;0.117)				TGTAGCCAGCGCAAACCAGGT	0.537													G|||	1	0.000199681	0.0	0.0	5008	,	,		21442	0.0		0.001	False		,,,				2504	0.0				p.A2591T		Atlas-SNP	.											.	HIVEP1	242	.	0			c.G7771A						PASS	.	G	THR/ALA	3,4009		0,3,2003	70.0	78.0	76.0		7771	3.3	0.0	6		76	31,8333		0,31,4151	yes	missense	HIVEP1	NM_002114.2	58	0,34,6154	AA,AG,GG		0.3706,0.0748,0.2747	benign	2591/2719	12164308	34,12342	2006	4182	6188	SO:0001583	missense	3096	exon9			GCCAGCGCAAACC	J05011	CCDS43426.1	6p24-p22.3	2012-10-05	2001-11-28		ENSG00000095951	ENSG00000095951		"""Zinc fingers, C2H2-type"""	4920	protein-coding gene	gene with protein product		194540	"""human immunodeficiency virus type I enhancer-binding protein 1"", ""zinc finger protein 40"""	ZNF40		2037300	Standard	XR_241895		Approved	CIRIP, MBP-1, CRYBP1, PRDII-BF1, ZAS1, Schnurri-1, ZNF40A	uc003nac.3	P15822	OTTHUMG00000014265	ENST00000379388.2:c.7771G>A	6.37:g.12164308G>A	ENSP00000368698:p.Ala2591Thr	120.0	0.0	0		117.0	58.0	0.495726	NM_002114	B2RTU3|Q14122|Q5MPB1|Q5VW60	Missense_Mutation	SNP	ENST00000379388.2	37	CCDS43426.1	1	4.578754578754579E-4	0	0.0	0	0.0	0	0.0	1	0.0013192612137203166	G	16.33	3.092661	0.56075	7.48E-4	0.003706	ENSG00000095951	ENST00000379388;ENST00000541134;ENST00000542327	T;T	0.31769	2.99;1.48	5.23	3.27	0.37495	.	0.224672	0.22869	N	0.054645	T	0.07007	0.0178	L	0.38175	1.15	0.09310	N	1	P	0.35155	0.487	B	0.20955	0.032	T	0.13098	-1.0522	10	0.37606	T	0.19	-6.4409	6.6498	0.22955	0.0763:0.2109:0.5992:0.1136	.	2591	P15822	ZEP1_HUMAN	T	2591;456;573	ENSP00000368698:A2591T;ENSP00000445617:A456T	ENSP00000368698:A2591T	A	+	1	0	HIVEP1	12272294	0.000000	0.05858	0.005000	0.12908	0.319000	0.28217	0.217000	0.17603	1.173000	0.42796	0.580000	0.79431	GCA	G|0.999;A|0.001	0.001	strong		0.537	HIVEP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000039870.2	NM_002114	
ADGB	79747	hgsc.bcm.edu	37	6	146993392	146993392	+	Silent	SNP	A	A	G	rs77104188	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	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		188.0	0.0	0		182.0	92.0	0.505495	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	
MYH9	4627	hgsc.bcm.edu	37	22	36689434	36689434	+	Missense_Mutation	SNP	C	C	T			TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr22:36689434C>T	ENST00000216181.5	-	30	4266	c.4036G>A	c.(4036-4038)Gag>Aag	p.E1346K		NM_002473.4	NP_002464.1	P35579	MYH9_HUMAN	myosin, heavy chain 9, non-muscle	1346					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						TCCTCCTCCTCCAGCTGCTCC	0.637			T	ALK	ALCL		"""Deafness, autosomal dominant 17, Epstein syndrome, Fechtner syndrome, May-Hegglin anomaly, Sebastian syndrome"""		Hereditary Macrothrombocytopenia, MYH9-associated																												p.E1346K		Atlas-SNP	.		Dom	yes		22	22q13.1	4627	"""myosin, heavy polypeptide 9, non-muscle"""	yes	L	.	MYH9	225	.	0			c.G4036A						PASS	.						80.0	76.0	77.0					22																	36689434		2203	4300	6503	SO:0001583	missense	4627	exon30	Familial Cancer Database	MYHIIA syndrome, incl. Fechtner Syndrome, FTNS, and May-Hegglin Anomaly, MHA	CCTCCTCCAGCTG		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.4036G>A	22.37:g.36689434C>T	ENSP00000216181:p.Glu1346Lys	75.0	0.0	0		100.0	4.0	0.04	NM_002473	A8K6E4|O60805|Q60FE2|Q86T83	Missense_Mutation	SNP	ENST00000216181.5	37	CCDS13927.1	.	.	.	.	.	.	.	.	.	.	C	26.7	4.763943	0.89932	.	.	ENSG00000100345	ENST00000216181	D	0.84070	-1.8	5.0	2.88	0.33553	Myosin tail (1);	0.000000	0.85682	D	0.000000	D	0.90974	0.7162	M	0.88906	2.99	0.80722	D	1	D	0.76494	0.999	D	0.79108	0.992	D	0.90771	0.4672	10	0.87932	D	0	.	10.4603	0.44575	0.0:0.7922:0.1347:0.0731	.	1346	P35579	MYH9_HUMAN	K	1346	ENSP00000216181:E1346K	ENSP00000216181:E1346K	E	-	1	0	MYH9	35019380	1.000000	0.71417	1.000000	0.80357	0.969000	0.65631	5.997000	0.70646	0.607000	0.29982	0.491000	0.48974	GAG	.	.	none		0.637	MYH9-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000259110.3	NM_002473	
FAM32A	26017	hgsc.bcm.edu	37	19	16301759	16301759	+	Missense_Mutation	SNP	C	C	T			TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr19:16301759C>T	ENST00000263384.7	+	4	357	c.332C>T	c.(331-333)aCg>aTg	p.T111M	FAM32A_ENST00000588367.1_Missense_Mutation_p.T93M|CTD-2562J15.4_ENST00000591038.1_RNA|FAM32A_ENST00000589852.1_Missense_Mutation_p.T91M	NM_014077.2	NP_054796.1	Q9Y421	FA32A_HUMAN	family with sequence similarity 32, member A	111					apoptotic process (GO:0006915)|cell cycle (GO:0007049)	intracellular membrane-bounded organelle (GO:0043231)|mitochondrion (GO:0005739)|nucleolus (GO:0005730)|nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)	p.T111M(1)		lung(1)	1						GTCAGCTGGACGAAGTAGCCG	0.557																																					p.T111M		Atlas-SNP	.											FAM32A,NS,carcinoma,0,1	FAM32A	6	1	1	Substitution - Missense(1)	lung(1)	c.C332T						PASS	.						73.0	61.0	65.0					19																	16301759		2203	4300	6503	SO:0001583	missense	26017	exon4			GCTGGACGAAGTA	BC000639	CCDS12341.1	19p13.12-p13.11	2013-09-19			ENSG00000105058	ENSG00000105058			24563	protein-coding gene	gene with protein product		614554				11230166, 10810093	Standard	NM_014077		Approved	DKFZP586O0120	uc002ndt.3	Q9Y421	OTTHUMG00000182279	ENST00000263384.7:c.332C>T	19.37:g.16301759C>T	ENSP00000263384:p.Thr111Met	127.0	0.0	0		131.0	53.0	0.40458	NM_014077	Q9BT02	Missense_Mutation	SNP	ENST00000263384.7	37	CCDS12341.1	.	.	.	.	.	.	.	.	.	.	C	16.01	2.999969	0.54147	.	.	ENSG00000105058	ENST00000263384	.	.	.	3.99	2.94	0.34122	.	0.000000	0.85682	D	0.000000	T	0.44307	0.1287	M	0.72576	2.205	0.80722	D	1	P	0.40144	0.704	B	0.28465	0.09	T	0.48747	-0.9008	9	0.66056	D	0.02	-16.2628	9.4497	0.38719	0.0:0.8985:0.0:0.1015	.	111	Q9Y421	FA32A_HUMAN	M	111	.	ENSP00000263384:T111M	T	+	2	0	FAM32A	16162759	1.000000	0.71417	0.841000	0.33234	0.578000	0.36192	5.807000	0.69157	0.793000	0.33875	0.462000	0.41574	ACG	.	.	none		0.557	FAM32A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000460346.1	NM_014077	
TUBB1	81027	hgsc.bcm.edu	37	20	57598808	57598808	+	Missense_Mutation	SNP	G	G	A	rs41303899	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr20:57598808G>A	ENST00000217133.1	+	4	595	c.326G>A	c.(325-327)gGa>gAa	p.G109E		NM_030773.3	NP_110400.1	Q9H4B7	TBB1_HUMAN	tubulin, beta 1 class VI	109					'de novo' posttranslational protein folding (GO:0051084)|cellular protein metabolic process (GO:0044267)|protein folding (GO:0006457)|protein polymerization (GO:0051258)|spindle assembly (GO:0051225)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|microtubule (GO:0005874)	GTP binding (GO:0005525)|GTPase activity (GO:0003924)|structural constituent of cytoskeleton (GO:0005200)			endometrium(1)|kidney(1)|large_intestine(2)|lung(7)|ovary(1)|prostate(2)|skin(2)	16	all_lung(29;0.00711)		Colorectal(105;0.109)		Cabazitaxel(DB06772)|Colchicine(DB01394)|Docetaxel(DB01248)|Paclitaxel(DB01229)|Vindesine(DB00309)	TACACGGAGGGAGCCGAGCTG	0.592													G|||	4	0.000798722	0.0	0.0029	5008	,	,		16838	0.0		0.002	False		,,,				2504	0.0				p.G109E		Atlas-SNP	.											TUBB1,mucosal,malignant_melanoma,+1,1	TUBB1	42	1	0			c.G326A						PASS	.	G	GLU/GLY	2,4404	4.2+/-10.8	0,2,2201	83.0	91.0	89.0		326	5.4	1.0	20	dbSNP_127	89	12,8588	9.1+/-34.3	0,12,4288	yes	missense	TUBB1	NM_030773.3	98	0,14,6489	AA,AG,GG		0.1395,0.0454,0.1076	probably-damaging	109/452	57598808	14,12992	2203	4300	6503	SO:0001583	missense	81027	exon4			CGGAGGGAGCCGA	AJ292757	CCDS13475.1	20q13.32	2014-09-17	2011-10-10		ENSG00000101162	ENSG00000101162		"""Tubulins"""	16257	protein-coding gene	gene with protein product	"""class VI beta-tubulin"""	612901	"""tubulin, beta 1"""				Standard	NM_030773		Approved	dJ543J19.4	uc002yak.3	Q9H4B7	OTTHUMG00000032860	ENST00000217133.1:c.326G>A	20.37:g.57598808G>A	ENSP00000217133:p.Gly109Glu	113.0	0.0	0		124.0	59.0	0.475806	NM_030773		Missense_Mutation	SNP	ENST00000217133.1	37	CCDS13475.1	2	9.157509157509158E-4	0	0.0	0	0.0	0	0.0	2	0.002638522427440633	G	17.48	3.399586	0.62177	4.54E-4	0.001395	ENSG00000101162	ENST00000217133	T	0.75821	-0.97	5.39	5.39	0.77823	Tubulin/FtsZ, GTPase domain (4);	0.000000	0.85682	D	0.000000	D	0.94374	0.8191	H	0.99993	5.38	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.97591	1.0117	10	0.87932	D	0	.	18.1143	0.89546	0.0:0.0:1.0:0.0	rs41303899	109	Q9H4B7	TBB1_HUMAN	E	109	ENSP00000217133:G109E	ENSP00000217133:G109E	G	+	2	0	TUBB1	57032203	1.000000	0.71417	0.952000	0.39060	0.158000	0.22134	9.824000	0.99380	2.537000	0.85549	0.655000	0.94253	GGA	G|0.999;A|0.001	0.001	strong		0.592	TUBB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079903.1	NM_030773	
CNNM2	54805	hgsc.bcm.edu	37	10	104678801	104678801	+	Silent	SNP	C	C	T	rs117691462	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr10:104678801C>T	ENST00000369878.4	+	1	752	c.564C>T	c.(562-564)tcC>tcT	p.S188S	CNNM2_ENST00000433628.2_Silent_p.S188S|CNNM2_ENST00000369875.3_Silent_p.S188S	NM_017649.4	NP_060119.3	Q9H8M5	CNNM2_HUMAN	cyclin and CBS domain divalent metal cation transport mediator 2	188					magnesium ion homeostasis (GO:0010960)|magnesium ion transport (GO:0015693)	basolateral plasma membrane (GO:0016323)|integral component of membrane (GO:0016021)	adenyl nucleotide binding (GO:0030554)			central_nervous_system(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(5)|lung(7)|ovary(1)|prostate(2)|urinary_tract(1)	19		Colorectal(252;0.103)|all_hematologic(284;0.152)|Breast(234;0.198)		Epithelial(162;7.89e-09)|all cancers(201;1.82e-07)|BRCA - Breast invasive adenocarcinoma(275;0.215)		AGAGCAAGTCCTATTACCTGT	0.652													C|||	8	0.00159744	0.0008	0.0	5008	,	,		13685	0.0		0.007	False		,,,				2504	0.0				p.S188S		Atlas-SNP	.											.	CNNM2	119	.	0			c.C564T						PASS	.	C	,,	2,4402		0,2,2200	96.0	104.0	102.0		564,564,564	2.6	1.0	10	dbSNP_132	102	46,8548		0,46,4251	no	coding-synonymous,coding-synonymous,coding-synonymous	CNNM2	NM_017649.3,NM_199076.1,NM_199077.1	,,	0,48,6451	TT,TC,CC		0.5353,0.0454,0.3693	,,	188/876,188/854,188/553	104678801	48,12950	2202	4297	6499	SO:0001819	synonymous_variant	54805	exon1			CAAGTCCTATTAC	AF216962	CCDS7543.1, CCDS44474.1, CCDS44475.1	10q24.32	2014-08-08	2014-08-07		ENSG00000148842	ENSG00000148842			103	protein-coding gene	gene with protein product		607803	"""cyclin M2"""	ACDP2		21393841, 24699222	Standard	NM_017649		Approved		uc001kwm.3	Q9H8M5	OTTHUMG00000018976	ENST00000369878.4:c.564C>T	10.37:g.104678801C>T		134.0	0.0	0		75.0	62.0	0.826667	NM_199076	Q5T569|Q5T570|Q8WU59|Q9H952|Q9NRK5|Q9NXT4	Silent	SNP	ENST00000369878.4	37	CCDS44474.1																																																																																			C|0.996;T|0.004	0.004	strong		0.652	CNNM2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000050113.3	NM_017649	
USP31	57478	hgsc.bcm.edu	37	16	23091371	23091371	+	Missense_Mutation	SNP	G	G	A			TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr16:23091371G>A	ENST00000219689.7	-	13	2071	c.2072C>T	c.(2071-2073)cCg>cTg	p.P691L		NM_020718.3	NP_065769.3	Q86UV5	UBP48_HUMAN	ubiquitin specific peptidase 31	333	DUSP 2. {ECO:0000255|PROSITE- ProRule:PRU00613}.				ubiquitin-dependent protein catabolic process (GO:0006511)	cytoplasm (GO:0005737)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	ubiquitin-specific protease activity (GO:0004843)			breast(4)|central_nervous_system(2)|cervix(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(13)|lung(17)|ovary(4)|pancreas(1)|prostate(1)|skin(2)|stomach(1)|urinary_tract(2)	57				GBM - Glioblastoma multiforme(48;0.0187)		CCGTCTCCACGGGGACCAATG	0.562																																					p.P691L		Atlas-SNP	.											.	USP31	122	.	0			c.C2072T						PASS	.						126.0	109.0	114.0					16																	23091371		2197	4300	6497	SO:0001583	missense	57478	exon13			CTCCACGGGGACC	AB033029	CCDS10607.1	16p12.3	2008-02-05	2005-08-08		ENSG00000103404	ENSG00000103404		"""Ubiquitin-specific peptidases"""	20060	protein-coding gene	gene with protein product			"""ubiquitin specific protease 31"""			12838346	Standard	NM_020718		Approved	KIAA1203	uc002dll.3	Q70CQ4	OTTHUMG00000094793	ENST00000219689.7:c.2072C>T	16.37:g.23091371G>A	ENSP00000219689:p.Pro691Leu	248.0	0.0	0		264.0	15.0	0.0568182	NM_020718	B7ZKS7|Q2M3I4|Q5SZI4|Q5T3T5|Q6NX53|Q8N3F6|Q96F64|Q96IQ3|Q9H5N3|Q9H5T7|Q9NUJ6|Q9NXR0	Missense_Mutation	SNP	ENST00000219689.7	37	CCDS10607.1	.	.	.	.	.	.	.	.	.	.	G	23.3	4.393555	0.83011	.	.	ENSG00000103404	ENST00000219689	T	0.10005	2.92	4.91	3.96	0.45880	Peptidase C19, ubiquitin carboxyl-terminal hydrolase 2 (2);	0.000000	0.85682	U	0.000000	T	0.25791	0.0628	L	0.50993	1.605	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	T	0.00641	-1.1631	10	0.59425	D	0.04	-16.8435	12.2435	0.54558	0.0829:0.0:0.9171:0.0	.	691	Q70CQ4	UBP31_HUMAN	L	691	ENSP00000219689:P691L	ENSP00000219689:P691L	P	-	2	0	USP31	22998872	1.000000	0.71417	0.997000	0.53966	0.998000	0.95712	9.471000	0.97696	1.058000	0.40530	0.557000	0.71058	CCG	.	.	none		0.562	USP31-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000211607.1	NM_020718	
EBNA1BP2	10969	hgsc.bcm.edu	37	1	43630156	43630156	+	Silent	SNP	A	A	C	rs11559311	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr1:43630156A>C	ENST00000236051.2	-	9	1020	c.879T>G	c.(877-879)ccT>ccG	p.P293P	EBNA1BP2_ENST00000431635.2_Silent_p.P348P	NM_006824.2	NP_006815.2	Q99848	EBP2_HUMAN	EBNA1 binding protein 2	293					ribosome biogenesis (GO:0042254)	membrane (GO:0016020)|nucleolus (GO:0005730)|nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)			endometrium(1)|kidney(2)|large_intestine(4)|lung(9)	16	Ovarian(52;0.00579)|all_hematologic(146;0.0977)|Acute lymphoblastic leukemia(166;0.155)	Myeloproliferative disorder(586;0.0505)				TTCGTTTTCCAGGTCTCTTCT	0.443													A|||	410	0.081869	0.2405	0.0605	5008	,	,		19601	0.001		0.0368	False		,,,				2504	0.0123				p.P348P		Atlas-SNP	.											.	EBNA1BP2	37	.	0			c.T1044G						PASS	.	A	,	913,3493	351.1+/-311.1	102,709,1392	176.0	155.0	162.0		1044,879	-0.3	1.0	1	dbSNP_120	162	356,8244	119.7+/-179.0	6,344,3950	no	coding-synonymous,coding-synonymous	EBNA1BP2	NM_001159936.1,NM_006824.2	,	108,1053,5342	CC,CA,AA		4.1395,20.7217,9.757	,	348/362,293/307	43630156	1269,11737	2203	4300	6503	SO:0001819	synonymous_variant	10969	exon10			TTTTCCAGGTCTC	U86602	CCDS478.1, CCDS53308.1	1p35-p33	2011-02-10	2001-11-28		ENSG00000117395	ENSG00000117395			15531	protein-coding gene	gene with protein product		614443	"""EBNA1-binding protein 2"""			10074103, 11438656	Standard	NM_001159936		Approved	NOBP, EBP2, P40	uc010ojx.2	Q99848	OTTHUMG00000007284	ENST00000236051.2:c.879T>G	1.37:g.43630156A>C		148.0	0.0	0		119.0	87.0	0.731092	NM_001159936	Q96A66	Silent	SNP	ENST00000236051.2	37	CCDS478.1																																																																																			A|0.912;C|0.088	0.088	strong		0.443	EBNA1BP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000019015.1		
SLC26A9	115019	hgsc.bcm.edu	37	1	205884508	205884508	+	Missense_Mutation	SNP	C	C	T	rs147005854		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr1:205884508C>T	ENST00000367135.3	-	21	2466	c.2353G>A	c.(2353-2355)Gca>Aca	p.A785T	SLC26A9_ENST00000340781.4_Missense_Mutation_p.A785T|SLC26A9_ENST00000367134.2_Missense_Mutation_p.A785T	NM_052934.3	NP_443166.1	Q7LBE3	S26A9_HUMAN	solute carrier family 26 (anion exchanger), member 9	785					anion transport (GO:0006820)|bicarbonate transport (GO:0015701)|chloride transmembrane transport (GO:1902476)|chloride transport (GO:0006821)|ion transport (GO:0006811)|positive regulation of gene expression (GO:0010628)|regulation of pH (GO:0006885)|transmembrane transport (GO:0055085)	apical plasma membrane (GO:0016324)|cell surface (GO:0009986)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	anion:anion antiporter activity (GO:0015301)|ATPase binding (GO:0051117)|bicarbonate transmembrane transporter activity (GO:0015106)|chloride channel activity (GO:0005254)|secondary active sulfate transmembrane transporter activity (GO:0008271)			NS(1)|breast(3)|endometrium(11)|kidney(1)|large_intestine(6)|lung(17)|ovary(1)|skin(7)|urinary_tract(5)	52	Breast(84;0.201)		BRCA - Breast invasive adenocarcinoma(75;0.0458)			AGGGTCTCTGCGTGAAACATG	0.577													C|||	1	0.000199681	0.0	0.0	5008	,	,		19734	0.0		0.001	False		,,,				2504	0.0				p.A785T		Atlas-SNP	.											.	SLC26A9	176	.	0			c.G2353A						PASS	.	C	THR/ALA,THR/ALA	1,4405	2.1+/-5.4	0,1,2202	108.0	98.0	102.0		2353,2353	-10.9	0.0	1	dbSNP_134	102	8,8592	5.7+/-21.5	0,8,4292	yes	missense,missense	SLC26A9	NM_052934.3,NM_134325.2	58,58	0,9,6494	TT,TC,CC		0.093,0.0227,0.0692	benign,benign	785/792,785/888	205884508	9,12997	2203	4300	6503	SO:0001583	missense	115019	exon21			TCTCTGCGTGAAA	AF331525	CCDS30989.1, CCDS30990.1	1q32.1	2013-07-18	2013-07-18		ENSG00000174502	ENSG00000174502		"""Solute carriers"""	14469	protein-coding gene	gene with protein product	"""anion transporter/exchanger-9"""	608481	"""solute carrier family 26, member 9"""			11834742	Standard	NM_134325		Approved		uc001hdp.3	Q7LBE3	OTTHUMG00000036001	ENST00000367135.3:c.2353G>A	1.37:g.205884508C>T	ENSP00000356103:p.Ala785Thr	180.0	0.0	0		254.0	88.0	0.346457	NM_134325	A7E2V6|B1AVM8|B1AVM9|B7ZKK2|Q96PK9|Q96RN0	Missense_Mutation	SNP	ENST00000367135.3	37	CCDS30990.1	1	4.578754578754579E-4	0	0.0	0	0.0	0	0.0	1	0.0013192612137203166	C	3.411	-0.120195	0.06838	2.27E-4	9.3E-4	ENSG00000174502	ENST00000340781;ENST00000367135;ENST00000367134	D;D;D	0.92699	-3.09;-2.98;-3.09	5.44	-10.9	0.00192	.	1.255410	0.05466	N	0.552214	T	0.76772	0.4034	N	0.04508	-0.205	0.09310	N	1	B;B	0.02656	0.0;0.0	B;B	0.04013	0.0;0.001	T	0.65307	-0.6200	10	0.11794	T	0.64	.	10.9011	0.47051	0.2271:0.5876:0.0:0.1853	.	785;785	Q7LBE3;B1AVM8	S26A9_HUMAN;.	T	785	ENSP00000341682:A785T;ENSP00000356103:A785T;ENSP00000356102:A785T	ENSP00000341682:A785T	A	-	1	0	SLC26A9	204151131	0.000000	0.05858	0.035000	0.18076	0.935000	0.57460	-2.719000	0.00812	-3.835000	0.00101	-1.327000	0.01280	GCA	C|0.999;T|0.001	0.001	strong		0.577	SLC26A9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000087742.1	NM_052934	
PIAS1	8554	hgsc.bcm.edu	37	15	68479959	68479959	+	Missense_Mutation	SNP	T	T	C			TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr15:68479959T>C	ENST00000249636.6	+	14	1890	c.1742T>C	c.(1741-1743)tTc>tCc	p.F581S	PIAS1_ENST00000545237.1_Missense_Mutation_p.F583S	NM_016166.1	NP_057250.1	O75925	PIAS1_HUMAN	protein inhibitor of activated STAT, 1	581	4 X 4 AA repeats of N-T-S-L.|Ser-rich.				androgen receptor signaling pathway (GO:0030521)|cytokine-mediated signaling pathway (GO:0019221)|interferon-gamma-mediated signaling pathway (GO:0060333)|JAK-STAT cascade (GO:0007259)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of proteasomal ubiquitin-dependent protein catabolic process (GO:0032436)|positive regulation of protein sumoylation (GO:0033235)|positive regulation of smooth muscle cell differentiation (GO:0051152)|positive regulation of transcription, DNA-templated (GO:0045893)|protein sumoylation (GO:0016925)|protein-DNA complex assembly (GO:0065004)|regulation of cell proliferation (GO:0042127)|regulation of interferon-gamma-mediated signaling pathway (GO:0060334)|spermatogenesis (GO:0007283)|transcription, DNA-templated (GO:0006351)	nucleoplasm (GO:0005654)|nucleus (GO:0005634)|PML body (GO:0016605)	androgen receptor binding (GO:0050681)|DNA binding (GO:0003677)|enzyme binding (GO:0019899)|SUMO ligase activity (GO:0019789)|transcription coactivator activity (GO:0003713)|transcription corepressor activity (GO:0003714)|zinc ion binding (GO:0008270)			breast(2)|endometrium(5)|kidney(3)|large_intestine(5)|lung(8)|ovary(1)	24						TCTCGGTTTTTCCCGTATACC	0.498																																					p.F581S		Atlas-SNP	.											PIAS1,NS,carcinoma,-1,1	PIAS1	42	1	0			c.T1742C						PASS	.						87.0	84.0	85.0					15																	68479959		1919	4137	6056	SO:0001583	missense	8554	exon14			GGTTTTTCCCGTA	AF077951	CCDS45290.1	15q	2011-10-11	2002-04-19	2002-04-19		ENSG00000033800		"""Zinc fingers, MIZ-type"""	2752	protein-coding gene	gene with protein product	"""zinc finger, MIZ-type containing 3"""	603566	"""DEAD/H (Asp-Glu-Ala-Asp/His) box binding protein 1"""	DDXBP1		9724754, 9177271	Standard	XM_005254735		Approved	GBP, GU/RH-II, ZMIZ3	uc002aqz.3	O75925		ENST00000249636.6:c.1742T>C	15.37:g.68479959T>C	ENSP00000249636:p.Phe581Ser	272.0	0.0	0		171.0	16.0	0.0935673	NM_016166	B2RB67|B3KSY9|C5J4B4|Q147X4|Q99751|Q9UN02	Missense_Mutation	SNP	ENST00000249636.6	37	CCDS45290.1	.	.	.	.	.	.	.	.	.	.	T	17.16	3.317953	0.60524	.	.	ENSG00000033800	ENST00000249636;ENST00000545237	T;T	0.33216	1.43;1.42	5.74	5.74	0.90152	.	0.103576	0.64402	D	0.000002	T	0.26011	0.0634	L	0.39898	1.24	0.51233	D	0.999913	P	0.40000	0.698	B	0.32211	0.142	T	0.07233	-1.0783	10	0.87932	D	0	-15.7775	16.0292	0.80564	0.0:0.0:0.0:1.0	.	581	O75925	PIAS1_HUMAN	S	581;583	ENSP00000249636:F581S;ENSP00000438574:F583S	ENSP00000249636:F581S	F	+	2	0	PIAS1	66267013	1.000000	0.71417	0.918000	0.36340	0.518000	0.34316	7.420000	0.80191	2.187000	0.69744	0.533000	0.62120	TTC	.	.	none		0.498	PIAS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000419642.2		
KLC1	3831	hgsc.bcm.edu	37	14	104143806	104143806	+	Silent	SNP	C	C	T			TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr14:104143806C>T	ENST00000348520.6	+	12	1753	c.1434C>T	c.(1432-1434)ggC>ggT	p.G478G	KLC1_ENST00000452929.2_Silent_p.G478G|KLC1_ENST00000553286.1_Silent_p.G478G|KLC1_ENST00000380038.3_Silent_p.G478G|RP11-73M18.2_ENST00000472726.2_Silent_p.G650G|KLC1_ENST00000347839.6_Silent_p.G478G|KLC1_ENST00000554280.1_Silent_p.G478G|KLC1_ENST00000557575.1_Silent_p.G478G|KLC1_ENST00000555836.1_Silent_p.G478G|KLC1_ENST00000445352.4_Silent_p.G476G|KLC1_ENST00000557450.1_Silent_p.G478G|KLC1_ENST00000246489.7_Silent_p.G478G|KLC1_ENST00000334553.6_Silent_p.G478G|KLC1_ENST00000389744.4_Silent_p.G478G	NM_182923.3	NP_891553.2	Q07866	KLC1_HUMAN	kinesin light chain 1	478					antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|blood coagulation (GO:0007596)|metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)|stress granule disassembly (GO:0035617)|viral process (GO:0016032)	cytoplasmic vesicle (GO:0031410)|cytosol (GO:0005829)|growth cone (GO:0030426)|kinesin complex (GO:0005871)|membrane (GO:0016020)|microtubule (GO:0005874)	microtubule motor activity (GO:0003777)|motor activity (GO:0003774)		KLC1/ALK(2)	NS(1)|endometrium(1)|kidney(3)|large_intestine(3)|lung(2)|prostate(1)|urinary_tract(1)	12		Melanoma(154;0.155)|all_epithelial(191;0.19)				GACGTCAAGGCAAATTTGAAG	0.418																																					p.G478G		Atlas-SNP	.											.	KLC1	54	.	0			c.C1434T						PASS	.						145.0	141.0	143.0					14																	104143806		2203	4300	6503	SO:0001819	synonymous_variant	3831	exon12			TCAAGGCAAATTT	AF267530	CCDS32165.1, CCDS41996.1, CCDS45168.1	14q32.3	2013-01-10	2007-03-09	2007-03-09	ENSG00000126214	ENSG00000126214		"""Tetratricopeptide (TTC) repeat domain containing"""	6387	protein-coding gene	gene with protein product		600025	"""kinesin 2 60/70kDa"", ""kinesin 2"""	KNS2		8274221, 11106729	Standard	NM_005552		Approved	KNS2A, KLC, hKLC1S, hKLC1N, hKLC1P, hKLC1G, hKLC1R, hKLC1J, hKLC1B	uc010tyf.2	Q07866	OTTHUMG00000169227	ENST00000348520.6:c.1434C>T	14.37:g.104143806C>T		98.0	0.0	0		126.0	35.0	0.277778	NM_182923	A6NF62|F8VTM4|Q7RTM2|Q7RTM3|Q7RTM5|Q7RTP9|Q7RTQ3|Q7RTQ5|Q7RTQ6|Q86SF5|Q86TF5|Q86V74|Q86V75|Q86V76|Q86V77|Q86V78|Q86V79|Q96H62	Silent	SNP	ENST00000348520.6	37	CCDS41996.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	10.60|10.60	1.396952|1.396952	0.25205|0.25205	.|.	.|.	ENSG00000126214|ENSG00000126214	ENST00000553325;ENST00000553436;ENST00000555856|ENST00000537046	.|.	.|.	.|.	5.52|5.52	2.56|2.56	0.30785|0.30785	.|.	.|.	.|.	.|.	.|.	T|.	0.72350|.	0.3449|.	.|.	.|.	.|.	0.80722|0.80722	D|D	1|1	.|.	.|.	.|.	.|.	.|.	.|.	T|.	0.71869|.	-0.4462|.	4|.	.|.	.|.	.|.	-15.9577|-15.9577	17.9404|17.9404	0.89025|0.89025	0.0:0.7802:0.2198:0.0|0.0:0.7802:0.2198:0.0	.|.	.|.	.|.	.|.	V|X	58;54;52|84	.|.	.|.	A|Q	+|+	2|1	0|0	KLC1|KLC1	103213559|103213559	1.000000|1.000000	0.71417|0.71417	0.999000|0.999000	0.59377|0.59377	0.964000|0.964000	0.63967|0.63967	1.666000|1.666000	0.37460|0.37460	0.313000|0.313000	0.23062|0.23062	0.655000|0.655000	0.94253|0.94253	GCA|CAA	.	.	none		0.418	KLC1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000402947.2	NM_005552	
RBM44	375316	hgsc.bcm.edu	37	2	238742968	238742968	+	Missense_Mutation	SNP	G	G	A			TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr2:238742968G>A	ENST00000409864.1	+	15	3337	c.3083G>A	c.(3082-3084)gGt>gAt	p.G1028D	RBM44_ENST00000316997.4_Missense_Mutation_p.G1028D			Q6ZP01	RBM44_HUMAN	RNA binding motif protein 44	1027						cytoplasm (GO:0005737)|intercellular bridge (GO:0045171)	nucleotide binding (GO:0000166)|protein homodimerization activity (GO:0042803)|RNA binding (GO:0003723)			breast(1)|endometrium(4)|kidney(4)|large_intestine(11)|lung(7)|ovary(4)|upper_aerodigestive_tract(1)|urinary_tract(1)	33		Breast(86;0.0042)|Renal(207;0.00571)|Ovarian(221;0.17)|all_hematologic(139;0.182)		Epithelial(121;3.74e-22)|OV - Ovarian serous cystadenocarcinoma(60;5.3e-11)|Kidney(56;3.04e-09)|KIRC - Kidney renal clear cell carcinoma(57;6.5e-08)|BRCA - Breast invasive adenocarcinoma(100;0.000118)|Lung(119;0.0112)|LUSC - Lung squamous cell carcinoma(224;0.0266)		AGACATAAAGGTTTTCTGAAT	0.318																																					p.G1028D		Atlas-SNP	.											.	RBM44	167	.	0			c.G3083A						PASS	.						38.0	37.0	37.0					2																	238742968		1804	4054	5858	SO:0001583	missense	375316	exon15			ATAAAGGTTTTCT	AK097730	CCDS46554.1	2q37.3	2013-02-12			ENSG00000177483	ENSG00000177483		"""RNA binding motif (RRM) containing"""	24756	protein-coding gene	gene with protein product							Standard	NM_001080504		Approved	FLJ40411	uc002vxi.4	Q6ZP01	OTTHUMG00000152937	ENST00000409864.1:c.3083G>A	2.37:g.238742968G>A	ENSP00000386727:p.Gly1028Asp	297.0	1.0	0.003367		262.0	128.0	0.48855	NM_001080504	A0AUW3	Missense_Mutation	SNP	ENST00000409864.1	37	CCDS46554.1	.	.	.	.	.	.	.	.	.	.	G	20.3	3.962568	0.74016	.	.	ENSG00000177483	ENST00000316997;ENST00000409864	T;T	0.69561	-0.41;-0.41	4.96	4.96	0.65561	.	.	.	.	.	T	0.81351	0.4804	M	0.74881	2.28	0.43275	D	0.995234	D	0.89917	1.0	D	0.91635	0.999	D	0.83952	0.0317	9	0.87932	D	0	-15.9804	15.6834	0.77391	0.0:0.0:1.0:0.0	.	1027	Q6ZP01	RBM44_HUMAN	D	1028	ENSP00000321179:G1028D;ENSP00000386727:G1028D	ENSP00000321179:G1028D	G	+	2	0	RBM44	238407707	1.000000	0.71417	0.812000	0.32479	0.977000	0.68977	6.062000	0.71155	2.297000	0.77311	0.484000	0.47621	GGT	.	.	none		0.318	RBM44-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000328733.2	NM_001080504	
SFN	2810	hgsc.bcm.edu	37	1	27190196	27190196	+	Missense_Mutation	SNP	A	A	T	rs77755255		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr1:27190196A>T	ENST00000339276.4	+	1	564	c.493A>T	c.(493-495)Acc>Tcc	p.T165S		NM_006142.3	NP_006133.1	Q9Y3B8	ORN_HUMAN	stratifin	0	Exonuclease.				nucleic acid phosphodiester bond hydrolysis (GO:0090305)|nucleobase-containing compound metabolic process (GO:0006139)|nucleotide metabolic process (GO:0009117)	focal adhesion (GO:0005925)|mitochondrion (GO:0005739)|nucleolus (GO:0005730)|nucleus (GO:0005634)	3'-5' exonuclease activity (GO:0008408)|nucleic acid binding (GO:0003676)			breast(1)|cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|lung(3)|skin(2)	9		all_cancers(24;1.23e-26)|all_epithelial(13;1.19e-23)|Colorectal(325;3.46e-05)|all_lung(284;5.94e-05)|Lung NSC(340;7.26e-05)|Breast(348;0.00017)|Renal(390;0.0007)|Ovarian(437;0.00764)|Myeloproliferative disorder(586;0.0255)|all_neural(195;0.0381)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0178)|all cancers(4;2.1e-52)|Epithelial(14;2.31e-52)|OV - Ovarian serous cystadenocarcinoma(117;8.22e-30)|Colorectal(126;1.31e-09)|COAD - Colon adenocarcinoma(152;3.45e-07)|BRCA - Breast invasive adenocarcinoma(304;0.000501)|STAD - Stomach adenocarcinoma(196;0.000588)|KIRC - Kidney renal clear cell carcinoma(1967;0.000716)|READ - Rectum adenocarcinoma(331;0.0419)|GBM - Glioblastoma multiforme(114;0.0767)|Lung(427;0.215)		GATGCCGCCCACCAACCCCAT	0.617																																					p.T165S		Atlas-SNP	.											.	SFN	20	.	0			c.A493T						PASS	.						90.0	84.0	86.0					1																	27190196		2203	4300	6503	SO:0001583	missense	2810	exon1			CCGCCCACCAACC	BC023552	CCDS288.1	1p36.11	2008-02-05			ENSG00000175793	ENSG00000175793			10773	protein-coding gene	gene with protein product	"""14-3-3 sigma"""	601290				8515476	Standard	NM_006142		Approved	YWHAS	uc001bnc.1	P31947	OTTHUMG00000004093	ENST00000339276.4:c.493A>T	1.37:g.27190196A>T	ENSP00000340989:p.Thr165Ser	59.0	0.0	0		37.0	6.0	0.162162	NM_006142	B2R532|Q32Q18|Q53FT1|Q6FIC6|Q9UFY7	Missense_Mutation	SNP	ENST00000339276.4	37	CCDS288.1	.	.	.	.	.	.	.	.	.	.	A	28.4	4.919577	0.92249	.	.	ENSG00000175793	ENST00000339276;ENST00000538651	T	0.46819	0.86	5.91	5.91	0.95273	14-3-3 domain (4);	0.000000	0.85682	D	0.000000	T	0.73938	0.3651	M	0.89715	3.055	0.36736	D	0.881953	D	0.53885	0.963	D	0.65443	0.935	T	0.83349	-0.0004	10	0.87932	D	0	-45.3648	16.0112	0.80404	1.0:0.0:0.0:0.0	.	165	P31947	1433S_HUMAN	S	165;133	ENSP00000340989:T165S	ENSP00000340989:T165S	T	+	1	0	SFN	27062783	1.000000	0.71417	1.000000	0.80357	0.980000	0.70556	9.335000	0.96500	2.255000	0.74692	0.533000	0.62120	ACC	.	.	weak		0.617	SFN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000011709.1	NM_006142	
SPRY4	81848	hgsc.bcm.edu	37	5	141693948	141693948	+	Silent	SNP	G	G	A	rs145360326	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr5:141693948G>A	ENST00000434127.2	-	2	969	c.726C>T	c.(724-726)tcC>tcT	p.S242S	SPRY4_ENST00000344120.4_Silent_p.S265S|SPRY4_ENST00000503582.1_5'Flank	NM_001127496.1	NP_001120968.1	Q9C004	SPY4_HUMAN	sprouty homolog 4 (Drosophila)	242	Cys-rich.|SPR. {ECO:0000255|PROSITE- ProRule:PRU00572}.				multicellular organismal development (GO:0007275)|negative regulation of MAP kinase activity (GO:0043407)	cell projection (GO:0042995)|cytoplasm (GO:0005737)|focal adhesion (GO:0005925)|Golgi apparatus (GO:0005794)|plasma membrane (GO:0005886)		p.S265S(3)		breast(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(3)|large_intestine(3)|lung(7)|ovary(1)	18		all_hematologic(541;0.118)	KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			GCAGCACCACGGAGAGAGCAC	0.682									Testicular Cancer, Familial Clustering of																												p.S265S		Atlas-SNP	.											SPRY4,rectum,carcinoma,0,2	SPRY4	31	2	3	Substitution - coding silent(3)	lung(2)|large_intestine(1)	c.C795T						PASS	.	G	,	2,4404	4.2+/-10.8	0,2,2201	60.0	60.0	60.0		726,795	0.7	1.0	5	dbSNP_134	60	5,8595	4.3+/-15.6	0,5,4295	no	coding-synonymous,coding-synonymous	SPRY4	NM_001127496.1,NM_030964.3	,	0,7,6496	AA,AG,GG		0.0581,0.0454,0.0538	,	242/300,265/323	141693948	7,12999	2203	4300	6503	SO:0001819	synonymous_variant	81848	exon3	Familial Cancer Database		CACCACGGAGAGA	AF227516	CCDS4274.1, CCDS47296.1	5q31.3	2010-08-05			ENSG00000187678	ENSG00000187678			15533	protein-coding gene	gene with protein product		607984				16465403	Standard	NM_030964		Approved		uc010jgi.1	Q9C004	OTTHUMG00000129663	ENST00000434127.2:c.726C>T	5.37:g.141693948G>A		251.0	0.0	0		229.0	108.0	0.471616	NM_030964	A4FVB2|A4FVB3|Q6QIX2|Q9C003	Silent	SNP	ENST00000434127.2	37	CCDS47296.1																																																																																			G|0.999;A|0.001	0.001	strong		0.682	SPRY4-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000370652.1		
MEF2A	4205	hgsc.bcm.edu	37	15	100250918	100250918	+	Silent	SNP	G	G	A			TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr15:100250918G>A	ENST00000557785.1	+	10	1414	c.1065G>A	c.(1063-1065)tcG>tcA	p.S355S	MEF2A_ENST00000557942.1_Silent_p.S363S|MEF2A_ENST00000453228.2_Silent_p.S355S|MEF2A_ENST00000558812.1_Silent_p.S295S|MEF2A_ENST00000354410.5_Silent_p.S357S|MEF2A_ENST00000338042.6_Silent_p.S364S|MEF2A_ENST00000449277.2_Silent_p.S287S	NM_001171894.1	NP_001165365.1	Q02078	MEF2A_HUMAN	myocyte enhancer factor 2A	365					apoptotic process (GO:0006915)|cardiac conduction (GO:0061337)|cellular response to calcium ion (GO:0071277)|dendrite morphogenesis (GO:0048813)|ERK5 cascade (GO:0070375)|heart development (GO:0007507)|innate immune response (GO:0045087)|MAPK cascade (GO:0000165)|mitochondrial genome maintenance (GO:0000002)|mitochondrion distribution (GO:0048311)|muscle cell differentiation (GO:0042692)|muscle organ development (GO:0007517)|MyD88-dependent toll-like receptor signaling pathway (GO:0002755)|MyD88-independent toll-like receptor signaling pathway (GO:0002756)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of muscle cell differentiation (GO:0051149)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|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)|transcription from RNA polymerase II promoter (GO:0006366)|transcription, DNA-templated (GO:0006351)|TRIF-dependent toll-like receptor signaling pathway (GO:0035666)|ventricular cardiac myofibril assembly (GO:0055005)	cytoplasm (GO:0005737)|nuclear chromatin (GO:0000790)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	activating transcription factor binding (GO:0033613)|chromatin binding (GO:0003682)|histone acetyltransferase binding (GO:0035035)|histone deacetylase binding (GO:0042826)|protein heterodimerization activity (GO:0046982)|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)|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 coactivator activity (GO:0001105)|RNA polymerase II transcription factor binding (GO:0001085)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0000981)|sequence-specific DNA binding transcription factor activity (GO:0003700)|SMAD binding (GO:0046332)			endometrium(2)|large_intestine(2)|lung(7)|ovary(1)	12	Lung NSC(78;0.00335)|all_lung(78;0.00659)|Melanoma(26;0.00778)|Medulloblastoma(229;0.163)		OV - Ovarian serous cystadenocarcinoma(32;0.00085)			GACAGGTGTCGGCCTGGCAGC	0.537																																					p.S357S		Atlas-SNP	.											.	MEF2A	138	.	0			c.G1071A						PASS	.						51.0	53.0	53.0					15																	100250918		2046	4203	6249	SO:0001819	synonymous_variant	4205	exon10			GGTGTCGGCCTGG		CCDS45362.1, CCDS45363.1, CCDS53978.1, CCDS58401.1	15q26	2008-02-05	2007-04-24			ENSG00000068305		"""Myocyte enhancer factors"""	6993	protein-coding gene	gene with protein product		600660				1516833	Standard	NM_005587		Approved	RSRFC4, RSRFC9	uc002bvf.3	Q02078		ENST00000557785.1:c.1065G>A	15.37:g.100250918G>A		139.0	0.0	0		97.0	71.0	0.731959	NM_005587	B4DFQ7|F6XG23|O43814|Q14223|Q14224|Q59GX4|Q7Z6C9|Q96D14	Silent	SNP	ENST00000557785.1	37	CCDS53978.1																																																																																			.	.	none		0.537	MEF2A-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000415985.1		
SAMD9	54809	hgsc.bcm.edu	37	7	92734358	92734358	+	Silent	SNP	G	G	A	rs200454238		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr7:92734358G>A	ENST00000379958.2	-	3	1322	c.1053C>T	c.(1051-1053)gaC>gaT	p.D351D		NM_001193307.1|NM_017654.3	NP_001180236.1|NP_060124.2	Q5K651	SAMD9_HUMAN	sterile alpha motif domain containing 9	351						cytoplasm (GO:0005737)|intracellular membrane-bounded organelle (GO:0043231)		p.S348fs*47(1)		NS(1)|breast(4)|central_nervous_system(3)|endometrium(5)|haematopoietic_and_lymphoid_tissue(2)|kidney(7)|large_intestine(20)|lung(32)|ovary(4)|prostate(1)|skin(5)|upper_aerodigestive_tract(2)|urinary_tract(2)	88	all_cancers(62;5.71e-11)|all_epithelial(64;3.25e-10)|Breast(17;0.000675)|Lung NSC(181;0.0969)|all_lung(186;0.125)		STAD - Stomach adenocarcinoma(171;0.000302)			TTTTCGTAATGTCCTTAGAGC	0.323																																					p.D351D		Atlas-SNP	.											.	SAMD9	239	.	1	Deletion - Frameshift(1)	breast(1)	c.C1053T						PASS	.	G	,	0,4402		0,0,2201	97.0	95.0	96.0		1053,1053	2.4	0.1	7		96	4,8594	3.7+/-12.6	0,4,4295	no	coding-synonymous,coding-synonymous	SAMD9	NM_001193307.1,NM_017654.3	,	0,4,6496	AA,AG,GG		0.0465,0.0,0.0308	,	351/1590,351/1590	92734358	4,12996	2201	4299	6500	SO:0001819	synonymous_variant	54809	exon2			CGTAATGTCCTTA	AB095925	CCDS34680.1	7q21.2	2013-01-10	2004-07-15	2004-07-16	ENSG00000205413	ENSG00000205413		"""Sterile alpha motif (SAM) domain containing"""	1348	protein-coding gene	gene with protein product		610456	"""chromosome 7 open reading frame 5"""	C7orf5			Standard	NM_017654		Approved	KIAA2004, FLJ20073	uc003umg.3	Q5K651	OTTHUMG00000155809	ENST00000379958.2:c.1053C>T	7.37:g.92734358G>A		128.0	0.0	0		198.0	68.0	0.343434	NM_001193307	A2RU68|Q5K649|Q6P080|Q75N21|Q8IVG6|Q9NXS8	Silent	SNP	ENST00000379958.2	37	CCDS34680.1																																																																																			G|0.999;A|0.001	0.001	weak		0.323	SAMD9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000341761.1	NM_017654	
RHBDF2	79651	hgsc.bcm.edu	37	17	74473329	74473329	+	Missense_Mutation	SNP	C	C	T	rs140433374		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr17:74473329C>T	ENST00000313080.4	-	8	1213	c.940G>A	c.(940-942)Gcc>Acc	p.A314T	RHBDF2_ENST00000389760.4_Missense_Mutation_p.A285T|RHBDF2_ENST00000592378.1_5'Flank|RHBDF2_ENST00000591885.1_Missense_Mutation_p.A285T	NM_024599.5	NP_078875.4	Q6PJF5	RHDF2_HUMAN	rhomboid 5 homolog 2 (Drosophila)	314					negative regulation of protein secretion (GO:0050709)|protein transport (GO:0015031)	endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	serine-type endopeptidase activity (GO:0004252)			cervix(1)|endometrium(1)|kidney(1)|large_intestine(5)|lung(13)|ovary(1)|prostate(4)|skin(1)	27						AAGTAGCTGGCAGAGAGTGGG	0.582													C|||	1	0.000199681	0.0	0.0014	5008	,	,		17105	0.0		0.0	False		,,,				2504	0.0				p.A314T		Atlas-SNP	.											.	RHBDF2	57	.	0			c.G940A						PASS	.	C	THR/ALA,THR/ALA	0,4404		0,0,2202	30.0	35.0	33.0		853,940	5.5	1.0	17	dbSNP_134	33	9,8591	6.4+/-24.3	0,9,4291	yes	missense,missense	RHBDF2	NM_001005498.3,NM_024599.5	58,58	0,9,6493	TT,TC,CC		0.1047,0.0,0.0692	possibly-damaging,possibly-damaging	285/828,314/857	74473329	9,12995	2202	4300	6502	SO:0001583	missense	79651	exon8			AGCTGGCAGAGAG	BC016034	CCDS32743.1, CCDS32744.1	17q25.3	2014-09-17	2006-02-22	2006-02-22		ENSG00000129667			20788	protein-coding gene	gene with protein product		614404	"""rhomboid, veinlet-like 6 (Drosophila)"", ""tylosis with oesophageal cancer"""	RHBDL6, TOC		12838346, 22265016	Standard	NM_024599		Approved	FLJ22341, RHBDL5, TOCG	uc002jrq.2	Q6PJF5		ENST00000313080.4:c.940G>A	17.37:g.74473329C>T	ENSP00000322775:p.Ala314Thr	158.0	0.0	0		138.0	74.0	0.536232	NM_024599	A6NEM3|A8K801|Q5U607|Q5YGQ8|Q9H6E9	Missense_Mutation	SNP	ENST00000313080.4	37	CCDS32743.1	1	4.578754578754579E-4	0	0.0	1	0.0027624309392265192	0	0.0	0	0.0	C	27.4	4.830924	0.91036	0.0	0.001047	ENSG00000129667	ENST00000313080;ENST00000389760;ENST00000389762	T;T	0.69561	-0.41;-0.41	5.54	5.54	0.83059	.	0.000000	0.85682	D	0.000000	T	0.78566	0.4303	L	0.56769	1.78	0.50632	D	0.999886	D;P;P;P	0.69078	0.997;0.866;0.891;0.799	D;P;B;P	0.67548	0.952;0.507;0.439;0.615	T	0.73920	-0.3830	10	0.26408	T	0.33	-38.8792	19.4819	0.95013	0.0:1.0:0.0:0.0	.	285;260;314;285	B7Z8H4;Q6ZWP8;Q6PJF5;Q6PJF5-2	.;.;RHDF2_HUMAN;.	T	314;285;260	ENSP00000322775:A314T;ENSP00000374410:A285T	ENSP00000322775:A314T	A	-	1	0	RHBDF2	71984924	1.000000	0.71417	1.000000	0.80357	0.988000	0.76386	5.534000	0.67167	2.595000	0.87683	0.655000	0.94253	GCC	C|0.999;T|0.001	0.001	strong		0.582	RHBDF2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000450134.1	NM_024599	
MTHFSD	64779	hgsc.bcm.edu	37	16	86585743	86585743	+	Missense_Mutation	SNP	G	G	C	rs34005514	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr16:86585743G>C	ENST00000360900.6	-	3	158	c.133C>G	c.(133-135)Ctg>Gtg	p.L45V	MTHFSD_ENST00000543303.2_Intron|MTHFSD_ENST00000568037.1_Intron|MTHFSD_ENST00000322911.6_Missense_Mutation_p.L44V|MTHFSD_ENST00000381214.5_Intron|MTHFSD_ENST00000546093.1_Intron	NM_001159380.1	NP_001152852.1	Q2M296	MTHSD_HUMAN	methenyltetrahydrofolate synthetase domain containing	45			L -> V (in dbSNP:rs34005514).				nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)			endometrium(1)|large_intestine(3)|lung(6)|skin(1)	11						TGGCAAGCCAGATAAGACCCC	0.473													G|||	95	0.0189696	0.0053	0.0274	5008	,	,		19532	0.004		0.0517	False		,,,				2504	0.0133				p.L45V		Atlas-SNP	.											.	MTHFSD	52	.	0			c.C133G						PASS	.	G	VAL/LEU,,,VAL/LEU,VAL/LEU	43,3753		0,43,1855	151.0	153.0	152.0		133,,,73,130	-0.4	0.6	16	dbSNP_126	152	398,7840		14,370,3735	yes	missense,intron,intron,missense,missense	MTHFSD	NM_001159377.1,NM_001159378.1,NM_001159379.1,NM_001159380.1,NM_022764.2	32,,,32,32	14,413,5590	CC,CG,GG		4.8313,1.1328,3.6646	,,,,	45/384,,,25/364,44/383	86585743	441,11593	1898	4119	6017	SO:0001583	missense	64779	exon3			AAGCCAGATAAGA	AK023060	CCDS54047.1, CCDS54048.1, CCDS58490.1	16q24.1	2013-02-12				ENSG00000103248		"""RNA binding motif (RRM) containing"""	25778	protein-coding gene	gene with protein product						12477932	Standard	NM_022764		Approved	FLJ12998	uc010vor.2	Q2M296		ENST00000360900.6:c.133C>G	16.37:g.86585743G>C	ENSP00000354152:p.Leu45Val	130.0	0.0	0		142.0	113.0	0.795775	NM_001159377	A8MQ77|B7ZLC0|B7ZLC2|D3DUM9|E9PAM1|Q9H878|Q9H954	Missense_Mutation	SNP	ENST00000360900.6	37	CCDS54047.1	55	0.025183150183150184	2	0.0040650406504065045	8	0.022099447513812154	4	0.006993006993006993	41	0.05408970976253298	G	10.80	1.453214	0.26161	0.011328	0.048313	ENSG00000103248	ENST00000543303;ENST00000360900;ENST00000322911	T;T	0.41400	1.0;1.0	5.93	-0.438	0.12268	5-formyltetrahydrofolate cyclo-ligase-like domain (1);	1.474430	0.04126	N	0.317098	T	0.04724	0.0128	N	0.04297	-0.235	0.09310	N	1	B;B	0.17465	0.022;0.017	B;B	0.23852	0.049;0.029	T	0.23726	-1.0180	10	0.35671	T	0.21	-11.0693	14.9226	0.70851	0.0:0.419:0.4829:0.0981	rs34005514	45;44	Q2M296;Q2M296-2	MTHSD_HUMAN;.	V	43;45;44	ENSP00000354152:L45V;ENSP00000326777:L44V	ENSP00000326777:L44V	L	-	1	2	MTHFSD	85143244	0.057000	0.20700	0.564000	0.28396	0.964000	0.63967	0.453000	0.21811	0.070000	0.16634	0.655000	0.94253	CTG	G|0.968;C|0.032	0.032	strong		0.473	MTHFSD-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000432182.1	NM_022764	
LPAR2	9170	hgsc.bcm.edu	37	19	19737992	19737992	+	Silent	SNP	G	G	A	rs150741448	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr19:19737992G>A	ENST00000542587.1	-	5	1004	c.102C>T	c.(100-102)gtC>gtT	p.V34V	LPAR2_ENST00000407877.3_Silent_p.V34V|LPAR2_ENST00000589311.1_5'Flank|LPAR2_ENST00000586703.1_Silent_p.V34V			Q9HBW0	LPAR2_HUMAN	lysophosphatidic acid receptor 2	34					activation of MAPK activity (GO:0000187)|activation of phospholipase C activity (GO:0007202)|G-protein coupled receptor signaling pathway (GO:0007186)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|positive regulation of Rho protein signal transduction (GO:0035025)	cell surface (GO:0009986)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|lipid binding (GO:0008289)|lysophosphatidic acid receptor activity (GO:0070915)			breast(1)|endometrium(2)|large_intestine(2)|lung(2)|ovary(1)|prostate(1)|urinary_tract(1)	10						GTGCCACCACGACCACATCCT	0.592													G|||	7	0.00139776	0.0	0.0029	5008	,	,		18269	0.0		0.005	False		,,,				2504	0.0				p.V34V		Atlas-SNP	.											.	LPAR2	28	.	0			c.C102T						PASS	.	G		4,4400	6.2+/-15.9	0,4,2198	33.0	32.0	33.0		102	-8.9	0.4	19	dbSNP_134	33	39,8561	24.0+/-70.4	0,39,4261	no	coding-synonymous	LPAR2	NM_004720.5		0,43,6459	AA,AG,GG		0.4535,0.0908,0.3307		34/352	19737992	43,12961	2202	4300	6502	SO:0001819	synonymous_variant	9170	exon2			CACCACGACCACA	AF011466	CCDS12407.1	19p12	2012-08-08	2008-04-11	2008-04-11		ENSG00000064547		"""GPCR / Class A : Lysophospholipid receptors : Lysophosphatidic acid"""	3168	protein-coding gene	gene with protein product		605110	"""endothelial differentiation, lysophosphatidic acid G-protein-coupled receptor, 4"""	EDG4		9525886, 9804623	Standard	NM_004720		Approved	EDG-4, LPA2	uc002nnb.4	Q9HBW0		ENST00000542587.1:c.102C>T	19.37:g.19737992G>A		66.0	0.0	0		75.0	35.0	0.466667	NM_004720	O00543|O43431	Silent	SNP	ENST00000542587.1	37	CCDS12407.1																																																																																			G|0.997;A|0.003	0.003	strong		0.592	LPAR2-003	KNOWN	alternative_5_UTR|non_canonical_TEC|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000460544.1	NM_004720	
LRRC16B	90668	hgsc.bcm.edu	37	14	24534270	24534270	+	Missense_Mutation	SNP	C	C	T	rs117833529	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr14:24534270C>T	ENST00000342740.5	+	33	3338	c.3184C>T	c.(3184-3186)Cgg>Tgg	p.R1062W	LRRC16B_ENST00000334420.7_Missense_Mutation_p.R158W	NM_138360.3	NP_612369.3	Q8ND23	LR16B_HUMAN	leucine rich repeat containing 16B	1062				R -> W (in Ref. 2; CAD38886). {ECO:0000305}.		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)		TCGCCGGCCCCGGAGCTTCAA	0.716													C|||	108	0.0215655	0.0015	0.0418	5008	,	,		8025	0.0		0.0368	False		,,,				2504	0.0409				p.R1062W		Atlas-SNP	.											.	LRRC16B	120	.	0			c.C3184T						PASS	.	C	TRP/ARG	23,3751		0,23,1864	19.0	24.0	22.0		3184	2.8	1.0	14	dbSNP_132	22	255,7637		2,251,3693	yes	missense	LRRC16B	NM_138360.3	101	2,274,5557	TT,TC,CC		3.2311,0.6094,2.383	probably-damaging	1062/1373	24534270	278,11388	1887	3946	5833	SO:0001583	missense	90668	exon33			CGGCCCCGGAGCT	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.3184C>T	14.37:g.24534270C>T	ENSP00000340467:p.Arg1062Trp	59.0	0.0	0		69.0	35.0	0.507246	NM_138360	Q8TEF7|Q96HS9	Missense_Mutation	SNP	ENST00000342740.5	37	CCDS32054.1	46	0.021062271062271064	2	0.0040650406504065045	19	0.052486187845303865	0	0.0	25	0.032981530343007916	C	12.56	1.973870	0.34848	0.006094	0.032311	ENSG00000186648	ENST00000342740;ENST00000334420	T;T	0.60797	1.2;0.16	4.66	2.77	0.32553	.	0.254810	0.20948	N	0.082818	T	0.29389	0.0732	L	0.59436	1.845	0.28233	N	0.926034	D;D	0.89917	1.0;0.999	D;P	0.80764	0.994;0.876	T	0.48725	-0.9010	10	0.87932	D	0	-13.2657	9.764	0.40550	0.3756:0.6244:0.0:0.0	.	158;1062	Q8ND23-2;Q8ND23	.;LR16B_HUMAN	W	1062;158	ENSP00000340467:R1062W;ENSP00000334701:R158W	ENSP00000334701:R158W	R	+	1	2	LRRC16B	23604110	0.999000	0.42202	1.000000	0.80357	0.602000	0.36980	1.625000	0.37029	0.375000	0.24679	-0.348000	0.07805	CGG	C|0.976;T|0.024	0.024	strong		0.716	LRRC16B-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000416527.1	NM_138360	
PCDHA12	56137	hgsc.bcm.edu	37	5	140256807	140256807	+	Missense_Mutation	SNP	T	T	A	rs199811254		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr5:140256807T>A	ENST00000398631.2	+	1	1750	c.1750T>A	c.(1750-1752)Tcg>Acg	p.S584T	PCDHA1_ENST00000394633.3_Intron|PCDHA2_ENST00000526136.1_Intron|PCDHA10_ENST00000307360.5_Intron|PCDHA5_ENST00000529859.1_Intron|PCDHA1_ENST00000504120.2_Intron|PCDHA4_ENST00000512229.2_Intron|PCDHA5_ENST00000529619.1_Intron|PCDHA10_ENST00000506939.2_Intron|PCDHA11_ENST00000398640.2_Intron|PCDHA7_ENST00000525929.1_Intron|PCDHA6_ENST00000527624.1_Intron|PCDHA6_ENST00000529310.1_Intron|PCDHA3_ENST00000522353.2_Intron|PCDHA8_ENST00000531613.1_Intron|PCDHA9_ENST00000532602.1_Intron|PCDHA4_ENST00000530339.1_Intron	NM_018903.2|NM_031864.2	NP_061726.1|NP_114070.1	Q9UN75	PCDAC_HUMAN	protocadherin alpha 12	584	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)			NS(4)|breast(2)|cervix(1)|endometrium(19)|kidney(8)|large_intestine(8)|liver(2)|lung(25)|prostate(1)|skin(3)|upper_aerodigestive_tract(4)|urinary_tract(1)	78			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			GGTACCGCGGTCGGTGGGTGC	0.682													.|||	1	0.000199681	0.0	0.0	5008	,	,		17689	0.0		0.001	False		,,,				2504	0.0				p.S584T	Pancreas(113;759 1672 13322 24104 50104)	Atlas-SNP	.											PCDHA12,NS,carcinoma,-1,2	PCDHA12	196	2	0			c.T1750A						PASS	.	T	,,,THR/SER,,,,,,,,,,,,THR/SER	1,4405	2.1+/-5.4	0,1,2202	221.0	209.0	213.0		,,,1750,,,,,,,,,,,,1750	-1.4	0.0	5		213	5,8591	4.3+/-15.6	0,5,4293	no	intron,intron,intron,missense,intron,intron,intron,intron,intron,intron,intron,intron,intron,intron,intron,missense	PCDHA9,PCDHA12,PCDHA11,PCDHA10,PCDHA8,PCDHA7,PCDHA6,PCDHA5,PCDHA4,PCDHA3,PCDHA2,PCDHA1	NM_018900.2,NM_018901.2,NM_018902.3,NM_018903.2,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_031864.1	,,,58,,,,,,,,,,,,58	0,6,6495	AA,AT,TT		0.0582,0.0227,0.0461	,,,,,,,,,,,,,,,	,,,584/942,,,,,,,,,,,,584/793	140256807	6,12996	2203	4298	6501	SO:0001583	missense	56137	exon1			CCGCGGTCGGTGG	AF152477	CCDS47285.1, CCDS75327.1	5q31	2010-11-26			ENSG00000251664	ENSG00000251664		"""Cadherins / Protocadherins : Clustered"""	8666	other	complex locus constituent	"""KIAA0345-like 2"""	606318				10380929	Standard	NM_018903		Approved	PCDH-ALPHA12	uc003lic.2	Q9UN75	OTTHUMG00000163366	ENST00000398631.2:c.1750T>A	5.37:g.140256807T>A	ENSP00000381628:p.Ser584Thr	295.0	0.0	0		224.0	117.0	0.522321	NM_018903	O75278|Q2M1N8	Missense_Mutation	SNP	ENST00000398631.2	37	CCDS47285.1	1	4.578754578754579E-4	0	0.0	0	0.0	0	0.0	1	0.0013192612137203166	T	4.945	0.175589	0.09391	2.27E-4	5.82E-4	ENSG00000251664	ENST00000398631	T	0.39229	1.09	4.71	-1.37	0.09056	Cadherin (2);Cadherin-like (1);	.	.	.	.	T	0.33760	0.0874	M	0.69185	2.1	0.09310	N	1	B;B	0.33212	0.232;0.402	B;B	0.32762	0.152;0.082	T	0.37549	-0.9701	9	0.59425	D	0.04	.	1.4327	0.02337	0.276:0.0817:0.2678:0.3745	.	584;584	Q9UN75-2;Q9UN75	.;PCDAC_HUMAN	T	584	ENSP00000381628:S584T	ENSP00000381628:S584T	S	+	1	0	PCDHA12	140236991	0.000000	0.05858	0.000000	0.03702	0.012000	0.07955	-0.529000	0.06186	-0.138000	0.11434	-0.516000	0.04426	TCG	T|0.999;A|0.001	0.001	strong		0.682	PCDHA12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000372882.2	NM_018903	
MUC17	140453	hgsc.bcm.edu	37	7	100682117	100682117	+	Missense_Mutation	SNP	G	G	A	rs555953599	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr7:100682117G>A	ENST00000306151.4	+	3	7484	c.7420G>A	c.(7420-7422)Ggc>Agc	p.G2474S		NM_001040105.1	NP_001035194.1	Q685J3	MUC17_HUMAN	mucin 17, cell surface associated	2474	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)					TTCTGAGGCTGGCACCCTTTC	0.522													N|||	3	0.000599042	0.0	0.0	5008	,	,		27478	0.0		0.0	False		,,,				2504	0.0031				p.G2474S		Atlas-SNP	.											MUC17,right_upper_lobe,carcinoma,-2,1	MUC17	804	1	0			c.G7420A						scavenged	.																																			SO:0001583	missense	140453	exon3			GAGGCTGGCACCC	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.7420G>A	7.37:g.100682117G>A	ENSP00000302716:p.Gly2474Ser	187.0	0.0	0		238.0	15.0	0.0630252	NM_001040105	O14761|Q685J2|Q8TDH7	Missense_Mutation	SNP	ENST00000306151.4	37	CCDS34711.1	.	.	.	.	.	.	.	.	.	.	N	2.617	-0.289370	0.05605	.	.	ENSG00000169876	ENST00000306151	T	0.03468	3.92	0.869	-0.297	0.12820	.	.	.	.	.	T	0.01254	0.0041	N	0.02916	-0.46	0.09310	N	1	B	0.27286	0.174	B	0.19148	0.024	T	0.45131	-0.9282	9	0.02654	T	1	.	5.8185	0.18514	0.4085:0.0:0.5915:0.0	.	2474	Q685J3	MUC17_HUMAN	S	2474	ENSP00000302716:G2474S	ENSP00000302716:G2474S	G	+	1	0	MUC17	100468837	0.000000	0.05858	0.000000	0.03702	0.022000	0.10575	-0.476000	0.06591	-0.655000	0.05387	-1.616000	0.00795	GGC	.	.	none		0.522	MUC17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347161.1	NM_001040105	
PKHD1L1	93035	hgsc.bcm.edu	37	8	110510964	110510964	+	Missense_Mutation	SNP	A	A	C	rs191412861	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	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	149.0	0.0	0		217.0	73.0	0.336406	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	
PADI2	11240	hgsc.bcm.edu	37	1	17410253	17410253	+	Nonsense_Mutation	SNP	G	G	A	rs142403504	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr1:17410253G>A	ENST00000375486.4	-	9	1081	c.1018C>T	c.(1018-1020)Cag>Tag	p.Q340*	PADI2_ENST00000375481.1_Nonsense_Mutation_p.Q340*|PADI2_ENST00000444885.2_Nonsense_Mutation_p.Q224*|PADI2_ENST00000466151.1_5'Flank	NM_007365.2	NP_031391.2	Q9Y2J8	PADI2_HUMAN	peptidyl arginine deiminase, type II	340					chromatin-mediated maintenance of transcription (GO:0048096)|histone H3-R26 citrullination (GO:0036413)|intracellular estrogen receptor signaling pathway (GO:0030520)|negative regulation of chemokine-mediated signaling pathway (GO:0070100)|negative regulation of lymphocyte chemotaxis (GO:1901624)|protein citrullination (GO:0018101)|regulation of chromatin disassembly (GO:0010848)|substantia nigra development (GO:0021762)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|transcriptionally active chromatin (GO:0035327)	calcium ion binding (GO:0005509)|estrogen receptor binding (GO:0030331)|protein-arginine deiminase activity (GO:0004668)			breast(1)|central_nervous_system(1)|endometrium(1)|large_intestine(1)|lung(12)|ovary(4)|pancreas(1)|skin(5)|urinary_tract(3)	29		Colorectal(325;3.46e-05)|Breast(348;0.000162)|Lung NSC(340;0.000422)|Renal(390;0.000518)|all_lung(284;0.000546)|Ovarian(437;0.00671)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.00583)|BRCA - Breast invasive adenocarcinoma(304;1.49e-05)|COAD - Colon adenocarcinoma(227;1.54e-05)|Kidney(64;0.000258)|KIRC - Kidney renal clear cell carcinoma(64;0.00348)|STAD - Stomach adenocarcinoma(196;0.0072)|READ - Rectum adenocarcinoma(331;0.0698)|Lung(427;0.201)	L-Citrulline(DB00155)	TTTAGGTACTGGAAGCAGACC	0.522													G|||	4	0.000798722	0.0	0.0	5008	,	,		20901	0.0		0.001	False		,,,				2504	0.0031				p.Q340X		Atlas-SNP	.											.	PADI2	72	.	0			c.C1018T						PASS	.	G	stop/GLN	1,4405	2.1+/-5.4	0,1,2202	140.0	133.0	135.0		1018	5.8	1.0	1	dbSNP_134	135	30,8570	21.0+/-64.5	0,30,4270	yes	stop-gained	PADI2	NM_007365.2		0,31,6472	AA,AG,GG		0.3488,0.0227,0.2384		340/666	17410253	31,12975	2203	4300	6503	SO:0001587	stop_gained	11240	exon9			GGTACTGGAAGCA	AB030176	CCDS177.1	1p35.2-p35.1	2008-02-05			ENSG00000117115	ENSG00000117115	3.5.3.15	"""Peptidyl arginine deiminases"""	18341	protein-coding gene	gene with protein product		607935				2768262	Standard	NM_007365		Approved	KIAA0994, PDI2	uc001baf.3	Q9Y2J8	OTTHUMG00000002295	ENST00000375486.4:c.1018C>T	1.37:g.17410253G>A	ENSP00000364635:p.Gln340*	219.0	0.0	0		121.0	35.0	0.289256	NM_007365	Q96DA7|Q9UPN2	Nonsense_Mutation	SNP	ENST00000375486.4	37	CCDS177.1	1	4.578754578754579E-4	0	0.0	0	0.0	0	0.0	1	0.0013192612137203166	G	38	7.248142	0.98161	2.27E-4	0.003488	ENSG00000117115	ENST00000375486;ENST00000444885;ENST00000375481	.	.	.	5.77	5.77	0.91146	.	0.267496	0.41605	D	0.000847	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.13853	T	0.58	-37.1678	13.5666	0.61822	0.0:0.2539:0.7461:0.0	.	.	.	.	X	340;224;340	.	ENSP00000364630:Q340X	Q	-	1	0	PADI2	17282840	1.000000	0.71417	1.000000	0.80357	0.990000	0.78478	5.120000	0.64685	2.724000	0.93272	0.561000	0.74099	CAG	G|0.998;A|0.002	0.002	strong		0.522	PADI2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000006624.1		
XIRP2	129446	hgsc.bcm.edu	37	2	168115158	168115158	+	Missense_Mutation	SNP	A	A	C			TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr2:168115158A>C	ENST00000409728.1	+	11	2290	c.2201A>C	c.(2200-2202)aAa>aCa	p.K734T	XIRP2_ENST00000409273.1_3'UTR|XIRP2_ENST00000420519.1_Missense_Mutation_p.K734T|XIRP2_ENST00000409605.1_Missense_Mutation_p.K479T|XIRP2_ENST00000409043.1_Missense_Mutation_p.K701T|XIRP2_ENST00000295237.9_3'UTR|XIRP2_ENST00000409756.2_Missense_Mutation_p.K701T|XIRP2_ENST00000409195.1_3'UTR	NM_001199143.1	NP_001186072.1	A4UGR9	XIRP2_HUMAN	xin actin-binding repeat containing 2	0					actin cytoskeleton organization (GO:0030036)|cardiac muscle tissue morphogenesis (GO:0055008)|cell-cell junction organization (GO:0045216)|ventricular septum development (GO:0003281)	cell junction (GO:0030054)|Z disc (GO:0030018)				NS(3)|biliary_tract(2)|breast(5)|cervix(3)|endometrium(16)|haematopoietic_and_lymphoid_tissue(2)|kidney(18)|large_intestine(51)|lung(160)|ovary(7)|pancreas(3)|prostate(11)|skin(14)|stomach(5)|upper_aerodigestive_tract(8)|urinary_tract(7)	315						GAAAATCATAAAGAAAATTTG	0.294																																					p.K734T		Atlas-SNP	.											.	XIRP2	914	.	0			c.A2201C						PASS	.						28.0	27.0	27.0					2																	168115158		1807	4068	5875	SO:0001583	missense	129446	exon11			ATCATAAAGAAAA	AK056582	CCDS42768.1, CCDS42769.1, CCDS56143.1, CCDS56144.1, CCDS56145.1	2q31.1	2013-10-25	2007-06-27	2007-06-27	ENSG00000163092	ENSG00000163092			14303	protein-coding gene	gene with protein product	"""myomaxin"""	609778	"""cardiomyopathy associated 3"""	CMYA3		17046827, 12203715, 15454575	Standard	NM_001079810		Approved		uc002udx.3	A4UGR9	OTTHUMG00000154027	ENST00000409728.1:c.2201A>C	2.37:g.168115158A>C	ENSP00000386619:p.Lys734Thr	88.0	0.0	0		85.0	37.0	0.435294	NM_001199143	A0PJ94|B2BBS0|B2BBS1|B2BBS4|B3KVH0|J3KNB1|Q53R52|Q5MJ67|Q702N7|Q86T36|Q86T38|Q86T46|Q86T51|Q86T53|Q86T55|Q86T79|Q86TB6|Q8N1M9|Q8N3R5|Q8TBV6	Missense_Mutation	SNP	ENST00000409728.1	37	CCDS56143.1	.	.	.	.	.	.	.	.	.	.	A	14.20	2.463028	0.43736	.	.	ENSG00000163092	ENST00000409043;ENST00000409728;ENST00000409756;ENST00000420519;ENST00000409605	D;D;D;D;D	0.82167	-1.54;-1.54;-1.54;-1.54;-1.58	5.61	3.21	0.36854	.	.	.	.	.	D	0.87597	0.6217	.	.	.	0.80722	D	1	D;D	0.67145	0.996;0.996	P;P	0.62298	0.9;0.9	D	0.85431	0.1149	8	0.87932	D	0	.	5.8857	0.18880	0.7743:0.0:0.0791:0.1466	.	701;734	A4UGR9-4;A4UGR9-6	.;.	T	701;734;701;734;479	ENSP00000386454:K701T;ENSP00000386619:K734T;ENSP00000386724:K701T;ENSP00000415541:K734T;ENSP00000386981:K479T	ENSP00000386454:K701T	K	+	2	0	XIRP2	167823404	1.000000	0.71417	0.366000	0.25914	0.381000	0.30169	2.375000	0.44283	0.407000	0.25591	0.418000	0.28097	AAA	.	.	none		0.294	XIRP2-006	NOVEL	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000333552.1	NM_152381	
DMPK	1760	hgsc.bcm.edu	37	19	46273740	46273740	+	3'UTR	SNP	T	T	C			TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr19:46273740T>C	ENST00000291270.4	-	0	2021				DMPK_ENST00000600757.1_Nonstop_Mutation_p.*636W|SIX5_ENST00000560168.1_5'Flank|DMPK_ENST00000458663.2_Nonstop_Mutation_p.*626W|AC074212.6_ENST00000586251.1_RNA|DMPK_ENST00000354227.5_3'UTR|SIX5_ENST00000317578.6_5'Flank|AC074212.5_ENST00000559756.1_RNA|AC074212.5_ENST00000592217.2_RNA|DMPK_ENST00000447742.2_3'UTR|AC074212.6_ENST00000591530.1_RNA|DMPK_ENST00000343373.4_3'UTR|AC074212.6_ENST00000586498.1_RNA|AC074212.6_ENST00000590076.1_RNA	NM_004409.3	NP_004400.4	Q09013	DMPK_HUMAN	dystrophia myotonica-protein kinase						cellular calcium ion homeostasis (GO:0006874)|muscle cell apoptotic process (GO:0010657)|nuclear envelope organization (GO:0006998)|protein phosphorylation (GO:0006468)|regulation of catalytic activity (GO:0050790)|regulation of excitatory postsynaptic membrane potential involved in skeletal muscle contraction (GO:0014853)|regulation of heart contraction (GO:0008016)|regulation of myotube differentiation (GO:0010830)|regulation of skeletal muscle contraction by calcium ion signaling (GO:0014722)|regulation of sodium ion transport (GO:0002028)|regulation of synapse structural plasticity (GO:0051823)	cytosol (GO:0005829)|endoplasmic reticulum membrane (GO:0005789)|integral component of mitochondrial outer membrane (GO:0031307)|nuclear membrane (GO:0031965)|plasma membrane (GO:0005886)|sarcoplasmic reticulum membrane (GO:0033017)	ATP binding (GO:0005524)|metal ion binding (GO:0046872)|myosin phosphatase regulator activity (GO:0017020)|protein serine/threonine kinase activity (GO:0004674)			endometrium(5)|kidney(1)|large_intestine(1)|lung(6)|stomach(1)|urinary_tract(2)	16		Ovarian(192;0.0308)|all_neural(266;0.112)		OV - Ovarian serous cystadenocarcinoma(262;0.00616)|GBM - Glioblastoma multiforme(486;0.0825)|Epithelial(262;0.24)		AAGACAGTTCTAGGGTTCAGG	0.716											OREG0025561	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.X626W	Esophageal Squamous(35;307 869 9153 24033 28903)	Atlas-SNP	.											.	DMPK	74	.	0			c.A1877G						PASS	.						7.0	8.0	8.0					19																	46273740		1840	3549	5389	SO:0001624	3_prime_UTR_variant	1760	exon15			CAGTTCTAGGGTT	L19268	CCDS12674.1, CCDS46117.1, CCDS46118.1, CCDS46119.1, CCDS74400.1	19q13.3	2014-02-05					2.7.11.1		2933	protein-coding gene	gene with protein product	"""dystrophia myotonica 1"", ""DM protein kinase"", ""myotonin protein kinase A"", ""myotonic dystrophy associated protein kinase"", ""thymopoietin homolog"""	605377	"""dystrophia myotonica 1 (includes dystrophia myotonia protein kinase)"""	DM1, DM		1546325, 1546326	Standard	NM_001288765		Approved	DMK, DM1PK, MDPK, MT-PK	uc002pdf.1	Q09013		ENST00000291270.4:c.*6A>G	19.37:g.46273740T>C		157.0	0.0	0	938	95.0	45.0	0.473684	NM_001081562	E5KR08|Q16205|Q6P5Z6	Missense_Mutation	SNP	ENST00000291270.4	37	CCDS12674.1	.	.	.	.	.	.	.	.	.	.	t	17.91	3.504333	0.64410	.	.	ENSG00000104936	ENST00000458663	.	.	.	4.05	4.05	0.47172	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	9.3258	0.37993	0.0:0.0:0.0:1.0	.	.	.	.	W	626	.	.	X	-	2	0	DMPK	50965580	1.000000	0.71417	0.967000	0.41034	0.514000	0.34195	1.865000	0.39479	1.712000	0.51347	0.454000	0.30748	TAG	.	.	none		0.716	DMPK-004	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000460572.1	NM_004409	
CACNA2D1	781	hgsc.bcm.edu	37	7	81635083	81635083	+	Missense_Mutation	SNP	T	T	C			TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr7:81635083T>C	ENST00000356253.5	-	17	1768	c.1513A>G	c.(1513-1515)Aca>Gca	p.T505A	CACNA2D1_ENST00000356860.3_Missense_Mutation_p.T505A|CACNA2D1_ENST00000464354.1_5'UTR			P54289	CA2D1_HUMAN	calcium channel, voltage-dependent, alpha 2/delta subunit 1	505	Cache.				calcium ion transport (GO:0006816)|regulation of calcium ion transport (GO:0051924)	extracellular vesicular exosome (GO:0070062)|sarcoplasmic reticulum (GO:0016529)|T-tubule (GO:0030315)|voltage-gated calcium channel complex (GO:0005891)	metal ion binding (GO:0046872)|voltage-gated calcium channel activity (GO:0005245)			breast(2)|cervix(1)|endometrium(1)|kidney(2)|large_intestine(15)|liver(1)|lung(42)|ovary(6)|pancreas(1)|prostate(2)|skin(4)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	81					Amlodipine(DB00381)|Cyclandelate(DB04838)|Felodipine(DB01023)|Gabapentin(DB00996)|Ibutilide(DB00308)|Isradipine(DB00270)|Magnesium Sulfate(DB00653)|Nicardipine(DB00622)|Nifedipine(DB01115)|Nilvadipine(DB06712)|Nisoldipine(DB00401)|Nitrendipine(DB01054)|Spironolactone(DB00421)	CATCTTACTGTAAAACGTGGT	0.358																																					p.T505A		Atlas-SNP	.											.	CACNA2D1	191	.	0			c.A1513G						PASS	.						123.0	117.0	119.0					7																	81635083		2203	4299	6502	SO:0001583	missense	781	exon17			TTACTGTAAAACG	M76559	CCDS5598.1	7q21-q22	2014-09-17			ENSG00000153956	ENSG00000153956		"""Calcium channel subunits"""	1399	protein-coding gene	gene with protein product		114204	"""long intergenic non-protein coding RNA 1112"""	CACNL2A, CACNA2, MHS3, LINC01112		8188232	Standard	XM_005250570		Approved	lncRNA-N3	uc003uhr.1	P54289	OTTHUMG00000023622	ENST00000356253.5:c.1513A>G	7.37:g.81635083T>C	ENSP00000348589:p.Thr505Ala	380.0	0.0	0		475.0	107.0	0.225263	NM_000722	Q17R45|Q9UD80|Q9UD81|Q9UD82	Missense_Mutation	SNP	ENST00000356253.5	37		.	.	.	.	.	.	.	.	.	.	T	17.74	3.464121	0.63513	.	.	ENSG00000153956	ENST00000356860;ENST00000284088;ENST00000356253	T;T	0.06608	3.28;3.28	5.38	5.38	0.77491	.	0.000000	0.85682	D	0.000000	T	0.10165	0.0249	L	0.58669	1.825	0.80722	D	1	B	0.19445	0.036	B	0.20384	0.029	T	0.02885	-1.1098	10	0.56958	D	0.05	-20.1301	15.0578	0.71927	0.0:0.0:0.0:1.0	.	505	P54289-2	.	A	505	ENSP00000349320:T505A;ENSP00000348589:T505A	ENSP00000284088:T505A	T	-	1	0	CACNA2D1	81473019	1.000000	0.71417	1.000000	0.80357	0.963000	0.63663	7.672000	0.83956	2.040000	0.60383	0.482000	0.46254	ACA	.	.	none		0.358	CACNA2D1-201	KNOWN	basic	protein_coding	protein_coding			
MXRA5	25878	hgsc.bcm.edu	37	X	3248333	3248333	+	Silent	SNP	T	T	C	rs372395776		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chrX:3248333T>C	ENST00000217939.6	-	4	589	c.435A>G	c.(433-435)caA>caG	p.Q145Q		NM_015419.3	NP_056234.2	Q9NR99	MXRA5_HUMAN	matrix-remodelling associated 5	145						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)				CGTTGAAAGCTTGAGGGTGGA	0.488																																					p.Q145Q		Atlas-SNP	.											.	MXRA5	815	.	0			c.A435G						PASS	.	T		1,3834		0,0,1,1632,570	118.0	96.0	103.0		435	-7.1	0.0	X		103	1,6727		0,0,1,2428,1871	no	coding-synonymous	MXRA5	NM_015419.3		0,0,2,4060,2441	CC,CT,C,TT,T		0.0149,0.0261,0.0189		145/2829	3248333	2,10561	2203	4300	6503	SO:0001819	synonymous_variant	25878	exon4			GAAAGCTTGAGGG	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.435A>G	X.37:g.3248333T>C		397.0	2.0	0.00503778		176.0	171.0	0.971591	NM_015419	Q6P1M7|Q9Y3Y8	Silent	SNP	ENST00000217939.6	37	CCDS14124.1																																																																																			.	.	weak		0.488	MXRA5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055655.2	NM_015419	
PDE8A	5151	hgsc.bcm.edu	37	15	85610349	85610349	+	Silent	SNP	C	C	T	rs35666574	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr15:85610349C>T	ENST00000310298.4	+	4	600	c.348C>T	c.(346-348)gtC>gtT	p.V116V	PDE8A_ENST00000557957.1_Silent_p.V44V|PDE8A_ENST00000394553.1_Silent_p.V116V|PDE8A_ENST00000557819.2_3'UTR|PDE8A_ENST00000339708.5_Silent_p.V116V			O60658	PDE8A_HUMAN	phosphodiesterase 8A	116					cAMP catabolic process (GO:0006198)|cyclic nucleotide metabolic process (GO:0009187)|phosphorelay signal transduction system (GO:0000160)|regulation of transcription, DNA-templated (GO:0006355)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)	3',5'-cyclic-AMP phosphodiesterase activity (GO:0004115)|3',5'-cyclic-nucleotide phosphodiesterase activity (GO:0004114)|metal ion binding (GO:0046872)|signal transducer activity (GO:0004871)			NS(1)|central_nervous_system(1)|endometrium(2)|kidney(3)|large_intestine(4)|lung(8)|ovary(2)|pancreas(1)|prostate(1)|skin(2)	25	Colorectal(223;0.227)		BRCA - Breast invasive adenocarcinoma(143;0.0608)		Caffeine(DB00201)|Ketotifen(DB00920)	CTCAGGCTGTCCTTGCCTGTT	0.448													C|||	64	0.0127796	0.0098	0.0058	5008	,	,		19685	0.0		0.0408	False		,,,				2504	0.0061				p.V116V		Atlas-SNP	.											.	PDE8A	50	.	0			c.C348T						PASS	.	C	,	60,4346	58.1+/-94.6	0,60,2143	164.0	138.0	147.0		348,348	0.2	1.0	15	dbSNP_126	147	280,8318	105.6+/-166.5	7,266,4026	no	coding-synonymous,coding-synonymous	PDE8A	NM_002605.2,NM_173454.1	,	7,326,6169	TT,TC,CC		3.2566,1.3618,2.6146	,	116/830,116/784	85610349	340,12664	2203	4299	6502	SO:0001819	synonymous_variant	5151	exon3			GGCTGTCCTTGCC	AF056490	CCDS10336.1, CCDS10337.1, CCDS58397.1	15q25.3	2008-05-14			ENSG00000073417	ENSG00000073417	3.1.4.17	"""Phosphodiesterases"""	8793	protein-coding gene	gene with protein product		602972				9618252	Standard	NM_001243137		Approved	HsT19550	uc002blh.3	O60658	OTTHUMG00000148670	ENST00000310298.4:c.348C>T	15.37:g.85610349C>T		105.0	0.0	0		73.0	62.0	0.849315	NM_173454	B3KXE6|H0YMZ7|Q6P9H3|Q969I1|Q96PC9|Q96PD0|Q96PD1|Q96T71|Q9UMB7|Q9UMC3	Silent	SNP	ENST00000310298.4	37	CCDS10336.1																																																																																			C|0.976;T|0.024	0.024	strong		0.448	PDE8A-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000309018.1	NM_002605	
MUC17	140453	hgsc.bcm.edu	37	7	100678988	100678988	+	Missense_Mutation	SNP	G	G	A	rs71286276		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr7:100678988G>A	ENST00000306151.4	+	3	4355	c.4291G>A	c.(4291-4293)Gct>Act	p.A1431T		NM_001040105.1	NP_001035194.1	Q685J3	MUC17_HUMAN	mucin 17, cell surface associated	1431	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)	p.A1431T(1)		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)					GACCACTTCTGCTGAAGCCAC	0.488																																					p.A1431T		Atlas-SNP	.											MUC17,NS,carcinoma,0,2	MUC17	804	2	1	Substitution - Missense(1)	kidney(1)	c.G4291A						scavenged	.						207.0	222.0	217.0					7																	100678988		2203	4300	6503	SO:0001583	missense	140453	exon3			ACTTCTGCTGAAG	AJ606307	CCDS34711.1	7q22	2007-01-17	2006-03-14		ENSG00000169876	ENSG00000169876		"""Mucins"""	16800	protein-coding gene	gene with protein product		608424				11855812	Standard	NM_001040105		Approved		uc003uxp.1	Q685J3	OTTHUMG00000157030	ENST00000306151.4:c.4291G>A	7.37:g.100678988G>A	ENSP00000302716:p.Ala1431Thr	120.0	0.0	0		205.0	12.0	0.0585366	NM_001040105	O14761|Q685J2|Q8TDH7	Missense_Mutation	SNP	ENST00000306151.4	37	CCDS34711.1	.	.	.	.	.	.	.	.	.	.	a	3.722	-0.057377	0.07317	.	.	ENSG00000169876	ENST00000306151	T	0.02656	4.21	0.982	-0.425	0.12317	.	.	.	.	.	T	0.01558	0.0050	N	0.19112	0.55	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.48779	-0.9005	9	0.02654	T	1	.	4.4511	0.11621	0.488:0.0:0.512:0.0	.	1431	Q685J3	MUC17_HUMAN	T	1431	ENSP00000302716:A1431T	ENSP00000302716:A1431T	A	+	1	0	MUC17	100465708	0.000000	0.05858	0.001000	0.08648	0.001000	0.01503	-2.968000	0.00669	-0.790000	0.04492	-1.616000	0.00795	GCT	.	.	none		0.488	MUC17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347161.1	NM_001040105	
MTX3	345778	hgsc.bcm.edu	37	5	79286042	79286042	+	Missense_Mutation	SNP	T	T	A	rs371364933		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr5:79286042T>A	ENST00000512528.1	-	3	189	c.169A>T	c.(169-171)Aca>Tca	p.T57S	MTX3_ENST00000512560.1_5'UTR|MTX3_ENST00000509852.1_Missense_Mutation_p.T57S			Q5HYI7	MTX3_HUMAN	metaxin 3	57					protein targeting to mitochondrion (GO:0006626)	mitochondrial outer membrane (GO:0005741)				endometrium(1)|large_intestine(3)|lung(2)|urinary_tract(1)	7		Lung NSC(167;0.00428)|all_lung(232;0.00455)|Ovarian(174;0.0261)		OV - Ovarian serous cystadenocarcinoma(54;1.63e-45)|Epithelial(54;2.9e-40)|all cancers(79;4.68e-35)		TCTTCAGTTGTCAAAATTGGT	0.358																																					p.T57S		Atlas-SNP	.											.	MTX3	29	.	0			c.A169T						PASS	.	T	SER/THR,	0,3672		0,0,1836	86.0	78.0	81.0		169,	4.7	1.0	5		81	2,8158		0,2,4078	no	missense,utr-5	MTX3	NM_001010891.4,NM_001167741.1	58,	0,2,5914	AA,AT,TT		0.0245,0.0,0.0169	benign,	57/249,	79286042	2,11830	1836	4080	5916	SO:0001583	missense	345778	exon3			CAGTTGTCAAAAT	BX538064	CCDS47239.1, CCDS47239.2, CCDS54872.1	5q14.1	2004-08-18				ENSG00000177034			24812	protein-coding gene	gene with protein product						15087125	Standard	NM_001010891		Approved		uc010jah.3	Q5HYI7		ENST00000512528.1:c.169A>T	5.37:g.79286042T>A	ENSP00000424798:p.Thr57Ser	380.0	0.0	0		349.0	162.0	0.464183	NM_001010891	B4DL65|E9PB57|Q7Z380|Q8NB92	Missense_Mutation	SNP	ENST00000512528.1	37		.	.	.	.	.	.	.	.	.	.	T	8.983	0.975725	0.18736	0.0	2.45E-4	ENSG00000177034	ENST00000328496;ENST00000509852;ENST00000512528;ENST00000418095	T;T	0.42513	0.97;0.97	5.86	4.69	0.59074	.	0.541563	0.21589	N	0.072127	T	0.30885	0.0779	L	0.35644	1.08	0.28755	N	0.901208	B;B	0.10296	0.003;0.001	B;B	0.09377	0.002;0.004	T	0.18116	-1.0347	10	0.33141	T	0.24	-2.1085	8.1501	0.31134	0.1203:0.0663:0.0:0.8134	.	57;57	Q5HYI7-4;Q5HYI7	.;MTX3_HUMAN	S	57	ENSP00000423302:T57S;ENSP00000424798:T57S	ENSP00000331672:T57S	T	-	1	0	MTX3	79321798	1.000000	0.71417	1.000000	0.80357	0.987000	0.75469	1.676000	0.37565	1.036000	0.39998	-0.290000	0.09829	ACA	.	.	weak		0.358	MTX3-005	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000372567.1	XM_293971	
CHTF18	63922	hgsc.bcm.edu	37	16	841238	841238	+	Silent	SNP	G	G	A	rs151271197	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr16:841238G>A	ENST00000262315.9	+	8	1035	c.972G>A	c.(970-972)aaG>aaA	p.K324K	RPUSD1_ENST00000007264.2_5'Flank|RPUSD1_ENST00000567114.1_5'Flank|CHTF18_ENST00000455171.2_Silent_p.K352K|RPUSD1_ENST00000565809.1_5'Flank|CHTF18_ENST00000317063.6_Silent_p.K519K|CHTF18_ENST00000491530.1_3'UTR	NM_022092.2	NP_071375.1	Q8WVB6	CTF18_HUMAN	CTF18, chromosome transmission fidelity factor 18 homolog (S. cerevisiae)	324					cell cycle (GO:0007049)|DNA replication (GO:0006260)	cytoplasm (GO:0005737)|membrane (GO:0016020)|nucleus (GO:0005634)	ATP binding (GO:0005524)|DNA binding (GO:0003677)			endometrium(1)|kidney(3)|liver(2)|lung(4)|prostate(1)	11		Hepatocellular(780;0.00335)				CTTCCCGGAAGCCCAGGCCCA	0.642													G|||	27	0.00539137	0.0	0.0058	5008	,	,		18196	0.0		0.008	False		,,,				2504	0.0153				p.K324K		Atlas-SNP	.											.	CHTF18	52	.	0			c.G972A						PASS	.	G		5,4119		0,5,2057	19.0	24.0	22.0		972	1.3	1.0	16	dbSNP_134	22	86,8280		1,84,4098	no	coding-synonymous	CHTF18	NM_022092.2		1,89,6155	AA,AG,GG		1.028,0.1212,0.7286		324/976	841238	91,12399	2062	4183	6245	SO:0001819	synonymous_variant	63922	exon8			CCGGAAGCCCAGG	BC018184	CCDS45371.1	16p13.3	2010-04-21	2003-12-09		ENSG00000127586	ENSG00000127586		"""ATPases / AAA-type"""	18435	protein-coding gene	gene with protein product		613201	"""chromosome 16 open reading frame 41"""	C16orf41		12171929	Standard	NM_022092		Approved	CHL12, C321D2.4, Ctf18	uc002cke.4	Q8WVB6	OTTHUMG00000047838	ENST00000262315.9:c.972G>A	16.37:g.841238G>A		76.0	0.0	0		79.0	41.0	0.518987	NM_022092	B7ZBA2|D3DU68|Q7Z6Y4|Q7Z6Y6|Q9BR83|Q9BRG5|Q9H7K3	Silent	SNP	ENST00000262315.9	37	CCDS45371.1	10	0.004578754578754579	0	0.0	3	0.008287292817679558	0	0.0	7	0.009234828496042216	G	1.548	-0.540090	0.04053	0.001212	0.01028	ENSG00000127586	ENST00000426047	.	.	.	4.85	1.28	0.21552	.	.	.	.	.	T	0.43787	0.1263	.	.	.	0.41571	D	0.988681	.	.	.	.	.	.	T	0.36768	-0.9734	4	.	.	.	-39.2725	5.5091	0.16870	0.4904:0.0:0.5096:0.0	.	.	.	.	T	220	.	.	A	+	1	0	CHTF18	781239	0.890000	0.30428	0.994000	0.49952	0.848000	0.48234	0.510000	0.22723	0.579000	0.29504	0.579000	0.79373	GCC	G|0.995;A|0.005	0.005	strong		0.642	CHTF18-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000109061.3	NM_022092	
TREML4	285852	hgsc.bcm.edu	37	6	41196169	41196169	+	Missense_Mutation	SNP	G	G	T	rs112680060	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr6:41196169G>T	ENST00000341495.2	+	1	108	c.4G>T	c.(4-6)Gcc>Tcc	p.A2S	TREML4_ENST00000448827.2_Missense_Mutation_p.A2S	NM_198153.2	NP_937796.1	Q6UXN2	TRML4_HUMAN	triggering receptor expressed on myeloid cells-like 4	2						extracellular region (GO:0005576)				breast(1)|endometrium(1)|large_intestine(1)|lung(4)|skin(1)	8	Ovarian(28;0.0327)|Colorectal(47;0.196)					GGCTGGAATGGCCTGGGGTGG	0.607													G|||	141	0.028155	0.0	0.0159	5008	,	,		17102	0.006		0.0129	False		,,,				2504	0.1135				p.A2S		Atlas-SNP	.											.	TREML4	25	.	0			c.G4T						PASS	.	G	SER/ALA	7,4399		0,7,2196	37.0	37.0	37.0		4	2.0	0.3	6	dbSNP_132	37	57,8543		0,57,4243	yes	missense	TREML4	NM_198153.2	99	0,64,6439	TT,TG,GG		0.6628,0.1589,0.4921	possibly-damaging	2/201	41196169	64,12942	2203	4300	6503	SO:0001583	missense	285852	exon1			GGAATGGCCTGGG	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.4G>T	6.37:g.41196169G>T	ENSP00000342570:p.Ala2Ser	75.0	0.0	0		85.0	46.0	0.541176	NM_198153	B7ZL92	Missense_Mutation	SNP	ENST00000341495.2	37	CCDS34446.1	16	0.007326007326007326	0	0.0	6	0.016574585635359115	0	0.0	10	0.013192612137203167	.	12.79	2.044341	0.36085	0.001589	0.006628	ENSG00000188056	ENST00000341495;ENST00000445267;ENST00000448827	T;T	0.09445	2.98;2.98	3.94	2.05	0.26809	.	.	.	.	.	T	0.05273	0.0140	N	0.14661	0.345	0.09310	N	1	D	0.76494	0.999	D	0.63381	0.914	T	0.22800	-1.0206	9	0.72032	D	0.01	-18.3792	4.7235	0.12929	0.1155:0.0:0.6718:0.2127	.	2	Q6UXN2	TRML4_HUMAN	S	2	ENSP00000342570:A2S;ENSP00000418078:A2S	ENSP00000342570:A2S	A	+	1	0	TREML4	41304147	0.595000	0.26857	0.269000	0.24586	0.017000	0.09413	0.825000	0.27393	0.395000	0.25257	0.591000	0.81541	GCC	G|0.995;T|0.005	0.005	strong		0.607	TREML4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000043873.2		
SPACA3	124912	hgsc.bcm.edu	37	17	31322691	31322691	+	Missense_Mutation	SNP	A	A	G	rs28963	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr17:31322691A>G	ENST00000269053.3	+	2	369	c.299A>G	c.(298-300)cAt>cGt	p.H100R	SPACA3_ENST00000394637.2_3'UTR|SPACA3_ENST00000580599.1_Missense_Mutation_p.H31R|SPACA3_ENST00000394638.1_Intron	NM_173847.3	NP_776246.1	Q8IXA5	SACA3_HUMAN	sperm acrosome associated 3	100			H -> R (in dbSNP:rs28963).		cell wall macromolecule catabolic process (GO:0016998)|defense response to Gram-positive bacterium (GO:0050830)|monocyte activation (GO:0042117)|peptidoglycan catabolic process (GO:0009253)|positive regulation of macrophage activation (GO:0043032)|positive regulation of phagocytosis (GO:0050766)|response to virus (GO:0009615)|sperm-egg recognition (GO:0035036)	acrosomal vesicle (GO:0001669)|extracellular region (GO:0005576)|integral component of membrane (GO:0016021)|lysosome (GO:0005764)|secretory granule (GO:0030141)	lysozyme activity (GO:0003796)			breast(1)|endometrium(1)|large_intestine(3)|lung(10)|ovary(2)|urinary_tract(1)	18			BRCA - Breast invasive adenocarcinoma(9;0.193)			AGAGTGCTACATGACTTCGGG	0.612																																					p.H100R		Atlas-SNP	.											.	SPACA3	35	.	0			c.A299G						PASS	.	A	ARG/HIS	1,4405	2.1+/-5.4	0,1,2202	102.0	67.0	79.0		299	-1.0	0.0	17	dbSNP_76	79	14,8586	10.5+/-38.8	0,14,4286	yes	missense	SPACA3	NM_173847.3	29	0,15,6488	GG,GA,AA		0.1628,0.0227,0.1153	benign	100/216	31322691	15,12991	2203	4300	6503	SO:0001583	missense	124912	exon2			TGCTACATGACTT	AF216311, AF099029	CCDS11275.1	17q12	2014-07-23			ENSG00000141316	ENSG00000141316			16260	protein-coding gene	gene with protein product	"""cancer/testis antigen 54"", ""sperm lyzozyme-like acrosomal protein 1"""	612749				12606493	Standard	NM_173847		Approved	ALLP17, SLLP1, LYC3, LYZL3, CT54	uc002hhs.1	Q8IXA5	OTTHUMG00000132886	ENST00000269053.3:c.299A>G	17.37:g.31322691A>G	ENSP00000269053:p.His100Arg	245.0	0.0	0		203.0	101.0	0.497537	NM_173847	Q7Z4Y5	Missense_Mutation	SNP	ENST00000269053.3	37	CCDS11275.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	a|a	2.934|2.934	-0.220387|-0.220387	0.06061|0.06061	2.27E-4|2.27E-4	0.001628|0.001628	ENSG00000141316|ENSG00000141316	ENST00000269053;ENST00000394637|ENST00000411740	T|.	0.67345|.	-0.26|.	3.82|3.82	-0.968|-0.968	0.10313|0.10313	Lysozyme-like domain (1);|.	0.660523|.	0.13489|.	N|.	0.384114|.	T|T	0.16642|0.16642	0.0400|0.0400	N|N	0.05230|0.05230	-0.09|-0.09	0.09310|0.09310	N|N	1|1	B|.	0.06786|.	0.001|.	B|.	0.08055|.	0.003|.	T|T	0.20739|0.20739	-1.0266|-1.0266	10|6	0.39692|0.87932	T|D	0.17|0	-7.1977|-7.1977	3.9109|3.9109	0.09202|0.09202	0.4882:0.1912:0.3206:0.0|0.4882:0.1912:0.3206:0.0	rs28963;rs52826872;rs28963|rs28963;rs52826872;rs28963	100|.	Q8IXA5|.	SACA3_HUMAN|.	R|V	100;101|1	ENSP00000269053:H100R|.	ENSP00000269053:H100R|ENSP00000392807:M1V	H|M	+|+	2|1	0|0	SPACA3|SPACA3	28346804|28346804	0.026000|0.026000	0.19158|0.19158	0.000000|0.000000	0.03702|0.03702	0.607000|0.607000	0.37147|0.37147	2.419000|2.419000	0.44671|0.44671	-0.692000|-0.692000	0.05128|0.05128	-0.443000|-0.443000	0.05667|0.05667	CAT|ATG	A|0.998;G|0.002	0.002	strong		0.612	SPACA3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256380.1	NM_173847	
CHST13	166012	hgsc.bcm.edu	37	3	126260995	126260995	+	Silent	SNP	C	C	T	rs7614066	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr3:126260995C>T	ENST00000319340.2	+	3	650	c.600C>T	c.(598-600)taC>taT	p.Y200Y		NM_152889.2	NP_690849.1	Q8NET6	CHSTD_HUMAN	carbohydrate (chondroitin 4) sulfotransferase 13	200					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)		AGAGGCGCTACGGTGCACGCA	0.721													C|||	273	0.0545128	0.1248	0.0288	5008	,	,		7896	0.002		0.0258	False		,,,				2504	0.0613				p.Y200Y		Atlas-SNP	.											.	CHST13	21	.	0			c.C600T						PASS	.	C		331,3793		10,311,1741	6.0	7.0	6.0		600	-5.3	0.2	3	dbSNP_116	6	189,7819		2,185,3817	no	coding-synonymous	CHST13	NM_152889.2		12,496,5558	TT,TC,CC		2.3601,8.0262,4.2862		200/342	126260995	520,11612	2062	4004	6066	SO:0001819	synonymous_variant	166012	exon3			GCGCTACGGTGCA	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.600C>T	3.37:g.126260995C>T		16.0	0.0	0		18.0	11.0	0.611111	NM_152889	Q3SYA3|Q3SYA5	Silent	SNP	ENST00000319340.2	37	CCDS3039.1																																																																																			C|0.956;T|0.044	0.044	strong		0.721	CHST13-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000370201.2	NM_152889	
TRIO	7204	hgsc.bcm.edu	37	5	14304588	14304588	+	Missense_Mutation	SNP	T	T	G			TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr5:14304588T>G	ENST00000344204.4	+	8	1411	c.1387T>G	c.(1387-1389)Tca>Gca	p.S463A	TRIO_ENST00000509967.2_Missense_Mutation_p.S414A|TRIO_ENST00000537187.1_Missense_Mutation_p.S463A	NM_007118.2	NP_009049.2	O75962	TRIO_HUMAN	trio Rho guanine nucleotide exchange factor	463					apoptotic signaling pathway (GO:0097190)|axon guidance (GO:0007411)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of apoptotic process (GO:0043065)|positive regulation of GTPase activity (GO:0043547)|regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)|transmembrane receptor protein tyrosine phosphatase signaling pathway (GO:0007185)	cytosol (GO:0005829)	ATP binding (GO:0005524)|guanyl-nucleotide exchange factor activity (GO:0005085)|protein serine/threonine kinase activity (GO:0004674)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)			NS(2)|breast(6)|central_nervous_system(4)|endometrium(16)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(21)|lung(34)|ovary(4)|prostate(2)|skin(11)|stomach(3)|upper_aerodigestive_tract(3)|urinary_tract(4)	118	Lung NSC(4;0.000742)					CAACGTGGATTCATGGTGTAA	0.373																																					p.S463A		Atlas-SNP	.											.	TRIO	305	.	0			c.T1387G						PASS	.						177.0	160.0	166.0					5																	14304588		2203	4300	6503	SO:0001583	missense	7204	exon8			GTGGATTCATGGT	AF091395	CCDS3883.1	5p14-p15.1	2013-01-11	2012-07-12		ENSG00000038382	ENSG00000038382		"""Rho guanine nucleotide exchange factors"", ""Immunoglobulin superfamily / I-set domain containing"""	12303	protein-coding gene	gene with protein product		601893	"""triple functional domain (PTPRF interacting)"""			8643598	Standard	NM_007118		Approved	ARHGEF23	uc003jff.3	O75962	OTTHUMG00000131057	ENST00000344204.4:c.1387T>G	5.37:g.14304588T>G	ENSP00000339299:p.Ser463Ala	151.0	0.0	0		168.0	81.0	0.482143	NM_007118	D3DTD1|Q13458|Q59EQ7|Q6PJC9|Q6ZN05|Q8IWK8	Missense_Mutation	SNP	ENST00000344204.4	37	CCDS3883.1	.	.	.	.	.	.	.	.	.	.	T	12.03	1.816676	0.32145	.	.	ENSG00000038382	ENST00000344204;ENST00000537187;ENST00000509967;ENST00000513206	T;T;T	0.65178	-0.14;-0.11;0.53	5.18	5.18	0.71444	.	0.080894	0.56097	D	0.000034	T	0.43366	0.1244	N	0.12831	0.26	0.48135	D	0.999591	B;B;B	0.22983	0.0;0.078;0.004	B;B;B	0.27380	0.002;0.079;0.001	T	0.35351	-0.9792	10	0.08599	T	0.76	.	15.0541	0.71897	0.0:0.0:0.0:1.0	.	414;463;463	F5H228;O75962-5;O75962	.;.;TRIO_HUMAN	A	463;463;414;150	ENSP00000339299:S463A;ENSP00000446348:S463A;ENSP00000445592:S414A	ENSP00000339299:S463A	S	+	1	0	TRIO	14357588	1.000000	0.71417	0.995000	0.50966	0.971000	0.66376	2.719000	0.47244	1.966000	0.57179	0.528000	0.53228	TCA	.	.	none		0.373	TRIO-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253711.2	NM_007118	
PKD1L2	114780	hgsc.bcm.edu	37	16	81232294	81232294	+	RNA	SNP	T	T	C	rs61734110	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr16:81232294T>C	ENST00000525539.1	-	0	1515				PKD1L2_ENST00000337114.4_RNA	NM_052892.3	NP_443124.3	Q7Z442	PK1L2_HUMAN	polycystic kidney disease 1-like 2						ion transport (GO:0006811)|neuropeptide signaling pathway (GO:0007218)	integral component of membrane (GO:0016021)	calcium ion binding (GO:0005509)|carbohydrate binding (GO:0030246)			breast(2)|central_nervous_system(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(9)|lung(20)|ovary(2)|pancreas(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	44						AGGCGGCAAATCCCAAATGGC	0.582													T|||	154	0.0307508	0.0325	0.0317	5008	,	,		20196	0.004		0.0716	False		,,,				2504	0.0133				p.I506V		Atlas-SNP	.											.	PKD1L2	361	.	0			c.A1516G						PASS	.	T	VAL/ILE,VAL/ILE	168,3844		1,166,1839	51.0	52.0	51.0		1516,1516	2.8	0.5	16	dbSNP_129	51	526,7782		17,492,3645	yes	missense,missense	PKD1L2	NM_001076780.1,NM_052892.3	29,29	18,658,5484	CC,CT,TT		6.3312,4.1874,5.6331	benign,benign	506/992,506/2460	81232294	694,11626	2006	4154	6160			114780	exon7			GGCAAATCCCAAA	AY164483	CCDS61998.1, CCDS61999.1	16q23.2	2014-09-11			ENSG00000166473	ENSG00000166473			21715	protein-coding gene	gene with protein product		607894				12782129	Standard	NM_052892		Approved	KIAA1879	uc002fgf.1	Q7Z442	OTTHUMG00000166126		16.37:g.81232294T>C		122.0	0.0	0		109.0	88.0	0.807339	NM_001076780	Q6UEE1|Q6ZN46|Q6ZSP2|Q8N1H9|Q96CL2|Q96Q08	Missense_Mutation	SNP	ENST00000525539.1	37		85|85	0.03891941391941392|0.03891941391941392	17|17	0.034552845528455285|0.034552845528455285	16|16	0.04419889502762431|0.04419889502762431	1|1	0.0017482517482517483|0.0017482517482517483	51|51	0.06728232189973615|0.06728232189973615	T|T	0.006|0.006	-2.058861|-2.058861	0.00390|0.00390	0.041874|0.041874	0.063312|0.063312	ENSG00000166473|ENSG00000166473	ENST00000526632|ENST00000337114	.|T	.|0.01279	.|5.06	5.08|5.08	2.75|2.75	0.32379|0.32379	.|Egg jelly receptor, REJ-like (1);	.|1.001100	.|0.08058	.|N	.|0.997623	T|T	0.00144|0.00144	0.0004|0.0004	.|.	.|.	.|.	0.09310|0.09310	N|N	1|1	.|B;B	.|0.16603	.|0.018;0.006	.|B;B	.|0.17722	.|0.019;0.004	T|T	0.50127|0.50127	-0.8864|-0.8864	4|9	.|0.22706	.|T	.|0.39	-3.0E-4|-3.0E-4	8.8296|8.8296	0.35076|0.35076	0.0:0.2087:0.0:0.7913|0.0:0.2087:0.0:0.7913	.|.	.|506;506	.|Q7Z442-3;Q7Z442	.|.;PK1L2_HUMAN	G|V	33|506	.|ENSP00000337397:I506V	.|ENSP00000337397:I506V	D|I	-|-	2|1	0|0	PKD1L2|PKD1L2	79789795|79789795	0.000000|0.000000	0.05858|0.05858	0.487000|0.487000	0.27428|0.27428	0.041000|0.041000	0.13682|0.13682	0.422000|0.422000	0.21296|0.21296	0.790000|0.790000	0.33803|0.33803	-0.398000|-0.398000	0.06409|0.06409	GAT|ATT	T|0.956;C|0.044	0.044	strong		0.582	PKD1L2-001	KNOWN	non_canonical_polymorphism|basic	polymorphic_pseudogene	polymorphic_pseudogene	OTTHUMT00000387972.2		
RHPN1	114822	hgsc.bcm.edu	37	8	144462841	144462841	+	Silent	SNP	G	G	A	rs117282246	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr8:144462841G>A	ENST00000289013.6	+	11	1400	c.1299G>A	c.(1297-1299)gtG>gtA	p.V433V		NM_052924.2	NP_443156.2	Q8TCX5	RHPN1_HUMAN	rhophilin, Rho GTPase binding protein 1	458	BRO1. {ECO:0000255|PROSITE- ProRule:PRU00526}.				signal transduction (GO:0007165)		small GTPase regulator activity (GO:0005083)			endometrium(1)|large_intestine(1)|lung(7)	9	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;0.156)			TGCGCGAGGTGGACCTGCTTC	0.687													g|||	20	0.00399361	0.0	0.0	5008	,	,		17518	0.0		0.0129	False		,,,				2504	0.0072				p.V433V		Atlas-SNP	.											.	RHPN1	76	.	0			c.G1299A						PASS	.	G		7,4217		0,7,2105	19.0	23.0	21.0		1299	2.5	0.9	8	dbSNP_132	21	71,8371		0,71,4150	no	coding-synonymous	RHPN1	NM_052924.2		0,78,6255	AA,AG,GG		0.841,0.1657,0.6158		433/671	144462841	78,12588	2112	4221	6333	SO:0001819	synonymous_variant	114822	exon11			CGAGGTGGACCTG	AB067516	CCDS47927.1	8q24.3	2003-02-06			ENSG00000158106	ENSG00000158106			19973	protein-coding gene	gene with protein product		601031				11572484	Standard	NM_052924		Approved	KIAA1929, RHPN, ODF5	uc003yyb.3	Q8TCX5	OTTHUMG00000165006	ENST00000289013.6:c.1299G>A	8.37:g.144462841G>A		233.0	0.0	0		210.0	95.0	0.452381	NM_052924	Q8TAV1|Q96PV9	Silent	SNP	ENST00000289013.6	37	CCDS47927.1																																																																																			G|0.994;A|0.006	0.006	strong		0.687	RHPN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000381417.1		
KAT2A	2648	hgsc.bcm.edu	37	17	40265751	40265751	+	Silent	SNP	C	C	T	rs147642400	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr17:40265751C>T	ENST00000225916.5	-	18	2483	c.2430G>A	c.(2428-2430)ccG>ccA	p.P810P	DHX58_ENST00000251642.3_5'Flank	NM_021078.2	NP_066564.2	Q92830	KAT2A_HUMAN	K(lysine) acetyltransferase 2A	810	Bromo. {ECO:0000255|PROSITE- ProRule:PRU00035}.				cell proliferation (GO:0008283)|chromatin organization (GO:0006325)|chromatin remodeling (GO:0006338)|histone deubiquitination (GO:0016578)|histone H3 acetylation (GO:0043966)|histone H3-K14 acetylation (GO:0044154)|in utero embryonic development (GO:0001701)|metencephalon development (GO:0022037)|midbrain development (GO:0030901)|multicellular organism growth (GO:0035264)|neural tube closure (GO:0001843)|positive regulation of gluconeogenesis (GO:0045722)|regulation of protein stability (GO:0031647)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|somitogenesis (GO:0001756)|telencephalon development (GO:0021537)|transcription from RNA polymerase II promoter (GO:0006366)|viral process (GO:0016032)	Ada2/Gcn5/Ada3 transcription activator complex (GO:0005671)|extracellular space (GO:0005615)|mitotic spindle (GO:0072686)|nucleoplasm (GO:0005654)|STAGA complex (GO:0030914)|transcription factor TFTC complex (GO:0033276)	chromatin binding (GO:0003682)|H3 histone acetyltransferase activity (GO:0010484)|histone acetyltransferase activity (GO:0004402)|histone acetyltransferase activity (H4-K12 specific) (GO:0043997)|histone deacetylase binding (GO:0042826)|transcription coactivator activity (GO:0003713)			central_nervous_system(1)|endometrium(3)|large_intestine(1)|lung(4)|ovary(1)|prostate(3)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	18						ACTCGCTGTCCGGGGGGTTGT	0.612													C|||	7	0.00139776	0.0008	0.0029	5008	,	,		17799	0.0		0.004	False		,,,				2504	0.0				p.P810P		Atlas-SNP	.											.	KAT2A	54	.	0			c.G2430A						PASS	.	C		1,4405	2.1+/-5.4	0,1,2202	34.0	35.0	34.0		2430	-10.1	0.6	17	dbSNP_134	34	54,8546	32.3+/-84.9	0,54,4246	no	coding-synonymous	KAT2A	NM_021078.2		0,55,6448	TT,TC,CC		0.6279,0.0227,0.4229		810/838	40265751	55,12951	2203	4300	6503	SO:0001819	synonymous_variant	2648	exon18			GCTGTCCGGGGGG	AF029777	CCDS11417.1	17q12-q21	2011-07-01	2008-07-04	2008-07-04	ENSG00000108773	ENSG00000108773		"""Chromatin-modifying enzymes / K-acetyltransferases"""	4201	protein-coding gene	gene with protein product		602301	"""GCN5 general control of amino-acid synthesis 5-like 2 (yeast)"""	GCN5L2		8552087	Standard	NM_021078		Approved	GCN5, PCAF-b	uc002hyx.2	Q92830	OTTHUMG00000133504	ENST00000225916.5:c.2430G>A	17.37:g.40265751C>T		35.0	0.0	0		54.0	15.0	0.277778	NM_021078	Q8N1A2|Q9UCW1	Silent	SNP	ENST00000225916.5	37	CCDS11417.1																																																																																			C|0.998;T|0.002	0.002	strong		0.612	KAT2A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257458.1	NM_021078	
CSF3R	1441	hgsc.bcm.edu	37	1	36937106	36937106	+	Missense_Mutation	SNP	C	C	T	rs3918019	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr1:36937106C>T	ENST00000373106.1	-	10	1760	c.1213G>A	c.(1213-1215)Gag>Aag	p.E405K	CSF3R_ENST00000373103.1_Missense_Mutation_p.E405K|CSF3R_ENST00000331941.5_Missense_Mutation_p.E405K|CSF3R_ENST00000418048.2_Missense_Mutation_p.E405K|CSF3R_ENST00000338937.5_Missense_Mutation_p.E405K|CSF3R_ENST00000373104.1_Missense_Mutation_p.E405K|CSF3R_ENST00000487540.2_5'UTR|CSF3R_ENST00000361632.4_Missense_Mutation_p.E405K|CSF3R_ENST00000440588.2_Missense_Mutation_p.E405K	NM_000760.3	NP_000751.1	Q99062	CSF3R_HUMAN	colony stimulating factor 3 receptor (granulocyte)	405	Fibronectin type-III 3. {ECO:0000255|PROSITE-ProRule:PRU00316}.		E -> K (in dbSNP:rs3918019). {ECO:0000269|Ref.4}.		cell adhesion (GO:0007155)|defense response (GO:0006952)|neutrophil chemotaxis (GO:0030593)|odontogenesis of dentin-containing tooth (GO:0042475)|signal transduction (GO:0007165)	extracellular region (GO:0005576)|integral component of plasma membrane (GO:0005887)	cytokine receptor activity (GO:0004896)|receptor activity (GO:0004872)			central_nervous_system(3)|endometrium(2)|kidney(3)|large_intestine(9)|lung(16)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	38		Myeloproliferative disorder(586;0.0255)|all_neural(195;0.164)			Filgrastim(DB00099)|Pegfilgrastim(DB00019)	AGGGCCACCTCCTGGGCTTCT	0.612													C|||	8	0.00159744	0.0	0.0014	5008	,	,		17751	0.0		0.007	False		,,,				2504	0.0				p.E405K		Atlas-SNP	.											.	CSF3R	157	.	0			c.G1213A						PASS	.	C	LYS/GLU,LYS/GLU,LYS/GLU	3,4403	6.2+/-15.9	0,3,2200	103.0	111.0	108.0		1213,1213,1213	3.3	0.9	1	dbSNP_108	108	37,8563	25.7+/-73.6	1,35,4264	yes	missense,missense,missense	CSF3R	NM_000760.3,NM_156039.3,NM_172313.2	56,56,56	1,38,6464	TT,TC,CC		0.4302,0.0681,0.3076	possibly-damaging,possibly-damaging,possibly-damaging	405/837,405/864,405/784	36937106	40,12966	2203	4300	6503	SO:0001583	missense	1441	exon10			CCACCTCCTGGGC	M59820	CCDS412.1, CCDS413.1, CCDS414.1	1p35-p34.3	2014-09-17			ENSG00000119535	ENSG00000119535		"""CD molecules"", ""Fibronectin type III domain containing"""	2439	protein-coding gene	gene with protein product		138971		CD114		1371413	Standard	NM_000760		Approved	GCSFR	uc001cax.2	Q99062	OTTHUMG00000008010	ENST00000373106.1:c.1213G>A	1.37:g.36937106C>T	ENSP00000362198:p.Glu405Lys	105.0	0.0	0		73.0	50.0	0.684932	NM_156039		Missense_Mutation	SNP	ENST00000373106.1	37	CCDS413.1	7	0.003205128205128205	0	0.0	1	0.0027624309392265192	0	0.0	6	0.0079155672823219	C	15.35	2.808248	0.50421	6.81E-4	0.004302	ENSG00000119535	ENST00000373106;ENST00000373104;ENST00000373103;ENST00000361632;ENST00000331941;ENST00000418048;ENST00000338937;ENST00000440588	T;T;T;T;T;T;T;T	0.18338	2.22;2.22;2.22;2.22;2.22;2.22;2.22;2.22	5.2	3.3	0.37823	Fibronectin, type III (3);Immunoglobulin-like fold (1);	0.580572	0.20168	N	0.097787	T	0.05686	0.0149	L	0.33485	1.01	0.25352	N	0.988858	P;P;P;B	0.48764	0.915;0.902;0.651;0.028	B;B;B;B	0.36092	0.217;0.194;0.057;0.038	T	0.14952	-1.0454	10	0.06236	T	0.91	-11.2121	7.3658	0.26772	0.0:0.7939:0.0:0.2061	rs3918019;rs3918019	405;405;405;405	E1B6W6;Q99062-3;Q99062;Q99062-4	.;.;CSF3R_HUMAN;.	K	405	ENSP00000362198:E405K;ENSP00000362196:E405K;ENSP00000362195:E405K;ENSP00000355406:E405K;ENSP00000332180:E405K;ENSP00000401588:E405K;ENSP00000345013:E405K;ENSP00000397568:E405K	ENSP00000332180:E405K	E	-	1	0	CSF3R	36709693	0.102000	0.21896	0.923000	0.36655	0.788000	0.44548	1.384000	0.34396	0.561000	0.29186	-0.258000	0.10820	GAG	C|0.996;T|0.004	0.004	strong		0.612	CSF3R-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000021997.2	NM_156039	
MYO7A	4647	hgsc.bcm.edu	37	11	76918411	76918411	+	Silent	SNP	A	A	G			TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr11:76918411A>G	ENST00000409709.3	+	42	6092	c.5820A>G	c.(5818-5820)tcA>tcG	p.S1940S	MYO7A_ENST00000605744.1_3'UTR|MYO7A_ENST00000409619.2_Silent_p.S1891S|MYO7A_ENST00000458637.2_Silent_p.S1902S	NM_000260.3	NP_000251.3	Q13402	MYO7A_HUMAN	myosin VIIA	1940	FERM 2. {ECO:0000255|PROSITE- ProRule:PRU00084}.				actin filament-based movement (GO:0030048)|auditory receptor cell stereocilium organization (GO:0060088)|equilibrioception (GO:0050957)|eye photoreceptor cell development (GO:0042462)|intracellular protein transport (GO:0006886)|lysosome organization (GO:0007040)|metabolic process (GO:0008152)|phagolysosome assembly (GO:0001845)|pigment granule transport (GO:0051904)|post-embryonic organ morphogenesis (GO:0048563)|sensory perception of light stimulus (GO:0050953)|sensory perception of sound (GO:0007605)|visual perception (GO:0007601)	apical plasma membrane (GO:0016324)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|lysosomal membrane (GO:0005765)|melanosome (GO:0042470)|myosin VII complex (GO:0031477)|photoreceptor connecting cilium (GO:0032391)|photoreceptor inner segment (GO:0001917)|photoreceptor outer segment (GO:0001750)|stereocilium (GO:0032420)|synapse (GO:0045202)	actin filament binding (GO:0051015)|actin-dependent ATPase activity (GO:0030898)|ADP binding (GO:0043531)|ATP binding (GO:0005524)|calmodulin binding (GO:0005516)|microfilament motor activity (GO:0000146)|spectrin binding (GO:0030507)			NS(2)|breast(2)|central_nervous_system(1)|endometrium(7)|kidney(1)|large_intestine(10)|lung(32)|ovary(4)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	64						TCAAGTCCTCAGAGGGATTCA	0.572																																					p.S1940S		Atlas-SNP	.											.	MYO7A	164	.	0			c.A5820G						PASS	.						40.0	45.0	43.0					11																	76918411		2062	4191	6253	SO:0001819	synonymous_variant	4647	exon42			GTCCTCAGAGGGA	U39226	CCDS53683.1, CCDS53684.1, CCDS53685.1	11q13.5	2013-01-08	2005-09-12		ENSG00000137474	ENSG00000137474		"""A-kinase anchor proteins"", ""Myosins / Myosin superfamily : Class VII"""	7606	protein-coding gene	gene with protein product		276903	"""myosin VIIA (Usher syndrome 1B (autosomal recessive, severe))"""	USH1B, DFNB2, DFNA11		8884266	Standard	NM_000260		Approved	NSRD2	uc001oyb.2	Q13402	OTTHUMG00000152822	ENST00000409709.3:c.5820A>G	11.37:g.76918411A>G		112.0	0.0	0		118.0	72.0	0.610169	NM_000260	B9A011|F8VUN5|P78427|Q13321|Q14785|Q92821|Q92822	Silent	SNP	ENST00000409709.3	37	CCDS53683.1																																																																																			.	.	none		0.572	MYO7A-001	KNOWN	non_canonical_conserved|basic|CCDS	protein_coding	protein_coding	OTTHUMT00000328133.1	NM_000260	
HEATR6	63897	hgsc.bcm.edu	37	17	58156228	58156228	+	Silent	SNP	C	C	T	rs116476597	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr17:58156228C>T	ENST00000184956.6	-	1	64	c.48G>A	c.(46-48)cgG>cgA	p.R16R	CTD-2319I12.2_ENST00000589740.1_lincRNA|HEATR6_ENST00000585712.1_5'UTR|HEATR6_ENST00000585976.1_Silent_p.R16R	NM_022070.4	NP_071353.4	Q6AI08	HEAT6_HUMAN	HEAT repeat containing 6	16							poly(A) RNA binding (GO:0044822)			NS(1)|breast(4)|endometrium(5)|kidney(2)|large_intestine(4)|lung(7)|ovary(2)|pancreas(1)|prostate(4)|skin(10)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	44	all_cancers(5;2.25e-13)|Breast(5;4.84e-25)|all_neural(34;0.0878)|Medulloblastoma(34;0.0922)		BRCA - Breast invasive adenocarcinoma(1;5.93e-19)|Epithelial(12;7.59e-12)|all cancers(12;1.26e-10)			GCGGTGCCTCCCGCGGCTGCA	0.662													C|||	16	0.00319489	0.0	0.0086	5008	,	,		7336	0.0		0.0099	False		,,,				2504	0.0				p.R16R		Atlas-SNP	.											.	HEATR6	98	.	0			c.G48A						PASS	.	C		10,4394		0,10,2192	22.0	20.0	21.0		48	-5.8	0.0	17	dbSNP_132	21	61,8535		0,61,4237	no	coding-synonymous	HEATR6	NM_022070.4		0,71,6429	TT,TC,CC		0.7096,0.2271,0.5462		16/1182	58156228	71,12929	2202	4298	6500	SO:0001819	synonymous_variant	63897	exon1			TGCCTCCCGCGGC	BX640819	CCDS11623.1	17q23.2	2007-05-01				ENSG00000068097			24076	protein-coding gene	gene with protein product	"""amplified in breast cancer 1"""					12755490	Standard	NM_022070		Approved	ABC1, FLJ22087	uc002iyk.1	Q6AI08		ENST00000184956.6:c.48G>A	17.37:g.58156228C>T		93.0	0.0	0		88.0	52.0	0.590909	NM_022070	B3KXP3|Q6MZX1|Q6MZY2|Q8TDM9|Q9H6B3|Q9H6M7	Silent	SNP	ENST00000184956.6	37	CCDS11623.1																																																																																			C|0.996;T|0.004	0.004	strong		0.662	HEATR6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000449165.1	NM_022070	
PALD1	27143	hgsc.bcm.edu	37	10	72291172	72291172	+	Missense_Mutation	SNP	G	G	A	rs61737673	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr10:72291172G>A	ENST00000263563.6	+	5	863	c.595G>A	c.(595-597)Gtc>Atc	p.V199I		NM_014431.2	NP_055246.2	Q9ULE6	PALD_HUMAN	phosphatase domain containing, paladin 1	199						cytosol (GO:0005829)											TGGACCCGGGGTCCGGGTGGA	0.602													G|||	67	0.0133786	0.003	0.0216	5008	,	,		18858	0.0		0.0388	False		,,,				2504	0.0092				p.V199I		Atlas-SNP	.											.	.	.	.	0			c.G595A						PASS	.	G	ILE/VAL	38,4368	41.6+/-74.8	0,38,2165	64.0	58.0	60.0		595	1.1	0.0	10	dbSNP_129	60	276,8324	104.2+/-165.2	3,270,4027	yes	missense	KIAA1274	NM_014431.2	29	3,308,6192	AA,AG,GG		3.2093,0.8625,2.4143	benign	199/857	72291172	314,12692	2203	4300	6503	SO:0001583	missense	27143	exon5			CCCGGGGTCCGGG	AB033100	CCDS31215.1	10q22.2	2012-07-17	2012-07-17	2012-07-17	ENSG00000107719	ENSG00000107719			23530	protein-coding gene	gene with protein product		614656	"""paladin"", ""KIAA1274"""	PALD, KIAA1274			Standard	NM_014431		Approved		uc001jrd.4	Q9ULE6	OTTHUMG00000018411	ENST00000263563.6:c.595G>A	10.37:g.72291172G>A	ENSP00000263563:p.Val199Ile	92.0	0.0	0		54.0	13.0	0.240741	NM_014431	B2RMS1|B9EGC6|Q5JTK7|Q5JTK8	Missense_Mutation	SNP	ENST00000263563.6	37	CCDS31215.1	33	0.01510989010989011	0	0.0	10	0.027624309392265192	0	0.0	23	0.030343007915567283	G	2.180	-0.387703	0.04932	0.008625	0.032093	ENSG00000107719	ENST00000263563;ENST00000373214	T	0.21932	1.98	5.08	1.08	0.20341	.	0.896709	0.09766	N	0.758599	T	0.04588	0.0125	L	0.33753	1.03	0.09310	N	1	B	0.09022	0.002	B	0.11329	0.006	T	0.37033	-0.9723	10	0.18710	T	0.47	-16.1671	6.6817	0.23123	0.2174:0.3405:0.442:0.0	rs61737673	199	Q9ULE6	PALD_HUMAN	I	199	ENSP00000263563:V199I	ENSP00000263563:V199I	V	+	1	0	KIAA1274	71961178	0.013000	0.17824	0.003000	0.11579	0.070000	0.16714	0.778000	0.26732	0.091000	0.17302	0.655000	0.94253	GTC	G|0.979;A|0.021	0.021	strong		0.602	PALD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048515.2	NM_014431	
CSPG4	1464	hgsc.bcm.edu	37	15	75982119	75982119	+	Silent	SNP	G	G	T	rs199778089	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr15:75982119G>T	ENST00000308508.5	-	3	1379	c.1287C>A	c.(1285-1287)acC>acA	p.T429T		NM_001897.4	NP_001888.2	Q6UVK1	CSPG4_HUMAN	chondroitin sulfate proteoglycan 4	429	Globular or compact configuration stabilized by disulfide bonds.|Neurite growth inhibition. {ECO:0000250}.				activation of MAPK activity (GO:0000187)|angiogenesis (GO:0001525)|carbohydrate metabolic process (GO:0005975)|cell proliferation (GO:0008283)|chondroitin sulfate biosynthetic process (GO:0030206)|chondroitin sulfate catabolic process (GO:0030207)|chondroitin sulfate metabolic process (GO:0030204)|dermatan sulfate biosynthetic process (GO:0030208)|glial cell migration (GO:0008347)|glycosaminoglycan metabolic process (GO:0030203)|intracellular signal transduction (GO:0035556)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|small molecule metabolic process (GO:0044281)|tissue remodeling (GO:0048771)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)	cell projection (GO:0042995)|cell surface (GO:0009986)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|Golgi lumen (GO:0005796)|integral component of plasma membrane (GO:0005887)|lysosomal lumen (GO:0043202)	protein kinase binding (GO:0019901)|signal transducer activity (GO:0004871)			breast(1)|cervix(2)|endometrium(5)|kidney(5)|large_intestine(3)|liver(2)|lung(18)|ovary(2)|pancreas(2)|prostate(4)|skin(4)	48						TCAGCAGCTGGGTGAAATTGG	0.642																																					p.T429T		Atlas-SNP	.											CSPG4,NS,neuroblastoma,0,1	CSPG4	175	1	0			c.C1287A						PASS	.						34.0	34.0	34.0					15																	75982119		2197	4291	6488	SO:0001819	synonymous_variant	1464	exon3			CAGCTGGGTGAAA	X96753, AY359468	CCDS10284.1	15q24.2	2010-04-19	2007-02-16		ENSG00000173546	ENSG00000173546		"""Proteoglycans / Cell surface : Other"""	2466	protein-coding gene	gene with protein product	"""melanoma-associated chondroitin sulfate proteoglycan"""	601172	"""chondroitin sulfate proteoglycan 4 (melanoma-associated)"""			8790396, 16407841	Standard	NM_001897		Approved	MCSPG, MEL-CSPG, MSK16, NG2, MCSP, HMW-MAA	uc002baw.3	Q6UVK1	OTTHUMG00000142836	ENST00000308508.5:c.1287C>A	15.37:g.75982119G>T		134.0	0.0	0		88.0	15.0	0.170455	NM_001897	D3DW77|Q92675	Silent	SNP	ENST00000308508.5	37	CCDS10284.1																																																																																			G|0.997;T|0.003	0.003	strong		0.642	CSPG4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000286472.1	NM_001897	
DLEC1	9940	hgsc.bcm.edu	37	3	38125704	38125704	+	Missense_Mutation	SNP	C	C	T			TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr3:38125704C>T	ENST00000308059.6	+	7	1250	c.1229C>T	c.(1228-1230)cCg>cTg	p.P410L	DLEC1_ENST00000346219.3_Missense_Mutation_p.P410L|DLEC1_ENST00000452631.2_Missense_Mutation_p.P410L|DLEC1_ENST00000469151.1_3'UTR					deleted in lung and esophageal cancer 1											NS(1)|breast(3)|central_nervous_system(3)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(9)|lung(14)|ovary(3)|pancreas(3)|prostate(1)|skin(5)|upper_aerodigestive_tract(2)	51				KIRC - Kidney renal clear cell carcinoma(284;0.0664)|Kidney(284;0.0827)		CGAGTCCTCCCGCCTTCCACG	0.453																																					p.P410L		Atlas-SNP	.											.	DLEC1	278	.	0			c.C1229T						PASS	.						110.0	121.0	117.0					3																	38125704		2083	4217	6300	SO:0001583	missense	9940	exon7			TCCTCCCGCCTTC	AB020522	CCDS2672.2	3p21.3	2014-07-31			ENSG00000008226	ENSG00000008226			2899	protein-coding gene	gene with protein product	"""cilia and flagella associated protein 81"""	604050				10213508	Standard	XM_005265630		Approved	DLC1, CFAP81	uc003chp.1	Q9Y238	OTTHUMG00000131085	ENST00000308059.6:c.1229C>T	3.37:g.38125704C>T	ENSP00000308597:p.Pro410Leu	159.0	0.0	0		178.0	89.0	0.5	NM_007337		Missense_Mutation	SNP	ENST00000308059.6	37	CCDS2672.2	.	.	.	.	.	.	.	.	.	.	c	23.3	4.394599	0.83011	.	.	ENSG00000008226	ENST00000308059;ENST00000346219;ENST00000452631	T;T;T	0.08984	3.03;3.05;3.27	5.4	5.4	0.78164	.	0.060013	0.64402	D	0.000002	T	0.32882	0.0844	M	0.80422	2.495	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;0.999	T	0.03545	-1.1026	10	0.56958	D	0.05	-17.7606	17.9203	0.88964	0.0:1.0:0.0:0.0	.	410;410;410;410	A1L305;F8W6T4;Q9Y238-3;Q9Y238	.;.;.;DLEC1_HUMAN	L	410	ENSP00000308597:P410L;ENSP00000315914:P410L;ENSP00000410427:P410L	ENSP00000308597:P410L	P	+	2	0	DLEC1	38100708	0.999000	0.42202	0.891000	0.34965	0.768000	0.43524	5.469000	0.66749	2.532000	0.85374	0.524000	0.50904	CCG	.	.	none		0.453	DLEC1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000253745.3	NM_007337	
CDH19	28513	hgsc.bcm.edu	37	18	64172434	64172434	+	Missense_Mutation	SNP	C	C	G	rs55874520	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr18:64172434C>G	ENST00000262150.2	-	12	2226	c.1934G>C	c.(1933-1935)gGg>gCg	p.G645A	CDH19_ENST00000540086.1_3'UTR	NM_021153.3	NP_066976.1	Q96JQ0	PCD16_HUMAN	cadherin 19, type 2	0	Cadherin 6. {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)				TTCTCCACCCCCTTCATCATC	0.403													c|||	35	0.00698882	0.0015	0.0101	5008	,	,		14403	0.0		0.0258	False		,,,				2504	0.0				p.G645A		Atlas-SNP	.											.	CDH19	141	.	0			c.G1934C						PASS	.	C	ALA/GLY	26,4380	29.0+/-57.7	0,26,2177	169.0	169.0	169.0		1934	5.2	0.8	18	dbSNP_129	169	219,8381	83.1+/-145.7	3,213,4084	yes	missense	CDH19	NM_021153.2	60	3,239,6261	GG,GC,CC		2.5465,0.5901,1.8837	probably-damaging	645/773	64172434	245,12761	2203	4300	6503	SO:0001583	missense	28513	exon12			CCACCCCCTTCAT	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.1934G>C	18.37:g.64172434C>G	ENSP00000262150:p.Gly645Ala	239.0	0.0	0		201.0	97.0	0.482587	NM_021153	O15098	Missense_Mutation	SNP	ENST00000262150.2	37	CCDS11994.1	25	0.011446886446886446	0	0.0	5	0.013812154696132596	0	0.0	20	0.026385224274406333	c	19.92	3.917129	0.73098	0.005901	0.025465	ENSG00000071991	ENST00000262150	D	0.85556	-2.0	5.18	5.18	0.71444	Cadherin, cytoplasmic domain (1);	0.000000	0.85682	D	0.000000	D	0.87030	0.6076	M	0.91717	3.235	0.80722	D	1	D	0.76494	0.999	D	0.79784	0.993	D	0.90204	0.4259	10	0.87932	D	0	.	19.0693	0.93126	0.0:1.0:0.0:0.0	rs55874520	645	Q9H159	CAD19_HUMAN	A	645	ENSP00000262150:G645A	ENSP00000262150:G645A	G	-	2	0	CDH19	62323414	1.000000	0.71417	0.759000	0.31340	0.423000	0.31445	7.284000	0.78650	2.564000	0.86499	0.650000	0.86243	GGG	C|0.983;G|0.017	0.017	strong		0.403	CDH19-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256219.1	NM_021153	
GTF3C4	9329	hgsc.bcm.edu	37	9	135546021	135546021	+	Silent	SNP	G	G	A	rs146201597	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr9:135546021G>A	ENST00000372146.4	+	1	600	c.36G>A	c.(34-36)gcG>gcA	p.A12A	DDX31_ENST00000544003.1_5'Flank|DDX31_ENST00000372153.1_5'Flank|DDX31_ENST00000480876.1_5'Flank|GTF3C4_ENST00000483873.2_Silent_p.A12A|DDX31_ENST00000310532.2_5'Flank|DDX31_ENST00000372159.3_5'Flank	NM_012204.2	NP_036336.2	Q9UKN8	TF3C4_HUMAN	general transcription factor IIIC, polypeptide 4, 90kDa	12					5S class rRNA transcription from RNA polymerase III type 1 promoter (GO:0042791)|gene expression (GO:0010467)|histone acetylation (GO:0016573)|positive regulation of catalytic activity (GO:0043085)|transcription from RNA polymerase III promoter (GO:0006383)|transcription initiation from RNA polymerase III promoter (GO:0006384)|transcription, DNA-templated (GO:0006351)|tRNA transcription from RNA polymerase III promoter (GO:0042797)	nucleoplasm (GO:0005654)|transcription factor TFIIIC complex (GO:0000127)	DNA binding (GO:0003677)|enzyme activator activity (GO:0008047)|histone acetyltransferase activity (GO:0004402)			breast(1)|central_nervous_system(2)|cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(4)|lung(7)|ovary(1)|skin(1)	20				OV - Ovarian serous cystadenocarcinoma(145;8.15e-07)|Epithelial(140;2.6e-05)		TGGGGCCCGCGGACGACGGGC	0.771													G|||	81	0.0161741	0.0045	0.0202	5008	,	,		9102	0.0		0.0338	False		,,,				2504	0.0276				p.A12A	Pancreas(142;417 1875 11086 31973 47667)	Atlas-SNP	.											.	GTF3C4	53	.	0			c.G36A						PASS	.	G		13,2385		0,13,1186	3.0	4.0	4.0		36	2.4	0.9	9	dbSNP_134	4	168,5390		0,168,2611	no	coding-synonymous	GTF3C4	NM_012204.2		0,181,3797	AA,AG,GG		3.0227,0.5421,2.275		12/823	135546021	181,7775	1199	2779	3978	SO:0001819	synonymous_variant	9329	exon1			GCCCGCGGACGAC	AF142328	CCDS6953.1	9q34.3	2011-07-01	2002-08-29		ENSG00000125484	ENSG00000125484		"""Chromatin-modifying enzymes / K-acetyltransferases"", ""General transcription factors"""	4667	protein-coding gene	gene with protein product		604892	"""general transcription factor IIIC, polypeptide 4 (90kD)"""			10523658	Standard	NM_012204		Approved	TFIIIC90, KAT12	uc010mzv.3	Q9UKN8	OTTHUMG00000020842	ENST00000372146.4:c.36G>A	9.37:g.135546021G>A		13.0	0.0	0		9.0	8.0	0.888889	NM_012204	Q5VZJ7	Silent	SNP	ENST00000372146.4	37	CCDS6953.1																																																																																			G|0.986;A|0.014	0.014	strong		0.771	GTF3C4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054792.1		
GBGT1	26301	hgsc.bcm.edu	37	9	136029138	136029138	+	Silent	SNP	G	G	A	rs35902535	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr9:136029138G>A	ENST00000372040.3	-	7	1181	c.870C>T	c.(868-870)ggC>ggT	p.G290G	GBGT1_ENST00000540636.1_Silent_p.G273G|GBGT1_ENST00000372043.3_Missense_Mutation_p.A284V|RALGDS_ENST00000542690.1_Intron|GBGT1_ENST00000472281.1_5'UTR	NM_001282629.1	NP_001269558.1	Q8N5D6	GBGT1_HUMAN	globoside alpha-1,3-N-acetylgalactosaminyltransferase 1	290					glycolipid biosynthetic process (GO:0009247)|protein glycosylation (GO:0006486)	Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)	globoside alpha-N-acetylgalactosaminyltransferase activity (GO:0047277)|metal ion binding (GO:0046872)			breast(2)|endometrium(1)|kidney(4)|lung(2)|skin(1)	10				OV - Ovarian serous cystadenocarcinoma(145;3.49e-06)|Epithelial(140;2.59e-05)		CAGCCATGATGCCATTGGCCT	0.587													G|||	210	0.0419329	0.0333	0.0403	5008	,	,		17659	0.002		0.0795	False		,,,				2504	0.0573				p.G290G		Atlas-SNP	.											.	GBGT1	25	.	0			c.C870T						PASS	.	G		200,4206	124.9+/-162.1	8,184,2011	121.0	113.0	116.0		870	2.3	1.0	9	dbSNP_126	116	618,7982	160.3+/-213.4	16,586,3698	no	coding-synonymous	GBGT1	NM_021996.4		24,770,5709	AA,AG,GG		7.186,4.5393,6.2894		290/348	136029138	818,12188	2203	4300	6503	SO:0001819	synonymous_variant	26301	exon7			CATGATGCCATTG	AY358175	CCDS6960.1, CCDS65175.1, CCDS65176.1	9q34.13-q34.3	2014-07-18			ENSG00000148288	ENSG00000148288		"""Glycosyltransferase family 6 domain containing"""	20460	protein-coding gene	gene with protein product	"""Forssman glycolipid synthetase (FS)"", ""Forssman synthetase"""	606074				10506200, 8855242	Standard	NM_021996		Approved	UDP-GalNAc, A3GALNT, MGC44848, FS		Q8N5D6	OTTHUMG00000020853	ENST00000372040.3:c.870C>T	9.37:g.136029138G>A		122.0	0.0	0		140.0	68.0	0.485714	NM_021996	A8K633|B2RA95|B7Z8S5|Q45F07|Q5T7U9|Q5T7V1|Q8N2K4|Q9UKI5	Silent	SNP	ENST00000372040.3	37	CCDS6960.1	105	0.04807692307692308	21	0.042682926829268296	15	0.04143646408839779	2	0.0034965034965034965	67	0.08839050131926121	G	12.72	2.022220	0.35701	0.045393	0.07186	ENSG00000148288	ENST00000372043	T	0.23348	1.91	5.38	2.31	0.28768	.	.	.	.	.	T	0.01287	0.0042	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.00460	-1.1726	6	0.87932	D	0	-15.1162	5.0909	0.14708	0.2677:0.3054:0.4269:0.0	rs35902535;rs62638711	.	.	.	V	284	ENSP00000361113:A284V	ENSP00000361113:A284V	A	-	2	0	GBGT1	135018959	0.629000	0.27146	0.992000	0.48379	0.929000	0.56500	0.761000	0.26489	0.542000	0.28846	0.561000	0.74099	GCA	G|0.944;A|0.056	0.056	strong		0.587	GBGT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054815.1	NM_021996	
GLRA1	2741	hgsc.bcm.edu	37	5	151208500	151208500	+	Silent	SNP	C	C	T	rs75463357	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr5:151208500C>T	ENST00000455880.2	-	8	1327	c.1041G>A	c.(1039-1041)agG>agA	p.R347R	GLRA1_ENST00000545569.1_Silent_p.R264R|GLRA1_ENST00000274576.4_Silent_p.R347R			P23415	GLRA1_HUMAN	glycine receptor, alpha 1	347					acrosome reaction (GO:0007340)|action potential (GO:0001508)|adult walking behavior (GO:0007628)|chloride transmembrane transport (GO:1902476)|chloride transport (GO:0006821)|ion transmembrane transport (GO:0034220)|ion transport (GO:0006811)|muscle contraction (GO:0006936)|negative regulation of transmission of nerve impulse (GO:0051970)|neuromuscular process controlling posture (GO:0050884)|neuropeptide signaling pathway (GO:0007218)|positive regulation of acrosome reaction (GO:2000344)|regulation of inhibitory postsynaptic membrane potential (GO:0060080)|regulation of membrane potential (GO:0042391)|regulation of respiratory gaseous exchange by neurological system process (GO:0002087)|righting reflex (GO:0060013)|startle response (GO:0001964)|synaptic transmission, glycinergic (GO:0060012)|transmembrane transport (GO:0055085)|visual perception (GO:0007601)	cell junction (GO:0030054)|chloride channel complex (GO:0034707)|external side of plasma membrane (GO:0009897)|inhibitory synapse (GO:0060077)|integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|intracellular membrane-bounded organelle (GO:0043231)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)	extracellular-glycine-gated chloride channel activity (GO:0016934)|glycine binding (GO:0016594)|taurine binding (GO:0030977)|transmitter-gated ion channel activity (GO:0022824)			breast(1)|central_nervous_system(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(2)|lung(6)|ovary(1)|prostate(1)|skin(3)|urinary_tract(1)	23		all_hematologic(541;0.0341)|Medulloblastoma(196;0.0912)	Kidney(363;0.000171)|KIRC - Kidney renal clear cell carcinoma(527;0.000785)		Desflurane(DB01189)|Enflurane(DB00228)|Ethanol(DB00898)|Ginkgo biloba(DB01381)|Glycine(DB00145)|Halothane(DB01159)|Isoflurane(DB00753)|Lindane(DB00431)|Methoxyflurane(DB01028)|Sevoflurane(DB01236)	GTCTCCGCTTCCTCCTGAATC	0.468													C|||	42	0.00838658	0.0008	0.0159	5008	,	,		21283	0.0		0.0258	False		,,,				2504	0.0041				p.R347R		Atlas-SNP	.											.	GLRA1	61	.	0			c.G1041A						PASS	.	C	,	23,4383	30.8+/-60.4	0,23,2180	172.0	167.0	169.0		1041,1041	4.2	1.0	5	dbSNP_132	169	209,8391	89.2+/-151.4	5,199,4096	no	coding-synonymous,coding-synonymous	GLRA1	NM_000171.3,NM_001146040.1	,	5,222,6276	TT,TC,CC		2.4302,0.522,1.7838	,	347/450,347/458	151208500	232,12774	2203	4300	6503	SO:0001819	synonymous_variant	2741	exon8			CCGCTTCCTCCTG		CCDS4320.1, CCDS54942.1	5q33.1	2012-02-07	2008-01-24		ENSG00000145888	ENSG00000145888		"""Ligand-gated ion channels / Glycine receptors"""	4326	protein-coding gene	gene with protein product	"""startle disease/hyperekplexia"", ""stiff person syndrome"""	138491	"""glycine receptor, alpha 1 (startle disease/hyperekplexia)"""	STHE		1355335, 8298642	Standard	NM_000171		Approved		uc003lut.3	P23415	OTTHUMG00000130121	ENST00000455880.2:c.1041G>A	5.37:g.151208500C>T		66.0	0.0	0		71.0	35.0	0.492958	NM_000171	B2R6T3|Q14C77|Q6DJV9	Silent	SNP	ENST00000455880.2	37	CCDS54942.1																																																																																			C|0.983;T|0.017	0.017	strong		0.468	GLRA1-004	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000373959.1		
MYH10	4628	hgsc.bcm.edu	37	17	8396176	8396176	+	Missense_Mutation	SNP	T	T	C			TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr17:8396176T>C	ENST00000269243.4	-	31	4421	c.4283A>G	c.(4282-4284)gAg>gGg	p.E1428G	MYH10_ENST00000396239.1_Missense_Mutation_p.E1449G|MYH10_ENST00000360416.3_Missense_Mutation_p.E1459G|MYH10_ENST00000379980.4_Missense_Mutation_p.E1444G	NM_005964.3	NP_005955.3	P35580	MYH10_HUMAN	myosin, heavy chain 10, non-muscle	1428					actin filament-based movement (GO:0030048)|actomyosin structure organization (GO:0031032)|adult heart development (GO:0007512)|ATP catabolic process (GO:0006200)|axon guidance (GO:0007411)|cardiac myofibril assembly (GO:0055003)|cell adhesion (GO:0007155)|cell proliferation (GO:0008283)|cerebellar Purkinje cell layer development (GO:0021680)|exocytosis (GO:0006887)|fourth ventricle development (GO:0021592)|in utero embryonic development (GO:0001701)|lateral ventricle development (GO:0021670)|mitotic cytokinesis (GO:0000281)|neuromuscular process controlling balance (GO:0050885)|neuron migration (GO:0001764)|nuclear migration (GO:0007097)|plasma membrane repair (GO:0001778)|regulation of cell shape (GO:0008360)|retina development in camera-type eye (GO:0060041)|substrate-dependent cell migration, cell extension (GO:0006930)|third ventricle development (GO:0021678)|ventricular cardiac muscle cell development (GO:0055015)	actomyosin (GO:0042641)|axon (GO:0030424)|cell cortex (GO:0005938)|cleavage furrow (GO:0032154)|cytoplasm (GO:0005737)|dendritic spine (GO:0043197)|extracellular vesicular exosome (GO:0070062)|growth cone (GO:0030426)|midbody (GO:0030496)|myosin complex (GO:0016459)|myosin II complex (GO:0016460)|myosin II filament (GO:0097513)|neuromuscular junction (GO:0031594)|neuronal cell body (GO:0043025)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|spindle (GO:0005819)|stress fiber (GO:0001725)	actin binding (GO:0003779)|actin filament binding (GO:0051015)|actin-dependent ATPase activity (GO:0030898)|ADP binding (GO:0043531)|ATP binding (GO:0005524)|microfilament motor activity (GO:0000146)			breast(5)|endometrium(9)|kidney(2)|large_intestine(16)|lung(9)|ovary(3)|prostate(3)|skin(4)|stomach(1)	52						GTCGTCCAGCTCCTGCTGCAG	0.607																																					p.E1459G		Atlas-SNP	.											.	MYH10	148	.	0			c.A4376G						PASS	.						80.0	71.0	74.0					17																	8396176		2203	4300	6503	SO:0001583	missense	4628	exon33			TCCAGCTCCTGCT	M69181	CCDS11144.1, CCDS58515.1, CCDS73984.1	17p13	2011-09-27	2006-09-29		ENSG00000133026	ENSG00000133026		"""Myosins / Myosin superfamily : Class II"""	7568	protein-coding gene	gene with protein product		160776	"""myosin, heavy polypeptide 10, non-muscle"""			1860190	Standard	NM_001256012		Approved	NMMHCB	uc002glm.4	P35580	OTTHUMG00000108195	ENST00000269243.4:c.4283A>G	17.37:g.8396176T>C	ENSP00000269243:p.Glu1428Gly	125.0	0.0	0		91.0	4.0	0.043956	NM_001256012	B2RWP9|D3DTS1|F8VTL3|Q12989|Q149N3|Q149N4|Q16087|Q4LE45|Q6PK16|Q9BWG0	Missense_Mutation	SNP	ENST00000269243.4	37	CCDS11144.1	.	.	.	.	.	.	.	.	.	.	T	31	5.091155	0.94149	.	.	ENSG00000133026	ENST00000269243;ENST00000360416;ENST00000396239;ENST00000379980	D;D;D;D	0.85629	-2.01;-2.01;-2.01;-2.01	5.31	5.31	0.75309	Myosin tail (1);	0.000000	0.85682	D	0.000000	D	0.94820	0.8327	H	0.95917	3.74	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.97110	1.0;1.0;1.0	D	0.96370	0.9273	10	0.87932	D	0	.	15.4317	0.75105	0.0:0.0:0.0:1.0	.	1437;1459;1428	B2RWP9;F8VTL3;P35580	.;.;MYH10_HUMAN	G	1428;1459;1449;1444	ENSP00000269243:E1428G;ENSP00000353590:E1459G;ENSP00000379539:E1449G;ENSP00000369315:E1444G	ENSP00000269243:E1428G	E	-	2	0	MYH10	8336901	1.000000	0.71417	1.000000	0.80357	0.957000	0.61999	7.825000	0.86693	2.224000	0.72417	0.528000	0.53228	GAG	.	.	none		0.607	MYH10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000227001.2		
DNAH6	1768	hgsc.bcm.edu	37	2	84926756	84926756	+	Silent	SNP	G	G	A	rs74514752	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr2:84926756G>A	ENST00000237449.6	+	47	7724	c.7716G>A	c.(7714-7716)ctG>ctA	p.L2572L	DNAH6_ENST00000389394.3_Silent_p.L2572L			Q9C0G6	DYH6_HUMAN	dynein, axonemal, heavy chain 6	2572	AAA 4. {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(9)|central_nervous_system(2)|endometrium(11)|haematopoietic_and_lymphoid_tissue(2)|kidney(7)|large_intestine(3)|lung(14)|pancreas(1)|prostate(2)|skin(3)|upper_aerodigestive_tract(1)	57						GTCAGAAGCTGCACATTGTTC	0.408													G|||	23	0.00459265	0.0023	0.0101	5008	,	,		20442	0.0		0.0109	False		,,,				2504	0.002				p.L2572L		Atlas-SNP	.											.	DNAH6	194	.	0			c.G7716A						PASS	.	G		3,1381		0,3,689	113.0	92.0	99.0		7716	-0.2	1.0	2	dbSNP_132	99	43,3139		1,41,1549	no	coding-synonymous	DNAH6	NM_001370.1		1,44,2238	AA,AG,GG		1.3514,0.2168,1.0074		2572/4159	84926756	46,4520	692	1591	2283	SO:0001819	synonymous_variant	1768	exon48			GAAGCTGCACATT	U61736	CCDS46348.1	2p11.2	2011-05-24	2006-09-04		ENSG00000115423	ENSG00000115423		"""Axonemal dyneins"""	2951	protein-coding gene	gene with protein product		603336	"""dynein, axonemal, heavy polypeptide 6"", ""dynein heavy chain-like 1"""	DNHL1		8812413	Standard	NM_001370		Approved	Dnahc6, HL-2, FLJ37357	uc010fgb.3	Q9C0G6	OTTHUMG00000128957	ENST00000237449.6:c.7716G>A	2.37:g.84926756G>A		94.0	0.0	0		85.0	38.0	0.447059	NM_001370	A0PJN9|B5MEE0|B7ZL99|O95493|Q53QZ1|Q53TE5|Q8N1W6|Q92861|Q96BL6|Q9H030|Q9H5E1	Silent	SNP	ENST00000237449.6	37	CCDS46348.1																																																																																			G|0.994;A|0.006	0.006	strong		0.408	DNAH6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000328537.2	NM_001370	
VWCE	220001	hgsc.bcm.edu	37	11	61053895	61053895	+	Silent	SNP	G	G	A	rs146572904	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr11:61053895G>A	ENST00000335613.5	-	5	818	c.432C>T	c.(430-432)gaC>gaT	p.D144D		NM_152718.2	NP_689931.2	Q96DN2	VWCE_HUMAN	von Willebrand factor C and EGF domains	144	EGF-like 2; calcium-binding. {ECO:0000255|PROSITE-ProRule:PRU00076}.					extracellular region (GO:0005576)	calcium ion binding (GO:0005509)			biliary_tract(1)|endometrium(5)|kidney(1)|large_intestine(5)|lung(17)|ovary(3)|prostate(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	37						TTACACATTCGTCAATGTCTG	0.547													g|||	6	0.00119808	0.0	0.0014	5008	,	,		23016	0.0		0.005	False		,,,				2504	0.0				p.D144D		Atlas-SNP	.											.	VWCE	84	.	0			c.C432T						PASS	.	A		2,4404	4.2+/-10.8	0,2,2201	89.0	77.0	81.0		432	-10.6	0.0	11	dbSNP_134	81	22,8576	16.6+/-54.9	0,22,4277	no	coding-synonymous	VWCE	NM_152718.2		0,24,6478	AA,AG,GG		0.2559,0.0454,0.1846		144/956	61053895	24,12980	2203	4299	6502	SO:0001819	synonymous_variant	220001	exon5			ACATTCGTCAATG	AK056571	CCDS8002.1	11q12.2	2006-08-04			ENSG00000167992	ENSG00000167992			26487	protein-coding gene	gene with protein product		611115				12869306	Standard	NM_152718		Approved	URG11, FLJ32009, VWC1	uc001nra.3	Q96DN2	OTTHUMG00000168208	ENST00000335613.5:c.432C>T	11.37:g.61053895G>A		56.0	0.0	0		64.0	26.0	0.40625	NM_152718	A5PKV0|Q7Z7L6|Q86WK8	Silent	SNP	ENST00000335613.5	37	CCDS8002.1																																																																																			G|0.998;A|0.002	0.002	strong		0.547	VWCE-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000398811.1	NM_152718	
COL5A1	1289	hgsc.bcm.edu	37	9	137734084	137734084	+	Missense_Mutation	SNP	A	A	G			TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr9:137734084A>G	ENST00000371817.3	+	66	5866	c.5452A>G	c.(5452-5454)Aat>Gat	p.N1818D		NM_000093.3|NM_001278074.1	NP_000084.3|NP_001265003.1	P20908	CO5A1_HUMAN	collagen, type V, alpha 1	1818	Fibrillar collagen NC1. {ECO:0000255|PROSITE-ProRule:PRU00793}.				axon guidance (GO:0007411)|blood vessel development (GO:0001568)|cell adhesion (GO:0007155)|cell migration (GO:0016477)|collagen biosynthetic process (GO:0032964)|collagen catabolic process (GO:0030574)|collagen fibril organization (GO:0030199)|extracellular fibril organization (GO:0043206)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|eye morphogenesis (GO:0048592)|heart morphogenesis (GO:0003007)|integrin biosynthetic process (GO:0045112)|negative regulation of endodermal cell differentiation (GO:1903225)|regulation of cellular component organization (GO:0051128)|skin development (GO:0043588)|tendon development (GO:0035989)|wound healing, spreading of epidermal cells (GO:0035313)	basement membrane (GO:0005604)|collagen type V trimer (GO:0005588)|endoplasmic reticulum lumen (GO:0005788)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)	extracellular matrix structural constituent (GO:0005201)|heparin binding (GO:0008201)|integrin binding (GO:0005178)|metal ion binding (GO:0046872)|platelet-derived growth factor binding (GO:0048407)|proteoglycan binding (GO:0043394)			NS(1)|breast(3)|central_nervous_system(1)|cervix(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(26)|liver(2)|lung(36)|ovary(4)|pancreas(4)|prostate(5)|skin(10)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(4)	115		Myeloproliferative disorder(178;0.0341)		all cancers(34;2.28e-08)|OV - Ovarian serous cystadenocarcinoma(145;6.03e-08)|Epithelial(140;6.4e-08)|GBM - Glioblastoma multiforme(294;0.131)		CATCATGTTCAATGACTTCGG	0.577																																					p.N1818D		Atlas-SNP	.											.	COL5A1	323	.	0			c.A5452G						PASS	.						129.0	125.0	126.0					9																	137734084		2203	4300	6503	SO:0001583	missense	1289	exon66			ATGTTCAATGACT	D90279	CCDS6982.1, CCDS75932.1	9q34.2-q34.3	2014-09-17			ENSG00000130635	ENSG00000130635		"""Collagens"""	2209	protein-coding gene	gene with protein product	"""alpha 1 type V collagen"""	120215				1572660	Standard	NM_001278074		Approved		uc031tfl.1	P20908	OTTHUMG00000020891	ENST00000371817.3:c.5452A>G	9.37:g.137734084A>G	ENSP00000360882:p.Asn1818Asp	156.0	0.0	0		144.0	68.0	0.472222	NM_000093	Q15094|Q5SUX4	Missense_Mutation	SNP	ENST00000371817.3	37	CCDS6982.1	.	.	.	.	.	.	.	.	.	.	A	16.41	3.114962	0.56505	.	.	ENSG00000130635	ENST00000371817;ENST00000355306	T	0.73152	-0.72	4.72	4.72	0.59763	Fibrillar collagen, C-terminal (4);	0.069214	0.53938	U	0.000046	T	0.69278	0.3093	M	0.70595	2.14	0.42323	D	0.992266	P	0.38280	0.625	B	0.37508	0.252	T	0.70575	-0.4834	10	0.33940	T	0.23	.	14.1846	0.65598	1.0:0.0:0.0:0.0	.	1818	P20908	CO5A1_HUMAN	D	1818;355	ENSP00000360882:N1818D	ENSP00000347458:N355D	N	+	1	0	COL5A1	136873905	1.000000	0.71417	0.986000	0.45419	0.997000	0.91878	9.057000	0.93889	1.765000	0.52091	0.460000	0.39030	AAT	.	.	none		0.577	COL5A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054954.2	NM_000093	
HLA-DRB5	3127	hgsc.bcm.edu	37	6	32489754	32489754	+	Missense_Mutation	SNP	T	T	C	rs41551116|rs201925120	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr6:32489754T>C	ENST00000374975.3	-	2	360	c.298A>G	c.(298-300)Agg>Ggg	p.R100G		NM_002125.3	NP_002116.2			major histocompatibility complex, class II, DR beta 5											NS(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(1)|lung(3)|pancreas(1)|prostate(1)|stomach(2)	10						GCGGCGCGCCTGTCTTCCAGG	0.667													T|||	280	0.0559105	0.084	0.0605	5008	,	,		4296	0.0317		0.0626	False		,,,				2504	0.0327				p.R100G		Atlas-SNP	.											.	HLA-DRB5	31	.	0			c.A298G						PASS	.						36.0	32.0	33.0					6																	32489754		1942	3732	5674	SO:0001583	missense	3127	exon2			CGCGCCTGTCTTC		CCDS4751.1	6p21.3	2013-01-11			ENSG00000198502	ENSG00000198502		"""Histocompatibility complex"", ""Immunoglobulin superfamily / C1-set domain containing"""	4953	protein-coding gene	gene with protein product		604776					Standard	NM_002125		Approved		uc003obj.3	Q30154	OTTHUMG00000031027	ENST00000374975.3:c.298A>G	6.37:g.32489754T>C	ENSP00000364114:p.Arg100Gly	2.0	0.0	0		29.0	27.0	0.931035	NM_002125		Missense_Mutation	SNP	ENST00000374975.3	37	CCDS4751.1	.	.	.	.	.	.	.	.	.	.	.	10.39	1.336269	0.24253	.	.	ENSG00000198502	ENST00000374975	T	0.00349	7.99	4.72	-9.43	0.00607	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);	5.372110	0.00166	N	0.000006	T	0.00300	0.0009	H	0.95950	3.745	0.09310	N	1	P;B	0.35155	0.487;0.304	B;P	0.58266	0.344;0.836	T	0.48536	-0.9027	10	0.66056	D	0.02	.	0.4687	0.00528	0.2086:0.2516:0.2378:0.302	rs41551116	27;100	Q29973;Q30154	.;DRB5_HUMAN	G	100	ENSP00000364114:R100G	ENSP00000364114:R100G	R	-	1	2	HLA-DRB5	32597732	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-6.530000	0.00062	-5.722000	0.00010	-3.428000	0.00037	AGG	T|0.952;C|0.047	0.047	strong		0.667	HLA-DRB5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076022.2	NM_002125	
EHBP1L1	254102	hgsc.bcm.edu	37	11	65349037	65349037	+	Silent	SNP	G	G	A	rs74684453	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	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		195.0	0.0	0		209.0	92.0	0.440191	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	
PPP1R3A	5506	hgsc.bcm.edu	37	7	113519637	113519637	+	Missense_Mutation	SNP	C	C	G	rs371962450		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr7:113519637C>G	ENST00000284601.3	-	4	1578	c.1510G>C	c.(1510-1512)Gga>Cga	p.G504R		NM_002711.3	NP_002702.2	Q16821	PPR3A_HUMAN	protein phosphatase 1, regulatory subunit 3A	504					glycogen metabolic process (GO:0005977)	integral component of membrane (GO:0016021)				NS(2)|breast(8)|cervix(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(14)|liver(1)|lung(43)|ovary(10)|pancreas(7)|prostate(3)|skin(15)|stomach(1)|upper_aerodigestive_tract(2)	121						TTAGAAGATCCTTCTTCTGTT	0.318																																					p.G504R		Atlas-SNP	.											.	PPP1R3A	317	.	0			c.G1510C						PASS	.						63.0	60.0	61.0					7																	113519637		2203	4299	6502	SO:0001583	missense	5506	exon4			AAGATCCTTCTTC	AF024578	CCDS5759.1	7q31.1	2012-04-17	2011-10-04	2001-07-02	ENSG00000154415	ENSG00000154415	3.1.3.16	"""Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"""	9291	protein-coding gene	gene with protein product	"""glycogen-associated regulatory subunit of protein phosphatase-1"", ""protein phosphatase 1 regulatory subunit GM"""	600917	"""protein phosphatase 1, regulatory (inhibitor) subunit 3A (glycogen and sarcoplasmic reticulum binding subunit, skeletal muscle)"", ""protein phosphatase 1, regulatory (inhibitor) subunit 3A"""	PPP1R3		7926294	Standard	NM_002711		Approved	GM	uc010ljy.1	Q16821	OTTHUMG00000156944	ENST00000284601.3:c.1510G>C	7.37:g.113519637C>G	ENSP00000284601:p.Gly504Arg	188.0	0.0	0		181.0	53.0	0.292818	NM_002711	A0AVQ2|A4D0T6|O43476|Q75LN8|Q7KYM8|Q86UI6	Missense_Mutation	SNP	ENST00000284601.3	37	CCDS5759.1	.	.	.	.	.	.	.	.	.	.	C	9.621	1.133935	0.21123	.	.	ENSG00000154415	ENST00000284601;ENST00000449795	T;T	0.29655	2.51;1.56	6.02	2.73	0.32206	.	0.930568	0.09052	N	0.855709	T	0.19604	0.0471	N	0.25144	0.715	0.09310	N	1	B	0.06786	0.001	B	0.04013	0.001	T	0.28586	-1.0039	10	0.13853	T	0.58	-0.2141	9.1988	0.37244	0.0:0.6562:0.0:0.3437	.	504	Q16821	PPR3A_HUMAN	R	504;183	ENSP00000284601:G504R;ENSP00000401278:G183R	ENSP00000284601:G504R	G	-	1	0	PPP1R3A	113306873	0.000000	0.05858	0.001000	0.08648	0.001000	0.01503	0.331000	0.19733	0.826000	0.34661	0.655000	0.94253	GGA	.	.	none		0.318	PPP1R3A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000346724.1	NM_002711	
TOP2A	7153	hgsc.bcm.edu	37	17	38564363	38564363	+	Silent	SNP	G	G	A			TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr17:38564363G>A	ENST00000423485.1	-	12	1514	c.1356C>T	c.(1354-1356)tcC>tcT	p.S452S		NM_001067.3	NP_001058.2	P11388	TOP2A_HUMAN	topoisomerase (DNA) II alpha 170kDa	452					apoptotic chromosome condensation (GO:0030263)|ATP catabolic process (GO:0006200)|cellular response to DNA damage stimulus (GO:0006974)|chromosome segregation (GO:0007059)|DNA ligation (GO:0006266)|DNA topological change (GO:0006265)|DNA unwinding involved in DNA replication (GO:0006268)|embryonic cleavage (GO:0040016)|hematopoietic progenitor cell differentiation (GO:0002244)|mitotic cell cycle (GO:0000278)|mitotic DNA integrity checkpoint (GO:0044774)|mitotic recombination (GO:0006312)|positive regulation of apoptotic process (GO:0043065)|positive regulation of single stranded viral RNA replication via double stranded DNA intermediate (GO:0045870)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of viral genome replication (GO:0045070)|resolution of meiotic recombination intermediates (GO:0000712)|sister chromatid segregation (GO:0000819)	condensed chromosome (GO:0000793)|cytoplasm (GO:0005737)|DNA topoisomerase complex (ATP-hydrolyzing) (GO:0009330)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|protein complex (GO:0043234)	ATP binding (GO:0005524)|chromatin binding (GO:0003682)|DNA binding (GO:0003677)|DNA binding, bending (GO:0008301)|DNA topoisomerase type II (ATP-hydrolyzing) activity (GO:0003918)|DNA-dependent ATPase activity (GO:0008094)|drug binding (GO:0008144)|enzyme binding (GO:0019899)|histone deacetylase binding (GO:0042826)|magnesium ion binding (GO:0000287)|poly(A) RNA binding (GO:0044822)|protein C-terminus binding (GO:0008022)|protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)|protein kinase C binding (GO:0005080)|ubiquitin binding (GO:0043130)			breast(2)|central_nervous_system(1)|cervix(1)|endometrium(3)|kidney(2)|large_intestine(8)|lung(9)|ovary(5)|pancreas(2)|prostate(3)|skin(1)|upper_aerodigestive_tract(2)	39		Breast(137;0.00328)	STAD - Stomach adenocarcinoma(5;0.00183)		Amsacrine(DB00276)|Ciprofloxacin(DB00537)|Dactinomycin(DB00970)|Daunorubicin(DB00694)|Dexrazoxane(DB00380)|Doxorubicin(DB00997)|Enoxacin(DB00467)|Epirubicin(DB00445)|Etoposide(DB00773)|Fleroxacin(DB04576)|Idarubicin(DB01177)|Levofloxacin(DB01137)|Lomefloxacin(DB00978)|Lucanthone(DB04967)|Mitoxantrone(DB01204)|Moxifloxacin(DB00218)|Norfloxacin(DB01059)|Ofloxacin(DB01165)|Pefloxacin(DB00487)|Podofilox(DB01179)|Sparfloxacin(DB01208)|Teniposide(DB00444)|Trovafloxacin(DB00685)|Valrubicin(DB00385)	TACACTCAGTGGAGTTTCGGC	0.403																																					p.S452S		Atlas-SNP	.											.	TOP2A	124	.	0			c.C1356T						PASS	.						39.0	37.0	37.0					17																	38564363		1832	4080	5912	SO:0001819	synonymous_variant	7153	exon12			CTCAGTGGAGTTT		CCDS45672.1	17q21-q22	2008-08-06	2002-08-29		ENSG00000131747	ENSG00000131747	5.99.1.2		11989	protein-coding gene	gene with protein product		126430	"""topoisomerase (DNA) II alpha (170kD)"""	TOP2			Standard	NM_001067		Approved		uc002huq.3	P11388	OTTHUMG00000155008	ENST00000423485.1:c.1356C>T	17.37:g.38564363G>A		43.0	0.0	0		58.0	27.0	0.465517	NM_001067	B2RTS1|Q71UN1|Q71UQ5|Q9HB24|Q9HB25|Q9HB26|Q9UP44|Q9UQP9	Silent	SNP	ENST00000423485.1	37	CCDS45672.1																																																																																			.	.	none		0.403	TOP2A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000338035.1		
NOL4L	140688	hgsc.bcm.edu	37	20	31044059	31044059	+	Silent	SNP	G	G	A	rs570929204	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr20:31044059G>A	ENST00000359676.5	-	3	391	c.249C>T	c.(247-249)gcC>gcT	p.A83A	RP5-1184F4.5_ENST00000442179.1_RNA|C20orf112_ENST00000475781.1_5'UTR	NM_001256798.1|NM_080616.4	NP_001243727.1|NP_542183.2	Q96MY1	NOL4L_HUMAN		83						cytoplasm (GO:0005737)|nucleus (GO:0005634)				endometrium(3)|kidney(2)|large_intestine(5)|lung(5)	15						GATCCTCGGCGGCCGTGGTGA	0.687													G|||	4	0.000798722	0.0	0.0	5008	,	,		17312	0.0		0.0	False		,,,				2504	0.0041				p.A327A		Atlas-SNP	.											.	C20orf112	39	.	0			c.C981T						PASS	.						43.0	40.0	41.0					20																	31044059		2203	4298	6501	SO:0001819	synonymous_variant	140688	exon6			CTCGGCGGCCGTG																												ENST00000359676.5:c.249C>T	20.37:g.31044059G>A		181.0	0.0	0		152.0	71.0	0.467105	NM_001256798	Q5JYB7|Q6P0Y4|Q9BR34|Q9NQF6	Silent	SNP	ENST00000359676.5	37	CCDS13202.1																																																																																			.	.	none		0.687	C20orf112-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000078628.2		
ISM2	145501	hgsc.bcm.edu	37	14	77942316	77942316	+	Silent	SNP	G	G	A	rs3742732	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr14:77942316G>A	ENST00000342219.4	-	7	1394	c.1338C>T	c.(1336-1338)gaC>gaT	p.D446D	ISM2_ENST00000493585.1_3'UTR|ISM2_ENST00000393684.3_Silent_p.D358D|ISM2_ENST00000412904.1_Silent_p.D365D|ISM2_ENST00000429906.1_Silent_p.D365D	NM_199296.2	NP_954993.1	Q6H9L7	ISM2_HUMAN	isthmin 2	446	AMOP. {ECO:0000255|PROSITE- ProRule:PRU00347}.					extracellular region (GO:0005576)				endometrium(3)|large_intestine(4)|lung(11)|prostate(1)|skin(1)|urinary_tract(1)	21						CCTGGTGCTCGTCCTGTAGGC	0.652													G|||	322	0.0642971	0.0363	0.1571	5008	,	,		17437	0.0149		0.0765	False		,,,				2504	0.0746				p.D446D		Atlas-SNP	.											.	ISM2	68	.	0			c.C1338T						PASS	.	G	,	210,4196	127.8+/-164.7	6,198,1999	36.0	38.0	37.0		,1338	-3.0	0.3	14	dbSNP_107	37	775,7825	179.2+/-228.4	32,711,3557	no	utr-3,coding-synonymous	ISM2	NM_182509.3,NM_199296.2	,	38,909,5556	AA,AG,GG		9.0116,4.7662,7.5734	,	,446/572	77942316	985,12021	2203	4300	6503	SO:0001819	synonymous_variant	145501	exon7			GTGCTCGTCCTGT	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.1338C>T	14.37:g.77942316G>A		12.0	0.0	0		14.0	7.0	0.5	NM_199296	A8K6D5|O95432|Q495U5|Q68CN3|Q86TQ7|Q86TW3|Q86TW4|Q8N501|Q8NBL0	Silent	SNP	ENST00000342219.4	37	CCDS9864.1																																																																																			G|0.930;A|0.070	0.070	strong		0.652	ISM2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000351309.1	NM_182509	
ITGA11	22801	hgsc.bcm.edu	37	15	68606192	68606192	+	Missense_Mutation	SNP	C	C	T	rs368307734		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr15:68606192C>T	ENST00000315757.7	-	23	2893	c.2807G>A	c.(2806-2808)cGg>cAg	p.R936Q	ITGA11_ENST00000423218.2_Missense_Mutation_p.R936Q	NM_001004439.1	NP_001004439.1	Q9UKX5	ITA11_HUMAN	integrin, alpha 11	936					cell adhesion (GO:0007155)|cell adhesion mediated by integrin (GO:0033627)|cell-matrix adhesion (GO:0007160)|collagen-activated signaling pathway (GO:0038065)|extracellular matrix organization (GO:0030198)|integrin-mediated signaling pathway (GO:0007229)|muscle organ development (GO:0007517)|osteoblast differentiation (GO:0001649)|substrate-dependent cell migration (GO:0006929)	focal adhesion (GO:0005925)|integrin alpha11-beta1 complex (GO:0034681)|integrin complex (GO:0008305)|membrane (GO:0016020)|plasma membrane (GO:0005886)	collagen binding (GO:0005518)|collagen binding involved in cell-matrix adhesion (GO:0098639)|collagen receptor activity (GO:0038064)|metal ion binding (GO:0046872)			NS(2)|breast(1)|central_nervous_system(1)|endometrium(7)|kidney(6)|large_intestine(6)|lung(22)|pancreas(1)|prostate(1)|upper_aerodigestive_tract(3)|urinary_tract(2)	52						GGTGCTGTCCCGCTCATTACT	0.637																																					p.R936Q		Atlas-SNP	.											.	ITGA11	110	.	0			c.G2807A						PASS	.	C	GLN/ARG	0,4316		0,0,2158	80.0	84.0	83.0		2807	2.6	1.0	15		83	2,8508		0,2,4253	no	missense	ITGA11	NM_001004439.1	43	0,2,6411	TT,TC,CC		0.0235,0.0,0.0156	benign	936/1189	68606192	2,12824	2158	4255	6413	SO:0001583	missense	22801	exon23			CTGTCCCGCTCAT	AF109681	CCDS45291.1	15q22.3-q23	2010-03-23				ENSG00000137809		"""Integrins"""	6136	protein-coding gene	gene with protein product		604789				10486209	Standard	NM_001004439		Approved	HsT18964	uc002ari.3	Q9UKX5		ENST00000315757.7:c.2807G>A	15.37:g.68606192C>T	ENSP00000327290:p.Arg936Gln	158.0	0.0	0		100.0	78.0	0.78	NM_001004439	J3KQM2|Q8WYI8|Q9UKQ1	Missense_Mutation	SNP	ENST00000315757.7	37	CCDS45291.1	.	.	.	.	.	.	.	.	.	.	C	10.57	1.386513	0.25031	0.0	2.35E-4	ENSG00000137809	ENST00000315757;ENST00000423218;ENST00000535491	T;T	0.39997	1.05;1.05	4.94	2.58	0.30949	Integrin alpha-2 (1);	0.362684	0.31071	N	0.008308	T	0.14657	0.0354	N	0.02539	-0.55	0.22581	N	0.998964	B;B	0.09022	0.002;0.0	B;B	0.13407	0.009;0.001	T	0.24297	-1.0164	10	0.15499	T	0.54	.	5.5239	0.16947	0.1525:0.0858:0.0:0.7617	.	936;936	A8K8T0;Q9UKX5	.;ITA11_HUMAN	Q	936;936;571	ENSP00000327290:R936Q;ENSP00000403392:R936Q	ENSP00000327290:R936Q	R	-	2	0	ITGA11	66393246	0.984000	0.35163	0.987000	0.45799	0.698000	0.40448	2.853000	0.48317	0.228000	0.21019	-0.367000	0.07326	CGG	.	.	weak		0.637	ITGA11-201	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding		NM_012211	
HDHD3	81932	hgsc.bcm.edu	37	9	116136262	116136262	+	Missense_Mutation	SNP	G	G	A			TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr9:116136262G>A	ENST00000238379.5	-	2	1270	c.373C>T	c.(373-375)Cgc>Tgc	p.R125C	HDHD3_ENST00000374180.3_Missense_Mutation_p.R125C|HDHD3_ENST00000485934.1_5'UTR	NM_031219.2	NP_112496.1	Q9BSH5	HDHD3_HUMAN	haloacid dehalogenase-like hydrolase domain containing 3	125						mitochondrion (GO:0005739)	hydrolase activity (GO:0016787)			large_intestine(2)|liver(1)	3						CCCCGTGTGCGGCACTCCCTC	0.597																																					p.R125C		Atlas-SNP	.											.	HDHD3	10	.	0			c.C373T						PASS	.						120.0	127.0	125.0					9																	116136262		2203	4300	6503	SO:0001583	missense	81932	exon2			GTGTGCGGCACTC	AK097067	CCDS6793.1	9q33.1	2006-04-12	2004-08-09	2004-08-12	ENSG00000119431	ENSG00000119431			28171	protein-coding gene	gene with protein product			"""chromosome 9 open reading frame 158"""	C9orf158		12477932	Standard	NM_031219		Approved	MGC12904	uc004bhi.1	Q9BSH5	OTTHUMG00000020524	ENST00000238379.5:c.373C>T	9.37:g.116136262G>A	ENSP00000238379:p.Arg125Cys	116.0	0.0	0		145.0	75.0	0.517241	NM_031219	B2RD47	Missense_Mutation	SNP	ENST00000238379.5	37	CCDS6793.1	.	.	.	.	.	.	.	.	.	.	G	14.42	2.529009	0.44969	.	.	ENSG00000119431	ENST00000238379;ENST00000374180	T;T	0.06687	3.27;3.27	5.76	5.76	0.90799	Haloacid dehalogenase-like hydrolase (1);HAD-like domain (2);	0.421114	0.26963	N	0.021610	T	0.34861	0.0912	M	0.92507	3.315	0.53688	D	0.999974	D	0.89917	1.0	P	0.62089	0.898	T	0.34775	-0.9815	10	0.87932	D	0	-14.3793	13.8598	0.63552	0.0:0.0:0.8475:0.1525	.	125	Q9BSH5	HDHD3_HUMAN	C	125	ENSP00000238379:R125C;ENSP00000363295:R125C	ENSP00000238379:R125C	R	-	1	0	HDHD3	115176083	0.955000	0.32602	0.998000	0.56505	0.238000	0.25445	1.482000	0.35486	2.721000	0.93114	0.655000	0.94253	CGC	.	.	none		0.597	HDHD3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053731.1	NM_031219	
KRTAP10-3	386682	hgsc.bcm.edu	37	21	45978210	45978210	+	Missense_Mutation	SNP	G	G	C	rs200250794		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr21:45978210G>C	ENST00000391620.1	-	1	433	c.389C>G	c.(388-390)tCt>tGt	p.S130C	TSPEAR_ENST00000397916.1_Intron|TSPEAR_ENST00000323084.4_Intron	NM_198696.2	NP_941969.2	P60369	KR103_HUMAN	keratin associated protein 10-3	130	18 X 5 AA repeats of C-C-X(3).					keratin filament (GO:0045095)				kidney(1)|lung(4)|prostate(1)|skin(1)	7						GGAAGCCCCAGAgcagacggg	0.657																																					p.S130C		Atlas-SNP	.											.	KRTAP10-3	17	.	0			c.C389G						PASS	.	G	,CYS/SER	0,4406		0,0,2203	154.0	157.0	156.0		,389	0.3	0.9	21		156	4,8596	3.7+/-12.6	0,4,4296	no	intron,missense	TSPEAR,KRTAP10-3	NM_144991.2,NM_198696.2	,112	0,4,6499	CC,CG,GG		0.0465,0.0,0.0308	,benign	,130/222	45978210	4,13002	2203	4300	6503	SO:0001583	missense	386682	exon1			GCCCCAGAGCAGA	AJ566383	CCDS42956.1	21q22.3	2007-10-05			ENSG00000212935	ENSG00000212935		"""Keratin associated proteins"""	22968	protein-coding gene	gene with protein product				KRTAP18-3			Standard	NM_198696		Approved	KAP10.3, KAP18.3	uc002zfj.1	P60369	OTTHUMG00000057628	ENST00000391620.1:c.389C>G	21.37:g.45978210G>C	ENSP00000375478:p.Ser130Cys	165.0	0.0	0		199.0	118.0	0.592965	NM_198696	A3KN67|Q70LJ4	Missense_Mutation	SNP	ENST00000391620.1	37	CCDS42956.1	.	.	.	.	.	.	.	.	.	.	g	0.926	-0.714347	0.03206	0.0	4.65E-4	ENSG00000212935	ENST00000391620	T	0.00672	5.89	3.53	0.295	0.15752	.	.	.	.	.	T	0.00496	0.0016	N	0.13168	0.305	0.24401	N	0.994705	B	0.09022	0.002	B	0.12156	0.007	T	0.43972	-0.9358	9	0.02654	T	1	.	7.3519	0.26695	0.0:0.4413:0.4219:0.1367	.	130	P60369	KR103_HUMAN	C	130	ENSP00000375478:S130C	ENSP00000375478:S130C	S	-	2	0	KRTAP10-3	44802638	0.172000	0.23043	0.877000	0.34402	0.106000	0.19336	1.422000	0.34826	0.267000	0.21916	0.561000	0.74099	TCT	G|0.999;C|0.001	0.001	weak		0.657	KRTAP10-3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000128031.1		
SSPO	23145	hgsc.bcm.edu	37	7	149489540	149489540	+	RNA	SNP	G	G	A	rs199795943	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr7:149489540G>A	ENST00000378016.2	+	0	5693							A2VEC9	SSPO_HUMAN	SCO-spondin						cell adhesion (GO:0007155)	extracellular space (GO:0005615)	peptidase inhibitor activity (GO:0030414)					Melanoma(164;0.165)|Ovarian(565;0.177)		OV - Ovarian serous cystadenocarcinoma(82;0.00625)			GGACGGCCCCGACGCTGCCGA	0.692													G|||	7	0.00139776	0.0	0.0014	5008	,	,		15662	0.0		0.005	False		,,,				2504	0.001				p.R1898Q		Atlas-SNP	.											.	.	.	.	0			c.G5693A						PASS	.	G		2,4260		0,2,2129	14.0	21.0	19.0		5697	-0.2	0.1	7		19	30,8422		0,30,4196	no	coding-notMod3	SSPO	NM_198455.2		0,32,6325	AA,AG,GG		0.3549,0.0469,0.2517			149489540	32,12682	2131	4226	6357			23145	exon37			GGCCCCGACGCTG	AK093431		7q36.1	2013-08-07	2013-08-06		ENSG00000197558	ENSG00000197558			21998	protein-coding gene	gene with protein product	"""subcommissural organ spondin"", ""SCO protein, thrombospondin domain containing"""		"""SCO-spondin homolog (Bos taurus)"""			8743952, 11008217	Standard	NM_198455		Approved	SCO-spondin, KIAA0543, FLJ36112	uc010lpk.3	A2VEC9	OTTHUMG00000157884		7.37:g.149489540G>A		27.0	0.0	0		7.0	5.0	0.714286	NM_198455	Q76B61	Missense_Mutation	SNP	ENST00000378016.2	37																																																																																				G|0.998;A|0.002	0.002	weak		0.692	SSPO-202	KNOWN	basic	processed_transcript	processed_transcript			
CCDC9	26093	hgsc.bcm.edu	37	19	47774358	47774358	+	Missense_Mutation	SNP	G	G	C			TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr19:47774358G>C	ENST00000221922.6	+	11	1327	c.1105G>C	c.(1105-1107)Gag>Cag	p.E369Q		NM_015603.2	NP_056418.1	Q9Y3X0	CCDC9_HUMAN	coiled-coil domain containing 9	369							poly(A) RNA binding (GO:0044822)			endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(5)|lung(2)|ovary(1)|pancreas(1)|urinary_tract(1)	12		all_cancers(25;0.0432)|all_epithelial(76;0.00812)|Medulloblastoma(540;0.0208)|all_neural(266;0.0416)|Hepatocellular(1079;0.114)		OV - Ovarian serous cystadenocarcinoma(262;8.51e-95)|Epithelial(262;1.15e-92)|all cancers(93;7.67e-84)|GBM - Glioblastoma multiforme(486;0.024)|STAD - Stomach adenocarcinoma(1328;0.183)		TGACCGCTGGGAGACAAAAGA	0.622																																					p.E369Q		Atlas-SNP	.											.	CCDC9	37	.	0			c.G1105C						PASS	.						35.0	35.0	35.0					19																	47774358		2198	4285	6483	SO:0001583	missense	26093	exon11			CGCTGGGAGACAA	AL050284	CCDS12698.1	19q13.33	2008-02-05				ENSG00000105321			24560	protein-coding gene	gene with protein product						11230166	Standard	NM_015603		Approved	DKFZP586M1019	uc010xym.2	Q9Y3X0		ENST00000221922.6:c.1105G>C	19.37:g.47774358G>C	ENSP00000221922:p.Glu369Gln	150.0	0.0	0		145.0	72.0	0.496552	NM_015603		Missense_Mutation	SNP	ENST00000221922.6	37	CCDS12698.1	.	.	.	.	.	.	.	.	.	.	.	13.05	2.122654	0.37436	.	.	ENSG00000105321	ENST00000221922;ENST00000504556	T	0.58358	0.34	4.34	4.34	0.51931	.	0.059852	0.64402	D	0.000005	T	0.69043	0.3067	M	0.69823	2.125	0.45025	D	0.998043	D	0.67145	0.996	D	0.75484	0.986	T	0.72080	-0.4398	10	0.62326	D	0.03	-22.8191	12.1997	0.54317	0.0:0.0:1.0:0.0	.	369	Q9Y3X0	CCDC9_HUMAN	Q	369;351	ENSP00000221922:E369Q	ENSP00000221922:E369Q	E	+	1	0	CCDC9	52466198	1.000000	0.71417	1.000000	0.80357	0.463000	0.32649	2.962000	0.49176	2.213000	0.71641	0.305000	0.20034	GAG	.	.	none		0.622	CCDC9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466917.1	NM_015603	
RPS24	6229	hgsc.bcm.edu	37	10	79814612	79814612	+	Silent	SNP	T	T	C	rs2257155	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr10:79814612T>C	ENST00000440692.1	+	5	856	c.714T>C	c.(712-714)ggT>ggC	p.G238G	RPS24_ENST00000476545.1_3'UTR	NM_001142285.1	NP_001135757.1	P62847	RS24_HUMAN	ribosomal protein S24	0					cellular protein metabolic process (GO:0044267)|erythrocyte homeostasis (GO:0034101)|gene expression (GO:0010467)|maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) (GO:0000462)|mRNA metabolic process (GO:0016071)|nuclear-transcribed mRNA catabolic process, nonsense-mediated decay (GO:0000184)|ribosomal small subunit biogenesis (GO:0042274)|RNA metabolic process (GO:0016070)|rRNA processing (GO:0006364)|SRP-dependent cotranslational protein targeting to membrane (GO:0006614)|translation (GO:0006412)|translational elongation (GO:0006414)|translational initiation (GO:0006413)|translational termination (GO:0006415)|viral life cycle (GO:0019058)|viral process (GO:0016032)|viral transcription (GO:0019083)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|cytosolic small ribosomal subunit (GO:0022627)|membrane (GO:0016020)|nucleolus (GO:0005730)|nucleus (GO:0005634)|small ribosomal subunit (GO:0015935)	nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)|structural constituent of ribosome (GO:0003735)|translation initiation factor binding (GO:0031369)			endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|ovary(2)|skin(1)	5	all_cancers(46;0.0343)|all_epithelial(25;0.000959)|Breast(12;0.00113)|Prostate(51;0.0095)		Epithelial(14;0.00128)|OV - Ovarian serous cystadenocarcinoma(4;0.00248)|all cancers(16;0.00428)			ctgtggacggtgacttggtcc	0.572													T|||	3	0.000599042	0.0	0.0014	5008	,	,		17704	0.0		0.002	False		,,,				2504	0.0				p.G238G		Atlas-SNP	.											.	RPS24	23	.	0			c.T714C						PASS	.	T		0,1384		0,0,692	105.0	103.0	104.0		714	-1.1	0.0	10	dbSNP_100	104	10,3172		0,10,1581	no	coding-synonymous	RPS24	NM_001142285.1		0,10,2273	CC,CT,TT		0.3143,0.0,0.219		238/290	79814612	10,4556	692	1591	2283	SO:0001819	synonymous_variant	6229	exon5			GGACGGTGACTTG	AB007159	CCDS7355.1, CCDS7356.1, CCDS44443.1	10q22	2011-04-06			ENSG00000138326	ENSG00000138326		"""S ribosomal proteins"""	10411	protein-coding gene	gene with protein product		602412				9027498, 9582194	Standard	NM_001142283		Approved	S24	uc001jzs.3	P62847	OTTHUMG00000018549	ENST00000440692.1:c.714T>C	10.37:g.79814612T>C		169.0	0.0	0		94.0	67.0	0.712766	NM_001142285	E7EPK6|P16632|Q5T0P7|Q5T0P8|Q7Z3D1	Silent	SNP	ENST00000440692.1	37	CCDS44443.1																																																																																			T|1.000;|0.000	.	weak		0.572	RPS24-202	KNOWN	basic|CCDS	protein_coding	protein_coding		NM_001026	
KHSRP	8570	hgsc.bcm.edu	37	19	6415735	6415735	+	Silent	SNP	A	A	G	rs145698454	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr19:6415735A>G	ENST00000398148.3	-	17	1790	c.1698T>C	c.(1696-1698)gcT>gcC	p.A566A	MIR3940_ENST00000579148.1_RNA	NM_003685.2	NP_003676.2	Q92945	FUBP2_HUMAN	KH-type splicing regulatory protein	566	Ala/Gly/Pro-rich.				gene expression (GO:0010467)|mRNA catabolic process (GO:0006402)|mRNA metabolic process (GO:0016071)|mRNA processing (GO:0006397)|mRNA transport (GO:0051028)|regulation of miRNA metabolic process (GO:2000628)|regulation of transcription, DNA-templated (GO:0006355)|RNA metabolic process (GO:0016070)|RNA splicing (GO:0008380)|RNA splicing, via transesterification reactions (GO:0000375)|transcription, DNA-templated (GO:0006351)	cytoplasmic stress granule (GO:0010494)|cytosol (GO:0005829)|membrane (GO:0016020)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	DNA binding (GO:0003677)|mRNA binding (GO:0003729)|poly(A) RNA binding (GO:0044822)	p.A566A(1)		breast(1)|central_nervous_system(2)|endometrium(2)|large_intestine(3)|liver(1)|lung(6)|skin(1)|soft_tissue(1)	17						CGGCCGCTGCAGCTGCTTTGC	0.706													A|||	32	0.00638978	0.0008	0.0144	5008	,	,		11509	0.0		0.0139	False		,,,				2504	0.0072				p.A566A	Colon(55;593 1006 2067 9135 22980)	Atlas-SNP	.											KHSRP,brain,primitive_neuroectodermal_tumour-medulloblastoma,0,1	KHSRP	51	1	1	Substitution - coding silent(1)	central_nervous_system(1)	c.T1698C						PASS	.	A		3,3369		0,3,1683	4.0	6.0	5.0		1698	-10.1	0.0	19	dbSNP_134	5	31,7415		0,31,3692	no	coding-synonymous	KHSRP	NM_003685.2		0,34,5375	GG,GA,AA		0.4163,0.089,0.3143		566/712	6415735	34,10784	1686	3723	5409	SO:0001819	synonymous_variant	8570	exon17			CGCTGCAGCTGCT	U94832	CCDS45936.1	19p13.3	2010-11-23	2008-02-04		ENSG00000088247	ENSG00000088247			6316	protein-coding gene	gene with protein product	"""FUSE binding protein 2"""	603445				9136930, 8940189	Standard	NM_003685		Approved	KSRP, FBP2, FUBP2	uc002mer.4	Q92945		ENST00000398148.3:c.1698T>C	19.37:g.6415735A>G		48.0	0.0	0		31.0	10.0	0.322581	NM_003685	O00301|Q59EZ9|Q5U4P6|Q9UNT5|Q9UQH5	Silent	SNP	ENST00000398148.3	37	CCDS45936.1																																																																																			A|0.994;G|0.006	0.006	strong		0.706	KHSRP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000453305.1		
DUSP19	142679	hgsc.bcm.edu	37	2	183951796	183951796	+	Missense_Mutation	SNP	G	G	A	rs368865344		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr2:183951796G>A	ENST00000354221.4	+	3	477	c.302G>A	c.(301-303)gGa>gAa	p.G101E	DUSP19_ENST00000342619.6_Intron|AC064871.3_ENST00000444562.1_RNA|DUSP19_ENST00000469344.1_Intron	NM_080876.3	NP_543152.1	Q8WTR2	DUS19_HUMAN	dual specificity phosphatase 19	101					inactivation of MAPK activity (GO:0000188)|JNK cascade (GO:0007254)|negative regulation of JNK cascade (GO:0046329)|negative regulation of JUN kinase activity (GO:0043508)|negative regulation of protein kinase activity (GO:0006469)|positive regulation of JNK cascade (GO:0046330)|positive regulation of JUN kinase activity (GO:0043507)|positive regulation of MAPK cascade (GO:0043410)|positive regulation of protein kinase activity (GO:0045860)|protein dephosphorylation (GO:0006470)	cytoplasm (GO:0005737)	JUN kinase phosphatase activity (GO:0008579)|MAP-kinase scaffold activity (GO:0005078)|mitogen-activated protein kinase kinase kinase binding (GO:0031435)|protein kinase activator activity (GO:0030295)|protein kinase inhibitor activity (GO:0004860)|protein tyrosine phosphatase activity (GO:0004725)|protein tyrosine/threonine phosphatase activity (GO:0008330)			breast(1)|kidney(2)|large_intestine(3)|lung(6)|ovary(4)|pancreas(1)	17						GTTGCATATGGAGTTGAAAAT	0.333																																					p.G101E		Atlas-SNP	.											.	DUSP19	41	.	0			c.G302A						PASS	.		GLU/GLY,	0,4404		0,0,2202	112.0	111.0	111.0		302,	5.4	1.0	2		111	1,8599	1.2+/-3.3	0,1,4299	no	missense,intron	DUSP19	NM_080876.3,NM_001142314.1	98,	0,1,6501	AA,AG,GG		0.0116,0.0,0.0077	possibly-damaging,	101/218,	183951796	1,13003	2202	4300	6502	SO:0001583	missense	142679	exon3			CATATGGAGTTGA	AB038770	CCDS2289.1, CCDS46469.1	2q32.1	2011-06-09			ENSG00000162999	ENSG00000162999		"""Protein tyrosine phosphatases / Class I Cys-based PTPs : Atypical dual specificity phosphatases"""	18894	protein-coding gene	gene with protein product		611437					Standard	NM_080876		Approved	SKRP1, DUSP17	uc002upd.3	Q8WTR2	OTTHUMG00000132622	ENST00000354221.4:c.302G>A	2.37:g.183951796G>A	ENSP00000346160:p.Gly101Glu	57.0	0.0	0		48.0	17.0	0.354167	NM_080876	B2RA79|Q547H4|Q8WYN4	Missense_Mutation	SNP	ENST00000354221.4	37	CCDS2289.1	.	.	.	.	.	.	.	.	.	.	g	18.99	3.739002	0.69304	0.0	1.16E-4	ENSG00000162999	ENST00000354221	D	0.83506	-1.73	5.38	5.38	0.77491	Dual specificity phosphatase, catalytic domain (1);Dual specificity phosphatase, subgroup, catalytic domain (2);	0.199838	0.53938	D	0.000058	T	0.79106	0.4390	L	0.35341	1.055	0.80722	D	1	P	0.42908	0.793	P	0.46885	0.53	T	0.74284	-0.3715	10	0.02654	T	1	.	19.5054	0.95113	0.0:0.0:1.0:0.0	.	101	Q8WTR2	DUS19_HUMAN	E	101	ENSP00000346160:G101E	ENSP00000346160:G101E	G	+	2	0	DUSP19	183660041	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	8.691000	0.91279	2.674000	0.91012	0.651000	0.88453	GGA	.	.	weak		0.333	DUSP19-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255866.1		
ZNF33A	7581	hgsc.bcm.edu	37	10	38345409	38345409	+	Missense_Mutation	SNP	A	A	G	rs71491230	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr10:38345409A>G	ENST00000458705.2	+	5	2512	c.2354A>G	c.(2353-2355)cAg>cGg	p.Q785R	ZNF33A_ENST00000469037.2_Intron|ZNF33A_ENST00000432900.2_Missense_Mutation_p.Q792R|ZNF33A_ENST00000374618.3_Missense_Mutation_p.Q786R|ZNF33A_ENST00000307441.9_Missense_Mutation_p.Q785R			Q06730	ZN33A_HUMAN	zinc finger protein 33A	785					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)	p.Q785R(1)		cervix(2)|endometrium(2)|large_intestine(8)|liver(2)|lung(27)|ovary(2)|prostate(1)|skin(2)	46						AGAAATTTCCAGCCACAAGTC	0.383													A|||	3	0.000599042	0.0	0.0	5008	,	,		18653	0.0		0.003	False		,,,				2504	0.0				p.Q786R		Atlas-SNP	.											ZNF33A,NS,carcinoma,0,1	ZNF33A	103	1	1	Substitution - Missense(1)	lung(1)	c.A2357G						PASS	.	A	ARG/GLN,ARG/GLN	2,4404	4.2+/-10.8	0,2,2201	61.0	61.0	61.0		2357,2354	0.6	0.0	10	dbSNP_130	61	25,8575	17.3+/-56.4	0,25,4275	yes	missense,missense	ZNF33A	NM_006954.1,NM_006974.2	43,43	0,27,6476	GG,GA,AA		0.2907,0.0454,0.2076	benign,benign	786/812,785/811	38345409	27,12979	2203	4300	6503	SO:0001583	missense	7581	exon5			ATTTCCAGCCACA	D31763	CCDS31182.1, CCDS60514.1, CCDS73088.1, CCDS73089.1	10p11.2	2013-01-08	2005-03-18		ENSG00000189180	ENSG00000189180		"""Zinc fingers, C2H2-type"", ""-"""	13096	protein-coding gene	gene with protein product	"""zinc finger and ZAK associated protein with KRAB domain"""	194521	"""zinc finger protein 33a (KOX 31)"", ""zinc finger protein 11A"""	ZNF33, ZNF11A		2014798, 8464732	Standard	NM_006974		Approved	KOX5, KOX31, KIAA0065, FLJ23404, ZZAPK	uc031pui.1	Q06730	OTTHUMG00000017983	ENST00000458705.2:c.2354A>G	10.37:g.38345409A>G	ENSP00000387713:p.Gln785Arg	162.0	0.0	0		95.0	24.0	0.252632	NM_006954	A8K9X9|B4E0M8|F6TH33|F8WAJ5|P17013|Q5VZ86	Missense_Mutation	SNP	ENST00000458705.2	37	CCDS31182.1	3	0.0013736263736263737	0	0.0	0	0.0	0	0.0	3	0.00395778364116095	A	7.459	0.644218	0.14451	4.54E-4	0.002907	ENSG00000189180	ENST00000374618;ENST00000432900;ENST00000458705;ENST00000307441	T;T;T;T	0.07327	3.2;3.46;3.2;3.2	1.92	0.561	0.17285	.	.	.	.	.	T	0.03827	0.0108	N	0.08118	0	0.09310	N	1	B;B;B	0.15141	0.012;0.007;0.012	B;B;B	0.09377	0.004;0.002;0.004	T	0.40961	-0.9535	9	0.87932	D	0	.	2.6079	0.04883	0.4659:0.2692:0.0:0.2649	.	792;785;786	F6TH33;Q06730;F8WAJ5	.;ZN33A_HUMAN;.	R	786;792;785;785	ENSP00000363747:Q786R;ENSP00000402467:Q792R;ENSP00000387713:Q785R;ENSP00000304268:Q785R	ENSP00000304268:Q785R	Q	+	2	0	ZNF33A	38385415	0.000000	0.05858	0.007000	0.13788	0.142000	0.21351	-0.152000	0.10159	-0.018000	0.14079	0.260000	0.18958	CAG	A|0.998;G|0.002	0.002	strong		0.383	ZNF33A-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000047614.1	NM_006974	
SF3B4	10262	hgsc.bcm.edu	37	1	149895866	149895866	+	Silent	SNP	G	G	A			TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr1:149895866G>A	ENST00000271628.8	-	5	1538	c.954C>T	c.(952-954)ggC>ggT	p.G318G		NM_005850.4	NP_005841.1	Q15427	SF3B4_HUMAN	splicing factor 3b, subunit 4, 49kDa	318					gene expression (GO:0010467)|mRNA processing (GO:0006397)|mRNA splicing, via spliceosome (GO:0000398)|RNA splicing (GO:0008380)|RNA splicing, via transesterification reactions (GO:0000375)	nucleoplasm (GO:0005654)|spliceosomal complex (GO:0005681)|U12-type spliceosomal complex (GO:0005689)	nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)			endometrium(2)|large_intestine(4)|lung(7)|ovary(2)|prostate(1)|skin(1)	17	Breast(34;0.0009)|all_hematologic(923;0.0597)|Hepatocellular(266;0.161)|Colorectal(459;0.171)		LUSC - Lung squamous cell carcinoma(543;0.221)|STAD - Stomach adenocarcinoma(528;0.247)			GATGTCCTAAGCCATGAGGGC	0.542																																					p.G318G		Atlas-SNP	.											.	SF3B4	37	.	0			c.C954T						PASS	.						12.0	13.0	13.0					1																	149895866		2197	4296	6493	SO:0001819	synonymous_variant	10262	exon5			TCCTAAGCCATGA	L35013	CCDS72900.1	1q21.2	2013-02-12	2002-08-29		ENSG00000143368	ENSG00000143368		"""RNA binding motif (RRM) containing"""	10771	protein-coding gene	gene with protein product		605593	"""splicing factor 3b, subunit 4, 49kD"""			7958871	Standard	NM_005850		Approved	SAP49, SF3b49, Hsh49	uc001etk.2	Q15427	OTTHUMG00000012208	ENST00000271628.8:c.954C>T	1.37:g.149895866G>A		101.0	0.0	0		120.0	31.0	0.258333	NM_005850	Q5SZ63	Silent	SNP	ENST00000271628.8	37	CCDS941.1																																																																																			.	.	none		0.542	SF3B4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000033753.1	NM_005850	
ZNF85	7639	hgsc.bcm.edu	37	19	21133078	21133078	+	Missense_Mutation	SNP	A	A	G	rs142868740	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr19:21133078A>G	ENST00000328178.8	+	4	1871	c.1758A>G	c.(1756-1758)atA>atG	p.I586M	ZNF85_ENST00000601023.1_Missense_Mutation_p.I527M|ZNF85_ENST00000345030.6_Missense_Mutation_p.I553M	NM_001256173.1|NM_003429.4	NP_001243102.1|NP_003420.2	Q03923	ZNF85_HUMAN	zinc finger protein 85	586					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)|transcription corepressor activity (GO:0003714)			breast(1)|central_nervous_system(1)|large_intestine(5)|lung(10)|ovary(1)|prostate(2)	20						AACATAAGATAATTCATACCG	0.284													.|||	2	0.000399361	0.0	0.0	5008	,	,		18633	0.0		0.001	False		,,,				2504	0.001				p.I616M		Atlas-SNP	.											.	ZNF85	72	.	0			c.A1848G						PASS	.	A	MET/ILE	0,4396		0,0,2198	18.0	19.0	19.0		1758	1.3	0.0	19	dbSNP_134	19	12,8550		0,12,4269	yes	missense	ZNF85	NM_003429.4	10	0,12,6467	GG,GA,AA		0.1402,0.0,0.0926	benign	586/596	21133078	12,12946	2198	4281	6479	SO:0001583	missense	7639	exon5			TAAGATAATTCAT	U35376	CCDS32977.1, CCDS58657.1	19p12	2013-01-08	2006-05-12			ENSG00000105750		"""Zinc fingers, C2H2-type"", ""-"""	13160	protein-coding gene	gene with protein product		603899	"""zinc finger protein 85 (HPF4, HTF1)"""			2505992	Standard	NM_003429		Approved	HPF4, HTF1	uc031rjx.1	Q03923		ENST00000328178.8:c.1758A>G	19.37:g.21133078A>G	ENSP00000329793:p.Ile586Met	99.0	0.0	0		98.0	46.0	0.469388	NM_001256171	B9ZVP4|Q6NVI0	Missense_Mutation	SNP	ENST00000328178.8	37	CCDS32977.1	1	4.578754578754579E-4	0	0.0	0	0.0	0	0.0	1	0.0013192612137203166	.	0.029	-1.346964	0.01266	0.0	0.001402	ENSG00000105750	ENST00000328178;ENST00000345030;ENST00000421385	T;T	0.07444	3.19;3.19	1.27	1.27	0.21489	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.04407	0.0121	N	0.12471	0.22	0.80722	D	1	P;B;P	0.44816	0.478;0.082;0.844	B;B;B	0.40165	0.272;0.002;0.321	T	0.48906	-0.8993	9	0.72032	D	0.01	.	5.3151	0.15850	0.7085:0.2915:0.0:0.0	.	553;527;586	Q03923-2;Q49A12;Q03923	.;.;ZNF85_HUMAN	M	586;553;461	ENSP00000329793:I586M;ENSP00000342340:I553M	ENSP00000329793:I586M	I	+	3	3	ZNF85	20924918	0.001000	0.12720	0.044000	0.18714	0.048000	0.14542	0.031000	0.13710	0.528000	0.28580	0.329000	0.21502	ATA	A|0.999;G|0.001	0.001	strong		0.284	ZNF85-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000463430.1	NM_003429	
TJP1	7082	hgsc.bcm.edu	37	15	30026582	30026582	+	Missense_Mutation	SNP	T	T	C	rs2229517	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr15:30026582T>C	ENST00000346128.6	-	12	1886	c.1412A>G	c.(1411-1413)aAc>aGc	p.N471S	TJP1_ENST00000400011.2_Missense_Mutation_p.N475S|TJP1_ENST00000356107.6_Missense_Mutation_p.N471S|TJP1_ENST00000545208.2_Missense_Mutation_p.N471S	NM_003257.3|NM_175610.2	NP_003248.3|NP_783297.2	Q07157	ZO1_HUMAN	tight junction protein 1	471	PDZ 3. {ECO:0000255|PROSITE- ProRule:PRU00143}.		N -> S (in dbSNP:rs2229517). {ECO:0000269|Ref.3}.		apoptotic process (GO:0006915)|blastocyst formation (GO:0001825)|cell-cell junction assembly (GO:0007043)|cell-cell signaling involved in cell-cell junction organization (GO:1901350)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|cellular response to glucose stimulus (GO:0071333)|hippo signaling (GO:0035329)|membrane organization (GO:0061024)|negative regulation of vascular permeability (GO:0043116)|response to drug (GO:0042493)|response to ethanol (GO:0045471)|response to lipopolysaccharide (GO:0032496)|response to magnetism (GO:0071000)|sensory perception of sound (GO:0007605)	apical junction complex (GO:0043296)|apical part of cell (GO:0045177)|apical plasma membrane (GO:0016324)|apicolateral plasma membrane (GO:0016327)|basolateral plasma membrane (GO:0016323)|cell junction (GO:0030054)|cell-cell adherens junction (GO:0005913)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|gap junction (GO:0005921)|intercalated disc (GO:0014704)|intercellular canaliculus (GO:0046581)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|tight junction (GO:0005923)				breast(4)|central_nervous_system(2)|endometrium(8)|kidney(3)|large_intestine(12)|liver(1)|lung(29)|ovary(4)|pancreas(1)|prostate(3)|urinary_tract(1)	68		all_lung(180;7.48e-11)|Breast(32;0.000153)		all cancers(64;3.29e-10)|Epithelial(43;5.34e-09)|BRCA - Breast invasive adenocarcinoma(123;0.0034)|GBM - Glioblastoma multiforme(186;0.0139)|Lung(196;0.186)		ATCTACGTTGTTTACCTAATA	0.348													T|||	24	0.00479233	0.003	0.0014	5008	,	,		17609	0.0		0.0109	False		,,,				2504	0.0082				p.N471S	Melanoma(77;681 1843 6309 6570)	Atlas-SNP	.											.	TJP1	140	.	0			c.A1412G						PASS	.	T	SER/ASN,SER/ASN	7,3635		0,7,1814	99.0	89.0	92.0		1412,1412	5.4	1.0	15	dbSNP_98	92	108,8050		0,108,3971	yes	missense,missense	TJP1	NM_003257.3,NM_175610.2	46,46	0,115,5785	CC,CT,TT		1.3239,0.1922,0.9746	benign,benign	471/1749,471/1669	30026582	115,11685	1821	4079	5900	SO:0001583	missense	7082	exon12			ACGTTGTTTACCT		CCDS42007.1, CCDS45199.1, CCDS73702.1	15q13	2012-07-12	2012-07-12		ENSG00000104067	ENSG00000104067			11827	protein-coding gene	gene with protein product	"""zona occludens 1"", ""tight junction protein ZO-1"""	601009				8825647	Standard	XM_005254616		Approved	ZO-1, MGC133289, DKFZp686M05161	uc001zcr.3	Q07157	OTTHUMG00000137397	ENST00000346128.6:c.1412A>G	15.37:g.30026582T>C	ENSP00000281537:p.Asn471Ser	135.0	0.0	0		61.0	43.0	0.704918	NM_175610	B4E3K1|Q2NKP3|Q4ZGJ6	Missense_Mutation	SNP	ENST00000346128.6	37	CCDS42007.1	16	0.007326007326007326	3	0.006097560975609756	2	0.0055248618784530384	0	0.0	11	0.014511873350923483	T	16.63	3.176786	0.57692	0.001922	0.013239	ENSG00000104067	ENST00000346128;ENST00000400011;ENST00000545208;ENST00000400007;ENST00000356107	T;T;T;T	0.59224	0.28;0.28;0.28;0.28	5.36	5.36	0.76844	Src homology-3 domain (1);PDZ/DHR/GLGF (4);	0.000000	0.85682	D	0.000000	T	0.72550	0.3474	M	0.85945	2.785	0.80722	D	1	B;D;B;D	0.89917	0.009;1.0;0.009;0.998	B;D;B;D	0.87578	0.04;0.998;0.04;0.994	T	0.79434	-0.1805	9	.	.	.	.	15.6385	0.76977	0.0:0.0:0.0:1.0	rs2229517;rs45612033	464;471;471;475	A9CQZ8;Q07157-2;Q07157;G5E9E7	.;.;ZO1_HUMAN;.	S	471;475;471;471;471	ENSP00000281537:N471S;ENSP00000382890:N475S;ENSP00000441202:N471S;ENSP00000348416:N471S	.	N	-	2	0	TJP1	27813874	1.000000	0.71417	1.000000	0.80357	0.762000	0.43233	7.997000	0.88414	2.147000	0.66899	0.477000	0.44152	AAC	T|0.991;C|0.009	0.009	strong		0.348	TJP1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000268237.3	NM_003257	
SFN	2810	hgsc.bcm.edu	37	1	27190149	27190149	+	Missense_Mutation	SNP	C	C	T	rs78707984		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr1:27190149C>T	ENST00000339276.4	+	1	517	c.446C>T	c.(445-447)tCa>tTa	p.S149L		NM_006142.3	NP_006133.1	Q9Y3B8	ORN_HUMAN	stratifin	0	Exonuclease.				nucleic acid phosphodiester bond hydrolysis (GO:0090305)|nucleobase-containing compound metabolic process (GO:0006139)|nucleotide metabolic process (GO:0009117)	focal adhesion (GO:0005925)|mitochondrion (GO:0005739)|nucleolus (GO:0005730)|nucleus (GO:0005634)	3'-5' exonuclease activity (GO:0008408)|nucleic acid binding (GO:0003676)			breast(1)|cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|lung(3)|skin(2)	9		all_cancers(24;1.23e-26)|all_epithelial(13;1.19e-23)|Colorectal(325;3.46e-05)|all_lung(284;5.94e-05)|Lung NSC(340;7.26e-05)|Breast(348;0.00017)|Renal(390;0.0007)|Ovarian(437;0.00764)|Myeloproliferative disorder(586;0.0255)|all_neural(195;0.0381)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0178)|all cancers(4;2.1e-52)|Epithelial(14;2.31e-52)|OV - Ovarian serous cystadenocarcinoma(117;8.22e-30)|Colorectal(126;1.31e-09)|COAD - Colon adenocarcinoma(152;3.45e-07)|BRCA - Breast invasive adenocarcinoma(304;0.000501)|STAD - Stomach adenocarcinoma(196;0.000588)|KIRC - Kidney renal clear cell carcinoma(1967;0.000716)|READ - Rectum adenocarcinoma(331;0.0419)|GBM - Glioblastoma multiforme(114;0.0767)|Lung(427;0.215)		TCAGCCCGGTCAGCCTACCAG	0.602																																					p.S149L		Atlas-SNP	.											.	SFN	20	.	0			c.C446T						PASS	.	C	LEU/SER	0,4406		0,0,2203	85.0	83.0	84.0		446	5.1	0.7	1	dbSNP_131	84	2,8598	2.2+/-6.3	0,2,4298	yes	missense	SFN	NM_006142.3	145	0,2,6501	TT,TC,CC		0.0233,0.0,0.0154	benign	149/249	27190149	2,13004	2203	4300	6503	SO:0001583	missense	2810	exon1			CCCGGTCAGCCTA	BC023552	CCDS288.1	1p36.11	2008-02-05			ENSG00000175793	ENSG00000175793			10773	protein-coding gene	gene with protein product	"""14-3-3 sigma"""	601290				8515476	Standard	NM_006142		Approved	YWHAS	uc001bnc.1	P31947	OTTHUMG00000004093	ENST00000339276.4:c.446C>T	1.37:g.27190149C>T	ENSP00000340989:p.Ser149Leu	48.0	0.0	0		41.0	11.0	0.268293	NM_006142	B2R532|Q32Q18|Q53FT1|Q6FIC6|Q9UFY7	Missense_Mutation	SNP	ENST00000339276.4	37	CCDS288.1	.	.	.	.	.	.	.	.	.	.	C	12.17	1.858571	0.32791	0.0	2.33E-4	ENSG00000175793	ENST00000339276;ENST00000538651	T	0.43688	0.94	6.06	5.1	0.69264	14-3-3 domain (4);	0.906876	0.09400	N	0.807339	T	0.20780	0.0500	N	0.02368	-0.58	0.09310	N	1	B	0.02656	0.0	B	0.08055	0.003	T	0.05402	-1.0887	10	0.25751	T	0.34	-0.5242	11.3178	0.49403	0.1716:0.7101:0.1183:0.0	.	149	P31947	1433S_HUMAN	L	149;117	ENSP00000340989:S149L	ENSP00000340989:S149L	S	+	2	0	SFN	27062736	0.144000	0.22641	0.733000	0.30861	0.993000	0.82548	2.150000	0.42254	2.871000	0.98454	0.655000	0.94253	TCA	.	.	weak		0.602	SFN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000011709.1	NM_006142	
PRDM4	11108	hgsc.bcm.edu	37	12	108140191	108140191	+	Silent	SNP	C	C	T			TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr12:108140191C>T	ENST00000228437.5	-	6	1596	c.1137G>A	c.(1135-1137)ctG>ctA	p.L379L	RP11-864J10.4_ENST00000546714.1_RNA	NM_012406.3	NP_036538.3	Q9UKN5	PRDM4_HUMAN	PR domain containing 4	379					cell proliferation (GO:0008283)|negative regulation of cell cycle (GO:0045786)|neurotrophin TRK receptor signaling pathway (GO:0048011)|regulation of transcription, DNA-templated (GO:0006355)|signal transduction (GO:0007165)|transcription from RNA polymerase II promoter (GO:0006366)	nucleus (GO:0005634)	DNA binding (GO:0003677)|methyltransferase activity (GO:0008168)|zinc ion binding (GO:0008270)			biliary_tract(1)|breast(2)|endometrium(1)|kidney(2)|large_intestine(3)|lung(6)|prostate(2)|skin(2)|urinary_tract(1)	20						CGCGGTCACACAGAGTACACC	0.458																																					p.L379L		Atlas-SNP	.											PRDM4,bladder,carcinoma,-1,1	PRDM4	64	1	0			c.G1137A						PASS	.						86.0	83.0	84.0					12																	108140191		2203	4300	6503	SO:0001819	synonymous_variant	11108	exon6			GTCACACAGAGTA	AF144757	CCDS9115.1	12q23-q24.1	2013-01-08				ENSG00000110851		"""Zinc fingers, C2H2-type"""	9348	protein-coding gene	gene with protein product		605780				10552934	Standard	NM_012406		Approved	PFM1	uc001tmp.3	Q9UKN5	OTTHUMG00000169914	ENST00000228437.5:c.1137G>A	12.37:g.108140191C>T		122.0	0.0	0		109.0	46.0	0.422018	NM_012406	Q9UFA6	Silent	SNP	ENST00000228437.5	37	CCDS9115.1																																																																																			.	.	none		0.458	PRDM4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000406546.1	NM_012406	
SCAF1	58506	hgsc.bcm.edu	37	19	50154607	50154607	+	Missense_Mutation	SNP	C	C	T	rs146455893	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr19:50154607C>T	ENST00000360565.3	+	7	1085	c.961C>T	c.(961-963)Cgc>Tgc	p.R321C		NM_021228.2	NP_067051.2	Q9H7N4	SFR19_HUMAN	SR-related CTD-associated factor 1	321					mRNA processing (GO:0006397)|RNA splicing (GO:0008380)|transcription from RNA polymerase II promoter (GO:0006366)	nucleus (GO:0005634)	RNA binding (GO:0003723)			breast(1)|central_nervous_system(1)|cervix(1)|endometrium(2)|kidney(1)|large_intestine(4)|lung(2)|ovary(1)|prostate(2)|skin(3)|upper_aerodigestive_tract(2)	20		all_lung(116;1.05e-05)|Lung NSC(112;3.77e-05)|all_neural(266;0.196)|Ovarian(192;0.231)		OV - Ovarian serous cystadenocarcinoma(262;0.00113)|GBM - Glioblastoma multiforme(134;0.0204)		CGAGAGCCCCCGCCCGGACGC	0.697																																					p.R321C		Atlas-SNP	.											.	SCAF1	78	.	0			c.C961T						PASS	.	C	CYS/ARG	2,4400		0,2,2199	18.0	19.0	19.0		961	0.7	0.2	19	dbSNP_134	19	5,8591		0,5,4293	no	missense	SCAF1	NM_021228.2	180	0,7,6492	TT,TC,CC		0.0582,0.0454,0.0539	possibly-damaging	321/1313	50154607	7,12991	2201	4298	6499	SO:0001583	missense	58506	exon7			AGCCCCCGCCCGG	AK024444	CCDS33074.1	19q13.3-q13.4	2011-01-10			ENSG00000126461	ENSG00000126461			30403	protein-coding gene	gene with protein product						11461075	Standard	NM_021228		Approved	SR-A1, FLJ00034	uc002poq.3	Q9H7N4		ENST00000360565.3:c.961C>T	19.37:g.50154607C>T	ENSP00000353769:p.Arg321Cys	20.0	0.0	0		19.0	16.0	0.842105	NM_021228	Q7Z5V7|Q8WVA1|Q9NR59	Missense_Mutation	SNP	ENST00000360565.3	37	CCDS33074.1	.	.	.	.	.	.	.	.	.	.	C	14.64	2.595518	0.46318	4.54E-4	5.82E-4	ENSG00000126461	ENST00000360565	T	0.34275	1.37	4.47	0.683	0.17998	.	1.130880	0.06849	N	0.797016	T	0.19685	0.0473	N	0.08118	0	0.09310	N	0.999999	P	0.44281	0.831	B	0.36186	0.219	T	0.23547	-1.0185	9	.	.	.	-2.8823	14.2469	0.65995	0.0:0.4311:0.5689:0.0	.	321	Q9H7N4	SFR19_HUMAN	C	321	ENSP00000353769:R321C	.	R	+	1	0	SCAF1	54846419	0.000000	0.05858	0.200000	0.23457	0.964000	0.63967	-0.197000	0.09518	0.401000	0.25424	0.591000	0.81541	CGC	A|0.000;C|0.999;T|0.001	0.001	strong		0.697	SCAF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000465764.1	NM_021228	
CLDN19	149461	hgsc.bcm.edu	37	1	43201614	43201614	+	Silent	SNP	C	C	T	rs9660973	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr1:43201614C>T	ENST00000296387.1	-	4	751	c.561G>A	c.(559-561)ccG>ccA	p.P187P	CLDN19_ENST00000372539.3_Silent_p.P187P|CLDN19_ENST00000539749.1_Missense_Mutation_p.R159Q	NM_001123395.1|NM_148960.2	NP_001116867.1|NP_683763.2	Q8N6F1	CLD19_HUMAN	claudin 19	187					apical junction assembly (GO:0043297)|calcium-independent cell-cell adhesion (GO:0016338)|neuronal action potential propagation (GO:0019227)|response to stimulus (GO:0050896)|visual perception (GO:0007601)	apical junction complex (GO:0043296)|basolateral plasma membrane (GO:0016323)|cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)|nucleus (GO:0005634)|tight junction (GO:0005923)	identical protein binding (GO:0042802)|structural molecule activity (GO:0005198)			breast(2)|large_intestine(1)|lung(2)|skin(1)	6	Ovarian(52;0.00744)|all_hematologic(146;0.0977)|Acute lymphoblastic leukemia(166;0.155)	Myeloproliferative disorder(586;0.0505)				TCTCTGGCTCCGGGCATGTGC	0.677													c|||	260	0.0519169	0.1006	0.0389	5008	,	,		16585	0.001		0.0398	False		,,,				2504	0.0603				p.R159Q		Atlas-SNP	.											.	CLDN19	21	.	0			c.G476A						PASS	.		,GLN/ARG,	396,3984		9,378,1803	30.0	28.0	29.0		561,476,561	-8.6	0.0	1	dbSNP_119	29	351,8217		5,341,3938	yes	coding-synonymous,missense,coding-synonymous	CLDN19	NM_001123395.1,NM_001185117.1,NM_148960.2	,43,	14,719,5741	TT,TC,CC		4.0966,9.0411,5.7692	,,	187/212,159/219,187/225	43201614	747,12201	2190	4284	6474	SO:0001819	synonymous_variant	149461	exon3			TGGCTCCGGGCAT	AK096063	CCDS471.1, CCDS44125.1, CCDS53306.1	1p34.2	2008-05-14			ENSG00000164007	ENSG00000164007		"""Claudins"""	2040	protein-coding gene	gene with protein product		610036					Standard	NM_148960		Approved		uc001cht.1	Q8N6F1	OTTHUMG00000007524	ENST00000296387.1:c.561G>A	1.37:g.43201614C>T		216.0	0.0	0		134.0	45.0	0.335821	NM_001185117	B7Z5I2|F5H5P9|Q5QT57|Q8N8X0	Missense_Mutation	SNP	ENST00000296387.1	37	CCDS471.1	98	0.04487179487179487	48	0.0975609756097561	19	0.052486187845303865	0	0.0	31	0.040897097625329816	c	11.52	1.664047	0.29604	0.090411	0.040966	ENSG00000164007	ENST00000539749	D	0.86627	-2.15	4.31	-8.62	0.00881	.	.	.	.	.	T	0.07458	0.0188	.	.	.	0.23260	N	0.998023	B	0.10296	0.003	B	0.04013	0.001	T	0.48714	-0.9011	8	0.72032	D	0.01	.	2.721	0.05201	0.2173:0.0855:0.367:0.3302	rs9660973;rs9660973	159	F5H5P9	.	Q	159	ENSP00000443229:R159Q	ENSP00000443229:R159Q	R	-	2	0	CLDN19	42974201	0.000000	0.05858	0.016000	0.15963	0.624000	0.37722	-2.658000	0.00852	-3.151000	0.00230	-0.516000	0.04426	CGG	C|0.945;T|0.055	0.055	strong		0.677	CLDN19-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000019788.1	NM_148960	
TPCN1	53373	hgsc.bcm.edu	37	12	113733830	113733830	+	Silent	SNP	C	C	T	rs61943642	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr12:113733830C>T	ENST00000335509.6	+	28	2714	c.2400C>T	c.(2398-2400)ccC>ccT	p.P800P	TPCN1_ENST00000392569.4_Silent_p.P732P|TPCN1_ENST00000541517.1_Silent_p.P872P|TPCN1_ENST00000550785.1_Silent_p.P872P	NM_017901.4	NP_060371.2	Q9ULQ1	TPC1_HUMAN	two pore segment channel 1	800					calcium ion transport (GO:0006816)|ion transmembrane transport (GO:0034220)|membrane depolarization during action potential (GO:0086010)|transmembrane transport (GO:0055085)	endosome membrane (GO:0010008)|integral component of membrane (GO:0016021)|lysosomal membrane (GO:0005765)|plasma membrane (GO:0005886)	identical protein binding (GO:0042802)|NAADP-sensitive calcium-release channel activity (GO:0072345)|voltage-gated calcium channel activity (GO:0005245)			cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(7)|lung(16)|ovary(2)|prostate(3)|skin(3)|urinary_tract(1)	40						GTGCAGCCCCCGCCGCCCAGC	0.617													C|||	123	0.0245607	0.0023	0.0461	5008	,	,		11380	0.0		0.0775	False		,,,				2504	0.0102				p.P872P		Atlas-SNP	.											.	TPCN1	109	.	0			c.C2616T						PASS	.	C	,	60,4340	48.9+/-83.8	2,56,2142	27.0	32.0	30.0		2616,2400	0.7	0.0	12	dbSNP_129	30	498,8102	133.3+/-190.8	13,472,3815	no	coding-synonymous,coding-synonymous	TPCN1	NM_001143819.1,NM_017901.4	,	15,528,5957	TT,TC,CC		5.7907,1.3636,4.2923	,	872/889,800/817	113733830	558,12442	2200	4300	6500	SO:0001819	synonymous_variant	53373	exon29			AGCCCCCGCCGCC	AB032995	CCDS31908.1, CCDS44985.1	12q24.21	2011-07-05			ENSG00000186815	ENSG00000186815		"""Voltage-gated ion channels / Two-pore channels"""	18182	protein-coding gene	gene with protein product		609666				10574461, 10753632, 16382101	Standard	XM_005253905		Approved	KIAA1169, FLJ20612, TPC1	uc001tux.3	Q9ULQ1	OTTHUMG00000169625	ENST00000335509.6:c.2400C>T	12.37:g.113733830C>T		158.0	0.0	0		121.0	60.0	0.495868	NM_001143819	A7E258|Q86XS9|Q8NC20	Silent	SNP	ENST00000335509.6	37	CCDS31908.1																																																																																			C|0.958;T|0.042	0.042	strong		0.617	TPCN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000405156.3	NM_017901	
SAE1	10055	hgsc.bcm.edu	37	19	47700542	47700542	+	Silent	SNP	T	T	C	rs117605411	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr19:47700542T>C	ENST00000270225.7	+	7	854	c.786T>C	c.(784-786)taT>taC	p.Y262Y	SAE1_ENST00000392776.3_Intron|SAE1_ENST00000598840.1_Silent_p.Y181Y|SAE1_ENST00000540850.1_Silent_p.Y88Y|SAE1_ENST00000413379.3_Intron	NM_005500.2	NP_005491.1	Q9UBE0	SAE1_HUMAN	SUMO1 activating enzyme subunit 1	262					cellular protein metabolic process (GO:0044267)|positive regulation of catalytic activity (GO:0043085)|post-translational protein modification (GO:0043687)|protein sumoylation (GO:0016925)|protein ubiquitination (GO:0016567)|regulation of mitotic cell cycle (GO:0007346)|SMT3-dependent protein catabolic process (GO:0019950)	cytosol (GO:0005829)|intracellular membrane-bounded organelle (GO:0043231)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	ATP-dependent protein binding (GO:0043008)|enzyme activator activity (GO:0008047)|protein C-terminus binding (GO:0008022)|protein heterodimerization activity (GO:0046982)|ubiquitin activating enzyme activity (GO:0004839)			endometrium(3)|large_intestine(5)|lung(4)|ovary(1)	13		all_cancers(25;1.13e-05)|all_lung(116;0.000192)|all_epithelial(76;0.000274)|Lung NSC(112;0.000446)|all_neural(266;0.0652)|Ovarian(192;0.15)		all cancers(93;0.00013)|OV - Ovarian serous cystadenocarcinoma(262;0.000146)|Epithelial(262;0.00697)|GBM - Glioblastoma multiforme(486;0.0278)		CTGATACATATGAGGAAGATT	0.408													T|||	23	0.00459265	0.0	0.0014	5008	,	,		19443	0.001		0.005	False		,,,				2504	0.0164				p.Y262Y		Atlas-SNP	.											.	SAE1	50	.	0			c.T786C						PASS	.	T	,,	9,4397	14.3+/-33.2	0,9,2194	213.0	193.0	200.0		,,786	-4.8	0.0	19	dbSNP_132	200	27,8573	19.2+/-60.6	0,27,4273	no	intron,intron,coding-synonymous	SAE1	NM_001145713.1,NM_001145714.1,NM_005500.2	,,	0,36,6467	CC,CT,TT		0.314,0.2043,0.2768	,,	,,262/347	47700542	36,12970	2203	4300	6503	SO:0001819	synonymous_variant	10055	exon7			TACATATGAGGAA	BC018271	CCDS12696.1, CCDS54284.1, CCDS54285.1	19q13.32	2013-09-26				ENSG00000142230		"""Ubiquitin-like modifier activating enzymes"""	30660	protein-coding gene	gene with protein product	"""activator Of sumo 1"""	613294				10187858, 9920803, 10217437	Standard	NM_005500		Approved	AOS1, FLJ3091, Sua1	uc002pgc.3	Q9UBE0		ENST00000270225.7:c.786T>C	19.37:g.47700542T>C		238.0	0.0	0		190.0	74.0	0.389474	NM_005500	B2RDP5|B3KMQ2|F5GXX7|G3XAK6|O95717|Q9P020	Silent	SNP	ENST00000270225.7	37	CCDS12696.1																																																																																			T|0.997;C|0.003	0.003	strong		0.408	SAE1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466775.1	NM_005500	
IRF2BPL	64207	hgsc.bcm.edu	37	14	77493809	77493809	+	Silent	SNP	C	C	T	rs61991638		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr14:77493809C>T	ENST00000238647.3	-	1	1225	c.327G>A	c.(325-327)caG>caA	p.Q109Q		NM_024496.3	NP_078772.1	Q9H1B7	I2BPL_HUMAN	interferon regulatory factor 2 binding protein-like	109	Poly-Gln.				development of secondary female sexual characteristics (GO:0046543)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)	extracellular space (GO:0005615)|nucleus (GO:0005634)	metal ion binding (GO:0046872)			endometrium(2)|kidney(1)|lung(3)|ovary(1)|prostate(1)|skin(1)|urinary_tract(2)	11						gctgctgctgctgctgttgct	0.687																																					p.Q109Q		Atlas-SNP	.											.	IRF2BPL	40	.	0			c.G327A						PASS	.						2.0	2.0	2.0					14																	77493809		1179	2145	3324	SO:0001819	synonymous_variant	64207	exon1			CTGCTGCTGCTGT	AJ277365	CCDS9854.1	14q24.3	2011-02-23	2011-02-23	2011-02-23	ENSG00000119669	ENSG00000119669			14282	protein-coding gene	gene with protein product	"""enhanced at puberty 1"""	611720	"""chromosome 14 open reading frame 4"""	C14orf4		11095982, 17627301	Standard	NM_024496		Approved	EAP1, KIAA1865	uc001xsy.4	Q9H1B7		ENST00000238647.3:c.327G>A	14.37:g.77493809C>T		15.0	0.0	0		13.0	4.0	0.307692	NM_024496	Q8NDQ2|Q96JG2|Q9H3I7	Silent	SNP	ENST00000238647.3	37	CCDS9854.1																																																																																			C|0.978;T|0.022	0.022	strong		0.687	IRF2BPL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000414298.1	NM_024496	
PEX5	5830	hgsc.bcm.edu	37	12	7343153	7343153	+	Intron	SNP	A	A	G			TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr12:7343153A>G	ENST00000455147.2	+	3	727				PEX5_ENST00000434354.2_Silent_p.A60A|PEX5_ENST00000266563.5_Intron|RP11-273B20.3_ENST00000545794.1_RNA|PEX5_ENST00000412720.2_Intron|PEX5_ENST00000420616.2_Intron|PEX5_ENST00000266564.3_Intron|PEX5_ENST00000545220.1_Intron|RP11-273B20.3_ENST00000543061.1_RNA	NM_001131026.1	NP_001124498.1	P50542	PEX5_HUMAN	peroxisomal biogenesis factor 5						cell development (GO:0048468)|cerebral cortex cell migration (GO:0021795)|cerebral cortex neuron differentiation (GO:0021895)|endoplasmic reticulum organization (GO:0007029)|fatty acid beta-oxidation (GO:0006635)|mitochondrial membrane organization (GO:0007006)|negative regulation of protein homotetramerization (GO:1901094)|neuromuscular process (GO:0050905)|neuron migration (GO:0001764)|positive regulation of multicellular organism growth (GO:0040018)|protein import into peroxisome matrix (GO:0016558)|protein import into peroxisome matrix, docking (GO:0016560)|protein import into peroxisome matrix, translocation (GO:0016561)|protein import into peroxisome membrane (GO:0045046)|protein targeting to peroxisome (GO:0006625)|protein tetramerization (GO:0051262)|very long-chain fatty acid metabolic process (GO:0000038)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|Golgi apparatus (GO:0005794)|intracellular (GO:0005622)|membrane (GO:0016020)|mitochondrion (GO:0005739)|peroxisomal matrix (GO:0005782)|peroxisomal membrane (GO:0005778)|peroxisome (GO:0005777)|protein complex (GO:0043234)	enzyme binding (GO:0019899)|peroxisome matrix targeting signal-1 binding (GO:0005052)|peroxisome targeting sequence binding (GO:0000268)|protein C-terminus binding (GO:0008022)|protein N-terminus binding (GO:0047485)|small GTPase binding (GO:0031267)			breast(1)|endometrium(3)|kidney(1)|large_intestine(5)|lung(8)|ovary(1)|prostate(1)|skin(1)	21						GCCCAGGTGCAGCCTCTGAGG	0.627																																					p.A60A		Atlas-SNP	.											PEX5_ENST00000434354,colon,carcinoma,0,3	PEX5	63	3	0			c.A180G						scavenged	.						9.0	11.0	11.0					12																	7343153		2154	4209	6363	SO:0001627	intron_variant	5830	exon2			AGGTGCAGCCTCT	U19721	CCDS8576.1, CCDS44822.1, CCDS44823.1, CCDS44824.1, CCDS73433.1	12p	2013-01-10	2004-03-17	2004-03-19		ENSG00000139197		"""Tetratricopeptide (TTC) repeat domain containing"""	9719	protein-coding gene	gene with protein product		600414	"""peroxisome receptor 1"""	PXR1			Standard	NM_000319		Approved	PTS1R	uc010sgc.2	P50542		ENST00000455147.2:c.147+33A>G	12.37:g.7343153A>G		49.0	2.0	0.0408163		61.0	6.0	0.0983607	NM_001131023	A8K891|B4DZ45|B7ZAD5|D3DUT8|Q15115|Q15266|Q96FN7	Silent	SNP	ENST00000455147.2	37	CCDS44823.1																																																																																			.	.	none		0.627	PEX5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000398611.1	NM_000319	
ABCC11	85320	hgsc.bcm.edu	37	16	48226458	48226458	+	Silent	SNP	C	C	T	rs144318062		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr16:48226458C>T	ENST00000394747.1	-	19	3028	c.2679G>A	c.(2677-2679)acG>acA	p.T893T	ABCC11_ENST00000353782.5_Silent_p.T893T|ABCC11_ENST00000394748.1_Silent_p.T893T|ABCC11_ENST00000356608.2_Silent_p.T893T|ABCC11_ENST00000537808.1_3'UTR	NM_033151.3	NP_149163.2	Q96J66	ABCCB_HUMAN	ATP-binding cassette, sub-family C (CFTR/MRP), member 11	893	ABC transmembrane type-1 2. {ECO:0000255|PROSITE-ProRule:PRU00441}.				organic anion transport (GO:0015711)|purine nucleotide transport (GO:0015865)|transmembrane transport (GO:0055085)	extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|ATPase activity, coupled to transmembrane movement of substances (GO:0042626)|organic anion transmembrane transporter activity (GO:0008514)|purine nucleotide transmembrane transporter activity (GO:0015216)			breast(3)|central_nervous_system(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(12)|lung(42)|ovary(3)|prostate(2)|skin(5)|urinary_tract(2)	83		all_cancers(37;0.127)|all_lung(18;0.132)|Breast(268;0.166)			Conjugated Estrogens(DB00286)|Folic Acid(DB00158)|Indomethacin(DB00328)|Methotrexate(DB00563)|Probenecid(DB01032)	TGTGCAGGGCCGTGGATGCCT	0.552																																					p.T893T		Atlas-SNP	.											.	ABCC11	177	.	0			c.G2679A						PASS	.	C	,,	0,4402		0,0,2201	90.0	82.0	85.0		2679,2679,2679	-9.9	0.0	16	dbSNP_134	85	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous,coding-synonymous,coding-synonymous	ABCC11	NM_032583.3,NM_033151.3,NM_145186.2	,,	0,1,6500	TT,TC,CC		0.0116,0.0,0.0077	,,	893/1383,893/1383,893/1345	48226458	1,13001	2201	4300	6501	SO:0001819	synonymous_variant	85320	exon19			CAGGGCCGTGGAT	AF367202	CCDS10732.1, CCDS10733.1	16q12	2012-03-14			ENSG00000121270	ENSG00000121270		"""ATP binding cassette transporters / subfamily C"""	14639	protein-coding gene	gene with protein product		607040				11483364, 11435397	Standard	NM_033151		Approved	MRP8	uc002efg.1	Q96J66	OTTHUMG00000133146	ENST00000394747.1:c.2679G>A	16.37:g.48226458C>T		148.0	0.0	0		141.0	116.0	0.822695	NM_033151	Q8TDJ0|Q96JA6|Q9BX80	Silent	SNP	ENST00000394747.1	37	CCDS10732.1																																																																																			C|1.000;T|0.000	0.000	weak		0.552	ABCC11-004	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000429984.1	NM_032583	
SSPO	23145	hgsc.bcm.edu	37	7	149485557	149485557	+	RNA	SNP	C	C	T	rs73168056	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr7:149485557C>T	ENST00000378016.2	+	0	3963							A2VEC9	SSPO_HUMAN	SCO-spondin						cell adhesion (GO:0007155)	extracellular space (GO:0005615)	peptidase inhibitor activity (GO:0030414)					Melanoma(164;0.165)|Ovarian(565;0.177)		OV - Ovarian serous cystadenocarcinoma(82;0.00625)			CTCTGCTGCACGGTGTGTAGA	0.652													C|||	65	0.0129792	0.0008	0.0548	5008	,	,		20320	0.0		0.0209	False		,,,				2504	0.0051				p.H1321H		Atlas-SNP	.											.	.	.	.	0			c.C3963T						PASS	.	C		18,4176		1,16,2080	34.0	41.0	39.0		3967	-6.3	0.6	7	dbSNP_130	39	136,8306		1,134,4086	yes	coding-notMod3-near-splice	SSPO	NM_198455.2		2,150,6166	TT,TC,CC		1.611,0.4292,1.2187			149485557	154,12482	2097	4221	6318			23145	exon27			GCTGCACGGTGTG	AK093431		7q36.1	2013-08-07	2013-08-06		ENSG00000197558	ENSG00000197558			21998	protein-coding gene	gene with protein product	"""subcommissural organ spondin"", ""SCO protein, thrombospondin domain containing"""		"""SCO-spondin homolog (Bos taurus)"""			8743952, 11008217	Standard	NM_198455		Approved	SCO-spondin, KIAA0543, FLJ36112	uc010lpk.3	A2VEC9	OTTHUMG00000157884		7.37:g.149485557C>T		117.0	0.0	0		86.0	15.0	0.174419	NM_198455	Q76B61	Silent	SNP	ENST00000378016.2	37																																																																																				C|0.986;T|0.014	0.014	strong		0.652	SSPO-202	KNOWN	basic	processed_transcript	processed_transcript			
CGRRF1	10668	hgsc.bcm.edu	37	14	55005083	55005083	+	Silent	SNP	C	C	T	rs202061859		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr14:55005083C>T	ENST00000216420.7	+	6	1113	c.981C>T	c.(979-981)gaC>gaT	p.D327D		NM_006568.2	NP_006559.1	Q99675	CGRF1_HUMAN	cell growth regulator with ring finger domain 1	327					cell cycle arrest (GO:0007050)|negative regulation of cell proliferation (GO:0008285)|response to stress (GO:0006950)	intracellular membrane-bounded organelle (GO:0043231)|nucleus (GO:0005634)	zinc ion binding (GO:0008270)			endometrium(3)|kidney(2)|lung(5)|ovary(2)|stomach(1)	13						AAGATAAAGACAAACCGAAGA	0.383																																					p.D327D		Atlas-SNP	.											.	CGRRF1	30	.	0			c.C981T						PASS	.	C		0,4406		0,0,2203	71.0	67.0	69.0		981	1.5	0.2	14		69	2,8598	1.2+/-3.3	0,2,4298	no	coding-synonymous	CGRRF1	NM_006568.2		0,2,6501	TT,TC,CC		0.0233,0.0,0.0154		327/333	55005083	2,13004	2203	4300	6503	SO:0001819	synonymous_variant	10668	exon6			TAAAGACAAACCG	BC015063	CCDS9719.1	14q22.2	2013-09-20			ENSG00000100532	ENSG00000100532		"""RING-type (C3HC4) zinc fingers"""	15528	protein-coding gene	gene with protein product		606138				8968090	Standard	NM_006568		Approved	CGR19, RNF197	uc001xay.3	Q99675	OTTHUMG00000140308	ENST00000216420.7:c.981C>T	14.37:g.55005083C>T		87.0	0.0	0		98.0	32.0	0.326531	NM_006568	Q96BX2	Silent	SNP	ENST00000216420.7	37	CCDS9719.1																																																																																			C|0.999;T|0.001	0.001	weak		0.383	CGRRF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276905.2	NM_006568	
SSPO	23145	hgsc.bcm.edu	37	7	149519742	149519742	+	RNA	SNP	G	G	A	rs201102091	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr7:149519742G>A	ENST00000378016.2	+	0	13232							A2VEC9	SSPO_HUMAN	SCO-spondin						cell adhesion (GO:0007155)	extracellular space (GO:0005615)	peptidase inhibitor activity (GO:0030414)					Melanoma(164;0.165)|Ovarian(565;0.177)		OV - Ovarian serous cystadenocarcinoma(82;0.00625)			GGCCACTTCCGGCCTTGCCTT	0.687													G|||	6	0.00119808	0.0	0.0029	5008	,	,		15642	0.0		0.003	False		,,,				2504	0.001				p.R4411Q		Atlas-SNP	.											.	.	.	.	0			c.G13232A						PASS	.	G		5,3807		0,5,1901	6.0	8.0	8.0		13246	4.0	1.0	7		8	36,8100		0,36,4032	yes	coding-notMod3	SSPO	NM_198455.2		0,41,5933	AA,AG,GG		0.4425,0.1312,0.3432			149519742	41,11907	1906	4068	5974			23145	exon91			ACTTCCGGCCTTG	AK093431		7q36.1	2013-08-07	2013-08-06		ENSG00000197558	ENSG00000197558			21998	protein-coding gene	gene with protein product	"""subcommissural organ spondin"", ""SCO protein, thrombospondin domain containing"""		"""SCO-spondin homolog (Bos taurus)"""			8743952, 11008217	Standard	NM_198455		Approved	SCO-spondin, KIAA0543, FLJ36112	uc010lpk.3	A2VEC9	OTTHUMG00000157884		7.37:g.149519742G>A		118.0	0.0	0		48.0	11.0	0.229167	NM_198455	Q76B61	Missense_Mutation	SNP	ENST00000378016.2	37																																																																																				.	.	weak		0.687	SSPO-202	KNOWN	basic	processed_transcript	processed_transcript			
MAP2K1	5604	hgsc.bcm.edu	37	15	66727483	66727483	+	Missense_Mutation	SNP	G	G	A			TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr15:66727483G>A	ENST00000307102.5	+	2	730	c.199G>A	c.(199-201)Gac>Aac	p.D67N		NM_002755.3	NP_002746.1	Q02750	MP2K1_HUMAN	mitogen-activated protein kinase kinase 1	67					activation of MAPK activity (GO:0000187)|activation of MAPKK activity (GO:0000186)|axon guidance (GO:0007411)|cell cycle arrest (GO:0007050)|cell motility (GO:0048870)|cell proliferation (GO:0008283)|cellular component movement (GO:0006928)|cellular senescence (GO:0090398)|chemotaxis (GO:0006935)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|Golgi inheritance (GO:0048313)|innate immune response (GO:0045087)|insulin receptor signaling pathway (GO:0008286)|keratinocyte differentiation (GO:0030216)|labyrinthine layer development (GO:0060711)|MAPK cascade (GO:0000165)|melanosome transport (GO:0032402)|mitotic nuclear division (GO:0007067)|MyD88-dependent toll-like receptor signaling pathway (GO:0002755)|MyD88-independent toll-like receptor signaling pathway (GO:0002756)|negative regulation of cell proliferation (GO:0008285)|negative regulation of homotypic cell-cell adhesion (GO:0034111)|neurotrophin TRK receptor signaling pathway (GO:0048011)|placenta blood vessel development (GO:0060674)|positive regulation of cell differentiation (GO:0045597)|positive regulation of cell migration (GO:0030335)|positive regulation of gene expression (GO:0010628)|positive regulation of protein serine/threonine kinase activity (GO:0071902)|positive regulation of Ras GTPase activity (GO:0032320)|positive regulation of Ras protein signal transduction (GO:0046579)|positive regulation of transcription elongation from RNA polymerase II promoter (GO:0032968)|protein heterooligomerization (GO:0051291)|Ras protein signal transduction (GO:0007265)|regulation of early endosome to late endosome transport (GO:2000641)|regulation of Golgi inheritance (GO:0090170)|regulation of stress-activated MAPK cascade (GO:0032872)|regulation of vascular smooth muscle contraction (GO:0003056)|response to axon injury (GO:0048678)|response to glucocorticoid (GO:0051384)|response to oxidative stress (GO:0006979)|signal transduction (GO:0007165)|small GTPase mediated signal transduction (GO:0007264)|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)|TRIF-dependent toll-like receptor signaling pathway (GO:0035666)|vesicle transport along microtubule (GO:0047496)	cell cortex (GO:0005938)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|dendrite cytoplasm (GO:0032839)|early endosome (GO:0005769)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|Golgi apparatus (GO:0005794)|late endosome (GO:0005770)|mitochondrion (GO:0005739)|nucleus (GO:0005634)|perikaryon (GO:0043204)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|MAP kinase kinase activity (GO:0004708)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activator activity (GO:0043539)|protein serine/threonine kinase activity (GO:0004674)|protein serine/threonine/tyrosine kinase activity (GO:0004712)|protein tyrosine kinase activity (GO:0004713)|receptor signaling protein tyrosine phosphatase activity (GO:0004728)	p.D67N(1)		endometrium(2)|kidney(1)|large_intestine(1)|lung(6)|prostate(1)|skin(8)|urinary_tract(1)	20					Bosutinib(DB06616)|Trametinib(DB08911)	GAAGGATGACGACTTTGAGAA	0.547																																					p.D67N		Atlas-SNP	.											MAP2K1,NS,lymphoid_neoplasm,0,5	MAP2K1	115	5	1	Substitution - Missense(1)	large_intestine(1)	c.G199A	GRCh37	CM076269	MAP2K1	M		PASS	.						188.0	174.0	179.0					15																	66727483		2201	4299	6500	SO:0001583	missense	5604	exon2			GATGACGACTTTG	L11284	CCDS10216.1	15q22.1-q22.33	2014-09-17			ENSG00000169032	ENSG00000169032	2.7.12.2	"""Mitogen-activated protein kinase cascade / Kinase kinases"""	6840	protein-coding gene	gene with protein product		176872		PRKMK1		9465908, 8388392	Standard	NM_002755		Approved	MEK1, MAPKK1	uc010bhq.3	Q02750	OTTHUMG00000133196	ENST00000307102.5:c.199G>A	15.37:g.66727483G>A	ENSP00000302486:p.Asp67Asn	141.0	0.0	0		97.0	54.0	0.556701	NM_002755		Missense_Mutation	SNP	ENST00000307102.5	37	CCDS10216.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	36|36	5.691697|5.691697	0.96793|0.96793	.|.	.|.	ENSG00000169032|ENSG00000169032	ENST00000307102|ENST00000425818	D|.	0.93859|.	-3.3|.	5.24|5.24	5.24|5.24	0.73138|0.73138	Protein kinase-like domain (1);|.	0.091006|.	0.85682|.	D|.	0.000000|.	T|T	0.76133|0.76133	0.3945|0.3945	M|M	0.73962|0.73962	2.25|2.25	0.80722|0.80722	D|D	1|1	D;D|.	0.76494|.	0.999;0.993|.	D;P|.	0.64687|.	0.928;0.638|.	T|T	0.76211|0.76211	-0.3042|-0.3042	10|5	0.72032|.	D|.	0.01|.	-32.7633|-32.7633	17.8302|17.8302	0.88680|0.88680	0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0	.|.	45;67|.	B4DFY5;Q02750|.	.;MP2K1_HUMAN|.	N|Q	67|6	ENSP00000302486:D67N|.	ENSP00000302486:D67N|.	D|R	+|+	1|2	0|0	MAP2K1|MAP2K1	64514537|64514537	1.000000|1.000000	0.71417|0.71417	0.993000|0.993000	0.49108|0.49108	0.983000|0.983000	0.72400|0.72400	9.723000|9.723000	0.98772|0.98772	2.443000|2.443000	0.82685|0.82685	0.591000|0.591000	0.81541|0.81541	GAC|CGA	.	.	none		0.547	MAP2K1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256906.4		
ABCA3	21	hgsc.bcm.edu	37	16	2329071	2329071	+	Missense_Mutation	SNP	G	G	A	rs146709251	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr16:2329071G>A	ENST00000301732.5	-	29	5120	c.4420C>T	c.(4420-4422)Cgg>Tgg	p.R1474W	ABCA3_ENST00000382381.3_Missense_Mutation_p.R1416W	NM_001089.2	NP_001080.2	Q99758	ABCA3_HUMAN	ATP-binding cassette, sub-family A (ABC1), member 3	1474	ABC transporter 2. {ECO:0000255|PROSITE- ProRule:PRU00434}.				response to drug (GO:0042493)|transmembrane transport (GO:0055085)|transport (GO:0006810)	alveolar lamellar body (GO:0097208)|alveolar lamellar body membrane (GO:0097233)|extracellular space (GO:0005615)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|ATPase activity, coupled to transmembrane movement of substances (GO:0042626)|transporter activity (GO:0005215)			breast(7)|central_nervous_system(4)|cervix(1)|endometrium(5)|kidney(2)|large_intestine(11)|liver(1)|lung(20)|ovary(7)|prostate(5)|skin(6)|upper_aerodigestive_tract(1)	70		Ovarian(90;0.17)			Imatinib(DB00619)	AGCATCTCCCGGCCTGTCATG	0.677													G|||	11	0.00219649	0.0	0.0	5008	,	,		18482	0.0		0.0109	False		,,,				2504	0.0				p.R1474W		Atlas-SNP	.											.	ABCA3	176	.	0			c.C4420T						PASS	.	G	TRP/ARG	1,4395	2.1+/-5.4	0,1,2197	56.0	57.0	57.0		4420	3.3	1.0	16	dbSNP_134	57	31,8569	22.2+/-67.0	0,31,4269	yes	missense	ABCA3	NM_001089.2	101	0,32,6466	AA,AG,GG		0.3605,0.0227,0.2462	probably-damaging	1474/1705	2329071	32,12964	2198	4300	6498	SO:0001583	missense	21	exon29			TCTCCCGGCCTGT	U78735	CCDS10466.1	16p13.3	2012-03-14			ENSG00000167972	ENSG00000167972		"""ATP binding cassette transporters / subfamily A"""	33	protein-coding gene	gene with protein product		601615		ABC3		8706931	Standard	NM_001089		Approved	ABC-C, EST111653, LBM180	uc002cpy.1	Q99758	OTTHUMG00000128845	ENST00000301732.5:c.4420C>T	16.37:g.2329071G>A	ENSP00000301732:p.Arg1474Trp	134.0	0.0	0		143.0	67.0	0.468531	NM_001089	B2RU09|Q54A95|Q6P5P9|Q92473	Missense_Mutation	SNP	ENST00000301732.5	37	CCDS10466.1	8	0.003663003663003663	0	0.0	0	0.0	0	0.0	8	0.010554089709762533	G	13.04	2.118520	0.37436	2.27E-4	0.003605	ENSG00000167972	ENST00000301732;ENST00000382381	D	0.94613	-3.47	5.35	3.32	0.38043	ATPase, AAA+ type, core (1);ABC transporter-like (2);	0.057559	0.64402	N	0.000002	D	0.92414	0.7592	M	0.76328	2.33	0.80722	D	1	P;P	0.43024	0.798;0.689	P;P	0.47573	0.55;0.466	D	0.90607	0.4549	10	0.56958	D	0.05	.	9.1349	0.36868	0.0781:0.0:0.7721:0.1498	.	1478;1474	Q4LE27;Q99758	.;ABCA3_HUMAN	W	1474;1478	ENSP00000301732:R1474W	ENSP00000301732:R1474W	R	-	1	2	ABCA3	2269072	1.000000	0.71417	0.998000	0.56505	0.958000	0.62258	2.466000	0.45084	0.580000	0.29522	0.561000	0.74099	CGG	G|0.997;A|0.003	0.003	strong		0.677	ABCA3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250784.2	NM_001089	
PRB3	5544	hgsc.bcm.edu	37	12	11421004	11421004	+	Missense_Mutation	SNP	C	C	T	rs71455364		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr12:11421004C>T	ENST00000279573.7	-	3	314	c.179G>A	c.(178-180)cGa>cAa	p.R60Q	PRB3_ENST00000538488.1_Missense_Mutation_p.R60Q|PRB3_ENST00000381842.3_Missense_Mutation_p.R60Q|PRB3_ENST00000440870.3_5'UTR			Q04118	PRB3_HUMAN	proline-rich protein BstNI subfamily 3	60	10 X 21 AA tandem repeats of [RH]-P-G-K- P-[EQ]-G-[PQS]-P-[PS]-Q-[GE]-G-N-[QK]- [SP]-[QR]-[GR]-P-P-P.|Pro-rich.			R -> P (in Ref. 1; CAA30728). {ECO:0000305}.	defense response to Gram-negative bacterium (GO:0050829)	extracellular region (GO:0005576)				breast(2)|endometrium(1)|kidney(2)|large_intestine(1)|lung(13)|ovary(1)|skin(5)	25			OV - Ovarian serous cystadenocarcinoma(49;0.201)			TTGTGGGGGTCGTCCTTCTGG	0.627																																					p.R60Q		Atlas-SNP	.											.	PRB3	84	.	0			c.G179A						PASS	.						160.0	173.0	168.0					12																	11421004		2198	4296	6494	SO:0001583	missense	5544	exon3			GGGGGTCGTCCTT			12p13.2	2012-10-02				ENSG00000197870			9339	protein-coding gene	gene with protein product		168840				1894623	Standard	NM_006249		Approved	PRG	uc001qzs.3	Q04118		ENST00000279573.7:c.179G>A	12.37:g.11421004C>T	ENSP00000279573:p.Arg60Gln	108.0	0.0	0		73.0	27.0	0.369863	NM_006249	Q15188|Q4VAY3|Q4VAY4|Q7M4M9|Q9UCT9	Missense_Mutation	SNP	ENST00000279573.7	37		.	.	.	.	.	.	.	.	.	.	.	3.985	-0.005638	0.07773	.	.	ENSG00000197870	ENST00000381842;ENST00000538488	T;T	0.04119	3.7;3.7	0.763	-1.53	0.08611	.	0.242690	0.19335	U	0.116811	T	0.02610	0.0079	.	.	.	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.46233	-0.9206	9	0.13470	T	0.59	.	5.5053	0.16850	0.0:0.3072:0.4664:0.2265	.	60	Q04118	PRB3_HUMAN	Q	60	ENSP00000371264:R60Q;ENSP00000442626:R60Q	ENSP00000279573:R60Q	R	-	2	0	PRB3	11312271	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-4.005000	0.00315	-4.132000	0.00071	-2.937000	0.00087	CGA	C|0.500;G|0.500	.	alt		0.627	PRB3-001	KNOWN	basic|appris_candidate	protein_coding	protein_coding	OTTHUMT00000402119.5	NM_006249	
YAP1	10413	hgsc.bcm.edu	37	11	102094424	102094424	+	Silent	SNP	C	C	T	rs61749258	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr11:102094424C>T	ENST00000282441.5	+	7	1492	c.1104C>T	c.(1102-1104)ccC>ccT	p.P368P	YAP1_ENST00000526343.1_Silent_p.P314P|YAP1_ENST00000524575.1_Silent_p.P190P|YAP1_ENST00000531439.1_Silent_p.P352P|YAP1_ENST00000537274.1_Silent_p.P356P|YAP1_ENST00000345877.2_Silent_p.P318P	NM_001130145.2|NM_001282101.1	NP_001123617.1|NP_001269030.1	P46937	YAP1_HUMAN	Yes-associated protein 1	368	Transactivation domain.				cell proliferation (GO:0008283)|cellular response to DNA damage stimulus (GO:0006974)|cellular response to gamma radiation (GO:0071480)|contact inhibition (GO:0060242)|embryonic heart tube morphogenesis (GO:0003143)|gene expression (GO:0010467)|hippo signaling (GO:0035329)|keratinocyte differentiation (GO:0030216)|lateral mesoderm development (GO:0048368)|negative regulation of epithelial cell differentiation (GO:0030857)|negative regulation of extrinsic apoptotic signaling pathway (GO:2001237)|notochord development (GO:0030903)|paraxial mesoderm development (GO:0048339)|positive regulation of canonical Wnt signaling pathway (GO:0090263)|positive regulation of cell proliferation (GO:0008284)|positive regulation of organ growth (GO:0046622)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of keratinocyte proliferation (GO:0010837)|regulation of metanephric nephron tubule epithelial cell differentiation (GO:0072307)|regulation of stem cell proliferation (GO:0072091)|somatic stem cell maintenance (GO:0035019)|transcription initiation from RNA polymerase II promoter (GO:0006367)|vasculogenesis (GO:0001570)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|membrane (GO:0016020)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	chromatin binding (GO:0003682)|RNA polymerase II transcription factor binding transcription factor activity (GO:0001076)|transcription coactivator activity (GO:0003713)|transcription corepressor activity (GO:0003714)|transcription regulatory region DNA binding (GO:0044212)			central_nervous_system(1)|large_intestine(1)|lung(1)|ovary(1)	4	all_cancers(8;0.000575)|all_epithelial(12;0.00564)	Acute lymphoblastic leukemia(157;0.000994)|all_hematologic(158;0.00936)	Lung(13;0.245)	BRCA - Breast invasive adenocarcinoma(274;0.0189)		TGTCTTCTCCCGGGATGTCTC	0.438													C|||	15	0.00299521	0.0	0.0029	5008	,	,		20533	0.0		0.008	False		,,,				2504	0.0051				p.P368P	Colon(50;247 1103 7861 28956)	Atlas-SNP	.											.	YAP1	45	.	0			c.C1104T						PASS	.	C	,,,	13,4393	20.2+/-43.8	0,13,2190	108.0	97.0	101.0		1104,1056,570,942	-11.0	0.2	11	dbSNP_129	101	81,8517	46.7+/-105.8	0,81,4218	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	YAP1	NM_001130145.2,NM_001195044.1,NM_001195045.1,NM_006106.4	,,,	0,94,6408	TT,TC,CC		0.9421,0.2951,0.7229	,,,	368/505,352/489,190/327,314/451	102094424	94,12910	2203	4299	6502	SO:0001819	synonymous_variant	10413	exon7			TTCTCCCGGGATG		CCDS8314.1, CCDS44716.1, CCDS8314.2, CCDS53699.1, CCDS53700.1, CCDS60944.1, CCDS73373.1, CCDS73374.1	11q13	2010-03-19	2010-03-19		ENSG00000137693	ENSG00000137693			16262	protein-coding gene	gene with protein product		606608	"""Yes-associated protein 1, 65kDa"""			7782338	Standard	NM_001130145		Approved	YAP65	uc001pgt.3	P46937	OTTHUMG00000167322	ENST00000282441.5:c.1104C>T	11.37:g.102094424C>T		156.0	1.0	0.00641026		316.0	209.0	0.661392	NM_001130145	B4DTY1|B7ZA01|E3WEB5|E3WEB6|E9PRV2|F5H202|K0KQ18|K0KYZ8|K0L195|K0L1G3|Q7Z574|Q8IUY9	Silent	SNP	ENST00000282441.5	37	CCDS44716.1	7	0.003205128205128205	0	0.0	2	0.0055248618784530384	0	0.0	5	0.006596306068601583	C	8.228	0.803942	0.16467	0.002951	0.009421	ENSG00000137693	ENST00000529029	.	.	.	5.49	-11.0	0.00169	.	0.114641	0.64402	D	0.000010	T	0.27866	0.0686	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.56019	-0.8048	6	0.39692	T	0.17	.	1.2473	0.01975	0.1961:0.1395:0.2166:0.4477	rs61749258	.	.	.	L	122	.	ENSP00000431626:P122L	P	+	2	0	YAP1	101599634	0.700000	0.27796	0.231000	0.23993	0.968000	0.65278	-0.459000	0.06728	-2.745000	0.00377	-1.083000	0.02208	CCG	C|0.995;T|0.005	0.005	strong		0.438	YAP1-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000394151.1	NM_006106	
GBGT1	26301	hgsc.bcm.edu	37	9	136029645	136029645	+	Nonsense_Mutation	SNP	G	G	T	rs35898523	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr9:136029645G>T	ENST00000372040.3	-	7	674	c.363C>A	c.(361-363)taC>taA	p.Y121*	GBGT1_ENST00000540636.1_Nonsense_Mutation_p.Y104*|GBGT1_ENST00000372043.3_Intron|RALGDS_ENST00000542690.1_Intron|GBGT1_ENST00000372038.3_Missense_Mutation_p.H134N|GBGT1_ENST00000472281.1_5'UTR	NM_001282629.1	NP_001269558.1	Q8N5D6	GBGT1_HUMAN	globoside alpha-1,3-N-acetylgalactosaminyltransferase 1	121					glycolipid biosynthetic process (GO:0009247)|protein glycosylation (GO:0006486)	Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)	globoside alpha-N-acetylgalactosaminyltransferase activity (GO:0047277)|metal ion binding (GO:0046872)			breast(2)|endometrium(1)|kidney(4)|lung(2)|skin(1)	10				OV - Ovarian serous cystadenocarcinoma(145;3.49e-06)|Epithelial(140;2.59e-05)		TGAAATGAGTGTACCTAGTGA	0.587													G|||	215	0.0429313	0.034	0.0418	5008	,	,		18455	0.002		0.0815	False		,,,				2504	0.0583				p.Y121X		Atlas-SNP	.											GBGT1,NS,carcinoma,-2,1	GBGT1	25	1	0			c.C363A						PASS	.	G	stop/TYR	199,4207	121.7+/-159.2	8,183,2012	39.0	40.0	39.0		363	1.5	0.9	9	dbSNP_126	39	629,7971	155.7+/-209.7	18,593,3689	yes	stop-gained	GBGT1	NM_021996.4		26,776,5701	TT,TG,GG		7.314,4.5166,6.3663		121/348	136029645	828,12178	2203	4300	6503	SO:0001587	stop_gained	26301	exon7			ATGAGTGTACCTA	AY358175	CCDS6960.1, CCDS65175.1, CCDS65176.1	9q34.13-q34.3	2014-07-18			ENSG00000148288	ENSG00000148288		"""Glycosyltransferase family 6 domain containing"""	20460	protein-coding gene	gene with protein product	"""Forssman glycolipid synthetase (FS)"", ""Forssman synthetase"""	606074				10506200, 8855242	Standard	NM_021996		Approved	UDP-GalNAc, A3GALNT, MGC44848, FS		Q8N5D6	OTTHUMG00000020853	ENST00000372040.3:c.363C>A	9.37:g.136029645G>T	ENSP00000361110:p.Tyr121*	24.0	0.0	0		23.0	7.0	0.304348	NM_021996	A8K633|B2RA95|B7Z8S5|Q45F07|Q5T7U9|Q5T7V1|Q8N2K4|Q9UKI5	Nonsense_Mutation	SNP	ENST00000372040.3	37	CCDS6960.1	108|108	0.04945054945054945|0.04945054945054945	23|23	0.046747967479674794|0.046747967479674794	16|16	0.04419889502762431|0.04419889502762431	2|2	0.0034965034965034965|0.0034965034965034965	67|67	0.08839050131926121|0.08839050131926121	G|G	17.35|17.35	3.367115|3.367115	0.61513|0.61513	0.045166|0.045166	0.07314|0.07314	ENSG00000148288|ENSG00000148288	ENST00000372038|ENST00000372040;ENST00000540636	T|.	0.36157|.	1.27|.	5.38|5.38	1.47|1.47	0.22746|0.22746	.|.	.|0.137701	.|0.50627	.|D	.|0.000106	T|.	0.01156|.	0.0038|.	.|.	.|.	.|.	0.80722|0.80722	D|D	1|1	.|.	.|.	.|.	.|.	.|.	.|.	T|.	0.02358|.	-1.1171|.	6|.	0.05833|0.07813	T|T	0.94|0.8	-15.2709|-15.2709	6.0904|6.0904	0.19991|0.19991	0.2143:0.0:0.6535:0.1322|0.2143:0.0:0.6535:0.1322	rs35898523;rs62638704|rs35898523;rs62638704	.|.	.|.	.|.	N|X	134|121;104	ENSP00000361108:H134N|.	ENSP00000361108:H134N|ENSP00000361110:Y121X	H|Y	-|-	1|3	0|2	GBGT1|GBGT1	135019466|135019466	0.883000|0.883000	0.30277|0.30277	0.900000|0.900000	0.35374|0.35374	0.243000|0.243000	0.25628|0.25628	0.687000|0.687000	0.25407|0.25407	0.008000|0.008000	0.14787|0.14787	0.491000|0.491000	0.48974|0.48974	CAC|TAC	G|0.941;T|0.059	0.059	strong		0.587	GBGT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054815.1	NM_021996	
WRAP73	49856	hgsc.bcm.edu	37	1	3551828	3551828	+	Missense_Mutation	SNP	G	G	A			TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr1:3551828G>A	ENST00000270708.7	-	7	707	c.634C>T	c.(634-636)Cgg>Tgg	p.R212W	WRAP73_ENST00000378322.3_Missense_Mutation_p.R212W	NM_017818.3	NP_060288.3	Q9P2S5	WRP73_HUMAN	WD repeat containing, antisense to TP73	212						centrosome (GO:0005813)|cytoplasm (GO:0005737)				endometrium(2)|kidney(1)|large_intestine(5)|lung(3)|pancreas(1)	12						GACAACAACCGGCCATCCAAT	0.542																																					p.R212W		Atlas-SNP	.											WRAP73,NS,carcinoma,+1,1	WRAP73	43	1	0			c.C634T						PASS	.						80.0	80.0	80.0					1																	3551828		2203	4300	6503	SO:0001583	missense	49856	exon7			ACAACCGGCCATC	AB034912, EF494669	CCDS48.1	1p36.3	2013-05-21	2011-04-13	2011-04-13	ENSG00000116213	ENSG00000116213		"""WD repeat domain containing"""	12759	protein-coding gene	gene with protein product		606040	"""WD repeat domain 8"""	WDR8			Standard	NM_017818		Approved		uc001ako.3	Q9P2S5	OTTHUMG00000000612	ENST00000270708.7:c.634C>T	1.37:g.3551828G>A	ENSP00000270708:p.Arg212Trp	157.0	0.0	0		118.0	48.0	0.40678	NM_017818	Q5T0D6|Q9BUH7|Q9NTK7|Q9NX56	Missense_Mutation	SNP	ENST00000270708.7	37	CCDS48.1	.	.	.	.	.	.	.	.	.	.	G	16.60	3.168380	0.57584	.	.	ENSG00000116213	ENST00000270708;ENST00000378322;ENST00000419924	T;T	0.49139	3.34;0.79	5.65	5.65	0.86999	Six-bladed beta-propeller, TolB-like (1);	0.000000	0.85682	D	0.000000	T	0.77226	0.4099	H	0.94423	3.535	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.83414	0.0029	10	0.87932	D	0	-63.099	15.1585	0.72761	0.0:0.0:0.8584:0.1416	.	212	Q9P2S5	WRP73_HUMAN	W	212;212;183	ENSP00000270708:R212W;ENSP00000367573:R212W	ENSP00000270708:R212W	R	-	1	2	WRAP73	3541688	1.000000	0.71417	1.000000	0.80357	0.053000	0.15095	5.938000	0.70170	2.652000	0.90054	0.655000	0.94253	CGG	.	.	none		0.542	WRAP73-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000001470.1		
PCM1	5108	hgsc.bcm.edu	37	8	17847418	17847418	+	Silent	SNP	A	A	G	rs145539051	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr8:17847418A>G	ENST00000519253.1	+	27	4712	c.4461A>G	c.(4459-4461)caA>caG	p.Q1487Q	PCM1_ENST00000325083.8_Silent_p.Q1487Q|PCM1_ENST00000327578.8_Silent_p.Q186Q|PCM1_ENST00000524226.1_Silent_p.Q1433Q			Q15154	PCM1_HUMAN	pericentriolar material 1	1487	Interaction with HAP1.				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)		TAAGTGAGCAAAATGATGCTG	0.308			T	"""RET, JAK2"""	"""papillary thyroid, CML, MPD"""								A|||	18	0.00359425	0.0015	0.0058	5008	,	,		18234	0.0		0.0099	False		,,,				2504	0.002				p.Q1487Q		Atlas-SNP	.		Dom	yes		8	8p22-p21.3	5108	pericentriolar material 1  (PTC4)		"""E, L"""	.	PCM1	120	.	0			c.A4461G						PASS	.	A		13,3403		0,13,1695	86.0	80.0	82.0		4461	-1.6	1.0	8	dbSNP_134	82	106,7508		0,106,3701	no	coding-synonymous	PCM1	NM_006197.3		0,119,5396	GG,GA,AA		1.3922,0.3806,1.0789		1487/2025	17847418	119,10911	1708	3807	5515	SO:0001819	synonymous_variant	5108	exon27			TGAGCAAAATGAT		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.4461A>G	8.37:g.17847418A>G		79.0	0.0	0		97.0	45.0	0.463918	NM_006197	Q58F13|Q6P1K7|Q8NB85|Q9BWC1|Q9H4A2	Silent	SNP	ENST00000519253.1	37		13	0.005952380952380952	1	0.0020325203252032522	1	0.0027624309392265192	0	0.0	11	0.014511873350923483	A	5.205	0.223287	0.09863	0.003806	0.013922	ENSG00000078674	ENST00000522275	.	.	.	5.17	-1.58	0.08479	.	.	.	.	.	T	0.33498	0.0865	.	.	.	0.52099	D	0.999945	.	.	.	.	.	.	T	0.24476	-1.0159	4	.	.	.	-4.1258	2.8152	0.05454	0.5136:0.1104:0.2686:0.1075	.	.	.	.	R	227	.	.	K	+	2	0	PCM1	17891698	0.998000	0.40836	0.990000	0.47175	0.774000	0.43823	0.689000	0.25437	-0.140000	0.11394	-2.258000	0.00281	AAA	A|0.991;G|0.009	0.009	strong		0.308	PCM1-003	NOVEL	basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000374800.1	NM_006197	
CBS	875	hgsc.bcm.edu	37	21	44483101	44483101	+	Missense_Mutation	SNP	T	T	C			TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr21:44483101T>C	ENST00000398165.3	-	10	1175	c.916A>G	c.(916-918)Atc>Gtc	p.I306V	CBS_ENST00000352178.5_Missense_Mutation_p.I306V|CBS_ENST00000398158.1_Missense_Mutation_p.I306V|CBS_ENST00000359624.3_Missense_Mutation_p.I306V|CBS_ENST00000544202.1_Missense_Mutation_p.I218V|CBS_ENST00000398168.1_Missense_Mutation_p.I306V	NM_000071.2	NP_000062.1	P35520	CBS_HUMAN	cystathionine-beta-synthase	306					cellular nitrogen compound metabolic process (GO:0034641)|cysteine biosynthetic process from serine (GO:0006535)|cysteine biosynthetic process via cystathionine (GO:0019343)|homocysteine catabolic process (GO:0043418)|homocysteine metabolic process (GO:0050667)|hydrogen sulfide biosynthetic process (GO:0070814)|L-cysteine catabolic process (GO:0019448)|L-serine catabolic process (GO:0006565)|L-serine metabolic process (GO:0006563)|small molecule metabolic process (GO:0044281)|sulfur amino acid metabolic process (GO:0000096)|transsulfuration (GO:0019346)	cytosol (GO:0005829)|nucleus (GO:0005634)	adenyl nucleotide binding (GO:0030554)|cystathionine beta-synthase activity (GO:0004122)|enzyme binding (GO:0019899)|heme binding (GO:0020037)|identical protein binding (GO:0042802)|metal ion binding (GO:0046872)|modified amino acid binding (GO:0072341)|protein homodimerization activity (GO:0042803)|pyridoxal phosphate binding (GO:0030170)|ubiquitin protein ligase binding (GO:0031625)			endometrium(4)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(2)|lung(8)	17					L-Cysteine(DB00151)|L-Serine(DB00133)|S-Adenosylmethionine(DB00118)	TCGTAGCCGATCCCTTCCACC	0.632																																					p.I306V		Atlas-SNP	.											.	CBS	85	.	0			c.A916G						PASS	.						145.0	121.0	129.0					21																	44483101		2203	4300	6503	SO:0001583	missense	875	exon10			AGCCGATCCCTTC	L14577	CCDS13693.1	21q22.3	2014-09-17			ENSG00000160200	ENSG00000160200	4.2.1.22		1550	protein-coding gene	gene with protein product		613381				9790750	Standard	NM_000071		Approved	HIP4	uc002zcv.2	P35520	OTTHUMG00000086834	ENST00000398165.3:c.916A>G	21.37:g.44483101T>C	ENSP00000381231:p.Ile306Val	106.0	0.0	0		120.0	27.0	0.225	NM_000071	B2R993|D3DSK4|Q99425|Q9BWC5	Missense_Mutation	SNP	ENST00000398165.3	37	CCDS13693.1	.	.	.	.	.	.	.	.	.	.	T	17.87	3.494781	0.64186	.	.	ENSG00000160200	ENST00000398158;ENST00000398165;ENST00000359624;ENST00000352178;ENST00000398168;ENST00000539520;ENST00000544202	D;D;D;D;D;D	0.97066	-4.23;-4.23;-4.23;-4.23;-4.23;-4.23	4.67	4.67	0.58626	Pyridoxal phosphate-dependent enzyme, beta subunit (2);	0.000000	0.85682	D	0.000000	D	0.97766	0.9267	M	0.82056	2.57	0.49798	D	0.99982	P;P	0.46784	0.573;0.884	P;P	0.57720	0.775;0.826	D	0.97377	0.9980	10	0.38643	T	0.18	-21.5015	12.3672	0.55234	0.0:0.0:0.0:1.0	.	306;263	P35520;B7Z2D6	CBS_HUMAN;.	V	306;306;306;306;306;263;218	ENSP00000381225:I306V;ENSP00000381231:I306V;ENSP00000352643:I306V;ENSP00000344460:I306V;ENSP00000381234:I306V;ENSP00000439332:I218V	ENSP00000344460:I306V	I	-	1	0	CBS	43356170	1.000000	0.71417	0.122000	0.21767	0.415000	0.31203	6.807000	0.75201	1.740000	0.51718	0.482000	0.46254	ATC	.	.	none		0.632	CBS-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000195525.1	NM_000071	
DFNA5	1687	hgsc.bcm.edu	37	7	24789386	24789386	+	Missense_Mutation	SNP	G	G	A			TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr7:24789386G>A	ENST00000342947.3	-	2	433	c.8C>T	c.(7-9)gCc>gTc	p.A3V	DFNA5_ENST00000409970.1_Intron|DFNA5_ENST00000409775.3_Missense_Mutation_p.A3V|DFNA5_ENST00000545231.1_5'UTR|DFNA5_ENST00000419307.1_Intron	NM_004403.2	NP_004394.1	O60443	DFNA5_HUMAN	deafness, autosomal dominant 5	3					apoptotic process (GO:0006915)|inner ear receptor cell differentiation (GO:0060113)|negative regulation of cell proliferation (GO:0008285)|positive regulation of intrinsic apoptotic signaling pathway (GO:2001244)|sensory perception of sound (GO:0007605)	cytoplasm (GO:0005737)				endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(4)|lung(6)|ovary(1)|prostate(3)|stomach(1)	19						GGTTGCTTTGGCAAACATTTT	0.333																																					p.A3V	GBM(78;184 1250 20134 20900 23600)	Atlas-SNP	.											.	DFNA5	51	.	0			c.C8T						PASS	.						79.0	85.0	83.0					7																	24789386		2203	4300	6503	SO:0001583	missense	1687	exon2			GCTTTGGCAAACA	AF007790	CCDS5389.1, CCDS47563.1	7p15	2011-07-01			ENSG00000105928	ENSG00000105928			2810	protein-coding gene	gene with protein product		608798				8589696, 9450185	Standard	NM_004403		Approved	ICERE-1	uc010kus.1	O60443	OTTHUMG00000023237	ENST00000342947.3:c.8C>T	7.37:g.24789386G>A	ENSP00000339587:p.Ala3Val	113.0	0.0	0		114.0	29.0	0.254386	NM_001127453	A4D156|B2RAX9|B3KT05|O14590|Q08AQ8|Q9UBV3	Missense_Mutation	SNP	ENST00000342947.3	37	CCDS5389.1	.	.	.	.	.	.	.	.	.	.	G	25.8	4.670665	0.88348	.	.	ENSG00000105928	ENST00000342947;ENST00000409775	T;T	0.25414	1.8;1.8	5.54	5.54	0.83059	.	0.000000	0.85682	D	0.000000	T	0.54498	0.1862	M	0.80847	2.515	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.87578	0.996;0.998	T	0.57230	-0.7847	10	0.59425	D	0.04	-24.0835	16.4772	0.84135	0.0:0.1308:0.8692:0.0	.	3;3	A4FTY0;O60443	.;DFNA5_HUMAN	V	3	ENSP00000339587:A3V;ENSP00000386670:A3V	ENSP00000339587:A3V	A	-	2	0	DFNA5	24755911	1.000000	0.71417	1.000000	0.80357	0.974000	0.67602	5.414000	0.66405	2.606000	0.88127	0.655000	0.94253	GCC	.	.	none		0.333	DFNA5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000214060.2	NM_004403	
DHX15	1665	hgsc.bcm.edu	37	4	24550580	24550580	+	Silent	SNP	G	G	A	rs33972724	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr4:24550580G>A	ENST00000336812.4	-	6	1302	c.1146C>T	c.(1144-1146)gaC>gaT	p.D382D		NM_001358.2	NP_001349.2	O43143	DHX15_HUMAN	DEAH (Asp-Glu-Ala-His) box helicase 15	382	Helicase C-terminal. {ECO:0000255|PROSITE-ProRule:PRU00542}.				mRNA processing (GO:0006397)|RNA splicing (GO:0008380)	nucleus (GO:0005634)|U12-type spliceosomal complex (GO:0005689)	ATP binding (GO:0005524)|ATP-dependent helicase activity (GO:0008026)|double-stranded RNA binding (GO:0003725)|poly(A) RNA binding (GO:0044822)|RNA helicase activity (GO:0003724)			breast(4)|endometrium(4)|haematopoietic_and_lymphoid_tissue(2)|kidney(6)|large_intestine(5)|liver(1)|lung(6)|ovary(1)|upper_aerodigestive_tract(1)	30		Breast(46;0.0503)				TGATTTTAATGTCACCAACTT	0.393													G|||	25	0.00499201	0.0015	0.013	5008	,	,		15491	0.0		0.0139	False		,,,				2504	0.0				p.D382D		Atlas-SNP	.											.	DHX15	69	.	0			c.C1146T						PASS	.	G		11,4395	17.9+/-39.9	0,11,2192	124.0	111.0	115.0		1146	3.2	1.0	4	dbSNP_126	115	108,8492	59.1+/-120.7	0,108,4192	no	coding-synonymous	DHX15	NM_001358.2		0,119,6384	AA,AG,GG		1.2558,0.2497,0.915		382/796	24550580	119,12887	2203	4300	6503	SO:0001819	synonymous_variant	1665	exon6			TTTAATGTCACCA	AB001636	CCDS33966.1	4p15.3	2013-05-13	2013-05-13	2003-06-20	ENSG00000109606	ENSG00000109606		"""DEAH-boxes"""	2738	protein-coding gene	gene with protein product		603403	"""DEAD/H (Asp-Glu-Ala-Asp/His) box polypeptide 15"", ""DEAH (Asp-Glu-Ala-His) box polypeptide 15"""	DDX15		9388478	Standard	NM_001358		Approved	HRH2, DBP1, PRP43, PrPp43p, PRPF43	uc003gqx.3	O43143	OTTHUMG00000160304	ENST00000336812.4:c.1146C>T	4.37:g.24550580G>A		102.0	0.0	0		92.0	39.0	0.423913	NM_001358	Q9NQT7	Silent	SNP	ENST00000336812.4	37	CCDS33966.1																																																																																			G|0.991;A|0.009	0.009	strong		0.393	DHX15-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000360143.1	NM_001358	
FAM188B	84182	hgsc.bcm.edu	37	7	30868352	30868352	+	Splice_Site	SNP	C	C	T	rs201645679		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr7:30868352C>T	ENST00000265299.6	+	6	1208	c.1131C>T	c.(1129-1131)ctC>ctT	p.L377L	INMT-FAM188B_ENST00000458257.1_3'UTR	NM_032222.2	NP_115598.2	Q4G0A6	F188B_HUMAN	family with sequence similarity 188, member B	377										endometrium(1)|large_intestine(5)|lung(19)|prostate(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	29						CCCTGCGGCTCGGTAGGTGCA	0.582																																					p.L377L		Atlas-SNP	.											.	FAM188B	62	.	0			c.C1131T						PASS	.	C		0,4054		0,0,2027	115.0	119.0	118.0		1131	-6.6	0.3	7		118	1,8369		0,1,4184	yes	coding-synonymous-near-splice	FAM188B	NM_032222.2		0,1,6211	TT,TC,CC		0.0119,0.0,0.0080		377/758	30868352	1,12423	2027	4185	6212	SO:0001630	splice_region_variant	84182	exon6			GCGGCTCGGTAGG	AK026027	CCDS43565.1	7p14.3	2010-08-17	2009-07-14	2009-07-14	ENSG00000106125	ENSG00000106125			21916	protein-coding gene	gene with protein product			"""chromosome 7 open reading frame 67"""	C7orf67			Standard	NM_032222		Approved	FLJ22374	uc003tbt.3	Q4G0A6	OTTHUMG00000152800	ENST00000265299.6:c.1132+1C>T	7.37:g.30868352C>T		80.0	0.0	0		98.0	48.0	0.489796	NM_032222	Q71AZ7|Q9H6D2	Silent	SNP	ENST00000265299.6	37	CCDS43565.1																																																																																			C|0.999;T|0.001	0.001	weak		0.582	FAM188B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000327962.1	NM_032222	Silent
IKBKB	3551	hgsc.bcm.edu	37	8	42174380	42174380	+	Silent	SNP	G	G	A	rs56230731	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr8:42174380G>A	ENST00000520810.1	+	11	1269	c.1083G>A	c.(1081-1083)ttG>ttA	p.L361L	IKBKB_ENST00000522147.1_Intron|IKBKB_ENST00000416505.2_Silent_p.L302L|IKBKB_ENST00000520835.1_Silent_p.L359L|IKBKB_ENST00000379708.3_Silent_p.L138L	NM_001556.2	NP_001547.1	O14920	IKKB_HUMAN	inhibitor of kappa light polypeptide gene enhancer in B-cells, kinase beta	361					B cell homeostasis (GO:0001782)|cellular response to tumor necrosis factor (GO:0071356)|Fc-epsilon receptor signaling pathway (GO:0038095)|I-kappaB kinase/NF-kappaB signaling (GO:0007249)|I-kappaB phosphorylation (GO:0007252)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|MyD88-dependent toll-like receptor signaling pathway (GO:0002755)|MyD88-independent toll-like receptor signaling pathway (GO:0002756)|negative regulation of apoptotic process (GO:0043066)|neurotrophin TRK receptor signaling pathway (GO:0048011)|nucleotide-binding domain, leucine rich repeat containing receptor signaling pathway (GO:0035872)|nucleotide-binding oligomerization domain containing signaling pathway (GO:0070423)|positive regulation of cation channel activity (GO:2001259)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of sodium ion transport (GO:0010765)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of type I interferon production (GO:0032481)|protein phosphorylation (GO:0006468)|response to virus (GO:0009615)|serine phosphorylation of STAT protein (GO:0042501)|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)	CD40 receptor complex (GO:0035631)|cytoplasm (GO:0005737)|cytoplasmic side of plasma membrane (GO:0009898)|cytosol (GO:0005829)|IkappaB kinase complex (GO:0008385)|nucleus (GO:0005634)	ATP binding (GO:0005524)|IkappaB kinase activity (GO:0008384)|protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)|protein kinase activity (GO:0004672)|protein kinase binding (GO:0019901)|protein serine/threonine kinase activity (GO:0004674)|scaffold protein binding (GO:0097110)			breast(4)|lung(1)|ovary(2)|skin(1)	8	all_cancers(6;1.42e-24)|all_epithelial(6;1.02e-25)|all_lung(13;6.21e-12)|Lung NSC(13;1.04e-10)|Ovarian(28;0.00769)|Prostate(17;0.0119)|Colorectal(14;0.0468)|Lung SC(25;0.211)	all_lung(54;0.000434)|Lung NSC(58;0.00161)|Hepatocellular(245;0.0524)|Renal(179;0.0822)|Esophageal squamous(32;0.0954)	BRCA - Breast invasive adenocarcinoma(8;1.37e-10)|Colorectal(10;0.00102)|OV - Ovarian serous cystadenocarcinoma(14;0.00168)|Lung(22;0.00467)|LUSC - Lung squamous cell carcinoma(45;0.024)|COAD - Colon adenocarcinoma(11;0.0264)		Acetylcysteine(DB06151)|Acetylsalicylic acid(DB00945)|Arsenic trioxide(DB01169)|Auranofin(DB00995)|Mesalazine(DB00244)|Sulfasalazine(DB00795)	GCCTGGCGTTGATCCCCGATA	0.582													G|||	19	0.00379393	0.0008	0.0014	5008	,	,		17740	0.0		0.0169	False		,,,				2504	0.0				p.L361L		Atlas-SNP	.											.	IKBKB	88	.	0			c.G1083A						PASS	.	G	,,	14,4392	21.2+/-45.6	0,14,2189	82.0	76.0	78.0		1077,906,1083	4.6	1.0	8	dbSNP_129	78	128,8472	65.6+/-127.9	1,126,4173	no	coding-synonymous,coding-synonymous,coding-synonymous	IKBKB	NM_001190720.2,NM_001242778.1,NM_001556.2	,,	1,140,6362	AA,AG,GG		1.4884,0.3177,1.0918	,,	359/755,302/698,361/757	42174380	142,12864	2203	4300	6503	SO:0001819	synonymous_variant	3551	exon11			GGCGTTGATCCCC	AF029684	CCDS6128.1, CCDS55228.1, CCDS56535.1	8p11.2	2008-08-18			ENSG00000104365	ENSG00000104365			5960	protein-coding gene	gene with protein product		603258				9878263, 9763654	Standard	NM_001556		Approved	IKK2, NFKBIKB, IKK-beta, IKKB	uc003xow.2	O14920	OTTHUMG00000164092	ENST00000520810.1:c.1083G>A	8.37:g.42174380G>A		106.0	0.0	0		115.0	37.0	0.321739	NM_001556	B4DZ30|B4E0U4|O75327	Silent	SNP	ENST00000520810.1	37	CCDS6128.1																																																																																			G|0.991;A|0.009	0.009	strong		0.582	IKBKB-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000377214.1		
PARP3	10039	hgsc.bcm.edu	37	3	51981769	51981769	+	Silent	SNP	G	G	A			TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr3:51981769G>A	ENST00000417220.2	+	11	1778	c.1290G>A	c.(1288-1290)aaG>aaA	p.K430K	PARP3_ENST00000398755.3_Silent_p.K437K|PARP3_ENST00000486510.1_3'UTR|PARP3_ENST00000431474.1_Silent_p.K430K			Q9Y6F1	PARP3_HUMAN	poly (ADP-ribose) polymerase family, member 3	430	PARP catalytic. {ECO:0000255|PROSITE- ProRule:PRU00397}.				DNA repair (GO:0006281)|double-strand break repair (GO:0006302)|positive regulation of DNA ligation (GO:0051106)|protein ADP-ribosylation (GO:0006471)|protein localization to site of double-strand break (GO:1990166)|regulation of mitotic spindle organization (GO:0060236)|telomere maintenance (GO:0000723)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|nucleus (GO:0005634)|site of double-strand break (GO:0035861)	catalytic activity (GO:0003824)|NAD+ ADP-ribosyltransferase activity (GO:0003950)			ovary(1)	1				BRCA - Breast invasive adenocarcinoma(193;8.01e-05)|Kidney(197;0.000541)|KIRC - Kidney renal clear cell carcinoma(197;0.000716)		TTGGCATGAAGTGTGGGGCCC	0.602																																					p.K437K		Atlas-SNP	.											.	PARP3	90	.	0			c.G1311A						PASS	.						95.0	100.0	98.0					3																	51981769		2053	4189	6242	SO:0001819	synonymous_variant	10039	exon10			CATGAAGTGTGGG	AF083068	CCDS43097.1, CCDS46839.1	3p22.2-p21.1	2010-07-14	2004-08-20	2004-08-26	ENSG00000041880	ENSG00000041880	2.4.2.30	"""Poly (ADP-ribose) polymerases"""	273	protein-coding gene	gene with protein product	"""poly(ADP-ribose) synthetase-3"", ""NAD+ ADP-ribosyltransferase 3"", ""poly(ADP-ribose) polymerase 3"""	607726	"""ADP-ribosyltransferase (NAD+; poly (ADP-ribose) polymerase)-like 3"""	ADPRTL3		10329013	Standard	NM_001003931		Approved	ADPRT3, IRT1, hPARP-3, pADPRT-3	uc003dbz.3	Q9Y6F1	OTTHUMG00000156931	ENST00000417220.2:c.1290G>A	3.37:g.51981769G>A		103.0	0.0	0		97.0	57.0	0.587629	NM_001003931	Q8NER9|Q96CG2|Q9UG81	Silent	SNP	ENST00000417220.2	37	CCDS43097.1																																																																																			.	.	none		0.602	PARP3-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000348612.2	NM_005485.4	
SCYL1	57410	hgsc.bcm.edu	37	11	65293819	65293819	+	Silent	SNP	G	G	A	rs75169347	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr11:65293819G>A	ENST00000270176.5	+	4	677	c.600G>A	c.(598-600)aaG>aaA	p.K200K	SCYL1_ENST00000527009.1_Silent_p.K57K|SCYL1_ENST00000533862.1_Silent_p.K200K|SCYL1_ENST00000525364.1_Silent_p.K200K|SCYL1_ENST00000524944.1_Silent_p.K200K|SCYL1_ENST00000279270.6_Silent_p.K200K|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		141.0	0.0	0		140.0	64.0	0.457143	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	
MUC17	140453	hgsc.bcm.edu	37	7	100680463	100680463	+	Missense_Mutation	SNP	G	G	T	rs368849364	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr7:100680463G>T	ENST00000306151.4	+	3	5830	c.5766G>T	c.(5764-5766)agG>agT	p.R1922S		NM_001040105.1	NP_001035194.1	Q685J3	MUC17_HUMAN	mucin 17, cell surface associated	1922	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)					CAACTCCTAGGGAAGGAAGGC	0.507																																					p.R1922S		Atlas-SNP	.											.	MUC17	804	.	0			c.G5766T						PASS	.						242.0	242.0	242.0					7																	100680463		2203	4300	6503	SO:0001583	missense	140453	exon3			TCCTAGGGAAGGA	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.5766G>T	7.37:g.100680463G>T	ENSP00000302716:p.Arg1922Ser	157.0	0.0	0		204.0	19.0	0.0931373	NM_001040105	O14761|Q685J2|Q8TDH7	Missense_Mutation	SNP	ENST00000306151.4	37	CCDS34711.1	.	.	.	.	.	.	.	.	.	.	N	0.015	-1.561399	0.00903	.	.	ENSG00000169876	ENST00000306151	T	0.02787	4.16	0.932	-1.86	0.07760	.	.	.	.	.	T	0.00998	0.0033	N	0.02539	-0.55	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.39210	-0.9625	9	0.06494	T	0.89	.	3.4094	0.07353	0.2058:0.0:0.3687:0.4255	.	1922	Q685J3	MUC17_HUMAN	S	1922	ENSP00000302716:R1922S	ENSP00000302716:R1922S	R	+	3	2	MUC17	100467183	0.000000	0.05858	0.000000	0.03702	0.002000	0.02628	-3.905000	0.00338	-2.952000	0.00293	-2.056000	0.00403	AGG	.	.	alt		0.507	MUC17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347161.1	NM_001040105	
PANX2	56666	hgsc.bcm.edu	37	22	50617671	50617671	+	Missense_Mutation	SNP	G	G	A			TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr22:50617671G>A	ENST00000395842.2	+	3	1999	c.1999G>A	c.(1999-2001)Gag>Aag	p.E667K	PANX2_ENST00000159647.5_Silent_p.T638T	NM_052839.3	NP_443071.2	Q96RD6	PANX2_HUMAN	pannexin 2	667					ion transport (GO:0006811)|protein hexamerization (GO:0034214)|response to ischemia (GO:0002931)|synaptic transmission (GO:0007268)	cytoplasm (GO:0005737)|gap junction (GO:0005921)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	gap junction hemi-channel activity (GO:0055077)			breast(1)|central_nervous_system(1)|endometrium(2)|large_intestine(1)|lung(1)|skin(1)	7		all_cancers(38;1.14e-10)|all_epithelial(38;2.12e-09)|all_lung(38;7.01e-05)|Breast(42;0.000523)|Lung NSC(38;0.0018)|Ovarian(80;0.0365)|Lung SC(80;0.113)		LUAD - Lung adenocarcinoma(64;0.105)		CACCTTCGACGAGCCGAGAAC	0.697																																					p.E667K		Atlas-SNP	.											.	PANX2	69	.	0			c.G1999A						PASS	.						49.0	43.0	45.0					22																	50617671		2203	4297	6500	SO:0001583	missense	56666	exon3			TTCGACGAGCCGA		CCDS14085.2, CCDS54544.1	22q13.33	2011-12-05			ENSG00000073150	ENSG00000073150		"""Ion channels / Pannexins"""	8600	protein-coding gene	gene with protein product		608421				14702039, 14597722	Standard	NM_052839		Approved	hPANX2, PX2	uc003bjn.4	Q96RD6	OTTHUMG00000044649	ENST00000395842.2:c.1999G>A	22.37:g.50617671G>A	ENSP00000379183:p.Glu667Lys	146.0	0.0	0		127.0	44.0	0.346457	NM_052839	B7Z684|Q96RD5|Q9UGX8	Missense_Mutation	SNP	ENST00000395842.2	37	CCDS14085.2	.	.	.	.	.	.	.	.	.	.	G	22.1	4.250501	0.80024	.	.	ENSG00000073150	ENST00000395842;ENST00000401643	T	0.33216	1.42	3.72	3.72	0.42706	.	0.000000	0.37304	U	0.002153	T	0.55529	0.1926	.	.	.	0.46279	D	0.998968	D	0.76494	0.999	D	0.68621	0.959	T	0.64744	-0.6335	9	0.87932	D	0	-23.7117	15.9969	0.80256	0.0:0.0:1.0:0.0	.	667	Q96RD6	PANX2_HUMAN	K	667;344	ENSP00000379183:E667K	ENSP00000379183:E667K	E	+	1	0	PANX2	48959798	1.000000	0.71417	0.946000	0.38457	0.282000	0.26991	6.495000	0.73665	2.081000	0.62600	0.313000	0.20887	GAG	.	.	none		0.697	PANX2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000075010.3	NM_052839	
TGM4	7047	hgsc.bcm.edu	37	3	44948563	44948563	+	Missense_Mutation	SNP	A	A	G			TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr3:44948563A>G	ENST00000296125.4	+	10	1266	c.1198A>G	c.(1198-1200)Atg>Gtg	p.M400V		NM_003241.3	NP_003232.2	P49221	TGM4_HUMAN	transglutaminase 4	400					mating plug formation (GO:0042628)|peptide cross-linking (GO:0018149)	cytoplasm (GO:0005737)|extracellular matrix (GO:0031012)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)	metal ion binding (GO:0046872)|protein-glutamine gamma-glutamyltransferase activity (GO:0003810)			NS(1)|breast(1)|endometrium(2)|large_intestine(9)|lung(21)|ovary(2)|stomach(1)|upper_aerodigestive_tract(1)	38				BRCA - Breast invasive adenocarcinoma(193;0.00963)|KIRC - Kidney renal clear cell carcinoma(197;0.0546)|Kidney(197;0.0686)	L-Glutamine(DB00130)	GTTGGTGAAGATGGTGAATGG	0.498																																					p.M400V		Atlas-SNP	.											.	TGM4	82	.	0			c.A1198G						PASS	.						140.0	128.0	132.0					3																	44948563		2203	4300	6503	SO:0001583	missense	7047	exon10			GTGAAGATGGTGA	BC007003	CCDS2723.1	3p22-p21.33	2013-05-02	2013-05-02		ENSG00000163810	ENSG00000163810	2.3.2.13	"""Transglutaminases"""	11780	protein-coding gene	gene with protein product		600585	"""transglutaminase 4 (prostate)"""			7665178, 7916568	Standard	NM_003241		Approved	TGP	uc003coc.4	P49221	OTTHUMG00000133096	ENST00000296125.4:c.1198A>G	3.37:g.44948563A>G	ENSP00000296125:p.Met400Val	270.0	0.0	0		230.0	117.0	0.508696	NM_003241	Q16707|Q96QN4	Missense_Mutation	SNP	ENST00000296125.4	37	CCDS2723.1	.	.	.	.	.	.	.	.	.	.	A	5.841	0.339412	0.11069	.	.	ENSG00000163810	ENST00000296125	T	0.20738	2.05	2.03	-4.07	0.03975	.	0.468908	0.16456	U	0.213616	T	0.04048	0.0113	N	0.01048	-1.04	0.09310	N	1	B	0.19073	0.033	B	0.08055	0.003	T	0.22765	-1.0207	10	0.33141	T	0.24	.	0.4585	0.00512	0.3471:0.1383:0.2793:0.2353	.	400	P49221	TGM4_HUMAN	V	400	ENSP00000296125:M400V	ENSP00000296125:M400V	M	+	1	0	TGM4	44923567	0.002000	0.14202	0.000000	0.03702	0.112000	0.19704	-0.168000	0.09925	-1.271000	0.02430	-0.710000	0.03640	ATG	.	.	none		0.498	TGM4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256755.2	NM_003241	
HNRNPA1	3178	hgsc.bcm.edu	37	12	54676630	54676630	+	Silent	SNP	G	G	A			TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr12:54676630G>A	ENST00000340913.6	+	7	776	c.723G>A	c.(721-723)ggG>ggA	p.G241G	HNRNPA1_ENST00000330752.8_Silent_p.G228G|RP11-968A15.8_ENST00000553061.1_RNA|HNRNPA1_ENST00000546500.1_Silent_p.G241G|CBX5_ENST00000209875.4_5'Flank|HNRNPA1_ENST00000547276.1_Intron	NM_002136.2|NM_031157.2	NP_002127.1|NP_112420.1	P09651	ROA1_HUMAN	heterogeneous nuclear ribonucleoprotein A1	241	Gly-rich.				cell death (GO:0008219)|gene expression (GO:0010467)|mRNA processing (GO:0006397)|mRNA splicing, via spliceosome (GO:0000398)|mRNA transport (GO:0051028)|nuclear export (GO:0051168)|nuclear import (GO:0051170)|RNA export from nucleus (GO:0006405)|RNA splicing (GO:0008380)|viral process (GO:0016032)	catalytic step 2 spliceosome (GO:0071013)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|intermediate filament cytoskeleton (GO:0045111)|membrane (GO:0016020)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|ribonucleoprotein complex (GO:0030529)|spliceosomal complex (GO:0005681)	nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)|single-stranded DNA binding (GO:0003697)|single-stranded RNA binding (GO:0003727)			endometrium(3)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(4)|lung(6)|ovary(1)|skin(2)|upper_aerodigestive_tract(1)	20						gtggcagtggggatggctata	0.398																																					p.G241G	Colon(83;502 1289 8436 16406 24870)	Atlas-SNP	.											.	HNRNPA1	72	.	0			c.G723A						PASS	.						34.0	33.0	34.0					12																	54676630		2008	3945	5953	SO:0001819	synonymous_variant	3178	exon7			CAGTGGGGATGGC	BC009600	CCDS41793.1, CCDS44909.1	12q13.1	2013-10-11		2007-08-16	ENSG00000135486	ENSG00000135486		"""RNA binding motif (RRM) containing"""	5031	protein-coding gene	gene with protein product		164017		HNRPA1		1733858	Standard	XR_245923		Approved	hnRNPA1, hnRNP-A1	uc001sfl.3	P09651		ENST00000340913.6:c.723G>A	12.37:g.54676630G>A		125.0	0.0	0		104.0	38.0	0.365385	NM_002136	A8K4Z8|Q3MIB7|Q6PJZ7	Silent	SNP	ENST00000340913.6	37	CCDS44909.1																																																																																			.	.	none		0.398	HNRNPA1-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000405480.1	NM_031157	
TMEM45A	55076	hgsc.bcm.edu	37	3	100274090	100274090	+	Missense_Mutation	SNP	C	C	A	rs200878698		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr3:100274090C>A	ENST00000323523.4	+	2	348	c.35C>A	c.(34-36)aCc>aAc	p.T12N	TMEM45A_ENST00000462884.1_3'UTR|TMEM45A_ENST00000403410.1_Missense_Mutation_p.T28N	NM_018004.1	NP_060474.1	Q9NWC5	TM45A_HUMAN	transmembrane protein 45A	12						integral component of membrane (GO:0016021)				breast(1)|kidney(1)|large_intestine(1)|lung(5)|ovary(1)|skin(2)	11						CTCCCTGGAACCTTCTTTTTT	0.368																																					p.T12N		Atlas-SNP	.											TMEM45A,NS,carcinoma,+1,1	TMEM45A	35	1	0			c.C35A						PASS	.	C	ASN/THR	0,4406		0,0,2203	166.0	176.0	172.0		35	-0.4	0.6	3		172	2,8598	2.2+/-6.3	0,2,4298	yes	missense	TMEM45A	NM_018004.1	65	0,2,6501	AA,AC,CC		0.0233,0.0,0.0154	benign	12/276	100274090	2,13004	2203	4300	6503	SO:0001583	missense	55076	exon2			CTGGAACCTTCTT	AK000996	CCDS2937.1	3q12.2	2005-02-04			ENSG00000181458	ENSG00000181458			25480	protein-coding gene	gene with protein product						12477932	Standard	XM_005247568		Approved	FLJ10134, DERP7	uc003dtz.1	Q9NWC5	OTTHUMG00000150327	ENST00000323523.4:c.35C>A	3.37:g.100274090C>A	ENSP00000319009:p.Thr12Asn	195.0	0.0	0		156.0	68.0	0.435897	NM_018004	Q53YW5	Missense_Mutation	SNP	ENST00000323523.4	37	CCDS2937.1	.	.	.	.	.	.	.	.	.	.	C	11.78	1.740553	0.30865	0.0	2.33E-4	ENSG00000181458	ENST00000323523;ENST00000403410;ENST00000449609	T;T;T	0.50001	1.39;1.38;0.76	5.84	-0.364	0.12553	.	0.370601	0.35349	N	0.003273	T	0.45135	0.1327	M	0.62723	1.935	0.25270	N	0.989529	B;P	0.47106	0.22;0.89	B;B	0.39876	0.036;0.312	T	0.52711	-0.8539	10	0.59425	D	0.04	0.3845	17.6844	0.88253	0.0:0.1546:0.7715:0.0738	.	28;12	C9J9Z5;Q9NWC5	.;TM45A_HUMAN	N	12;28;28	ENSP00000319009:T12N;ENSP00000385089:T28N;ENSP00000405597:T28N	ENSP00000319009:T12N	T	+	2	0	TMEM45A	101756780	1.000000	0.71417	0.567000	0.28434	0.432000	0.31715	0.710000	0.25748	-0.406000	0.07588	-0.150000	0.13652	ACC	.	.	weak		0.368	TMEM45A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000317571.1	NM_018004	
HENMT1	113802	hgsc.bcm.edu	37	1	109200108	109200108	+	Missense_Mutation	SNP	C	C	T	rs36100901	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr1:109200108C>T	ENST00000370032.5	-	3	535	c.115G>A	c.(115-117)Gtt>Att	p.V39I	HENMT1_ENST00000493676.1_5'UTR|HENMT1_ENST00000402983.1_Missense_Mutation_p.V39I|HENMT1_ENST00000370031.1_Missense_Mutation_p.V39I	NM_144584.2	NP_653185.2	Q5T8I9	HENMT_HUMAN	HEN1 methyltransferase homolog 1 (Arabidopsis)	39					gene silencing by RNA (GO:0031047)|piRNA metabolic process (GO:0034587)|RNA methylation (GO:0001510)	P granule (GO:0043186)	metal ion binding (GO:0046872)|O-methyltransferase activity (GO:0008171)|RNA binding (GO:0003723)|RNA methyltransferase activity (GO:0008173)			central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(1)|lung(6)|ovary(2)|prostate(1)|skin(2)|stomach(1)	16						AAATTTTTAACGAACTGGTAC	0.383													C|||	62	0.0123802	0.0053	0.0202	5008	,	,		17554	0.0		0.0288	False		,,,				2504	0.0123				p.V39I		Atlas-SNP	.											.	HENMT1	38	.	0			c.G115A						PASS	.	C	ILE/VAL,ILE/VAL	22,4384	29.0+/-57.7	0,22,2181	112.0	113.0	113.0		115,115	3.7	0.2	1	dbSNP_126	113	219,8381	91.4+/-153.5	2,215,4083	yes	missense,missense	HENMT1	NM_001102592.1,NM_144584.2	29,29	2,237,6264	TT,TC,CC		2.5465,0.4993,1.853	possibly-damaging,possibly-damaging	39/394,39/394	109200108	241,12765	2203	4300	6503	SO:0001583	missense	113802	exon3			TTTTAACGAACTG		CCDS787.1	1p13.3	2011-01-28	2011-01-28	2011-01-28	ENSG00000162639	ENSG00000162639			26400	protein-coding gene	gene with protein product	"""HEN1 methyltransferase homolog (Arabidopsis)"""	612178	"""chromosome 1 open reading frame 59"""	C1orf59			Standard	NM_144584		Approved	FLJ30525, HEN1	uc001dvt.4	Q5T8I9	OTTHUMG00000011123	ENST00000370032.5:c.115G>A	1.37:g.109200108C>T	ENSP00000359049:p.Val39Ile	111.0	0.0	0		69.0	53.0	0.768116	NM_144584	A8MRR6|B1AM16|B1AM17|Q96EJ7|Q96NN0	Missense_Mutation	SNP	ENST00000370032.5	37	CCDS787.1	29	0.013278388278388278	4	0.008130081300813009	4	0.011049723756906077	0	0.0	21	0.027704485488126648	C	15.44	2.833273	0.50951	0.004993	0.025465	ENSG00000162639	ENST00000402983;ENST00000370031;ENST00000370032;ENST00000420055	T;T;T;T	0.38077	1.16;1.16;1.16;1.16	5.62	3.68	0.42216	.	0.067024	0.64402	D	0.000015	T	0.31327	0.0793	L	0.41573	1.285	0.48185	D	0.999609	D	0.76494	0.999	D	0.66979	0.948	T	0.05733	-1.0867	10	0.32370	T	0.25	.	8.5831	0.33642	0.0:0.813:0.0:0.187	rs36100901	39	Q5T8I9	HENMT_HUMAN	I	39	ENSP00000385655:V39I;ENSP00000359048:V39I;ENSP00000359049:V39I;ENSP00000403953:V39I	ENSP00000359048:V39I	V	-	1	0	HENMT1	109001631	0.607000	0.26958	0.229000	0.23960	0.264000	0.26372	0.956000	0.29202	1.292000	0.44672	0.655000	0.94253	GTT	C|0.984;T|0.016	0.016	strong		0.383	HENMT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000030592.1	NM_144584	
XKR9	389668	hgsc.bcm.edu	37	8	71646201	71646201	+	Missense_Mutation	SNP	C	C	T	rs61734026	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr8:71646201C>T	ENST00000408926.3	+	5	1198	c.664C>T	c.(664-666)Ctt>Ttt	p.L222F	XKR9_ENST00000520273.1_Intron|XKR9_ENST00000520030.1_Missense_Mutation_p.L222F	NM_001011720.1	NP_001011720.1	Q5GH70	XKR9_HUMAN	XK, Kell blood group complex subunit-related family, member 9	222						integral component of membrane (GO:0016021)				breast(1)|endometrium(1)|kidney(1)|large_intestine(5)|liver(2)|lung(4)|ovary(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	19	Breast(64;0.0716)		Epithelial(68;0.00301)|all cancers(69;0.0165)|OV - Ovarian serous cystadenocarcinoma(28;0.0524)|BRCA - Breast invasive adenocarcinoma(89;0.166)			GAGTGTTGTACTTCTACTATT	0.313													C|||	24	0.00479233	0.0	0.0101	5008	,	,		16387	0.0		0.0149	False		,,,				2504	0.002				p.L222F		Atlas-SNP	.											.	XKR9	43	.	0			c.C664T						PASS	.	C	PHE/LEU	7,4399	15.5+/-35.6	0,7,2196	189.0	188.0	188.0		664	4.7	1.0	8	dbSNP_129	188	110,8486	57.5+/-118.9	1,108,4189	yes	missense	XKR9	NM_001011720.1	22	1,115,6385	TT,TC,CC		1.2797,0.1589,0.8999	possibly-damaging	222/374	71646201	117,12885	2203	4298	6501	SO:0001583	missense	389668	exon5			GTTGTACTTCTAC	AY534247	CCDS34905.1	8q13.3	2006-01-12	2006-01-12			ENSG00000221947			20937	protein-coding gene	gene with protein product			"""X Kell blood group precursor-related family, member 9"""				Standard	NM_001287258		Approved		uc003xyq.3	Q5GH70		ENST00000408926.3:c.664C>T	8.37:g.71646201C>T	ENSP00000386141:p.Leu222Phe	365.0	0.0	0		461.0	266.0	0.577007	NM_001011720	B2RNS9|B9EH74	Missense_Mutation	SNP	ENST00000408926.3	37	CCDS34905.1	12	0.005494505494505495	0	0.0	3	0.008287292817679558	0	0.0	9	0.011873350923482849	C	14.17	2.456518	0.43634	0.001589	0.012797	ENSG00000221947	ENST00000408926;ENST00000520030	T;T	0.70749	-0.51;-0.51	4.69	4.69	0.59074	.	0.000000	0.85682	D	0.000000	T	0.57975	0.2090	M	0.62723	1.935	0.53688	D	0.999976	P	0.42993	0.797	B	0.39840	0.311	T	0.66097	-0.6008	10	0.49607	T	0.09	-22.2782	9.9909	0.41870	0.0:0.8431:0.0:0.1569	rs61734026	222	Q5GH70	XKR9_HUMAN	F	222	ENSP00000386141:L222F;ENSP00000431088:L222F	ENSP00000386141:L222F	L	+	1	0	XKR9	71808755	0.999000	0.42202	1.000000	0.80357	0.982000	0.71751	1.792000	0.38754	2.597000	0.87782	0.563000	0.77884	CTT	C|0.990;T|0.010	0.010	strong		0.313	XKR9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000378752.1	NM_001011720	
C9orf172	389813	hgsc.bcm.edu	37	9	139740436	139740436	+	Missense_Mutation	SNP	G	G	A	rs375030600		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr9:139740436G>A	ENST00000436881.1	+	1	1570	c.1570G>A	c.(1570-1572)Ggc>Agc	p.G524S	PHPT1_ENST00000371661.1_5'Flank|PHPT1_ENST00000545326.1_5'Flank	NM_001080482.2	NP_001073951.2	C9J069	CI172_HUMAN	chromosome 9 open reading frame 172	524										endometrium(2)|large_intestine(1)|lung(6)	9						CGAGGGCCTGGGCCGCAACTG	0.711																																					p.G524S		Atlas-SNP	.											.	C9orf172	23	.	0			c.G1570A						PASS	.	G	SER/GLY	0,3880		0,0,1940	7.0	8.0	8.0		1570	1.4	1.0	9		8	1,8013		0,1,4006	no	missense	C9orf172	NM_001080482.2	56	0,1,5946	AA,AG,GG		0.0125,0.0,0.0084	possibly-damaging	524/977	139740436	1,11893	1940	4007	5947	SO:0001583	missense	389813	exon1			GGCCTGGGCCGCA		CCDS48059.1	9q34.3	2012-04-03			ENSG00000232434	ENSG00000232434			37284	protein-coding gene	gene with protein product							Standard	NM_001080482		Approved		uc011meh.2	C9J069		ENST00000436881.1:c.1570G>A	9.37:g.139740436G>A	ENSP00000412388:p.Gly524Ser	81.0	0.0	0		63.0	37.0	0.587302	NM_001080482		Missense_Mutation	SNP	ENST00000436881.1	37	CCDS48059.1	.	.	.	.	.	.	.	.	.	.	.	7.729	0.698804	0.15106	0.0	1.25E-4	ENSG00000232434	ENST00000436881	.	.	.	3.54	1.41	0.22369	.	.	.	.	.	T	0.18718	0.0449	N	0.12746	0.255	0.26736	N	0.970498	P	0.36683	0.565	B	0.34385	0.181	T	0.12319	-1.0552	8	0.30078	T	0.28	-13.7135	9.0585	0.36421	0.2261:0.0:0.7739:0.0	.	524	C9J069	CI172_HUMAN	S	524	.	ENSP00000412388:G524S	G	+	1	0	C9orf172	138860257	0.337000	0.24766	0.990000	0.47175	0.802000	0.45316	0.645000	0.24782	0.670000	0.31165	0.472000	0.43445	GGC	.	.	weak		0.711	C9orf172-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_001080482	
MBD1	4152	hgsc.bcm.edu	37	18	47796399	47796399	+	3'UTR	SNP	A	A	C	rs183864846	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr18:47796399A>C	ENST00000591416.1	-	0	3721				MBD1_ENST00000590208.1_Intron|MBD1_ENST00000382948.5_Intron|MBD1_ENST00000588937.1_Intron|MBD1_ENST00000269468.5_Intron|MBD1_ENST00000349085.2_Intron|MBD1_ENST00000585672.1_Intron|MBD1_ENST00000269471.5_Intron|MBD1_ENST00000585595.1_Intron|MBD1_ENST00000339998.6_Missense_Mutation_p.I545M|MBD1_ENST00000424334.2_Intron|MBD1_ENST00000436910.1_Intron|MBD1_ENST00000347968.3_Intron|MBD1_ENST00000587605.1_Intron|MBD1_ENST00000353909.3_Intron			Q9UIS9	MBD1_HUMAN	methyl-CpG binding domain protein 1						negative regulation of transcription, DNA-templated (GO:0045892)|transcription from RNA polymerase II promoter (GO:0006366)	cytoplasm (GO:0005737)|heterochromatin (GO:0000792)|nuclear matrix (GO:0016363)|nuclear speck (GO:0016607)|nucleus (GO:0005634)	DNA binding (GO:0003677)|methyl-CpG binding (GO:0008327)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription corepressor activity (GO:0003714)|zinc ion binding (GO:0008270)			breast(3)|central_nervous_system(1)|endometrium(6)|kidney(2)|large_intestine(5)|lung(14)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(2)	36						CAATCAAATAAATTTCATATA	0.378													A|||	14	0.00279553	0.0	0.0029	5008	,	,		20091	0.0		0.006	False		,,,				2504	0.0061				p.I545M		Atlas-SNP	.											MBD1_ENST00000339998,NS,carcinoma,-1,1	MBD1	228	1	0			c.T1635G						scavenged	.	A	,,,MET/ILE,,,,,,	2,1750		0,2,874	110.0	109.0	110.0		,,,1635,,,,,,	1.4	0.0	18		110	31,3951		0,31,1960	yes	intron,intron,intron,missense,intron,intron,intron,intron,intron,intron	MBD1	NM_001204136.1,NM_001204139.1,NM_001204141.1,NM_001204142.1,NM_001204143.1,NM_002384.2,NM_015844.2,NM_015845.3,NM_015846.3,NM_015847.3	,,,10,,,,,,	0,33,2834	CC,CA,AA		0.7785,0.1142,0.5755	,,,,,,,,,	,,,545/551,,,,,,	47796399	33,5701	876	1991	2867	SO:0001624	3_prime_UTR_variant	4152	exon14			CAAATAAATTTCA	Y10746	CCDS11941.1, CCDS11942.1, CCDS11943.1, CCDS11944.1, CCDS32832.1, CCDS56071.1, CCDS56072.1, CCDS56073.1, CCDS59318.1, CCDS59319.1, CCDS59320.1	18q21	2014-02-18			ENSG00000141644	ENSG00000141644			6916	protein-coding gene	gene with protein product		156535				9207790, 10441743	Standard	NM_015844		Approved	PCM1, CXXC3	uc002lem.4	Q9UIS9	OTTHUMG00000132669	ENST00000591416.1:c.*1472T>G	18.37:g.47796399A>C		5.0	0.0	0		5.0	4.0	0.8	NM_001204142	A4UTZ0|B4DXJ5|E9PEC5|K7ELI2|K7EQZ4|K7ESN0|O15248|O95241|Q7Z7B5|Q8N4W4|Q9UNZ6|Q9UNZ7|Q9UNZ8|Q9UNZ9	Missense_Mutation	SNP	ENST00000591416.1	37	CCDS11943.1	7	0.003205128205128205	0	0.0	1	0.0027624309392265192	0	0.0	6	0.0079155672823219	A	9.230	1.035529	0.19590	0.001142	0.007785	ENSG00000141644	ENST00000339998	D	0.95756	-3.8	4.03	1.44	0.22558	.	.	.	.	.	D	0.87981	0.6315	.	.	.	0.18873	N	0.999987	B	0.24368	0.102	B	0.18561	0.022	T	0.81816	-0.0759	8	0.87932	D	0	.	4.6182	0.12437	0.5301:0.2952:0.0:0.1746	.	545	Q9UIS9-6	.	M	545	ENSP00000339546:I545M	ENSP00000339546:I545M	I	-	3	3	MBD1	46050397	0.000000	0.05858	0.010000	0.14722	0.703000	0.40648	-0.694000	0.05115	0.273000	0.22049	0.482000	0.46254	ATT	A|0.993;C|0.007	0.007	strong		0.378	MBD1-004	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000255926.3	NM_015846	
FAM134A	79137	hgsc.bcm.edu	37	2	220046155	220046155	+	Silent	SNP	C	C	T	rs548711754		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr2:220046155C>T	ENST00000430297.2	+	7	985	c.849C>T	c.(847-849)agC>agT	p.S283S		NM_024293.4	NP_077269.3	Q8NC44	F134A_HUMAN	family with sequence similarity 134, member A	283						integral component of membrane (GO:0016021)				central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(4)|lung(9)|ovary(1)|prostate(2)	19		Renal(207;0.0915)		Epithelial(149;8.92e-07)|all cancers(144;0.000151)|LUSC - Lung squamous cell carcinoma(224;0.008)|Lung(261;0.00942)		AGAGTGAAAGCGAGGCAGAGC	0.542													C|||	1	0.000199681	0.0	0.0	5008	,	,		18963	0.0		0.0	False		,,,				2504	0.001				p.S283S		Atlas-SNP	.											FAM134A,colon,carcinoma,0,1	FAM134A	34	1	0			c.C849T						PASS	.						56.0	57.0	57.0					2																	220046155		2203	4300	6503	SO:0001819	synonymous_variant	79137	exon7			TGAAAGCGAGGCA	AK074983	CCDS2434.1	2q36.1	2008-02-05	2007-05-01	2007-05-01	ENSG00000144567	ENSG00000144567			28450	protein-coding gene	gene with protein product			"""chromosome 2 open reading frame 17"""	C2orf17			Standard	NM_024293		Approved	MGC3035	uc002vjw.4	Q8NC44	OTTHUMG00000154577	ENST00000430297.2:c.849C>T	2.37:g.220046155C>T		82.0	0.0	0		74.0	18.0	0.243243	NM_024293	Q6P1P5|Q9H0K7	Silent	SNP	ENST00000430297.2	37	CCDS2434.1																																																																																			.	.	none		0.542	FAM134A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000336147.2	NM_024293	
MEP1B	4225	hgsc.bcm.edu	37	18	29782953	29782953	+	Missense_Mutation	SNP	A	A	G	rs71361372	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr18:29782953A>G	ENST00000269202.6	+	6	395	c.348A>G	c.(346-348)atA>atG	p.I116M	MEP1B_ENST00000581447.1_Missense_Mutation_p.I116M	NM_005925.2	NP_005916.2	Q16820	MEP1B_HUMAN	meprin A, beta	116	Metalloprotease.				digestion (GO:0007586)|inflammatory response (GO:0006954)	extracellular space (GO:0005615)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	metalloendopeptidase activity (GO:0004222)|zinc ion binding (GO:0008270)			cervix(1)|endometrium(1)|kidney(2)|large_intestine(6)|lung(9)|ovary(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	23						CAAACTATATATCAGTGTTCA	0.413													A|||	36	0.0071885	0.0015	0.0086	5008	,	,		20162	0.0		0.0129	False		,,,				2504	0.0153				p.I116M		Atlas-SNP	.											.	MEP1B	54	.	0			c.A348G						PASS	.	A	MET/ILE	13,3787		0,13,1887	83.0	81.0	82.0		348	1.2	1.0	18	dbSNP_130	82	141,8103		3,135,3984	yes	missense	MEP1B	NM_005925.2	10	3,148,5871	GG,GA,AA		1.7103,0.3421,1.2786	probably-damaging	116/702	29782953	154,11890	1900	4122	6022	SO:0001583	missense	4225	exon6			CTATATATCAGTG	X81333	CCDS45846.1	18q12.2-q12.3	2003-12-17				ENSG00000141434	3.4.24.18		7020	protein-coding gene	gene with protein product		600389				7774936	Standard	NM_005925		Approved		uc002kxj.4	Q16820		ENST00000269202.6:c.348A>G	18.37:g.29782953A>G	ENSP00000269202:p.Ile116Met	37.0	0.0	0		39.0	24.0	0.615385	NM_005925	B7ZM35|B9EGL6|Q670J1	Missense_Mutation	SNP	ENST00000269202.6	37	CCDS45846.1	16	0.007326007326007326	0	0.0	5	0.013812154696132596	0	0.0	11	0.014511873350923483	A	18.72	3.684857	0.68157	0.003421	0.017103	ENSG00000141434	ENST00000269202	T	0.70749	-0.51	5.72	1.22	0.21188	Peptidase, metallopeptidase (1);Peptidase M12A, astacin (1);Metallopeptidase, catalytic domain (1);	0.000000	0.85682	D	0.000000	T	0.74199	0.3685	M	0.91972	3.26	0.38390	D	0.945362	D	0.89917	1.0	D	0.81914	0.995	T	0.80837	-0.1204	10	0.87932	D	0	-18.6302	8.2453	0.31684	0.5426:0.3346:0.0:0.1228	.	116	Q16820	MEP1B_HUMAN	M	116	ENSP00000269202:I116M	ENSP00000269202:I116M	I	+	3	3	MEP1B	28036951	1.000000	0.71417	0.998000	0.56505	0.974000	0.67602	1.052000	0.30429	0.376000	0.24707	0.533000	0.62120	ATA	A|0.992;G|0.008	0.008	strong		0.413	MEP1B-001	KNOWN	NAGNAG_splice_site|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000447755.1	NM_005925	
LEPRE1	64175	hgsc.bcm.edu	37	1	43223489	43223489	+	Missense_Mutation	SNP	C	C	T	rs6700677	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr1:43223489C>T	ENST00000296388.5	-	5	1096	c.1045G>A	c.(1045-1047)Gga>Aga	p.G349R	LEPRE1_ENST00000397054.3_Missense_Mutation_p.G349R|LEPRE1_ENST00000236040.4_Missense_Mutation_p.G349R			Q32P28	P3H1_HUMAN	leucine proline-enriched proteoglycan (leprecan) 1	349			G -> R (in dbSNP:rs6700677).		bone development (GO:0060348)|cell growth (GO:0016049)|chaperone-mediated protein folding (GO:0061077)|collagen fibril organization (GO:0030199)|collagen metabolic process (GO:0032963)|extracellular matrix organization (GO:0030198)|negative regulation of cell proliferation (GO:0008285)|negative regulation of post-translational protein modification (GO:1901874)|peptidyl-proline hydroxylation (GO:0019511)|protein folding (GO:0006457)|protein hydroxylation (GO:0018126)|protein stabilization (GO:0050821)|regulation of ossification (GO:0030278)|regulation of protein secretion (GO:0050708)	endoplasmic reticulum (GO:0005783)|endoplasmic reticulum lumen (GO:0005788)|extracellular vesicular exosome (GO:0070062)|macromolecular complex (GO:0032991)|membrane (GO:0016020)|nucleus (GO:0005634)|proteinaceous extracellular matrix (GO:0005578)	iron ion binding (GO:0005506)|L-ascorbic acid binding (GO:0031418)|procollagen-proline 3-dioxygenase activity (GO:0019797)|protein complex binding (GO:0032403)			large_intestine(2)|lung(15)|ovary(5)|prostate(1)|urinary_tract(3)	26	Ovarian(52;0.00744)|all_hematologic(146;0.0977)|Acute lymphoblastic leukemia(166;0.155)	Myeloproliferative disorder(586;0.0505)			L-Proline(DB00172)|Succinic acid(DB00139)|Vitamin C(DB00126)	TGTTCTTCTCCAAGCATAGCT	0.498											OREG0013423	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	C|||	275	0.0549121	0.112	0.0389	5008	,	,		22023	0.001		0.0388	False		,,,				2504	0.0613				p.G349R		Atlas-SNP	.											LEPRE1_ENST00000296388,colon,carcinoma,0,8	LEPRE1	130	8	0			c.G1045A						PASS	.	C	ARG/GLY,ARG/GLY	478,3928	223.9+/-240.3	18,442,1743	253.0	211.0	225.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	1045,1045	5.8	1.0	1	dbSNP_116	225	374,8226	122.0+/-181.0	6,362,3932	yes	missense,missense	LEPRE1	NM_001146289.1,NM_022356.3	125,125	24,804,5675	TT,TC,CC		4.3488,10.8488,6.5508	probably-damaging,probably-damaging	349/698,349/737	43223489	852,12154	2203	4300	6503	SO:0001583	missense	64175	exon5			CTTCTCCAAGCAT	AK027648	CCDS472.2, CCDS53307.1, CCDS57986.1	1p34.1	2014-09-17			ENSG00000117385	ENSG00000117385			19316	protein-coding gene	gene with protein product	"""prolyl 3-hydroxylase 1"", ""growth suppressor 1"""	610339				10951563	Standard	NM_022356		Approved	GROS1, P3H1, LEPRECAN, MGC117314	uc001chx.4	Q32P28	OTTHUMG00000007525	ENST00000296388.5:c.1045G>A	1.37:g.43223489C>T	ENSP00000296388:p.Gly349Arg	170.0	0.0	0	914	98.0	20.0	0.204082	NM_001146289	Q7KZR4|Q96BR8|Q96SK8|Q96SL5|Q96SN3|Q9H6K3|Q9HC86|Q9HC87	Missense_Mutation	SNP	ENST00000296388.5	37	CCDS472.2	97	0.044413919413919416	48	0.0975609756097561	19	0.052486187845303865	0	0.0	30	0.0395778364116095	C	23.0	4.365718	0.82463	0.108488	0.043488	ENSG00000117385	ENST00000397054;ENST00000236040;ENST00000296388;ENST00000540027	D;D;D	0.82893	-1.66;-1.66;-1.66	5.84	5.84	0.93424	Tetratricopeptide-like helical (1);	0.000000	0.85682	D	0.000000	T	0.27384	0.0672	M	0.87547	2.89	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.97110	1.0;0.999;0.999	T	0.68618	-0.5361	10	0.87932	D	0	-19.1499	17.6432	0.88142	0.0:1.0:0.0:0.0	rs6700677;rs52814052;rs56872967;rs6700677	349;214;349	Q32P28-3;B4DNM8;Q32P28	.;.;P3H1_HUMAN	R	349;349;349;214	ENSP00000380245:G349R;ENSP00000236040:G349R;ENSP00000296388:G349R	ENSP00000236040:G349R	G	-	1	0	LEPRE1	42996076	1.000000	0.71417	0.993000	0.49108	0.473000	0.32948	7.487000	0.81328	2.769000	0.95229	0.462000	0.41574	GGA	C|0.940;T|0.060	0.060	strong		0.498	LEPRE1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000019790.2	NM_022356	
PTH1R	5745	hgsc.bcm.edu	37	3	46939456	46939456	+	Splice_Site	SNP	G	G	C	rs201472450		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr3:46939456G>C	ENST00000313049.5	+	4	627		c.e4+1		PTH1R_ENST00000418619.1_Splice_Site|PTH1R_ENST00000490109.1_Splice_Site|PTH1R_ENST00000449590.1_Splice_Site|PTH1R_ENST00000430002.2_Splice_Site			Q03431	PTH1R_HUMAN	parathyroid hormone 1 receptor						adenylate cyclase-activating G-protein coupled receptor signaling pathway (GO:0007189)|adenylate cyclase-modulating G-protein coupled receptor signaling pathway (GO:0007188)|aging (GO:0007568)|bone mineralization (GO:0030282)|bone resorption (GO:0045453)|cell maturation (GO:0048469)|chondrocyte differentiation (GO:0002062)|G-protein coupled receptor signaling pathway (GO:0007186)|G-protein coupled receptor signaling pathway, coupled to cyclic nucleotide second messenger (GO:0007187)|negative regulation of cell proliferation (GO:0008285)|osteoblast development (GO:0002076)|phospholipase C-activating G-protein coupled receptor signaling pathway (GO:0007200)|positive regulation of cell proliferation (GO:0008284)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|positive regulation of inositol phosphate biosynthetic process (GO:0060732)|skeletal system development (GO:0001501)	apical plasma membrane (GO:0016324)|basolateral plasma membrane (GO:0016323)|brush border membrane (GO:0031526)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	parathyroid hormone receptor activity (GO:0004991)|peptide hormone binding (GO:0017046)|protein self-association (GO:0043621)			breast(1)|central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(3)|liver(1)|lung(5)|skin(2)|stomach(1)|urinary_tract(2)	19					Preotact(DB05829)|Teriparatide(DB06285)	AATCACAAAGGTGAGGCCTGC	0.612																																					.		Atlas-SNP	.											.	PTH1R	49	.	0			c.424+1G>C						PASS	.						61.0	63.0	62.0					3																	46939456		2203	4300	6503	SO:0001630	splice_region_variant	5745	exon6			ACAAAGGTGAGGC		CCDS2747.1	3p22-p21.1	2012-08-10	2008-11-18	2008-11-18	ENSG00000160801	ENSG00000160801		"""GPCR / Class B : Parathyroid hormone receptors"""	9608	protein-coding gene	gene with protein product		168468	"""parathyroid hormone receptor 1"""	PTHR, PTHR1		8020952	Standard	NM_001184744		Approved		uc021wxg.1	Q03431	OTTHUMG00000133515	ENST00000313049.5:c.424+1G>C	3.37:g.46939456G>C		123.0	0.0	0		147.0	49.0	0.333333	NM_000316	Q2M1U3	Splice_Site	SNP	ENST00000313049.5	37	CCDS2747.1	.	.	.	.	.	.	.	.	.	.	G	21.8	4.198211	0.79015	.	.	ENSG00000160801	ENST00000449590;ENST00000418619;ENST00000427125;ENST00000430002;ENST00000313049	.	.	.	5.24	5.24	0.73138	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	16.3295	0.83004	0.0:0.0:1.0:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	PTH1R	46914460	1.000000	0.71417	1.000000	0.80357	0.918000	0.54935	9.292000	0.96076	2.448000	0.82819	0.561000	0.74099	.	.	.	weak		0.612	PTH1R-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257481.1	NM_000316	Intron
TMPRSS13	84000	hgsc.bcm.edu	37	11	117789345	117789345	+	Missense_Mutation	SNP	G	G	C	rs61900347	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr11:117789345G>C	ENST00000430170.2	-	2	317	c.230C>G	c.(229-231)gCc>gGc	p.A77G	TMPRSS13_ENST00000445164.2_Missense_Mutation_p.A77G|TMPRSS13_ENST00000526090.1_Missense_Mutation_p.A77G|TMPRSS13_ENST00000524993.1_Missense_Mutation_p.A77G|TMPRSS13_ENST00000528626.1_Missense_Mutation_p.A77G	NM_001244995.1	NP_001231924.1	Q9BYE2	TMPSD_HUMAN	transmembrane protease, serine 13	77	13 X 5 AA repeats of A-S-P-A-[GLQR].|Ala-rich.					blood microparticle (GO:0072562)|integral component of membrane (GO:0016021)	scavenger receptor activity (GO:0005044)|serine-type endopeptidase activity (GO:0004252)			endometrium(1)|kidney(3)|large_intestine(6)|lung(7)|pancreas(1)|prostate(1)|urinary_tract(1)	20	all_hematologic(175;0.0487)	Medulloblastoma(222;0.0425)|all_hematologic(192;0.196)|all_neural(223;0.234)		BRCA - Breast invasive adenocarcinoma(274;1.78e-05)|Epithelial(105;0.00106)		AGATGCCTGGGCTGGAGATGC	0.672													G|||	2	0.000399361	0.0	0.0	5008	,	,		14255	0.002		0.0	False		,,,				2504	0.0				p.A77G		Atlas-SNP	.											TMPRSS13_ENST00000445164,NS,carcinoma,0,2	TMPRSS13	75	2	0			c.C230G						PASS	.						39.0	48.0	45.0					11																	117789345		1921	4109	6030	SO:0001583	missense	84000	exon2			GCCTGGGCTGGAG	AB048796	CCDS41721.1, CCDS55788.1, CCDS55789.1, CCDS58185.1	11q23	2010-04-13	2005-03-11	2005-03-12	ENSG00000137747	ENSG00000137747		"""Serine peptidases / Transmembrane"""	29808	protein-coding gene	gene with protein product		610050	"""transmembrane protease, serine 11"""	TMPRSS11		11267681	Standard	NM_001077263		Approved	MSPL	uc001prs.2	Q9BYE2	OTTHUMG00000166992	ENST00000430170.2:c.230C>G	11.37:g.117789345G>C	ENSP00000387702:p.Ala77Gly	144.0	0.0	0		243.0	27.0	0.111111	NM_001206790	B4DTM9|E9PIJ5|F8WAJ3|Q86YM4|Q96JY8|Q9BYE1	Missense_Mutation	SNP	ENST00000430170.2	37	CCDS58185.1	219|219	0.10027472527472528|0.10027472527472528	67|67	0.13617886178861788|0.13617886178861788	52|52	0.143646408839779|0.143646408839779	45|45	0.07867132867132867|0.07867132867132867	55|55	0.07255936675461741|0.07255936675461741	G|G	4.978|4.978	0.181711|0.181711	0.09495|0.09495	.|.	.|.	ENSG00000137747|ENSG00000137747	ENST00000336500|ENST00000528626;ENST00000524993;ENST00000430170;ENST00000445164;ENST00000526090	.|D;D;D;D;D	.|0.88431	.|-2.38;-2.36;-2.36;-2.34;-2.24	3.11|3.11	1.04|1.04	0.20106|0.20106	.|.	.|1.049680	.|0.07486	.|N	.|0.904837	.|T	.|0.02380	.|0.0073	L|L	0.32530|0.32530	0.975|0.975	0.80722|0.80722	P|P	0.0|0.0	.|B	.|0.02656	.|0.0	.|B	.|0.04013	.|0.001	.|T	.|0.28776	.|-1.0033	.|9	.|0.20046	.|T	.|0.44	.|.	6.0296|6.0296	0.19673|0.19673	0.1228:0.2258:0.6514:0.0|0.1228:0.2258:0.6514:0.0	rs61900347|rs61900347	.|77	.|E9PRA0	.|.	.|G	-1|77	.|ENSP00000435813:A77G;ENSP00000434279:A77G;ENSP00000387702:A77G;ENSP00000394114:A77G;ENSP00000436502:A77G	.|ENSP00000387702:A77G	.|A	-|-	.|2	.|0	TMPRSS13|TMPRSS13	117294555|117294555	0.000000|0.000000	0.05858|0.05858	0.000000|0.000000	0.03702|0.03702	0.000000|0.000000	0.00434|0.00434	0.105000|0.105000	0.15333|0.15333	-0.045000|-0.045000	0.13468|0.13468	-0.189000|-0.189000	0.12847|0.12847	.|GCC	G|0.899;C|0.101	0.101	strong		0.672	TMPRSS13-006	PUTATIVE	basic|appris_candidate|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000392318.1	NM_032046	
PAX8	7849	hgsc.bcm.edu	37	2	113976146	113976146	+	Silent	SNP	T	T	C	rs368201100	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr2:113976146T>C	ENST00000429538.3	-	12	1511	c.1317A>G	c.(1315-1317)gcA>gcG	p.A439A	PAX8_ENST00000397647.3_3'UTR|PAX8_ENST00000263335.7_3'UTR|PAX8_ENST00000348715.5_3'UTR|AC016683.6_ENST00000456685.1_RNA	NM_003466.3	NP_003457.1	Q06710	PAX8_HUMAN	paired box 8	439					anatomical structure morphogenesis (GO:0009653)|branching involved in ureteric bud morphogenesis (GO:0001658)|cellular response to gonadotropin stimulus (GO:0071371)|central nervous system development (GO:0007417)|inner ear morphogenesis (GO:0042472)|kidney development (GO:0001822)|mesenchymal to epithelial transition involved in metanephros morphogenesis (GO:0003337)|mesonephros development (GO:0001823)|metanephric comma-shaped body morphogenesis (GO:0072278)|metanephric distal convoluted tubule development (GO:0072221)|metanephric epithelium development (GO:0072207)|metanephric nephron tubule formation (GO:0072289)|metanephric S-shaped body morphogenesis (GO:0072284)|negative regulation of apoptotic process involved in metanephric collecting duct development (GO:1900215)|negative regulation of apoptotic process involved in metanephric nephron tubule development (GO:1900218)|negative regulation of mesenchymal cell apoptotic process involved in metanephric nephron morphogenesis (GO:0072305)|negative regulation of mesenchymal cell apoptotic process involved in metanephros development (GO:1900212)|otic vesicle development (GO:0071599)|positive regulation of branching involved in ureteric bud morphogenesis (GO:0090190)|positive regulation of mesenchymal to epithelial transition involved in metanephros morphogenesis (GO:0072108)|positive regulation of metanephric DCT cell differentiation (GO:2000594)|positive regulation of thyroid hormone generation (GO:2000611)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|pronephric field specification (GO:0039003)|pronephros development (GO:0048793)|regulation of apoptotic process (GO:0042981)|regulation of metanephric nephron tubule epithelial cell differentiation (GO:0072307)|regulation of thyroid-stimulating hormone secretion (GO:2000612)|thyroid gland development (GO:0030878)|thyroid-stimulating hormone signaling pathway (GO:0038194)|transcription, DNA-templated (GO:0006351)|urogenital system development (GO:0001655)	nucleoplasm (GO:0005654)|nucleus (GO:0005634)	DNA binding (GO:0003677)|RNA polymerase II core promoter sequence-specific DNA binding (GO:0000979)|sequence-specific DNA binding transcription factor activity (GO:0003700)|thyroid-stimulating hormone receptor activity (GO:0004996)|transcription regulatory region DNA binding (GO:0044212)		PAX8/PPARG(117)	breast(1)|endometrium(4)|kidney(2)|large_intestine(1)|liver(1)|lung(9)|ovary(1)|skin(1)	20						TGGTGGGCGGTGCACTCGGCC	0.517			T	PPARG	follicular thyroid		Thyroid dysgenesis						T|||	8	0.00159744	0.0	0.0014	5008	,	,		17403	0.0		0.006	False		,,,				2504	0.001				p.A439A	Ovarian(188;7 2067 9084 29802 29892)	Atlas-SNP	.		Dom	yes		2	2q12-q14	7849	paired box gene 8	yes	E	.	PAX8	42	.	0			c.A1317G						PASS	.	T	,,,	6,3874		0,6,1934	34.0	40.0	38.0		1317,,,	-6.1	0.0	2		38	37,8203		0,37,4083	no	coding-synonymous,utr-3,utr-3,utr-3	PAX8	NM_003466.3,NM_013952.3,NM_013953.3,NM_013992.3	,,,	0,43,6017	CC,CT,TT		0.449,0.1546,0.3548	,,,	439/451,,,	113976146	43,12077	1940	4120	6060	SO:0001819	synonymous_variant	7849	exon12			GGGCGGTGCACTC	X69699	CCDS42735.1, CCDS42736.1, CCDS46398.1, CCDS46399.1	2q13	2011-06-20	2007-07-12		ENSG00000125618	ENSG00000125618		"""Paired boxes"", ""Homeoboxes / PRD class"""	8622	protein-coding gene	gene with protein product		167415	"""paired box gene 8"""			8431641, 7981748	Standard	NM_003466		Approved		uc010yxt.2	Q06710	OTTHUMG00000128529	ENST00000429538.3:c.1317A>G	2.37:g.113976146T>C		54.0	0.0	0		70.0	32.0	0.457143	NM_003466	Q09155|Q16337|Q16338|Q16339|Q4ZG35|Q96J49	Silent	SNP	ENST00000429538.3	37	CCDS46398.1	.	.	.	.	.	.	.	.	.	.	T	0.123	-1.122781	0.01785	0.001546	0.00449	ENSG00000125618	ENST00000468980	.	.	.	5.34	-6.12	0.02124	.	.	.	.	.	T	0.51907	0.1702	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.56056	-0.8042	4	.	.	.	.	10.6988	0.45915	0.1148:0.5796:0.0:0.3056	.	.	.	.	A	162	.	.	T	-	1	0	PAX8	113692617	0.000000	0.05858	0.014000	0.15608	0.065000	0.16274	-4.294000	0.00258	-0.902000	0.03886	-1.054000	0.02325	ACC	.	.	weak		0.517	PAX8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250353.5		
AKR1B15	441282	hgsc.bcm.edu	37	7	134261174	134261174	+	Missense_Mutation	SNP	A	A	G	rs2458502	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr7:134261174A>G	ENST00000457545.2	+	9	1077	c.817A>G	c.(817-819)Aca>Gca	p.T273A	AKR1B15_ENST00000423958.1_Missense_Mutation_p.T245A	NM_001080538.2	NP_001074007.2	C9JRZ8	AK1BF_HUMAN	aldo-keto reductase family 1, member B15	273							oxidoreductase activity (GO:0016491)			endometrium(1)|kidney(3)|large_intestine(2)|lung(10)|ovary(1)|urinary_tract(1)	18						CAAAAAAACCACAGCCCAGGT	0.448													A|||	5	0.000998403	0.0	0.0029	5008	,	,		21387	0.0		0.003	False		,,,				2504	0.0				p.T273A		Atlas-SNP	.											.	AKR1B15	105	.	0			c.A817G						PASS	.	A	ALA/THR	7,4399	12.9+/-30.5	0,7,2196	64.0	71.0	68.0		817	-6.9	0.0	7	dbSNP_100	68	48,8552	31.2+/-83.2	0,48,4252	no	missense	AKR1B15	NM_001080538.2	58	0,55,6448	GG,GA,AA		0.5581,0.1589,0.4229	benign	273/345	134261174	55,12951	2203	4300	6503	SO:0001583	missense	441282	exon9			AAAACCACAGCCC		CCDS47715.1, CCDS47715.2	7q33	2009-09-09			ENSG00000227471	ENSG00000227471		"""Aldo-keto reductases"""	37281	protein-coding gene	gene with protein product							Standard	NM_001080538		Approved		uc011kpr.2	C9JRZ8	OTTHUMG00000155376	ENST00000457545.2:c.817A>G	7.37:g.134261174A>G	ENSP00000389289:p.Thr273Ala	91.0	0.0	0		77.0	17.0	0.220779	NM_001080538	C9J3V2	Missense_Mutation	SNP	ENST00000457545.2	37	CCDS47715.2	2	9.157509157509158E-4	0	0.0	1	0.0027624309392265192	0	0.0	1	0.0013192612137203166	a	0.028	-1.354403	0.01256	0.001589	0.005581	ENSG00000227471	ENST00000457545;ENST00000423958	T;T	0.16324	2.35;2.35	3.46	-6.91	0.01649	NADP-dependent oxidoreductase domain (3);	.	.	.	.	T	0.03178	0.0093	N	0.03071	-0.42	0.09310	N	0.999998	B;B	0.10296	0.0;0.003	B;B	0.12156	0.001;0.007	T	0.33904	-0.9850	9	0.33141	T	0.24	.	2.4069	0.04414	0.2716:0.2406:0.3777:0.1102	rs2458502	245;273	C9JRZ8-2;C9JRZ8	.;AK1BF_HUMAN	A	273;245	ENSP00000389289:T273A;ENSP00000397009:T245A	ENSP00000397009:T245A	T	+	1	0	AKR1B15	133911714	0.000000	0.05858	0.001000	0.08648	0.157000	0.22087	-5.815000	0.00096	-2.183000	0.00763	-1.140000	0.01884	ACA	A|0.998;G|0.002	0.002	strong		0.448	AKR1B15-001	PUTATIVE	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000339726.2		
CCDC178	374864	hgsc.bcm.edu	37	18	30928852	30928852	+	Splice_Site	SNP	A	A	G	rs140419270	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr18:30928852A>G	ENST00000383096.3	-	8	640		c.e8+1		CCDC178_ENST00000300227.8_Splice_Site|CCDC178_ENST00000406524.2_Splice_Site|CCDC178_ENST00000583930.1_Splice_Site|CCDC178_ENST00000402325.1_Splice_Site|CCDC178_ENST00000579916.1_Intron|CCDC178_ENST00000403303.1_Splice_Site|CCDC178_ENST00000579947.1_Splice_Site			Q5BJE1	CC178_HUMAN	coiled-coil domain containing 178									p.?(2)									GAACAACTTTACCTCTCTTTT	0.323													A|||	8	0.00159744	0.0	0.0029	5008	,	,		15391	0.0		0.005	False		,,,				2504	0.001				.		Atlas-SNP	.											.	.	.	.	2	Unknown(2)	lung(2)	c.457+2T>C						PASS	.	A	,	5,4401	9.9+/-24.2	0,5,2198	132.0	111.0	118.0		,	4.2	0.8	18	dbSNP_134	118	31,8569	21.6+/-65.8	0,31,4269	yes	splice-5,splice-5	C18orf34	NM_001105528.1,NM_198995.2	,	0,36,6467	GG,GA,AA		0.3605,0.1135,0.2768	,	,	30928852	36,12970	2203	4300	6503	SO:0001630	splice_region_variant	374864	exon8			AACTTTACCTCTC	AK126038	CCDS11906.1, CCDS42424.1	18q12.1	2012-10-15	2012-10-15	2012-10-15	ENSG00000166960	ENSG00000166960			29588	protein-coding gene	gene with protein product			"""chromosome 18 open reading frame 34"""	C18orf34			Standard	NM_198995		Approved	FLJ44050	uc002kxn.2	Q5BJE1	OTTHUMG00000132279	ENST00000383096.3:c.457+1T>C	18.37:g.30928852A>G		77.0	0.0	0		62.0	24.0	0.387097	NM_001105528	A6NDC6|J3KS92|Q6ZP67|Q6ZU20	Splice_Site	SNP	ENST00000383096.3	37	CCDS42424.1	5	0.0022893772893772895	0	0.0	0	0.0	0	0.0	5	0.006596306068601583	A	12.87	2.068210	0.36470	0.001135	0.003605	ENSG00000166960	ENST00000403303;ENST00000383096;ENST00000300227;ENST00000406524;ENST00000402325;ENST00000399177	.	.	.	4.24	4.24	0.50183	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	10.0289	0.42087	1.0:0.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	-	.	.	C18orf34	29182850	0.994000	0.37717	0.791000	0.31998	0.061000	0.15899	3.552000	0.53705	2.144000	0.66660	0.533000	0.62120	.	A|0.997;G|0.003	0.003	strong		0.323	CCDC178-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000255373.2	NM_198995	Intron
PAGE5	90737	hgsc.bcm.edu	37	X	55247817	55247817	+	Missense_Mutation	SNP	T	T	C	rs61745114	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chrX:55247817T>C	ENST00000289619.5	+	2	307	c.62T>C	c.(61-63)aTg>aCg	p.M21T	PAGE5_ENST00000374952.1_Start_Codon_SNP_p.M1T|PAGE5_ENST00000374955.3_Start_Codon_SNP_p.M1T	NM_130467.3	NP_569734.2	Q96GU1	PAGE5_HUMAN	P antigen family, member 5 (prostate associated)	21										breast(1)|endometrium(1)|kidney(1)|large_intestine(2)|lung(3)	8						GTGAGAGATATGAGTGAGCAT	0.363													T|||	7	0.0018543	0.0	0.0	3775	,	,		11913	0.0		0.006	False		,,,				2504	0.001				p.M21T		Atlas-SNP	.											.	PAGE5	20	.	0			c.T62C						PASS	.	T	THR/MET,THR/MET	11,3824		0,11,0,1621,571	98.0	80.0	86.0		2,62	1.1	0.0	X	dbSNP_129	86	80,6648		0,52,28,2376,1844	yes	missense,missense	PAGE5	NM_001013435.1,NM_130467.3	81,81	0,63,28,3997,2415	CC,CT,C,TT,T		1.1891,0.2868,0.8615	probably-damaging,probably-damaging	1/111,21/131	55247817	91,10472	2203	4300	6503	SO:0001583	missense	90737	exon2			GAGATATGAGTGA	AJ344352	CCDS14368.1, CCDS35306.1	Xp11.22	2009-08-18			ENSG00000158639	ENSG00000158639			29992	protein-coding gene	gene with protein product	"""cancer/testis antigen family 16, member 1"", ""cancer/testis antigen family 16, member 2"""					11920606, 11992404	Standard	XM_006724613		Approved	PAGE-5, CT16.1, CT16.2	uc004duk.3	Q96GU1	OTTHUMG00000021650	ENST00000289619.5:c.62T>C	X.37:g.55247817T>C	ENSP00000289619:p.Met21Thr	622.0	0.0	0		278.0	272.0	0.978417	NM_130467	Q2NL97|Q5JUL0|Q8WWL9	Missense_Mutation	SNP	ENST00000289619.5	37	CCDS14368.1	4	0.0024110910186859553	0	0.0	0	0.0	0	0.0	5	0.006596306068601583	.	9.512	1.106093	0.20632	0.002868	0.011891	ENSG00000158639	ENST00000289619;ENST00000374955;ENST00000374952	T;T;T	0.50813	1.66;1.75;0.73	1.09	1.09	0.20402	.	.	.	.	.	T	0.49081	0.1536	M	0.67397	2.05	0.54753	D	0.999989	D	0.60160	0.987	D	0.66196	0.942	T	0.55205	-0.8177	9	0.87932	D	0	.	4.0529	0.09803	0.0:0.0:0.0:1.0	rs61745114	21	Q96GU1	GGEE1_HUMAN	T	21;1;1	ENSP00000289619:M21T;ENSP00000364093:M1T;ENSP00000364090:M1T	ENSP00000289619:M21T	M	+	2	0	PAGE5	55264542	0.381000	0.25140	0.020000	0.16555	0.069000	0.16628	0.969000	0.29370	0.677000	0.31305	0.231000	0.17811	ATG	T|0.994;C|0.006	0.006	strong		0.363	PAGE5-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000056861.1	NM_130467	
HLA-DRB5	3127	hgsc.bcm.edu	37	6	32489753	32489753	+	Missense_Mutation	SNP	C	C	T	rs41544215	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr6:32489753C>T	ENST00000374975.3	-	2	361	c.299G>A	c.(298-300)aGg>aAg	p.R100K		NM_002125.3	NP_002116.2			major histocompatibility complex, class II, DR beta 5											NS(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(1)|lung(3)|pancreas(1)|prostate(1)|stomach(2)	10						CGCGGCGCGCCTGTCTTCCAG	0.662																																					p.R100K		Atlas-SNP	.											.	HLA-DRB5	31	.	0			c.G299A						PASS	.	C	LYS/ARG	193,3701		62,69,1816	36.0	32.0	33.0		299	-9.4	0.0	6	dbSNP_127	33	210,7310		48,114,3598	no	missense	HLA-DRB5	NM_002125.3	26	110,183,5414	TT,TC,CC		2.7926,4.9563,3.5308	benign	100/267	32489753	403,11011	1947	3760	5707	SO:0001583	missense	3127	exon2			GCGCGCCTGTCTT		CCDS4751.1	6p21.3	2013-01-11			ENSG00000198502	ENSG00000198502		"""Histocompatibility complex"", ""Immunoglobulin superfamily / C1-set domain containing"""	4953	protein-coding gene	gene with protein product		604776					Standard	NM_002125		Approved		uc003obj.3	Q30154	OTTHUMG00000031027	ENST00000374975.3:c.299G>A	6.37:g.32489753C>T	ENSP00000364114:p.Arg100Lys	2.0	0.0	0		27.0	25.0	0.925926	NM_002125		Missense_Mutation	SNP	ENST00000374975.3	37	CCDS4751.1	92	0.04212454212454213	32	0.06504065040650407	21	0.058011049723756904	9	0.015734265734265736	30	0.0395778364116095	.	4.604	0.112185	0.08831	0.049563	0.027926	ENSG00000198502	ENST00000374975	T	0.00314	8.14	4.72	-9.43	0.00607	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);	5.372110	0.00166	N	0.000006	T	0.00039	0.0001	N	0.11756	0.17	0.09310	N	1	B;B	0.06786	0.001;0.001	B;B	0.29942	0.006;0.109	T	0.39014	-0.9634	10	0.10636	T	0.68	.	2.9021	0.05709	0.1516:0.3667:0.2298:0.2519	.	27;100	Q29973;Q30154	.;DRB5_HUMAN	K	100	ENSP00000364114:R100K	ENSP00000364114:R100K	R	-	2	0	HLA-DRB5	32597731	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-12.951000	0.00001	-4.402000	0.00051	-2.111000	0.00353	AGG	T|0.078;C|0.922	0.078	strong		0.662	HLA-DRB5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076022.2	NM_002125	
QPCTL	54814	hgsc.bcm.edu	37	19	46202131	46202131	+	Missense_Mutation	SNP	C	C	T	rs145016874	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr19:46202131C>T	ENST00000012049.5	+	5	1080	c.859C>T	c.(859-861)Cgc>Tgc	p.R287C	QPCTL_ENST00000366382.4_Missense_Mutation_p.R193C	NM_017659.3	NP_060129.2	Q9NXS2	QPCTL_HUMAN	glutaminyl-peptide cyclotransferase-like	287					peptidyl-pyroglutamic acid biosynthetic process, using glutaminyl-peptide cyclotransferase (GO:0017186)	Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|membrane (GO:0016020)	glutaminyl-peptide cyclotransferase activity (GO:0016603)|zinc ion binding (GO:0008270)			breast(1)|cervix(2)|endometrium(1)|lung(5)|skin(1)|stomach(1)	11		Ovarian(192;0.051)|all_neural(266;0.112)		OV - Ovarian serous cystadenocarcinoma(262;0.0059)|GBM - Glioblastoma multiforme(486;0.0882)|Epithelial(262;0.208)		TCGCACGGTCCGCTGGTTCCA	0.617													C|||	3	0.000599042	0.0	0.0	5008	,	,		15872	0.0		0.002	False		,,,				2504	0.001				p.R287C		Atlas-SNP	.											.	QPCTL	24	.	0			c.C859T						PASS	.	C	CYS/ARG,CYS/ARG	2,4404	4.2+/-10.8	0,2,2201	81.0	80.0	81.0		577,859	3.8	1.0	19	dbSNP_134	81	11,8589	8.4+/-32.0	0,11,4289	yes	missense,missense	QPCTL	NM_001163377.1,NM_017659.3	180,180	0,13,6490	TT,TC,CC		0.1279,0.0454,0.1	probably-damaging,probably-damaging	193/289,287/383	46202131	13,12993	2203	4300	6503	SO:0001583	missense	54814	exon5			ACGGTCCGCTGGT	AK000091	CCDS12672.1, CCDS54282.1	19q13.32	2014-09-04			ENSG00000011478	ENSG00000011478			25952	protein-coding gene	gene with protein product	"""glutaminyl cyclase-like"""						Standard	NM_017659		Approved	FLJ20084	uc010xxr.2	Q9NXS2	OTTHUMG00000182131	ENST00000012049.5:c.859C>T	19.37:g.46202131C>T	ENSP00000012049:p.Arg287Cys	113.0	0.0	0		92.0	45.0	0.48913	NM_017659	Q53HE4|Q96F74	Missense_Mutation	SNP	ENST00000012049.5	37	CCDS12672.1	1	4.578754578754579E-4	0	0.0	0	0.0	0	0.0	1	0.0013192612137203166	C	17.33	3.362347	0.61403	4.54E-4	0.001279	ENSG00000011478	ENST00000012049;ENST00000366382	T;T	0.51071	0.72;0.72	5.93	3.83	0.44106	Peptidase M28 (1);	0.342596	0.33772	N	0.004570	T	0.63212	0.2492	M	0.88450	2.955	0.58432	D	0.999993	D	0.71674	0.998	P	0.56700	0.804	T	0.64580	-0.6374	10	0.39692	T	0.17	-1.3625	8.816	0.34996	0.0:0.8542:0.0:0.1458	.	287	Q9NXS2	QPCTL_HUMAN	C	287;193	ENSP00000012049:R287C;ENSP00000387944:R193C	ENSP00000012049:R287C	R	+	1	0	QPCTL	50893971	0.932000	0.31603	0.997000	0.53966	0.627000	0.37826	1.506000	0.35747	2.826000	0.97356	0.655000	0.94253	CGC	C|0.999;T|0.001	0.001	strong		0.617	QPCTL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000459656.1	NM_017659	
CYP2D6	1565	hgsc.bcm.edu	37	22	42526775	42526775	+	Missense_Mutation	SNP	C	C	T	rs72549358	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr22:42526775C>T	ENST00000360608.5	-	1	133	c.19G>A	c.(19-21)Gtg>Atg	p.V7M	CYP2D6_ENST00000389970.3_Missense_Mutation_p.V7M|CYP2D6_ENST00000359033.4_Missense_Mutation_p.V7M|NDUFA6-AS1_ENST00000608288.1_RNA|NDUFA6-AS1_ENST00000416037.2_RNA|NDUFA6-AS1_ENST00000608491.1_RNA|NDUFA6-AS1_ENST00000439129.1_RNA	NM_000106.5	NP_000097	P10635	CP2D6_HUMAN	cytochrome P450, family 2, subfamily D, polypeptide 6	7					alkaloid catabolic process (GO:0009822)|alkaloid metabolic process (GO:0009820)|coumarin metabolic process (GO:0009804)|drug catabolic process (GO:0042737)|drug metabolic process (GO:0017144)|heterocycle metabolic process (GO:0046483)|isoquinoline alkaloid metabolic process (GO:0033076)|monoterpenoid metabolic process (GO:0016098)|negative regulation of binding (GO:0051100)|negative regulation of cellular organofluorine metabolic process (GO:0090350)|oxidation-reduction process (GO:0055114)|oxidative demethylation (GO:0070989)|small molecule metabolic process (GO:0044281)|steroid metabolic process (GO:0008202)|xenobiotic metabolic process (GO:0006805)	endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|mitochondrion (GO:0005739)	aromatase activity (GO:0070330)|drug binding (GO:0008144)|heme binding (GO:0020037)|iron ion binding (GO:0005506)|monooxygenase activity (GO:0004497)|oxidoreductase activity (GO:0016491)			NS(1)|breast(2)|endometrium(1)|large_intestine(2)|lung(4)|prostate(7)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	21					Abiraterone(DB05812)|Acebutolol(DB01193)|Acetaminophen(DB00316)|Ajmaline(DB01426)|Almotriptan(DB00918)|Alogliptin(DB06203)|Alprenolol(DB00866)|Aminophenazone(DB01424)|Amiodarone(DB01118)|Amitriptyline(DB00321)|Amlodipine(DB00381)|Amodiaquine(DB00613)|Amoxapine(DB00543)|Amphetamine(DB00182)|Amprenavir(DB00701)|Amsacrine(DB00276)|Antipyrine(DB01435)|Aprindine(DB01429)|Arformoterol(DB01274)|Aripiprazole(DB01238)|Artemether(DB06697)|Asenapine(DB06216)|Astemizole(DB00637)|Atomoxetine(DB00289)|Atorvastatin(DB01076)|Azelastine(DB00972)|Benzatropine(DB00245)|Benzyl alcohol(DB06770)|Bepridil(DB01244)|Betaxolol(DB00195)|Bicalutamide(DB01128)|Biperiden(DB00810)|Bisoprolol(DB00612)|Bortezomib(DB00188)|Brompheniramine(DB00835)|Bupivacaine(DB00297)|Buprenorphine(DB00921)|Bupropion(DB01156)|Buspirone(DB00490)|Caffeine(DB00201)|Captopril(DB01197)|Carbinoxamine(DB00748)|Carteolol(DB00521)|Carvedilol(DB01136)|Celecoxib(DB00482)|Cephalexin(DB00567)|Cevimeline(DB00185)|Chlordiazepoxide(DB00475)|Chloroquine(DB00608)|Chlorphenamine(DB01114)|Chlorpromazine(DB00477)|Chlorzoxazone(DB00356)|Cholecalciferol(DB00169)|Ciclesonide(DB01410)|Cilostazol(DB01166)|Cimetidine(DB00501)|Cinacalcet(DB01012)|Cinnarizine(DB00568)|Cisapride(DB00604)|Citalopram(DB00215)|Clemastine(DB00283)|Clevidipine(DB04920)|Clomipramine(DB01242)|Clonidine(DB00575)|Clotrimazole(DB00257)|Clozapine(DB00363)|Cocaine(DB00907)|Codeine(DB00318)|Cyclobenzaprine(DB00924)|Cyclophosphamide(DB00531)|Cyclosporine(DB00091)|Dapagliflozin(DB06292)|Darifenacin(DB00496)|Debrisoquin(DB04840)|Delavirdine(DB00705)|Desipramine(DB01151)|Desloratadine(DB00967)|Dexamethasone(DB01234)|Dexfenfluramine(DB01191)|Dexmedetomidine(DB00633)|Dexmethylphenidate(DB06701)|Dextroamphetamine(DB01576)|Dextromethorphan(DB00514)|Dextropropoxyphene(DB00647)|Dihydrocodeine(DB01551)|Diltiazem(DB00343)|Dimethyl sulfoxide(DB01093)|Diphenhydramine(DB01075)|Dolasetron(DB00757)|Domperidone(DB01184)|Donepezil(DB00843)|Dopamine(DB00988)|Doxazosin(DB00590)|Doxepin(DB01142)|Doxorubicin(DB00997)|Dronedarone(DB04855)|Duloxetine(DB00476)|Efavirenz(DB00625)|Eletriptan(DB00216)|Encainide(DB01228)|Enzalutamide(DB08899)|Epinastine(DB00751)|Erlotinib(DB00530)|Escitalopram(DB01175)|Ethylmorphine(DB01466)|Etoricoxib(DB01628)|Felodipine(DB01023)|Fesoterodine(DB06702)|Fexofenadine(DB00950)|Fingolimod(DB08868)|Flecainide(DB01195)|Flunarizine(DB04841)|Fluoxetine(DB00472)|Fluphenazine(DB00623)|Fluvastatin(DB01095)|Fluvoxamine(DB00176)|Formoterol(DB00983)|Galantamine(DB00674)|Gefitinib(DB00317)|Glutethimide(DB01437)|Granisetron(DB00889)|Halofantrine(DB01218)|Haloperidol(DB00502)|Halothane(DB01159)|Histamine Phosphate(DB00667)|Hydrocodone(DB00956)|Hydromorphone(DB00327)|Hydroxychloroquine(DB01611)|Hydroxyurea(DB01005)|Hydroxyzine(DB00557)|Idarubicin(DB01177)|Iloperidone(DB04946)|Imatinib(DB00619)|Imipramine(DB00458)|Indinavir(DB00224)|Ipratropium bromide(DB00332)|Irbesartan(DB01029)|Isoniazid(DB00951)|Itraconazole(DB01167)|Ketoconazole(DB01026)|L-DOPA(DB01235)|Labetalol(DB00598)|Lansoprazole(DB00448)|Lercanidipine(DB00528)|Levomilnacipran(DB08918)|Lidocaine(DB00281)|Lisuride(DB00589)|Lomustine(DB01206)|Loperamide(DB00836)|Lopinavir(DB01601)|Loratadine(DB00455)|Lorcaserin(DB04871)|Lovastatin(DB00227)|Lumefantrine(DB06708)|Maprotiline(DB00934)|Mefloquine(DB00358)|Mepyramine(DB06691)|Mequitazine(DB01071)|Mesoridazine(DB00933)|Methadone(DB00333)|Methamphetamine(DB01577)|Methazolamide(DB00703)|Methimazole(DB00763)|Methotrimeprazine(DB01403)|Methoxyflurane(DB01028)|Methylnaltrexone(DB06800)|Methylphenidate(DB00422)|Methyprylon(DB01107)|Metoclopramide(DB01233)|Metoprolol(DB00264)|Mexiletine(DB00379)|Mianserin(DB06148)|Miconazole(DB01110)|Midodrine(DB00211)|Mifepristone(DB00834)|Minaprine(DB00805)|Mirabegron(DB08893)|Mirtazapine(DB00370)|Moclobemide(DB01171)|Morphine(DB00295)|Nateglinide(DB00731)|Nebivolol(DB04861)|Nefazodone(DB01149)|Nelfinavir(DB00220)|Nevirapine(DB00238)|Niacin(DB00627)|Nicardipine(DB00622)|Nicergoline(DB00699)|Nicotine(DB00184)|Nifedipine(DB01115)|Nilotinib(DB04868)|Nitrofural(DB00336)|Nortriptyline(DB00540)|Olanzapine(DB00334)|Omeprazole(DB00338)|Ondansetron(DB00904)|Oxamniquine(DB01096)|Oxprenolol(DB01580)|Oxybutynin(DB01062)|Oxycodone(DB00497)|Oxymorphone(DB01192)|Paliperidone(DB01267)|Palonosetron(DB00377)|Paroxetine(DB00715)|Pazopanib(DB06589)|Pentamidine(DB00738)|Pergolide(DB01186)|Perhexiline(DB01074)|Perphenazine(DB00850)|Pethidine(DB00454)|Phenformin(DB00914)|Phentermine(DB00191)|Pimozide(DB01100)|Pindolol(DB00960)|Pioglitazone(DB01132)|Piperazine(DB00592)|Pipotiazine(DB01621)|Ponatinib(DB08901)|Pravastatin(DB00175)|Praziquantel(DB01058)|Primaquine(DB01087)|Procainamide(DB01035)|Prochlorperazine(DB00433)|Progesterone(DB00396)|Proguanil(DB01131)|Promethazine(DB01069)|Propafenone(DB01182)|Propofol(DB00818)|Propranolol(DB00571)|Protriptyline(DB00344)|Pseudoephedrine(DB00852)|Pyrimethamine(DB00205)|Quetiapine(DB01224)|Quinidine(DB00908)|Quinine(DB00468)|Rabeprazole(DB01129)|Ranitidine(DB00863)|Ranolazine(DB00243)|Reboxetine(DB00234)|Remoxipride(DB00409)|Rifapentine(DB01201)|Risperidone(DB00734)|Ritonavir(DB00503)|Rivastigmine(DB00989)|Ropinirole(DB00268)|Ropivacaine(DB00296)|Rosiglitazone(DB00412)|Rotigotine(DB05271)|Saquinavir(DB01232)|Selegiline(DB01037)|Sertindole(DB06144)|Sertraline(DB01104)|Sildenafil(DB00203)|Simvastatin(DB00641)|Sorafenib(DB00398)|Sulfanilamide(DB00259)|Sulfaphenazole(DB06729)|Tamoxifen(DB00675)|Tamsulosin(DB00706)|Tapentadol(DB06204)|Telithromycin(DB00976)|Temsirolimus(DB06287)|Terbinafine(DB00857)|Tetrabenazine(DB04844)|Theophylline(DB00277)|Thioridazine(DB00679)|Thiothixene(DB01623)|Ticlopidine(DB00208)|Timolol(DB00373)|Tiotropium(DB01409)|Tipranavir(DB00932)|Tolterodine(DB01036)|Trabectedin(DB05109)|Tramadol(DB00193)|Tranylcypromine(DB00752)|Trazodone(DB00656)|Trimipramine(DB00726)|Tripelennamine(DB00792)|Triprolidine(DB00427)|Trospium(DB00209)|Vemurafenib(DB08881)|Venlafaxine(DB00285)|Verapamil(DB00661)|Vilazodone(DB06684)|Vinblastine(DB00570)|Vinorelbine(DB00361)|Yohimbine(DB01392)|Zafirlukast(DB00549)|Zalcitabine(DB00943)|Ziprasidone(DB00246)|Zolpidem(DB00425)	GCCAGGGGCACCAGTGCTTCT	0.652													C|||	6	0.00119808	0.0	0.0014	5008	,	,		19268	0.0		0.005	False		,,,				2504	0.0				p.V7M		Atlas-SNP	.											.	CYP2D6	104	.	0			c.G19A						PASS	.	C	MET/VAL,MET/VAL	6,4376		0,6,2185	37.0	37.0	37.0		19,19	0.1	0.0	22	dbSNP_130	37	27,8549		0,27,4261	no	missense,missense	CYP2D6	NM_001025161.1,NM_000106.4	21,21	0,33,6446	TT,TC,CC		0.3148,0.1369,0.2547	benign,benign	7/447,7/498	42526775	33,12925	2191	4288	6479	SO:0001583	missense	1565	exon1			GGGGCACCAGTGC	M20403	CCDS33657.1, CCDS46721.1	22q13.1	2014-09-17	2003-01-14		ENSG00000100197	ENSG00000100197		"""Cytochrome P450s"""	2625	protein-coding gene	gene with protein product		124030	"""cytochrome P450, subfamily IID (debrisoquine, sparteine, etc., -metabolizing), polypeptide 6"", ""cytochrome P450, family 2, subfamily D, polypeptide 7 pseudogene 2"", ""cytochrome P450, subfamily II (debrisoquine, sparteine, etc., -metabolising), polypeptide 7 pseudogene 2"", ""cytochrome P450, family 2, subfamily D, polypeptide 8 pseudogene 2"", ""cytochrome P450, subfamily IID (debrisoquine, sparteine, etc., -metabolising), polypeptide 8 pseudogene 2"""	CYP2DL1, CYP2D7P2, CYP2D7BP, CYP2D8P2, CYP2D7AP		8449513	Standard	NM_000106		Approved	CPD6, P450-DB1, CYP2D, P450C2D	uc003bce.3	P10635	OTTHUMG00000150918	ENST00000360608.5:c.19G>A	22.37:g.42526775C>T	ENSP00000353820:p.Val7Met	308.0	1.0	0.00324675		289.0	154.0	0.532872	NM_000106	Q16752|Q2XND6|Q2XND7|Q2XNE0|Q6B012|Q6NXU8	Missense_Mutation	SNP	ENST00000360608.5	37	CCDS46721.1	.	.	.	.	.	.	.	.	.	.	C	1.817	-0.473201	0.04445	0.001369	0.003148	ENSG00000100197	ENST00000360608;ENST00000389970;ENST00000359033	T;T;T	0.37058	1.22;1.22;1.22	3.46	0.0648	0.14354	.	3.717790	0.00802	N	0.001421	T	0.18964	0.0455	N	0.08118	0	0.09310	N	1	B;B	0.13145	0.007;0.007	B;B	0.08055	0.003;0.002	T	0.12578	-1.0542	10	0.34782	T	0.22	.	2.8284	0.05491	0.2852:0.448:0.0:0.2668	.	7;7	Q6NXU8;Q6NWU0	.;.	M	7	ENSP00000353820:V7M;ENSP00000374620:V7M;ENSP00000351927:V7M	ENSP00000351927:V7M	V	-	1	0	CYP2D6	40856719	0.001000	0.12720	0.013000	0.15412	0.004000	0.04260	-0.451000	0.06795	0.050000	0.15949	-0.350000	0.07774	GTG	C|0.996;T|0.004	0.004	strong		0.652	CYP2D6-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000320525.1		
CSMD1	64478	hgsc.bcm.edu	37	8	3267108	3267108	+	Silent	SNP	A	A	G	rs190257069	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr8:3267108A>G	ENST00000520002.1	-	14	2139	c.1584T>C	c.(1582-1584)tgT>tgC	p.C528C	CSMD1_ENST00000602557.1_Silent_p.C528C|CSMD1_ENST00000537824.1_Silent_p.C527C|CSMD1_ENST00000539096.1_Silent_p.C527C|CSMD1_ENST00000602723.1_Silent_p.C528C|CSMD1_ENST00000400186.3_Silent_p.C528C|CSMD1_ENST00000542608.1_Silent_p.C527C			Q96PZ7	CSMD1_HUMAN	CUB and Sushi multiple domains 1	528	Sushi 3. {ECO:0000255|PROSITE- ProRule:PRU00302}.					integral component of membrane (GO:0016021)				breast(20)|large_intestine(5)	25		all_cancers(1;5.7e-41)|all_epithelial(1;2.54e-36)|Lung NSC(1;7.54e-11)|all_lung(1;3.2e-10)|Hepatocellular(1;3.78e-05)|Breast(1;0.000196)|Myeloproliferative disorder(4;0.000374)|Esophageal squamous(1;0.0157)|Ovarian(12;0.091)|Renal(68;0.144)|Colorectal(14;0.234)		all cancers(1;5.03e-41)|Epithelial(1;4.78e-31)|Lung(1;1.14e-14)|LUSC - Lung squamous cell carcinoma(1;2.34e-14)|GBM - Glioblastoma multiforme(1;4.49e-10)|Colorectal(4;1.18e-07)|OV - Ovarian serous cystadenocarcinoma(1;3.2e-07)|BRCA - Breast invasive adenocarcinoma(1;6.17e-07)|COAD - Colon adenocarcinoma(4;0.000539)|READ - Rectum adenocarcinoma(4;0.00896)|Kidney(5;0.00957)|KIRC - Kidney renal clear cell carcinoma(5;0.0689)		CAGGATCCCCACACCCTCCCT	0.453													A|||	3	0.000599042	0.0008	0.0014	5008	,	,		16262	0.0		0.001	False		,,,				2504	0.0				p.C527C		Atlas-SNP	.											.	CSMD1	1469	.	0			c.T1581C						PASS	.	A		1,3679		0,1,1839	23.0	24.0	24.0		1581	-0.3	0.9	8		24	17,8143		0,17,4063	no	coding-synonymous	CSMD1	NM_033225.5		0,18,5902	GG,GA,AA		0.2083,0.0272,0.152		527/3565	3267108	18,11822	1840	4080	5920	SO:0001819	synonymous_variant	64478	exon13			ATCCCCACACCCT			8p23.2	2012-04-17			ENSG00000183117	ENSG00000183117		"""Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"""	14026	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 24"""	608397					Standard	NM_033225		Approved	KIAA1890, PPP1R24	uc022aqr.1	Q96PZ7	OTTHUMG00000163605	ENST00000520002.1:c.1584T>C	8.37:g.3267108A>G		90.0	0.0	0		102.0	38.0	0.372549	NM_033225	Q0H0J5|Q96QU9|Q96RM4	Silent	SNP	ENST00000520002.1	37		3	0.0013736263736263737	1	0.0020325203252032522	1	0.0027624309392265192	0	0.0	1	0.0013192612137203166	A	10.20	1.285284	0.23478	2.72E-4	0.002083	ENSG00000183117	ENST00000335551	.	.	.	5.26	-0.303	0.12792	.	.	.	.	.	T	0.56804	0.2010	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.49725	-0.8909	4	.	.	.	.	9.8509	0.41057	0.7465:0.0:0.2535:0.0	.	.	.	.	R	8	.	.	W	-	1	0	CSMD1	3254516	0.997000	0.39634	0.924000	0.36721	0.977000	0.68977	0.529000	0.23019	-0.300000	0.08895	0.467000	0.42956	TGG	A|0.999;G|0.001	0.001	strong		0.453	CSMD1-001	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000374500.2	NM_033225	
KIAA0895	23366	hgsc.bcm.edu	37	7	36366404	36366404	+	Missense_Mutation	SNP	C	C	T	rs191576648		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr7:36366404C>T	ENST00000297063.6	-	7	1578	c.1528G>A	c.(1528-1530)Gaa>Aaa	p.E510K	KIAA0895_ENST00000453212.1_Missense_Mutation_p.E265K|KIAA0895_ENST00000338533.5_Missense_Mutation_p.E497K|KIAA0895_ENST00000440378.1_Missense_Mutation_p.E507K|KIAA0895_ENST00000317020.6_Missense_Mutation_p.E459K|KIAA0895_ENST00000436884.1_Missense_Mutation_p.E407K	NM_001100425.1	NP_001093895.1	Q8NCT3	K0895_HUMAN	KIAA0895	510										breast(2)|endometrium(1)|kidney(1)|large_intestine(6)|liver(1)|lung(11)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	26						TCAGTCAGTTCATTCACTTCC	0.418													C|||	1	0.000199681	0.0	0.0014	5008	,	,		16857	0.0		0.0	False		,,,				2504	0.0				p.E510K		Atlas-SNP	.											.	KIAA0895	89	.	0			c.G1528A						PASS	.	C	LYS/GLU,LYS/GLU,LYS/GLU,LYS/GLU,LYS/GLU	0,3788		0,0,1894	180.0	169.0	172.0		1528,1519,1489,1219,1375	5.6	1.0	7		172	1,8201		0,1,4100	no	missense,missense,missense,missense,missense	KIAA0895	NM_001100425.1,NM_001199706.1,NM_001199707.1,NM_001199708.1,NM_015314.2	56,56,56,56,56	0,1,5994	TT,TC,CC		0.0122,0.0,0.0083	probably-damaging,probably-damaging,probably-damaging,probably-damaging,probably-damaging	510/521,507/518,497/508,407/418,459/470	36366404	1,11989	1894	4101	5995	SO:0001583	missense	23366	exon7			TCAGTTCATTCAC	BC028678	CCDS43570.1, CCDS47573.1, CCDS56482.1, CCDS56483.1, CCDS56484.1, CCDS75583.1	7p14.2	2008-11-27			ENSG00000164542	ENSG00000164542			22206	protein-coding gene	gene with protein product							Standard	NM_015314		Approved		uc003tfd.2	Q8NCT3	OTTHUMG00000154939	ENST00000297063.6:c.1528G>A	7.37:g.36366404C>T	ENSP00000297063:p.Glu510Lys	171.0	0.0	0		246.0	100.0	0.406504	NM_001100425	B4DF35|B7ZLT4|B9EGB9|O94969|Q0VGC1|Q7Z4L2	Missense_Mutation	SNP	ENST00000297063.6	37	CCDS43570.1	1	4.578754578754579E-4	0	0.0	1	0.0027624309392265192	0	0.0	0	0.0	C	15.36	2.811535	0.50527	0.0	1.22E-4	ENSG00000164542	ENST00000297063;ENST00000338533;ENST00000317020;ENST00000440378;ENST00000436884;ENST00000453212	.	.	.	5.6	5.6	0.85130	.	0.205140	0.51477	D	0.000096	T	0.45856	0.1363	L	0.33485	1.01	0.80722	D	1	B;B;B;B;B	0.31548	0.018;0.019;0.009;0.328;0.001	B;B;B;B;B	0.30495	0.023;0.023;0.015;0.116;0.004	T	0.43310	-0.9399	9	0.02654	T	1	-22.975	19.9925	0.97371	0.0:1.0:0.0:0.0	.	507;407;510;497;459	B7ZLT4;B4DF35;Q8NCT3;Q8NCT3-2;Q8NCT3-3	.;.;K0895_HUMAN;.;.	K	510;497;459;507;407;265	.	ENSP00000297063:E510K	E	-	1	0	KIAA0895	36332929	0.998000	0.40836	0.990000	0.47175	0.994000	0.84299	1.435000	0.34969	2.818000	0.97014	0.655000	0.94253	GAA	C|1.000;T|0.000	0.000	strong		0.418	KIAA0895-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000337717.1	NM_015314	
OSGIN1	29948	hgsc.bcm.edu	37	16	83999548	83999548	+	Missense_Mutation	SNP	T	T	C	rs62640905	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr16:83999548T>C	ENST00000343939.2	+	7	2002	c.1619T>C	c.(1618-1620)gTg>gCg	p.V540A	NECAB2_ENST00000305202.4_5'Flank|OSGIN1_ENST00000393306.1_Missense_Mutation_p.V457A|OSGIN1_ENST00000361711.3_Missense_Mutation_p.V457A			Q9UJX0	OSGI1_HUMAN	oxidative stress induced growth inhibitor 1	540					cell differentiation (GO:0030154)|multicellular organismal development (GO:0007275)|negative regulation of cell growth (GO:0030308)|positive regulation of apoptotic process (GO:0043065)		growth factor activity (GO:0008083)			autonomic_ganglia(1)|large_intestine(1)|lung(7)|prostate(2)|upper_aerodigestive_tract(1)	12						GTGAGGTTTGTGCAGGGGGGC	0.662													T|||	40	0.00798722	0.0	0.013	5008	,	,		17559	0.0		0.0278	False		,,,				2504	0.0031				p.V457A		Atlas-SNP	.											.	OSGIN1	33	.	0			c.T1370C						PASS	.	T	ALA/VAL,ALA/VAL,ALA/VAL	14,4370		0,14,2178	14.0	15.0	15.0		1619,1370,1370	4.4	1.0	16	dbSNP_129	15	218,8354		5,208,4073	yes	missense,missense,missense	OSGIN1	NM_013370.3,NM_182980.2,NM_182981.2	64,64,64	5,222,6251	CC,CT,TT		2.5432,0.3193,1.7907	possibly-damaging,possibly-damaging,possibly-damaging	540/561,457/478,457/478	83999548	232,12724	2192	4286	6478	SO:0001583	missense	29948	exon6			GGTTTGTGCAGGG	AY258066	CCDS10939.1	16q23.3	2010-11-23			ENSG00000140961	ENSG00000140961			30093	protein-coding gene	gene with protein product	"""bone marrow stromal cell-derived growth inhibitor"", ""pregnancy induced growth inhibitor"""	607975				11459809, 14570898	Standard	NM_182981		Approved	BDGI, OKL38	uc002fhc.3	Q9UJX0	OTTHUMG00000137640	ENST00000343939.2:c.1619T>C	16.37:g.83999548T>C	ENSP00000343376:p.Val540Ala	76.0	0.0	0		53.0	43.0	0.811321	NM_182981	Q52M33|Q86UQ1|Q96S88|Q9BZ70	Missense_Mutation	SNP	ENST00000343939.2	37		27	0.012362637362637362	0	0.0	6	0.016574585635359115	0	0.0	21	0.027704485488126648	T	16.86	3.238732	0.58995	0.003193	0.025432	ENSG00000140961	ENST00000343939;ENST00000361711;ENST00000393306	T;T;T	0.37411	1.2;1.2;1.2	4.37	4.37	0.52481	.	0.065516	0.64402	D	0.000009	T	0.15739	0.0379	M	0.63428	1.95	0.80722	D	1	D	0.58268	0.982	B	0.44315	0.446	T	0.04811	-1.0925	10	0.24483	T	0.36	-26.2537	12.7349	0.57218	0.0:0.0:0.0:1.0	rs62640905	540	Q9UJX0	OSGI1_HUMAN	A	540;457;457	ENSP00000343376:V540A;ENSP00000355374:V457A;ENSP00000376983:V457A	ENSP00000343376:V540A	V	+	2	0	OSGIN1	82557049	1.000000	0.71417	0.954000	0.39281	0.681000	0.39784	7.645000	0.83430	1.606000	0.50161	0.260000	0.18958	GTG	T|0.985;C|0.015	0.015	strong		0.662	OSGIN1-001	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000269081.1	NM_013370	
GAB3	139716	hgsc.bcm.edu	37	X	153925443	153925443	+	Missense_Mutation	SNP	T	T	C			TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chrX:153925443T>C	ENST00000369575.3	-	7	1419	c.1388A>G	c.(1387-1389)gAa>gGa	p.E463G	GAB3_ENST00000496390.1_5'UTR|GAB3_ENST00000424127.2_Missense_Mutation_p.E464G	NM_001081573.1|NM_080612.2	NP_001075042.1|NP_542179.1	Q8WWW8	GAB3_HUMAN	GRB2-associated binding protein 3	463					macrophage differentiation (GO:0030225)					NS(1)|breast(3)|central_nervous_system(1)|cervix(1)|endometrium(2)|large_intestine(7)|lung(6)|ovary(2)|prostate(1)|skin(1)	25	all_cancers(53;8.15e-17)|all_epithelial(53;1.1e-10)|all_lung(58;6.63e-07)|Lung NSC(58;2.08e-06)|all_hematologic(71;2.45e-06)|Acute lymphoblastic leukemia(192;6.56e-05)|Breast(217;0.176)|Renal(33;0.214)					AGATGCATGTTCCCGGATGAT	0.537																																					p.E464G		Atlas-SNP	.											.	GAB3	73	.	0			c.A1391G						PASS	.						146.0	123.0	131.0					X																	153925443		2203	4300	6503	SO:0001583	missense	139716	exon7			GCATGTTCCCGGA	AY057989	CCDS14760.1, CCDS48198.1, CCDS65357.1	Xq28	2013-01-10			ENSG00000160219	ENSG00000160219		"""Pleckstrin homology (PH) domain containing"""	17515	protein-coding gene	gene with protein product	"""DOS/Gab family member 3"", ""Gab3 scaffolding protein"""	300482				11739737	Standard	XM_005274648		Approved		uc004fmk.1	Q8WWW8	OTTHUMG00000024245	ENST00000369575.3:c.1388A>G	X.37:g.153925443T>C	ENSP00000358588:p.Glu463Gly	158.0	0.0	0		74.0	4.0	0.0540541	NM_001081573	A6NHF8|E9PB44	Missense_Mutation	SNP	ENST00000369575.3	37	CCDS14760.1	.	.	.	.	.	.	.	.	.	.	T	14.91	2.675913	0.47886	.	.	ENSG00000160219	ENST00000369575;ENST00000369568;ENST00000424127	T;T;T	0.30448	1.53;1.53;1.53	5.1	5.1	0.69264	.	0.000000	0.85682	D	0.000000	T	0.60418	0.2267	M	0.88031	2.925	0.39665	D	0.970665	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.85130	0.996;0.997;0.996	T	0.69884	-0.5024	10	0.87932	D	0	-15.0336	12.0037	0.53246	0.0:0.0:0.0:1.0	.	464;464;463	A6NHF8;E9PB44;Q8WWW8	.;.;GAB3_HUMAN	G	463;464;464	ENSP00000358588:E463G;ENSP00000358581:E464G;ENSP00000399588:E464G	ENSP00000358581:E464G	E	-	2	0	GAB3	153578637	1.000000	0.71417	0.875000	0.34327	0.065000	0.16274	5.325000	0.65869	1.808000	0.52836	0.486000	0.48141	GAA	.	.	none		0.537	GAB3-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000061192.2	NM_001081573	
NDST3	9348	hgsc.bcm.edu	37	4	118975189	118975189	+	Nonsense_Mutation	SNP	G	G	T			TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr4:118975189G>T	ENST00000296499.5	+	2	527	c.124G>T	c.(124-126)Gaa>Taa	p.E42*	NDST3_ENST00000433996.2_Nonsense_Mutation_p.E42*	NM_004784.2	NP_004775.1	O95803	NDST3_HUMAN	N-deacetylase/N-sulfotransferase (heparan glucosaminyl) 3	42	Heparan sulfate N-deacetylase 3.				heparan sulfate proteoglycan biosynthetic process (GO:0015012)|heparin biosynthetic process (GO:0030210)	Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)	[heparan sulfate]-glucosamine N-sulfotransferase activity (GO:0015016)|deacetylase activity (GO:0019213)			NS(1)|breast(3)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(11)|lung(23)|prostate(1)|skin(3)|upper_aerodigestive_tract(3)|urinary_tract(1)	54						ACAGGAAAATGAACTCTCTGA	0.423																																					p.E42X		Atlas-SNP	.											.	NDST3	107	.	0			c.G124T						PASS	.						122.0	119.0	120.0					4																	118975189		2203	4300	6503	SO:0001587	stop_gained	9348	exon2			GAAAATGAACTCT	AF074924	CCDS3708.1	4q26	2008-08-04			ENSG00000164100	ENSG00000164100		"""Sulfotransferases, membrane-bound"""	7682	protein-coding gene	gene with protein product		603950				9915799	Standard	NM_004784		Approved	HSST3	uc003ibx.3	O95803	OTTHUMG00000132959	ENST00000296499.5:c.124G>T	4.37:g.118975189G>T	ENSP00000296499:p.Glu42*	224.0	1.0	0.00446429		123.0	60.0	0.487805	NM_004784	B4DI67|Q4W5C1|Q4W5D0|Q6UWC5|Q9UP21	Nonsense_Mutation	SNP	ENST00000296499.5	37	CCDS3708.1	.	.	.	.	.	.	.	.	.	.	G	36	5.624220	0.96660	.	.	ENSG00000164100	ENST00000296499;ENST00000433996	.	.	.	5.82	4.98	0.66077	.	0.262983	0.39083	N	0.001477	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.09084	T	0.74	.	11.9424	0.52909	0.0:0.1318:0.7311:0.1371	.	.	.	.	X	42	.	ENSP00000296499:E42X	E	+	1	0	NDST3	119194637	1.000000	0.71417	0.305000	0.25099	0.920000	0.55202	7.237000	0.78164	1.441000	0.47550	0.650000	0.86243	GAA	.	.	none		0.423	NDST3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256517.4	NM_004784	
MYO9B	4650	hgsc.bcm.edu	37	19	17306074	17306074	+	Missense_Mutation	SNP	G	G	A	rs112900956	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr19:17306074G>A	ENST00000594824.1	+	22	3985	c.3838G>A	c.(3838-3840)Ggc>Agc	p.G1280S	MYO9B_ENST00000397274.2_Missense_Mutation_p.G1280S|MYO9B_ENST00000595618.1_Missense_Mutation_p.G1280S			Q13459	MYO9B_HUMAN	myosin IXB	1280	Tail.				actin filament-based movement (GO:0030048)|establishment of cell polarity (GO:0030010)|lamellipodium morphogenesis (GO:0072673)|macrophage chemotaxis (GO:0048246)|monocyte chemotaxis (GO:0002548)|regulation of small GTPase mediated signal transduction (GO:0051056)|Rho protein signal transduction (GO:0007266)|small GTPase mediated signal transduction (GO:0007264)	actin cytoskeleton (GO:0015629)|cell cortex (GO:0005938)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|filamentous actin (GO:0031941)|filopodium tip (GO:0032433)|lamellipodium (GO:0030027)|membrane (GO:0016020)|myosin complex (GO:0016459)|perinuclear region of cytoplasm (GO:0048471)|ruffle (GO:0001726)	actin binding (GO:0003779)|actin-dependent ATPase activity (GO:0030898)|ADP binding (GO:0043531)|ATP binding (GO:0005524)|ATPase activity (GO:0016887)|calmodulin binding (GO:0005516)|microfilament motor activity (GO:0000146)|Rho GTPase activator activity (GO:0005100)|zinc ion binding (GO:0008270)			breast(3)|endometrium(9)|kidney(2)|large_intestine(1)|lung(19)|soft_tissue(1)|urinary_tract(4)	39						CAAACCATGTGGCAGCCCAAG	0.701													G|||	19	0.00379393	0.0008	0.0029	5008	,	,		13079	0.0		0.0129	False		,,,				2504	0.0031				p.G1280S		Atlas-SNP	.											MYO9B_ENST00000319396,adrenal_gland,adrenal_cortical_adenoma,0,2	MYO9B	264	2	0			c.G3838A						PASS	.	G	SER/GLY,SER/GLY	11,3783		0,11,1886	20.0	27.0	25.0		3838,3838	-3.2	0.0	19	dbSNP_132	25	119,8027		0,119,3954	yes	missense,missense	MYO9B	NM_001130065.1,NM_004145.3	56,56	0,130,5840	AA,AG,GG		1.4608,0.2899,1.0888	benign,benign	1280/2023,1280/2158	17306074	130,11810	1897	4073	5970	SO:0001583	missense	4650	exon22			CCATGTGGCAGCC		CCDS46010.1	19p13.1	2011-09-27				ENSG00000099331		"""Myosins / Myosin superfamily : Class IX"""	7609	protein-coding gene	gene with protein product		602129		CELIAC4		9226381	Standard	NM_004145		Approved		uc010eak.3	Q13459		ENST00000594824.1:c.3838G>A	19.37:g.17306074G>A	ENSP00000471367:p.Gly1280Ser	89.0	0.0	0		65.0	40.0	0.615385	NM_001130065	O75314|Q9NUJ2|Q9UHN0	Missense_Mutation	SNP	ENST00000594824.1	37		12	0.005494505494505495	0	0.0	2	0.0055248618784530384	0	0.0	10	0.013192612137203167	G	5.753	0.323409	0.10900	0.002899	0.014608	ENSG00000099331	ENST00000397274	D	0.83673	-1.75	5.28	-3.16	0.05217	.	1.740110	0.03022	N	0.150866	T	0.65123	0.2661	L	0.34521	1.04	0.09310	N	1	B;B;B	0.06786	0.0;0.0;0.001	B;B;B	0.06405	0.0;0.0;0.002	T	0.56932	-0.7897	10	0.07030	T	0.85	.	10.5091	0.44851	0.645:0.0:0.355:0.0	.	1280;1280;1286	Q13459;B0I1T6;Q4LE74	MYO9B_HUMAN;.;.	S	1280	ENSP00000380444:G1280S	ENSP00000380444:G1280S	G	+	1	0	MYO9B	17167074	0.000000	0.05858	0.000000	0.03702	0.003000	0.03518	-0.479000	0.06567	-0.339000	0.08401	-0.367000	0.07326	GGC	G|0.994;A|0.006	0.006	strong		0.701	MYO9B-002	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000463236.1		
POU4F2	5458	hgsc.bcm.edu	37	4	147561804	147561804	+	Silent	SNP	C	C	T			TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr4:147561804C>T	ENST00000281321.3	+	2	1322	c.1074C>T	c.(1072-1074)cgC>cgT	p.R358R	AC093887.1_ENST00000584185.1_RNA	NM_004575.2	NP_004566.2	Q12837	PO4F2_HUMAN	POU class 4 homeobox 2	358					axon extension (GO:0048675)|axon guidance (GO:0007411)|intracellular estrogen receptor signaling pathway (GO:0030520)|MAPK cascade (GO:0000165)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|neuromuscular process controlling balance (GO:0050885)|neuron differentiation (GO:0030182)|positive regulation of cell differentiation (GO:0045597)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|retina development in camera-type eye (GO:0060041)|retinal ganglion cell axon guidance (GO:0031290)|sensory perception of sound (GO:0007605)	nucleus (GO:0005634)	chromatin binding (GO:0003682)|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)			NS(1)|breast(1)|endometrium(7)|kidney(3)|large_intestine(11)|lung(8)|skin(1)|upper_aerodigestive_tract(1)	33	all_hematologic(180;0.151)					CAGAGAAGCGCTCGCTCGAAG	0.602																																					p.R358R		Atlas-SNP	.											POU4F2,caecum,carcinoma,+1,1	POU4F2	83	1	0			c.C1074T						scavenged	.						74.0	77.0	76.0					4																	147561804		2203	4300	6503	SO:0001819	synonymous_variant	5458	exon2			GAAGCGCTCGCTC	U06233	CCDS34074.1	4q31.22	2011-06-20	2007-07-13					"""Homeoboxes / POU class"""	9219	protein-coding gene	gene with protein product		113725	"""POU domain, class 4, transcription factor 2"", ""POU domain class 4, transcription factor 2"""	BRN3B		8332509	Standard	NM_004575		Approved	Brn-3b	uc003ikv.3	Q12837		ENST00000281321.3:c.1074C>T	4.37:g.147561804C>T		74.0	0.0	0		55.0	3.0	0.0545455	NM_004575	B1PJR6|B2RC84|Q13883|Q14987	Silent	SNP	ENST00000281321.3	37	CCDS34074.1																																																																																			.	.	none		0.602	POU4F2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000367020.1	NM_004575	
ZNF493	284443	hgsc.bcm.edu	37	19	21607252	21607252	+	Missense_Mutation	SNP	T	T	A	rs142288436	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr19:21607252T>A	ENST00000355504.4	+	2	1673	c.1407T>A	c.(1405-1407)gaT>gaA	p.D469E	ZNF493_ENST00000392288.2_Missense_Mutation_p.D597E|CTD-2561J22.3_ENST00000600810.1_Intron	NM_175910.6	NP_787106.4	Q6ZR52	ZN493_HUMAN	zinc finger protein 493	469					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)			central_nervous_system(2)|cervix(1)|endometrium(1)|kidney(1)|large_intestine(6)|lung(10)|ovary(1)|prostate(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	30						TTCATACTGATAAGAAACCCT	0.333													.|||	3	0.000599042	0.0	0.0	5008	,	,		19829	0.0		0.003	False		,,,				2504	0.0				p.D597E		Atlas-SNP	.											.	ZNF493	178	.	0			c.T1791A						PASS	.						33.0	33.0	33.0					19																	21607252		2200	4298	6498	SO:0001583	missense	284443	exon4			TACTGATAAGAAA	AK093823, BC006408, BC022394	CCDS12412.1, CCDS42536.1, CCDS12411.1	19p12	2013-01-08			ENSG00000196268	ENSG00000196268		"""Zinc fingers, C2H2-type"", ""-"""	23708	protein-coding gene	gene with protein product							Standard	NM_001076678		Approved	FLJ36504	uc002npw.3	Q6ZR52	OTTHUMG00000141297	ENST00000355504.4:c.1407T>A	19.37:g.21607252T>A	ENSP00000347691:p.Asp469Glu	77.0	0.0	0		66.0	11.0	0.166667	NM_001076678	G5E974|Q59GM3|Q6ZSF6|Q8N1Z6|Q8N965|Q9BR99	Missense_Mutation	SNP	ENST00000355504.4	37	CCDS12412.1	.	.	.	.	.	.	.	.	.	.	N	1.434	-0.569466	0.03910	.	.	ENSG00000196268	ENST00000392288;ENST00000355504	T;T	0.16897	2.31;2.31	1.06	-2.12	0.07165	Zinc finger, C2H2 (1);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.05731	0.0150	N	0.02674	-0.535	0.09310	N	1	B;B	0.09022	0.001;0.002	B;B	0.08055	0.003;0.002	T	0.31336	-0.9947	9	0.66056	D	0.02	.	3.2801	0.06912	0.5296:0.0:0.2843:0.1862	.	469;597	Q6ZR52;Q6ZR52-2	ZN493_HUMAN;.	E	597;469	ENSP00000376110:D597E;ENSP00000347691:D469E	ENSP00000347691:D469E	D	+	3	2	ZNF493	21399092	0.001000	0.12720	0.000000	0.03702	0.000000	0.00434	-1.688000	0.01925	-3.330000	0.00186	-3.393000	0.00039	GAT	.	.	weak		0.333	ZNF493-003	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000280563.1	NM_175910	
USP40	55230	hgsc.bcm.edu	37	2	234429744	234429744	+	Missense_Mutation	SNP	C	C	T			TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr2:234429744C>T	ENST00000427112.2	-	16	2250	c.2215G>A	c.(2215-2217)Gag>Aag	p.E739K	USP40_ENST00000251722.6_Missense_Mutation_p.E739K|USP40_ENST00000450966.1_Missense_Mutation_p.E751K			Q9NVE5	UBP40_HUMAN	ubiquitin specific peptidase 40	739					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)		ACCCATTTCTCTTCCTTGGTC	0.368																																					p.E751K		Atlas-SNP	.											USP40_ENST00000450966,caecum,carcinoma,+2,2	USP40	174	2	0			c.G2251A						scavenged	.						84.0	77.0	79.0					2																	234429744		1842	4083	5925	SO:0001583	missense	55230	exon16			ATTTCTCTTCCTT	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.2215G>A	2.37:g.234429744C>T	ENSP00000387898:p.Glu739Lys	60.0	0.0	0		67.0	6.0	0.0895522	NM_018218	Q6NX38|Q70EL0	Missense_Mutation	SNP	ENST00000427112.2	37	CCDS46547.1	.	.	.	.	.	.	.	.	.	.	C	8.295	0.818600	0.16607	.	.	ENSG00000085982	ENST00000450966;ENST00000251722;ENST00000427112;ENST00000452724	T;T;T;T	0.50548	0.74;0.74;0.74;0.74	4.75	2.88	0.33553	.	2.303910	0.01545	N	0.019397	T	0.37376	0.1001	L	0.29908	0.895	0.09310	N	1	B;B	0.28055	0.126;0.199	B;B	0.26770	0.033;0.073	T	0.22836	-1.0205	10	0.12430	T	0.62	.	9.1947	0.37220	0.0:0.8191:0.0:0.1809	.	739;751	Q9NVE5;Q9NVE5-3	UBP40_HUMAN;.	K	751;739;739;34	ENSP00000415434:E751K;ENSP00000251722:E739K;ENSP00000387898:E739K;ENSP00000408853:E34K	ENSP00000251722:E739K	E	-	1	0	USP40	234094483	0.026000	0.19158	0.801000	0.32222	0.504000	0.33889	1.443000	0.35057	1.208000	0.43306	0.585000	0.79938	GAG	.	.	none		0.368	USP40-017	KNOWN	alternative_5_UTR|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000397235.1	XM_114294	
CCR2	729230	hgsc.bcm.edu	37	3	46399226	46399226	+	Missense_Mutation	SNP	T	T	G			TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr3:46399226T>G	ENST00000400888.2	+	1	247	c.208T>G	c.(208-210)Tgc>Ggc	p.C70G	CCR2_ENST00000445132.2_Missense_Mutation_p.C70G|CCR2_ENST00000465202.1_Intron|CCR2_ENST00000292301.4_Missense_Mutation_p.C70G			P41597	CCR2_HUMAN	chemokine (C-C motif) receptor 2	70					blood vessel remodeling (GO:0001974)|cellular calcium ion homeostasis (GO:0006874)|cellular defense response (GO:0006968)|cellular homeostasis (GO:0019725)|chemokine-mediated signaling pathway (GO:0070098)|chemotaxis (GO:0006935)|cytokine-mediated signaling pathway (GO:0019221)|dendritic cell chemotaxis (GO:0002407)|immune response (GO:0006955)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|JAK-STAT cascade (GO:0007259)|negative regulation of adenylate cyclase activity (GO:0007194)|negative regulation of angiogenesis (GO:0016525)|negative regulation of eosinophil degranulation (GO:0043310)|negative regulation of type 2 immune response (GO:0002829)|positive regulation of alpha-beta T cell proliferation (GO:0046641)|positive regulation of astrocyte chemotaxis (GO:2000464)|positive regulation of CD8-positive, alpha-beta T cell extravasation (GO:2000451)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|positive regulation of hematopoietic stem cell migration (GO:2000473)|positive regulation of immune complex clearance by monocytes and macrophages (GO:0090265)|positive regulation of inflammatory response (GO:0050729)|positive regulation of interferon-gamma production (GO:0032729)|positive regulation of interleukin-2 production (GO:0032743)|positive regulation of monocyte chemotaxis (GO:0090026)|positive regulation of monocyte extravasation (GO:2000439)|positive regulation of T cell activation (GO:0050870)|positive regulation of T cell chemotaxis (GO:0010820)|positive regulation of T-helper 1 type immune response (GO:0002827)|positive regulation of tumor necrosis factor biosynthetic process (GO:0042535)|regulation of vascular endothelial growth factor production (GO:0010574)|response to wounding (GO:0009611)|T-helper 17 cell chemotaxis (GO:0035705)|viral process (GO:0016032)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|dendrite (GO:0030425)|integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|neuronal cell body (GO:0043025)|perikaryon (GO:0043204)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)	C-C chemokine receptor activity (GO:0016493)|CCR2 chemokine receptor binding (GO:0031727)|chemokine receptor activity (GO:0004950)|protein homodimerization activity (GO:0042803)			breast(3)|endometrium(1)|large_intestine(1)|liver(2)|lung(7)	14				BRCA - Breast invasive adenocarcinoma(193;0.00114)|KIRC - Kidney renal clear cell carcinoma(197;0.0174)|Kidney(197;0.0206)		CTTAATAAACTGCAAAAAGCT	0.488																																					p.C70G		Atlas-SNP	.											.	CCR2	103	.	0			c.T208G						PASS	.						199.0	182.0	188.0					3																	46399226		1568	3582	5150	SO:0001583	missense	729230	exon2			ATAAACTGCAAAA		CCDS43078.1, CCDS46813.1	3p21	2012-08-08			ENSG00000121807	ENSG00000121807		"""GPCR / Class A : Chemokine receptors : C-C motif"", ""CD molecules"""	1603	protein-coding gene	gene with protein product		601267		CMKBR2		8146186	Standard	NM_001123041		Approved	CC-CKR-2, CKR2, MCP-1-R, CD192, FLJ78302	uc003cpn.4	P41597	OTTHUMG00000156466	ENST00000400888.2:c.208T>G	3.37:g.46399226T>G	ENSP00000383681:p.Cys70Gly	380.0	1.0	0.00263158		353.0	141.0	0.399433	NM_001123041	A0AVQ3|B2RMT0|Q4VBL2	Missense_Mutation	SNP	ENST00000400888.2	37	CCDS43078.1	.	.	.	.	.	.	.	.	.	.	T	15.03	2.712653	0.48517	.	.	ENSG00000121807	ENST00000445132;ENST00000292301;ENST00000421659;ENST00000400888	T;T;T;T	0.71461	-0.57;-0.57;-0.57;-0.57	4.41	4.41	0.53225	GPCR, rhodopsin-like superfamily (1);	0.097576	0.46145	D	0.000305	T	0.81403	0.4815	M	0.73430	2.235	0.31410	N	0.675649	D;P	0.76494	0.999;0.851	D;P	0.71184	0.972;0.794	T	0.80899	-0.1176	10	0.25106	T	0.35	.	13.9659	0.64209	0.0:0.0:0.0:1.0	.	70;70	P41597;Q4VBL2	CCR2_HUMAN;.	G	70	ENSP00000399285:C70G;ENSP00000292301:C70G;ENSP00000396736:C70G;ENSP00000383681:C70G	ENSP00000292301:C70G	C	+	1	0	CCR2	46374230	1.000000	0.71417	0.988000	0.46212	0.949000	0.60115	1.614000	0.36911	1.774000	0.52232	0.528000	0.53228	TGC	.	.	none		0.488	CCR2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000344292.1	NM_000647	
AHCTF1	25909	hgsc.bcm.edu	37	1	247051714	247051714	+	Silent	SNP	A	A	G	rs144599339	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr1:247051714A>G	ENST00000391829.2	-	18	2373	c.2250T>C	c.(2248-2250)taT>taC	p.Y750Y	AHCTF1_ENST00000470300.1_5'UTR|AHCTF1_ENST00000326225.3_Silent_p.Y759Y|AHCTF1_ENST00000366508.1_Silent_p.Y785Y			Q8WYP5	ELYS_HUMAN	AT hook containing transcription factor 1	750	Necessary for cytoplasmic localization. {ECO:0000250}.				cytokinesis (GO:0000910)|mitotic cell cycle (GO:0000278)|mRNA transport (GO:0051028)|nuclear pore complex assembly (GO:0051292)|protein transport (GO:0015031)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|kinetochore (GO:0000776)|nuclear matrix (GO:0016363)|nuclear membrane (GO:0031965)|nuclear pore (GO:0005643)|nucleus (GO:0005634)	DNA binding (GO:0003677)|sequence-specific DNA binding transcription factor activity (GO:0003700)			NS(1)|breast(6)|cervix(3)|endometrium(8)|kidney(6)|large_intestine(12)|liver(2)|lung(21)|ovary(5)|prostate(1)|skin(6)|upper_aerodigestive_tract(1)|urinary_tract(2)	74	all_cancers(71;3.05e-05)|all_epithelial(71;6.72e-06)|Ovarian(71;0.0173)|Breast(184;0.0318)|all_lung(81;0.0458)|Lung NSC(105;0.0518)	all_cancers(173;0.0266)	OV - Ovarian serous cystadenocarcinoma(106;0.00271)			TAGCAGGAGGATATTTTCCTG	0.463													A|||	13	0.00259585	0.0	0.0014	5008	,	,		18465	0.0		0.006	False		,,,				2504	0.0061				p.Y759Y	Colon(145;197 1800 4745 15099 26333)	Atlas-SNP	.											.	AHCTF1	187	.	0			c.T2277C						PASS	.	A		3,4403	6.2+/-15.9	0,3,2200	134.0	125.0	128.0		2277	-1.4	1.0	1	dbSNP_134	128	54,8546	33.8+/-87.4	0,54,4246	no	coding-synonymous	AHCTF1	NM_015446.4		0,57,6446	GG,GA,AA		0.6279,0.0681,0.4383		759/2276	247051714	57,12949	2203	4300	6503	SO:0001819	synonymous_variant	25909	exon18			AGGAGGATATTTT		CCDS1629.1, CCDS1629.2	1q44	2008-09-09			ENSG00000153207	ENSG00000153207			24618	protein-coding gene	gene with protein product	"""ELYS transcription factor like protein TMBS62"""	610853				11952839	Standard	NM_015446		Approved	ELYS	uc001ibv.2	Q8WYP5	OTTHUMG00000040706	ENST00000391829.2:c.2250T>C	1.37:g.247051714A>G		477.0	1.0	0.00209644		565.0	328.0	0.580531	NM_015446	A6NGM0|A8MSG9|A8MZ86|Q7Z4E3|Q8IZA4|Q96EH9|Q9Y4Q6	Silent	SNP	ENST00000391829.2	37																																																																																				A|0.997;G|0.003	0.003	strong		0.463	AHCTF1-201	KNOWN	basic|appris_candidate	protein_coding	protein_coding		NM_015446	
TMEM52B	120939	hgsc.bcm.edu	37	12	10332198	10332198	+	Missense_Mutation	SNP	G	G	T	rs140071448		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr12:10332198G>T	ENST00000381923.2	+	2	429	c.25G>T	c.(25-27)Gcg>Tcg	p.A9S	TMEM52B_ENST00000298530.3_Missense_Mutation_p.W3C|TMEM52B_ENST00000536952.1_Missense_Mutation_p.A9S			Q4KMG9	TM52B_HUMAN	transmembrane protein 52B	9						extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)											TCATGTCGTGGCGGCCTCAGC	0.478													G|||	1	0.000199681	0.0	0.0	5008	,	,		17529	0.0		0.001	False		,,,				2504	0.0				p.W3C		Atlas-SNP	.											.	.	.	.	0			c.G9T						PASS	.	G	CYS/TRP	0,4406		0,0,2203	183.0	173.0	176.0		9	-5.3	0.0	12	dbSNP_134	176	3,8597	3.0+/-9.4	0,3,4297	yes	missense	C12orf59	NM_153022.2	215	0,3,6500	TT,TG,GG		0.0349,0.0,0.0231	benign	3/164	10332198	3,13003	2203	4300	6503	SO:0001583	missense	120939	exon1			GTCGTGGCGGCCT	AY358845	CCDS8619.1, CCDS66314.1	12p13.2	2012-08-15	2012-08-15	2012-08-15	ENSG00000165685	ENSG00000165685			26438	protein-coding gene	gene with protein product			"""chromosome 12 open reading frame 59"""	C12orf59		12975309	Standard	XM_005253299		Approved	FLJ31166	uc001qxq.3	Q4KMG9	OTTHUMG00000168410	ENST00000381923.2:c.25G>T	12.37:g.10332198G>T	ENSP00000371348:p.Ala9Ser	163.0	0.0	0		118.0	54.0	0.457627	NM_153022	Q96NA7	Missense_Mutation	SNP	ENST00000381923.2	37		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	G|G	8.571|8.571	0.879998|0.879998	0.17467|0.17467	0.0|0.0	3.49E-4|3.49E-4	ENSG00000165685|ENSG00000165685	ENST00000381923;ENST00000543484;ENST00000536952|ENST00000298530	.|.	.|.	.|.	5.3|5.3	-5.3|-5.3	0.02738|0.02738	.|.	1.353820|.	0.04491|.	N|.	0.379462|.	T|T	0.25754|0.25754	0.0627|0.0627	.|.	.|.	.|.	0.09310|0.09310	N|N	1|1	B|B	0.02656|0.02656	0.0|0.0	B|B	0.01281|0.01281	0.0|0.0	T|T	0.29366|0.29366	-1.0014|-1.0014	8|7	0.38643|0.87932	T|D	0.18|0	1.6513|1.6513	4.7738|4.7738	0.13169|0.13169	0.3682:0.0:0.3801:0.2518|0.3682:0.0:0.3801:0.2518	.|.	9|3	Q4KMG9|Q4KMG9-2	CL059_HUMAN|.	S|C	9|3	.|.	ENSP00000371348:A9S|ENSP00000298530:W3C	A|W	+|+	1|3	0|0	C12orf59|C12orf59	10223465|10223465	0.000000|0.000000	0.05858|0.05858	0.000000|0.000000	0.03702|0.03702	0.000000|0.000000	0.00434|0.00434	-0.493000|-0.493000	0.06459|0.06459	-1.165000|-1.165000	0.02786|0.02786	-1.197000|-1.197000	0.01672|0.01672	GCG|TGG	G|1.000;T|0.000	0.000	strong		0.478	TMEM52B-002	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000399645.1	NM_153022	
NAV2	89797	hgsc.bcm.edu	37	11	19735325	19735325	+	Silent	SNP	C	C	A	rs11828836	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr11:19735325C>A	ENST00000396087.3	+	1	183	c.84C>A	c.(82-84)ccC>ccA	p.P28P	RP11-359E10.1_ENST00000603468.1_lincRNA|NAV2_ENST00000349880.4_Silent_p.P28P|NAV2_ENST00000360655.4_Intron|NAV2_ENST00000396085.1_Silent_p.P28P	NM_001244963.1	NP_001231892.1	Q8IVL1	NAV2_HUMAN	neuron navigator 2	28					glossopharyngeal nerve development (GO:0021563)|locomotory behavior (GO:0007626)|optic nerve development (GO:0021554)|regulation of systemic arterial blood pressure by baroreceptor feedback (GO:0003025)|sensory perception of smell (GO:0007608)|sensory perception of sound (GO:0007605)|vagus nerve development (GO:0021564)	interstitial matrix (GO:0005614)|nucleus (GO:0005634)	ATP binding (GO:0005524)|helicase activity (GO:0004386)|heparin binding (GO:0008201)			NS(1)|breast(2)|central_nervous_system(5)|endometrium(15)|haematopoietic_and_lymphoid_tissue(2)|kidney(7)|large_intestine(26)|lung(38)|ovary(3)|pancreas(1)|prostate(7)|skin(5)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	116						TGCACGTgcccccggcccggg	0.662													C|||	112	0.0223642	0.0825	0.0043	5008	,	,		13608	0.0		0.0	False		,,,				2504	0.0				p.P28P		Atlas-SNP	.											.	NAV2	255	.	0			c.C84A						PASS	.	C	,,	269,4121		8,253,1934	20.0	22.0	21.0		,84,84	4.4	1.0	11	dbSNP_120	21	5,8571		0,5,4283	no	intron,coding-synonymous,coding-synonymous	NAV2	NM_001111018.1,NM_145117.4,NM_182964.5	,,	8,258,6217	AA,AC,CC		0.0583,6.1276,2.1132	,,	,28/2430,28/2433	19735325	274,12692	2195	4288	6483	SO:0001819	synonymous_variant	89797	exon1			CGTGCCCCCGGCC	AB037840	CCDS7850.1, CCDS7851.2, CCDS44552.1, CCDS53612.1, CCDS58126.1	11p15.1	2008-07-18			ENSG00000166833	ENSG00000166833	3.6.1.1		15997	protein-coding gene	gene with protein product	"""pore membrane and/or filament interacting like protein 2"", ""retinoic acid inducible gene in neuroblastoma 1"", ""helicase, APC down-regulated 1"""	607026				12079279, 12062803	Standard	NM_145117		Approved	FLJ10633, FLJ11030, HELAD1, KIAA1419, POMFIL2, RAINB1, FLJ23707	uc010rdm.2	Q8IVL1	OTTHUMG00000151837	ENST00000396087.3:c.84C>A	11.37:g.19735325C>A		38.0	0.0	0		21.0	9.0	0.428571	NM_145117	A6NEC1|Q8IVK3|Q8IVK4|Q8IVK5|Q8IVK6|Q8IVK7|Q8IVK8|Q8NHC9|Q8NHD0|Q8TDE9|Q8TDF0|Q8TEB3|Q96B30|Q9NUZ6|Q9NVM7|Q9P2C8	Silent	SNP	ENST00000396087.3	37	CCDS58126.1																																																																																			C|0.975;A|0.025	0.025	strong		0.662	NAV2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000324112.1	NM_145117	
ARHGAP5	394	hgsc.bcm.edu	37	14	32561313	32561313	+	Nonsense_Mutation	SNP	C	C	T	rs201986816	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr14:32561313C>T	ENST00000345122.3	+	2	1753	c.1438C>T	c.(1438-1440)Cga>Tga	p.R480*	ARHGAP5_ENST00000433497.1_Intron|ARHGAP5_ENST00000539826.2_Nonsense_Mutation_p.R480*|ARHGAP5_ENST00000432921.1_Nonsense_Mutation_p.R480*|ARHGAP5_ENST00000556611.1_Nonsense_Mutation_p.R480*|ARHGAP5_ENST00000396582.2_Intron	NM_001030055.1	NP_001025226.1	Q13017	RHG05_HUMAN	Rho GTPase activating protein 5	480	FF 3.				cell adhesion (GO:0007155)|GTP catabolic process (GO:0006184)|mammary gland development (GO:0030879)|positive regulation of cell migration (GO:0030335)|positive regulation of mesenchymal cell proliferation (GO:0002053)|positive regulation of Rho GTPase activity (GO:0032321)|regulation of cell size (GO:0008361)|regulation of small GTPase mediated signal transduction (GO:0051056)|Rho protein signal transduction (GO:0007266)|small GTPase mediated signal transduction (GO:0007264)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|membrane (GO:0016020)	GTP binding (GO:0005525)|GTPase activity (GO:0003924)|Rho GTPase activator activity (GO:0005100)|SH2 domain binding (GO:0042169)			NS(2)|breast(10)|central_nervous_system(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(10)|lung(12)|ovary(4)|skin(1)|stomach(1)|urinary_tract(4)	55	Hepatocellular(127;0.0604)|Prostate(35;0.15)|Breast(36;0.186)		LUAD - Lung adenocarcinoma(48;0.00192)|Lung(238;0.00714)|BRCA - Breast invasive adenocarcinoma(188;0.0952)|STAD - Stomach adenocarcinoma(7;0.173)	GBM - Glioblastoma multiforme(265;0.00566)		TAGGCATCAGCGAGAAATAGT	0.383																																					p.R480X	NSCLC(9;77 350 3443 29227 41353)	Atlas-SNP	.											.	ARHGAP5	166	.	0			c.C1438T						PASS	.						70.0	72.0	71.0					14																	32561313		2203	4298	6501	SO:0001587	stop_gained	394	exon2			CATCAGCGAGAAA	U17032	CCDS32062.1, CCDS45095.1	14q12	2010-02-05						"""Rho GTPase activating proteins"""	675	protein-coding gene	gene with protein product		602680	"""growth factor independent 2"""	GFI2		8537347	Standard	XM_005267635		Approved	RhoGAP5, p190-B, p190BRhoGAP	uc001wrn.3	Q13017		ENST00000345122.3:c.1438C>T	14.37:g.32561313C>T	ENSP00000371897:p.Arg480*	116.0	0.0	0		126.0	7.0	0.0555556	NM_001173	A1L375|A1L376|A8KAA1|D3DS89|D3DS90|Q05BE8|Q05BU8|Q59ER0|Q6DHZ3	Nonsense_Mutation	SNP	ENST00000345122.3	37	CCDS32062.1	.	.	.	.	.	.	.	.	.	.	C	39	7.554307	0.98355	.	.	ENSG00000100852	ENST00000556611;ENST00000539826;ENST00000345122;ENST00000432921	.	.	.	6.02	5.11	0.69529	.	0.057780	0.64402	D	0.000001	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.06891	T	0.86	.	14.0719	0.64865	0.3873:0.6127:0.0:0.0	.	.	.	.	X	480	.	ENSP00000371897:R480X	R	+	1	2	ARHGAP5	31631064	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	2.567000	0.45956	1.483000	0.48342	0.650000	0.86243	CGA	C|0.998;T|0.002	0.002	strong		0.383	ARHGAP5-201	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000409735.1	NM_001030055	
RNGTT	8732	hgsc.bcm.edu	37	6	89614521	89614521	+	Silent	SNP	G	G	A	rs139029923		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr6:89614521G>A	ENST00000369485.4	-	6	783	c.597C>T	c.(595-597)gaC>gaT	p.D199D	RNGTT_ENST00000538899.1_Silent_p.D139D|RNGTT_ENST00000369475.3_Silent_p.D199D|RNGTT_ENST00000265607.6_Silent_p.D199D	NM_003800.3	NP_003791.3	O60942	MCE1_HUMAN	RNA guanylyltransferase and 5'-phosphatase	199	Asp/Glu-rich.|TPase.				7-methylguanosine mRNA capping (GO:0006370)|gene expression (GO:0010467)|RNA processing (GO:0006396)|transcription from RNA polymerase II promoter (GO:0006366)|viral process (GO:0016032)	nucleoplasm (GO:0005654)|nucleus (GO:0005634)	GTP binding (GO:0005525)|mRNA guanylyltransferase activity (GO:0004484)|polynucleotide 5'-phosphatase activity (GO:0004651)|protein tyrosine phosphatase activity (GO:0004725)|protein tyrosine/serine/threonine phosphatase activity (GO:0008138)|RNA guanylyltransferase activity (GO:0008192)|triphosphatase activity (GO:0050355)			endometrium(1)|large_intestine(7)|lung(6)|ovary(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(3)	21		all_cancers(76;4.07e-09)|Prostate(29;1.16e-10)|Acute lymphoblastic leukemia(125;1.49e-10)|all_hematologic(105;7.79e-07)|all_epithelial(107;6.86e-05)		BRCA - Breast invasive adenocarcinoma(108;0.151)		CCTCATCTTCGTCTTCATCAT	0.428																																					p.D199D		Atlas-SNP	.											.	RNGTT	52	.	0			c.C597T						PASS	.	G		0,4406		0,0,2203	108.0	91.0	97.0		597	-10.6	0.9	6	dbSNP_134	97	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous	RNGTT	NM_003800.3		0,1,6502	AA,AG,GG		0.0116,0.0,0.0077		199/598	89614521	1,13005	2203	4300	6503	SO:0001819	synonymous_variant	8732	exon6			ATCTTCGTCTTCA	AF025654	CCDS5017.1	6q16	2011-06-09			ENSG00000111880	ENSG00000111880	2.7.7.50	"""Protein tyrosine phosphatases / Class I Cys-based PTPs : Atypical dual specificity phosphatases"""	10073	protein-coding gene	gene with protein product		603512				9828141, 9512541	Standard	NM_001286428		Approved	HCE, HCE1, hCAP	uc003pmr.2	O60942	OTTHUMG00000015190	ENST00000369485.4:c.597C>T	6.37:g.89614521G>A		227.0	0.0	0		206.0	103.0	0.5	NM_003800	E1P513|E1P514|O43483|O60257|O60351|Q5TCW8|Q8WUM8	Silent	SNP	ENST00000369485.4	37	CCDS5017.1																																																																																			G|1.000;A|0.000	0.000	weak		0.428	RNGTT-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041469.1		
CTNNA3	29119	hgsc.bcm.edu	37	10	68535222	68535222	+	Missense_Mutation	SNP	T	T	C			TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr10:68535222T>C	ENST00000433211.2	-	8	1282	c.1108A>G	c.(1108-1110)Aca>Gca	p.T370A	CTNNA3_ENST00000373744.4_Missense_Mutation_p.T370A	NM_013266.2	NP_037398.2			catenin (cadherin-associated protein), alpha 3											breast(1)|central_nervous_system(1)|cervix(2)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(14)|liver(1)|lung(50)|ovary(2)|pancreas(2)|prostate(2)|skin(7)|stomach(1)|urinary_tract(1)	95						AGGTCTCTTGTCTTCTTACAC	0.378																																					p.T370A		Atlas-SNP	.											.	CTNNA3	401	.	0			c.A1108G						PASS	.						187.0	177.0	180.0					10																	68535222		2203	4300	6503	SO:0001583	missense	29119	exon8			CTCTTGTCTTCTT	AF091606	CCDS7269.1	10q21	2006-11-24			ENSG00000183230	ENSG00000183230			2511	protein-coding gene	gene with protein product		607667				12596047, 11590244	Standard	XM_005269717		Approved	VR22, MGC26194	uc001jmw.2	Q9UI47	OTTHUMG00000018334	ENST00000433211.2:c.1108A>G	10.37:g.68535222T>C	ENSP00000389714:p.Thr370Ala	175.0	0.0	0		102.0	6.0	0.0588235	NM_013266		Missense_Mutation	SNP	ENST00000433211.2	37	CCDS7269.1	.	.	.	.	.	.	.	.	.	.	T	15.09	2.731133	0.48939	.	.	ENSG00000183230	ENST00000433211;ENST00000373744	T;T	0.40756	1.02;1.02	6.16	5.04	0.67666	.	0.092451	0.47093	D	0.000247	T	0.48607	0.1509	M	0.82716	2.605	0.80722	D	1	B;B	0.26744	0.158;0.006	B;B	0.33196	0.159;0.012	T	0.53287	-0.8460	10	0.52906	T	0.07	-22.6925	9.8846	0.41253	0.0:0.0786:0.0:0.9214	.	370;370	Q9UI47-2;Q9UI47	.;CTNA3_HUMAN	A	370	ENSP00000389714:T370A;ENSP00000362849:T370A	ENSP00000362849:T370A	T	-	1	0	CTNNA3	68205228	1.000000	0.71417	1.000000	0.80357	0.985000	0.73830	4.998000	0.63927	2.367000	0.80283	0.528000	0.53228	ACA	.	.	none		0.378	CTNNA3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048282.2	NM_013266	
RUFY2	55680	hgsc.bcm.edu	37	10	70143826	70143826	+	Silent	SNP	T	T	C			TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr10:70143826T>C	ENST00000602465.1	-	9	904	c.804A>G	c.(802-804)aaA>aaG	p.K268K	RUFY2_ENST00000472394.2_5'UTR|RUFY2_ENST00000454950.2_Silent_p.K210K|RUFY2_ENST00000388768.2_Silent_p.K303K|RUFY2_ENST00000399200.2_Silent_p.K234K			Q8WXA3	RUFY2_HUMAN	RUN and FYVE domain containing 2	317						nucleus (GO:0005634)	metal ion binding (GO:0046872)			NS(1)|endometrium(2)|kidney(3)|large_intestine(1)|lung(10)|ovary(1)|upper_aerodigestive_tract(2)	20						GCTGCTGTGTTTTCATTAAAA	0.323																																					p.K303K		Atlas-SNP	.											.	RUFY2	58	.	0			c.A909G						PASS	.						146.0	131.0	136.0					10																	70143826		1832	4084	5916	SO:0001819	synonymous_variant	55680	exon9			CTGTGTTTTCATT	AF461266	CCDS41534.1, CCDS44414.1, CCDS60544.1	10q22.2	2007-01-29			ENSG00000204130	ENSG00000204130		"""Zinc fingers, FYVE domain containing"""	19761	protein-coding gene	gene with protein product		610328				11877430	Standard	NM_001042417		Approved	RABIP4R, FLJ10063, KIAA1537, ZFYVE13	uc001job.3	Q8WXA3	OTTHUMG00000018353	ENST00000602465.1:c.804A>G	10.37:g.70143826T>C		132.0	0.0	0		84.0	4.0	0.047619	NM_017987	B3KXB2|B4DFR0|Q5TC48|Q8IW33|Q96P51|Q9P1Z1	Silent	SNP	ENST00000602465.1	37																																																																																				.	.	none		0.323	RUFY2-010	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000467567.1	NM_017987	
AGPAT4	56895	hgsc.bcm.edu	37	6	161567601	161567601	+	Silent	SNP	G	G	A	rs16892215	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr6:161567601G>A	ENST00000320285.4	-	7	1010	c.798C>T	c.(796-798)gaC>gaT	p.D266D	AGPAT4_ENST00000457520.2_Silent_p.D104D|AGPAT4_ENST00000366911.5_3'UTR|AGPAT4_ENST00000366908.5_3'UTR	NM_020133.2	NP_064518.1	Q9NRZ5	PLCD_HUMAN	1-acylglycerol-3-phosphate O-acyltransferase 4	266					CDP-diacylglycerol biosynthetic process (GO:0016024)|cellular lipid metabolic process (GO:0044255)|glycerophospholipid biosynthetic process (GO:0046474)|phosphatidic acid biosynthetic process (GO:0006654)|phospholipid biosynthetic process (GO:0008654)|phospholipid metabolic process (GO:0006644)|small molecule metabolic process (GO:0044281)|triglyceride biosynthetic process (GO:0019432)	endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)	1-acylglycerol-3-phosphate O-acyltransferase activity (GO:0003841)			endometrium(1)|large_intestine(10)|lung(10)|ovary(2)|skin(2)	25		Breast(66;0.000289)|Ovarian(120;0.0266)|Prostate(117;0.0285)		OV - Ovarian serous cystadenocarcinoma(65;2.23e-17)|BRCA - Breast invasive adenocarcinoma(81;3.58e-05)		ACTCGTCATCGTCTTCAGGGA	0.592													G|||	117	0.0233626	0.0802	0.0072	5008	,	,		18454	0.006		0.0	False		,,,				2504	0.0				p.D266D		Atlas-SNP	.											.	AGPAT4	50	.	0			c.C798T						PASS	.	G		263,4143	150.3+/-184.3	10,243,1950	126.0	102.0	110.0		798	-9.9	0.0	6	dbSNP_123	110	2,8598	1.2+/-3.3	0,2,4298	no	coding-synonymous	AGPAT4	NM_020133.2		10,245,6248	AA,AG,GG		0.0233,5.9691,2.0375		266/379	161567601	265,12741	2203	4300	6503	SO:0001819	synonymous_variant	56895	exon7			GTCATCGTCTTCA	AF156776	CCDS5280.1	6q25.3	2013-02-05	2013-02-05		ENSG00000026652	ENSG00000026652	2.3.1.51	"""1-acylglycerol-3-phosphate O-acyltransferases"""	20885	protein-coding gene	gene with protein product	"""lysophosphatidic acid acyltransferase, delta"""	614795	"""1-acylglycerol-3-phosphate O-acyltransferase 4 (lysophosphatidic acid acyltransferase, delta)"""				Standard	XM_005267052		Approved	LPAAT-delta, dJ473J16.2	uc003qtr.1	Q9NRZ5	OTTHUMG00000015966	ENST00000320285.4:c.798C>T	6.37:g.161567601G>A		77.0	0.0	0		76.0	36.0	0.473684	NM_020133	B4DSF9|Q5TEF0	Silent	SNP	ENST00000320285.4	37	CCDS5280.1	47	0.02152014652014652	37	0.07520325203252033	4	0.011049723756906077	6	0.01048951048951049	0	0.0	G	0.145	-1.097373	0.01843	0.059691	2.33E-4	ENSG00000026652	ENST00000437165	.	.	.	4.95	-9.9	0.00461	.	.	.	.	.	T	0.43366	0.1244	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.68112	-0.5495	4	.	.	.	-42.6356	14.5465	0.68035	0.7342:0.1664:0.0994:0.0	rs16892215;rs16892215	.	.	.	M	45	.	.	T	-	2	0	AGPAT4	161487591	0.004000	0.15560	0.014000	0.15608	0.025000	0.11179	-1.069000	0.03444	-3.051000	0.00260	-0.997000	0.02515	ACG	G|0.975;A|0.025	0.025	strong		0.592	AGPAT4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042983.1	NM_020133	
GLI2	2736	hgsc.bcm.edu	37	2	121742124	121742124	+	Silent	SNP	G	G	A	rs61732852	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr2:121742124G>A	ENST00000452319.1	+	12	1821	c.1761G>A	c.(1759-1761)acG>acA	p.T587T	GLI2_ENST00000314490.11_Silent_p.T259T|GLI2_ENST00000361492.4_Silent_p.T587T|GLI2_ENST00000435313.2_3'UTR					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		206.0	0.0	0		180.0	83.0	0.461111	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	
BIRC3	330	hgsc.bcm.edu	37	11	102195297	102195297	+	Silent	SNP	G	G	A			TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr11:102195297G>A	ENST00000263464.3	+	2	2807	c.57G>A	c.(55-57)acG>acA	p.T19T	BIRC3_ENST00000532808.1_Silent_p.T19T	NM_001165.4	NP_001156.1	Q13489	BIRC3_HUMAN	baculoviral IAP repeat containing 3	19					apoptotic process (GO:0006915)|cell surface receptor signaling pathway (GO:0007166)|innate immune response (GO:0045087)|MyD88-independent toll-like receptor signaling pathway (GO:0002756)|necroptotic process (GO:0070266)|negative regulation of apoptotic process (GO:0043066)|negative regulation of necroptotic process (GO:0060546)|negative regulation of phosphorylation (GO:0042326)|negative regulation of reactive oxygen species metabolic process (GO:2000378)|NIK/NF-kappaB signaling (GO:0038061)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of protein ubiquitination (GO:0031398)|protein heterooligomerization (GO:0051291)|protein ubiquitination (GO:0016567)|regulation of apoptotic process (GO:0042981)|regulation of cysteine-type endopeptidase activity (GO:2000116)|regulation of inflammatory response (GO:0050727)|regulation of innate immune response (GO:0045088)|regulation of necroptotic process (GO:0060544)|regulation of nucleotide-binding oligomerization domain containing signaling pathway (GO:0070424)|regulation of RIG-I signaling pathway (GO:0039535)|regulation of toll-like receptor signaling pathway (GO:0034121)|spermatogenesis (GO:0007283)|toll-like receptor 3 signaling pathway (GO:0034138)|toll-like receptor 4 signaling pathway (GO:0034142)|toll-like receptor signaling pathway (GO:0002224)|TRIF-dependent toll-like receptor signaling pathway (GO:0035666)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|membrane raft (GO:0045121)|nucleus (GO:0005634)|protein complex (GO:0043234)	ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			endometrium(3)|kidney(2)|large_intestine(7)|lung(5)|ovary(3)|skin(1)	21	all_cancers(8;0.00044)|all_epithelial(12;0.00348)|Lung NSC(15;0.227)	Acute lymphoblastic leukemia(157;0.000967)|all_hematologic(158;0.0093)	Lung(13;0.109)|LUSC - Lung squamous cell carcinoma(19;0.151)	BRCA - Breast invasive adenocarcinoma(274;0.0146)		GCGCCAACACGTTTGAACTGA	0.413			T	MALT1	MALT																																p.T19T		Atlas-SNP	.		Dom	yes		11	11q22-q23	330	baculoviral IAP repeat-containing 3		L	.	BIRC3	56	.	0			c.G57A						PASS	.						144.0	129.0	134.0					11																	102195297		2203	4299	6502	SO:0001819	synonymous_variant	330	exon2			CAACACGTTTGAA	L49432	CCDS8315.1	11q22	2011-01-25	2011-01-25			ENSG00000023445		"""Baculoviral IAP repeat containing"", ""RING-type (C3HC4) zinc fingers"""	591	protein-coding gene	gene with protein product	"""apoptosis inhibitor 2"", ""TNFR2-TRAF signaling complex protein"", ""mammalian IAP homolog C"", ""inhibitor of apoptosis protein 1"""	601721	"""baculoviral IAP repeat-containing 3"""	API2		8552191, 8548810	Standard	NM_001165		Approved	cIAP2, hiap-1, MIHC, RNF49, MALT2, c-IAP2	uc001pgx.3	Q13489		ENST00000263464.3:c.57G>A	11.37:g.102195297G>A		315.0	0.0	0		442.0	95.0	0.214932	NM_001165	Q16628|Q9HC27|Q9UP46	Silent	SNP	ENST00000263464.3	37	CCDS8315.1																																																																																			.	.	none		0.413	BIRC3-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000394159.1	NM_001165	
GBP7	388646	hgsc.bcm.edu	37	1	89599013	89599013	+	Silent	SNP	G	G	T	rs115671591	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr1:89599013G>T	ENST00000294671.2	-	10	1728	c.1590C>A	c.(1588-1590)ctC>ctA	p.L530L		NM_207398.2	NP_997281.2	Q8N8V2	GBP7_HUMAN	guanylate binding protein 7	530						membrane (GO:0016020)	GTP binding (GO:0005525)|GTPase activity (GO:0003924)			NS(1)|breast(2)|central_nervous_system(1)|endometrium(2)|large_intestine(9)|lung(5)|ovary(1)|pancreas(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	27		Lung NSC(277;0.0908)		all cancers(265;0.00835)|Epithelial(280;0.0322)		TCTTCTTCTTGAGTTGAGCTA	0.438													G|||	103	0.0205671	0.0068	0.0159	5008	,	,		22297	0.0119		0.0278	False		,,,				2504	0.044				p.L530L		Atlas-SNP	.											.	GBP7	57	.	0			c.C1590A						PASS	.	G		38,4366	41.6+/-74.8	0,38,2164	290.0	265.0	273.0		1590	-6.5	0.0	1	dbSNP_132	273	216,8384	90.9+/-153.0	1,214,4085	no	coding-synonymous	GBP7	NM_207398.2		1,252,6249	TT,TG,GG		2.5116,0.8629,1.9532		530/639	89599013	254,12750	2202	4300	6502	SO:0001819	synonymous_variant	388646	exon10			CTTCTTGAGTTGA	AK096141	CCDS720.1	1p22.2	2008-02-05			ENSG00000213512	ENSG00000213512			29606	protein-coding gene	gene with protein product		612468					Standard	NM_207398		Approved	FLJ38822, GBP4L	uc001dna.2	Q8N8V2	OTTHUMG00000010659	ENST00000294671.2:c.1590C>A	1.37:g.89599013G>T		473.0	0.0	0		274.0	272.0	0.992701	NM_207398		Silent	SNP	ENST00000294671.2	37	CCDS720.1																																																																																			G|0.979;T|0.021	0.021	strong		0.438	GBP7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000029401.1	NM_207398	
SP140L	93349	hgsc.bcm.edu	37	2	231226371	231226371	+	Missense_Mutation	SNP	A	A	G	rs190007801	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr2:231226371A>G	ENST00000415673.2	+	5	568	c.482A>G	c.(481-483)gAa>gGa	p.E161G	SP140L_ENST00000444636.1_Missense_Mutation_p.E161G|SP140L_ENST00000396563.4_Missense_Mutation_p.E161G|SP140L_ENST00000458341.1_Missense_Mutation_p.E74G|SP140L_ENST00000243810.6_Missense_Mutation_p.E161G	NM_138402.4	NP_612411.4	Q9H930	SP14L_HUMAN	SP140 nuclear body protein-like	161						nucleus (GO:0005634)	DNA binding (GO:0003677)|zinc ion binding (GO:0008270)			central_nervous_system(1)|endometrium(1)|kidney(4)|large_intestine(5)|lung(7)|prostate(1)|skin(1)	20						GATCGAAAAGAAAGGGAAGAG	0.403													A|||	2	0.000399361	0.0015	0.0	5008	,	,		23304	0.0		0.0	False		,,,				2504	0.0				p.E161G		Atlas-SNP	.											.	SP140L	68	.	0			c.A482G						PASS	.	A	GLY/GLU	3,4039		0,3,2018	62.0	59.0	60.0		482	0.9	0.0	2		60	0,8456		0,0,4228	yes	missense	SP140L	NM_138402.4	98	0,3,6246	GG,GA,AA		0.0,0.0742,0.024	probably-damaging	161/581	231226371	3,12495	2021	4228	6249	SO:0001583	missense	93349	exon5			GAAAAGAAAGGGA	BC004921	CCDS46538.1	2q37.1	2013-01-28			ENSG00000185404	ENSG00000185404		"""Zinc fingers, PHD-type"""	25105	protein-coding gene	gene with protein product						12477932	Standard	NM_138402		Approved		uc010fxm.1	Q9H930	OTTHUMG00000153730	ENST00000415673.2:c.482A>G	2.37:g.231226371A>G	ENSP00000397911:p.Glu161Gly	103.0	0.0	0		89.0	4.0	0.0449438	NM_138402	Q2M375|Q4ZG65|Q9BSP3	Missense_Mutation	SNP	ENST00000415673.2	37	CCDS46538.1	2	9.157509157509158E-4	2	0.0040650406504065045	0	0.0	0	0.0	0	0.0	A	9.805	1.181709	0.21787	7.42E-4	0.0	ENSG00000185404	ENST00000444636;ENST00000415673;ENST00000243810;ENST00000396563;ENST00000458341	D;T;D;D;T	0.85171	-1.82;-1.45;-1.82;-1.95;0.58	2.13	0.943	0.19531	.	.	.	.	.	D	0.84284	0.5438	L	0.44542	1.39	0.09310	N	1	D;B	0.67145	0.996;0.028	P;B	0.61722	0.893;0.007	T	0.71220	-0.4657	9	0.31617	T	0.26	.	3.9572	0.09395	0.811:0.0:0.189:0.0	.	74;161	Q9H930-3;Q9H930-4	.;.	G	161;161;161;161;74	ENSP00000395195:E161G;ENSP00000397911:E161G;ENSP00000243810:E161G;ENSP00000379811:E161G;ENSP00000395223:E74G	ENSP00000243810:E161G	E	+	2	0	SP140L	230934615	0.001000	0.12720	0.001000	0.08648	0.010000	0.07245	0.491000	0.22419	0.268000	0.21939	0.254000	0.18369	GAA	A|0.999;G|0.001	0.001	strong		0.403	SP140L-009	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000374538.1	NM_138402	
BIRC3	330	hgsc.bcm.edu	37	11	102195984	102195984	+	Silent	SNP	T	T	A	rs147757750		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr11:102195984T>A	ENST00000263464.3	+	2	3494	c.744T>A	c.(742-744)tcT>tcA	p.S248S	BIRC3_ENST00000532808.1_Silent_p.S248S	NM_001165.4	NP_001156.1	Q13489	BIRC3_HUMAN	baculoviral IAP repeat containing 3	248					apoptotic process (GO:0006915)|cell surface receptor signaling pathway (GO:0007166)|innate immune response (GO:0045087)|MyD88-independent toll-like receptor signaling pathway (GO:0002756)|necroptotic process (GO:0070266)|negative regulation of apoptotic process (GO:0043066)|negative regulation of necroptotic process (GO:0060546)|negative regulation of phosphorylation (GO:0042326)|negative regulation of reactive oxygen species metabolic process (GO:2000378)|NIK/NF-kappaB signaling (GO:0038061)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of protein ubiquitination (GO:0031398)|protein heterooligomerization (GO:0051291)|protein ubiquitination (GO:0016567)|regulation of apoptotic process (GO:0042981)|regulation of cysteine-type endopeptidase activity (GO:2000116)|regulation of inflammatory response (GO:0050727)|regulation of innate immune response (GO:0045088)|regulation of necroptotic process (GO:0060544)|regulation of nucleotide-binding oligomerization domain containing signaling pathway (GO:0070424)|regulation of RIG-I signaling pathway (GO:0039535)|regulation of toll-like receptor signaling pathway (GO:0034121)|spermatogenesis (GO:0007283)|toll-like receptor 3 signaling pathway (GO:0034138)|toll-like receptor 4 signaling pathway (GO:0034142)|toll-like receptor signaling pathway (GO:0002224)|TRIF-dependent toll-like receptor signaling pathway (GO:0035666)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|membrane raft (GO:0045121)|nucleus (GO:0005634)|protein complex (GO:0043234)	ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			endometrium(3)|kidney(2)|large_intestine(7)|lung(5)|ovary(3)|skin(1)	21	all_cancers(8;0.00044)|all_epithelial(12;0.00348)|Lung NSC(15;0.227)	Acute lymphoblastic leukemia(157;0.000967)|all_hematologic(158;0.0093)	Lung(13;0.109)|LUSC - Lung squamous cell carcinoma(19;0.151)	BRCA - Breast invasive adenocarcinoma(274;0.0146)		ACACAGTTTCTAATCTGAGCA	0.423			T	MALT1	MALT																																p.S248S		Atlas-SNP	.		Dom	yes		11	11q22-q23	330	baculoviral IAP repeat-containing 3		L	BIRC3,colon,carcinoma,+2,2	BIRC3	56	2	0			c.T744A						PASS	.						75.0	76.0	76.0					11																	102195984		2203	4299	6502	SO:0001819	synonymous_variant	330	exon2			AGTTTCTAATCTG	L49432	CCDS8315.1	11q22	2011-01-25	2011-01-25			ENSG00000023445		"""Baculoviral IAP repeat containing"", ""RING-type (C3HC4) zinc fingers"""	591	protein-coding gene	gene with protein product	"""apoptosis inhibitor 2"", ""TNFR2-TRAF signaling complex protein"", ""mammalian IAP homolog C"", ""inhibitor of apoptosis protein 1"""	601721	"""baculoviral IAP repeat-containing 3"""	API2		8552191, 8548810	Standard	NM_001165		Approved	cIAP2, hiap-1, MIHC, RNF49, MALT2, c-IAP2	uc001pgx.3	Q13489		ENST00000263464.3:c.744T>A	11.37:g.102195984T>A		66.0	0.0	0		106.0	20.0	0.188679	NM_001165	Q16628|Q9HC27|Q9UP46	Silent	SNP	ENST00000263464.3	37	CCDS8315.1																																																																																			T|1.000;C|0.000	.	alt		0.423	BIRC3-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000394159.1	NM_001165	
NCKIPSD	51517	hgsc.bcm.edu	37	3	48717276	48717276	+	Silent	SNP	G	G	A	rs562394435		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr3:48717276G>A	ENST00000294129.2	-	7	1427	c.1308C>T	c.(1306-1308)aaC>aaT	p.N436N	NCKIPSD_ENST00000416649.2_Silent_p.N429N|NCKIPSD_ENST00000341520.4_Silent_p.N436N	NM_016453.2	NP_057537.1	Q9NZQ3	SPN90_HUMAN	NCK interacting protein with SH3 domain	436					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)		ACTCGAACTCGTTTCTCTTGC	0.522													G|||	1	0.000199681	0.0	0.0	5008	,	,		24484	0.0		0.0	False		,,,				2504	0.001				p.N436N		Atlas-SNP	.											.	NCKIPSD	52	.	0			c.C1308T						PASS	.						138.0	123.0	128.0					3																	48717276		2203	4300	6503	SO:0001819	synonymous_variant	51517	exon7			GAACTCGTTTCTC	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.1308C>T	3.37:g.48717276G>A		166.0	0.0	0		123.0	67.0	0.544715	NM_016453	B4DFL5|Q6GU34|Q6SPF3|Q8TC10|Q9UGM8	Silent	SNP	ENST00000294129.2	37	CCDS2776.1	.	.	.	.	.	.	.	.	.	.	G	5.849	0.340768	0.11069	.	.	ENSG00000213672	ENST00000415281	.	.	.	5.2	-3.89	0.04193	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	12.2642	0.54668	0.5461:0.0:0.4539:0.0	.	.	.	.	X	172	.	.	R	-	1	2	NCKIPSD	48692280	0.845000	0.29573	0.068000	0.19968	0.913000	0.54294	-0.007000	0.12810	-1.032000	0.03304	-1.326000	0.01283	CGA	.	.	none		0.522	NCKIPSD-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000257520.1	NM_016453	
KLHL33	123103	hgsc.bcm.edu	37	14	20897065	20897065	+	Silent	SNP	G	G	A	rs368179614		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr14:20897065G>A	ENST00000344581.4	-	4	1767	c.1545C>T	c.(1543-1545)ccC>ccT	p.P515P		NM_001109997.2	NP_001103467.2	A6NCF5	KLH33_HUMAN	kelch-like family member 33	515												all_cancers(95;0.00123)		Epithelial(56;7.57e-08)|all cancers(55;8.63e-07)	GBM - Glioblastoma multiforme(265;0.0223)|READ - Rectum adenocarcinoma(17;0.193)		GCTGCACAGCGGGCAGTGTCA	0.582																																					p.P515P		Atlas-SNP	.											.	KLHL33	37	.	0			c.C1545T						PASS	.	G		0,1384		0,0,692	73.0	70.0	71.0		1545	-5.4	0.0	14		71	1,3181		0,1,1590	no	coding-synonymous	KLHL33	NM_001109997.2		0,1,2282	AA,AG,GG		0.0314,0.0,0.0219		515/534	20897065	1,4565	692	1591	2283	SO:0001819	synonymous_variant	123103	exon4			CACAGCGGGCAGT		CCDS53882.1	14q11.2	2013-10-15	2013-02-22		ENSG00000185271	ENSG00000185271		"""Kelch-like"""	31952	protein-coding gene	gene with protein product			"""kelch-like 33 (Drosophila)"""				Standard	NM_001109997		Approved		uc010tli.2	A6NCF5	OTTHUMG00000170982	ENST00000344581.4:c.1545C>T	14.37:g.20897065G>A		246.0	0.0	0		302.0	123.0	0.407285	NM_001109997		Silent	SNP	ENST00000344581.4	37	CCDS53882.1																																																																																			.	.	weak		0.582	KLHL33-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000411038.1	XM_063481	
PCIF1	63935	hgsc.bcm.edu	37	20	44575932	44575932	+	Missense_Mutation	SNP	T	T	C			TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr20:44575932T>C	ENST00000372409.3	+	16	2102	c.1738T>C	c.(1738-1740)Tcc>Ccc	p.S580P	PCIF1_ENST00000479348.1_3'UTR	NM_022104.3	NP_071387.1	Q9H4Z3	PCIF1_HUMAN	PDX1 C-terminal inhibiting factor 1	580					negative regulation of phosphatase activity (GO:0010923)	intercellular bridge (GO:0045171)|microtubule cytoskeleton (GO:0015630)|nucleus (GO:0005634)				central_nervous_system(1)|endometrium(3)|large_intestine(5)|lung(4)|skin(2)|upper_aerodigestive_tract(3)|urinary_tract(2)	20						GGAGCCCCTGTCCTTCATCGT	0.622																																					p.S580P		Atlas-SNP	.											.	PCIF1	51	.	0			c.T1738C						PASS	.						79.0	81.0	80.0					20																	44575932		2203	4300	6503	SO:0001583	missense	63935	exon16			CCCCTGTCCTTCA	AB050014	CCDS13388.1	20q13.12	2014-06-13	2008-04-29	2008-04-29	ENSG00000100982	ENSG00000100982			16200	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 121"""		"""chromosome 20 open reading frame 67"""	C20orf67		12565871, 15121856	Standard	NM_022104		Approved	bA465L10.1, PPP1R121	uc002xqs.3	Q9H4Z3	OTTHUMG00000032635	ENST00000372409.3:c.1738T>C	20.37:g.44575932T>C	ENSP00000361486:p.Ser580Pro	110.0	0.0	0		104.0	6.0	0.0576923	NM_022104	E1P5P1|Q54AB9|Q9NT85	Missense_Mutation	SNP	ENST00000372409.3	37	CCDS13388.1	.	.	.	.	.	.	.	.	.	.	T	23.1	4.371687	0.82573	.	.	ENSG00000100982	ENST00000372409;ENST00000443130	.	.	.	5.03	5.03	0.67393	Phosphorylated CTD interacting factor 1, WW domain (1);	0.000000	0.85682	D	0.000000	D	0.84306	0.5443	M	0.90542	3.125	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;1.0	D	0.87621	0.2510	9	0.72032	D	0.01	-30.1299	14.0902	0.64984	0.0:0.0:0.0:1.0	.	580;580	B7Z5U5;Q9H4Z3	.;PCIF1_HUMAN	P	580	.	ENSP00000361486:S580P	S	+	1	0	PCIF1	44009339	1.000000	0.71417	1.000000	0.80357	0.896000	0.52359	5.925000	0.70062	2.114000	0.64651	0.374000	0.22700	TCC	.	.	none		0.622	PCIF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079550.1	NM_022104	
SAR1B	51128	hgsc.bcm.edu	37	5	133945288	133945288	+	Silent	SNP	C	C	T	rs140899111	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr5:133945288C>T	ENST00000402673.2	-	5	599	c.321G>A	c.(319-321)agG>agA	p.R107R	SAR1B_ENST00000502539.1_Silent_p.R39R|SAR1B_ENST00000439578.1_Silent_p.R107R|SAR1B_ENST00000509937.1_Silent_p.R39R|SAR1B_ENST00000507419.1_Silent_p.R39R	NM_016103.3	NP_057187.1	Q9Y6B6	SAR1B_HUMAN	secretion associated, Ras related GTPase 1B	107					antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|antigen processing and presentation of peptide antigen via MHC class I (GO:0002474)|cellular protein metabolic process (GO:0044267)|COPII vesicle coating (GO:0048208)|ER to Golgi vesicle-mediated transport (GO:0006888)|GTP catabolic process (GO:0006184)|intracellular protein transport (GO:0006886)|membrane organization (GO:0061024)|post-translational protein modification (GO:0043687)|protein N-linked glycosylation via asparagine (GO:0018279)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)|endoplasmic reticulum membrane (GO:0005789)|ER to Golgi transport vesicle membrane (GO:0012507)|Golgi membrane (GO:0000139)	GTP binding (GO:0005525)|GTPase activity (GO:0003924)|metal ion binding (GO:0046872)			kidney(2)|lung(2)|urinary_tract(1)	5			KIRC - Kidney renal clear cell carcinoma(527;0.0186)|Kidney(363;0.0365)			ACTCTAACAGCCTTTCGTGGT	0.393													C|||	4	0.000798722	0.0	0.0	5008	,	,		20631	0.0		0.004	False		,,,				2504	0.0				p.R107R		Atlas-SNP	.											.	SAR1B	19	.	0			c.G321A						PASS	.	C	,	1,4405	2.1+/-5.4	0,1,2202	129.0	118.0	122.0		321,321	1.9	1.0	5	dbSNP_134	122	15,8585	11.2+/-40.8	0,15,4285	no	coding-synonymous,coding-synonymous	SAR1B	NM_001033503.2,NM_016103.3	,	0,16,6487	TT,TC,CC		0.1744,0.0227,0.123	,	107/199,107/199	133945288	16,12990	2203	4300	6503	SO:0001819	synonymous_variant	51128	exon6			TAACAGCCTTTCG	AF092130	CCDS4177.1	5q31.1	2014-03-07	2014-03-07	2005-10-21	ENSG00000152700	ENSG00000152700			10535	protein-coding gene	gene with protein product		607690	"""SAR1a gene homolog (S. cerevisiae) 2"", ""SAR1a gene homolog 2 (S. cerevisiae)"", ""SAR1 homolog B (S. cerevisiae)"""	SARA2			Standard	NM_001033503		Approved		uc003kzr.3	Q9Y6B6	OTTHUMG00000129114	ENST00000402673.2:c.321G>A	5.37:g.133945288C>T		138.0	0.0	0		145.0	56.0	0.386207	NM_001033503	D3DQA4|Q567T4	Silent	SNP	ENST00000402673.2	37	CCDS4177.1																																																																																			C|0.999;T|0.001	0.001	strong		0.393	SAR1B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251158.2	NM_016103	
URB1	9875	hgsc.bcm.edu	37	21	33697576	33697576	+	Missense_Mutation	SNP	G	G	A	rs187640762	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr21:33697576G>A	ENST00000382751.3	-	31	5199	c.5084C>T	c.(5083-5085)tCg>tTg	p.S1695L		NM_014825.2	NP_055640.2	O60287	NPA1P_HUMAN	URB1 ribosome biogenesis 1 homolog (S. cerevisiae)	1695						nucleolus (GO:0005730)	poly(A) RNA binding (GO:0044822)			NS(1)|autonomic_ganglia(1)|breast(2)|central_nervous_system(1)|endometrium(9)|kidney(3)|skin(1)|stomach(1)	19						CTCCAAGTGCGAGTAGTAGGC	0.577													G|||	13	0.00259585	0.0	0.0029	5008	,	,		17029	0.0		0.006	False		,,,				2504	0.0051				p.S1695L		Atlas-SNP	.											.	URB1	176	.	0			c.C5084T						PASS	.	G	LEU/SER	0,1384		0,0,692	65.0	57.0	59.0		5084	4.2	1.0	21		59	29,3153		0,29,1562	yes	missense	URB1	NM_014825.2	145	0,29,2254	AA,AG,GG		0.9114,0.0,0.6351	probably-damaging	1695/2272	33697576	29,4537	692	1591	2283	SO:0001583	missense	9875	exon31			AAGTGCGAGTAGT	AB011111	CCDS46645.1	21q22.11	2006-11-28	2006-11-28	2006-11-28	ENSG00000142207	ENSG00000142207			17344	protein-coding gene	gene with protein product	nucleolar preribosomal-associated protein 1	608865	"""chromosome 21 open reading frame 108"""	C21orf108		9628581	Standard	NM_014825		Approved	KIAA0539, NPA1	uc002ypn.2	O60287	OTTHUMG00000064919	ENST00000382751.3:c.5084C>T	21.37:g.33697576G>A	ENSP00000372199:p.Ser1695Leu	67.0	0.0	0		88.0	34.0	0.386364	NM_014825	D3DSE5|Q96NX1|Q9NYQ1	Missense_Mutation	SNP	ENST00000382751.3	37	CCDS46645.1	8	0.003663003663003663	0	0.0	2	0.0055248618784530384	0	0.0	6	0.0079155672823219	G	17.73	3.461947	0.63513	0.0	0.009114	ENSG00000142207	ENST00000382751	T	0.32753	1.44	5.15	4.2	0.49525	.	0.247939	0.42548	D	0.000682	T	0.33876	0.0878	L	0.52011	1.625	0.47094	D	0.999315	D	0.76494	0.999	P	0.61397	0.888	T	0.06862	-1.0803	10	0.10636	T	0.68	-17.8842	15.4371	0.75155	0.0:0.1391:0.8609:0.0	.	1695	O60287	NPA1P_HUMAN	L	1695	ENSP00000372199:S1695L	ENSP00000372199:S1695L	S	-	2	0	URB1	32619447	1.000000	0.71417	0.960000	0.40013	0.441000	0.31987	3.473000	0.53122	2.555000	0.86185	0.655000	0.94253	TCG	G|0.995;A|0.005	0.005	strong		0.577	URB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000139400.2		
HOXB5	3215	hgsc.bcm.edu	37	17	46669730	46669730	+	Silent	SNP	G	G	T	rs36049616	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr17:46669730G>T	ENST00000239151.5	-	2	929	c.651C>A	c.(649-651)cgC>cgA	p.R217R	HOXB-AS3_ENST00000480872.1_RNA|HOXB3_ENST00000552000.2_Intron|HOXB3_ENST00000472863.1_5'Flank|HOXB-AS3_ENST00000476204.1_RNA|HOXB-AS3_ENST00000474040.1_RNA|HOXB-AS3_ENST00000467155.2_RNA|HOXB-AS3_ENST00000492897.3_RNA|HOXB3_ENST00000476342.1_5'Flank|HOXB-AS3_ENST00000487849.3_RNA|HOXB3_ENST00000498678.1_5'Flank|HOXB3_ENST00000460160.1_5'Flank|HOXB-AS3_ENST00000465846.2_RNA|HOXB-AS3_ENST00000429755.4_RNA	NM_002147.3	NP_002138.1	P09067	HXB5_HUMAN	homeobox B5	217					anatomical structure morphogenesis (GO:0009653)|anterior/posterior pattern specification (GO:0009952)|embryonic skeletal system morphogenesis (GO:0048704)|endothelial cell differentiation (GO:0045446)	nucleus (GO:0005634)	RNA polymerase II distal enhancer sequence-specific DNA binding (GO:0000980)|RNA polymerase II distal enhancer sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001205)			large_intestine(1)|lung(2)	3						GGGTCAGGTAGCGGTTGAAGT	0.612													G|||	144	0.028754	0.0734	0.0346	5008	,	,		11348	0.0		0.0179	False		,,,				2504	0.0051				p.R217R		Atlas-SNP	.											.	HOXB5	20	.	0			c.C651A						PASS	.	G		301,4105	165.8+/-197.2	13,275,1915	105.0	105.0	105.0		651	4.2	1.0	17	dbSNP_126	105	301,8299	109.4+/-169.9	6,289,4005	no	coding-synonymous	HOXB5	NM_002147.3		19,564,5920	TT,TG,GG		3.5,6.8316,4.6286		217/270	46669730	602,12404	2203	4300	6503	SO:0001819	synonymous_variant	3215	exon2			CAGGTAGCGGTTG		CCDS11530.1	17q21.32	2011-06-20	2005-12-22		ENSG00000120075	ENSG00000120075		"""Homeoboxes / ANTP class : HOXL subclass"""	5116	protein-coding gene	gene with protein product		142960	"""homeo box B5"""	HOX2, HOX2A		1973146, 1358459	Standard	NM_002147		Approved		uc002inr.3	P09067	OTTHUMG00000159913	ENST00000239151.5:c.651C>A	17.37:g.46669730G>T		187.0	0.0	0		203.0	76.0	0.374384	NM_002147	B2RC69|P09069|Q17RP4	Silent	SNP	ENST00000239151.5	37	CCDS11530.1																																																																																			G|0.960;T|0.040	0.040	strong		0.612	HOXB5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000358148.2		
VWA2	340706	hgsc.bcm.edu	37	10	116045993	116045993	+	Silent	SNP	G	G	A	rs566742651	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr10:116045993G>A	ENST00000392982.3	+	11	1543	c.1293G>A	c.(1291-1293)gaG>gaA	p.E431E	VWA2_ENST00000603594.1_Silent_p.E431E			Q5GFL6	VWA2_HUMAN	von Willebrand factor A domain containing 2	431	VWFA 2. {ECO:0000255|PROSITE- ProRule:PRU00219}.				calcium-independent cell-matrix adhesion (GO:0007161)|protein homooligomerization (GO:0051260)|regulation of insulin receptor signaling pathway (GO:0046626)	basement membrane (GO:0005604)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)	identical protein binding (GO:0042802)			central_nervous_system(1)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(7)|lung(6)|ovary(2)|prostate(1)|skin(1)|stomach(1)	26				Epithelial(162;0.036)|all cancers(201;0.0793)		AGGCGGCAGAGCGTGGCTTCG	0.662																																					p.E431E		Atlas-SNP	.											.	VWA2	64	.	0			c.G1293A						PASS	.						56.0	49.0	51.0					10																	116045993		2203	4299	6502	SO:0001819	synonymous_variant	340706	exon11			GGCAGAGCGTGGC	AK127756	CCDS7589.1, CCDS7589.2	10q25.3	2009-11-06			ENSG00000165816	ENSG00000165816			24709	protein-coding gene	gene with protein product						15580307, 14506275	Standard	NM_001272046		Approved	FLJ45857, FLJ16213, CCSP-2, AMACO, NET42	uc001lbl.2	Q5GFL6	OTTHUMG00000019082	ENST00000392982.3:c.1293G>A	10.37:g.116045993G>A		117.0	0.0	0		89.0	43.0	0.483146	NM_001272046	A1A5D4|B5MDJ8|Q6ZS39|Q6ZWJ7|Q708C5|Q70UZ8	Silent	SNP	ENST00000392982.3	37																																																																																				.	.	none		0.662	VWA2-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000050456.3	NM_198496	
GNB5	10681	hgsc.bcm.edu	37	15	52433397	52433397	+	Silent	SNP	C	C	T	rs17612637	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr15:52433397C>T	ENST00000261837.7	-	7	632	c.567G>A	c.(565-567)aaG>aaA	p.K189K	GNB5_ENST00000559348.1_5'Flank|GNB5_ENST00000396335.4_Intron|CTD-2184D3.7_ENST00000560613.1_RNA|GNB5_ENST00000358784.7_Silent_p.K147K|CTD-2184D3.7_ENST00000557898.1_RNA	NM_016194.3	NP_057278.2	O14775	GBB5_HUMAN	guanine nucleotide binding protein (G protein), beta 5	189					GTP catabolic process (GO:0006184)|negative regulation of voltage-gated calcium channel activity (GO:1901386)|phototransduction, visible light (GO:0007603)|regulation of rhodopsin mediated signaling pathway (GO:0022400)|rhodopsin mediated signaling pathway (GO:0016056)|signal transduction (GO:0007165)	nucleus (GO:0005634)|plasma membrane (GO:0005886)	chaperone binding (GO:0051087)|G-protein gamma-subunit binding (GO:0031682)|GTPase activity (GO:0003924)|signal transducer activity (GO:0004871)			large_intestine(1)|lung(1)	2				all cancers(107;0.0163)		TAGCAACAGACTTCTTTTTGG	0.473													C|||	82	0.0163738	0.0008	0.0389	5008	,	,		18151	0.0		0.0368	False		,,,				2504	0.0174				p.K189K		Atlas-SNP	.											.	GNB5	28	.	0			c.G567A						PASS	.	C	,	35,4355	39.2+/-71.8	1,33,2161	166.0	150.0	155.0		441,567	5.3	1.0	15	dbSNP_123	155	317,8269	112.5+/-172.7	4,309,3980	no	coding-synonymous,coding-synonymous	GNB5	NM_006578.3,NM_016194.3	,	5,342,6141	TT,TC,CC		3.6921,0.7973,2.7127	,	147/354,189/396	52433397	352,12624	2195	4293	6488	SO:0001819	synonymous_variant	10681	exon7			AACAGACTTCTTT	AF017656	CCDS10149.1, CCDS45261.1	15q21.1	2013-01-10			ENSG00000069966	ENSG00000069966		"""WD repeat domain containing"""	4401	protein-coding gene	gene with protein product		604447				9606987	Standard	NM_016194		Approved	GB5	uc031qrz.1	O14775	OTTHUMG00000131892	ENST00000261837.7:c.567G>A	15.37:g.52433397C>T		186.0	0.0	0		94.0	24.0	0.255319	NM_016194	B2RBR5|Q9HAU9|Q9UFT3	Silent	SNP	ENST00000261837.7	37	CCDS10149.1																																																																																			C|0.973;G|0.000;T|0.027	0.027	strong		0.473	GNB5-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000254842.1		
RCOR1	23186	hgsc.bcm.edu	37	14	103173756	103173756	+	Silent	SNP	C	C	A	rs149418829	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr14:103173756C>A	ENST00000570597.1	+	5	558	c.558C>A	c.(556-558)acC>acA	p.T186T	RCOR1_ENST00000262241.6_Silent_p.T189T			Q9UKL0	RCOR1_HUMAN	REST corepressor 1	186	ELM2. {ECO:0000255|PROSITE- ProRule:PRU00512}.|Interaction with HDAC1.				blood coagulation (GO:0007596)|histone H4 deacetylation (GO:0070933)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|viral process (GO:0016032)	nucleoplasm (GO:0005654)|nucleus (GO:0005634)|transcriptional repressor complex (GO:0017053)	chromatin binding (GO:0003682)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in negative regulation of transcription (GO:0001078)|transcription regulatory region DNA binding (GO:0044212)			NS(1)|central_nervous_system(1)|endometrium(1)|large_intestine(1)|lung(6)|ovary(1)|upper_aerodigestive_tract(1)	12						CCAACTTTACCCCTTTCCCAG	0.363													C|||	31	0.0061901	0.0	0.0202	5008	,	,		16191	0.0		0.0129	False		,,,				2504	0.0041				p.T189T		Atlas-SNP	.											.	RCOR1	39	.	0			c.C567A						PASS	.	C		14,4392	21.2+/-45.6	0,14,2189	134.0	136.0	136.0		558	3.1	1.0	14	dbSNP_134	136	96,8504	53.1+/-113.8	0,96,4204	no	coding-synonymous	RCOR1	NM_015156.3		0,110,6393	AA,AC,CC		1.1163,0.3177,0.8458		186/483	103173756	110,12896	2203	4300	6503	SO:0001819	synonymous_variant	23186	exon5			CTTTACCCCTTTC	AF155595	CCDS9974.1, CCDS9974.2	14q32.33	2004-04-16	2004-04-16	2004-04-16		ENSG00000089902			17441	protein-coding gene	gene with protein product		607675	"""REST corepressor"""	RCOR		10449787	Standard	NM_015156		Approved	COREST, KIAA0071	uc001ymb.4	Q9UKL0		ENST00000570597.1:c.558C>A	14.37:g.103173756C>A		161.0	0.0	0		162.0	51.0	0.314815	NM_015156	Q15044|Q6P2I9|Q86VG5	Silent	SNP	ENST00000570597.1	37																																																																																				C|0.990;A|0.010	0.010	strong		0.363	RCOR1-201	KNOWN	basic|appris_candidate	protein_coding	protein_coding		NM_015156	
KRT1	3848	hgsc.bcm.edu	37	12	53069243	53069243	+	Missense_Mutation	SNP	T	T	C	rs77846840|rs540699806|rs267607656	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr12:53069243T>C	ENST00000252244.3	-	9	1727	c.1669A>G	c.(1669-1671)Agc>Ggc	p.S557G		NM_006121.3	NP_006112.3	P04264	K2C1_HUMAN	keratin 1	557	Gly/Ser-rich.|Tail.				complement activation, lectin pathway (GO:0001867)|establishment of skin barrier (GO:0061436)|fibrinolysis (GO:0042730)|negative regulation of inflammatory response (GO:0050728)|regulation of angiogenesis (GO:0045765)|response to oxidative stress (GO:0006979)|retina homeostasis (GO:0001895)	blood microparticle (GO:0072562)|cytoskeleton (GO:0005856)|extracellular matrix (GO:0031012)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|keratin filament (GO:0045095)|membrane (GO:0016020)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	carbohydrate binding (GO:0030246)|receptor activity (GO:0004872)|structural molecule activity (GO:0005198)	p.S557_G563delSSYGSGG(3)		breast(2)|central_nervous_system(1)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(7)|lung(11)|ovary(1)|prostate(7)|skin(3)	39						ccgtagctgctacctccggag	0.682																																					p.S557G		Atlas-SNP	.											.	KRT1	110	.	3	Deletion - In frame(3)	prostate(2)|central_nervous_system(1)	c.A1669G						PASS	.						4.0	4.0	4.0					12																	53069243		1805	3566	5371	SO:0001583	missense	3848	exon9			AGCTGCTACCTCC	X69725	CCDS8836.1	12q13.13	2014-06-05	2008-08-01		ENSG00000167768	ENSG00000167768		"""-"", ""Intermediate filaments type II, keratins (basic)"""	6412	protein-coding gene	gene with protein product		139350	"""epidermolytic hyperkeratosis 1"""	EHK1		2461420, 2470667, 16831889	Standard	NM_006121		Approved	KRT1A	uc001sau.1	P04264	OTTHUMG00000169749	ENST00000252244.3:c.1669A>G	12.37:g.53069243T>C	ENSP00000252244:p.Ser557Gly	17.0	0.0	0		25.0	8.0	0.32	NM_006121	B2RA01|P85925|P86104|Q14720|Q6GSJ0|Q9H298	Missense_Mutation	SNP	ENST00000252244.3	37	CCDS8836.1	.	.	.	.	.	.	.	.	.	.	t	12.77	2.037794	0.35989	.	.	ENSG00000167768	ENST00000252244	T	0.81247	-1.47	3.63	0.628	0.17681	.	.	.	.	.	T	0.54711	0.1875	N	0.08118	0	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.48490	-0.9031	8	0.07644	T	0.81	.	5.639	0.17552	0.0:0.6406:0.1602:0.1993	.	557	P04264	K2C1_HUMAN	G	557	ENSP00000252244:S557G	ENSP00000252244:S557G	S	-	1	0	KRT1	51355510	0.000000	0.05858	0.034000	0.17996	0.201000	0.24016	-0.192000	0.09587	-0.104000	0.12154	-1.598000	0.00824	AGC	T|0.500;C|0.500	0.500	weak		0.682	KRT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000405706.1	NM_006121	
TRDMT1	1787	hgsc.bcm.edu	37	10	17243610	17243610	+	Silent	SNP	C	C	T			TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr10:17243610C>T	ENST00000377799.3	-	1	71	c.24G>A	c.(22-24)gaG>gaA	p.E8E	TRDMT1_ENST00000412821.3_Silent_p.E8E|TRDMT1_ENST00000457442.2_5'UTR|TRDMT1_ENST00000358282.7_Silent_p.E8E|TRDMT1_ENST00000351358.4_Silent_p.E8E|TRDMT1_ENST00000377766.5_Silent_p.E8E|TRDMT1_ENST00000488990.1_Silent_p.E8E	NM_004412.5	NP_004403.1	O14717	TRDMT_HUMAN	tRNA aspartic acid methyltransferase 1	8	SAM-dependent MTase C5-type. {ECO:0000255|PROSITE-ProRule:PRU01016}.				C-5 methylation of cytosine (GO:0090116)|response to amphetamine (GO:0001975)|tRNA methylation (GO:0030488)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	DNA (cytosine-5-)-methyltransferase activity (GO:0003886)|DNA binding (GO:0003677)|RNA binding (GO:0003723)|tRNA methyltransferase activity (GO:0008175)			breast(2)|endometrium(1)|kidney(3)|large_intestine(6)|lung(4)|ovary(1)|prostate(1)	18					Pentamidine(DB00738)	CGCTGTATAGCTCCAGCACCC	0.706																																					p.E8E		Atlas-SNP	.											.	TRDMT1	46	.	0			c.G24A						PASS	.						11.0	12.0	12.0					10																	17243610		1939	3647	5586	SO:0001819	synonymous_variant	1787	exon1			GTATAGCTCCAGC	AJ223333	CCDS7114.1	10p15.1	2006-10-23	2006-10-23	2006-10-23	ENSG00000107614	ENSG00000107614	2.1.1.37		2977	protein-coding gene	gene with protein product		602478	"""DNA (cytosine-5-)-methyltransferase 2"""	DNMT2		9425235, 9763678, 16424344	Standard	NM_004412		Approved	RNMT1	uc001iop.3	O14717	OTTHUMG00000017745	ENST00000377799.3:c.24G>A	10.37:g.17243610C>T		44.0	0.0	0		18.0	12.0	0.666667	NM_004412	B0YJ02|B0YJ03|B0YJ07|B0YJ08|O43669|Q86WW6	Silent	SNP	ENST00000377799.3	37	CCDS7114.1																																																																																			.	.	none		0.706	TRDMT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047024.3	NM_004412	
BPIFA2	140683	hgsc.bcm.edu	37	20	31761919	31761919	+	Missense_Mutation	SNP	A	A	G	rs17304572	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	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	148.0	0.0	0		126.0	58.0	0.460317	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	
INF2	64423	hgsc.bcm.edu	37	14	105179184	105179184	+	Missense_Mutation	SNP	G	G	A	rs142678449	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr14:105179184G>A	ENST00000392634.4	+	18	2742	c.2630G>A	c.(2629-2631)cGg>cAg	p.R877Q	INF2_ENST00000330634.7_Missense_Mutation_p.R877Q	NM_022489.3	NP_071934.3	Q27J81	INF2_HUMAN	inverted formin, FH2 and WH2 domain containing	877	FH2. {ECO:0000255|PROSITE- ProRule:PRU00774}.				actin cytoskeleton organization (GO:0030036)|cell death (GO:0008219)|regulation of cellular component size (GO:0032535)|regulation of mitochondrial fission (GO:0090140)	cytoplasm (GO:0005737)|endoplasmic reticulum (GO:0005783)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)				large_intestine(3)|lung(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	8		all_cancers(154;0.0896)|Melanoma(154;0.155)|all_epithelial(191;0.172)	all cancers(16;0.00188)|OV - Ovarian serous cystadenocarcinoma(23;0.0191)|Epithelial(46;0.047)|GBM - Glioblastoma multiforme(11;0.116)	Epithelial(152;0.176)		TCGGCCTTCCGGGCACTGGAT	0.677													G|||	28	0.00559105	0.0023	0.013	5008	,	,		17221	0.0		0.0089	False		,,,				2504	0.0072				p.R877Q		Atlas-SNP	.											.	INF2	148	.	0			c.G2630A						PASS	.	G	GLN/ARG,GLN/ARG	6,4024		0,6,2009	24.0	28.0	27.0		2630,2630	-4.1	0.0	14	dbSNP_134	27	89,8255		2,85,4085	yes	missense,missense	INF2	NM_022489.3,NM_001031714.3	43,43	2,91,6094	AA,AG,GG		1.0666,0.1489,0.7677	benign,benign	877/1250,877/1241	105179184	95,12279	2015	4172	6187	SO:0001583	missense	64423	exon18			CCTTCCGGGCACT	AK025709	CCDS9989.2, CCDS45173.1	14q32.33	2009-09-07	2007-11-29	2007-11-29	ENSG00000203485	ENSG00000203485			23791	protein-coding gene	gene with protein product	"""inverted formin 2"""	610982	"""chromosome 14 open reading frame 151"", ""chromosome 14 open reading frame 173"""	C14orf151, C14orf173		16818491	Standard	NM_001031714		Approved	MGC13251	uc001ypb.2	Q27J81	OTTHUMG00000029811	ENST00000392634.4:c.2630G>A	14.37:g.105179184G>A	ENSP00000376410:p.Arg877Gln	121.0	0.0	0		145.0	50.0	0.344828	NM_022489	Q27J83|Q69YL8|Q6P1X7|Q6PK22|Q86TR7|Q9BRM1|Q9H6N1	Missense_Mutation	SNP	ENST00000392634.4	37	CCDS9989.2	16	0.007326007326007326	1	0.0020325203252032522	9	0.024861878453038673	0	0.0	6	0.0079155672823219	G	13.65	2.300727	0.40694	0.001489	0.010666	ENSG00000203485	ENST00000330634;ENST00000392634	T;T	0.17213	2.29;2.29	5.06	-4.11	0.03928	Actin-binding FH2/DRF autoregulatory (1);Actin-binding FH2 (3);	1.264760	0.05384	N	0.537746	T	0.05731	0.0150	L	0.27053	0.805	0.09310	N	1	B;B	0.24882	0.093;0.113	B;B	0.17722	0.008;0.019	T	0.31308	-0.9948	10	0.17369	T	0.5	.	14.103	0.65070	0.6837:0.0:0.3163:0.0	.	877;877	Q27J81-2;Q27J81	.;INF2_HUMAN	Q	877	ENSP00000376406:R877Q;ENSP00000376410:R877Q	ENSP00000252527:R345Q	R	+	2	0	INF2	104250229	0.000000	0.05858	0.000000	0.03702	0.017000	0.09413	-0.660000	0.05317	-1.495000	0.01831	0.561000	0.74099	CGG	G|0.992;A|0.008	0.008	strong		0.677	INF2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000074371.4	NM_022489	
PCLO	27445	hgsc.bcm.edu	37	7	82451984	82451984	+	Missense_Mutation	SNP	T	T	G			TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr7:82451984T>G	ENST00000333891.9	-	20	14955	c.14618A>C	c.(14617-14619)gAg>gCg	p.E4873A	PCLO_ENST00000426442.2_5'UTR|PCLO_ENST00000423517.2_Missense_Mutation_p.E4873A	NM_033026.5	NP_149015.2			piccolo presynaptic cytomatrix protein											breast(3)|central_nervous_system(3)|cervix(5)|endometrium(19)|haematopoietic_and_lymphoid_tissue(3)|kidney(19)|large_intestine(35)|lung(145)|ovary(7)|prostate(4)|upper_aerodigestive_tract(14)|urinary_tract(2)	259						ATGGGATTTCTCAATGGTGGG	0.438																																					p.E4873A		Atlas-SNP	.											.	PCLO	1506	.	0			c.A14618C						PASS	.						231.0	226.0	228.0					7																	82451984		1967	4169	6136	SO:0001583	missense	27445	exon20			GATTTCTCAATGG	AB011131	CCDS47630.1, CCDS47631.1	7q11.23-q21.3	2013-01-07	2013-01-07		ENSG00000186472	ENSG00000186472			13406	protein-coding gene	gene with protein product	"""aczonin"""	604918	"""piccolo (presynaptic cytomatrix protein)"""			8900486, 9628581	Standard	NM_014510		Approved	KIAA0559, DKFZp779G1236, ACZ	uc003uhx.2	Q9Y6V0	OTTHUMG00000154853	ENST00000333891.9:c.14618A>C	7.37:g.82451984T>G	ENSP00000334319:p.Glu4873Ala	60.0	0.0	0		62.0	12.0	0.193548	NM_014510		Missense_Mutation	SNP	ENST00000333891.9	37	CCDS47630.1	.	.	.	.	.	.	.	.	.	.	T	14.77	2.635321	0.47049	.	.	ENSG00000186472	ENST00000333891;ENST00000423517;ENST00000380195	T;T	0.18174	2.29;2.23	5.05	5.05	0.67936	.	.	.	.	.	T	0.30823	0.0777	L	0.29908	0.895	0.80722	D	1	D;D;D;D	0.89917	1.0;1.0;0.998;0.997	D;D;D;D	0.87578	0.998;0.998;0.991;0.98	T	0.06826	-1.0805	9	0.87932	D	0	.	15.0845	0.72142	0.0:0.0:0.0:1.0	.	4873;4873;294;361	Q9Y6V0-5;Q9Y6V0-6;Q9Y6V0-3;Q32P40	.;.;.;.	A	4873;4873;360	ENSP00000334319:E4873A;ENSP00000388393:E4873A	ENSP00000334319:E4873A	E	-	2	0	PCLO	82289920	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.619000	0.83057	2.023000	0.59567	0.533000	0.62120	GAG	.	.	none		0.438	PCLO-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000337368.5	NM_014510	
SYT15	83849	hgsc.bcm.edu	37	10	46967514	46967514	+	Missense_Mutation	SNP	T	T	C			TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr10:46967514T>C	ENST00000374321.4	-	4	629	c.563A>G	c.(562-564)tAc>tGc	p.Y188C	SYT15_ENST00000503753.1_Missense_Mutation_p.Y188C|RP11-38L15.3_ENST00000506914.1_RNA|SYT15_ENST00000374323.4_Missense_Mutation_p.Y241C|SYT15_ENST00000374325.3_Missense_Mutation_p.Y188C	NM_031912.4	NP_114118.2	Q9BQS2	SYT15_HUMAN	synaptotagmin XV	188	C2 1. {ECO:0000255|PROSITE- ProRule:PRU00041}.					integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				cervix(1)|endometrium(5)|kidney(2)|lung(5)	13						GGGCAGCAGGTAGAGCTTCAC	0.592																																					p.Y188C	Ovarian(57;1152 1428 19651 37745)	Atlas-SNP	.											.	SYT15	165	.	0			c.A563G						PASS	.						68.0	81.0	77.0					10																	46967514		2071	4211	6282	SO:0001583	missense	83849	exon4			AGCAGGTAGAGCT	AJ303363	CCDS73103.1, CCDS73104.1	10q11.1	2013-01-21			ENSG00000204176	ENSG00000204176		"""Synaptotagmins"""	17167	protein-coding gene	gene with protein product		608081				11543631	Standard	NM_031912		Approved	CHR10SYT	uc001jea.3	Q9BQS2	OTTHUMG00000018103	ENST00000374321.4:c.563A>G	10.37:g.46967514T>C	ENSP00000363441:p.Tyr188Cys	141.0	0.0	0		145.0	15.0	0.103448	NM_031912	A5D6W8|Q5VY53|Q5VY55|Q7Z439|Q7Z440	Missense_Mutation	SNP	ENST00000374321.4	37	CCDS44376.1	.	.	.	.	.	.	.	.	.	.	.	15.71	2.913590	0.52439	.	.	ENSG00000204176	ENST00000416127;ENST00000374325;ENST00000503753;ENST00000374330;ENST00000374323;ENST00000374321;ENST00000512997	T;T;T;T;T	0.09073	3.02;3.02;3.02;3.02;3.02	4.92	4.92	0.64577	C2 membrane targeting protein (1);C2 calcium-dependent membrane targeting (2);C2 calcium/lipid-binding domain, CaLB (1);	0.238169	0.42964	D	0.000627	T	0.09818	0.0241	L	0.51914	1.62	0.34918	D	0.748104	B;B	0.20550	0.005;0.046	B;B	0.21708	0.013;0.036	T	0.12400	-1.0549	9	.	.	.	.	12.8277	0.57728	0.0:0.0:0.0:1.0	.	188;188	Q9BQS2;Q9BQS2-2	SYT15_HUMAN;.	C	188;188;188;27;241;188;72	ENSP00000363445:Y188C;ENSP00000427607:Y188C;ENSP00000363443:Y241C;ENSP00000363441:Y188C;ENSP00000424803:Y72C	.	Y	-	2	0	SYT15	46387520	1.000000	0.71417	0.996000	0.52242	0.871000	0.50021	5.085000	0.64468	1.974000	0.57490	0.533000	0.62120	TAC	.	.	none		0.592	SYT15-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000367008.1	NM_031912	
CTNS	1497	hgsc.bcm.edu	37	17	3563221	3563221	+	Missense_Mutation	SNP	G	G	A			TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr17:3563221G>A	ENST00000046640.3	+	11	1515	c.922G>A	c.(922-924)Ggg>Agg	p.G308R	CTNS_ENST00000381870.3_Missense_Mutation_p.G308R|CTNS_ENST00000441220.2_Missense_Mutation_p.G200R|CTNS_ENST00000414524.2_Missense_Mutation_p.G161R|RP11-235E17.6_ENST00000575741.1_RNA	NM_004937.2	NP_004928.2	O60931	CTNS_HUMAN	cystinosin, lysosomal cystine transporter	308	PQ-loop 2.		G -> R (in CTNS). {ECO:0000269|PubMed:10556299, ECO:0000269|PubMed:12825071, ECO:0000269|PubMed:9792862}.|G -> V (in CTNS). {ECO:0000269|PubMed:12204010}.		adult walking behavior (GO:0007628)|ATP metabolic process (GO:0046034)|brain development (GO:0007420)|cellular amino acid metabolic process (GO:0006520)|cognition (GO:0050890)|glutathione metabolic process (GO:0006749)|grooming behavior (GO:0007625)|L-cystine transport (GO:0015811)|lens development in camera-type eye (GO:0002088)|long-term memory (GO:0007616)|visual learning (GO:0008542)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|intermediate filament cytoskeleton (GO:0045111)|intracellular membrane-bounded organelle (GO:0043231)|late endosome (GO:0005770)|lysosomal membrane (GO:0005765)|lysosome (GO:0005764)|plasma membrane (GO:0005886)	L-cystine transmembrane transporter activity (GO:0015184)			NS(1)|cervix(1)|endometrium(3)|kidney(1)|large_intestine(2)|lung(2)	10				COAD - Colon adenocarcinoma(5;0.0829)	L-Cystine(DB00138)	GGACTTCACCGGGGGCAGCTT	0.617																																					p.G308R		Atlas-SNP	.											.	CTNS	42	.	0			c.G922A	GRCh37	CM980460	CTNS	M		PASS	.						59.0	57.0	58.0					17																	3563221		2203	4300	6503	SO:0001583	missense	1497	exon11			TTCACCGGGGGCA	AJ222967	CCDS11031.1, CCDS32530.1	17p13	2011-06-07	2011-06-07		ENSG00000040531	ENSG00000040531			2518	protein-coding gene	gene with protein product		606272	"""cystinosis, nephropathic"""			9537412, 15128704	Standard	NM_004937		Approved	CTNS-LSB, PQLC4	uc002fwa.3	O60931	OTTHUMG00000090693	ENST00000046640.3:c.922G>A	17.37:g.3563221G>A	ENSP00000046640:p.Gly308Arg	134.0	0.0	0		174.0	46.0	0.264368	NM_001031681	D3DTJ5|Q8IZ01|Q9UNK6	Missense_Mutation	SNP	ENST00000046640.3	37	CCDS11031.1	.	.	.	.	.	.	.	.	.	.	g	35	5.491019	0.96339	.	.	ENSG00000040531	ENST00000046640;ENST00000381870;ENST00000441220;ENST00000414524	D;D;D;D	0.99507	-6.04;-6.04;-6.04;-6.04	5.41	5.41	0.78517	.	0.000000	0.85682	D	0.000000	D	0.99684	0.9881	H	0.94345	3.525	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.97110	1.0;1.0;1.0	D	0.97688	1.0177	10	0.87932	D	0	-16.3759	18.5632	0.91108	0.0:0.0:1.0:0.0	.	200;308;308	F8W6Z1;O60931;O60931-2	.;CTNS_HUMAN;.	R	308;308;200;161	ENSP00000046640:G308R;ENSP00000371294:G308R;ENSP00000411465:G200R;ENSP00000395471:G161R	ENSP00000046640:G308R	G	+	1	0	CTNS	3509970	1.000000	0.71417	0.967000	0.41034	0.984000	0.73092	9.168000	0.94781	2.712000	0.92718	0.561000	0.74099	GGG	.	.	none		0.617	CTNS-001	KNOWN	upstream_ATG|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000317696.1	NM_004937	
CELA1	1990	hgsc.bcm.edu	37	12	51739625	51739625	+	Missense_Mutation	SNP	C	C	T	rs74336876	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr12:51739625C>T	ENST00000293636.1	-	2	93	c.53G>A	c.(52-54)cGc>cAc	p.R18H		NM_001971.5	NP_001962.3	Q9UNI1	CELA1_HUMAN	chymotrypsin-like elastase family, member 1	18					exocrine pancreas development (GO:0031017)|inflammatory response (GO:0006954)|multicellular organism growth (GO:0035264)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|pancreas morphogenesis (GO:0061113)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|post-embryonic development (GO:0009791)|regulation of cell differentiation (GO:0045595)|regulation of cell proliferation (GO:0042127)|Wnt signaling pathway (GO:0016055)	extracellular region (GO:0005576)	metal ion binding (GO:0046872)|serine-type endopeptidase activity (GO:0004252)			NS(1)|breast(3)|endometrium(2)|large_intestine(3)|lung(4)|ovary(1)|stomach(1)	15						TCCGACTACGCGGGCATTGGT	0.592													C|||	14	0.00279553	0.0	0.0043	5008	,	,		15127	0.0		0.0089	False		,,,				2504	0.002				p.R18H		Atlas-SNP	.											.	CELA1	39	.	0			c.G53A						PASS	.	C	HIS/ARG	12,4382		0,12,2185	58.0	52.0	54.0		53	5.0	1.0	12	dbSNP_131	54	66,8516		0,66,4225	yes	missense	CELA1	NM_001971.5	29	0,78,6410	TT,TC,CC		0.7691,0.2731,0.6011	probably-damaging	18/259	51739625	78,12898	2197	4291	6488	SO:0001583	missense	1990	exon2			ACTACGCGGGCAT		CCDS8812.1	12q13	2012-10-02	2009-05-05	2009-05-05	ENSG00000139610	ENSG00000139610			3308	protein-coding gene	gene with protein product		130120	"""elastase 1, pancreatic"""	ELA1			Standard	NM_001971		Approved		uc001ryi.1	Q9UNI1	OTTHUMG00000167523	ENST00000293636.1:c.53G>A	12.37:g.51739625C>T	ENSP00000293636:p.Arg18His	66.0	0.0	0		53.0	26.0	0.490566	NM_001971	Q5MLF0|Q6DJT0|Q6ISM6	Missense_Mutation	SNP	ENST00000293636.1	37	CCDS8812.1	8	0.003663003663003663	0	0.0	1	0.0027624309392265192	0	0.0	7	0.009234828496042216	C	27.9	4.875832	0.91664	0.002731	0.007691	ENSG00000139610	ENST00000293636	D	0.94966	-3.57	5.03	5.03	0.67393	Peptidase cysteine/serine, trypsin-like (1);Peptidase S1/S6, chymotrypsin/Hap (1);	0.000000	0.85682	D	0.000000	D	0.95950	0.8681	M	0.76002	2.32	0.58432	D	0.999999	D	0.89917	1.0	D	0.91635	0.999	D	0.95423	0.8509	10	0.87932	D	0	-29.8305	17.5406	0.87846	0.0:1.0:0.0:0.0	.	18	Q9UNI1	CELA1_HUMAN	H	18	ENSP00000293636:R18H	ENSP00000293636:R18H	R	-	2	0	CELA1	50025892	0.999000	0.42202	0.998000	0.56505	0.793000	0.44817	6.004000	0.70709	2.503000	0.84419	0.563000	0.77884	CGC	C|0.995;T|0.005	0.005	strong		0.592	CELA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000394901.1	NM_001971	
TRPM5	29850	hgsc.bcm.edu	37	11	2436464	2436464	+	Missense_Mutation	SNP	C	C	T	rs34551253	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr11:2436464C>T	ENST00000155858.6	-	9	1374	c.1366G>A	c.(1366-1368)Gcg>Acg	p.A456T	TRPM5_ENST00000452833.1_Missense_Mutation_p.A458T|TRPM5_ENST00000533060.1_Missense_Mutation_p.A456T|TRPM5_ENST00000528453.1_Missense_Mutation_p.A456T	NM_014555.3	NP_055370.1			transient receptor potential cation channel, subfamily M, member 5											breast(1)|central_nervous_system(1)|endometrium(4)|liver(1)|lung(8)|ovary(2)|prostate(2)|skin(2)|urinary_tract(2)	23		Medulloblastoma(188;0.0049)|Breast(177;0.00586)|all_epithelial(84;0.0075)|Ovarian(85;0.0256)|all_neural(188;0.0311)		BRCA - Breast invasive adenocarcinoma(625;0.00147)|LUSC - Lung squamous cell carcinoma(625;0.191)		GGTGGCCCCGCGGGTGGCTCC	0.716													C|||	54	0.0107827	0.0023	0.0245	5008	,	,		13476	0.001		0.0308	False		,,,				2504	0.002				p.A456T	NSCLC(1;49 61 17205 18850 43201)	Atlas-SNP	.											.	TRPM5	86	.	0			c.G1366A						PASS	.	C	THR/ALA	35,4235		1,33,2101	7.0	9.0	9.0		1366	-6.4	0.0	11	dbSNP_126	9	273,8141		6,261,3940	yes	missense	TRPM5	NM_014555.3	58	7,294,6041	TT,TC,CC		3.2446,0.8197,2.4283	benign	456/1166	2436464	308,12376	2135	4207	6342	SO:0001583	missense	29850	exon9			GCCCCGCGGGTGG	AF177473	CCDS31340.1	11p15.5	2011-12-14			ENSG00000070985	ENSG00000070985		"""Voltage-gated ion channels / Transient receptor potential cation channels"""	14323	protein-coding gene	gene with protein product		604600				10607831, 16382100	Standard	NM_014555		Approved	LTRPC5, MTR1	uc001lwm.4	Q9NZQ8	OTTHUMG00000009896	ENST00000155858.6:c.1366G>A	11.37:g.2436464C>T	ENSP00000155858:p.Ala456Thr	15.0	0.0	0		10.0	6.0	0.6	NM_014555		Missense_Mutation	SNP	ENST00000155858.6	37	CCDS31340.1	35	0.016025641025641024	1	0.0020325203252032522	12	0.03314917127071823	0	0.0	22	0.029023746701846966	C	0.009	-1.820965	0.00595	0.008197	0.032446	ENSG00000070985	ENST00000533881;ENST00000155858;ENST00000452833;ENST00000533060;ENST00000528453;ENST00000437542	T;T;T;T;T	0.68181	-0.31;-0.31;-0.31;-0.31;-0.31	3.19	-6.37	0.01963	.	1.134030	0.06672	N	0.766349	T	0.14227	0.0344	N	0.08118	0	0.09310	N	1	B;B;B	0.13594	0.005;0.005;0.008	B;B;B	0.09377	0.002;0.001;0.004	T	0.05517	-1.0880	10	0.14252	T	0.57	0.2166	1.5474	0.02568	0.2706:0.3676:0.1989:0.1629	rs34551253	456;458;456	E9PRW0;Q9NZQ8-2;Q9NZQ8	.;.;TRPM5_HUMAN	T	450;456;458;456;456;456	ENSP00000434383:A450T;ENSP00000155858:A456T;ENSP00000387965:A458T;ENSP00000434121:A456T;ENSP00000436809:A456T	ENSP00000155858:A456T	A	-	1	0	TRPM5	2393040	0.000000	0.05858	0.000000	0.03702	0.011000	0.07611	-2.025000	0.01435	-3.859000	0.00098	-1.579000	0.00862	GCG	C|0.983;T|0.017	0.017	strong		0.716	TRPM5-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000027378.1	NM_014555	
MRGPRF	116535	hgsc.bcm.edu	37	11	68773089	68773089	+	Missense_Mutation	SNP	C	C	T	rs151254404		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr11:68773089C>T	ENST00000309099.6	-	3	1071	c.689G>A	c.(688-690)cGg>cAg	p.R230Q	RP11-554A11.5_ENST00000562506.1_RNA|MRGPRF_ENST00000441623.1_Missense_Mutation_p.R230Q	NM_145015.4	NP_659452.3	Q96AM1	MRGRF_HUMAN	MAS-related GPR, member F	230						extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)			endometrium(3)|lung(4)	7			STAD - Stomach adenocarcinoma(18;0.0208)|LUAD - Lung adenocarcinoma(13;0.0713)			GCGCTGGCGCCGTCGGGCCCG	0.627																																					p.R230Q		Atlas-SNP	.											.	MRGPRF	22	.	0			c.G689A						PASS	.	C	GLN/ARG,GLN/ARG	0,4368		0,0,2184	33.0	26.0	28.0		689,689	3.3	0.9	11	dbSNP_134	28	4,8528		0,4,4262	yes	missense,missense	MRGPRF	NM_001098515.1,NM_145015.4	43,43	0,4,6446	TT,TC,CC		0.0469,0.0,0.031	probably-damaging,probably-damaging	230/344,230/344	68773089	4,12896	2184	4266	6450	SO:0001583	missense	116535	exon3			TGGCGCCGTCGGG	AK075492	CCDS8188.1	11q13.1	2014-03-13	2004-03-25		ENSG00000172935	ENSG00000172935		"""GPCR / Class A : Orphans"""	24828	protein-coding gene	gene with protein product		607233	"""G protein-coupled receptor 168"", ""G protein-coupled receptor 140"""	GPR168, GPR140		12477932	Standard	NM_001098515		Approved	MGC21621, mrgF	uc001oop.4	Q96AM1	OTTHUMG00000167897	ENST00000309099.6:c.689G>A	11.37:g.68773089C>T	ENSP00000309782:p.Arg230Gln	122.0	0.0	0		118.0	56.0	0.474576	NM_001098515	B3KV43|Q8NBK8	Missense_Mutation	SNP	ENST00000309099.6	37	CCDS8188.1	.	.	.	.	.	.	.	.	.	.	C	12.99	2.103907	0.37145	0.0	4.69E-4	ENSG00000172935	ENST00000441623;ENST00000309099;ENST00000421543	T;T	0.43294	0.95;0.95	5.25	3.27	0.37495	GPCR, rhodopsin-like superfamily (1);	0.000000	0.39146	N	0.001445	T	0.27765	0.0683	L	0.54323	1.7	0.25460	N	0.987926	P	0.38827	0.649	B	0.30572	0.117	T	0.10917	-1.0609	10	0.14656	T	0.56	-24.2612	6.393	0.21597	0.0:0.7165:0.1856:0.0979	.	230	Q96AM1	MRGRF_HUMAN	Q	230;230;202	ENSP00000403660:R230Q;ENSP00000309782:R230Q	ENSP00000309782:R230Q	R	-	2	0	MRGPRF	68529665	0.064000	0.20934	0.913000	0.36048	0.963000	0.63663	0.101000	0.15251	1.215000	0.43411	0.561000	0.74099	CGG	C|1.000;T|0.000	0.000	weak		0.627	MRGPRF-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000396875.1	NM_145015	
CCDC159	126075	hgsc.bcm.edu	37	19	11465311	11465311	+	Silent	SNP	C	C	T	rs374274390	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr19:11465311C>T	ENST00000588790.1	+	12	1275	c.828C>T	c.(826-828)tcC>tcT	p.S276S	DKFZP761J1410_ENST00000251473.5_5'Flank|DKFZP761J1410_ENST00000591608.1_5'Flank|CCDC159_ENST00000458408.1_Silent_p.S276S			P0C7I6	CC159_HUMAN	coiled-coil domain containing 159	391										endometrium(1)|large_intestine(1)|lung(2)|ovary(1)	5						ACTCTGACTCCGACTGTGACC	0.647													C|||	3	0.000599042	0.0	0.0	5008	,	,		16082	0.0		0.002	False		,,,				2504	0.001				p.S276S		Atlas-SNP	.											.	CCDC159	35	.	0			c.C828T						PASS	.	C		3,4397		0,3,2197	31.0	39.0	36.0		828	-8.8	0.0	19		36	33,8555		0,33,4261	no	coding-synonymous	CCDC159	NM_001080503.2		0,36,6458	TT,TC,CC		0.3843,0.0682,0.2772		276/298	11465311	36,12952	2200	4294	6494	SO:0001819	synonymous_variant	126075	exon10			TGACTCCGACTGT	BC038439	CCDS45976.1	19p13.2	2010-02-17			ENSG00000183401	ENSG00000183401			26996	protein-coding gene	gene with protein product							Standard	NM_001080503		Approved		uc010xlt.2	P0C7I6		ENST00000588790.1:c.828C>T	19.37:g.11465311C>T		133.0	0.0	0		124.0	59.0	0.475806	NM_001080503	B4DEG3|B4DWR8|B4E133|B7ZAM4	Silent	SNP	ENST00000588790.1	37	CCDS45976.1																																																																																			.	.	weak		0.647	CCDC159-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000458761.1	NM_001080503	
MUC17	140453	hgsc.bcm.edu	37	7	100678693	100678693	+	Silent	SNP	T	T	C	rs78176991	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr7:100678693T>C	ENST00000306151.4	+	3	4060	c.3996T>C	c.(3994-3996)taT>taC	p.Y1332Y		NM_001040105.1	NP_001035194.1	Q685J3	MUC17_HUMAN	mucin 17, cell surface associated	1332	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)					CCTCAACTTATAGTGAAGGAA	0.448																																					p.Y1332Y		Atlas-SNP	.											.	MUC17	804	.	0			c.T3996C						PASS	.						241.0	232.0	235.0					7																	100678693		2203	4300	6503	SO:0001819	synonymous_variant	140453	exon3			AACTTATAGTGAA	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.3996T>C	7.37:g.100678693T>C		200.0	0.0	0		264.0	39.0	0.147727	NM_001040105	O14761|Q685J2|Q8TDH7	Silent	SNP	ENST00000306151.4	37	CCDS34711.1																																																																																			T|0.994;C|0.006	0.006	strong		0.448	MUC17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347161.1	NM_001040105	
CEP164	22897	hgsc.bcm.edu	37	11	117222691	117222691	+	Missense_Mutation	SNP	C	C	A	rs143659874	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr11:117222691C>A	ENST00000278935.3	+	5	527	c.380C>A	c.(379-381)cCc>cAc	p.P127H		NM_001271933.1|NM_014956.4	NP_001258862.1|NP_055771.4	Q9UPV0	CE164_HUMAN	centrosomal protein 164kDa	127	Interaction with ATRIP.				cilium assembly (GO:0042384)|DNA repair (GO:0006281)|G2/M transition of mitotic cell cycle (GO:0000086)|mitotic cell cycle (GO:0000278)|mitotic nuclear division (GO:0007067)	centriole (GO:0005814)|centrosome (GO:0005813)|ciliary transition fiber (GO:0097539)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular space (GO:0005615)|nucleus (GO:0005634)				breast(3)|central_nervous_system(1)|kidney(7)|large_intestine(12)|lung(18)|ovary(3)|prostate(3)	47	all_hematologic(175;0.0487)	Breast(348;0.00908)|Medulloblastoma(222;0.0425)|all_hematologic(192;0.196)|all_neural(223;0.234)		BRCA - Breast invasive adenocarcinoma(274;4e-05)|Epithelial(105;0.0008)		AGAGACCCCCCCAAAAGTTCG	0.517													C|||	9	0.00179712	0.0	0.0014	5008	,	,		16611	0.0		0.008	False		,,,				2504	0.0				p.P127H		Atlas-SNP	.											.	CEP164	121	.	0			c.C380A						PASS	.	C	HIS/PRO	3,4385		0,3,2191	21.0	23.0	22.0		380	4.9	0.1	11	dbSNP_134	22	39,8503		0,39,4232	yes	missense	CEP164	NM_014956.4	77	0,42,6423	AA,AC,CC		0.4566,0.0684,0.3248	possibly-damaging	127/1461	117222691	42,12888	2194	4271	6465	SO:0001583	missense	22897	exon4			ACCCCCCCAAAAG	AB028975	CCDS31683.1	11q23.3	2014-02-20			ENSG00000110274	ENSG00000110274			29182	protein-coding gene	gene with protein product		614848				10470851, 14654843	Standard	NM_014956		Approved	KIAA1052, NPHP15	uc001prc.3	Q9UPV0	OTTHUMG00000167070	ENST00000278935.3:c.380C>A	11.37:g.117222691C>A	ENSP00000278935:p.Pro127His	35.0	0.0	0		49.0	38.0	0.77551	NM_001271933	Q6PKH9|Q7Z2X9|Q9NVS0|Q9UFJ6	Missense_Mutation	SNP	ENST00000278935.3	37	CCDS31683.1	7	0.003205128205128205	0	0.0	1	0.0027624309392265192	0	0.0	6	0.0079155672823219	C	10.48	1.362097	0.24684	6.84E-4	0.004566	ENSG00000110274	ENST00000533153;ENST00000278935;ENST00000525416;ENST00000545330;ENST00000529538	T;T;T	0.63744	-0.05;0.32;-0.06	5.81	4.89	0.63831	.	1.313720	0.05171	N	0.499480	T	0.60945	0.2308	L	0.36672	1.1	0.09310	N	1	P;P;D;P	0.63046	0.947;0.906;0.992;0.924	B;B;P;P	0.53146	0.36;0.258;0.719;0.562	T	0.57551	-0.7792	9	.	.	.	-0.0023	14.4821	0.67590	0.0:0.6025:0.3975:0.0	.	127;81;127;127	E9PI34;B7Z884;Q9UPV0;Q9UPV0-2	.;.;CE164_HUMAN;.	H	81;127;81;81;127	ENSP00000436034:P81H;ENSP00000278935:P127H;ENSP00000435759:P81H	.	P	+	2	0	CEP164	116727901	0.001000	0.12720	0.138000	0.22173	0.013000	0.08279	1.218000	0.32467	1.422000	0.47177	0.655000	0.94253	CCC	C|0.998;A|0.002	0.002	strong		0.517	CEP164-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000392893.1	NM_014956	
FAM46C	54855	hgsc.bcm.edu	37	1	118166385	118166385	+	Missense_Mutation	SNP	G	G	A	rs145471785	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr1:118166385G>A	ENST00000369448.3	+	2	1142	c.895G>A	c.(895-897)Gaa>Aaa	p.E299K		NM_017709.3	NP_060179.2	Q5VWP2	FA46C_HUMAN	family with sequence similarity 46, member C	299										endometrium(3)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(1)|lung(7)|ovary(1)|upper_aerodigestive_tract(1)	15	Lung SC(450;0.225)	all_cancers(81;0.000101)|all_lung(203;3.4e-06)|all_epithelial(167;4.98e-06)|Lung NSC(69;2.33e-05)		Lung(183;0.0576)|LUSC - Lung squamous cell carcinoma(189;0.192)|Colorectal(144;0.247)		CTTCGCTGAAGAAGAGAGAAG	0.517			"""Mis, F, O"""		MM					Multiple Myeloma(3;1.13e-06)			G|||	13	0.00259585	0.0	0.0029	5008	,	,		22262	0.0		0.0089	False		,,,				2504	0.002				p.E299K		Atlas-SNP	.		Rec	yes		1	1p12	54855	"""family with sequence similarity 46, member C"""		L	.	FAM46C	25	.	0			c.G895A						PASS	.	G	LYS/GLU	5,4401	9.9+/-24.2	0,5,2198	123.0	116.0	118.0		895	5.7	0.9	1	dbSNP_134	118	91,8509	51.1+/-111.2	1,89,4210	yes	missense	FAM46C	NM_017709.3	56	1,94,6408	AA,AG,GG		1.0581,0.1135,0.7381	possibly-damaging	299/392	118166385	96,12910	2203	4300	6503	SO:0001583	missense	54855	exon2			GCTGAAGAAGAGA	BC036516	CCDS896.1	1p12	2008-02-05			ENSG00000183508	ENSG00000183508			24712	protein-coding gene	gene with protein product		613952				12477932	Standard	NM_017709		Approved	FLJ20202	uc001ehe.3	Q5VWP2	OTTHUMG00000013703	ENST00000369448.3:c.895G>A	1.37:g.118166385G>A	ENSP00000358458:p.Glu299Lys	113.0	0.0	0		53.0	39.0	0.735849	NM_017709	A3KMG2|Q8NE25|Q9NXK0	Missense_Mutation	SNP	ENST00000369448.3	37	CCDS896.1	11	0.005036630036630037	0	0.0	2	0.0055248618784530384	0	0.0	9	0.011873350923482849	G	22.3	4.273089	0.80580	0.001135	0.010581	ENSG00000183508	ENST00000369448	T	0.22945	1.93	5.7	5.7	0.88788	Domain of unknown function DUF1693 (1);	0.079249	0.51477	D	0.000094	T	0.27454	0.0674	M	0.79693	2.465	0.80722	D	1	B	0.26902	0.163	B	0.34452	0.183	T	0.05131	-1.0904	10	0.33940	T	0.23	-11.7413	18.8168	0.92079	0.0:0.0:1.0:0.0	.	299	Q5VWP2	FA46C_HUMAN	K	299	ENSP00000358458:E299K	ENSP00000358458:E299K	E	+	1	0	FAM46C	117967908	1.000000	0.71417	0.894000	0.35097	0.979000	0.70002	5.244000	0.65400	2.686000	0.91538	0.655000	0.94253	GAA	G|0.995;A|0.005	0.005	strong		0.517	FAM46C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000038424.1	NM_017709	
THTPA	79178	hgsc.bcm.edu	37	14	24026046	24026046	+	Missense_Mutation	SNP	G	G	A			TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr14:24026046G>A	ENST00000288014.6	+	1	816	c.80G>A	c.(79-81)gGc>gAc	p.G27D	THTPA_ENST00000554789.1_Missense_Mutation_p.G27D|RP11-66N24.4_ENST00000553985.1_RNA|RP11-66N24.4_ENST00000555446.1_RNA|THTPA_ENST00000404535.3_Missense_Mutation_p.G27D|RP11-66N24.4_ENST00000556354.1_RNA|THTPA_ENST00000554970.1_Missense_Mutation_p.G27D|THTPA_ENST00000556015.1_Missense_Mutation_p.G27D			Q9BU02	THTPA_HUMAN	thiamine triphosphatase	27	CYTH. {ECO:0000255|PROSITE- ProRule:PRU01044}.				dephosphorylation (GO:0016311)|generation of precursor metabolites and energy (GO:0006091)|small molecule metabolic process (GO:0044281)|thiamine diphosphate metabolic process (GO:0042357)|thiamine metabolic process (GO:0006772)|thiamine-containing compound metabolic process (GO:0042723)|vitamin metabolic process (GO:0006766)|water-soluble vitamin metabolic process (GO:0006767)	cytosol (GO:0005829)	hydrolase activity (GO:0016787)|magnesium ion binding (GO:0000287)|thiamin-triphosphatase activity (GO:0050333)			large_intestine(1)|prostate(2)	3	all_cancers(95;0.000251)			GBM - Glioblastoma multiforme(265;0.00643)		GAGTTGGGGGGCACCCTGGAG	0.607																																					p.G27D		Atlas-SNP	.											.	THTPA	11	.	0			c.G80A						PASS	.						53.0	43.0	46.0					14																	24026046		2203	4300	6503	SO:0001583	missense	79178	exon2			TGGGGGGCACCCT	AF432862	CCDS32053.1, CCDS58306.1, CCDS58307.1	14q11.2	2011-04-28					3.6.1.28		18987	protein-coding gene	gene with protein product		611612				11827967	Standard	NR_046051		Approved	THTPASE	uc001wkh.5	Q9BU02		ENST00000288014.6:c.80G>A	14.37:g.24026046G>A	ENSP00000288014:p.Gly27Asp	126.0	0.0	0		158.0	93.0	0.588608	NM_001256321	D3DS50|G3V4J3	Missense_Mutation	SNP	ENST00000288014.6	37	CCDS32053.1	.	.	.	.	.	.	.	.	.	.	G	19.29	3.799652	0.70567	.	.	ENSG00000157306	ENST00000404535;ENST00000288014;ENST00000557630;ENST00000556015;ENST00000554970;ENST00000554789	T;T;T;T;T;T	0.49139	0.79;0.79;0.79;0.79;0.79;0.79	5.91	0.674	0.17946	CYTH domain (2);CYTH-like domain (1);	0.428933	0.25484	N	0.030357	T	0.66268	0.2772	M	0.76170	2.325	0.28533	N	0.91246	P;D	0.56746	0.928;0.977	P;P	0.60473	0.564;0.875	T	0.71155	-0.4675	10	0.62326	D	0.03	-1.7363	20.3036	0.98618	0.0:0.7093:0.2907:0.0	.	27;27	G3V4J3;Q9BU02	.;THTPA_HUMAN	D	27	ENSP00000384580:G27D;ENSP00000288014:G27D;ENSP00000452281:G27D;ENSP00000451835:G27D;ENSP00000452465:G27D;ENSP00000450459:G27D	ENSP00000288014:G27D	G	+	2	0	THTPA	23095886	0.623000	0.27094	0.764000	0.31436	0.880000	0.50808	0.727000	0.25999	-0.142000	0.11354	0.655000	0.94253	GGC	.	.	none		0.607	THTPA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000413800.2		
LIN9	286826	hgsc.bcm.edu	37	1	226474035	226474035	+	Splice_Site	SNP	T	T	C			TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr1:226474035T>C	ENST00000328205.5	-	6	1116	c.571A>G	c.(571-573)Aga>Gga	p.R191G	LIN9_ENST00000481685.1_Splice_Site_p.R156G|LIN9_ENST00000366801.1_Splice_Site_p.R140G	NM_173083.3	NP_775106.2	Q5TKA1	LIN9_HUMAN	lin-9 DREAM MuvB core complex component	175	Sufficient for interaction with RB1.				DNA replication (GO:0006260)|G2/M transition of mitotic cell cycle (GO:0000086)|mitotic cell cycle (GO:0000278)|regulation of cell cycle (GO:0051726)|transcription, DNA-templated (GO:0006351)	nucleoplasm (GO:0005654)|transcriptional repressor complex (GO:0017053)				breast(3)|endometrium(4)|kidney(2)|large_intestine(6)|lung(9)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	28	Breast(184;0.158)			GBM - Glioblastoma multiforme(131;0.131)		TATTTTTACCTCCGTGGTTTT	0.348																																					p.R191G	Ovarian(197;1696 2974 11248 14117)	Atlas-SNP	.											.	LIN9	57	.	0			c.A571G						PASS	.						50.0	55.0	53.0					1																	226474035		2202	4298	6500	SO:0001630	splice_region_variant	286826	exon6			TTTACCTCCGTGG	AY166858	CCDS1553.1	1q42	2014-07-17	2014-07-17		ENSG00000183814	ENSG00000183814			30830	protein-coding gene	gene with protein product	"""TUDOR gene similar"", ""rb related pathway actor"""	609375	"""lin-9 homolog (C. elegans)"""			15538385, 23667535	Standard	NM_173083		Approved	TGS	uc001hqa.3	Q5TKA1	OTTHUMG00000037557	ENST00000328205.5:c.572+1A>G	1.37:g.226474035T>C		79.0	0.0	0		99.0	5.0	0.050505	NM_173083	Q5U5L8|Q5U7E1|Q6PI55|Q6ZTV4|Q7Z3J1	Missense_Mutation	SNP	ENST00000328205.5	37	CCDS1553.1	.	.	.	.	.	.	.	.	.	.	T	16.75	3.208799	0.58343	.	.	ENSG00000183814	ENST00000460719;ENST00000328205;ENST00000366808;ENST00000366801;ENST00000481685;ENST00000366807	.	.	.	5.85	5.85	0.93711	.	0.042455	0.85682	D	0.000000	D	0.86033	0.5836	M	0.93062	3.375	0.80722	D	1	D;P;D	0.62365	0.989;0.884;0.991	D;P;D	0.78314	0.916;0.891;0.991	D	0.89383	0.3683	9	0.87932	D	0	.	16.2265	0.82298	0.0:0.0:0.0:1.0	.	156;175;325	C9J5J4;Q5TKA1;B1ANK3	.;LIN9_HUMAN;.	G	151;191;246;140;156;325	.	ENSP00000329102:R191G	R	-	1	2	LIN9	224540658	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	4.751000	0.62169	2.233000	0.73108	0.533000	0.62120	AGA	.	.	none		0.348	LIN9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000091523.2	NM_173083	Missense_Mutation
GPR162	27239	hgsc.bcm.edu	37	12	6935995	6935995	+	Missense_Mutation	SNP	G	G	A	rs138514784|rs138578985|rs58069762	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr12:6935995G>A	ENST00000311268.3	+	5	2180	c.1393G>A	c.(1393-1395)Gag>Aag	p.E465K	LEPREL2_ENST00000396725.2_RNA|LEPREL2_ENST00000606935.1_RNA|LEPREL2_ENST00000251761.8_RNA|GPR162_ENST00000382315.3_Missense_Mutation_p.E161K|GPR162_ENST00000428545.2_Missense_Mutation_p.E181K	NM_019858.1	NP_062832.1	Q16538	GP162_HUMAN	G protein-coupled receptor 162	465						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						GTTGGAGGACGAGGAGGACGA	0.652																																					p.E465K		Atlas-SNP	.											GPR162,bladder,carcinoma,0,1	GPR162	55	1	0			c.G1393A						scavenged	.	G	LYS/GLU,LYS/GLU	1,4405	2.1+/-5.4	0,1,2202	50.0	62.0	58.0		541,1393	3.8	0.9	12	dbSNP_134	58	3,8597	3.0+/-9.4	0,3,4297	yes	missense,missense	GPR162	NM_014449.1,NM_019858.1	56,56	0,4,6499	AA,AG,GG		0.0349,0.0227,0.0308	benign,benign	181/305,465/589	6935995	4,13002	2203	4300	6503	SO:0001583	missense	27239	exon5			GAGGACGAGGAGG	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.1393G>A	12.37:g.6935995G>A	ENSP00000311528:p.Glu465Lys	76.0	1.0	0.0131579		97.0	57.0	0.587629	NM_019858	Q16664|Q59EH5|Q66K56	Missense_Mutation	SNP	ENST00000311268.3	37	CCDS8563.1	.	.	.	.	.	.	.	.	.	.	G	7.227	0.598598	0.13939	2.27E-4	3.49E-4	ENSG00000250510	ENST00000311268;ENST00000428545;ENST00000382315	T;T;T	0.43688	3.1;0.94;0.94	4.7	3.79	0.43588	.	.	.	.	.	T	0.21145	0.0509	N	0.08118	0	0.22389	N	0.999148	B;B	0.27679	0.133;0.185	B;B	0.18561	0.022;0.013	T	0.10776	-1.0615	9	0.36615	T	0.2	.	7.9273	0.29883	0.0:0.268:0.5194:0.2126	.	181;465	Q16538-2;Q16538	.;GP162_HUMAN	K	465;181;161	ENSP00000311528:E465K;ENSP00000399670:E181K;ENSP00000371752:E161K	ENSP00000311528:E465K	E	+	1	0	GPR162	6806256	0.985000	0.35326	0.882000	0.34594	0.215000	0.24574	2.459000	0.45023	1.299000	0.44798	0.491000	0.48974	GAG	G|1.000;A|0.000	0.000	weak		0.652	GPR162-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000399478.1	NM_019858	
HIVEP3	59269	hgsc.bcm.edu	37	1	41978959	41978959	+	Missense_Mutation	SNP	C	C	T	rs144265546		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr1:41978959C>T	ENST00000372583.1	-	8	6818	c.5933G>A	c.(5932-5934)cGt>cAt	p.R1978H	HIVEP3_ENST00000429157.2_Missense_Mutation_p.R1978H|HIVEP3_ENST00000372584.1_Missense_Mutation_p.R1978H|HIVEP3_ENST00000247584.5_Missense_Mutation_p.R1978H|HIVEP3_ENST00000460604.1_5'UTR	NM_024503.4	NP_078779.2	Q5T1R4	ZEP3_HUMAN	human immunodeficiency virus type I enhancer binding protein 3	1978					positive regulation of transcription, DNA-templated (GO:0045893)|skeletal muscle cell differentiation (GO:0035914)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			NS(2)|breast(3)|central_nervous_system(5)|endometrium(13)|kidney(3)|large_intestine(13)|lung(33)|ovary(4)|prostate(5)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)	85	Ovarian(52;0.00769)|all_hematologic(146;0.109)|Acute lymphoblastic leukemia(166;0.155)	Myeloproliferative disorder(586;0.0367)				TAGTGGTGGACGGCTGCCTGC	0.612													C|||	1	0.000199681	0.0	0.0	5008	,	,		16700	0.001		0.0	False		,,,				2504	0.0				p.R1978H		Atlas-SNP	.											HIVEP3,NS,carcinoma,-1,1	HIVEP3	235	1	0			c.G5933A						PASS	.	C	HIS/ARG,HIS/ARG	0,4394		0,0,2197	59.0	66.0	64.0		5933,5933	0.9	0.1	1	dbSNP_134	64	1,8581		0,1,4290	no	missense,missense	HIVEP3	NM_001127714.2,NM_024503.4	29,29	0,1,6487	TT,TC,CC		0.0117,0.0,0.0077	benign,benign	1978/2406,1978/2407	41978959	1,12975	2197	4291	6488	SO:0001583	missense	59269	exon8			GGTGGACGGCTGC	AF278765	CCDS463.1, CCDS44124.1	1p34	2013-01-08	2001-11-28		ENSG00000127124	ENSG00000127124		"""Zinc fingers, C2H2-type"""	13561	protein-coding gene	gene with protein product	"""kappabinding protein-1"""	606649	"""human immunodeficiency virus type I enhancer-binding protein 3"""			11161801	Standard	NR_038260		Approved	KRC, KBP1, KBP-1, SHN3, FLJ16752, KIAA1555, ZAS3, Schnurri-3, ZNF40C	uc001cha.4	Q5T1R4	OTTHUMG00000006361	ENST00000372583.1:c.5933G>A	1.37:g.41978959C>T	ENSP00000361664:p.Arg1978His	398.0	1.0	0.00251256		266.0	194.0	0.729323	NM_024503	A7YY91|Q5T1R5|Q9BZS0|Q9HCL7	Missense_Mutation	SNP	ENST00000372583.1	37	CCDS463.1	.	.	.	.	.	.	.	.	.	.	C	3.314	-0.140096	0.06669	0.0	1.17E-4	ENSG00000127124	ENST00000372584;ENST00000372583;ENST00000247584;ENST00000429157	T;T;T;T	0.06849	3.27;3.25;3.25;3.27	4.9	0.906	0.19314	.	0.511179	0.16205	N	0.224759	T	0.04452	0.0122	N	0.17082	0.46	0.09310	N	1	B;B	0.15930	0.015;0.009	B;B	0.12156	0.007;0.003	T	0.43475	-0.9389	10	0.23891	T	0.37	-0.7167	5.8783	0.18842	0.0:0.5722:0.1291:0.2987	.	1978;1978	Q5T1R4-2;Q5T1R4	.;ZEP3_HUMAN	H	1978	ENSP00000361665:R1978H;ENSP00000361664:R1978H;ENSP00000247584:R1978H;ENSP00000410828:R1978H	ENSP00000247584:R1978H	R	-	2	0	HIVEP3	41751546	0.136000	0.22515	0.136000	0.22124	0.344000	0.29017	0.195000	0.17155	-0.021000	0.14009	-0.150000	0.13652	CGT	C|1.000;T|0.000	0.000	weak		0.612	HIVEP3-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000016978.1	NM_024503	
HS3ST5	222537	hgsc.bcm.edu	37	6	114378722	114378722	+	Missense_Mutation	SNP	A	A	T	rs17793043	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr6:114378722A>T	ENST00000312719.5	-	5	1928	c.740T>A	c.(739-741)aTt>aAt	p.I247N	RP3-399L15.3_ENST00000523087.1_RNA|RP3-399L15.3_ENST00000519104.1_RNA|RP3-399L15.3_ENST00000519270.1_RNA|HS3ST5_ENST00000411826.1_Missense_Mutation_p.I247N			Q8IZT8	HS3S5_HUMAN	heparan sulfate (glucosamine) 3-O-sulfotransferase 5	247			I -> N (in dbSNP:rs17793043).		carbohydrate metabolic process (GO:0005975)|glycosaminoglycan biosynthetic process (GO:0006024)|glycosaminoglycan metabolic process (GO:0030203)|heparan sulfate proteoglycan biosynthetic process, enzymatic modification (GO:0015015)|negative regulation of coagulation (GO:0050819)|protein sulfation (GO:0006477)|regulation of viral entry into host cell (GO:0046596)|small molecule metabolic process (GO:0044281)	Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)	3'-phosphoadenosine 5'-phosphosulfate binding (GO:0050656)|[heparan sulfate]-glucosamine 3-sulfotransferase 1 activity (GO:0008467)			breast(4)|endometrium(2)|kidney(1)|large_intestine(7)|lung(17)|ovary(1)|pancreas(1)|skin(4)|stomach(1)|upper_aerodigestive_tract(3)	41		all_cancers(87;0.0587)|Colorectal(196;0.0676)|all_epithelial(87;0.154)		OV - Ovarian serous cystadenocarcinoma(136;0.00937)|all cancers(137;0.0117)|Epithelial(106;0.0274)|GBM - Glioblastoma multiforme(226;0.143)		AAATTGCTCAATTGGAAAGTA	0.443													A|||	15	0.00299521	0.0	0.0043	5008	,	,		19731	0.0		0.0119	False		,,,				2504	0.0				p.I247N		Atlas-SNP	.											.	HS3ST5	80	.	0			c.T740A						PASS	.	A	ASN/ILE	7,4399	12.9+/-30.5	0,7,2196	192.0	185.0	187.0		740	6.1	1.0	6	dbSNP_123	187	90,8510	51.1+/-111.2	0,90,4210	yes	missense	HS3ST5	NM_153612.3	149	0,97,6406	TT,TA,AA		1.0465,0.1589,0.7458	possibly-damaging	247/347	114378722	97,12909	2203	4300	6503	SO:0001583	missense	222537	exon2			TGCTCAATTGGAA	AF503292	CCDS34517.1	6q21	2011-11-16			ENSG00000249853	ENSG00000249853		"""Sulfotransferases, membrane-bound"""	19419	protein-coding gene	gene with protein product		609407				12138164	Standard	NM_153612		Approved	3-OST-5	uc003pwg.4	Q8IZT8	OTTHUMG00000015412	ENST00000312719.5:c.740T>A	6.37:g.114378722A>T	ENSP00000427888:p.Ile247Asn	247.0	0.0	0		199.0	105.0	0.527638	NM_153612	A8K1J2|Q52LI2|Q8N285	Missense_Mutation	SNP	ENST00000312719.5	37	CCDS34517.1	12	0.005494505494505495	0	0.0	2	0.0055248618784530384	0	0.0	10	0.013192612137203167	A	11.94	1.789740	0.31685	0.001589	0.010465	ENSG00000249853	ENST00000312719;ENST00000411826	D;D	0.81579	-1.51;-1.51	6.06	6.06	0.98353	Sulfotransferase domain (1);	0.055484	0.64402	D	0.000001	T	0.65471	0.2694	L	0.58101	1.795	0.47698	D	0.999498	B	0.32302	0.363	B	0.27796	0.083	T	0.66826	-0.5825	10	0.15499	T	0.54	.	16.6093	0.84858	1.0:0.0:0.0:0.0	rs17793043;rs17793043	247	Q8IZT8	HS3S5_HUMAN	N	247	ENSP00000427888:I247N;ENSP00000440332:I247N	ENSP00000427888:I247N	I	-	2	0	HS3ST5	114485415	1.000000	0.71417	0.992000	0.48379	0.873000	0.50193	6.369000	0.73109	2.324000	0.78689	0.533000	0.62120	ATT	A|0.994;T|0.006	0.006	strong		0.443	HS3ST5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041911.2	NM_153612	
DNAJB1	3337	hgsc.bcm.edu	37	19	14629138	14629138	+	Silent	SNP	C	C	T	rs141518218	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr19:14629138C>T	ENST00000254322.2	-	1	94	c.24G>A	c.(22-24)acG>acA	p.T8T	DNAJB1_ENST00000396969.4_Intron	NM_006145.1	NP_006136.1	P25685	DNJB1_HUMAN	DnaJ (Hsp40) homolog, subfamily B, member 1	8	J. {ECO:0000255|PROSITE- ProRule:PRU00286}.				chaperone cofactor-dependent protein refolding (GO:0070389)|chaperone mediated protein folding requiring cofactor (GO:0051085)|negative regulation of inclusion body assembly (GO:0090084)|positive regulation of ATPase activity (GO:0032781)|response to unfolded protein (GO:0006986)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)	ATPase activator activity (GO:0001671)|ATPase binding (GO:0051117)|chaperone binding (GO:0051087)|Hsp70 protein binding (GO:0030544)|unfolded protein binding (GO:0051082)			NS(1)|breast(1)|cervix(3)|endometrium(1)|kidney(1)|lung(7)|prostate(1)|urinary_tract(1)	16				GBM - Glioblastoma multiforme(1328;0.0476)		CCAGGCCCAACGTCTGGTAGT	0.711													C|||	8	0.00159744	0.0	0.0014	5008	,	,		9495	0.0		0.004	False		,,,				2504	0.0031				p.T8T		Atlas-SNP	.											.	DNAJB1	38	.	0			c.G24A						PASS	.	C		8,4394		0,8,2193	27.0	26.0	27.0		24	1.7	1.0	19	dbSNP_134	27	67,8527		0,67,4230	no	coding-synonymous	DNAJB1	NM_006145.1		0,75,6423	TT,TC,CC		0.7796,0.1817,0.5771		8/341	14629138	75,12921	2201	4297	6498	SO:0001819	synonymous_variant	3337	exon1			GCCCAACGTCTGG	D49547	CCDS12312.1, CCDS74295.1	19p13.12	2014-08-12			ENSG00000132002	ENSG00000132002		"""Heat shock proteins / DNAJ (HSP40)"""	5270	protein-coding gene	gene with protein product	"""radial spoke 16 homolog B (Chlamydomonas)"""	604572		HSPF1		8975727, 8250930	Standard	XM_006722733		Approved	Hsp40, Sis1, RSPH16B	uc002myz.1	P25685	OTTHUMG00000183289	ENST00000254322.2:c.24G>A	19.37:g.14629138C>T		61.0	0.0	0		36.0	20.0	0.555556	NM_006145	B4DX52	Silent	SNP	ENST00000254322.2	37	CCDS12312.1																																																																																			C|0.995;T|0.005	0.005	strong		0.711	DNAJB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000465987.1	NM_006145	
TOP2A	7153	hgsc.bcm.edu	37	17	38546274	38546274	+	Silent	SNP	A	A	C	rs17680289	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr17:38546274A>C	ENST00000423485.1	-	34	4568	c.4410T>G	c.(4408-4410)acT>acG	p.T1470T	Y_RNA_ENST00000410949.1_RNA	NM_001067.3	NP_001058.2	P11388	TOP2A_HUMAN	topoisomerase (DNA) II alpha 170kDa	1470					apoptotic chromosome condensation (GO:0030263)|ATP catabolic process (GO:0006200)|cellular response to DNA damage stimulus (GO:0006974)|chromosome segregation (GO:0007059)|DNA ligation (GO:0006266)|DNA topological change (GO:0006265)|DNA unwinding involved in DNA replication (GO:0006268)|embryonic cleavage (GO:0040016)|hematopoietic progenitor cell differentiation (GO:0002244)|mitotic cell cycle (GO:0000278)|mitotic DNA integrity checkpoint (GO:0044774)|mitotic recombination (GO:0006312)|positive regulation of apoptotic process (GO:0043065)|positive regulation of single stranded viral RNA replication via double stranded DNA intermediate (GO:0045870)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of viral genome replication (GO:0045070)|resolution of meiotic recombination intermediates (GO:0000712)|sister chromatid segregation (GO:0000819)	condensed chromosome (GO:0000793)|cytoplasm (GO:0005737)|DNA topoisomerase complex (ATP-hydrolyzing) (GO:0009330)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|protein complex (GO:0043234)	ATP binding (GO:0005524)|chromatin binding (GO:0003682)|DNA binding (GO:0003677)|DNA binding, bending (GO:0008301)|DNA topoisomerase type II (ATP-hydrolyzing) activity (GO:0003918)|DNA-dependent ATPase activity (GO:0008094)|drug binding (GO:0008144)|enzyme binding (GO:0019899)|histone deacetylase binding (GO:0042826)|magnesium ion binding (GO:0000287)|poly(A) RNA binding (GO:0044822)|protein C-terminus binding (GO:0008022)|protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)|protein kinase C binding (GO:0005080)|ubiquitin binding (GO:0043130)			breast(2)|central_nervous_system(1)|cervix(1)|endometrium(3)|kidney(2)|large_intestine(8)|lung(9)|ovary(5)|pancreas(2)|prostate(3)|skin(1)|upper_aerodigestive_tract(2)	39		Breast(137;0.00328)	STAD - Stomach adenocarcinoma(5;0.00183)		Amsacrine(DB00276)|Ciprofloxacin(DB00537)|Dactinomycin(DB00970)|Daunorubicin(DB00694)|Dexrazoxane(DB00380)|Doxorubicin(DB00997)|Enoxacin(DB00467)|Epirubicin(DB00445)|Etoposide(DB00773)|Fleroxacin(DB04576)|Idarubicin(DB01177)|Levofloxacin(DB01137)|Lomefloxacin(DB00978)|Lucanthone(DB04967)|Mitoxantrone(DB01204)|Moxifloxacin(DB00218)|Norfloxacin(DB01059)|Ofloxacin(DB01165)|Pefloxacin(DB00487)|Podofilox(DB01179)|Sparfloxacin(DB01208)|Teniposide(DB00444)|Trovafloxacin(DB00685)|Valrubicin(DB00385)	AATCATCAGAAGTGGATGGCT	0.433													A|||	34	0.00678914	0.0015	0.0101	5008	,	,		17725	0.0		0.0209	False		,,,				2504	0.0041				p.T1470T		Atlas-SNP	.											.	TOP2A	124	.	0			c.T4410G						PASS	.	A		13,3797		0,13,1892	69.0	66.0	67.0		4410	0.4	0.8	17	dbSNP_123	67	163,8085		1,161,3962	no	coding-synonymous	TOP2A	NM_001067.3		1,174,5854	CC,CA,AA		1.9762,0.3412,1.4596		1470/1532	38546274	176,11882	1905	4124	6029	SO:0001819	synonymous_variant	7153	exon34			ATCAGAAGTGGAT		CCDS45672.1	17q21-q22	2008-08-06	2002-08-29		ENSG00000131747	ENSG00000131747	5.99.1.2		11989	protein-coding gene	gene with protein product		126430	"""topoisomerase (DNA) II alpha (170kD)"""	TOP2			Standard	NM_001067		Approved		uc002huq.3	P11388	OTTHUMG00000155008	ENST00000423485.1:c.4410T>G	17.37:g.38546274A>C		198.0	0.0	0		166.0	87.0	0.524096	NM_001067	B2RTS1|Q71UN1|Q71UQ5|Q9HB24|Q9HB25|Q9HB26|Q9UP44|Q9UQP9	Silent	SNP	ENST00000423485.1	37	CCDS45672.1																																																																																			A|0.988;C|0.012	0.012	strong		0.433	TOP2A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000338035.1		
CYP2A6	1548	hgsc.bcm.edu	37	19	41351321	41351321	+	Missense_Mutation	SNP	C	C	T	rs200267449		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr19:41351321C>T	ENST00000301141.5	-	7	1059	c.1039G>A	c.(1039-1041)Gcc>Acc	p.A347T	CTC-490E21.12_ENST00000601627.1_Intron	NM_000762.5	NP_000753	P11509	CP2A6_HUMAN	cytochrome P450, family 2, subfamily A, polypeptide 6	347					coumarin catabolic process (GO:0046226)|coumarin metabolic process (GO:0009804)|drug metabolic process (GO:0017144)|exogenous drug catabolic process (GO:0042738)|small molecule metabolic process (GO:0044281)|steroid metabolic process (GO:0008202)|xenobiotic metabolic process (GO:0006805)	cytoplasmic microtubule (GO:0005881)|endoplasmic reticulum membrane (GO:0005789)	coumarin 7-hydroxylase activity (GO:0008389)|enzyme binding (GO:0019899)|heme binding (GO:0020037)|iron ion binding (GO:0005506)|oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, reduced flavin or flavoprotein as one donor, and incorporation of one atom of oxygen (GO:0016712)			breast(1)|central_nervous_system(1)|endometrium(4)|kidney(3)|large_intestine(7)|lung(9)|ovary(3)|prostate(5)|skin(2)|upper_aerodigestive_tract(2)	37			LUSC - Lung squamous cell carcinoma(20;0.000219)|Lung(22;0.000959)		Acetaminophen(DB00316)|Amiodarone(DB01118)|Amlodipine(DB00381)|Amobarbital(DB01351)|Amphetamine(DB00182)|Antipyrine(DB01435)|Arformoterol(DB01274)|Azelastine(DB00972)|Azithromycin(DB00207)|Buprenorphine(DB00921)|Bupropion(DB01156)|Chlorzoxazone(DB00356)|Cinnarizine(DB00568)|Cisapride(DB00604)|Clofibrate(DB00636)|Clomifene(DB00882)|Clotrimazole(DB00257)|Clozapine(DB00363)|Cyclophosphamide(DB00531)|Dapagliflozin(DB06292)|Desipramine(DB01151)|Dexamethasone(DB01234)|Dexfenfluramine(DB01191)|Diethylstilbestrol(DB00255)|Dronabinol(DB00470)|Eletriptan(DB00216)|Ezogabine(DB04953)|Flunarizine(DB04841)|Flunitrazepam(DB01544)|Fluorouracil(DB00544)|Flurazepam(DB00690)|Fomepizole(DB01213)|Formoterol(DB00983)|Halothane(DB01159)|Ifosfamide(DB01181)|Isoniazid(DB00951)|Ketoconazole(DB01026)|Letrozole(DB01006)|Lidocaine(DB00281)|Lorcaserin(DB04871)|Memantine(DB01043)|Menadione(DB00170)|Methimazole(DB00763)|Methoxsalen(DB00553)|Methoxyflurane(DB01028)|Metyrapone(DB01011)|Miconazole(DB01110)|Montelukast(DB00471)|Nevirapine(DB00238)|Nicotine(DB00184)|Nifedipine(DB01115)|Nilvadipine(DB06712)|Norfloxacin(DB01059)|Pentobarbital(DB00312)|Phenobarbital(DB01174)|Pilocarpine(DB01085)|Prednisolone(DB00860)|Progesterone(DB00396)|Propofol(DB00818)|Rifampicin(DB01045)|Rosiglitazone(DB00412)|Selegiline(DB01037)|Sevoflurane(DB01236)|Sulfaphenazole(DB06729)|Tamoxifen(DB00675)|Tranylcypromine(DB00752)|Tretinoin(DB00755)|Troleandomycin(DB01361)|Valproic Acid(DB00313)|Zidovudine(DB00495)	GGCATCTTGGCCCGGTCCTCA	0.537																																					p.A347T		Atlas-SNP	.											.	CYP2A6	69	.	0			c.G1039A						PASS	.						115.0	104.0	108.0					19																	41351321		2203	4300	6503	SO:0001583	missense	1548	exon7			TCTTGGCCCGGTC	AF182275	CCDS12568.1	19q13.2	2013-11-11	2003-01-14		ENSG00000255974	ENSG00000255974		"""Cytochrome P450s"""	2610	protein-coding gene	gene with protein product		122720	"""cytochrome P450, subfamily IIA (phenobarbital-inducible), polypeptide 6"""	CYP2A3		7668294, 2748347	Standard	NM_000762		Approved	CPA6, CYP2A	uc002opl.4	P11509	OTTHUMG00000182713	ENST00000301141.5:c.1039G>A	19.37:g.41351321C>T	ENSP00000301141:p.Ala347Thr	283.0	0.0	0		298.0	34.0	0.114094	NM_000762	A7YAE5|B2R7F6|P00190|P10890|Q16803|Q4VAT9|Q4VAU0|Q4VAU1|Q9H1Z7|Q9UCU0|Q9UK48	Missense_Mutation	SNP	ENST00000301141.5	37	CCDS12568.1	.	.	.	.	.	.	.	.	.	.	-	4.025	0.002161	0.07819	.	.	ENSG00000255974	ENST00000301141	T	0.69306	-0.39	2.76	-2.87	0.05700	.	0.614141	0.16066	U	0.231229	T	0.43853	0.1266	L	0.31120	0.905	0.09310	N	1	B;B	0.02656	0.0;0.0	B;B	0.09377	0.002;0.004	T	0.17319	-1.0373	10	0.22706	T	0.39	.	4.9051	0.13795	0.0:0.2915:0.1649:0.5436	.	347;347	Q13120;P11509	.;CP2A6_HUMAN	T	347	ENSP00000301141:A347T	ENSP00000301141:A347T	A	-	1	0	CYP2A6	46043161	0.000000	0.05858	0.011000	0.14972	0.659000	0.38960	-1.191000	0.03055	-0.603000	0.05767	-0.912000	0.02778	GCC	C|0.500;T|0.500	0.500	strong		0.537	CYP2A6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000463259.1	NM_000762	
GRIN2D	2906	hgsc.bcm.edu	37	19	48945044	48945044	+	Silent	SNP	C	C	T	rs144676582	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr19:48945044C>T	ENST00000263269.3	+	11	2359	c.2271C>T	c.(2269-2271)atC>atT	p.I757I		NM_000836.2	NP_000827.2	O15399	NMDE4_HUMAN	glutamate receptor, ionotropic, N-methyl D-aspartate 2D	757					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)	ACGCCTTCATCTACGATGCTG	0.617													C|||	6	0.00119808	0.0	0.0058	5008	,	,		20158	0.0		0.002	False		,,,				2504	0.0				p.I757I		Atlas-SNP	.											.	GRIN2D	76	.	0			c.C2271T						PASS	.	C		2,4404	4.2+/-10.8	0,2,2201	55.0	46.0	49.0		2271	2.5	1.0	19	dbSNP_134	49	29,8571	19.2+/-60.6	0,29,4271	no	coding-synonymous	GRIN2D	NM_000836.2		0,31,6472	TT,TC,CC		0.3372,0.0454,0.2384		757/1337	48945044	31,12975	2203	4300	6503	SO:0001819	synonymous_variant	2906	exon11			CTTCATCTACGAT	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.2271C>T	19.37:g.48945044C>T		120.0	0.0	0		102.0	48.0	0.470588	NM_000836		Silent	SNP	ENST00000263269.3	37	CCDS12719.1																																																																																			C|0.998;T|0.002	0.002	strong		0.617	GRIN2D-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466121.1		
CYP24A1	1591	hgsc.bcm.edu	37	20	52790027	52790027	+	Missense_Mutation	SNP	G	G	A			TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr20:52790027G>A	ENST00000216862.3	-	1	485	c.92C>T	c.(91-93)aCg>aTg	p.T31M	CYP24A1_ENST00000395954.3_5'Flank|CYP24A1_ENST00000395955.3_Missense_Mutation_p.T31M	NM_000782.4	NP_000773.2	Q07973	CP24A_HUMAN	cytochrome P450, family 24, subfamily A, polypeptide 1	31					osteoblast differentiation (GO:0001649)|oxidation-reduction process (GO:0055114)|response to vitamin D (GO:0033280)|small molecule metabolic process (GO:0044281)|steroid metabolic process (GO:0008202)|vitamin D catabolic process (GO:0042369)|vitamin D metabolic process (GO:0042359)|vitamin D receptor signaling pathway (GO:0070561)|vitamin metabolic process (GO:0006766)|xenobiotic metabolic process (GO:0006805)	mitochondrial inner membrane (GO:0005743)	1-alpha,25-dihydroxyvitamin D3 24-hydroxylase activity (GO:0030342)|25-hydroxycholecalciferol-24-hydroxylase activity (GO:0008403)|heme binding (GO:0020037)|iron ion binding (GO:0005506)|oxidoreductase activity (GO:0016491)			breast(2)|endometrium(3)|large_intestine(4)|lung(9)|ovary(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)	24	Lung NSC(4;1.08e-05)|all_lung(4;2.7e-05)		STAD - Stomach adenocarcinoma(23;0.206)		Calcidiol(DB00146)|Calcipotriol(DB02300)|Calcitriol(DB00136)|Corticotropin(DB01285)|Ergocalciferol(DB00153)|Paricalcitol(DB00910)	CGTGTACGCCGTAGATGTCAC	0.701																																					p.T31M		Atlas-SNP	.											.	CYP24A1	75	.	0			c.C92T						PASS	.						11.0	10.0	10.0					20																	52790027		2182	4282	6464	SO:0001583	missense	1591	exon1			TACGCCGTAGATG	U60669	CCDS33491.1, CCDS46616.1	20q13.2-q13.3	2003-02-28	2003-02-14	2003-02-28	ENSG00000019186	ENSG00000019186		"""Cytochrome P450s"""	2602	protein-coding gene	gene with protein product		126065	"""cytochrome P450, subfamily XXIV (vitamin D 24-hydroxylase)"""	CYP24			Standard	NM_000782		Approved	CP24, P450-CC24	uc002xwv.2	Q07973	OTTHUMG00000032773	ENST00000216862.3:c.92C>T	20.37:g.52790027G>A	ENSP00000216862:p.Thr31Met	80.0	0.0	0		39.0	13.0	0.333333	NM_000782	Q15807|Q32ML3|Q5I2W7	Missense_Mutation	SNP	ENST00000216862.3	37	CCDS33491.1	.	.	.	.	.	.	.	.	.	.	G	8.351	0.830799	0.16820	.	.	ENSG00000019186	ENST00000216862;ENST00000395955	T;T	0.71222	-0.53;-0.55	5.27	-0.451	0.12214	.	0.815815	0.11464	N	0.561406	T	0.40372	0.1114	N	0.08118	0	0.09310	N	0.999999	P;P	0.43024	0.521;0.798	B;B	0.35182	0.128;0.197	T	0.29731	-1.0002	10	0.35671	T	0.21	-0.5016	3.5654	0.07897	0.0786:0.2999:0.3524:0.2691	.	31;31	Q32ML3;Q07973	.;CP24A_HUMAN	M	31	ENSP00000216862:T31M;ENSP00000379285:T31M	ENSP00000216862:T31M	T	-	2	0	CYP24A1	52223434	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	0.239000	0.18023	-0.332000	0.08489	-0.309000	0.09137	ACG	.	.	none		0.701	CYP24A1-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079769.2		
LILRA4	23547	hgsc.bcm.edu	37	19	54848144	54848144	+	Missense_Mutation	SNP	T	T	A	rs74869671	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr19:54848144T>A	ENST00000291759.4	-	6	1279	c.1223A>T	c.(1222-1224)cAc>cTc	p.H408L	AC008984.2_ENST00000507363.1_RNA	NM_012276.3	NP_036408.3	P59901	LIRA4_HUMAN	leukocyte immunoglobulin-like receptor, subfamily A (with TM domain), member 4	408	Ig-like C2-type 4.				immune system process (GO:0002376)	integral component of membrane (GO:0016021)				NS(2)|breast(1)|central_nervous_system(2)|endometrium(2)|large_intestine(5)|lung(13)|prostate(3)|skin(1)|upper_aerodigestive_tract(3)	32	Ovarian(34;0.19)			GBM - Glioblastoma multiforme(193;0.0565)		CTCACTGGGGTGAGACAGCAG	0.592													T|||	74	0.0147764	0.0333	0.0014	5008	,	,		17775	0.0		0.001	False		,,,				2504	0.0286				p.H408L		Atlas-SNP	.											.	LILRA4	91	.	0			c.A1223T						PASS	.	T	LEU/HIS	1,4405		0,1,2202	111.0	91.0	98.0		1223	-1.7	0.0	19	dbSNP_131	98	1,8599		0,1,4299	no	missense	LILRA4	NM_012276.3	99	0,2,6501	AA,AT,TT		0.0116,0.0227,0.0154	benign	408/500	54848144	2,13004	2203	4300	6503	SO:0001583	missense	23547	exon6			CTGGGGTGAGACA	AF041261	CCDS12890.1	19q13.4	2013-01-11			ENSG00000239961	ENSG00000239961		"""Leukocyte immunoglobulin-like receptors"", ""CD molecules"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	15503	protein-coding gene	gene with protein product		607517				10941842	Standard	NM_012276		Approved	ILT7, CD85g	uc002qfj.3	P59901	OTTHUMG00000065355	ENST00000291759.4:c.1223A>T	19.37:g.54848144T>A	ENSP00000291759:p.His408Leu	233.0	0.0	0		179.0	18.0	0.100559	NM_012276	Q32MC4	Missense_Mutation	SNP	ENST00000291759.4	37	CCDS12890.1	.	.	.	.	.	.	.	.	.	.	.	5.063	0.197370	0.09599	2.27E-4	1.16E-4	ENSG00000239961	ENST00000291759	T	0.00691	5.84	2.4	-1.74	0.08056	Immunoglobulin subtype (1);Immunoglobulin-like fold (1);	3.662820	0.00932	N	0.002721	T	0.00754	0.0025	L	0.35414	1.06	0.09310	N	1	B	0.02656	0.0	B	0.04013	0.001	T	0.49437	-0.8940	10	0.17832	T	0.49	.	3.0817	0.06265	0.4319:0.0:0.22:0.3481	.	408	P59901	LIRA4_HUMAN	L	408	ENSP00000291759:H408L	ENSP00000291759:H408L	H	-	2	0	LILRA4	59539956	0.000000	0.05858	0.001000	0.08648	0.029000	0.11900	-2.031000	0.01427	-0.517000	0.06461	-0.714000	0.03626	CAC	T|0.995;A|0.005	0.005	strong		0.592	LILRA4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000140229.2	NM_012276	
XIRP1	165904	hgsc.bcm.edu	37	3	39227495	39227495	+	Missense_Mutation	SNP	C	C	T	rs142860074	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr3:39227495C>T	ENST00000340369.3	-	2	3670	c.3442G>A	c.(3442-3444)Gtg>Atg	p.V1148M	XIRP1_ENST00000396251.1_Intron|XIRP1_ENST00000421646.1_Intron	NM_194293.2	NP_919269.2	Q702N8	XIRP1_HUMAN	xin actin-binding repeat containing 1	1148					cardiac muscle cell development (GO:0055013)|negative regulation of cell proliferation (GO:0008285)|regulation of membrane potential (GO:0042391)|sarcomere organization (GO:0045214)	fascia adherens (GO:0005916)	poly(A) RNA binding (GO:0044822)	p.V1148M(1)		breast(4)|central_nervous_system(2)|endometrium(9)|haematopoietic_and_lymphoid_tissue(3)|kidney(4)|large_intestine(14)|lung(22)|ovary(4)|pancreas(1)|prostate(2)|skin(6)	71				KIRC - Kidney renal clear cell carcinoma(284;0.0517)|Kidney(284;0.065)		AAGGTCCTCACGGGATGAGCG	0.617																																					p.V1148M		Atlas-SNP	.											XIRP1,colon,carcinoma,0,1	XIRP1	173	1	1	Substitution - Missense(1)	large_intestine(1)	c.G3442A						PASS	.	C	,MET/VAL	1,4405	2.1+/-5.4	0,1,2202	59.0	60.0	60.0		,3442	1.6	0.0	3	dbSNP_134	60	7,8593	5.7+/-21.5	0,7,4293	yes	intron,missense	XIRP1	NM_001198621.1,NM_194293.2	,21	0,8,6495	TT,TC,CC		0.0814,0.0227,0.0615	,possibly-damaging	,1148/1844	39227495	8,12998	2203	4300	6503	SO:0001583	missense	165904	exon2			TCCTCACGGGATG	AW755250	CCDS2683.1, CCDS56245.1	3p21.33	2008-02-05	2007-06-27	2007-06-27	ENSG00000168334	ENSG00000168334			14301	protein-coding gene	gene with protein product		609777	"""cardiomyopathy associated 1"""	CMYA1		12203715, 15454575	Standard	NM_001198621		Approved	DKFZp451D042, Xin	uc003cjk.2	Q702N8	OTTHUMG00000131297	ENST00000340369.3:c.3442G>A	3.37:g.39227495C>T	ENSP00000343140:p.Val1148Met	113.0	0.0	0		146.0	77.0	0.527397	NM_194293	A0JP25|A4QPE2|Q68DF2|Q6ZTR3|Q702N9|Q8IVN7|Q8N1N3|Q8N904|Q8TCG7	Missense_Mutation	SNP	ENST00000340369.3	37	CCDS2683.1	.	.	.	.	.	.	.	.	.	.	C	5.679	0.309769	0.10733	2.27E-4	8.14E-4	ENSG00000168334	ENST00000340369	T	0.06142	3.34	4.39	1.58	0.23477	.	0.713130	0.12138	U	0.496126	T	0.05686	0.0149	L	0.43152	1.355	0.09310	N	1	B	0.28208	0.203	B	0.14578	0.011	T	0.34054	-0.9844	10	0.45353	T	0.12	.	6.8454	0.23984	0.0:0.6999:0.0:0.3001	.	1148	Q702N8	XIRP1_HUMAN	M	1148	ENSP00000343140:V1148M	ENSP00000343140:V1148M	V	-	1	0	XIRP1	39202499	0.840000	0.29493	0.025000	0.17156	0.219000	0.24729	1.440000	0.35024	0.227000	0.20999	0.561000	0.74099	GTG	C|0.999;T|0.001	0.001	strong		0.617	XIRP1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000254065.1	XM_093522	
PTPN21	11099	hgsc.bcm.edu	37	14	88946343	88946343	+	Missense_Mutation	SNP	C	C	T			TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr14:88946343C>T	ENST00000556564.1	-	13	1716	c.1432G>A	c.(1432-1434)Ggc>Agc	p.G478S	PTPN21_ENST00000328736.3_Missense_Mutation_p.G478S	NM_007039.3	NP_008970.2	Q16825	PTN21_HUMAN	protein tyrosine phosphatase, non-receptor type 21	478					peptidyl-tyrosine dephosphorylation (GO:0035335)|protein dephosphorylation (GO:0006470)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)	protein tyrosine phosphatase activity (GO:0004725)			breast(1)|central_nervous_system(1)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(13)|liver(1)|lung(7)|ovary(4)|prostate(3)|skin(6)|upper_aerodigestive_tract(1)|urinary_tract(1)	45						TACGAGCTGCCGATGTTGAGG	0.667																																					p.G478S		Atlas-SNP	.											.	PTPN21	113	.	0			c.G1432A						PASS	.						36.0	37.0	37.0					14																	88946343		2203	4300	6503	SO:0001583	missense	11099	exon13			AGCTGCCGATGTT	X79510	CCDS9884.1	14q31	2011-06-09				ENSG00000070778		"""Protein tyrosine phosphatases / Class I Cys-based PTPs : Non-receptor"""	9651	protein-coding gene	gene with protein product		603271				7519780	Standard	NM_007039		Approved	PTPD1, PTPRL10	uc001xwv.4	Q16825		ENST00000556564.1:c.1432G>A	14.37:g.88946343C>T	ENSP00000452414:p.Gly478Ser	55.0	0.0	0		49.0	4.0	0.0816327	NM_007039		Missense_Mutation	SNP	ENST00000556564.1	37	CCDS9884.1	.	.	.	.	.	.	.	.	.	.	C	14.33	2.502634	0.44455	.	.	ENSG00000070778	ENST00000328736;ENST00000556564	T;T	0.72051	-0.62;-0.62	5.38	4.48	0.54585	.	0.111045	0.64402	D	0.000007	T	0.50000	0.1590	L	0.27053	0.805	0.47621	D	0.999473	P	0.41214	0.742	B	0.31946	0.138	T	0.49428	-0.8941	10	0.21014	T	0.42	.	10.7907	0.46432	0.0:0.8548:0.0:0.1452	.	478	Q16825	PTN21_HUMAN	S	478	ENSP00000330276:G478S;ENSP00000452414:G478S	ENSP00000330276:G478S	G	-	1	0	PTPN21	88016096	0.997000	0.39634	0.667000	0.29798	0.960000	0.62799	3.056000	0.49923	2.528000	0.85240	0.561000	0.74099	GGC	.	.	none		0.667	PTPN21-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000410303.1		
MUC17	140453	hgsc.bcm.edu	37	7	100682814	100682814	+	Missense_Mutation	SNP	A	A	G	rs201007776		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr7:100682814A>G	ENST00000306151.4	+	3	8181	c.8117A>G	c.(8116-8118)aAt>aGt	p.N2706S		NM_001040105.1	NP_001035194.1	Q685J3	MUC17_HUMAN	mucin 17, cell surface associated	2706	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)					CTGTTGGCCAATTCTGAGGCT	0.493																																					p.N2706S		Atlas-SNP	.											MUC17,NS,carcinoma,0,1	MUC17	804	1	0			c.A8117G						scavenged	.						245.0	255.0	251.0					7																	100682814		2203	4300	6503	SO:0001583	missense	140453	exon3			TGGCCAATTCTGA	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.8117A>G	7.37:g.100682814A>G	ENSP00000302716:p.Asn2706Ser	139.0	2.0	0.0143885		198.0	15.0	0.0757576	NM_001040105	O14761|Q685J2|Q8TDH7	Missense_Mutation	SNP	ENST00000306151.4	37	CCDS34711.1	.	.	.	.	.	.	.	.	.	.	G	0.044	-1.274581	0.01410	.	.	ENSG00000169876	ENST00000306151	T	0.02015	4.5	0.37	-0.741	0.11112	.	.	.	.	.	T	0.00754	0.0025	N	0.02539	-0.55	0.09310	N	1	B	0.17667	0.023	B	0.08055	0.003	T	0.43065	-0.9414	9	0.06236	T	0.91	.	0.1449	0.00087	0.2508:0.246:0.2581:0.2451	.	2706	Q685J3	MUC17_HUMAN	S	2706	ENSP00000302716:N2706S	ENSP00000302716:N2706S	N	+	2	0	MUC17	100469534	0.000000	0.05858	0.001000	0.08648	0.021000	0.10359	-0.783000	0.04638	-2.048000	0.00907	-1.389000	0.01157	AAT	A|0.999;G|0.001	0.001	weak		0.493	MUC17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347161.1	NM_001040105	
XDH	7498	hgsc.bcm.edu	37	2	31606682	31606682	+	Silent	SNP	A	A	G	rs145596057	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr2:31606682A>G	ENST00000379416.3	-	10	873	c.825T>C	c.(823-825)ttT>ttC	p.F275F	XDH_ENST00000491727.1_5'UTR	NM_000379.3	NP_000370.2	P47989	XDH_HUMAN	xanthine dehydrogenase	275	FAD-binding PCMH-type. {ECO:0000255|PROSITE-ProRule:PRU00718}.				activation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0006919)|lactation (GO:0007595)|negative regulation of endothelial cell differentiation (GO:0045602)|negative regulation of endothelial cell proliferation (GO:0001937)|negative regulation of gene expression (GO:0010629)|negative regulation of protein kinase B signaling (GO:0051898)|negative regulation of protein phosphorylation (GO:0001933)|negative regulation of vascular endothelial growth factor signaling pathway (GO:1900747)|negative regulation of vasculogenesis (GO:2001213)|nucleobase-containing small molecule metabolic process (GO:0055086)|positive regulation of p38MAPK cascade (GO:1900745)|positive regulation of reactive oxygen species metabolic process (GO:2000379)|purine nucleobase metabolic process (GO:0006144)|purine nucleotide catabolic process (GO:0006195)|small molecule metabolic process (GO:0044281)|xanthine catabolic process (GO:0009115)	cytosol (GO:0005829)|extracellular space (GO:0005615)|peroxisome (GO:0005777)	2 iron, 2 sulfur cluster binding (GO:0051537)|electron carrier activity (GO:0009055)|flavin adenine dinucleotide binding (GO:0050660)|iron ion binding (GO:0005506)|molybdopterin cofactor binding (GO:0043546)|protein homodimerization activity (GO:0042803)|UDP-N-acetylmuramate dehydrogenase activity (GO:0008762)|xanthine dehydrogenase activity (GO:0004854)|xanthine oxidase activity (GO:0004855)			breast(3)|central_nervous_system(2)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(13)|lung(31)|ovary(1)|pancreas(1)|prostate(3)|skin(9)|urinary_tract(1)	74	Acute lymphoblastic leukemia(172;0.155)				Aldesleukin(DB00041)|Allopurinol(DB00437)|Azathioprine(DB00993)|Carboplatin(DB00958)|Carvedilol(DB01136)|Chlorphenesin(DB00856)|Cisplatin(DB00515)|Daunorubicin(DB00694)|Deferoxamine(DB00746)|Doxorubicin(DB00997)|Flavin adenine dinucleotide(DB03147)|L-Carnitine(DB00583)|Menadione(DB00170)|Mercaptopurine(DB01033)|Nitrofural(DB00336)|Procarbazine(DB01168)|Pyrazinamide(DB00339)|Spermine(DB00127)|Trifluoperazine(DB00831)	CAATCATAGGAAACAGCATAT	0.493													A|||	2	0.000399361	0.0	0.0	5008	,	,		18724	0.0		0.002	False		,,,				2504	0.0				p.F275F	Colon(66;682 1445 30109 40147)	Atlas-SNP	.											.	XDH	191	.	0			c.T825C						PASS	.	A		1,4405	2.1+/-5.4	0,1,2202	115.0	101.0	106.0		825	0.8	0.9	2	dbSNP_134	106	14,8586	10.5+/-38.8	0,14,4286	no	coding-synonymous	XDH	NM_000379.3		0,15,6488	GG,GA,AA		0.1628,0.0227,0.1153		275/1334	31606682	15,12991	2203	4300	6503	SO:0001819	synonymous_variant	7498	exon10			CATAGGAAACAGC	D11456	CCDS1775.1	2p23.1	2009-07-10	2003-03-20		ENSG00000158125	ENSG00000158125	1.17.1.4		12805	protein-coding gene	gene with protein product		607633	"""xanthene dehydrogenase"""			8224915	Standard	NM_000379		Approved	XOR, XO	uc002rnv.1	P47989	OTTHUMG00000099385	ENST00000379416.3:c.825T>C	2.37:g.31606682A>G		165.0	0.0	0		166.0	85.0	0.512048	NM_000379	Q16681|Q16712|Q4PJ16	Silent	SNP	ENST00000379416.3	37	CCDS1775.1																																																																																			A|0.999;G|0.001	0.001	strong		0.493	XDH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000216840.1	NM_000379	
PLIN3	10226	hgsc.bcm.edu	37	19	4861381	4861381	+	Missense_Mutation	SNP	T	T	C			TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr19:4861381T>C	ENST00000221957.4	-	2	202	c.26A>G	c.(25-27)gAt>gGt	p.D9G	PLIN3_ENST00000592528.1_Missense_Mutation_p.D9G|PLIN3_ENST00000585479.1_Missense_Mutation_p.D9G	NM_001164189.1|NM_001164194.1|NM_005817.4	NP_001157661.1|NP_001157666.1|NP_005808.3	O60664	PLIN3_HUMAN	perilipin 3	9					vesicle-mediated transport (GO:0016192)	cytoplasm (GO:0005737)|endosome (GO:0005768)|Golgi apparatus (GO:0005794)|intracellular membrane-bounded organelle (GO:0043231)|lipid particle (GO:0005811)|membrane (GO:0016020)				cervix(1)|endometrium(2)|large_intestine(2)|lung(2)|ovary(1)|prostate(1)	9					Galsulfase(DB01279)|Idursulfase(DB01271)	GGTGCTGCCATCAGCCTCTGC	0.627																																					p.D9G		Atlas-SNP	.											PLIN3,NS,carcinoma,-1,1	PLIN3	36	1	0			c.A26G						PASS	.						113.0	91.0	98.0					19																	4861381		2203	4300	6503	SO:0001583	missense	10226	exon2			CTGCCATCAGCCT	AF051314	CCDS12137.1, CCDS59337.1, CCDS59338.1	19p13.3	2009-08-12	2009-08-12	2009-08-12		ENSG00000105355		"""Perilipins"""	16893	protein-coding gene	gene with protein product	"""cargo selection protein (mannose 6 phosphate receptor binding protein)"", ""placental protein 17"", ""MPR-BINDING PROTEIN, 47-KD"""	602702	"""mannose-6-phosphate receptor binding protein 1"""	M6PRBP1		9590177, 6856484, 19638644	Standard	NM_005817		Approved	TIP47, PP17	uc002mbj.2	O60664		ENST00000221957.4:c.26A>G	19.37:g.4861381T>C	ENSP00000221957:p.Asp9Gly	42.0	0.0	0		48.0	13.0	0.270833	NM_001164189	A8K4Y9|K7EQF4|Q53G77|Q9BS03|Q9UBD7|Q9UP92	Missense_Mutation	SNP	ENST00000221957.4	37	CCDS12137.1	.	.	.	.	.	.	.	.	.	.	T	7.718	0.696623	0.15106	.	.	ENSG00000105355	ENST00000221957	T	0.05925	3.37	3.24	-1.14	0.09741	.	1.247070	0.05815	U	0.614699	T	0.05135	0.0137	L	0.29908	0.895	0.09310	N	1	B;B	0.15930	0.015;0.009	B;B	0.16722	0.016;0.007	T	0.45731	-0.9241	10	0.27785	T	0.31	-22.7586	5.44	0.16501	0.0:0.161:0.5605:0.2785	.	9;9	O60664-3;O60664	.;PLIN3_HUMAN	G	9	ENSP00000221957:D9G	ENSP00000221957:D9G	D	-	2	0	PLIN3	4812381	0.000000	0.05858	0.000000	0.03702	0.106000	0.19336	0.176000	0.16782	0.042000	0.15717	0.379000	0.24179	GAT	.	.	none		0.627	PLIN3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000450436.1	NM_005817	
MUC12	10071	hgsc.bcm.edu	37	7	100635143	100635143	+	Silent	SNP	T	T	C	rs34337783	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr7:100635143T>C	ENST00000379442.3	+	5	1728	c.1728T>C	c.(1726-1728)cgT>cgC	p.R576R	MUC12_ENST00000536621.1_Silent_p.R433R			Q9UKN1	MUC12_HUMAN	mucin 12, cell surface associated	576	28 X 19 AA approximate tandem repeats of E-E-S-X-X-X-H-X-X-P-X-X-T-X-T-X-X-X-P.|Ser-rich.				cellular protein metabolic process (GO:0044267)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)|regulation of cell growth (GO:0001558)	Golgi lumen (GO:0005796)|integral component of plasma membrane (GO:0005887)				breast(6)|central_nervous_system(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|prostate(1)|stomach(13)	25						TCTCAGGCCGTAGTGAGGAAT	0.537													t|||	619	0.123602	0.2156	0.0922	5008	,	,		30398	0.0169		0.1352	False		,,,				2504	0.1196				p.R433R		Atlas-SNP	.											MUC12,NS,carcinoma,+2,1	MUC12	140	1	0			c.T1299C						PASS	.	T		262,1122		24,214,454	351.0	392.0	380.0		1299	0.1	0.0	7	dbSNP_126	380	454,2728		34,386,1171	no	coding-synonymous	MUC12	NM_001164462.1		58,600,1625	CC,CT,TT		14.2678,18.9306,15.6811		433/5336	100635143	716,3850	692	1591	2283	SO:0001819	synonymous_variant	10071	exon2			AGGCCGTAGTGAG	AF147790, AF147791	CCDS55139.1	7q22	2007-01-17	2006-03-14		ENSG00000205277	ENSG00000205277		"""Mucins"""	7510	protein-coding gene	gene with protein product		604609	"""mucin 11"""	MUC11		10463611	Standard	NM_001164462		Approved		uc003uxo.3	Q9UKN1	OTTHUMG00000157042	ENST00000379442.3:c.1728T>C	7.37:g.100635143T>C		0.0	0.0	.		4.0	4.0	1	NM_001164462	A6ND38|F5GWV9|Q9UKN0	Silent	SNP	ENST00000379442.3	37																																																																																				T|0.890;C|0.110	0.110	strong		0.537	MUC12-001	NOVEL	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000347234.1	XM_379904	
MYO18B	84700	hgsc.bcm.edu	37	22	26164700	26164700	+	Missense_Mutation	SNP	C	C	T			TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr22:26164700C>T	ENST00000407587.2	+	4	986	c.817C>T	c.(817-819)Ccc>Tcc	p.P273S	MYO18B_ENST00000335473.7_Missense_Mutation_p.P273S|MYO18B_ENST00000536101.1_Missense_Mutation_p.P273S			Q8IUG5	MY18B_HUMAN	myosin XVIIIB	273						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						AGCCCAAGGGCCCGGCGAGGG	0.627																																					p.P273S		Atlas-SNP	.											.	MYO18B	322	.	0			c.C817T						PASS	.						16.0	20.0	19.0					22																	26164700		1895	4089	5984	SO:0001583	missense	84700	exon4			CAAGGGCCCGGCG	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.817C>T	22.37:g.26164700C>T	ENSP00000386096:p.Pro273Ser	60.0	0.0	0		53.0	31.0	0.584906	NM_032608	B2RWP3|F5GYU7|Q8NDI8|Q8TE65|Q8WWS0|Q96KH2|Q96KR8|Q96KR9	Missense_Mutation	SNP	ENST00000407587.2	37		.	.	.	.	.	.	.	.	.	.	c	11.33	1.607898	0.28623	.	.	ENSG00000133454	ENST00000536101;ENST00000335473;ENST00000407587	D;D;D	0.86366	-2.09;-2.09;-2.11	3.13	-3.41	0.04839	.	0.695036	0.11932	N	0.515636	T	0.74176	0.3682	L	0.27053	0.805	0.09310	N	1	B;B;B	0.28291	0.131;0.103;0.206	B;B;B	0.25291	0.018;0.059;0.04	T	0.63278	-0.6673	10	0.66056	D	0.02	.	5.8765	0.18832	0.0:0.3595:0.3875:0.253	.	273;273;273	Q8IUG5;F5GXR6;F5GYU7	MY18B_HUMAN;.;.	S	273	ENSP00000441229:P273S;ENSP00000334563:P273S;ENSP00000386096:P273S	ENSP00000334563:P273S	P	+	1	0	MYO18B	24494700	0.000000	0.05858	0.001000	0.08648	0.367000	0.29736	-0.514000	0.06298	-0.256000	0.09473	0.306000	0.20318	CCC	.	.	none		0.627	MYO18B-006	NOVEL	non_canonical_conserved|basic|appris_candidate_longest|exp_conf	protein_coding	protein_coding	OTTHUMT00000400691.1	NM_032608	
FNDC3B	64778	hgsc.bcm.edu	37	3	172061988	172061988	+	Silent	SNP	C	C	T	rs200807692		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr3:172061988C>T	ENST00000336824.4	+	19	2289	c.2190C>T	c.(2188-2190)gtC>gtT	p.V730V	FNDC3B_ENST00000416957.1_Silent_p.V730V|FNDC3B_ENST00000415807.2_Silent_p.V730V	NM_001135095.1	NP_001128567.1	Q53EP0	FND3B_HUMAN	fibronectin type III domain containing 3B	730	Fibronectin type-III 5. {ECO:0000255|PROSITE-ProRule:PRU00316}.				cell migration (GO:0016477)|negative regulation of osteoblast differentiation (GO:0045668)|positive regulation of fat cell differentiation (GO:0045600)|positive regulation of fibroblast proliferation (GO:0048146)|substrate adhesion-dependent cell spreading (GO:0034446)|Type II pneumocyte differentiation (GO:0060510)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)	poly(A) RNA binding (GO:0044822)			breast(3)|cervix(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(12)|lung(26)|ovary(3)|prostate(2)|skin(3)|stomach(2)|upper_aerodigestive_tract(4)|urinary_tract(1)	69	all_cancers(22;1.01e-18)|Ovarian(172;0.00167)|Breast(254;0.165)		LUSC - Lung squamous cell carcinoma(14;3.57e-14)|Lung(28;9.39e-14)	GBM - Glioblastoma multiforme(1;0.0494)		AGTGCACCGTCGGCAACCTGC	0.567													C|||	1	0.000199681	0.0	0.0	5008	,	,		18074	0.001		0.0	False		,,,				2504	0.0				p.V730V		Atlas-SNP	.											.	FNDC3B	118	.	0			c.C2190T						PASS	.						183.0	166.0	172.0					3																	172061988		2203	4300	6503	SO:0001819	synonymous_variant	64778	exon19			CACCGTCGGCAAC	AF543840	CCDS3217.1	3q26.31	2013-11-06			ENSG00000075420	ENSG00000075420		"""Fibronectin type III domain containing"""	24670	protein-coding gene	gene with protein product		611909				15527760	Standard	NM_022763		Approved	FAD104, DKFZp762K137, FLJ23399, PRO4979, YVTM2421	uc003fhy.3	Q53EP0	OTTHUMG00000156761	ENST00000336824.4:c.2190C>T	3.37:g.172061988C>T		216.0	0.0	0		178.0	90.0	0.505618	NM_001135095	B2RB36|B3KXR8|D3DNQ7|Q5U5T8|Q6PIJ3|Q6UXG1|Q6UXZ5|Q8IXB2|Q8NBU7|Q96D78|Q9H5I7|Q9NSQ8	Silent	SNP	ENST00000336824.4	37	CCDS3217.1																																																																																			C|1.000;T|0.000	0.000	strong		0.567	FNDC3B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000345618.2	NM_022763	
DHX57	90957	hgsc.bcm.edu	37	2	39042718	39042718	+	Missense_Mutation	SNP	T	T	G	rs150735204	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr2:39042718T>G	ENST00000295373.6	-	20	3677	c.3551A>C	c.(3550-3552)gAa>gCa	p.E1184A		NM_198963.1	NP_945314.1	Q6P158	DHX57_HUMAN	DEAH (Asp-Glu-Ala-Asp/His) box polypeptide 57	1184							ATP binding (GO:0005524)|ATP-dependent helicase activity (GO:0008026)|metal ion binding (GO:0046872)|poly(A) RNA binding (GO:0044822)			NS(2)|breast(3)|central_nervous_system(1)|endometrium(9)|kidney(2)|large_intestine(15)|lung(20)|ovary(1)|prostate(3)|skin(4)|upper_aerodigestive_tract(1)|urinary_tract(1)	62		all_hematologic(82;0.248)				TTTCTCAATTTCCCTTGCTCT	0.453													T|||	11	0.00219649	0.0	0.0043	5008	,	,		19870	0.0		0.007	False		,,,				2504	0.001				p.E1184A	Melanoma(191;1090 2095 4375 23729 47341)	Atlas-SNP	.											DHX57,NS,carcinoma,0,1	DHX57	127	1	0			c.A3551C						PASS	.	T	ALA/GLU	5,4401	9.9+/-24.2	0,5,2198	222.0	207.0	212.0		3551	5.3	1.0	2	dbSNP_134	212	63,8537	39.3+/-95.6	0,63,4237	yes	missense	DHX57	NM_198963.1	107	0,68,6435	GG,GT,TT		0.7326,0.1135,0.5228	benign	1184/1387	39042718	68,12938	2203	4300	6503	SO:0001583	missense	90957	exon20			TCAATTTCCCTTG	AF070590	CCDS1800.1	2p22.3	2008-02-05			ENSG00000163214	ENSG00000163214		"""DEAH-boxes"""	20086	protein-coding gene	gene with protein product							Standard	NM_198963		Approved	DDX57	uc002rrf.3	Q6P158	OTTHUMG00000102103	ENST00000295373.6:c.3551A>C	2.37:g.39042718T>G	ENSP00000295373:p.Glu1184Ala	112.0	0.0	0		123.0	61.0	0.495935	NM_198963	A2RRC7|Q53SI4|Q6P9G1|Q7Z6H3|Q8NG17|Q96M33	Missense_Mutation	SNP	ENST00000295373.6	37	CCDS1800.1	3	0.0013736263736263737	0	0.0	0	0.0	0	0.0	3	0.00395778364116095	T	11.33	1.606871	0.28623	0.001135	0.007326	ENSG00000163214	ENST00000295373	T	0.02787	4.16	5.29	5.29	0.74685	Domain of unknown function DUF1605 (1);	0.241073	0.29046	N	0.013302	T	0.01489	0.0048	N	0.11560	0.145	0.46078	D	0.99885	B;B	0.10296	0.003;0.001	B;B	0.13407	0.009;0.001	T	0.57069	-0.7874	10	0.13470	T	0.59	.	15.5408	0.76043	0.0:0.0:0.0:1.0	.	1184;576	Q6P158;Q59G60	DHX57_HUMAN;.	A	1184	ENSP00000295373:E1184A	ENSP00000295373:E1184A	E	-	2	0	DHX57	38896222	1.000000	0.71417	0.992000	0.48379	0.948000	0.59901	5.728000	0.68531	2.120000	0.65058	0.460000	0.39030	GAA	T|0.996;G|0.004	0.004	strong		0.453	DHX57-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000219940.2	NM_145646	
MSH2	4436	hgsc.bcm.edu	37	2	47630528	47630528	+	Silent	SNP	C	C	T			TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr2:47630528C>T	ENST00000233146.2	+	1	421	c.198C>T	c.(196-198)taC>taT	p.Y66Y	MSH2_ENST00000543555.1_5'UTR|MSH2_ENST00000406134.1_Silent_p.Y66Y	NM_000251.2	NP_000242.1	P43246	MSH2_HUMAN	mutS homolog 2	66					ATP catabolic process (GO:0006200)|B cell differentiation (GO:0030183)|B cell mediated immunity (GO:0019724)|cell cycle arrest (GO:0007050)|determination of adult lifespan (GO:0008340)|DNA repair (GO:0006281)|double-strand break repair (GO:0006302)|germ cell development (GO:0007281)|in utero embryonic development (GO:0001701)|intra-S DNA damage checkpoint (GO:0031573)|intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator (GO:0042771)|isotype switching (GO:0045190)|maintenance of DNA repeat elements (GO:0043570)|male gonad development (GO:0008584)|meiotic gene conversion (GO:0006311)|meiotic mismatch repair (GO:0000710)|mismatch repair (GO:0006298)|negative regulation of DNA recombination (GO:0045910)|negative regulation of neuron apoptotic process (GO:0043524)|negative regulation of reciprocal meiotic recombination (GO:0045128)|oxidative phosphorylation (GO:0006119)|positive regulation of helicase activity (GO:0051096)|postreplication repair (GO:0006301)|response to UV-B (GO:0010224)|response to X-ray (GO:0010165)|somatic hypermutation of immunoglobulin genes (GO:0016446)|somatic recombination of immunoglobulin gene segments (GO:0016447)	membrane (GO:0016020)|MutSalpha complex (GO:0032301)|MutSbeta complex (GO:0032302)|nuclear chromosome (GO:0000228)	ATP binding (GO:0005524)|centromeric DNA binding (GO:0019237)|damaged DNA binding (GO:0003684)|DNA binding (GO:0003677)|DNA-dependent ATPase activity (GO:0008094)|double-strand/single-strand DNA junction binding (GO:0000406)|enzyme binding (GO:0019899)|guanine/thymine mispair binding (GO:0032137)|heteroduplex DNA loop binding (GO:0000404)|protein C-terminus binding (GO:0008022)|protein homodimerization activity (GO:0042803)|protein kinase binding (GO:0019901)|Y-form DNA binding (GO:0000403)	p.0?(2)|p.?(1)		NS(1)|breast(4)|central_nervous_system(2)|cervix(3)|endometrium(6)|haematopoietic_and_lymphoid_tissue(9)|kidney(5)|large_intestine(50)|lung(18)|ovary(5)|prostate(2)|skin(3)|small_intestine(1)|stomach(2)|urinary_tract(1)	112		all_hematologic(82;0.0359)|Acute lymphoblastic leukemia(82;0.175)	Lung(47;0.101)|LUSC - Lung squamous cell carcinoma(58;0.151)			TGATCAAGTACATGGGGCCGG	0.706			"""D, Mis, N, F, S"""		"""colorectal, endometrial, ovarian"""	"""colorectal, endometrial, ovarian"""		Mismatch excision repair (MMR)	Turcot syndrome;Muir-Torre syndrome;Lynch syndrome;Constitutional Mismatch Repair Deficiency Syndrome																												p.Y66Y		Atlas-SNP	.	yes	Rec	yes	Hereditary non-polyposis colorectal cancer	2	2p22-p21	4436	mutS homolog 2 (E. coli)		E	.	MSH2	198	.	3	Whole gene deletion(2)|Unknown(1)	haematopoietic_and_lymphoid_tissue(3)	c.C198T						PASS	.						9.0	12.0	11.0					2																	47630528		2186	4271	6457	SO:0001819	synonymous_variant	4436	exon1	Familial Cancer Database	Brain tumor-colorectal polyp(osis) syndrome; ;Hereditary Non-Polyposis Colorectal Cancer, HNPCC, Lynch syndromes 1 and 2 (= Cancer Family Syndrome), Hereditary Mismatch Repair Deficiency syndrome, HMRDS;Mismatch Repair Cancer syndrome, MMRCS, Childhood Cancer Syndrome, CCS, Biallelic Mismatch Repair Gene Mutations Associated Early Onset Cancer, Lynch syndrome type III	CAAGTACATGGGG	U03911	CCDS1834.1, CCDS58709.1	2p21	2014-09-17	2013-09-12		ENSG00000095002	ENSG00000095002			7325	protein-coding gene	gene with protein product		609309	"""mutS (E. coli) homolog 2 (colon cancer, nonpolyposis type 1)"", ""mutS homolog 2, colon cancer, nonpolyposis type 1 (E. coli)"""	COCA1		8484120, 9843200	Standard	NM_000251		Approved	HNPCC, HNPCC1	uc002rvy.2	P43246	OTTHUMG00000128861	ENST00000233146.2:c.198C>T	2.37:g.47630528C>T		171.0	0.0	0		111.0	62.0	0.558559	NM_000251	B4E2Z2|O75488	Silent	SNP	ENST00000233146.2	37	CCDS1834.1																																																																																			.	.	none		0.706	MSH2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250805.3		
DPF3	8110	hgsc.bcm.edu	37	14	73137882	73137882	+	Intron	SNP	G	G	A	rs202093453		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr14:73137882G>A	ENST00000556509.1	-	8	871				DPF3_ENST00000546183.1_Missense_Mutation_p.R356W|DPF3_ENST00000541685.1_Missense_Mutation_p.R346W|DPF3_ENST00000557704.1_5'UTR	NM_001280542.1	NP_001267471.1	Q92784	DPF3_HUMAN	D4, zinc and double PHD fingers, family 3						chromatin modification (GO:0016568)|nervous system development (GO:0007399)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nBAF complex (GO:0071565)	zinc ion binding (GO:0008270)			central_nervous_system(1)|cervix(1)|endometrium(2)|kidney(1)|large_intestine(3)|lung(13)|ovary(1)	22				BRCA - Breast invasive adenocarcinoma(234;0.00649)|OV - Ovarian serous cystadenocarcinoma(108;0.0654)		GGCGAACCCCGGCCACTGCGG	0.547													G|||	1	0.000199681	0.0	0.0014	5008	,	,		16614	0.0		0.0	False		,,,				2504	0.0				p.R346W		Atlas-SNP	.											.	DPF3	117	.	0			c.C1036T						PASS	.	G	TRP/ARG	1,4029		0,1,2014	55.0	57.0	56.0		1036	4.8	1.0	14		56	8,8334		0,8,4163	yes	missense	DPF3	NM_012074.3	101	0,9,6177	AA,AG,GG		0.0959,0.0248,0.0727	benign	346/358	73137882	9,12363	2015	4171	6186	SO:0001627	intron_variant	8110	exon9			AACCCCGGCCACT	U43919	CCDS45133.1, CCDS61495.1, CCDS61496.1, CCDS61497.1	14q24.2	2014-05-13			ENSG00000205683	ENSG00000205683		"""Zinc fingers, PHD-type"""	17427	protein-coding gene	gene with protein product		601672				11845289, 8812431	Standard	NM_012074		Approved	cer-d4, Cerd4, FLJ14079, BAF45c	uc010ari.1	Q92784		ENST00000556509.1:c.871+3065C>T	14.37:g.73137882G>A		86.0	0.0	0		139.0	91.0	0.654676	NM_012074	A8MSI3|B7Z276|F5H575|Q32UJ0|Q6P9E6|Q6ZT41|Q9H7Y5	Missense_Mutation	SNP	ENST00000556509.1	37		.	.	.	.	.	.	.	.	.	.	G	17.16	3.317391	0.60524	2.48E-4	9.59E-4	ENSG00000205683	ENST00000541685;ENST00000546183	T;T	0.67523	-0.25;-0.27	5.79	4.82	0.62117	.	.	.	.	.	T	0.47619	0.1455	N	0.08118	0	0.27889	N	0.939402	D;P	0.60160	0.987;0.923	P;B	0.44561	0.453;0.237	T	0.42155	-0.9468	9	0.87932	D	0	.	7.5751	0.27931	0.0:0.117:0.3984:0.4846	.	356;346	F5H575;Q92784-2	.;.	W	346;356	ENSP00000441640:R346W;ENSP00000444662:R356W	ENSP00000381791:R401W	R	-	1	2	DPF3	72207635	1.000000	0.71417	1.000000	0.80357	0.971000	0.66376	1.667000	0.37471	1.366000	0.46076	0.655000	0.94253	CGG	.	.	weak		0.547	DPF3-004	NOVEL	basic|appris_principal|exp_conf	protein_coding	protein_coding	OTTHUMT00000413152.2		
PALLD	23022	hgsc.bcm.edu	37	4	169819835	169819835	+	Silent	SNP	A	A	G	rs113676921	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr4:169819835A>G	ENST00000505667.1	+	14	2615	c.2442A>G	c.(2440-2442)acA>acG	p.T814T	PALLD_ENST00000507735.1_Silent_p.T310T|CBR4_ENST00000509108.1_Intron|PALLD_ENST00000261509.6_Silent_p.T797T|PALLD_ENST00000512127.1_Silent_p.T415T|PALLD_ENST00000335742.7_Silent_p.T639T			Q8WX93	PALLD_HUMAN	palladin, cytoskeletal associated protein	1021	Interaction with ARGBP2, SPIN90, SRC and PFN1.|Interaction with EPS8. {ECO:0000250}.|Pro-rich.				cytoskeleton organization (GO:0007010)	actin filament (GO:0005884)|cell projection (GO:0042995)|cytoplasm (GO:0005737)|focal adhesion (GO:0005925)|nucleus (GO:0005634)	muscle alpha-actinin binding (GO:0051371)			breast(4)|cervix(1)|endometrium(3)|kidney(4)|large_intestine(6)|liver(2)|lung(18)|ovary(3)|prostate(3)|skin(4)	48		Prostate(90;0.00996)|Renal(120;0.0203)|Melanoma(52;0.144)		GBM - Glioblastoma multiforme(119;0.204)		TAACTTTCACATGTAGAGTGG	0.423									Pancreatic Cancer, Familial Clustering of				A|||	7	0.00139776	0.0	0.0	5008	,	,		19745	0.0		0.007	False		,,,				2504	0.0				p.T814T	Esophageal Squamous(109;1482 1532 18347 40239 51172)	Atlas-SNP	.											.	PALLD	179	.	0			c.A2442G						PASS	.	A	,,,	3,4403	6.2+/-15.9	0,3,2200	103.0	98.0	100.0		2442,1245,930,2391	-7.0	0.9	4	dbSNP_132	100	48,8552	30.7+/-82.3	0,48,4252	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	PALLD	NM_001166108.1,NM_001166109.1,NM_001166110.1,NM_016081.3	,,,	0,51,6452	GG,GA,AA		0.5581,0.0681,0.3921	,,,	814/1124,415/778,310/673,797/1107	169819835	51,12955	2203	4300	6503	SO:0001819	synonymous_variant	23022	exon14	Familial Cancer Database	incl.: Hereditary Pancreatic Adenocarcinoma, Insulin-Dependent Diabetes Mellitus - Exocrine Insufficiency - Familial Pancreatic Cancer, PNCA1	TTTCACATGTAGA	AB023209	CCDS34098.1, CCDS54818.1, CCDS54819.1, CCDS54820.1	4q32.3	2013-01-11			ENSG00000129116	ENSG00000129116		"""Immunoglobulin superfamily / I-set domain containing"""	17068	protein-coding gene	gene with protein product		608092				10231032, 10931874	Standard	NM_001166108		Approved	KIAA0992, SIH002, CGI-151	uc011cjx.2	Q8WX93	OTTHUMG00000161097	ENST00000505667.1:c.2442A>G	4.37:g.169819835A>G		119.0	0.0	0		70.0	47.0	0.671429	NM_001166108	B3KTG2|B5MD56|B7ZMM5|Q7L3E0|Q7Z3W0|Q86WE8|Q8N1M2|Q9UGA0|Q9UQF5|Q9Y2J6|Q9Y3E9	Silent	SNP	ENST00000505667.1	37	CCDS54818.1																																																																																			A|0.996;G|0.004	0.004	strong		0.423	PALLD-002	NOVEL	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000363762.1	NM_016081	
LVRN	206338	hgsc.bcm.edu	37	5	115298898	115298898	+	Missense_Mutation	SNP	C	C	T	rs145336539	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr5:115298898C>T	ENST00000357872.4	+	1	708	c.584C>T	c.(583-585)cCc>cTc	p.P195L	AQPEP_ENST00000395528.2_5'UTR	NM_173800.4	NP_776161.3	Q6Q4G3	AMPQ_HUMAN		195						integral component of membrane (GO:0016021)	metallopeptidase activity (GO:0008237)|zinc ion binding (GO:0008270)										CTCAGTGAGCCCCTGAAACCT	0.622													C|||	16	0.00319489	0.0008	0.0086	5008	,	,		14129	0.0		0.008	False		,,,				2504	0.001				p.P195L		Atlas-SNP	.											.	.	.	.	0			c.C584T						PASS	.	C	LEU/PRO	3,4397		0,3,2197	21.0	22.0	22.0		584	4.6	0.9	5	dbSNP_134	22	39,8545		0,39,4253	yes	missense	AQPEP	NM_173800.4	98	0,42,6450	TT,TC,CC		0.4543,0.0682,0.3235	benign	195/991	115298898	42,12942	2200	4292	6492	SO:0001583	missense	0	exon1			GTGAGCCCCTGAA																												ENST00000357872.4:c.584C>T	5.37:g.115298898C>T	ENSP00000350541:p.Pro195Leu	131.0	0.0	0		131.0	56.0	0.427481	NM_173800	A8K6J0|C9JGD2|Q32MR1|Q4G0I9|Q4G0V2|Q86XA3|Q8NBZ2	Missense_Mutation	SNP	ENST00000357872.4	37	CCDS4124.1	7	0.003205128205128205	1	0.0020325203252032522	3	0.008287292817679558	0	0.0	3	0.00395778364116095	C	8.710	0.911797	0.17907	6.82E-4	0.004543	ENSG00000172901	ENST00000357872;ENST00000379578	T	0.02656	4.21	4.6	4.6	0.57074	Peptidase M1, membrane alanine aminopeptidase, N-terminal (1);	1.383950	0.04803	N	0.433838	T	0.03305	0.0096	L	0.43554	1.36	0.80722	D	1	B	0.27013	0.166	B	0.25614	0.062	T	0.41963	-0.9479	10	0.35671	T	0.21	.	12.9406	0.58340	0.0:1.0:0.0:0.0	.	195	Q6Q4G3	AMPQ_HUMAN	L	195;184	ENSP00000350541:P195L	ENSP00000350541:P195L	P	+	2	0	AC010282.1	115326797	0.002000	0.14202	0.891000	0.34965	0.178000	0.23041	1.441000	0.35035	2.105000	0.64084	0.655000	0.94253	CCC	C|0.997;T|0.003	0.003	strong		0.622	AQPEP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250852.1		
GPR20	2843	hgsc.bcm.edu	37	8	142367350	142367350	+	Missense_Mutation	SNP	C	C	T	rs201039593	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr8:142367350C>T	ENST00000377741.3	-	2	764	c.674G>A	c.(673-675)cGg>cAg	p.R225Q	CTD-3064M3.3_ENST00000562459.1_RNA	NM_005293.2	NP_005284.2	Q99678	GPR20_HUMAN	G protein-coupled receptor 20	225					G-protein coupled receptor signaling pathway (GO:0007186)	integral component of plasma membrane (GO:0005887)|receptor complex (GO:0043235)	G-protein coupled receptor activity (GO:0004930)			NS(1)|endometrium(3)|lung(4)|ovary(1)|prostate(1)|skin(3)|upper_aerodigestive_tract(2)	15	all_cancers(97;4.32e-16)|all_epithelial(106;6.61e-14)|Lung NSC(106;9.4e-06)|all_lung(105;1.35e-05)|Ovarian(258;0.0303)|Acute lymphoblastic leukemia(118;0.155)		BRCA - Breast invasive adenocarcinoma(115;0.0415)			CAGACCCGGCCGCGACAGTGC	0.652													C|||	4	0.000798722	0.0008	0.0	5008	,	,		18546	0.0		0.003	False		,,,				2504	0.0				p.R225Q		Atlas-SNP	.											.	GPR20	43	.	0			c.G674A						PASS	.	C	GLN/ARG	4,4162		0,4,2079	10.0	9.0	9.0		674	3.7	0.2	8	dbSNP_134	9	52,8166		1,50,4058	yes	missense	GPR20	NM_005293.2	43	1,54,6137	TT,TC,CC		0.6328,0.096,0.4522	probably-damaging	225/359	142367350	56,12328	2083	4109	6192	SO:0001583	missense	2843	exon2			CCCGGCCGCGACA	U66579	CCDS34949.1	8q24.3	2012-08-21				ENSG00000204882		"""GPCR / Class A : Orphans"""	4475	protein-coding gene	gene with protein product		601908				18347022	Standard	NM_005293		Approved		uc003ywf.3	Q99678		ENST00000377741.3:c.674G>A	8.37:g.142367350C>T	ENSP00000366970:p.Arg225Gln	20.0	0.0	0		20.0	20.0	1	NM_005293	Q17R96	Missense_Mutation	SNP	ENST00000377741.3	37	CCDS34949.1	.	.	.	.	.	.	.	.	.	.	C	10.82	1.459179	0.26248	9.6E-4	0.006328	ENSG00000204882	ENST00000377741	T	0.41400	1.0	4.77	3.67	0.42095	GPCR, rhodopsin-like superfamily (1);	0.643696	0.13570	U	0.378104	T	0.29684	0.0741	L	0.35793	1.09	0.09310	N	1	D	0.55800	0.973	P	0.48166	0.569	T	0.06588	-1.0818	10	0.32370	T	0.25	-20.3414	9.5849	0.39510	0.0:0.8396:0.0:0.1604	.	225	Q99678	GPR20_HUMAN	Q	225	ENSP00000366970:R225Q	ENSP00000366970:R225Q	R	-	2	0	GPR20	142436532	0.004000	0.15560	0.175000	0.22980	0.085000	0.17905	0.829000	0.27449	2.197000	0.70478	0.462000	0.41574	CGG	.	.	weak		0.652	GPR20-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000378968.1	NM_005293	
OGDHL	55753	hgsc.bcm.edu	37	10	50959965	50959965	+	Silent	SNP	C	C	T	rs7090775	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr10:50959965C>T	ENST00000374103.4	-	6	742	c.657G>A	c.(655-657)caG>caA	p.Q219Q	OGDHL_ENST00000419399.1_Silent_p.Q162Q|OGDHL_ENST00000432695.1_Silent_p.Q10Q	NM_018245.2	NP_060715.2	Q9ULD0	OGDHL_HUMAN	oxoglutarate dehydrogenase-like	219					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						GCCGGATCCACTGGCACTGCT	0.592													C|||	274	0.0547125	0.0877	0.0331	5008	,	,		19769	0.004		0.0219	False		,,,				2504	0.1115				p.Q219Q		Atlas-SNP	.											.	OGDHL	149	.	0			c.G657A						PASS	.	C	,,	263,4143	150.3+/-184.3	10,243,1950	193.0	187.0	189.0		486,30,657	4.7	1.0	10	dbSNP_116	189	287,8313	107.8+/-168.5	4,279,4017	no	coding-synonymous,coding-synonymous,coding-synonymous	OGDHL	NM_001143996.1,NM_001143997.1,NM_018245.2	,,	14,522,5967	TT,TC,CC		3.3372,5.9691,4.2288	,,	162/954,10/802,219/1011	50959965	550,12456	2203	4300	6503	SO:0001819	synonymous_variant	55753	exon6			GATCCACTGGCAC	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.657G>A	10.37:g.50959965C>T		184.0	0.0	0		92.0	73.0	0.793478	NM_018245	A8K2G1|B4DKG2|B4E193|Q8TAN9|Q9NVA0	Silent	SNP	ENST00000374103.4	37	CCDS7234.1																																																																																			C|0.960;T|0.040	0.040	strong		0.592	OGDHL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048007.1	NM_018245	
OR10V1	390201	hgsc.bcm.edu	37	11	59480759	59480759	+	Missense_Mutation	SNP	C	C	T	rs141649641	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr11:59480759C>T	ENST00000307552.2	-	1	578	c.560G>A	c.(559-561)cGc>cAc	p.R187H	STX3_ENST00000300150.7_5'Flank	NM_001005324.1	NP_001005324.1	Q8NGI7	O10V1_HUMAN	olfactory receptor, family 10, subfamily V, member 1	187						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			endometrium(1)|large_intestine(3)|liver(1)|lung(10)|skin(1)	16						ACAAGCCAGGCGCATGACTGC	0.483													C|||	3	0.000599042	0.0	0.0	5008	,	,		23804	0.0		0.003	False		,,,				2504	0.0				p.R187H		Atlas-SNP	.											.	OR10V1	40	.	0			c.G560A						PASS	.	C	HIS/ARG	5,4397	9.9+/-24.2	0,5,2196	104.0	89.0	94.0		560	-0.0	1.0	11	dbSNP_134	94	31,8559	21.6+/-65.8	0,31,4264	yes	missense	OR10V1	NM_001005324.1	29	0,36,6460	TT,TC,CC		0.3609,0.1136,0.2771	benign	187/310	59480759	36,12956	2201	4295	6496	SO:0001583	missense	390201	exon1			GCCAGGCGCATGA	AB065807	CCDS31565.1	11q12.1	2012-08-09			ENSG00000172289	ENSG00000172289		"""GPCR / Class A : Olfactory receptors"""	15136	protein-coding gene	gene with protein product							Standard	NM_001005324		Approved		uc001nof.1	Q8NGI7	OTTHUMG00000167406	ENST00000307552.2:c.560G>A	11.37:g.59480759C>T	ENSP00000302199:p.Arg187His	102.0	0.0	0		94.0	52.0	0.553191	NM_001005324	Q6IFD9|Q96R50	Missense_Mutation	SNP	ENST00000307552.2	37	CCDS31565.1	1	4.578754578754579E-4	0	0.0	0	0.0	0	0.0	1	0.0013192612137203166	C	9.722	1.159943	0.21454	0.001136	0.003609	ENSG00000172289	ENST00000307552	T	0.00137	8.68	4.47	-0.0376	0.13883	GPCR, rhodopsin-like superfamily (1);	0.258733	0.25869	N	0.027762	T	0.00109	0.0003	L	0.37800	1.135	0.24816	N	0.992619	B	0.31383	0.321	B	0.32149	0.141	T	0.28681	-1.0036	10	0.54805	T	0.06	.	5.0568	0.14537	0.142:0.5452:0.0:0.3128	.	187	Q8NGI7	O10V1_HUMAN	H	187	ENSP00000302199:R187H	ENSP00000302199:R187H	R	-	2	0	OR10V1	59237335	0.000000	0.05858	0.993000	0.49108	0.635000	0.38103	-1.103000	0.03329	-0.105000	0.12132	-0.545000	0.04230	CGC	C|0.998;T|0.002	0.002	strong		0.483	OR10V1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000394517.1	NM_001005324	
CASP12	100506742	hgsc.bcm.edu	37	11	104768098	104768098	+	Silent	SNP	T	T	C	rs555367	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr11:104768098T>C	ENST00000422698.2	-	2	123	c.105A>G	c.(103-105)gtA>gtG	p.V35V	CASP12_ENST00000447913.1_Intron|CASP12_ENST00000494737.1_Silent_p.V35V|CASP12_ENST00000508062.1_Intron|CASP12_ENST00000446862.1_Silent_p.V35V|CASP12_ENST00000448103.1_Silent_p.V35V|CASP12_ENST00000441710.1_Silent_p.V35V|CASP12_ENST00000433738.1_Intron|CASP12_ENST00000375726.2_Silent_p.V35V	NM_001191016.1	NP_001177945.1	Q6UXS9	CASPC_HUMAN	caspase 12 (gene/pseudogene)	35	CARD. {ECO:0000255|PROSITE- ProRule:PRU00046}.				endoplasmic reticulum unfolded protein response (GO:0030968)|intrinsic apoptotic signaling pathway in response to endoplasmic reticulum stress (GO:0070059)|regulation of apoptotic process (GO:0042981)	cytoplasm (GO:0005737)	cysteine-type endopeptidase activity (GO:0004197)			breast(1)	1						CTGTATTTAATACATTATTTT	0.383													C|||	4957	0.989816	0.9629	0.9971	5008	,	,		18743	1.0		1.0	False		,,,				2504	1.0				p.V35V		Atlas-SNP	.											.	CASP12	4	.	0			c.A105G						PASS	.																																			SO:0001819	synonymous_variant	100506742	exon2			ATTTAATACATTA	AF464191		11q22.3	2011-02-14	2007-12-17	2006-02-17	ENSG00000204403	ENSG00000204403		"""Caspases"""	19004	protein-coding gene	gene with protein product		608633	"""caspase 12 pseudogene 1"", ""caspase 12"""	CASP12P1		12054529, 9038361, 16917906, 16532395	Standard	NM_001191016		Approved		uc031qdo.1	Q6UXS9	OTTHUMG00000154965	ENST00000422698.2:c.105A>G	11.37:g.104768098T>C		0.0	0.0	.		4.0	4.0	1	NM_001191016	D6RBN7	Silent	SNP	ENST00000422698.2	37	CCDS55785.1																																																																																			T|0.010;C|0.990	0.990	strong		0.383	CASP12-008	KNOWN	non_canonical_genome_sequence_error|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000337832.2	NM_001191016	
DHRS4	10901	hgsc.bcm.edu	37	14	24435542	24435542	+	Missense_Mutation	SNP	G	G	T	rs11556285		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr14:24435542G>T	ENST00000313250.5	+	6	785	c.582G>T	c.(580-582)aaG>aaT	p.K194N	DHRS4_ENST00000559632.1_Intron|DHRS4_ENST00000397075.3_Intron|DHRS4_ENST00000558263.1_Intron|DHRS4_ENST00000421831.1_Missense_Mutation_p.K142N|DHRS4_ENST00000558581.1_Missense_Mutation_p.K160N|DHRS4_ENST00000543741.2_Intron|DHRS4_ENST00000308178.8_Intron|DHRS4_ENST00000382761.3_Intron|DHRS4_ENST00000397074.3_Intron|DHRS4_ENST00000397073.2_Intron	NM_021004.2	NP_066284.2	Q9BTZ2	DHRS4_HUMAN	dehydrogenase/reductase (SDR family) member 4	194					alcohol metabolic process (GO:0006066)|cellular ketone metabolic process (GO:0042180)|oxidation-reduction process (GO:0055114)|protein tetramerization (GO:0051262)|steroid metabolic process (GO:0008202)	extracellular vesicular exosome (GO:0070062)|intracellular membrane-bounded organelle (GO:0043231)|mitochondrion (GO:0005739)|nuclear membrane (GO:0031965)|nucleus (GO:0005634)|peroxisomal membrane (GO:0005778)|peroxisome (GO:0005777)	3-keto sterol reductase activity (GO:0000253)|alcohol dehydrogenase [NAD(P)+] activity (GO:0018455)|carbonyl reductase (NADPH) activity (GO:0004090)|oxidoreductase activity, acting on NAD(P)H, quinone or similar compound as acceptor (GO:0016655)|receptor binding (GO:0005102)			central_nervous_system(2)|endometrium(1)|kidney(3)|large_intestine(1)|lung(4)|ovary(1)|skin(1)|upper_aerodigestive_tract(1)	14				GBM - Glioblastoma multiforme(265;0.00962)	Vitamin A(DB00162)	GCCTGACCAAGACCCTGGCCA	0.502																																					p.K194N		Atlas-SNP	.											.	DHRS4	22	.	0			c.G582T						PASS	.																																			SO:0001583	missense	10901	exon6			GACCAAGACCCTG	AF044127	CCDS9605.1, CCDS61408.1, CCDS61409.1, CCDS61410.1, CCDS61411.1, CCDS61412.1	14q11.2	2013-06-14			ENSG00000157326	ENSG00000157326	1.1.1.184	"""Short chain dehydrogenase/reductase superfamily / Classical SDR fold cluster 1"""	16985	protein-coding gene	gene with protein product	"""short chain dehydrogenase/reductase family 25C, member 2"""	611596				10333503, 19027726	Standard	NM_021004		Approved	SCAD-SRL, SDR-SRL, humNRDR, FLJ11008, SDR25C2	uc001wla.3	Q9BTZ2	OTTHUMG00000028777	ENST00000313250.5:c.582G>T	14.37:g.24435542G>T	ENSP00000326219:p.Lys194Asn	1032.0	1.0	0.000968992		1415.0	159.0	0.112367	NM_021004	B2RB10|B7WNS9|D3YTB8|E2QRL8|O95162|Q20CR0|Q2LC19|Q2LE81|Q58IU4|Q6E0Y1|Q6UWU3|Q71UQ6|Q8TD03|Q9H3N5|Q9NV08	Missense_Mutation	SNP	ENST00000313250.5	37	CCDS9605.1	.	.	.	.	.	.	.	.	.	.	G	11.78	1.739826	0.30865	.	.	ENSG00000157326	ENST00000313250;ENST00000421831	T;T	0.46063	0.88;0.88	3.53	2.63	0.31362	Short-chain dehydrogenase/reductase, conserved site (1);NAD(P)-binding domain (1);	0.294117	0.30639	N	0.009188	T	0.54838	0.1883	M	0.82056	2.57	0.80722	D	1	B;P	0.39862	0.326;0.692	B;P	0.52823	0.238;0.71	T	0.54609	-0.8268	10	0.72032	D	0.01	.	5.9644	0.19316	0.251:0.0:0.749:0.0	rs11556285;rs11556285	160;194	Q9BTZ2-4;Q9BTZ2	.;DHRS4_HUMAN	N	194;142	ENSP00000326219:K194N;ENSP00000404147:K142N	ENSP00000326219:K194N	K	+	3	2	DHRS4	23505382	1.000000	0.71417	0.998000	0.56505	0.689000	0.40095	1.961000	0.40432	0.599000	0.29845	0.580000	0.79431	AAG	G|0.998;T|0.002	0.002	weak		0.502	DHRS4-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000071857.3		
PCDHA4	56144	hgsc.bcm.edu	37	5	140188353	140188353	+	Silent	SNP	G	G	A	rs561061447	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr5:140188353G>A	ENST00000530339.1	+	1	1581	c.1581G>A	c.(1579-1581)gaG>gaA	p.E527E	PCDHA4_ENST00000356878.4_Silent_p.E527E|PCDHA1_ENST00000504120.2_Intron|PCDHA2_ENST00000526136.1_Intron|PCDHA1_ENST00000394633.3_Intron|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		136.0	0.0	0		65.0	12.0	0.184615	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	
GPAA1	8733	hgsc.bcm.edu	37	8	145138063	145138063	+	Silent	SNP	G	G	A	rs138412600	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr8:145138063G>A	ENST00000355091.4	+	2	232	c.111G>A	c.(109-111)ttG>ttA	p.L37L	GPAA1_ENST00000361036.6_Intron	NM_003801.3	NP_003792.1	O43292	GPAA1_HUMAN	glycosylphosphatidylinositol anchor attachment 1	37					attachment of GPI anchor to protein (GO:0016255)|C-terminal protein lipidation (GO:0006501)|cellular protein metabolic process (GO:0044267)|post-translational protein modification (GO:0043687)|protein complex assembly (GO:0006461)|protein retention in ER lumen (GO:0006621)	endoplasmic reticulum membrane (GO:0005789)|GPI-anchor transamidase complex (GO:0042765)|membrane (GO:0016020)	tubulin binding (GO:0015631)			breast(1)|endometrium(2)|kidney(1)|large_intestine(3)|lung(10)|upper_aerodigestive_tract(2)	19	all_cancers(97;2.87e-11)|all_epithelial(106;2.16e-09)|Lung NSC(106;5.89e-05)|all_lung(105;0.000174)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155)		OV - Ovarian serous cystadenocarcinoma(54;3.38e-41)|Epithelial(56;6.02e-40)|all cancers(56;2.11e-35)|Colorectal(110;0.055)|BRCA - Breast invasive adenocarcinoma(115;0.105)			CCTGGTTCTTGGCGCTGGTTT	0.677													G|||	22	0.00439297	0.0008	0.0014	5008	,	,		12607	0.0		0.0189	False		,,,				2504	0.001				p.L37L		Atlas-SNP	.											.	GPAA1	40	.	0			c.G111A						PASS	.	G		16,4062		0,16,2023	24.0	29.0	27.0		111	4.0	1.0	8	dbSNP_134	27	153,8217		3,147,4035	no	coding-synonymous	GPAA1	NM_003801.3		3,163,6058	AA,AG,GG		1.828,0.3923,1.3576		37/622	145138063	169,12279	2039	4185	6224	SO:0001819	synonymous_variant	8733	exon2			GTTCTTGGCGCTG	AB006969	CCDS43776.1	8q24.3	2012-12-10	2012-12-10		ENSG00000197858	ENSG00000197858			4446	protein-coding gene	gene with protein product	"""GPI transamidase subunit"""	603048	"""anchor attachment protein 1 (Gaa1p, yeast) homolog"", ""GPAA1P anchor attachment protein 1 homolog (yeast)"", ""glycosylphosphatidylinositol anchor attachment protein 1 homolog (yeast)"""			9828142	Standard	NM_003801		Approved	GAA1, hGAA1	uc003zax.3	O43292	OTTHUMG00000165438	ENST00000355091.4:c.111G>A	8.37:g.145138063G>A		177.0	0.0	0		225.0	76.0	0.337778	NM_003801	Q9NSS0|Q9UQ31	Silent	SNP	ENST00000355091.4	37	CCDS43776.1																																																																																			G|0.993;A|0.007	0.007	strong		0.677	GPAA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000384070.1	NM_003801	
SYNJ2	8871	hgsc.bcm.edu	37	6	158516882	158516882	+	Missense_Mutation	SNP	C	C	T	rs137935231	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr6:158516882C>T	ENST00000355585.4	+	27	4052	c.3977C>T	c.(3976-3978)cCg>cTg	p.P1326L	SYNJ2_ENST00000367112.1_Missense_Mutation_p.P411L|SYNJ2_ENST00000367122.2_Missense_Mutation_p.P1281L	NM_001178088.1|NM_003898.3	NP_001171559.1|NP_003889.1	O15056	SYNJ2_HUMAN	synaptojanin 2	1326	Pro-rich.				phosphatidylinositol biosynthetic process (GO:0006661)|phosphatidylinositol dephosphorylation (GO:0046856)|phospholipid metabolic process (GO:0006644)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)|membrane (GO:0016020)	nucleotide binding (GO:0000166)|phosphatidylinositol-4,5-bisphosphate 5-phosphatase activity (GO:0004439)|RNA binding (GO:0003723)			biliary_tract(1)|endometrium(9)|kidney(3)|large_intestine(11)|lung(14)|ovary(1)|prostate(2)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	46				OV - Ovarian serous cystadenocarcinoma(65;4.42e-18)|BRCA - Breast invasive adenocarcinoma(81;4.23e-05)		CTGGAGGCGCCGCCTCTTGTG	0.657																																					p.P1326L		Atlas-SNP	.											.	SYNJ2	111	.	0			c.C3977T						PASS	.	C	LEU/PRO,LEU/PRO	5,4401	9.9+/-24.2	0,5,2198	42.0	50.0	48.0		3266,3977	2.8	0.0	6	dbSNP_134	48	23,8577	16.6+/-54.9	1,21,4278	yes	missense,missense	SYNJ2	NM_001178088.1,NM_003898.3	98,98	1,26,6476	TT,TC,CC		0.2674,0.1135,0.2153	benign,benign	1089/1260,1326/1497	158516882	28,12978	2203	4300	6503	SO:0001583	missense	8871	exon27			AGGCGCCGCCTCT	AB002346	CCDS5254.1	6q25.3	2008-05-15			ENSG00000078269	ENSG00000078269			11504	protein-coding gene	gene with protein product		609410					Standard	NM_003898		Approved	INPP5H	uc003qqx.2	O15056	OTTHUMG00000015904	ENST00000355585.4:c.3977C>T	6.37:g.158516882C>T	ENSP00000347792:p.Pro1326Leu	60.0	0.0	0		59.0	30.0	0.508475	NM_003898	Q5TA13|Q5TA16|Q5TA19|Q86XK0|Q8IZA8|Q9H226	Missense_Mutation	SNP	ENST00000355585.4	37	CCDS5254.1	.	.	.	.	.	.	.	.	.	.	C	13.26	2.185571	0.38609	0.001135	0.002674	ENSG00000078269	ENST00000367122;ENST00000355585;ENST00000367112	D;D;T	0.93133	-3.17;-3.16;0.83	5.57	2.76	0.32466	.	0.687143	0.13870	N	0.357073	T	0.79516	0.4459	L	0.55481	1.735	0.09310	N	1	B;P	0.48998	0.066;0.918	B;B	0.35510	0.01;0.204	T	0.67898	-0.5551	10	0.25106	T	0.35	.	9.5075	0.39056	0.0:0.7068:0.0:0.2932	.	721;1326	B4DLC4;O15056	.;SYNJ2_HUMAN	L	1281;1326;411	ENSP00000356089:P1281L;ENSP00000347792:P1326L;ENSP00000356079:P411L	ENSP00000347792:P1326L	P	+	2	0	SYNJ2	158436870	0.001000	0.12720	0.000000	0.03702	0.001000	0.01503	0.511000	0.22739	-1.335000	0.02241	-2.210000	0.00300	CCG	C|0.997;T|0.003	0.003	strong		0.657	SYNJ2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042858.2		
ANXA11	311	hgsc.bcm.edu	37	10	81917486	81917486	+	Missense_Mutation	SNP	T	T	C	rs1802932	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr10:81917486T>C	ENST00000438331.1	-	16	1851	c.1369A>G	c.(1369-1371)Atc>Gtc	p.I457V	ANXA11_ENST00000422982.3_Missense_Mutation_p.I457V|ANXA11_ENST00000372231.3_Missense_Mutation_p.I457V|ANXA11_ENST00000535999.1_Missense_Mutation_p.I457V|ANXA11_ENST00000360615.4_Missense_Mutation_p.I457V|ANXA11_ENST00000265447.4_Missense_Mutation_p.I457V|ANXA11_ENST00000537102.1_Missense_Mutation_p.I424V	NM_145869.1	NP_665876.1	P50995	ANX11_HUMAN	annexin A11	457			I -> V (in dbSNP:rs1802932).		cytokinesis, completion of separation (GO:0007109)|phagocytosis (GO:0006909)|response to calcium ion (GO:0051592)	azurophil granule (GO:0042582)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|midbody (GO:0030496)|nuclear envelope (GO:0005635)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|phagocytic vesicle (GO:0045335)|specific granule (GO:0042581)|spindle (GO:0005819)	calcium ion binding (GO:0005509)|calcium-dependent phospholipid binding (GO:0005544)|calcium-dependent protein binding (GO:0048306)|MHC class II protein complex binding (GO:0023026)|phosphatidylethanolamine binding (GO:0008429)|poly(A) RNA binding (GO:0044822)|S100 protein binding (GO:0044548)			endometrium(1)|large_intestine(5)|lung(6)|ovary(2)|prostate(2)|urinary_tract(1)	17	Prostate(51;0.00985)|all_epithelial(25;0.0951)		Colorectal(32;0.109)			GACACCATGATGCGAATCAGG	0.597													t|||	17	0.00339457	0.0	0.0029	5008	,	,		20944	0.0		0.0139	False		,,,				2504	0.001				p.I457V		Atlas-SNP	.											.	ANXA11	32	.	0			c.A1369G						PASS	.	T	VAL/ILE,VAL/ILE,VAL/ILE	13,4393	20.2+/-43.8	0,13,2190	127.0	110.0	116.0		1369,1369,1369	5.2	1.0	10	dbSNP_89	116	105,8495	57.5+/-118.9	1,103,4196	yes	missense,missense,missense	ANXA11	NM_001157.2,NM_145868.1,NM_145869.1	29,29,29	1,116,6386	CC,CT,TT		1.2209,0.2951,0.9073	benign,benign,benign	457/506,457/506,457/506	81917486	118,12888	2203	4300	6503	SO:0001583	missense	311	exon15			CCATGATGCGAAT	L19605	CCDS7364.1, CCDS60576.1	10q22.3	2005-11-09			ENSG00000122359	ENSG00000122359		"""Annexins"""	535	protein-coding gene	gene with protein product		602572		ANX11		7508441, 9503022	Standard	NM_001157		Approved		uc001kbt.1	P50995	OTTHUMG00000018604	ENST00000438331.1:c.1369A>G	10.37:g.81917486T>C	ENSP00000398610:p.Ile457Val	121.0	0.0	0		64.0	39.0	0.609375	NM_145868	B4DVE7	Missense_Mutation	SNP	ENST00000438331.1	37	CCDS7364.1	15	0.006868131868131868	1	0.0020325203252032522	2	0.0055248618784530384	0	0.0	12	0.0158311345646438	T	13.99	2.402389	0.42613	0.002951	0.012209	ENSG00000122359	ENST00000372231;ENST00000422982;ENST00000438331;ENST00000372234;ENST00000360615;ENST00000265447;ENST00000535999;ENST00000424188;ENST00000537102;ENST00000372219	T;T;T;T;T;T;T	0.08984	3.03;3.03;3.03;3.03;3.03;3.03;3.03	5.17	5.17	0.71159	Annexin repeat, conserved site (1);	0.000000	0.85682	D	0.000000	T	0.03739	0.0106	L	0.28192	0.835	0.50313	D	0.999865	B;B;B	0.33345	0.284;0.409;0.409	B;B;B	0.38225	0.103;0.268;0.268	T	0.45614	-0.9249	10	0.27082	T	0.32	.	13.2804	0.60210	0.0:0.0:0.0:1.0	rs1802932;rs1802932	557;457;457	B7Z6L0;Q5T0G8;P50995	.;.;ANX11_HUMAN	V	457;457;457;457;457;457;457;364;424;104	ENSP00000361305:I457V;ENSP00000404412:I457V;ENSP00000398610:I457V;ENSP00000353827:I457V;ENSP00000265447:I457V;ENSP00000441748:I457V;ENSP00000441400:I424V	ENSP00000265447:I457V	I	-	1	0	ANXA11	81907466	1.000000	0.71417	1.000000	0.80357	0.979000	0.70002	4.665000	0.61547	2.082000	0.62665	0.460000	0.39030	ATC	T|0.992;C|0.008	0.008	strong		0.597	ANXA11-003	KNOWN	alternative_5_UTR|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000049044.1	NM_145869	
REXO1	57455	hgsc.bcm.edu	37	19	1827927	1827927	+	Silent	SNP	T	T	G	rs144940979	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr19:1827927T>G	ENST00000170168.4	-	2	955	c.861A>C	c.(859-861)tcA>tcC	p.S287S	REXO1_ENST00000587524.1_5'UTR	NM_020695.3	NP_065746.3	Q8N1G1	REXO1_HUMAN	REX1, RNA exonuclease 1 homolog (S. cerevisiae)	287						nucleus (GO:0005634)	exonuclease activity (GO:0004527)|nucleic acid binding (GO:0003676)			breast(1)|endometrium(1)|kidney(1)|large_intestine(1)|lung(5)|skin(3)|upper_aerodigestive_tract(3)|urinary_tract(1)	16		Ovarian(11;1.78e-06)|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)		CTTCTGAGTCTGAGAACCTTG	0.672													.|||	3	0.000599042	0.0	0.0	5008	,	,		13621	0.0		0.003	False		,,,				2504	0.0				p.S287S		Atlas-SNP	.											.	REXO1	55	.	0			c.A861C						PASS	.	T		0,4404		0,0,2202	41.0	44.0	43.0		861	-8.3	0.1	19	dbSNP_134	43	14,8586	10.5+/-38.8	0,14,4286	no	coding-synonymous	REXO1	NM_020695.3		0,14,6488	GG,GT,TT		0.1628,0.0,0.1077		287/1222	1827927	14,12990	2202	4300	6502	SO:0001819	synonymous_variant	57455	exon2			TGAGTCTGAGAAC	AB032964	CCDS32866.1	19p13.3	2014-05-28	2005-08-22	2005-08-22	ENSG00000079313	ENSG00000079313			24616	protein-coding gene	gene with protein product	"""elongin A binding protein 1"""	609614	"""transcription elongation factor B polypeptide 3 binding protein 1"""	TCEB3BP1		10574461	Standard	NM_020695		Approved	EloA-BP1, KIAA1138	uc002lua.4	Q8N1G1	OTTHUMG00000179991	ENST00000170168.4:c.861A>C	19.37:g.1827927T>G		128.0	0.0	0		138.0	71.0	0.514493	NM_020695	Q9ULT2	Silent	SNP	ENST00000170168.4	37	CCDS32866.1																																																																																			T|0.999;G|0.001	0.001	strong		0.672	REXO1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000449200.1	NM_020695	
TYROBP	7305	hgsc.bcm.edu	37	19	36398454	36398454	+	Silent	SNP	G	G	C	rs111477177	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr19:36398454G>C	ENST00000262629.4	-	3	189	c.123C>G	c.(121-123)ggC>ggG	p.G41G	TYROBP_ENST00000424586.3_Silent_p.G30G|TYROBP_ENST00000589517.1_Silent_p.G41G|TYROBP_ENST00000544690.2_Silent_p.G30G|TYROBP_ENST00000585901.2_Silent_p.G41G	NM_003332.3|NM_198125.2	NP_003323.1|NP_937758.1	O43914	TYOBP_HUMAN	TYRO protein tyrosine kinase binding protein	41					axon guidance (GO:0007411)|cellular defense response (GO:0006968)|innate immune response (GO:0045087)|integrin-mediated signaling pathway (GO:0007229)|intracellular signal transduction (GO:0035556)|macrophage activation involved in immune response (GO:0002281)|neutrophil activation involved in immune response (GO:0002283)|regulation of immune response (GO:0050776)|regulation of osteoclast development (GO:2001204)|signal transduction (GO:0007165)	cell surface (GO:0009986)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	identical protein binding (GO:0042802)|receptor binding (GO:0005102)|receptor signaling protein activity (GO:0005057)			NS(1)|central_nervous_system(1)|large_intestine(1)|lung(4)|skin(1)	8	all_lung(56;7.14e-07)|Lung NSC(56;1.12e-06)|Esophageal squamous(110;0.162)		LUSC - Lung squamous cell carcinoma(66;0.0515)			CTGCCAGCACGCCCGGGCTCA	0.672													G|||	56	0.0111821	0.0008	0.0202	5008	,	,		16218	0.0		0.0348	False		,,,				2504	0.0061				p.G41G		Atlas-SNP	.											TYROBP,NS,carcinoma,-2,1	TYROBP	15	1	0			c.C123G						scavenged	.	G	,,,	36,4370	36.8+/-68.6	0,36,2167	36.0	38.0	37.0		90,90,123,123	-10.3	0.0	19	dbSNP_132	37	366,8234	115.9+/-175.7	8,350,3942	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	TYROBP	NM_001173514.1,NM_001173515.1,NM_003332.3,NM_198125.2	,,,	8,386,6109	CC,CG,GG		4.2558,0.8171,3.0909	,,,	30/103,30/102,41/114,41/113	36398454	402,12604	2203	4300	6503	SO:0001819	synonymous_variant	7305	exon3			CAGCACGCCCGGG	AF019563	CCDS12482.1, CCDS46058.1, CCDS54255.1, CCDS59378.1	19q13.1	2014-09-17				ENSG00000011600			12449	protein-coding gene	gene with protein product	"""killer activating receptor associated protein"", ""DNAX-activation protein 12"""	604142		PLOSL		9490415, 10888890	Standard	NM_003332		Approved	DAP12, PLO-SL, KARAP	uc002ocm.3	O43914		ENST00000262629.4:c.123C>G	19.37:g.36398454G>C		133.0	2.0	0.0150376		108.0	46.0	0.425926	NM_198125	A8K2X0|F5H389|Q6FGA5|Q9UMT3	Silent	SNP	ENST00000262629.4	37	CCDS12482.1																																																																																			A|0.000;C|0.024;G|0.976	0.024	strong		0.672	TYROBP-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000457397.1		
RSPH1	89765	hgsc.bcm.edu	37	21	43913112	43913112	+	Silent	SNP	G	G	A			TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr21:43913112G>A	ENST00000291536.3	-	2	299	c.132C>T	c.(130-132)taC>taT	p.Y44Y	RSPH1_ENST00000398352.3_Intron	NM_080860.2	NP_543136.1	Q8WYR4	RSPH1_HUMAN	radial spoke head 1 homolog (Chlamydomonas)	44					axoneme assembly (GO:0035082)|meiotic nuclear division (GO:0007126)	cytosol (GO:0005829)|motile cilium (GO:0031514)|nucleus (GO:0005634)				large_intestine(7)|lung(2)|ovary(1)|prostate(1)|stomach(1)	12						AGCTCCCTTCGTAGGTGTCCC	0.498																																					p.Y44Y	Esophageal Squamous(23;63 706 6286 10288 12913)	Atlas-SNP	.											RSPH1,NS,carcinoma,0,1	RSPH1	36	1	0			c.C132T						PASS	.						262.0	232.0	242.0					21																	43913112		2203	4300	6503	SO:0001819	synonymous_variant	89765	exon2			CCCTTCGTAGGTG	AB006536	CCDS13688.1, CCDS68210.1	21q22.3	2014-02-03	2007-06-25	2007-06-25	ENSG00000160188	ENSG00000160188			12371	protein-coding gene	gene with protein product	"""meichroacidin"""	609314	"""testis specific A2 homolog (mouse)"""	TSGA2		9403069, 9578619, 17451891	Standard	XM_005261208		Approved	FLJ32753, RSP44, RSPH10A, CILD24	uc002zbg.3	Q8WYR4	OTTHUMG00000086804	ENST00000291536.3:c.132C>T	21.37:g.43913112G>A		148.0	0.0	0		251.0	62.0	0.247012	NM_080860	A8MWV0|B2RBN9|Q3MJA1	Silent	SNP	ENST00000291536.3	37	CCDS13688.1																																																																																			.	.	none		0.498	RSPH1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000195379.1		
MTHFR	4524	hgsc.bcm.edu	37	1	11855269	11855269	+	Missense_Mutation	SNP	C	C	T			TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr1:11855269C>T	ENST00000376592.1	-	5	1045	c.917G>A	c.(916-918)tGc>tAc	p.C306Y	MTHFR_ENST00000376590.3_Missense_Mutation_p.C306Y|MTHFR_ENST00000376583.3_Missense_Mutation_p.C347Y|MTHFR_ENST00000376585.1_Missense_Mutation_p.C347Y			P42898	MTHR_HUMAN	methylenetetrahydrofolate reductase (NAD(P)H)	306					blood circulation (GO:0008015)|cellular amino acid metabolic process (GO:0006520)|folic acid metabolic process (GO:0046655)|homocysteine metabolic process (GO:0050667)|methionine biosynthetic process (GO:0009086)|response to drug (GO:0042493)|response to folic acid (GO:0051593)|response to hypoxia (GO:0001666)|response to interleukin-1 (GO:0070555)|response to vitamin B2 (GO:0033274)|S-adenosylmethionine metabolic process (GO:0046500)|small molecule metabolic process (GO:0044281)|tetrahydrofolate interconversion (GO:0035999)|vitamin metabolic process (GO:0006766)|water-soluble vitamin metabolic process (GO:0006767)	cytosol (GO:0005829)|neuron projection (GO:0043005)	flavin adenine dinucleotide binding (GO:0050660)|methylenetetrahydrofolate reductase (NAD(P)H) activity (GO:0004489)|modified amino acid binding (GO:0072341)|NADP binding (GO:0050661)			NS(4)|breast(1)|cervix(1)|endometrium(4)|kidney(1)|large_intestine(9)|lung(6)|prostate(2)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	33	Ovarian(185;0.249)	Lung NSC(185;8.69e-05)|all_lung(284;9.87e-05)|Renal(390;0.000147)|Breast(348;0.00093)|Colorectal(325;0.00205)|Hepatocellular(190;0.00826)|Ovarian(437;0.00965)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0228)|Colorectal(212;5.66e-06)|COAD - Colon adenocarcinoma(227;0.000261)|BRCA - Breast invasive adenocarcinoma(304;0.000304)|Kidney(185;0.000777)|KIRC - Kidney renal clear cell carcinoma(229;0.00261)|STAD - Stomach adenocarcinoma(313;0.0073)|READ - Rectum adenocarcinoma(331;0.0649)	Benazepril(DB00542)|Cyanocobalamin(DB00115)|Fluorouracil(DB00544)|Folic Acid(DB00158)|L-Methionine(DB00134)|Menadione(DB00170)|Methotrexate(DB00563)|Riboflavin(DB00140)|Tetrahydrofolic acid(DB00116)	AAGCTCCTGGCACAGGCTCAC	0.592																																					p.C306Y		Atlas-SNP	.											.	MTHFR	65	.	0			c.G917A						PASS	.						80.0	80.0	80.0					1																	11855269		2203	4300	6503	SO:0001583	missense	4524	exon6			TCCTGGCACAGGC	BC053509	CCDS137.1	1p36.3	2014-09-17	2010-05-04		ENSG00000177000	ENSG00000177000	1.5.1.20		7436	protein-coding gene	gene with protein product		607093	"""5,10-methylenetetrahydrofolate reductase (NADPH)"""			7920641	Standard	NM_005957		Approved		uc001atc.2	P42898	OTTHUMG00000002277	ENST00000376592.1:c.917G>A	1.37:g.11855269C>T	ENSP00000365777:p.Cys306Tyr	93.0	0.0	0		66.0	10.0	0.151515	NM_005957	B2R7A6|Q5SNW6|Q5SNW9|Q7Z6M6|Q8IU73|Q9UQR2	Missense_Mutation	SNP	ENST00000376592.1	37	CCDS137.1	.	.	.	.	.	.	.	.	.	.	C	25.1	4.600241	0.87055	.	.	ENSG00000177000	ENST00000376592;ENST00000376583;ENST00000376590;ENST00000376585	D;D;D;D	0.92495	-3.05;-3.05;-3.05;-3.05	5.09	5.09	0.68999	.	0.084158	0.85682	D	0.000000	D	0.97359	0.9136	H	0.96239	3.79	0.80722	D	1	D;D	0.69078	0.997;0.997	D;D	0.69479	0.964;0.963	D	0.98609	1.0662	10	0.87932	D	0	.	17.8468	0.88732	0.0:1.0:0.0:0.0	.	306;347	P42898;Q5SNW6	MTHR_HUMAN;.	Y	306;347;306;347	ENSP00000365777:C306Y;ENSP00000365767:C347Y;ENSP00000365775:C306Y;ENSP00000365770:C347Y	ENSP00000365767:C347Y	C	-	2	0	MTHFR	11777856	1.000000	0.71417	1.000000	0.80357	0.836000	0.47400	7.085000	0.76875	2.517000	0.84864	0.462000	0.41574	TGC	.	.	none		0.592	MTHFR-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000006538.1	NM_005957	
PTPN6	5777	hgsc.bcm.edu	37	12	7067226	7067226	+	Missense_Mutation	SNP	G	G	A	rs62621988		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr12:7067226G>A	ENST00000318974.9	+	11	1595	c.1351G>A	c.(1351-1353)Gtg>Atg	p.V451M	PTPN6_ENST00000456013.1_Missense_Mutation_p.V451M|PTPN6_ENST00000399448.1_Missense_Mutation_p.V453M|PTPN6_ENST00000447931.2_Missense_Mutation_p.V412M	NM_002831.5	NP_002822.2	P29350	PTN6_HUMAN	protein tyrosine phosphatase, non-receptor type 6	451	Tyrosine-protein phosphatase. {ECO:0000255|PROSITE-ProRule:PRU00160}.				abortive mitotic cell cycle (GO:0033277)|apoptotic process (GO:0006915)|B cell receptor signaling pathway (GO:0050853)|blood coagulation (GO:0007596)|cell differentiation (GO:0030154)|cell proliferation (GO:0008283)|cytokine-mediated signaling pathway (GO:0019221)|G-protein coupled receptor signaling pathway (GO:0007186)|interferon-gamma-mediated signaling pathway (GO:0060333)|JAK-STAT cascade involved in growth hormone signaling pathway (GO:0060397)|leukocyte migration (GO:0050900)|megakaryocyte development (GO:0035855)|natural killer cell mediated cytotoxicity (GO:0042267)|negative regulation of B cell receptor signaling pathway (GO:0050859)|negative regulation of cell proliferation (GO:0008285)|negative regulation of humoral immune response mediated by circulating immunoglobulin (GO:0002924)|negative regulation of MAP kinase activity (GO:0043407)|negative regulation of peptidyl-tyrosine phosphorylation (GO:0050732)|negative regulation of T cell proliferation (GO:0042130)|negative regulation of T cell receptor signaling pathway (GO:0050860)|peptidyl-tyrosine dephosphorylation (GO:0035335)|peptidyl-tyrosine phosphorylation (GO:0018108)|platelet aggregation (GO:0070527)|platelet formation (GO:0030220)|positive regulation of cell adhesion mediated by integrin (GO:0033630)|positive regulation of cell proliferation (GO:0008284)|positive regulation of phosphatidylinositol 3-kinase signaling (GO:0014068)|protein dephosphorylation (GO:0006470)|regulation of B cell differentiation (GO:0045577)|regulation of ERK1 and ERK2 cascade (GO:0070372)|regulation of G1/S transition of mitotic cell cycle (GO:2000045)|regulation of interferon-gamma-mediated signaling pathway (GO:0060334)|regulation of release of sequestered calcium ion into cytosol (GO:0051279)|regulation of type I interferon-mediated signaling pathway (GO:0060338)|T cell costimulation (GO:0031295)|type I interferon signaling pathway (GO:0060337)	alpha-beta T cell receptor complex (GO:0042105)|cell-cell junction (GO:0005911)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|nucleolus (GO:0005730)|nucleus (GO:0005634)	protein kinase binding (GO:0019901)|protein tyrosine phosphatase activity (GO:0004725)|transmembrane receptor protein tyrosine phosphatase activity (GO:0005001)			breast(1)|endometrium(3)|kidney(1)|large_intestine(5)|lung(5)|prostate(3)	18						GCCCATCATCGTGCACTGCAG	0.532													G|||	1	0.000199681	0.0	0.0	5008	,	,		-128	0.0		0.001	False		,,,				2504	0.0				p.V453M		Atlas-SNP	.											.	PTPN6	42	.	0			c.G1357A						PASS	.	G	MET/VAL,MET/VAL,MET/VAL	2,4098		0,2,2048	36.0	38.0	38.0		1351,1357,1351	5.1	1.0	12	dbSNP_129	38	12,8396		0,12,4192	yes	missense,missense,missense	PTPN6	NM_002831.5,NM_080548.4,NM_080549.3	21,21,21	0,14,6240	AA,AG,GG		0.1427,0.0488,0.1119	probably-damaging,probably-damaging,probably-damaging	451/596,453/598,451/625	7067226	14,12494	2050	4204	6254	SO:0001583	missense	5777	exon11			ATCATCGTGCACT		CCDS41744.1, CCDS44820.1, CCDS44821.1	12p13.31	2013-02-14			ENSG00000111679	ENSG00000111679		"""Protein tyrosine phosphatases / Class I Cys-based PTPs : Non-receptor"", ""SH2 domain containing"""	9658	protein-coding gene	gene with protein product		176883				1639416	Standard	NM_080548		Approved	HCP, HCPH, PTP-1C, SHP-1, SHP1	uc001qsa.1	P29350	OTTHUMG00000168518	ENST00000318974.9:c.1351G>A	12.37:g.7067226G>A	ENSP00000326010:p.Val451Met	41.0	0.0	0		22.0	11.0	0.5	NM_080548	A8K306|G3V0F8|Q969V8|Q9UK67	Missense_Mutation	SNP	ENST00000318974.9	37	CCDS44820.1	1	4.578754578754579E-4	0	0.0	0	0.0	0	0.0	1	0.0013192612137203166	G	19.88	3.908893	0.72868	4.88E-4	0.001427	ENSG00000111679	ENST00000399448;ENST00000447931;ENST00000318974;ENST00000456013	D;D;D;D	0.91124	-2.79;-2.79;-2.79;-2.79	5.08	5.08	0.68730	Protein-tyrosine phosphatase, receptor/non-receptor type (4);Protein-tyrosine/Dual-specificity phosphatase (1);	0.140227	0.48767	D	0.000171	D	0.97480	0.9175	H	0.98646	4.29	0.58432	D	0.999998	D;D;D;D;D	0.89917	1.0;1.0;1.0;1.0;1.0	D;D;D;D;D	0.91635	0.999;0.998;0.998;0.998;0.999	D	0.99410	1.0930	10	0.87932	D	0	.	18.4653	0.90752	0.0:0.0:1.0:0.0	rs62621988	439;412;451;451;453	B4DPS0;P29350-2;G3V0F8;P29350;Q53XS4	.;.;.;PTN6_HUMAN;.	M	453;412;451;451	ENSP00000382376:V453M;ENSP00000415979:V412M;ENSP00000326010:V451M;ENSP00000391592:V451M	ENSP00000326010:V451M	V	+	1	0	PTPN6	6937487	1.000000	0.71417	1.000000	0.80357	0.972000	0.66771	4.603000	0.61105	2.346000	0.79739	0.561000	0.74099	GTG	G|0.999;A|0.001	0.001	strong		0.532	PTPN6-008	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000400023.1	NM_002831	
ZNF845	91664	hgsc.bcm.edu	37	19	53856776	53856776	+	Missense_Mutation	SNP	A	A	G			TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr19:53856776A>G	ENST00000595091.1	+	5	3067	c.2848A>G	c.(2848-2850)Aag>Gag	p.K950E	ZNF845_ENST00000458035.1_Missense_Mutation_p.K950E			Q96IR2	ZN845_HUMAN	zinc finger protein 845	950					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(10)|lung(7)|pancreas(1)|prostate(1)|skin(2)|stomach(1)|urinary_tract(2)	26						TGAATGTGGCAAGGTTTTTAA	0.343																																					p.K950E		Atlas-SNP	.											.	ZNF845	101	.	0			c.A2848G						PASS	.						26.0	24.0	25.0					19																	53856776		692	1589	2281	SO:0001583	missense	91664	exon4			TGTGGCAAGGTTT	BC007307	CCDS46170.1	19q13.42	2013-01-08			ENSG00000213799	ENSG00000213799		"""Zinc fingers, C2H2-type"", ""-"""	25112	protein-coding gene	gene with protein product							Standard	NM_138374		Approved		uc010ydv.1	Q96IR2		ENST00000595091.1:c.2848A>G	19.37:g.53856776A>G	ENSP00000470005:p.Lys950Glu	145.0	0.0	0		156.0	7.0	0.0448718	NM_138374		Missense_Mutation	SNP	ENST00000595091.1	37	CCDS46170.1	.	.	.	.	.	.	.	.	.	.	A	12.64	1.999115	0.35226	.	.	ENSG00000213799	ENST00000458035;ENST00000427984	T	0.27104	1.69	2.04	2.04	0.26737	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.27933	0.0688	M	0.71036	2.16	0.21802	N	0.999532	B	0.02656	0.0	B	0.06405	0.002	T	0.25984	-1.0116	9	0.62326	D	0.03	.	8.7997	0.34901	1.0:0.0:0.0:0.0	.	950	Q96IR2	ZN845_HUMAN	E	950;866	ENSP00000388311:K950E	ENSP00000412086:K866E	K	+	1	0	ZNF845	58548588	0.001000	0.12720	0.001000	0.08648	0.060000	0.15804	1.472000	0.35376	0.918000	0.36919	0.338000	0.21704	AAG	.	.	none		0.343	ZNF845-001	KNOWN	upstream_uORF|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000464359.1	XM_039908	
CDH24	64403	hgsc.bcm.edu	37	14	23523353	23523353	+	Silent	SNP	G	G	T	rs139832060	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr14:23523353G>T	ENST00000267383.5	-	5	1061	c.969C>A	c.(967-969)cgC>cgA	p.R323R	CDH24_ENST00000554034.1_Silent_p.R323R|CDH24_ENST00000397359.3_Silent_p.R323R|CDH24_ENST00000487137.2_Silent_p.R323R			Q86UP0	CAD24_HUMAN	cadherin 24, type 2	323	Cadherin 3. {ECO:0000255|PROSITE- ProRule:PRU00043}.				adherens junction organization (GO:0034332)|cell junction assembly (GO:0034329)|cell-cell junction organization (GO:0045216)|homophilic cell adhesion (GO:0007156)|single organismal cell-cell adhesion (GO:0016337)	cell-cell junction (GO:0005911)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	alpha-catenin binding (GO:0045294)|beta-catenin binding (GO:0008013)|calcium ion binding (GO:0005509)|delta-catenin binding (GO:0070097)			breast(1)|central_nervous_system(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(3)|kidney(1)|large_intestine(6)|lung(5)|ovary(2)|prostate(1)|skin(1)|urinary_tract(1)	26	all_cancers(95;3.3e-05)			GBM - Glioblastoma multiforme(265;0.00654)		GGCTAACCTTGCGGACAGTGA	0.547													G|||	8	0.00159744	0.0	0.0029	5008	,	,		20441	0.0		0.0	False		,,,				2504	0.0061				p.R323R		Atlas-SNP	.											.	CDH24	129	.	0			c.C969A						PASS	.	G	,	4,4400		0,4,2198	78.0	72.0	74.0		969,969	0.3	1.0	14	dbSNP_134	74	41,8553		0,41,4256	yes	coding-synonymous,coding-synonymous	CDH24	NM_022478.3,NM_144985.3	,	0,45,6454	TT,TG,GG		0.4771,0.0908,0.3462	,	323/820,323/782	23523353	45,12953	2202	4297	6499	SO:0001819	synonymous_variant	64403	exon6			AACCTTGCGGACA	AL137477	CCDS9585.1, CCDS9586.1	14q11.2	2010-08-20	2009-11-20		ENSG00000139880	ENSG00000139880		"""Cadherins / Major cadherins"""	14265	protein-coding gene	gene with protein product			"""cadherin-like 24"""			12734196	Standard	NM_022478		Approved	CDH11L	uc001wil.3	Q86UP0	OTTHUMG00000028715	ENST00000267383.5:c.969C>A	14.37:g.23523353G>T		35.0	0.0	0		51.0	34.0	0.666667	NM_022478	D3DS44|Q86UP1|Q9NT84	Silent	SNP	ENST00000267383.5	37	CCDS9585.1																																																																																			G|0.997;T|0.003	0.003	strong		0.547	CDH24-006	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000257241.2	NM_022478	
HGS	9146	hgsc.bcm.edu	37	17	79660570	79660570	+	Missense_Mutation	SNP	C	C	T	rs150616739		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr17:79660570C>T	ENST00000329138.4	+	9	835	c.700C>T	c.(700-702)Ccc>Tcc	p.P234S		NM_004712.4	NP_004703.1	O14964	HGS_HUMAN	hepatocyte growth factor-regulated tyrosine kinase substrate	234	Interaction with SNX1. {ECO:0000250}.				endosomal transport (GO:0016197)|endosome to lysosome transport (GO:0008333)|epidermal growth factor receptor signaling pathway (GO:0007173)|membrane invagination (GO:0010324)|membrane organization (GO:0061024)|negative regulation of cell proliferation (GO:0008285)|negative regulation of epidermal growth factor receptor signaling pathway (GO:0042059)|negative regulation of JAK-STAT cascade (GO:0046426)|positive regulation of gene expression (GO:0010628)|protein localization to membrane (GO:0072657)|protein targeting to lysosome (GO:0006622)|regulation of protein catabolic process (GO:0042176)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|early endosome (GO:0005769)|endosome (GO:0005768)|extracellular vesicular exosome (GO:0070062)|intracellular membrane-bounded organelle (GO:0043231)|membrane (GO:0016020)|secretory granule (GO:0030141)	metal ion binding (GO:0046872)|protein domain specific binding (GO:0019904)			endometrium(2)|kidney(3)|lung(4)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)	12	all_neural(118;0.0878)|all_lung(278;0.23)		BRCA - Breast invasive adenocarcinoma(99;0.0101)|OV - Ovarian serous cystadenocarcinoma(97;0.0955)			CACTGAGCTGCCCCCCGAGTA	0.682																																					p.P234S		Atlas-SNP	.											.	HGS	54	.	0			c.C700T						PASS	.	C	SER/PRO	0,4406		0,0,2203	84.0	67.0	72.0		700	4.4	1.0	17	dbSNP_134	72	2,8598	2.2+/-6.3	0,2,4298	yes	missense	HGS	NM_004712.4	74	0,2,6501	TT,TC,CC		0.0233,0.0,0.0154	probably-damaging	234/778	79660570	2,13004	2203	4300	6503	SO:0001583	missense	9146	exon9			GAGCTGCCCCCCG	D84064	CCDS11784.1	17q25	2009-04-29				ENSG00000185359		"""Zinc fingers, FYVE domain containing"""	4897	protein-coding gene	gene with protein product		604375				9407053, 9630564	Standard	NM_004712		Approved	Hrs, ZFYVE8, Vps27	uc002kbg.3	O14964		ENST00000329138.4:c.700C>T	17.37:g.79660570C>T	ENSP00000331201:p.Pro234Ser	264.0	1.0	0.00378788		223.0	117.0	0.524664	NM_004712	Q9NR36	Missense_Mutation	SNP	ENST00000329138.4	37	CCDS11784.1	.	.	.	.	.	.	.	.	.	.	C	32	5.166816	0.94768	0.0	2.33E-4	ENSG00000185359	ENST00000329138;ENST00000442335	T	0.42900	0.96	4.39	4.39	0.52855	.	0.184051	0.48767	D	0.000171	T	0.61223	0.2330	M	0.82323	2.585	0.80722	D	1	P	0.47545	0.897	P	0.54924	0.764	T	0.65557	-0.6139	10	0.40728	T	0.16	-24.3068	16.3019	0.82825	0.0:1.0:0.0:0.0	.	234	O14964	HGS_HUMAN	S	234	ENSP00000331201:P234S	ENSP00000331201:P234S	P	+	1	0	HGS	77270975	1.000000	0.71417	1.000000	0.80357	0.951000	0.60555	7.258000	0.78371	2.138000	0.66242	0.655000	0.94253	CCC	C|1.000;T|0.000	0.000	weak		0.682	HGS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000440541.1	NM_004712	
AKAP9	10142	hgsc.bcm.edu	37	7	91660861	91660861	+	Silent	SNP	T	T	C			TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr7:91660861T>C	ENST00000359028.2	+	17	4542	c.4317T>C	c.(4315-4317)aaT>aaC	p.N1439N	AKAP9_ENST00000356239.3_Silent_p.N1427N|AKAP9_ENST00000358100.2_Silent_p.N1439N			Q99996	AKAP9_HUMAN	A kinase (PRKA) anchor protein 9	1439					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)			AGGAAACAAATATCGTTAAGT	0.284			T	BRAF	papillary thyroid																																p.N1427N		Atlas-SNP	.		Dom	yes		7	7q21-q22	10142	A kinase (PRKA) anchor protein (yotiao) 9		E	.	AKAP9	788	.	0			c.T4281C						PASS	.						121.0	128.0	126.0					7																	91660861		2202	4297	6499	SO:0001819	synonymous_variant	10142	exon16			AACAAATATCGTT	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.4317T>C	7.37:g.91660861T>C		87.0	0.0	0		91.0	6.0	0.0659341	NM_005751	A4D1F0|A4D1F2|A4D1F4|O14869|O43355|O94895|Q75N20|Q9UQH3|Q9UQQ4|Q9Y6B8|Q9Y6Y2	Silent	SNP	ENST00000359028.2	37																																																																																				.	.	none		0.284	AKAP9-202	KNOWN	basic	protein_coding	protein_coding		NM_005751	
SALL4	57167	hgsc.bcm.edu	37	20	50407255	50407255	+	Silent	SNP	G	G	A	rs201329321		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr20:50407255G>A	ENST00000217086.4	-	2	1878	c.1767C>T	c.(1765-1767)acC>acT	p.T589T	SALL4_ENST00000483130.1_5'Flank|SALL4_ENST00000395997.3_Intron|SALL4_ENST00000371539.3_Intron	NM_020436.3	NP_065169.1	Q9UJQ4	SALL4_HUMAN	spalt-like transcription factor 4	589					embryonic limb morphogenesis (GO:0030326)|inner cell mass cell proliferation (GO:0001833)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|neural tube closure (GO:0001843)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|stem cell maintenance (GO:0019827)|transcription, DNA-templated (GO:0006351)|ventricular septum development (GO:0003281)	cytoplasm (GO:0005737)|heterochromatin (GO:0000792)|nucleus (GO:0005634)|protein complex (GO:0043234)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(7)|lung(27)|ovary(5)|prostate(2)|skin(5)|upper_aerodigestive_tract(1)|urinary_tract(1)	63						GTCTCTCCCCGGTGTGGGTGC	0.507													G|||	1	0.000199681	0.0	0.0	5008	,	,		19405	0.001		0.0	False		,,,				2504	0.0				p.T589T		Atlas-SNP	.											.	SALL4	168	.	0			c.C1767T						PASS	.						93.0	82.0	86.0					20																	50407255		2203	4300	6503	SO:0001819	synonymous_variant	57167	exon2			CTCCCCGGTGTGG	AK001666	CCDS13438.1	20q13.2	2014-09-17	2013-10-17		ENSG00000101115	ENSG00000101115		"""Zinc fingers, C2H2-type"""	15924	protein-coding gene	gene with protein product		607343	"""sal (Drosophila)-like 4"", ""sal-like 4 (Drosophila)"""				Standard	NM_020436		Approved	dJ1112F19.1, ZNF797	uc002xwh.4	Q9UJQ4	OTTHUMG00000032752	ENST00000217086.4:c.1767C>T	20.37:g.50407255G>A		136.0	0.0	0		168.0	50.0	0.297619	NM_020436	A2A2D8|Q540H3|Q6Y8G6	Silent	SNP	ENST00000217086.4	37	CCDS13438.1																																																																																			G|1.000;A|0.000	0.000	strong		0.507	SALL4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079738.3		
DCD	117159	hgsc.bcm.edu	37	12	55038536	55038536	+	Silent	SNP	G	G	A	rs139716642		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr12:55038536G>A	ENST00000293371.6	-	5	483	c.294C>T	c.(292-294)gcC>gcT	p.A98A	DCD_ENST00000456047.2_Missense_Mutation_p.R120C	NM_053283.2	NP_444513.1	P81605	DCD_HUMAN	dermcidin	98					defense response to bacterium (GO:0042742)|defense response to fungus (GO:0050832)|killing of cells of other organism (GO:0031640)	extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)	peptidase activity (GO:0008233)|poly(A) RNA binding (GO:0044822)			large_intestine(2)|lung(2)|ovary(1)|skin(1)	6		Myeloproliferative disorder(1001;0.0255)				CGTCATGGACGGCTCCTAGGA	0.488																																					p.A98A		Atlas-SNP	.											.	DCD	20	.	0			c.C294T						PASS	.	G		1,4405	2.1+/-5.4	0,1,2202	31.0	28.0	29.0		294	-1.2	0.0	12	dbSNP_134	29	2,8596	2.2+/-6.3	0,2,4297	no	coding-synonymous	DCD	NM_053283.2		0,3,6499	AA,AG,GG		0.0233,0.0227,0.0231		98/111	55038536	3,13001	2203	4299	6502	SO:0001819	synonymous_variant	117159	exon5			ATGGACGGCTCCT	AF144011	CCDS8884.1, CCDS73478.1	12q13.1	2008-08-04				ENSG00000161634			14669	protein-coding gene	gene with protein product	"""proteolysis inducing factor"", ""preproteolysin"", ""diffusible survival/evasion peptide"", ""survival promoting peptide"""	606634				11694882	Standard	XM_005268627		Approved	AIDD, PIF, DSEP, HCAP, DCD-1	uc001sgj.3	P81605	OTTHUMG00000169937	ENST00000293371.6:c.294C>T	12.37:g.55038536G>A		214.0	0.0	0		238.0	120.0	0.504202	NM_053283	A5JHP2|A5JHP3|P58461|Q53YJ2	Silent	SNP	ENST00000293371.6	37	CCDS8884.1	.	.	.	.	.	.	.	.	.	.	G	3.323	-0.138330	0.06669	2.27E-4	2.33E-4	ENSG00000161634	ENST00000456047	.	.	.	2.5	-1.22	0.09494	.	.	.	.	.	T	0.28433	0.0703	.	.	.	0.09310	N	1	B	0.06786	0.001	B	0.04013	0.001	T	0.29212	-1.0019	7	0.87932	D	0	.	6.2481	0.20830	0.2528:0.0:0.7472:0.0	.	120	A5JHP3	.	C	120	.	ENSP00000406773:R120C	R	-	1	0	DCD	53324803	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-0.482000	0.06544	-0.129000	0.11620	-0.440000	0.05779	CGT	G|1.000;A|0.000	0.000	weak		0.488	DCD-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000406617.1	NM_053283	
CNTLN	54875	hgsc.bcm.edu	37	9	17135322	17135322	+	Missense_Mutation	SNP	A	A	G			TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr9:17135322A>G	ENST00000380647.3	+	1	343	c.259A>G	c.(259-261)Aga>Gga	p.R87G	CNTLN_ENST00000380641.4_Missense_Mutation_p.R87G|CNTLN_ENST00000425824.1_Missense_Mutation_p.R87G|CNTLN_ENST00000484374.1_3'UTR|CNTLN_ENST00000262360.5_Missense_Mutation_p.R87G			Q9NXG0	CNTLN_HUMAN	centlein, centrosomal protein	87					centriole-centriole cohesion (GO:0010457)|protein localization to organelle (GO:0033365)	centriole (GO:0005814)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)	phosphorelay sensor kinase activity (GO:0000155)|protein binding, bridging (GO:0030674)|protein domain specific binding (GO:0019904)|protein kinase binding (GO:0019901)			breast(6)|central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(5)|kidney(3)|large_intestine(10)|lung(17)|ovary(1)|pancreas(1)|prostate(3)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	53				GBM - Glioblastoma multiforme(50;6.14e-10)		CATGGGGTCCAGACGGCTAGA	0.652																																					p.R87G		Atlas-SNP	.											.	CNTLN	128	.	0			c.A259G						PASS	.						22.0	28.0	26.0					9																	17135322		1996	4163	6159	SO:0001583	missense	54875	exon1			GGGTCCAGACGGC	AK000283	CCDS43789.1, CCDS47953.1	9p22.2-p22.1	2008-11-11	2008-02-08	2008-02-08	ENSG00000044459	ENSG00000044459			23432	protein-coding gene	gene with protein product		611870	"""chromosome 9 open reading frame 101"", ""chromosome 9 open reading frame 39"""	C9orf101, C9orf39		18086554	Standard	XM_005251492		Approved	FLJ20276, bA340N12.1, OTTHUMG00000019597	uc003zmy.3	Q9NXG0	OTTHUMG00000019599	ENST00000380647.3:c.259A>G	9.37:g.17135322A>G	ENSP00000370021:p.Arg87Gly	76.0	0.0	0		49.0	12.0	0.244898	NM_017738	A5Z2X6|Q5VYJ0|Q8N1G9|Q9HAJ5	Missense_Mutation	SNP	ENST00000380647.3	37	CCDS43789.1	.	.	.	.	.	.	.	.	.	.	A	13.10	2.135748	0.37728	.	.	ENSG00000044459	ENST00000380647;ENST00000425824;ENST00000262360;ENST00000380641	T;T;T;T	0.14516	2.5;2.5;2.5;2.5	5.4	-5.91	0.02269	.	.	.	.	.	T	0.04182	0.0116	N	0.08118	0	0.09310	N	1	B;B;B;B	0.06786	0.0;0.0;0.0;0.001	B;B;B;B	0.04013	0.001;0.001;0.001;0.001	T	0.41395	-0.9511	9	0.13470	T	0.59	.	2.1611	0.03825	0.2599:0.2501:0.3609:0.1291	.	87;87;87;87	C9J1F9;Q9NXG0-2;Q9NXG0-3;B1AMC8	.;.;.;.	G	87	ENSP00000370021:R87G;ENSP00000392798:R87G;ENSP00000262360:R87G;ENSP00000370015:R87G	ENSP00000262360:R87G	R	+	1	2	CNTLN	17125322	0.756000	0.28383	0.210000	0.23637	0.766000	0.43426	-0.298000	0.08265	-1.336000	0.02238	-0.478000	0.04885	AGA	.	.	none		0.652	CNTLN-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000051793.3	NM_017738	
IFNGR1	3459	hgsc.bcm.edu	37	6	137540423	137540423	+	Silent	SNP	C	C	T	rs17181471	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr6:137540423C>T	ENST00000367739.4	-	1	163	c.42G>A	c.(40-42)gtG>gtA	p.V14V	IFNGR1_ENST00000367735.2_5'UTR|IFNGR1_ENST00000543628.1_5'Flank|IFNGR1_ENST00000478333.1_5'UTR	NM_000416.2	NP_000407.1	P15260	INGR1_HUMAN	interferon gamma receptor 1	14					cytokine-mediated signaling pathway (GO:0019221)|interferon-gamma-mediated signaling pathway (GO:0060333)|regulation of interferon-gamma-mediated signaling pathway (GO:0060334)|response to virus (GO:0009615)|signal transduction (GO:0007165)	dendrite (GO:0030425)|endoplasmic reticulum (GO:0005783)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|postsynaptic density (GO:0014069)|vesicle (GO:0031982)	interferon-gamma receptor activity (GO:0004906)			central_nervous_system(1)|kidney(3)|large_intestine(3)|lung(9)|skin(1)|upper_aerodigestive_tract(1)	18	Colorectal(23;0.24)			GBM - Glioblastoma multiforme(68;0.000829)|OV - Ovarian serous cystadenocarcinoma(155;0.00389)	Interferon gamma-1b(DB00033)	CAGCCCTGCTCACACCCTGCA	0.687													C|||	22	0.00439297	0.0015	0.0086	5008	,	,		14299	0.0		0.0119	False		,,,				2504	0.002				p.V14V		Atlas-SNP	.											.	IFNGR1	46	.	0			c.G42A						PASS	.	C		10,4392	15.5+/-35.6	0,10,2191	43.0	42.0	42.0		42	3.2	0.0	6	dbSNP_123	42	58,8542	32.8+/-85.7	0,58,4242	no	coding-synonymous	IFNGR1	NM_000416.2		0,68,6433	TT,TC,CC		0.6744,0.2272,0.523		14/490	137540423	68,12934	2201	4300	6501	SO:0001819	synonymous_variant	3459	exon1			CCTGCTCACACCC		CCDS5185.1	6q23-q24	2014-09-17			ENSG00000027697	ENSG00000027697		"""Interferons"", ""CD molecules"""	5439	protein-coding gene	gene with protein product		107470		IFNGR			Standard	NM_000416		Approved	CD119	uc003qho.2	P15260	OTTHUMG00000015656	ENST00000367739.4:c.42G>A	6.37:g.137540423C>T		179.0	0.0	0		131.0	52.0	0.396947	NM_000416	B4DFT7|E1P587|Q53Y96	Silent	SNP	ENST00000367739.4	37	CCDS5185.1																																																																																			C|0.995;T|0.005	0.005	strong		0.687	IFNGR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042401.1		
ADCYAP1R1	117	hgsc.bcm.edu	37	7	31104520	31104520	+	Missense_Mutation	SNP	A	A	G	rs144472289	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr7:31104520A>G	ENST00000304166.4	+	3	414	c.125A>G	c.(124-126)aAt>aGt	p.N42S	ADCYAP1R1_ENST00000409363.1_Missense_Mutation_p.N42S|ADCYAP1R1_ENST00000396211.2_Missense_Mutation_p.N42S|ADCYAP1R1_ENST00000409489.1_Missense_Mutation_p.N42S	NM_001118.4|NM_001199635.1|NM_001199636.1	NP_001109.2|NP_001186564.1|NP_001186565.1	P41586	PACR_HUMAN	adenylate cyclase activating polypeptide 1 (pituitary) receptor type I	42					activation of adenylate cyclase activity (GO:0007190)|cell differentiation (GO:0030154)|cell surface receptor signaling pathway (GO:0007166)|multicellular organismal development (GO:0007275)|neurotrophin TRK receptor signaling pathway (GO:0048011)|spermatogenesis (GO:0007283)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	receptor activity (GO:0004872)|vasoactive intestinal polypeptide receptor activity (GO:0004999)			endometrium(1)|large_intestine(4)|liver(2)|lung(24)|ovary(1)|skin(2)|stomach(1)	35						CAGAGGGCCAATGAGCTGATG	0.557													A|||	10	0.00199681	0.0	0.0014	5008	,	,		21493	0.0		0.0089	False		,,,				2504	0.0				p.N42S	Ovarian(44;225 1186 2158 11092)	Atlas-SNP	.											.	ADCYAP1R1	78	.	0			c.A125G						PASS	.	A	SER/ASN,SER/ASN,SER/ASN,SER/ASN	1,4405	2.1+/-5.4	0,1,2202	81.0	70.0	74.0		125,125,125,125	4.4	1.0	7	dbSNP_134	74	42,8556	27.4+/-76.7	0,42,4257	yes	missense,missense,missense,missense	ADCYAP1R1	NM_001118.4,NM_001199635.1,NM_001199636.1,NM_001199637.1	46,46,46,46	0,43,6459	GG,GA,AA		0.4885,0.0227,0.3307	benign,benign,benign,benign	42/469,42/497,42/496,42/448	31104520	43,12961	2203	4299	6502	SO:0001583	missense	117	exon3			GGGCCAATGAGCT		CCDS5433.1, CCDS56480.1, CCDS56481.1	7p14.3	2012-09-20			ENSG00000078549	ENSG00000078549		"""GPCR / Class B : VIP and PACAP (ADCYAP1) receptors"""	242	protein-coding gene	gene with protein product	"""PACAP receptor 1"""	102981				7902709	Standard	NM_001199635		Approved	PAC1, PACAPR, PAC1R	uc003tcg.3	P41586	OTTHUMG00000023884	ENST00000304166.4:c.125A>G	7.37:g.31104520A>G	ENSP00000306620:p.Asn42Ser	85.0	0.0	0		139.0	69.0	0.496403	NM_001118	A8K1Y1|B7ZLA7|B8ZZK3|Q17S10	Missense_Mutation	SNP	ENST00000304166.4	37	CCDS5433.1	10	0.004578754578754579	0	0.0	1	0.0027624309392265192	0	0.0	9	0.011873350923482849	A	13.14	2.147275	0.37923	2.27E-4	0.004885	ENSG00000078549	ENST00000304166;ENST00000409363;ENST00000431811;ENST00000396211;ENST00000409489	T;T;T;T;T	0.52057	0.68;1.16;0.98;0.68;0.68	5.58	4.36	0.52297	GPCR, family 2, extracellular hormone receptor domain (1);	0.257434	0.36066	N	0.002816	T	0.21186	0.0510	N	0.22421	0.69	0.30532	N	0.767307	B;B;B;B;B	0.11235	0.004;0.002;0.004;0.001;0.004	B;B;B;B;B	0.15052	0.012;0.007;0.007;0.0;0.004	T	0.14952	-1.0454	10	0.09590	T	0.72	.	8.9845	0.35986	0.8131:0.1869:0.0:0.0	.	42;42;42;42;42	B7ZLA7;Q17S10;E9PFU5;B8ZZK3;P41586	.;.;.;.;PACR_HUMAN	S	42	ENSP00000306620:N42S;ENSP00000387335:N42S;ENSP00000400893:N42S;ENSP00000379514:N42S;ENSP00000386395:N42S	ENSP00000306620:N42S	N	+	2	0	ADCYAP1R1	31071045	0.041000	0.20044	0.992000	0.48379	0.984000	0.73092	1.464000	0.35288	2.115000	0.64714	0.460000	0.39030	AAT	A|0.997;G|0.003	0.003	strong		0.557	ADCYAP1R1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000215041.3	NM_001118	
PCDHA4	56144	hgsc.bcm.edu	37	5	140188354	140188354	+	Missense_Mutation	SNP	C	C	G	rs142480630	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr5:140188354C>G	ENST00000530339.1	+	1	1582	c.1582C>G	c.(1582-1584)Cta>Gta	p.L528V	PCDHA4_ENST00000356878.4_Missense_Mutation_p.L528V|PCDHA1_ENST00000504120.2_Intron|PCDHA2_ENST00000526136.1_Intron|PCDHA1_ENST00000394633.3_Intron|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						PASS	.						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	133.0	0.0	0		64.0	11.0	0.171875	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	
KIAA0226	9711	hgsc.bcm.edu	37	3	197408085	197408085	+	Missense_Mutation	SNP	A	A	C			TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr3:197408085A>C	ENST00000296343.5	-	16	2344	c.2345T>G	c.(2344-2346)aTt>aGt	p.I782S	KIAA0226_ENST00000389665.5_Missense_Mutation_p.I807S|KIAA0226_ENST00000273582.5_Missense_Mutation_p.I737S	NM_014687.1	NP_055502.1	Q92622	RUBIC_HUMAN	KIAA0226	782					autophagy (GO:0006914)|cell death (GO:0008219)|endocytosis (GO:0006897)|negative regulation of autophagy (GO:0010507)|negative regulation of endocytosis (GO:0045806)	early endosome (GO:0005769)|late endosome (GO:0005770)|lysosome (GO:0005764)				NS(2)|central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(3)|lung(13)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	31	all_cancers(143;8.26e-10)|Ovarian(172;0.0418)|Breast(254;0.0976)		Epithelial(36;2.19e-23)|all cancers(36;1.39e-21)|OV - Ovarian serous cystadenocarcinoma(49;1.21e-18)|LUSC - Lung squamous cell carcinoma(58;1.51e-06)|Lung(62;1.95e-06)	GBM - Glioblastoma multiforme(93;0.0446)		CCAGATCTTAATGAGCAGGTC	0.517																																					p.I782S	Esophageal Squamous(3;167 355 3763 15924)	Atlas-SNP	.											.	KIAA0226	136	.	0			c.T2345G						PASS	.						149.0	144.0	145.0					3																	197408085		2034	4226	6260	SO:0001583	missense	9711	exon16			ATCTTAATGAGCA	D86979	CCDS43195.1, CCDS46987.1	3q29	2011-08-09			ENSG00000145016	ENSG00000145016			28991	protein-coding gene	gene with protein product	"""RUN domain and cysteine-rich domain containing, Beclin 1-interacting protein"""	613516				9039502, 19270693, 20826435	Standard	XM_005269374		Approved	rubicon, rundataxin	uc003fyc.2	Q92622	OTTHUMG00000155452	ENST00000296343.5:c.2345T>G	3.37:g.197408085A>C	ENSP00000296343:p.Ile782Ser	172.0	0.0	0		156.0	75.0	0.480769	NM_014687	Q96CK5	Missense_Mutation	SNP	ENST00000296343.5	37	CCDS43195.1	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	A|A|A	1.156|1.156|1.156	-0.645279|-0.645279|-0.645279	0.03531|0.03531|0.03531	.|.|.	.|.|.	ENSG00000145016|ENSG00000145016|ENSG00000145016	ENST00000413360|ENST00000273582;ENST00000296343;ENST00000389665|ENST00000415452	.|.|.	.|.|.	.|.|.	4.55|4.55|4.55	0.842|0.842|0.842	0.18927|0.18927|0.18927	.|.|.	.|0.449024|.	.|0.23137|.	.|N|.	.|0.051520|.	T|T|T	0.07052|0.07052|0.07052	0.0179|0.0179|0.0179	N|N|N	0.00413|0.00413|0.00413	-1.525|-1.525|-1.525	0.09310|0.09310|0.09310	N|N|N	1|1|1	.|B;B;B|.	.|0.06786|.	.|0.001;0.0;0.001|.	.|B;B;B|.	.|0.10450|.	.|0.003;0.0;0.005|.	T|T|T	0.39035|0.39035|0.39035	-0.9633|-0.9633|-0.9633	5|9|5	.|0.07990|.	.|T|.	.|0.79|.	.|.|.	5.7617|5.7617|5.7617	0.18203|0.18203|0.18203	0.394:0.4484:0.1575:0.0|0.394:0.4484:0.1575:0.0|0.394:0.4484:0.1575:0.0	.|.|.	.|807;737;782|.	.|Q92622-3;Q92622-2;Q92622|.	.|.;.;RUBIC_HUMAN|.	Q|S|V	743|737;782;807|566	.|.|.	.|ENSP00000273582:I737S|.	H|I|L	-|-|-	3|2|1	2|0|2	KIAA0226|KIAA0226|KIAA0226	198892482|198892482|198892482	0.950000|0.950000|0.950000	0.32346|0.32346|0.32346	0.220000|0.220000|0.220000	0.23810|0.23810|0.23810	0.992000|0.992000|0.992000	0.81027|0.81027|0.81027	1.068000|1.068000|1.068000	0.30629|0.30629|0.30629	0.353000|0.353000|0.353000	0.24079|0.24079|0.24079	0.454000|0.454000|0.454000	0.30748|0.30748|0.30748	CAT|ATT|TTA	.	.	none		0.517	KIAA0226-011	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000340184.1	XM_032901	
ASB6	140459	hgsc.bcm.edu	37	9	132401753	132401753	+	Silent	SNP	G	G	A	rs144137235		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr9:132401753G>A	ENST00000277458.4	-	3	495	c.330C>T	c.(328-330)gcC>gcT	p.A110A	ASB6_ENST00000277459.4_Silent_p.A110A|ASB6_ENST00000450050.2_Silent_p.A31A|RP11-483H20.4_ENST00000455074.1_RNA	NM_017873.3	NP_060343.1	Q9NWX5	ASB6_HUMAN	ankyrin repeat and SOCS box containing 6	110					intracellular signal transduction (GO:0035556)|protein ubiquitination (GO:0016567)	cytoplasm (GO:0005737)				NS(1)|endometrium(4)|kidney(1)|large_intestine(3)|lung(4)|prostate(2)	15		Ovarian(14;0.00556)				TCCGCAGGACGGCGATGTGCA	0.607													G|||	1	0.000199681	0.0	0.0	5008	,	,		18818	0.0		0.001	False		,,,				2504	0.0				p.A110A		Atlas-SNP	.											.	ASB6	31	.	0			c.C330T						PASS	.	G	,,	1,4405	2.1+/-5.4	0,1,2202	55.0	53.0	54.0		330,330,330	-7.5	0.4	9	dbSNP_134	54	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous,coding-synonymous,coding-synonymous	ASB6	NM_001202403.1,NM_017873.3,NM_177999.2	,,	0,2,6501	AA,AG,GG		0.0116,0.0227,0.0154	,,	110/393,110/422,110/198	132401753	2,13004	2203	4300	6503	SO:0001819	synonymous_variant	140459	exon3			CAGGACGGCGATG		CCDS6924.1, CCDS6925.1, CCDS75919.1	9q34.13	2013-01-10	2011-01-25		ENSG00000148331	ENSG00000148331		"""Ankyrin repeat domain containing"""	17181	protein-coding gene	gene with protein product		615051	"""ankyrin repeat and SOCS box-containing 6"""				Standard	NM_017873		Approved		uc004byf.2	Q9NWX5	OTTHUMG00000020787	ENST00000277458.4:c.330C>T	9.37:g.132401753G>A		82.0	0.0	0		81.0	34.0	0.419753	NM_017873	Q5SZB7|Q9BV15	Silent	SNP	ENST00000277458.4	37	CCDS6924.1																																																																																			G|0.999;A|0.001	0.001	strong		0.607	ASB6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054594.1	NM_017873	
BRD1	23774	hgsc.bcm.edu	37	22	50217387	50217387	+	Silent	SNP	G	G	A	rs11912787	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr22:50217387G>A	ENST00000216267.8	-	1	1065	c.579C>T	c.(577-579)ttC>ttT	p.F193F	BRD1_ENST00000342989.5_5'Flank|BRD1_ENST00000404034.1_Silent_p.F193F|BRD1_ENST00000542442.1_5'Flank|BRD1_ENST00000459821.1_5'Flank|BRD1_ENST00000404760.1_Silent_p.F193F|BRD1_ENST00000457780.2_Silent_p.F193F	NM_014577.1	NP_055392.1	O95696	BRD1_HUMAN	bromodomain containing 1	193					histone H3 acetylation (GO:0043966)	MOZ/MORF histone acetyltransferase complex (GO:0070776)|nucleus (GO:0005634)	histone binding (GO:0042393)|zinc ion binding (GO:0008270)			endometrium(6)|kidney(3)|large_intestine(5)|lung(17)|ovary(1)|pancreas(1)|prostate(3)|skin(1)	37		all_cancers(38;6.11e-10)|all_epithelial(38;8.06e-09)|all_lung(38;6.64e-05)|Lung NSC(38;0.0011)|Breast(42;0.00235)|Ovarian(80;0.0139)|Lung SC(80;0.164)		UCEC - Uterine corpus endometrioid carcinoma (28;0.0369)|BRCA - Breast invasive adenocarcinoma(115;0.21)		ACTCCTTCTCGAAGCGGTCCA	0.602													G|||	508	0.101438	0.1664	0.0432	5008	,	,		21111	0.003		0.0746	False		,,,				2504	0.184				p.F193F		Atlas-SNP	.											.	BRD1	144	.	0			c.C579T						PASS	.	G		801,3605	322.9+/-297.8	69,663,1471	72.0	61.0	65.0		579	-5.2	1.0	22	dbSNP_120	65	702,7898	172.6+/-223.3	31,640,3629	no	coding-synonymous	BRD1	NM_014577.1		100,1303,5100	AA,AG,GG		8.1628,18.1798,11.5562		193/1059	50217387	1503,11503	2203	4300	6503	SO:0001819	synonymous_variant	23774	exon1			CTTCTCGAAGCGG	AF005067	CCDS14080.1	22q13.33	2008-07-01	2002-01-14		ENSG00000100425	ENSG00000100425			1102	protein-coding gene	gene with protein product	"""BR140-like"""	604589	"""bromodomain-containing 1"""			10591208, 10602503	Standard	NM_014577		Approved	BRL, BRPF2	uc003biv.3	O95696	OTTHUMG00000150288	ENST00000216267.8:c.579C>T	22.37:g.50217387G>A		112.0	0.0	0		116.0	57.0	0.491379	NM_014577	A6ZJA4	Silent	SNP	ENST00000216267.8	37	CCDS14080.1																																																																																			G|0.899;A|0.101	0.101	strong		0.602	BRD1-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000317402.1	NM_014577	
MNDA	4332	hgsc.bcm.edu	37	1	158817521	158817521	+	Missense_Mutation	SNP	A	A	G			TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr1:158817521A>G	ENST00000368141.4	+	6	1252	c.991A>G	c.(991-993)Agc>Ggc	p.S331G		NM_002432.1	NP_002423.1	P41218	MNDA_HUMAN	myeloid cell nuclear differentiation antigen	331	HIN-200. {ECO:0000255|PROSITE- ProRule:PRU00106}.				B cell receptor signaling pathway (GO:0050853)|cellular defense response (GO:0006968)|cellular response to DNA damage stimulus (GO:0006974)|negative regulation of B cell proliferation (GO:0030889)|positive regulation of apoptotic process (GO:0043065)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)	DNA binding (GO:0003677)			NS(2)|breast(1)|cervix(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(9)|liver(1)|lung(26)|ovary(2)|prostate(4)|skin(3)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	65	all_hematologic(112;0.0378)					TTTGCAGAAAAGCGTACACAA	0.368																																					p.S331G		Atlas-SNP	.											MNDA,colon,carcinoma,0,2	MNDA	147	2	0			c.A991G						PASS	.						95.0	93.0	94.0					1																	158817521		2203	4300	6503	SO:0001583	missense	4332	exon6			CAGAAAAGCGTAC	BC032319	CCDS1177.1	1q22	2008-02-05			ENSG00000163563	ENSG00000163563			7183	protein-coding gene	gene with protein product		159553				1644857, 7512843	Standard	NM_002432		Approved	PYHIN3	uc001fsz.1	P41218	OTTHUMG00000022776	ENST00000368141.4:c.991A>G	1.37:g.158817521A>G	ENSP00000357123:p.Ser331Gly	77.0	0.0	0		120.0	5.0	0.0416667	NM_002432		Missense_Mutation	SNP	ENST00000368141.4	37	CCDS1177.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	4.768|4.768	0.142801|0.142801	0.09083|0.09083	.|.	.|.	ENSG00000163563|ENSG00000163563	ENST00000438394|ENST00000368141	T|T	0.19394|0.14766	2.15|2.48	4.15|4.15	0.259|0.259	0.15583|0.15583	.|HIN-200/IF120x (2);Nucleic acid-binding, OB-fold (1);	.|1.196580	.|0.06409	.|N	.|0.720183	T|T	0.02727|0.02727	0.0082|0.0082	N|N	0.24115|0.24115	0.695|0.695	0.09310|0.09310	N|N	0.999996|0.999996	.|B	.|0.33777	.|0.425	.|B	.|0.33121	.|0.158	T|T	0.45205|0.45205	-0.9277|-0.9277	7|10	0.72032|0.40728	D|T	0.01|0.16	0.0539|0.0539	5.0869|5.0869	0.14687|0.14687	0.4576:0.3654:0.0:0.1771|0.4576:0.3654:0.0:0.1771	.|.	.|331	.|P41218	.|MNDA_HUMAN	R|G	36|331	ENSP00000406800:K36R|ENSP00000357123:S331G	ENSP00000406800:K36R|ENSP00000357123:S331G	K|S	+|+	2|1	0|0	MNDA|MNDA	157084145|157084145	0.104000|0.104000	0.21937|0.21937	0.136000|0.136000	0.22124|0.22124	0.082000|0.082000	0.17680|0.17680	0.152000|0.152000	0.16302|0.16302	-0.064000|-0.064000	0.13043|0.13043	0.460000|0.460000	0.39030|0.39030	AAG|AGC	.	.	none		0.368	MNDA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000059069.1	NM_002432	
PIEZO1	9780	hgsc.bcm.edu	37	16	88789687	88789687	+	Missense_Mutation	SNP	C	C	T	rs188337046	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr16:88789687C>T	ENST00000301015.9	-	32	4631	c.4385G>A	c.(4384-4386)cGg>cAg	p.R1462Q	RP5-1142A6.9_ENST00000564984.1_RNA	NM_001142864.2	NP_001136336.2	Q92508	PIEZ1_HUMAN	piezo-type mechanosensitive ion channel component 1	1462					cation transmembrane transport (GO:0098655)|cation transport (GO:0006812)|detection of mechanical stimulus (GO:0050982)|positive regulation of cell-cell adhesion mediated by integrin (GO:0033634)|positive regulation of integrin activation (GO:0033625)|regulation of membrane potential (GO:0042391)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	cation channel activity (GO:0005261)|mechanically-gated ion channel activity (GO:0008381)			NS(1)|breast(3)|central_nervous_system(1)|endometrium(2)|prostate(2)|skin(1)	10						CTCCTGCTGCCGCCGCCTCAG	0.706													C|||	59	0.0117812	0.0325	0.0029	5008	,	,		13050	0.0		0.0139	False		,,,				2504	0.0				p.R1462Q		Atlas-SNP	.											.	PIEZO1	79	.	0			c.G4385A						PASS	.						18.0	26.0	24.0					16																	88789687		691	1585	2276	SO:0001583	missense	9780	exon32			TGCTGCCGCCGCC	D87071	CCDS54058.1	16q24.3	2011-08-31	2011-08-31	2011-08-31	ENSG00000103335	ENSG00000103335			28993	protein-coding gene	gene with protein product		611184	"""family with sequence similarity 38, member A"""	FAM38A		20813920, 21056836, 21299953, 21696149	Standard	NM_001142864		Approved	KIAA0233	uc010vpb.2	Q92508	OTTHUMG00000156776	ENST00000301015.9:c.4385G>A	16.37:g.88789687C>T	ENSP00000301015:p.Arg1462Gln	47.0	0.0	0		31.0	27.0	0.870968	NM_001142864	A6NHT9|A7E2B7|Q0KKZ9	Missense_Mutation	SNP	ENST00000301015.9	37	CCDS54058.1	38|38	0.0173992673992674|0.0173992673992674	21|21	0.042682926829268296|0.042682926829268296	4|4	0.011049723756906077|0.011049723756906077	3|3	0.005244755244755245|0.005244755244755245	10|10	0.013192612137203167|0.013192612137203167	C|C	10.95|10.95	1.494530|1.494530	0.26774|0.26774	.|.	.|.	ENSG00000103335|ENSG00000103335	ENST00000474606|ENST00000301015	.|T	.|0.75477	.|-0.94	4.92|4.92	-1.11|-1.11	0.09840|0.09840	.|.	.|0.239959	.|0.24988	.|N	.|0.034007	T|T	0.20047|0.20047	0.0482|0.0482	N|N	0.17723|0.17723	0.515|0.515	0.80722|0.80722	D|D	1|1	.|P	.|0.44429	.|0.835	.|B	.|0.26770	.|0.073	T|T	0.23797|0.23797	-1.0178|-1.0178	5|10	.|0.33940	.|T	.|0.23	-26.7276|-26.7276	16.9282|16.9282	0.86182|0.86182	0.0:0.8303:0.0:0.1697|0.0:0.8303:0.0:0.1697	.|.	.|1462	.|Q92508	.|PIEZ1_HUMAN	S|Q	136|1462	.|ENSP00000301015:R1462Q	.|ENSP00000301015:R1462Q	G|R	-|-	1|2	0|0	FAM38A|FAM38A	87317188|87317188	0.155000|0.155000	0.22806|0.22806	0.006000|0.006000	0.13384|0.13384	0.036000|0.036000	0.12997|0.12997	0.784000|0.784000	0.26816|0.26816	-0.731000|-0.731000	0.04862|0.04862	-1.134000|-1.134000	0.01955|0.01955	GGC|CGG	C|0.983;T|0.017	0.017	strong		0.706	PIEZO1-001	NOVEL	not_organism_supported|basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000345699.4	NM_014745	
CACUL1	143384	hgsc.bcm.edu	37	10	120489828	120489828	+	Silent	SNP	G	G	A	rs41284412	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr10:120489828G>A	ENST00000369151.3	-	2	945	c.462C>T	c.(460-462)gaC>gaT	p.D154D	CACUL1_ENST00000340214.4_Silent_p.D154D	NM_153810.4	NP_722517.3	Q86Y37	CACL1_HUMAN	CDK2-associated, cullin domain 1	154					G1/S transition of mitotic cell cycle (GO:0000082)|positive regulation of cell proliferation (GO:0008284)|positive regulation of protein kinase activity (GO:0045860)|ubiquitin-dependent protein catabolic process (GO:0006511)	cullin-RING ubiquitin ligase complex (GO:0031461)	protein kinase binding (GO:0019901)										TGGGGATATAGTCACCAGGAC	0.348													G|||	4	0.000798722	0.0	0.0	5008	,	,		19535	0.0		0.004	False		,,,				2504	0.0				p.D154D		Atlas-SNP	.											.	.	.	.	0			c.C462T						PASS	.	G		3,3659		0,3,1828	125.0	121.0	122.0		462	5.7	1.0	10	dbSNP_127	122	41,8135		0,41,4047	no	coding-synonymous	C10orf46	NM_153810.4		0,44,5875	AA,AG,GG		0.5015,0.0819,0.3717		154/370	120489828	44,11794	1831	4088	5919	SO:0001819	synonymous_variant	143384	exon2			GATATAGTCACCA	AK097728	CCDS41570.1	10q26.13	2012-06-12	2012-06-12	2012-06-12	ENSG00000151893	ENSG00000151893			23727	protein-coding gene	gene with protein product	"""Cdk-Associated Cullin1"""		"""chromosome 10 open reading frame 46"""	C10orf46		19829063	Standard	NM_153810		Approved	FLJ40409, MGC33215, CAC1	uc001lds.1	Q86Y37	OTTHUMG00000019138	ENST00000369151.3:c.462C>T	10.37:g.120489828G>A		137.0	0.0	0		104.0	54.0	0.519231	NM_153810	Q5XPL7|Q8IY11|Q8N7S4	Silent	SNP	ENST00000369151.3	37	CCDS41570.1																																																																																			G|0.998;A|0.002	0.002	strong		0.348	CACUL1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000050612.2	NM_153810	
CYP2D6	1565	hgsc.bcm.edu	37	22	42525089	42525089	+	Missense_Mutation	SNP	G	G	C	rs78482768	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr22:42525089G>C	ENST00000360608.5	-	3	565	c.451C>G	c.(451-453)Cag>Gag	p.Q151E	CYP2D6_ENST00000389970.3_Missense_Mutation_p.Q151E|CYP2D6_ENST00000359033.4_Intron|NDUFA6-AS1_ENST00000608288.1_RNA|NDUFA6-AS1_ENST00000416037.2_RNA|NDUFA6-AS1_ENST00000608491.1_RNA|NDUFA6-AS1_ENST00000439129.1_RNA	NM_000106.5	NP_000097	P10635	CP2D6_HUMAN	cytochrome P450, family 2, subfamily D, polypeptide 6	151					alkaloid catabolic process (GO:0009822)|alkaloid metabolic process (GO:0009820)|coumarin metabolic process (GO:0009804)|drug catabolic process (GO:0042737)|drug metabolic process (GO:0017144)|heterocycle metabolic process (GO:0046483)|isoquinoline alkaloid metabolic process (GO:0033076)|monoterpenoid metabolic process (GO:0016098)|negative regulation of binding (GO:0051100)|negative regulation of cellular organofluorine metabolic process (GO:0090350)|oxidation-reduction process (GO:0055114)|oxidative demethylation (GO:0070989)|small molecule metabolic process (GO:0044281)|steroid metabolic process (GO:0008202)|xenobiotic metabolic process (GO:0006805)	endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|mitochondrion (GO:0005739)	aromatase activity (GO:0070330)|drug binding (GO:0008144)|heme binding (GO:0020037)|iron ion binding (GO:0005506)|monooxygenase activity (GO:0004497)|oxidoreductase activity (GO:0016491)			NS(1)|breast(2)|endometrium(1)|large_intestine(2)|lung(4)|prostate(7)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	21					Abiraterone(DB05812)|Acebutolol(DB01193)|Acetaminophen(DB00316)|Ajmaline(DB01426)|Almotriptan(DB00918)|Alogliptin(DB06203)|Alprenolol(DB00866)|Aminophenazone(DB01424)|Amiodarone(DB01118)|Amitriptyline(DB00321)|Amlodipine(DB00381)|Amodiaquine(DB00613)|Amoxapine(DB00543)|Amphetamine(DB00182)|Amprenavir(DB00701)|Amsacrine(DB00276)|Antipyrine(DB01435)|Aprindine(DB01429)|Arformoterol(DB01274)|Aripiprazole(DB01238)|Artemether(DB06697)|Asenapine(DB06216)|Astemizole(DB00637)|Atomoxetine(DB00289)|Atorvastatin(DB01076)|Azelastine(DB00972)|Benzatropine(DB00245)|Benzyl alcohol(DB06770)|Bepridil(DB01244)|Betaxolol(DB00195)|Bicalutamide(DB01128)|Biperiden(DB00810)|Bisoprolol(DB00612)|Bortezomib(DB00188)|Brompheniramine(DB00835)|Bupivacaine(DB00297)|Buprenorphine(DB00921)|Bupropion(DB01156)|Buspirone(DB00490)|Caffeine(DB00201)|Captopril(DB01197)|Carbinoxamine(DB00748)|Carteolol(DB00521)|Carvedilol(DB01136)|Celecoxib(DB00482)|Cephalexin(DB00567)|Cevimeline(DB00185)|Chlordiazepoxide(DB00475)|Chloroquine(DB00608)|Chlorphenamine(DB01114)|Chlorpromazine(DB00477)|Chlorzoxazone(DB00356)|Cholecalciferol(DB00169)|Ciclesonide(DB01410)|Cilostazol(DB01166)|Cimetidine(DB00501)|Cinacalcet(DB01012)|Cinnarizine(DB00568)|Cisapride(DB00604)|Citalopram(DB00215)|Clemastine(DB00283)|Clevidipine(DB04920)|Clomipramine(DB01242)|Clonidine(DB00575)|Clotrimazole(DB00257)|Clozapine(DB00363)|Cocaine(DB00907)|Codeine(DB00318)|Cyclobenzaprine(DB00924)|Cyclophosphamide(DB00531)|Cyclosporine(DB00091)|Dapagliflozin(DB06292)|Darifenacin(DB00496)|Debrisoquin(DB04840)|Delavirdine(DB00705)|Desipramine(DB01151)|Desloratadine(DB00967)|Dexamethasone(DB01234)|Dexfenfluramine(DB01191)|Dexmedetomidine(DB00633)|Dexmethylphenidate(DB06701)|Dextroamphetamine(DB01576)|Dextromethorphan(DB00514)|Dextropropoxyphene(DB00647)|Dihydrocodeine(DB01551)|Diltiazem(DB00343)|Dimethyl sulfoxide(DB01093)|Diphenhydramine(DB01075)|Dolasetron(DB00757)|Domperidone(DB01184)|Donepezil(DB00843)|Dopamine(DB00988)|Doxazosin(DB00590)|Doxepin(DB01142)|Doxorubicin(DB00997)|Dronedarone(DB04855)|Duloxetine(DB00476)|Efavirenz(DB00625)|Eletriptan(DB00216)|Encainide(DB01228)|Enzalutamide(DB08899)|Epinastine(DB00751)|Erlotinib(DB00530)|Escitalopram(DB01175)|Ethylmorphine(DB01466)|Etoricoxib(DB01628)|Felodipine(DB01023)|Fesoterodine(DB06702)|Fexofenadine(DB00950)|Fingolimod(DB08868)|Flecainide(DB01195)|Flunarizine(DB04841)|Fluoxetine(DB00472)|Fluphenazine(DB00623)|Fluvastatin(DB01095)|Fluvoxamine(DB00176)|Formoterol(DB00983)|Galantamine(DB00674)|Gefitinib(DB00317)|Glutethimide(DB01437)|Granisetron(DB00889)|Halofantrine(DB01218)|Haloperidol(DB00502)|Halothane(DB01159)|Histamine Phosphate(DB00667)|Hydrocodone(DB00956)|Hydromorphone(DB00327)|Hydroxychloroquine(DB01611)|Hydroxyurea(DB01005)|Hydroxyzine(DB00557)|Idarubicin(DB01177)|Iloperidone(DB04946)|Imatinib(DB00619)|Imipramine(DB00458)|Indinavir(DB00224)|Ipratropium bromide(DB00332)|Irbesartan(DB01029)|Isoniazid(DB00951)|Itraconazole(DB01167)|Ketoconazole(DB01026)|L-DOPA(DB01235)|Labetalol(DB00598)|Lansoprazole(DB00448)|Lercanidipine(DB00528)|Levomilnacipran(DB08918)|Lidocaine(DB00281)|Lisuride(DB00589)|Lomustine(DB01206)|Loperamide(DB00836)|Lopinavir(DB01601)|Loratadine(DB00455)|Lorcaserin(DB04871)|Lovastatin(DB00227)|Lumefantrine(DB06708)|Maprotiline(DB00934)|Mefloquine(DB00358)|Mepyramine(DB06691)|Mequitazine(DB01071)|Mesoridazine(DB00933)|Methadone(DB00333)|Methamphetamine(DB01577)|Methazolamide(DB00703)|Methimazole(DB00763)|Methotrimeprazine(DB01403)|Methoxyflurane(DB01028)|Methylnaltrexone(DB06800)|Methylphenidate(DB00422)|Methyprylon(DB01107)|Metoclopramide(DB01233)|Metoprolol(DB00264)|Mexiletine(DB00379)|Mianserin(DB06148)|Miconazole(DB01110)|Midodrine(DB00211)|Mifepristone(DB00834)|Minaprine(DB00805)|Mirabegron(DB08893)|Mirtazapine(DB00370)|Moclobemide(DB01171)|Morphine(DB00295)|Nateglinide(DB00731)|Nebivolol(DB04861)|Nefazodone(DB01149)|Nelfinavir(DB00220)|Nevirapine(DB00238)|Niacin(DB00627)|Nicardipine(DB00622)|Nicergoline(DB00699)|Nicotine(DB00184)|Nifedipine(DB01115)|Nilotinib(DB04868)|Nitrofural(DB00336)|Nortriptyline(DB00540)|Olanzapine(DB00334)|Omeprazole(DB00338)|Ondansetron(DB00904)|Oxamniquine(DB01096)|Oxprenolol(DB01580)|Oxybutynin(DB01062)|Oxycodone(DB00497)|Oxymorphone(DB01192)|Paliperidone(DB01267)|Palonosetron(DB00377)|Paroxetine(DB00715)|Pazopanib(DB06589)|Pentamidine(DB00738)|Pergolide(DB01186)|Perhexiline(DB01074)|Perphenazine(DB00850)|Pethidine(DB00454)|Phenformin(DB00914)|Phentermine(DB00191)|Pimozide(DB01100)|Pindolol(DB00960)|Pioglitazone(DB01132)|Piperazine(DB00592)|Pipotiazine(DB01621)|Ponatinib(DB08901)|Pravastatin(DB00175)|Praziquantel(DB01058)|Primaquine(DB01087)|Procainamide(DB01035)|Prochlorperazine(DB00433)|Progesterone(DB00396)|Proguanil(DB01131)|Promethazine(DB01069)|Propafenone(DB01182)|Propofol(DB00818)|Propranolol(DB00571)|Protriptyline(DB00344)|Pseudoephedrine(DB00852)|Pyrimethamine(DB00205)|Quetiapine(DB01224)|Quinidine(DB00908)|Quinine(DB00468)|Rabeprazole(DB01129)|Ranitidine(DB00863)|Ranolazine(DB00243)|Reboxetine(DB00234)|Remoxipride(DB00409)|Rifapentine(DB01201)|Risperidone(DB00734)|Ritonavir(DB00503)|Rivastigmine(DB00989)|Ropinirole(DB00268)|Ropivacaine(DB00296)|Rosiglitazone(DB00412)|Rotigotine(DB05271)|Saquinavir(DB01232)|Selegiline(DB01037)|Sertindole(DB06144)|Sertraline(DB01104)|Sildenafil(DB00203)|Simvastatin(DB00641)|Sorafenib(DB00398)|Sulfanilamide(DB00259)|Sulfaphenazole(DB06729)|Tamoxifen(DB00675)|Tamsulosin(DB00706)|Tapentadol(DB06204)|Telithromycin(DB00976)|Temsirolimus(DB06287)|Terbinafine(DB00857)|Tetrabenazine(DB04844)|Theophylline(DB00277)|Thioridazine(DB00679)|Thiothixene(DB01623)|Ticlopidine(DB00208)|Timolol(DB00373)|Tiotropium(DB01409)|Tipranavir(DB00932)|Tolterodine(DB01036)|Trabectedin(DB05109)|Tramadol(DB00193)|Tranylcypromine(DB00752)|Trazodone(DB00656)|Trimipramine(DB00726)|Tripelennamine(DB00792)|Triprolidine(DB00427)|Trospium(DB00209)|Vemurafenib(DB08881)|Venlafaxine(DB00285)|Verapamil(DB00661)|Vilazodone(DB06684)|Vinblastine(DB00570)|Vinorelbine(DB00361)|Yohimbine(DB01392)|Zafirlukast(DB00549)|Zalcitabine(DB00943)|Ziprasidone(DB00246)|Zolpidem(DB00425)	GTCACCCACTGCTCCAGCGAC	0.677													G|||	6	0.00119808	0.0	0.0014	5008	,	,		16419	0.0		0.005	False		,,,				2504	0.0				p.Q151E		Atlas-SNP	.											.	CYP2D6	104	.	0			c.C451G						PASS	.	G	GLU/GLN,	5,4131		0,5,2063	19.0	23.0	22.0		451,	2.0	1.0	22	dbSNP_131	22	28,8350		1,26,4162	no	missense,intron	CYP2D6	NM_000106.4,NM_001025161.1	29,	1,31,6225	CC,CG,GG		0.3342,0.1209,0.2637	benign,	151/498,	42525089	33,12481	2068	4189	6257	SO:0001583	missense	1565	exon3			CCCACTGCTCCAG	M20403	CCDS33657.1, CCDS46721.1	22q13.1	2014-09-17	2003-01-14		ENSG00000100197	ENSG00000100197		"""Cytochrome P450s"""	2625	protein-coding gene	gene with protein product		124030	"""cytochrome P450, subfamily IID (debrisoquine, sparteine, etc., -metabolizing), polypeptide 6"", ""cytochrome P450, family 2, subfamily D, polypeptide 7 pseudogene 2"", ""cytochrome P450, subfamily II (debrisoquine, sparteine, etc., -metabolising), polypeptide 7 pseudogene 2"", ""cytochrome P450, family 2, subfamily D, polypeptide 8 pseudogene 2"", ""cytochrome P450, subfamily IID (debrisoquine, sparteine, etc., -metabolising), polypeptide 8 pseudogene 2"""	CYP2DL1, CYP2D7P2, CYP2D7BP, CYP2D8P2, CYP2D7AP		8449513	Standard	NM_000106		Approved	CPD6, P450-DB1, CYP2D, P450C2D	uc003bce.3	P10635	OTTHUMG00000150918	ENST00000360608.5:c.451C>G	22.37:g.42525089G>C	ENSP00000353820:p.Gln151Glu	119.0	0.0	0		102.0	52.0	0.509804	NM_000106	Q16752|Q2XND6|Q2XND7|Q2XNE0|Q6B012|Q6NXU8	Missense_Mutation	SNP	ENST00000360608.5	37	CCDS46721.1	.	.	.	.	.	.	.	.	.	.	g	0.009	-1.841892	0.00573	0.001209	0.003342	ENSG00000100197	ENST00000360608;ENST00000389970;ENST00000413640	T;T	0.77877	-1.13;-1.13	4.18	1.97	0.26223	.	0.756605	0.11656	N	0.542295	T	0.52008	0.1708	N	0.11341	0.13	0.22684	N	0.998852	B	0.10296	0.003	B	0.08055	0.003	T	0.38929	-0.9638	10	0.02654	T	1	.	6.6787	0.23108	0.1016:0.3458:0.5526:0.0	.	151	Q6NWU0	.	E	151;151;100	ENSP00000353820:Q151E;ENSP00000374620:Q151E	ENSP00000353820:Q151E	Q	-	1	0	CYP2D6	40855033	0.005000	0.15991	0.998000	0.56505	0.063000	0.16089	0.273000	0.18662	0.442000	0.26555	0.305000	0.20034	CAG	G|1.000;|0.000	.	weak		0.677	CYP2D6-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000320525.1		
IRX6	79190	hgsc.bcm.edu	37	16	55362625	55362625	+	Silent	SNP	C	C	T	rs199714803		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr16:55362625C>T	ENST00000290552.7	+	5	2067	c.735C>T	c.(733-735)agC>agT	p.S245S	RP11-26L20.3_ENST00000558730.2_RNA	NM_024335.2	NP_077311.2	P78412	IRX6_HUMAN	iroquois homeobox 6	245					regulation of transcription, DNA-templated (GO:0006355)	nucleus (GO:0005634)	sequence-specific DNA binding (GO:0043565)			breast(2)|central_nervous_system(5)|endometrium(3)|kidney(2)|large_intestine(6)|liver(2)|lung(10)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)	33						TTACTGCTAGCCAGGAGGCCC	0.582																																					p.S245S		Atlas-SNP	.											.	IRX6	66	.	0			c.C735T						PASS	.																																			SO:0001819	synonymous_variant	79190	exon5			TGCTAGCCAGGAG	AF319966	CCDS32449.1	16q12.2	2011-06-20	2007-07-13	2003-01-10		ENSG00000159387		"""Homeoboxes / TALE class"""	14675	protein-coding gene	gene with protein product		606196	"""iroquois homeobox protein 7"", ""iroquois homeobox protein 6"""	IRX7			Standard	NM_024335		Approved	IRX-3	uc002ehy.3	P78412		ENST00000290552.7:c.735C>T	16.37:g.55362625C>T		34.0	0.0	0		42.0	36.0	0.857143	NM_024335	B2RN06|Q7Z2K0	Silent	SNP	ENST00000290552.7	37	CCDS32449.1																																																																																			C|0.999;T|0.001	0.001	weak		0.582	IRX6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000417445.4	NM_024335	
S100PBP	64766	hgsc.bcm.edu	37	1	33292189	33292189	+	Silent	SNP	C	C	T	rs41265867	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr1:33292189C>T	ENST00000373475.5	+	3	743	c.489C>T	c.(487-489)gaC>gaT	p.D163D	S100PBP_ENST00000398243.3_Silent_p.D163D|S100PBP_ENST00000373476.1_Silent_p.D163D|S100PBP_ENST00000356689.3_3'UTR	NM_022753.3	NP_073590.2			S100P binding protein											endometrium(2)|kidney(1)|large_intestine(2)|lung(8)|ovary(1)|prostate(1)|stomach(1)	16		Myeloproliferative disorder(586;0.0255)|all_neural(195;0.0837)|Breast(348;0.244)				TTGATAAGGACGAGACTGATT	0.378													c|||	29	0.00579073	0.0008	0.0058	5008	,	,		22086	0.0		0.0159	False		,,,				2504	0.0082				p.D163D		Atlas-SNP	.											.	S100PBP	31	.	0			c.C489T						PASS	.	T	,	9,4397	15.5+/-35.6	0,9,2194	69.0	71.0	70.0		489,489	-8.8	0.3	1	dbSNP_127	70	67,8533	40.8+/-97.7	1,65,4234	no	coding-synonymous,coding-synonymous	S100PBP	NM_001017406.1,NM_022753.2	,	1,74,6428	TT,TC,CC		0.7791,0.2043,0.5843	,	163/342,163/409	33292189	76,12930	2203	4300	6503	SO:0001819	synonymous_variant	64766	exon3			TAAGGACGAGACT	BX647916	CCDS30666.1	1p35.1	2008-02-05			ENSG00000116497	ENSG00000116497			25768	protein-coding gene	gene with protein product	"""S100P binding protein 1"""	611889				12477932	Standard	NM_022753		Approved	FLJ12903, S100PBPR	uc001bwc.4	Q96BU1	OTTHUMG00000003955	ENST00000373475.5:c.489C>T	1.37:g.33292189C>T		36.0	0.0	0		26.0	20.0	0.769231	NM_001256121		Silent	SNP	ENST00000373475.5	37	CCDS30666.1																																																																																			C|0.992;T|0.008	0.008	strong		0.378	S100PBP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000011266.1	NM_022753	
MYLK	4638	hgsc.bcm.edu	37	3	123419422	123419422	+	Missense_Mutation	SNP	T	T	C			TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr3:123419422T>C	ENST00000475616.1	-	15	2892	c.2893A>G	c.(2893-2895)Acc>Gcc	p.T965A	MYLK_ENST00000346322.5_Missense_Mutation_p.T896A|MYLK_ENST00000510775.1_5'Flank|MYLK_ENST00000360304.3_Missense_Mutation_p.T965A|MYLK_ENST00000360772.3_Missense_Mutation_p.T965A|MYLK_ENST00000359169.1_Missense_Mutation_p.T965A			Q15746	MYLK_HUMAN	myosin light chain kinase	965	5 X 28 AA approximate tandem repeats.				actin filament organization (GO:0007015)|aorta smooth muscle tissue morphogenesis (GO:0060414)|bleb assembly (GO:0032060)|cellular hypotonic response (GO:0071476)|muscle contraction (GO:0006936)|positive regulation of calcium ion transport (GO:0051928)|positive regulation of cell migration (GO:0030335)|positive regulation of wound healing (GO:0090303)|protein phosphorylation (GO:0006468)|smooth muscle contraction (GO:0006939)|tonic smooth muscle contraction (GO:0014820)	cell-cell junction (GO:0005911)|cleavage furrow (GO:0032154)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|lamellipodium (GO:0030027)|stress fiber (GO:0001725)	ATP binding (GO:0005524)|calmodulin-dependent protein kinase activity (GO:0004683)|metal ion binding (GO:0046872)|myosin light chain kinase activity (GO:0004687)			NS(2)|breast(4)|central_nervous_system(1)|endometrium(24)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(17)|lung(37)|ovary(7)|prostate(3)|skin(5)|stomach(1)|upper_aerodigestive_tract(5)|urinary_tract(2)	113		Lung NSC(201;0.0496)		GBM - Glioblastoma multiforme(114;0.0736)		GGCACGGGGGTCTTGGAAGTC	0.572																																					p.T965A		Atlas-SNP	.											.	MYLK	224	.	0			c.A2893G						PASS	.						49.0	48.0	48.0					3																	123419422		2203	4300	6503	SO:0001583	missense	4638	exon18			CGGGGGTCTTGGA	X85337	CCDS3023.1, CCDS43141.1, CCDS46896.1, CCDS46897.1, CCDS58849.1	3q21	2013-02-11	2008-01-23		ENSG00000065534	ENSG00000065534	2.7.11.18	"""Immunoglobulin superfamily / I-set domain containing"", ""Fibronectin type III domain containing"""	7590	protein-coding gene	gene with protein product	"""smooth muscle myosin light chain kinase"""	600922	"""myosin, light polypeptide kinase"""			8575746	Standard	NM_053026		Approved	MLCK, smMLCK, MYLK1, MLCK1	uc003ego.3	Q15746	OTTHUMG00000141304	ENST00000475616.1:c.2893A>G	3.37:g.123419422T>C	ENSP00000418335:p.Thr965Ala	76.0	0.0	0		71.0	5.0	0.0704225	NM_053025	B4DUE3|D3DN97|O95796|O95797|O95798|O95799|Q14844|Q16794|Q17S15|Q3ZCP9|Q5MY99|Q5MYA0|Q6P2N0|Q7Z4J0|Q9C0L5|Q9UBG5|Q9UBY6|Q9UIT9	Missense_Mutation	SNP	ENST00000475616.1	37	CCDS46896.1	.	.	.	.	.	.	.	.	.	.	T	6.416	0.444842	0.12164	.	.	ENSG00000065534	ENST00000360772;ENST00000360304;ENST00000359169;ENST00000346322;ENST00000475616	T;T;T;T;T	0.64260	-0.09;-0.04;-0.09;-0.04;-0.04	5.2	2.46	0.29980	.	.	.	.	.	T	0.43344	0.1243	L	0.28556	0.865	0.80722	D	1	B;B;B;B;B;B	0.15141	0.0;0.001;0.005;0.012;0.003;0.0	B;B;B;B;B;B	0.14023	0.001;0.005;0.01;0.006;0.004;0.001	T	0.14364	-1.0475	9	0.15499	T	0.54	.	7.056	0.25099	0.0:0.1566:0.1276:0.7157	.	965;43;896;965;896;965	Q15746-6;Q15746-7;Q15746-4;Q15746-3;Q15746-2;Q15746	.;.;.;.;.;MYLK_HUMAN	A	965;965;965;896;965	ENSP00000354004:T965A;ENSP00000353452:T965A;ENSP00000352088:T965A;ENSP00000320622:T896A;ENSP00000418335:T965A	ENSP00000320622:T896A	T	-	1	0	MYLK	124902112	0.997000	0.39634	1.000000	0.80357	0.951000	0.60555	0.367000	0.20382	0.835000	0.34877	-0.434000	0.05882	ACC	.	.	none		0.572	MYLK-004	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000356464.1	NM_053025	
CTC1	80169	hgsc.bcm.edu	37	17	8135446	8135446	+	Silent	SNP	G	G	A	rs3027235	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr17:8135446G>A	ENST00000315684.8	-	13	2167	c.2160C>T	c.(2158-2160)acC>acT	p.T720T		NM_025099.5	NP_079375.3	Q2NKJ3	CTC1_HUMAN	CTS telomere maintenance complex component 1	720					bone marrow development (GO:0048539)|cellular response to DNA damage stimulus (GO:0006974)|hematopoietic stem cell proliferation (GO:0071425)|multicellular organism growth (GO:0035264)|positive regulation of DNA replication (GO:0045740)|positive regulation of fibroblast proliferation (GO:0048146)|regulation of G2/M transition of mitotic cell cycle (GO:0010389)|replicative senescence (GO:0090399)|spleen development (GO:0048536)|telomere maintenance (GO:0000723)|telomere maintenance via telomere lengthening (GO:0010833)|thymus development (GO:0048538)	nuclear chromosome, telomeric region (GO:0000784)|nucleus (GO:0005634)|Stn1-Ten1 complex (GO:0070188)	single-stranded DNA binding (GO:0003697)			NS(1)|endometrium(6)|kidney(3)|large_intestine(6)|lung(8)|ovary(1)|skin(4)	29						CCTCTGGGCCGGTGGGATCTG	0.577													G|||	217	0.0433307	0.087	0.1009	5008	,	,		17092	0.0099		0.0139	False		,,,				2504	0.0082				p.T720T		Atlas-SNP	.											.	CTC1	75	.	0			c.C2160T						PASS	.	G		260,3684		9,242,1721	21.0	22.0	22.0		2160	2.3	0.0	17	dbSNP_102	22	124,8160		3,118,4021	no	coding-synonymous	CTC1	NM_025099.5		12,360,5742	AA,AG,GG		1.4969,6.5923,3.1403		720/1218	8135446	384,11844	1972	4142	6114	SO:0001819	synonymous_variant	80169	exon13			TGGGCCGGTGGGA	AL831955	CCDS42259.1	17p13.1	2011-02-21	2011-02-21	2011-02-21	ENSG00000178971	ENSG00000178971			26169	protein-coding gene	gene with protein product	"""conserved telomere maintenance component 1"", ""alpha accessory factor 132"", ""conserved telomere capping protein 1"""	613129	"""tmp494178"", ""chromosome 17 open reading frame 68"""	C17orf68		19854130, 19854131	Standard	NM_025099		Approved	FLJ22170, AAF132	uc002gkq.4	Q2NKJ3		ENST00000315684.8:c.2160C>T	17.37:g.8135446G>A		79.0	0.0	0		73.0	28.0	0.383562	NM_025099	B3KR66|C9JEX5|Q1PCD1|Q2TBE3|Q8N3S6|Q9H6L0	Silent	SNP	ENST00000315684.8	37	CCDS42259.1																																																																																			G|0.964;A|0.036	0.036	strong		0.577	CTC1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000442012.1	NM_025099	
FGFR3	2261	hgsc.bcm.edu	37	4	1803704	1803704	+	Silent	SNP	T	T	C	rs2234909	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr4:1803704T>C	ENST00000260795.2	+	6	984	c.882T>C	c.(880-882)aaT>aaC	p.N294N	FGFR3_ENST00000352904.1_Silent_p.N294N|FGFR3_ENST00000440486.2_Silent_p.N294N|FGFR3_ENST00000474521.1_3'UTR|FGFR3_ENST00000481110.2_Silent_p.N294N|FGFR3_ENST00000412135.2_Silent_p.N294N|FGFR3_ENST00000340107.4_Silent_p.N294N			P22607	FGFR3_HUMAN	fibroblast growth factor receptor 3	294	Ig-like C2-type 3.				alveolar secondary septum development (GO:0061144)|axonogenesis involved in innervation (GO:0060385)|bone maturation (GO:0070977)|bone mineralization (GO:0030282)|bone morphogenesis (GO:0060349)|cell-cell signaling (GO:0007267)|central nervous system myelination (GO:0022010)|chondrocyte differentiation (GO:0002062)|chondrocyte proliferation (GO:0035988)|cochlea development (GO:0090102)|digestive tract morphogenesis (GO:0048546)|endochondral bone growth (GO:0003416)|endochondral ossification (GO:0001958)|epidermal growth factor receptor signaling pathway (GO:0007173)|epithelial cell fate commitment (GO:0072148)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor apoptotic signaling pathway (GO:1902178)|fibroblast growth factor receptor signaling pathway (GO:0008543)|innate immune response (GO:0045087)|inner ear receptor cell differentiation (GO:0060113)|insulin receptor signaling pathway (GO:0008286)|JAK-STAT cascade (GO:0007259)|lens fiber cell development (GO:0070307)|lens morphogenesis in camera-type eye (GO:0002089)|MAPK cascade (GO:0000165)|morphogenesis of an epithelium (GO:0002009)|negative regulation of astrocyte differentiation (GO:0048712)|negative regulation of developmental growth (GO:0048640)|negative regulation of epithelial cell proliferation (GO:0050680)|negative regulation of mitosis (GO:0045839)|negative regulation of smoothened signaling pathway (GO:0045879)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|neurotrophin TRK receptor signaling pathway (GO:0048011)|peptidyl-tyrosine phosphorylation (GO:0018108)|phosphatidylinositol-mediated signaling (GO:0048015)|positive regulation of canonical Wnt signaling pathway (GO:0090263)|positive regulation of cell differentiation (GO:0045597)|positive regulation of cell proliferation (GO:0008284)|positive regulation of endothelial cell proliferation (GO:0001938)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of MAPK cascade (GO:0043410)|positive regulation of MAPKKK cascade by fibroblast growth factor receptor signaling pathway (GO:0090080)|positive regulation of neuron apoptotic process (GO:0043525)|positive regulation of phosphatidylinositol 3-kinase activity (GO:0043552)|positive regulation of phospholipase activity (GO:0010518)|positive regulation of protein ubiquitination (GO:0031398)|positive regulation of tyrosine phosphorylation of Stat1 protein (GO:0042511)|positive regulation of tyrosine phosphorylation of Stat3 protein (GO:0042517)|protein autophosphorylation (GO:0046777)|response to axon injury (GO:0048678)|skeletal system development (GO:0001501)|somatic stem cell maintenance (GO:0035019)|substantia nigra development (GO:0021762)	cell surface (GO:0009986)|cytoplasmic side of plasma membrane (GO:0009898)|cytoplasmic vesicle (GO:0031410)|endoplasmic reticulum (GO:0005783)|extracellular region (GO:0005576)|integral component of plasma membrane (GO:0005887)|lysosome (GO:0005764)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|fibroblast growth factor binding (GO:0017134)|fibroblast growth factor-activated receptor activity (GO:0005007)|protein tyrosine kinase activity (GO:0004713)	p.N294N(5)		NS(1)|central_nervous_system(5)|cervix(6)|endometrium(2)|haematopoietic_and_lymphoid_tissue(40)|kidney(1)|large_intestine(5)|lung(9)|ovary(1)|pancreas(2)|prostate(9)|skin(339)|soft_tissue(4)|testis(2)|upper_aerodigestive_tract(58)|urinary_tract(2607)	3091		Breast(71;0.212)|all_epithelial(65;0.241)	all cancers(2;0.000145)|OV - Ovarian serous cystadenocarcinoma(23;0.0019)|Epithelial(3;0.00221)|GBM - Glioblastoma multiforme(2;0.234)		Palifermin(DB00039)|Pazopanib(DB06589)|Ponatinib(DB08901)	TGGAGGTGAATGGCAGCAAGG	0.672		1	"""Mis, T"""	"""IGH@, ETV6"""	"""bladder, MM, T-cell lymphoma"""		"""Hypochondroplasia, Thanatophoric dysplasia"""		Saethre-Chotzen syndrome;Muenke syndrome				N|||	1039	0.207468	0.3707	0.1441	5008	,	,		12849	0.0744		0.17	False		,,,				2504	0.2076				p.N294N		Atlas-SNP	.		Dom	yes		4	4p16.3	2261	fibroblast growth factor receptor 3	yes	"""L, E"""	FGFR3_ENST00000340107,caecum,carcinoma,+2,11	FGFR3	3320	11	5	Substitution - coding silent(5)	upper_aerodigestive_tract(3)|skin(2)	c.T882C						scavenged	.	C	,,	1504,2902	654.3+/-399.7	251,1002,950	47.0	42.0	44.0		882,882,882	-6.8	0.9	4	dbSNP_98	44	1278,7320	749.7+/-407.4	98,1082,3119	no	coding-synonymous,coding-synonymous,coding-synonymous	FGFR3	NM_000142.4,NM_001163213.1,NM_022965.3	,,	349,2084,4069	CC,CT,TT		14.8639,34.1353,21.3934	,,	294/807,294/809,294/695	1803704	2782,10222	2203	4299	6502	SO:0001819	synonymous_variant	2261	exon7	Familial Cancer Database	Acrocephalosyndactyly type III;Muenke Nonsyndromic Coronal Craniosynostosis, FGFR3-related Craniosynostosis	GGTGAATGGCAGC	M64347	CCDS3353.1, CCDS3354.1, CCDS54706.1	4p16.3	2013-01-11	2008-08-01		ENSG00000068078	ENSG00000068078		"""CD molecules"", ""Immunoglobulin superfamily / I-set domain containing"""	3690	protein-coding gene	gene with protein product		134934	"""achondroplasia, thanatophoric dwarfism"""	ACH		1847508	Standard	NM_000142		Approved	CEK2, JTK4, CD333	uc003gdu.2	P22607	OTTHUMG00000121148	ENST00000260795.2:c.882T>C	4.37:g.1803704T>C		211.0	2.0	0.00947867		152.0	72.0	0.473684	NM_001163213	D3DVP9|D3DVQ0|Q14308|Q16294|Q16608|Q59FL9	Silent	SNP	ENST00000260795.2	37	CCDS3353.1																																																																																			T|0.799;C|0.201	0.201	strong		0.672	FGFR3-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000241632.2	NM_000142	
SLC44A3	126969	hgsc.bcm.edu	37	1	95322903	95322903	+	Missense_Mutation	SNP	T	T	C			TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr1:95322903T>C	ENST00000271227.6	+	10	1187	c.1085T>C	c.(1084-1086)gTt>gCt	p.V362A	SLC44A3_ENST00000530397.1_3'UTR|SLC44A3_ENST00000446120.2_Missense_Mutation_p.V326A|RP11-465K1.2_ENST00000422162.1_RNA|SLC44A3_ENST00000532427.1_Missense_Mutation_p.V282A|SLC44A3_ENST00000529450.1_Missense_Mutation_p.V330A|SLC44A3_ENST00000467909.1_Missense_Mutation_p.V314A|SLC44A3_ENST00000527077.1_Missense_Mutation_p.V294A	NM_001114106.2|NM_001258340.1|NM_001258341.1	NP_001107578.1|NP_001245269.1|NP_001245270.1	Q8N4M1	CTL3_HUMAN	solute carrier family 44, member 3	362					glycerophospholipid biosynthetic process (GO:0046474)|phosphatidylcholine biosynthetic process (GO:0006656)|phospholipid metabolic process (GO:0006644)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				breast(1)|endometrium(2)|kidney(4)|large_intestine(6)|lung(6)|prostate(2)|stomach(1)|urinary_tract(1)	23		all_lung(203;0.000712)|Lung NSC(277;0.00316)		all cancers(265;0.039)|Epithelial(280;0.124)	Choline(DB00122)	GCTGCCCAGGTTATGGAAGGC	0.443																																					p.V362A		Atlas-SNP	.											.	SLC44A3	109	.	0			c.T1085C						PASS	.						114.0	102.0	106.0					1																	95322903		2203	4300	6503	SO:0001583	missense	126969	exon10			CCCAGGTTATGGA	BC033858	CCDS751.1, CCDS44176.1, CCDS58011.1, CCDS58012.1, CCDS58013.1, CCDS72827.1	1p22.1	2013-05-22	2005-09-06		ENSG00000143036	ENSG00000143036		"""Solute carriers"""	28689	protein-coding gene	gene with protein product			"""solute carrier family, member 3"""			15715662, 12975309	Standard	NM_001114106		Approved	MGC45474, CTL3	uc001dqv.5	Q8N4M1	OTTHUMG00000010700	ENST00000271227.6:c.1085T>C	1.37:g.95322903T>C	ENSP00000271227:p.Val362Ala	213.0	1.0	0.00469484		112.0	59.0	0.526786	NM_001114106	B4DVY4|B4E1M4|B7ZA08|E9PJH2|E9PJY8|Q6UWT1|Q7Z6C5|Q9BWY7	Missense_Mutation	SNP	ENST00000271227.6	37	CCDS44176.1	.	.	.	.	.	.	.	.	.	.	T	4.282	0.051417	0.08291	.	.	ENSG00000143036	ENST00000446120;ENST00000271227;ENST00000527077;ENST00000529450;ENST00000467909;ENST00000532427	T;T;T;T;T;T	0.21191	2.02;2.02;2.02;2.02;2.02;2.02	4.7	3.58	0.41010	.	0.152963	0.30401	N	0.009710	T	0.07593	0.0191	L	0.59436	1.845	0.09310	N	0.999997	P;B;B;P;P	0.34462	0.454;0.05;0.007;0.454;0.454	B;B;B;B;B	0.34931	0.192;0.037;0.011;0.192;0.192	T	0.25293	-1.0136	10	0.20519	T	0.43	-12.261	8.0786	0.30731	0.0:0.1799:0.0:0.8201	.	282;326;294;330;362	E9PIC5;Q8N4M1-3;E9PJY8;E9PJH2;Q8N4M1	.;.;.;.;CTL3_HUMAN	A	326;362;294;330;314;282	ENSP00000389143:V326A;ENSP00000271227:V362A;ENSP00000433641:V294A;ENSP00000431836:V330A;ENSP00000432789:V314A;ENSP00000436661:V282A	ENSP00000271227:V362A	V	+	2	0	SLC44A3	95095491	0.928000	0.31464	0.625000	0.29200	0.926000	0.56050	1.389000	0.34453	0.851000	0.35264	0.533000	0.62120	GTT	.	.	none		0.443	SLC44A3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000029544.3	NM_152369	
PCED1B	91523	hgsc.bcm.edu	37	12	47471287	47471287	+	5'Flank	SNP	G	G	A			TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr12:47471287G>A	ENST00000546455.1	+	0	0				AMIGO2_ENST00000429635.1_Missense_Mutation_p.T500M|AMIGO2_ENST00000321382.3_Missense_Mutation_p.T500M|AMIGO2_ENST00000550413.1_Missense_Mutation_p.T500M|AMIGO2_ENST00000266581.4_Missense_Mutation_p.T500M			Q96HM7	PED1B_HUMAN	PC-esterase domain containing 1B								hydrolase activity (GO:0016787)										TTTCCCCCTCGTGGACTTTAG	0.468																																					p.T500M		Atlas-SNP	.											AMIGO2,NS,carcinoma,-1,1	AMIGO2	50	1	0			c.C1499T						PASS	.						70.0	66.0	67.0					12																	47471287		2203	4300	6503	SO:0001631	upstream_gene_variant	347902	exon2			CCCCTCGTGGACT	BC016154	CCDS8752.1	12q13.11	2012-06-11	2012-06-11	2012-06-11	ENSG00000179715	ENSG00000179715			28255	protein-coding gene	gene with protein product			"""family with sequence similarity 113, member B"""	FAM113B		20056006	Standard	NM_138371		Approved	MGC16044	uc001rpq.3	Q96HM7	OTTHUMG00000169617		12.37:g.47471287G>A	Exception_encountered	167.0	0.0	0		130.0	56.0	0.430769	NM_181847	Q96B20	Missense_Mutation	SNP	ENST00000546455.1	37	CCDS8752.1	.	.	.	.	.	.	.	.	.	.	G	13.07	2.126383	0.37533	.	.	ENSG00000139211	ENST00000266581;ENST00000550413;ENST00000429635;ENST00000321382	T;T;T;T	0.49432	0.78;0.78;0.78;0.78	5.09	5.09	0.68999	.	0.380800	0.28647	N	0.014620	T	0.40839	0.1133	L	0.44542	1.39	0.25929	N	0.983015	P	0.47910	0.902	B	0.36666	0.23	T	0.47209	-0.9135	10	0.51188	T	0.08	-0.3923	18.3695	0.90402	0.0:0.0:1.0:0.0	.	500	Q86SJ2	AMGO2_HUMAN	M	500	ENSP00000266581:T500M;ENSP00000449034:T500M;ENSP00000406020:T500M;ENSP00000320848:T500M	ENSP00000266581:T500M	T	-	2	0	AMIGO2	45757554	0.970000	0.33590	0.047000	0.18901	0.988000	0.76386	4.115000	0.57865	2.745000	0.94114	0.561000	0.74099	ACG	.	.	none		0.468	PCED1B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000405079.1	NM_138371	
CLTCL1	8218	hgsc.bcm.edu	37	22	19175095	19175095	+	Missense_Mutation	SNP	A	A	C	rs182434700	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr22:19175095A>C	ENST00000263200.10	-	29	4652	c.4580T>G	c.(4579-4581)cTc>cGc	p.L1527R	CLTCL1_ENST00000427926.1_Missense_Mutation_p.L1527R|CLTCL1_ENST00000353891.5_Intron|CLTCL1_ENST00000442042.2_Intron	NM_007098.3	NP_009029.3	P53675	CLH2_HUMAN	clathrin, heavy chain-like 1	1527	Heavy chain arm.|Proximal segment.				anatomical structure morphogenesis (GO:0009653)|intracellular protein transport (GO:0006886)|mitotic nuclear division (GO:0007067)|positive regulation of glucose import (GO:0046326)|receptor-mediated endocytosis (GO:0006898)|signal transduction (GO:0007165)	clathrin coat of coated pit (GO:0030132)|clathrin coat of trans-Golgi network vesicle (GO:0030130)|clathrin-coated vesicle (GO:0030136)|coated pit (GO:0005905)|coated vesicle (GO:0030135)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|spindle (GO:0005819)|trans-Golgi network (GO:0005802)	signal transducer activity (GO:0004871)|structural molecule activity (GO:0005198)			breast(2)|central_nervous_system(3)|cervix(2)|endometrium(9)|kidney(3)|large_intestine(11)|lung(9)|ovary(5)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	49	Colorectal(54;0.0993)					CTTCTTGCAGAGCTCCACGCT	0.572			T	?	ALCL								A|||	5	0.000998403	0.0038	0.0	5008	,	,		20542	0.0		0.0	False		,,,				2504	0.0				p.L1527R		Atlas-SNP	.		Dom	yes		22	22q11.21	8218	"""clathrin, heavy polypeptide-like 1"""		L	.	CLTCL1	115	.	0			c.T4580G						PASS	.	A	ARG/LEU,	6,4150		0,6,2072	102.0	110.0	107.0		4580,	4.1	1.0	22		107	2,8418		0,2,4208	yes	missense,intron	CLTCL1	NM_007098.3,NM_001835.3	102,	0,8,6280	CC,CA,AA		0.0238,0.1444,0.0636	probably-damaging,	1527/1641,	19175095	8,12568	2078	4210	6288	SO:0001583	missense	8218	exon29			TTGCAGAGCTCCA		CCDS46662.1, CCDS54497.1, CCDS46662.2, CCDS54497.2	22q11.2	2008-06-10	2006-09-29		ENSG00000070371	ENSG00000070371			2093	protein-coding gene	gene with protein product		601273	"""clathrin, heavy polypeptide-like 1"""	CLTCL		8844170, 15133132	Standard	NM_007098		Approved	CLTD, CLH22, CHC22	uc021wle.1	P53675	OTTHUMG00000150109	ENST00000263200.10:c.4580T>G	22.37:g.19175095A>C	ENSP00000445677:p.Leu1527Arg	209.0	1.0	0.00478469		185.0	90.0	0.486486	NM_007098	B7Z7U5|Q14017|Q15808|Q15809	Missense_Mutation	SNP	ENST00000263200.10	37	CCDS46662.1	1	4.578754578754579E-4	1	0.0020325203252032522	0	0.0	0	0.0	0	0.0	A	23.2	4.381943	0.82792	0.001444	2.38E-4	ENSG00000070371	ENST00000263200;ENST00000427926	T;T	0.29917	1.55;1.55	4.13	4.13	0.48395	.	0.000000	0.64402	D	0.000002	T	0.62392	0.2424	M	0.91038	3.17	0.80722	D	1	D	0.76494	0.999	D	0.83275	0.996	T	0.72434	-0.4295	10	0.87932	D	0	-15.1854	13.2908	0.60270	1.0:0.0:0.0:0.0	.	1527	P53675	CLH2_HUMAN	R	1527	ENSP00000445677:L1527R;ENSP00000441158:L1527R	ENSP00000445677:L1527R	L	-	2	0	CLTCL1	17555095	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	8.286000	0.89916	1.738000	0.51689	0.533000	0.62120	CTC	A|0.999;C|0.001	0.001	strong		0.572	CLTCL1-001	KNOWN	non_canonical_genome_sequence_error|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000316397.5	NM_007098	
