#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
TTLL9	164395	hgsc.bcm.edu	37	20	30510797	30510798	+	Frame_Shift_Del	DEL	AT	AT	-			TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	AT	AT	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr20:30510797_30510798delAT	ENST00000375938.4	+	8	858_859	c.605_606delAT	c.(604-606)gatfs	p.D202fs	TTLL9_ENST00000535842.1_Frame_Shift_Del_p.D202fs|TTLL9_ENST00000375934.4_Frame_Shift_Del_p.D184fs|TTLL9_ENST00000375921.2_Frame_Shift_Del_p.D129fs|TTLL9_ENST00000310998.4_Frame_Shift_Del_p.D152fs|TTLL9_ENST00000375922.4_Frame_Shift_Del_p.D129fs			Q3SXZ7	TTLL9_HUMAN	tubulin tyrosine ligase-like family, member 9	202	TTL. {ECO:0000255|PROSITE- ProRule:PRU00568}.				cellular protein modification process (GO:0006464)	cilium (GO:0005929)|cytoplasm (GO:0005737)|microtubule (GO:0005874)	ligase activity (GO:0016874)			breast(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(8)|lung(8)|ovary(2)|prostate(1)|upper_aerodigestive_tract(1)	26			Colorectal(19;0.00306)|COAD - Colon adenocarcinoma(19;0.0347)			CAGAAAGATGATATTCCCGTGG	0.401																																					p.202_202del		Pindel,Atlas-Indel	.											.	TTLL9	95	.	0			c.604_605del						PASS	.																																			SO:0001589	frameshift_variant	164395	exon8			.	AL031658	CCDS42863.1	20q11	2013-02-14	2005-07-28	2005-07-28		ENSG00000131044		"""Tubulin tyrosine ligase-like family"""	16118	protein-coding gene	gene with protein product			"""chromosome 20 open reading frame 125"""	C20orf125		15890843	Standard	NM_001008409		Approved	dJ310O13.1	uc010gdx.1	Q3SXZ7		ENST00000375938.4:c.605_606delAT	20.37:g.30510799_30510800delAT	ENSP00000365105:p.Asp202fs	80.0	0.0	.		101.0	34.0	0.337	NM_001008409	A6NH06|A6NIS5|B3KSG8|Q3SXZ8|Q5JYS3|Q5JYS4	Frame_Shift_Del	DEL	ENST00000375938.4	37	CCDS42863.1																																																																																			.	.	none		0.401	TTLL9-205	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_001008409	
GTF3C3	9330	hgsc.bcm.edu	37	2	197657762	197657767	+	In_Frame_Del	DEL	TCCTCC	TCCTCC	-	rs372304935|rs555178972		TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	TCCTCC	TCCTCC	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr2:197657762_197657767delTCCTCC	ENST00000263956.3	-	3	413_418	c.324_329delGGAGGA	c.(322-330)gaggaggaa>gaa	p.108_110EEE>E	GTF3C3_ENST00000409364.3_In_Frame_Del_p.108_110EEE>E|GTF3C3_ENST00000470386.1_5'Flank	NM_012086.4	NP_036218.1	Q9Y5Q9	TF3C3_HUMAN	general transcription factor IIIC, polypeptide 3, 102kDa	108	Glu-rich.				5S class rRNA transcription from RNA polymerase III type 1 promoter (GO:0042791)|gene expression (GO:0010467)|transcription from RNA polymerase III promoter (GO:0006383)|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)	p.E109E(1)		breast(4)|endometrium(3)|kidney(1)|large_intestine(9)|lung(5)|ovary(3)|pancreas(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(3)	33						AGGTGTTtcttcctcctcctcctcct	0.437																																					p.109_110del		Pindel,Atlas-Indel	.											.	GTF3C3	96	.	1	Substitution - coding silent(1)	large_intestine(1)	c.325_330del						PASS	.																																			SO:0001651	inframe_deletion	9330	exon3			.	AF133123	CCDS2316.1, CCDS56153.1	2q33.1	2013-01-10	2002-08-29		ENSG00000119041	ENSG00000119041		"""General transcription factors"", ""Tetratricopeptide (TTC) repeat domain containing"""	4666	protein-coding gene	gene with protein product		604888	"""general transcription factor IIIC, polypeptide 3 (102kD)"""			10373544	Standard	NM_001206774		Approved	TFiiiC2-102, TFIIIC102	uc002uts.3	Q9Y5Q9	OTTHUMG00000154633	ENST00000263956.3:c.324_329delGGAGGA	2.37:g.197657768_197657773delTCCTCC	ENSP00000263956:p.Glu110_Glu111del	314.0	0.0	.		276.0	66.0	0.239	NM_012086	Q4ZG48|Q86XJ8|Q8WX84|Q96B44|Q9H5I8|Q9NT97	In_Frame_Del	DEL	ENST00000263956.3	37	CCDS2316.1																																																																																			.	.	alt		0.437	GTF3C3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256104.1		
KRTAP4-3	85290	hgsc.bcm.edu	37	17	39324346	39324347	+	In_Frame_Ins	INS	-	-	TTT			TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr17:39324346_39324347insTTT	ENST00000391356.2	-	1	77_78	c.78_79insAAA	c.(76-81)cgcccc>cgcAAAccc	p.26_27RP>RKP		NM_033187.1	NP_149443.1	Q9BYR4	KRA43_HUMAN	keratin associated protein 4-3	26					aging (GO:0007568)|hair cycle (GO:0042633)	keratin filament (GO:0045095)				breast(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(4)|lung(2)|upper_aerodigestive_tract(1)	12		Breast(137;0.000496)	STAD - Stomach adenocarcinoma(17;0.000449)			CAGCAGCTGGGGCGGCAGCAGC	0.639																																					p.P27delinsKP		Atlas-Indel	.											KRTAP4-3,NS,carcinoma,+2,1	KRTAP4-3	40	1	0			c.79_80insAAA						PASS	.																																			SO:0001652	inframe_insertion	85290	exon1			.	AJ406935	CCDS42331.1	17q21.2	2013-06-25			ENSG00000196156	ENSG00000196156		"""Keratin associated proteins"""	18908	protein-coding gene	gene with protein product							Standard	NM_033187		Approved	KAP4.3	uc010cxl.3	Q9BYR4	OTTHUMG00000133639	ENST00000391356.2:c.78_79insAAA	17.37:g.39324346_39324347insTTT	ENSP00000375151:p.Arg26_Pro27insLys	203.0	0.0	0		196.0	18.0	0.0918367	NM_033187		In_Frame_Ins	INS	ENST00000391356.2	37	CCDS42331.1																																																																																			.	.	none		0.639	KRTAP4-3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257784.1		
TNP2	7142	hgsc.bcm.edu	37	16	11362797	11362797	+	Frame_Shift_Del	DEL	T	T	-			TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr16:11362797delT	ENST00000312693.3	-	1	392	c.323delA	c.(322-324)aacfs	p.N108fs	RMI2_ENST00000572173.1_Intron	NM_005425.4	NP_005416.1	Q05952	STP2_HUMAN	transition protein 2 (during histone to protamine replacement)	108					acrosome reaction (GO:0007340)|binding of sperm to zona pellucida (GO:0007339)|cell differentiation (GO:0030154)|multicellular organismal development (GO:0007275)|penetration of zona pellucida (GO:0007341)|sperm motility (GO:0030317)|spermatogenesis (GO:0007283)	nucleosome (GO:0000786)|nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)	p.0?(1)		large_intestine(2)|lung(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	6						GCCTTCCAAGTTCTTTCTGTT	0.522																																					p.N108fs		Pindel,Atlas-Indel	.											.	TNP2	15	.	1	Whole gene deletion(1)	haematopoietic_and_lymphoid_tissue(1)	c.324delC						PASS	.						77.0	77.0	77.0					16																	11362797		1957	4150	6107	SO:0001589	frameshift_variant	7142	exon1			.		CCDS45410.1	16p13.13	2008-08-01				ENSG00000178279			11952	protein-coding gene	gene with protein product		190232				1395729, 2250010	Standard	NM_005425		Approved	TP2	uc002das.3	Q05952		ENST00000312693.3:c.323delA	16.37:g.11362797delT	ENSP00000325738:p.Asn108fs	232.0	0.0	.		266.0	47.0	0.177	NM_005425	Q9NZB0	Frame_Shift_Del	DEL	ENST00000312693.3	37	CCDS45410.1																																																																																			.	.	none		0.522	TNP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000417806.1	NM_005425	
EXO5	64789	hgsc.bcm.edu	37	1	40981245	40981246	+	Frame_Shift_Ins	INS	-	-	G	rs150018949	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr1:40981245_40981246insG	ENST00000372703.1	+	2	2103_2104	c.1029_1030insG	c.(1030-1032)cggfs	p.R344fs	RP11-656D10.6_ENST00000437060.1_RNA|EXO5_ENST00000296380.4_Frame_Shift_Ins_p.R344fs|RP11-656D10.5_ENST00000453437.1_RNA|EXO5_ENST00000358527.2_Frame_Shift_Ins_p.R344fs			Q9H790	EXO5_HUMAN	exonuclease 5	344					DNA catabolic process, exonucleolytic (GO:0000738)|interstrand cross-link repair (GO:0036297)	cytosol (GO:0005829)|nucleus (GO:0005634)	4 iron, 4 sulfur cluster binding (GO:0051539)|DNA binding (GO:0003677)|metal ion binding (GO:0046872)|protein homodimerization activity (GO:0042803)|single-stranded DNA 3'-5' exodeoxyribonuclease activity (GO:0008310)|single-stranded DNA 5'-3' exodeoxyribonuclease activity (GO:0045145)										CTTGGAAGTGCCGGACGTGTAC	0.54													-|-|G|insertion	42	0.00838658	0.0015	0.0144	5008	,	,		19343	0.0		0.0209	False		,,,				2504	0.0092				p.C343fs		Pindel,Atlas-Indel	.											.	.	.	.	0			c.1029_1030insG						PASS	.			17,4249		0,17,2116						0.4	0.4		dbSNP_134	52	186,8064		3,180,3942	no	frameshift	DEM1	NM_022774.1		3,197,6058	A1A1,A1R,RR		2.2545,0.3985,1.6219				203,12313				SO:0001589	frameshift_variant	64789	exon3			.	AK024797	CCDS453.1	1p34.2	2012-11-02	2012-10-30	2012-10-30	ENSG00000164002	ENSG00000164002			26115	protein-coding gene	gene with protein product			"""chromosome 1 open reading frame 176"", ""defects in morphology 1 homolog (S. cerevisiae)"""	C1orf176, DEM1		23095756	Standard	NM_022774		Approved	FLJ21144	uc001cfp.3	Q9H790	OTTHUMG00000007305	Exception_encountered	1.37:g.40981245_40981246insG	ENSP00000361788:p.Arg344fs	114.0	0.0	.		89.0	29.0	0.326	NM_022774	D3DPV4|Q5SWM7|Q5SWM8|Q5SWM9|Q5SWN0|Q5SWN1|Q8WTW9	Frame_Shift_Ins	INS	ENST00000372703.1	37	CCDS453.1																																																																																			-|0.989;G|0.011	0.011	strong		0.540	EXO5-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000019087.1	NM_022774	
ITGA7	3679	hgsc.bcm.edu	37	12	56091333	56091333	+	Intron	DEL	G	G	-			TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr12:56091333delG	ENST00000555728.1	-	11	1570				ITGA7_ENST00000553804.1_Intron|ITGA7_ENST00000394230.2_Intron|ITGA7_ENST00000347027.6_Intron|ITGA7_ENST00000257879.6_Intron|ITGA7_ENST00000257880.7_Intron|ITGA7_ENST00000394229.2_Intron|ITGA7_ENST00000452168.2_Intron			Q13683	ITA7_HUMAN	integrin, alpha 7						blood vessel morphogenesis (GO:0048514)|cell migration (GO:0016477)|cell-matrix adhesion (GO:0007160)|endodermal cell differentiation (GO:0035987)|extracellular matrix organization (GO:0030198)|heterotypic cell-cell adhesion (GO:0034113)|integrin-mediated signaling pathway (GO:0007229)|muscle organ development (GO:0007517)|regulation of cell shape (GO:0008360)|skeletal muscle tissue development (GO:0007519)	cell surface (GO:0009986)|cytoplasm (GO:0005737)|integrin alpha7-beta1 complex (GO:0034677)|muscle tendon junction (GO:0005927)|neuromuscular junction (GO:0031594)|plasma membrane (GO:0005886)|sarcolemma (GO:0042383)	metal ion binding (GO:0046872)			breast(2)|central_nervous_system(1)|cervix(1)|endometrium(6)|kidney(1)|large_intestine(10)|lung(16)|ovary(2)|prostate(2)|skin(5)|soft_tissue(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	50						GTCTGGCCCTGGGATTGGGGA	0.562																																					.		Pindel,Atlas-Indel	.											.	ITGA7	194	.	0			c.1422-2C>-						PASS	.		,,	0,4264		0,0,2132	57.0	56.0	57.0		,,	4.6	1.0	12		57	36,8218		1,34,4092	no	intron,intron,intron	ITGA7	NM_002206.2,NM_001144997.1,NM_001144996.1	,,	1,34,6224	A1A1,A1R,RR		0.4362,0.0,0.2876	,,	,,	56091333	36,12482	2203	4300	6503	SO:0001627	intron_variant	3679	exon11			.		CCDS8888.1, CCDS44914.1, CCDS55832.1	12q13	2014-09-17				ENSG00000135424		"""Integrins"""	6143	protein-coding gene	gene with protein product		600536				7607681	Standard	NM_002206		Approved		uc001shh.3	Q13683		ENST00000555728.1:c.1542-3C>-	12.37:g.56091333delG		63.0	0.0	.		68.0	26.0	0.382	NM_001144996	B4E3U0|C9JMD3|C9JMZ6|O43197|Q86W93|Q9NY89|Q9UET0|Q9UEV2	Splice_Site	DEL	ENST00000555728.1	37																																																																																				.	.	none		0.562	ITGA7-014	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000410138.1	NM_002206	
NEIL3	55247	hgsc.bcm.edu	37	4	178256864	178256864	+	Frame_Shift_Del	DEL	T	T	-			TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr4:178256864delT	ENST00000264596.3	+	3	419	c.301delT	c.(301-303)ttcfs	p.F101fs		NM_018248.2	NP_060718	Q8TAT5	NEIL3_HUMAN	nei endonuclease VIII-like 3 (E. coli)	101					base-excision repair (GO:0006284)|DNA catabolic process, endonucleolytic (GO:0000737)|nucleotide-excision repair (GO:0006289)	nucleus (GO:0005634)	bubble DNA binding (GO:0000405)|damaged DNA binding (GO:0003684)|DNA N-glycosylase activity (GO:0019104)|DNA-(apurinic or apyrimidinic site) lyase activity (GO:0003906)|double-stranded DNA binding (GO:0003690)|single-stranded DNA binding (GO:0003697)|zinc ion binding (GO:0008270)			breast(1)|central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(4)|lung(14)|ovary(1)|prostate(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	29		Breast(14;6.27e-05)|Melanoma(52;0.00102)|Renal(120;0.00988)|Prostate(90;0.00996)|all_hematologic(60;0.014)|all_neural(102;0.164)		all cancers(43;1.96e-23)|Epithelial(43;2.52e-20)|OV - Ovarian serous cystadenocarcinoma(60;1.89e-11)|GBM - Glioblastoma multiforme(59;9.49e-05)|Colorectal(24;0.00013)|COAD - Colon adenocarcinoma(29;0.000696)|STAD - Stomach adenocarcinoma(60;0.00308)|LUSC - Lung squamous cell carcinoma(193;0.0398)|READ - Rectum adenocarcinoma(43;0.191)		AATGAAAGGCTTCATCATGAT	0.323								Base excision repair (BER), DNA glycosylases																													p.G100fs		Pindel,Atlas-Indel	.											.	NEIL3	89	.	0			c.300delC						PASS	.						61.0	69.0	66.0					4																	178256864		2200	4300	6500	SO:0001589	frameshift_variant	55247	exon3			.	AB079071	CCDS3828.1	4q34	2014-02-18			ENSG00000109674	ENSG00000109674			24573	protein-coding gene	gene with protein product	"""zinc finger, GRF-type containing 3"""	608934				12713815, 12509226	Standard	NM_018248		Approved	FLJ10858, hFPG2, FPG2, hNEI3, ZGRF3	uc003iut.2	Q8TAT5	OTTHUMG00000160722	ENST00000264596.3:c.301delT	4.37:g.178256864delT	ENSP00000264596:p.Phe101fs	157.0	0.0	.		178.0	53.0	0.298	NM_018248	Q2PPJ3|Q8NG51|Q9NV95	Frame_Shift_Del	DEL	ENST00000264596.3	37	CCDS3828.1																																																																																			.	.	none		0.323	NEIL3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000361914.1	NM_018248	
ZSCAN18	65982	hgsc.bcm.edu	37	19	58598358	58598369	+	In_Frame_Del	DEL	TGGAAAGGACTT	TGGAAAGGACTT	-	rs368736992	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	TGGAAAGGACTT	TGGAAAGGACTT	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr19:58598358_58598369delTGGAAAGGACTT	ENST00000240727.6	-	5	1048_1059	c.649_660delAAGTCCTTTCCA	c.(649-660)aagtcctttccadel	p.KSFP217del	ZSCAN18_ENST00000601144.1_In_Frame_Del_p.KSFP217del|ZSCAN18_ENST00000421612.2_In_Frame_Del_p.KSFP82del|ZSCAN18_ENST00000600404.1_In_Frame_Del_p.KSFP273del	NM_023926.4	NP_076415.3	Q8TBC5	ZSC18_HUMAN	zinc finger and SCAN domain containing 18	217					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)			NS(1)|endometrium(2)|kidney(1)|large_intestine(4)|lung(8)|skin(3)	19		Colorectal(82;0.000256)|all_neural(62;0.0412)|Breast(46;0.114)|Ovarian(87;0.156)		UCEC - Uterine corpus endometrioid carcinoma (67;0.168)|GBM - Glioblastoma multiforme(193;0.0152)		GAGGGTCCTCTGGAAAGGACTTCAGCTTCTGA	0.637														7	0.00139776	0.0	0.0	5008	,	,		18211	0.0		0.0	False		,,,				2504	0.0072				p.273_277del		Pindel,Atlas-Indel	.											.	ZSCAN18	104	.	0			c.818_829del						PASS	.																																			SO:0001651	inframe_deletion	65982	exon5			.	AY280799, AY279352	CCDS12971.1, CCDS46214.1, CCDS46215.1	19q13.43	2013-01-09	2007-02-20	2007-02-20		ENSG00000121413		"""-"", ""Zinc fingers, C2H2-type"""	21037	protein-coding gene	gene with protein product			"""zinc finger protein 447"""	ZNF447			Standard	NM_001145542		Approved	FLJ12895	uc010yht.1	Q8TBC5		ENST00000240727.6:c.649_660delAAGTCCTTTCCA	19.37:g.58598358_58598369delTGGAAAGGACTT	ENSP00000240727:p.Lys217_Pro220del	77.0	0.0	.		44.0	11.0	0.250	NM_001145542	B4DG23|E9PBI0|Q9BRK7|Q9H9A0	In_Frame_Del	DEL	ENST00000240727.6	37	CCDS12971.1																																																																																			.	.	weak		0.637	ZSCAN18-003	KNOWN	alternative_5_UTR|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000466706.1	NM_023926	
MN1	4330	hgsc.bcm.edu	37	22	28194962	28194963	+	In_Frame_Ins	INS	-	-	CTGCTG			TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr22:28194962_28194963insCTGCTG	ENST00000302326.4	-	1	2523_2524	c.1569_1570insCAGCAG	c.(1567-1572)caacag>caaCAGCAGcag	p.523_524QQ>QQQQ		NM_002430.2	NP_002421.3	Q10571	MN1_HUMAN	meningioma (disrupted in balanced translocation) 1	523	Poly-Gln.				intramembranous ossification (GO:0001957)					NS(1)|breast(2)|central_nervous_system(3)|endometrium(4)|kidney(3)|large_intestine(6)|lung(15)|ovary(3)|prostate(4)|skin(3)|upper_aerodigestive_tract(1)	45						tgctgctgctgttgcAGGGACT	0.668			T	ETV6	"""AML, meningioma"""																																p.Q524delinsQQQ		Atlas-Indel	.		Dom	yes		22	22q13	4330	meningioma (disrupted in balanced translocation) 1		"""L, O"""	MN1,NS,carcinoma,+2,1	MN1	122	1	0			c.1570_1571insCAGCAG						PASS	.																																			SO:0001652	inframe_insertion	4330	exon1			.	X82209	CCDS42998.1	22q12.1	2010-09-29			ENSG00000169184	ENSG00000169184			7180	protein-coding gene	gene with protein product	"""probable tumor suppressor protein MN1"""	156100	"""meningioma chromosome region"""	MGCR		7731706, 12569362	Standard	NM_002430		Approved	MGCR1-PEN, MGCR1	uc003adj.3	Q10571	OTTHUMG00000150975	ENST00000302326.4:c.1564_1569dupCAGCAG	22.37:g.28194957_28194962dupCTGCTG	ENSP00000304956:p.Gln549_Gln550dup	76.0	0.0	0		81.0	10.0	0.123457	NM_002430	A9Z1V9	In_Frame_Ins	INS	ENST00000302326.4	37	CCDS42998.1																																																																																			.	.	none		0.668	MN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000320737.1	NM_002430	
KRTAP4-4	84616	hgsc.bcm.edu	37	17	39316851	39316865	+	In_Frame_Del	DEL	GCAGCAGGTGGTCTG	GCAGCAGGTGGTCTG	-	rs199889274|rs201042607	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	GCAGCAGGTGGTCTG	GCAGCAGGTGGTCTG	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr17:39316851_39316865delGCAGCAGGTGGTCTG	ENST00000390661.3	-	1	118_132	c.79_93delCAGACCACCTGCTGC	c.(79-93)cagaccacctgctgcdel	p.QTTCC27del		NM_032524.1	NP_115913.1	Q9BYR3	KRA44_HUMAN	keratin associated protein 4-4	27	26 X 5 AA repeats of C-C-[GRQVCH]-[SPT]- [VSTQR].					keratin filament (GO:0045095)				kidney(1)|large_intestine(1)|lung(5)	7		Breast(137;0.000496)	STAD - Stomach adenocarcinoma(17;0.000449)			AGGTGGTCCTGCAGCAGGTGGTCTGGCAGTAGCTG	0.637																																					p.27_32del		Pindel,Atlas-Indel	.											.	KRTAP4-4	21	.	0			c.80_94del						PASS	.			19,4221		3,13,2104						-0.9	0.6			51	51,8203		5,41,4081	no	coding	KRTAP4-4	NM_032524.1		8,54,6185	A1A1,A1R,RR		0.6179,0.4481,0.5603				70,12424				SO:0001651	inframe_deletion	84616	exon1			.	AJ406936	CCDS11383.1	17q21.2	2013-06-25			ENSG00000171396	ENSG00000171396		"""Keratin associated proteins"""	16928	protein-coding gene	gene with protein product			"""keratin associated protein 4-13"""	KRTAP4-13		11279113	Standard	NM_032524		Approved	KAP4.4, KAP4.13	uc002hwc.3	Q9BYR3	OTTHUMG00000133428	ENST00000390661.3:c.79_93delCAGACCACCTGCTGC	17.37:g.39316851_39316865delGCAGCAGGTGGTCTG	ENSP00000375076:p.Gln27_Cys31del	120.0	0.0	.		130.0	24.0	0.185	NM_032524	Q9BYU7	In_Frame_Del	DEL	ENST00000390661.3	37	CCDS11383.1																																																																																			.	.	none		0.637	KRTAP4-4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257291.1		
HLA-G	3135	hgsc.bcm.edu	37	6	29796435	29796435	+	Frame_Shift_Del	DEL	C	C	-	rs41557518	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr6:29796435delC	ENST00000360323.6	+	3	483	c.459delC	c.(457-459)gacfs	p.D153fs	HLA-G_ENST00000428701.1_Frame_Shift_Del_p.D153fs|HLA-G_ENST00000376828.2_Frame_Shift_Del_p.D158fs|HLA-G_ENST00000376815.3_Intron|HLA-G_ENST00000376818.3_Intron			P17693	HLAG_HUMAN	major histocompatibility complex, class I, G	153	Alpha-2.				antigen processing and presentation of exogenous peptide antigen via MHC class I (GO:0042590)|antigen processing and presentation of exogenous peptide antigen via MHC class I, TAP-dependent (GO:0002479)|antigen processing and presentation of exogenous peptide antigen via MHC class I, TAP-independent (GO:0002480)|antigen processing and presentation of peptide antigen via MHC class I (GO:0002474)|cellular defense response (GO:0006968)|cytokine-mediated signaling pathway (GO:0019221)|immune response-inhibiting cell surface receptor signaling pathway (GO:0002767)|interferon-gamma-mediated signaling pathway (GO:0060333)|negative regulation of dendritic cell differentiation (GO:2001199)|negative regulation of T cell proliferation (GO:0042130)|positive regulation of interleukin-12 production (GO:0032735)|positive regulation of regulatory T cell differentiation (GO:0045591)|positive regulation of T cell mediated cytotoxicity (GO:0001916)|positive regulation of T cell tolerance induction (GO:0002666)|regulation of immune response (GO:0050776)|type I interferon signaling pathway (GO:0060337)	early endosome membrane (GO:0031901)|ER to Golgi transport vesicle membrane (GO:0012507)|Golgi membrane (GO:0000139)|integral component of lumenal side of endoplasmic reticulum membrane (GO:0071556)|membrane (GO:0016020)|MHC class I protein complex (GO:0042612)|phagocytic vesicle membrane (GO:0030670)|plasma membrane (GO:0005886)	peptide antigen binding (GO:0042605)|protein homodimerization activity (GO:0042803)|receptor binding (GO:0005102)	p.L154fs*60(1)		central_nervous_system(1)|endometrium(1)|large_intestine(5)|lung(4)|ovary(3)|pancreas(1)|prostate(5)|skin(1)	21						TGAACGAGGACCTGCGCTCCT	0.617													cc|CC|C|deletion	142	0.0283546	0.0741	0.013	5008	,	,		16865	0.0149		0.0119	False		,,,				2504	0.0082				p.D153fs		Pindel,Atlas-Indel	.											.	HLA-G	90	.	1	Deletion - Frameshift(1)	pancreas(1)	c.458delA						PASS	.			272,3948		19,234,1857	107.0	99.0	102.0			1.7	0.8	6	dbSNP_134	105	112,8078		11,90,3994	no	frameshift	HLA-G	NM_002127.5		30,324,5851	A1A1,A1R,RR		1.3675,6.4455,3.0943			29796435	384,12026	1510	2709	4219	SO:0001589	frameshift_variant	3135	exon4			.		CCDS4668.1	6p21.3	2013-01-11	2007-12-12		ENSG00000204632	ENSG00000204632		"""Histocompatibility complex"", ""Immunoglobulin superfamily / C1-set domain containing"""	4964	protein-coding gene	gene with protein product	"""b2 microglobulin"""	142871	"""HLA-G histocompatibility antigen, class I, G"""				Standard	NM_002127		Approved		uc003nnw.2	P17693	OTTHUMG00000031157	ENST00000360323.6:c.459delC	6.37:g.29796435delC	ENSP00000353472:p.Asp153fs	177.0	0.0	.		226.0	74.0	0.327	NM_002127		Frame_Shift_Del	DEL	ENST00000360323.6	37	CCDS4668.1																																																																																			C|0.967;-|0.033	0.033	strong		0.617	HLA-G-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076286.2	NM_002127	
KREMEN2	79412	hgsc.bcm.edu	37	16	3017836	3017836	+	Frame_Shift_Del	DEL	G	G	-			TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr16:3017836delG	ENST00000303746.5	+	9	1781	c.1204delG	c.(1204-1206)gggfs	p.G402fs	PKMYT1_ENST00000571102.1_5'Flank|KREMEN2_ENST00000571007.1_Frame_Shift_Del_p.G363fs|KREMEN2_ENST00000575769.1_3'UTR|KREMEN2_ENST00000572045.1_3'UTR|PAQR4_ENST00000576565.1_5'Flank|PAQR4_ENST00000293978.8_5'Flank|KREMEN2_ENST00000319500.6_Frame_Shift_Del_p.K375fs|KREMEN2_ENST00000575885.1_Frame_Shift_Del_p.K336fs|PAQR4_ENST00000318782.8_5'Flank|PAQR4_ENST00000572687.1_5'Flank			Q8NCW0	KREM2_HUMAN	kringle containing transmembrane protein 2	402					Wnt signaling pathway (GO:0016055)	integral component of membrane (GO:0016021)				central_nervous_system(2)|endometrium(1)|large_intestine(1)	4						TCCGGGAAAAGGGCCCCCGGC	0.706																																					p.K401fs		Pindel,Atlas-Indel	.											.	KREMEN2	13	.	0			c.1203delA						PASS	.						8.0	8.0	8.0					16																	3017836		2028	4033	6061	SO:0001589	frameshift_variant	79412	exon9			.	BC003533	CCDS10483.1, CCDS10484.1, CCDS58412.1, CCDS58413.1	16p13.11	2008-08-04			ENSG00000131650	ENSG00000131650			18797	protein-coding gene	gene with protein product		609899				12050670	Standard	NM_172229		Approved	MGC10791, KRM2	uc002csg.3	Q8NCW0	OTTHUMG00000128976	ENST00000303746.5:c.1204delG	16.37:g.3017836delG	ENSP00000304422:p.Gly402fs	136.0	0.0	.		130.0	41.0	0.315	NM_172229	B4DXF6|I3L2S2|Q8N2J4|Q8NCW1|Q96GL8|Q9BTP9	Frame_Shift_Del	DEL	ENST00000303746.5	37	CCDS10483.1																																																																																			.	.	none		0.706	KREMEN2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000250964.2	NM_145347	
ATF7IP2	80063	hgsc.bcm.edu	37	16	10565979	10565981	+	In_Frame_Del	DEL	TGT	TGT	-	rs566280429|rs199605421	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	TGT	TGT	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr16:10565979_10565981delTGT	ENST00000396560.2	+	8	1592_1594	c.1365_1367delTGT	c.(1363-1368)gatgtt>gat	p.V456del	ATF7IP2_ENST00000543967.1_5'UTR|ATF7IP2_ENST00000396559.1_In_Frame_Del_p.V456del|ATF7IP2_ENST00000324570.5_In_Frame_Del_p.V456del|ATF7IP2_ENST00000356427.2_In_Frame_Del_p.V456del	NM_024997.3	NP_079273.2	Q5U623	MCAF2_HUMAN	activating transcription factor 7 interacting protein 2	456					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)				large_intestine(3)	3						ACAATGATGATGTTATGTTGATT	0.296														25	0.00499201	0.0008	0.0086	5008	,	,		16695	0.001		0.0099	False		,,,				2504	0.0072				p.455_456del		Pindel,Atlas-Indel	.											.	ATF7IP2	40	.	0			c.1364_1366del						PASS	.			6,4252		0,6,2123						2.3	1.0			67	99,8125		1,97,4014	no	coding	ATF7IP2	NM_024997.2		1,103,6137	A1A1,A1R,RR		1.2038,0.1409,0.8412				105,12377				SO:0001651	inframe_deletion	80063	exon9			.	AK022730	CCDS10540.1, CCDS58422.1	16p13.2	2008-02-05			ENSG00000166669	ENSG00000166669			20397	protein-coding gene	gene with protein product		613645					Standard	NM_001256160		Approved	FLJ12668	uc002czu.3	Q5U623	OTTHUMG00000129749	ENST00000396560.2:c.1365_1367delTGT	16.37:g.10565979_10565981delTGT	ENSP00000379808:p.Val456del	21.0	0.0	.		26.0	10.0	0.385	NM_001256160	B2RNR2|Q53EZ7|Q658U2|Q6IS97|Q8N9X8|Q9H9L6	In_Frame_Del	DEL	ENST00000396560.2	37	CCDS10540.1																																																																																			.	.	none		0.296	ATF7IP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251961.1	NM_024997	
ZNF570	148268	hgsc.bcm.edu	37	19	37976121	37976123	+	In_Frame_Del	DEL	CAC	CAC	-			TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	CAC	CAC	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr19:37976121_37976123delCAC	ENST00000330173.1	+	5	2126_2128	c.1597_1599delCAC	c.(1597-1599)cacdel	p.H533del	ZNF570_ENST00000388801.3_In_Frame_Del_p.H330del|CTD-2086O20.3_ENST00000591976.1_lincRNA|ZNF570_ENST00000586475.1_In_Frame_Del_p.H589del	NM_144694.1	NP_653295.1	Q96NI8	ZN570_HUMAN	zinc finger protein 570	533					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			endometrium(3)|kidney(3)|large_intestine(6)|lung(12)|ovary(1)|prostate(1)|skin(1)	27			COAD - Colon adenocarcinoma(19;0.114)|Colorectal(19;0.177)			cccagtcaatcaccaagtcctat	0.404																																					p.532_533del		Pindel,Atlas-Indel	.											ZNF570,NS,carcinoma,+2,1	ZNF570	58	1	0			c.1596_1598del						PASS	.																																			SO:0001651	inframe_deletion	148268	exon5			.	AK055353	CCDS12504.1, CCDS74355.1	19q13.12	2013-09-20			ENSG00000171827	ENSG00000171827		"""Zinc fingers, C2H2-type"", ""-"""	26416	protein-coding gene	gene with protein product							Standard	XM_005258567		Approved	FLJ30791	uc002ogk.1	Q96NI8	OTTHUMG00000048176	ENST00000330173.1:c.1597_1599delCAC	19.37:g.37976121_37976123delCAC	ENSP00000331540:p.His533del	80.0	0.0	.		81.0	25.0	0.309	NM_144694	A1L472|B4DMP1	In_Frame_Del	DEL	ENST00000330173.1	37	CCDS12504.1																																																																																			.	.	none		0.404	ZNF570-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000109600.1	NM_144694	
HOXA1	3198	hgsc.bcm.edu	37	7	27135317	27135319	+	In_Frame_Del	DEL	TGG	TGG	-	rs2074398|rs587777901|rs544314279	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	TGG	TGG	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr7:27135317_27135319delTGG	ENST00000343060.4	-	1	274_276	c.213_215delCCA	c.(211-216)caccat>cat	p.71_72HH>H	HOXA1_ENST00000355633.5_In_Frame_Del_p.71_72HH>H|HOTAIRM1_ENST00000429611.3_RNA|HOTAIRM1_ENST00000425358.2_RNA|HOTAIRM1_ENST00000434063.3_RNA|HOTAIRM1_ENST00000495032.1_RNA	NM_005522.4	NP_005513	P49639	HXA1_HUMAN	homeobox A1	71	Poly-His.				abducens nerve formation (GO:0021599)|anatomical structure morphogenesis (GO:0009653)|anterior/posterior pattern specification (GO:0009952)|artery development (GO:0060840)|artery morphogenesis (GO:0048844)|central nervous system neuron differentiation (GO:0021953)|cochlea development (GO:0090102)|cochlea morphogenesis (GO:0090103)|cognition (GO:0050890)|embryonic neurocranium morphogenesis (GO:0048702)|facial nerve structural organization (GO:0021612)|facial nucleus development (GO:0021754)|inner ear development (GO:0048839)|motor neuron axon guidance (GO:0008045)|multicellular organismal development (GO:0007275)|neuromuscular process (GO:0050905)|optokinetic behavior (GO:0007634)|outer ear morphogenesis (GO:0042473)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of behavior (GO:0050795)|rhombomere 3 development (GO:0021569)|rhombomere 4 development (GO:0021570)|rhombomere 5 development (GO:0021571)|semicircular canal formation (GO:0060876)|sensory perception of sound (GO:0007605)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	sequence-specific DNA binding (GO:0043565)			endometrium(2)|kidney(2)|large_intestine(4)|liver(1)|lung(14)|ovary(4)|prostate(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	31						ggggtggcgatggtggtggtggt	0.64											OREG0003750	type=REGULATORY REGION|Gene=BC031342|Dataset=Stanford ENCODE Dataset|EvidenceSubtype=Transient transfection luciferase assay																									p.72_72del		Pindel	.											.	HOXA1	64	.	0			c.214_216del						PASS	.																																			SO:0001651	inframe_deletion	3198	exon1			.		CCDS5401.1, CCDS5402.2	7p15.2	2011-06-20	2005-12-22		ENSG00000105991	ENSG00000105991		"""Homeoboxes / ANTP class : HOXL subclass"""	5099	protein-coding gene	gene with protein product		142955	"""homeo box A1"""	HOX1F, HOX1		1973146	Standard	NM_153620		Approved		uc003sye.3	P49639	OTTHUMG00000023207	ENST00000343060.4:c.213_215delCCA	7.37:g.27135326_27135328delTGG	ENSP00000343246:p.His72del	42.0	0.0	.	792	61.0	26.0	0.426	NM_005522	A4D184|B2R8U7|O43363	In_Frame_Del	DEL	ENST00000343060.4	37	CCDS5401.1																																																																																			.	.	none		0.640	HOXA1-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000358454.1		
ZNF644	84146	hgsc.bcm.edu	37	1	91404352	91404352	+	Silent	SNP	A	A	G	rs149082287	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr1:91404352A>G	ENST00000370440.1	-	3	2776	c.2559T>C	c.(2557-2559)taT>taC	p.Y853Y	ZNF644_ENST00000361321.5_Intron|ZNF644_ENST00000347275.5_Intron|ZNF644_ENST00000467231.1_Intron|ZNF644_ENST00000337393.5_Silent_p.Y853Y			Q9H582	ZN644_HUMAN	zinc finger protein 644	853					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(4)|endometrium(2)|large_intestine(10)|lung(21)|ovary(2)|skin(5)|upper_aerodigestive_tract(1)|urinary_tract(2)	47		all_lung(203;0.00206)|Lung NSC(277;0.0519)|Lung SC(238;0.101)		all cancers(265;0.00102)|Epithelial(280;0.00766)|KIRC - Kidney renal clear cell carcinoma(1967;0.147)|OV - Ovarian serous cystadenocarcinoma(397;0.173)		CTTCTGTTTCATAACTATCTT	0.363																																					p.Y853Y		Atlas-SNP	.											.	ZNF644	120	.	0			c.T2559C						PASS	.	A	,,	0,4406		0,0,2203	77.0	80.0	79.0		,,2559	2.0	1.0	1	dbSNP_134	79	4,8594	3.7+/-12.6	0,4,4295	no	intron,intron,coding-synonymous	ZNF644	NM_016620.3,NM_032186.4,NM_201269.2	,,	0,4,6498	GG,GA,AA		0.0465,0.0,0.0308	,,	,,853/1328	91404352	4,13000	2203	4299	6502	SO:0001819	synonymous_variant	84146	exon3			TGTTTCATAACTA	AB033047	CCDS731.1, CCDS732.1	1p22.2	2008-02-05			ENSG00000122482	ENSG00000122482			29222	protein-coding gene	gene with protein product		614159				10574462	Standard	NM_032186		Approved	KIAA1221, BM-005, MGC60165, MGC70410	uc001dnw.3	Q9H582	OTTHUMG00000010078	ENST00000370440.1:c.2559T>C	1.37:g.91404352A>G		88.0	0.0	0		82.0	42.0	0.512195	NM_201269	A2RU71|Q2TAM0|Q5TCC0|Q6BEP7|Q6P446|Q6PI06|Q7LG67|Q9ULJ9	Silent	SNP	ENST00000370440.1	37	CCDS731.1																																																																																			A|0.999;G|0.001	0.001	strong		0.363	ZNF644-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000027846.2	NM_032186	
EIF4G1	1981	hgsc.bcm.edu	37	3	184049807	184049807	+	Silent	SNP	C	C	T	rs11559218	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr3:184049807C>T	ENST00000346169.2	+	32	4822	c.4551C>T	c.(4549-4551)gaC>gaT	p.D1517D	EIF4G1_ENST00000319274.6_Silent_p.D1517D|EIF4G1_ENST00000342981.4_Silent_p.D1518D|EIF4G1_ENST00000411531.1_Silent_p.D1478D|EIF2B5_ENST00000444495.1_Intron|EIF4G1_ENST00000441154.1_Silent_p.D1354D|EIF4G1_ENST00000392537.2_Silent_p.D1430D|EIF4G1_ENST00000424196.1_Silent_p.D1524D|EIF4G1_ENST00000352767.3_Silent_p.D1524D|EIF4G1_ENST00000382330.3_Silent_p.D1524D|EIF4G1_ENST00000427845.1_Silent_p.D1431D|EIF4G1_ENST00000350481.5_Silent_p.D1353D|EIF4G1_ENST00000414031.1_Silent_p.D1477D|EIF4G1_ENST00000434061.2_Silent_p.D1322D|EIF4G1_ENST00000435046.2_Silent_p.D1321D	NM_198241.2	NP_937884	Q04637	IF4G1_HUMAN	eukaryotic translation initiation factor 4 gamma, 1	1517	EIF4A-binding.|W2. {ECO:0000255|PROSITE- ProRule:PRU00695}.				cell death (GO:0008219)|cellular protein metabolic process (GO:0044267)|cytokine-mediated signaling pathway (GO:0019221)|gene expression (GO:0010467)|insulin receptor signaling pathway (GO:0008286)|lung development (GO:0030324)|mRNA metabolic process (GO:0016071)|nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay (GO:0000288)|nuclear-transcribed mRNA catabolic process, nonsense-mediated decay (GO:0000184)|nuclear-transcribed mRNA poly(A) tail shortening (GO:0000289)|regulation of translational initiation (GO:0006446)|response to ethanol (GO:0045471)|RNA metabolic process (GO:0016070)|translation (GO:0006412)|translational initiation (GO:0006413)|viral process (GO:0016032)	cytosol (GO:0005829)|eukaryotic translation initiation factor 4F complex (GO:0016281)|membrane (GO:0016020)	poly(A) RNA binding (GO:0044822)|translation factor activity, nucleic acid binding (GO:0008135)|translation initiation factor activity (GO:0003743)			central_nervous_system(1)|cervix(2)|endometrium(3)|kidney(5)|large_intestine(14)|lung(41)|ovary(2)|prostate(1)|skin(5)|upper_aerodigestive_tract(1)	75	all_cancers(143;1.06e-10)|Ovarian(172;0.0339)		Epithelial(37;1.53e-33)|OV - Ovarian serous cystadenocarcinoma(80;2.72e-22)			ACCTGTGTGACGAGCAGAAGG	0.587													C|||	12	0.00239617	0.0	0.0072	5008	,	,		20060	0.0		0.006	False		,,,				2504	0.001				p.D1524D		Atlas-SNP	.											.	EIF4G1	151	.	0			c.C4572T						PASS	.	C	,,,,,,	9,4397	15.5+/-35.6	0,9,2194	64.0	61.0	62.0		4572,4572,3966,4554,4551,4059,4290	-9.6	0.7	3	dbSNP_120	62	69,8531	42.2+/-99.7	0,69,4231	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	EIF4G1	NM_001194946.1,NM_001194947.1,NM_004953.4,NM_182917.4,NM_198241.2,NM_198242.2,NM_198244.2	,,,,,,	0,78,6425	TT,TC,CC		0.8023,0.2043,0.5997	,,,,,,	1524/1607,1524/1607,1322/1405,1518/1601,1517/1600,1353/1436,1430/1513	184049807	78,12928	2203	4300	6503	SO:0001819	synonymous_variant	1981	exon33			GTGTGACGAGCAG	D12686	CCDS3259.1, CCDS3260.1, CCDS3261.1, CCDS46970.1, CCDS46970.2, CCDS54687.1, CCDS54688.1	3q27.1	2013-09-19			ENSG00000114867	ENSG00000114867		"""Parkinson disease"""	3296	protein-coding gene	gene with protein product		600495		EIF4G, EIF4F		1429670, 9372926, 21907011	Standard	NM_182917		Approved	p220, PARK18	uc010hxy.3	Q04637	OTTHUMG00000156784	ENST00000346169.2:c.4551C>T	3.37:g.184049807C>T		114.0	0.0	0		107.0	44.0	0.411215	NM_001194946	D3DNT2|D3DNT4|D3DNT5|E9PFM1|G5E9S1|O43177|O95066|Q5HYG0|Q6ZN21|Q8N102	Silent	SNP	ENST00000346169.2	37	CCDS3259.1																																																																																			C|0.995;T|0.005	0.005	strong		0.587	EIF4G1-007	NOVEL	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000345733.1	NM_182917	
CHMP6	79643	hgsc.bcm.edu	37	17	78968837	78968837	+	Silent	SNP	C	C	A	rs146625286	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr17:78968837C>A	ENST00000325167.5	+	3	270	c.192C>A	c.(190-192)ctC>ctA	p.L64L		NM_024591.4	NP_078867.2	Q96FZ7	CHMP6_HUMAN	charged multivesicular body protein 6	64					endosomal transport (GO:0016197)|membrane organization (GO:0061024)|protein transport (GO:0015031)|viral life cycle (GO:0019058)|viral process (GO:0016032)	cytosol (GO:0005829)|endosome (GO:0005768)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)	protein N-terminus binding (GO:0047485)			lung(2)|ovary(1)	3	all_neural(118;0.101)		BRCA - Breast invasive adenocarcinoma(99;0.0175)|OV - Ovarian serous cystadenocarcinoma(97;0.0524)			AGCTGCTGCTCAAGAAGAAGC	0.687													C|||	7	0.00139776	0.0	0.0058	5008	,	,		10104	0.0		0.003	False		,,,				2504	0.0				p.L64L		Atlas-SNP	.											.	CHMP6	16	.	0			c.C192A						PASS	.	C		1,4383		0,1,2191	34.0	33.0	34.0		192	-0.4	1.0	17	dbSNP_134	34	10,8570		0,10,4280	no	coding-synonymous	CHMP6	NM_024591.4		0,11,6471	AA,AC,CC		0.1166,0.0228,0.0849		64/202	78968837	11,12953	2192	4290	6482	SO:0001819	synonymous_variant	79643	exon3			GCTGCTCAAGAAG	BC010108	CCDS11774.1	17q25.3	2014-08-13	2011-09-21		ENSG00000176108	ENSG00000176108		"""Charged multivesicular body proteins"""	25675	protein-coding gene	gene with protein product		610901	"""chromatin modifying protein 6"""			11559748, 15511219	Standard	NM_024591		Approved	FLJ11749, VPS20	uc002jyw.4	Q96FZ7	OTTHUMG00000177645	ENST00000325167.5:c.192C>A	17.37:g.78968837C>A		161.0	0.0	0		173.0	78.0	0.450867	NM_024591	A8K7U0|Q53FU4|Q9HAE8	Silent	SNP	ENST00000325167.5	37	CCDS11774.1																																																																																			C|0.999;A|0.001	0.001	strong		0.687	CHMP6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000438215.1	NM_024591	
ECE2	9718	hgsc.bcm.edu	37	3	183995839	183995839	+	Splice_Site	SNP	T	T	C	rs56080981		TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr3:183995839T>C	ENST00000402825.3	+	5	957		c.e5+2		ECE2_ENST00000359140.4_Splice_Site|EIF2B5_ENST00000444495.1_Intron|ECE2_ENST00000404464.3_Splice_Site|ECE2_ENST00000357474.5_Splice_Site	NM_014693.3	NP_055508.3	O60344	ECE2_HUMAN	endothelin converting enzyme 2						brain development (GO:0007420)|cardioblast differentiation (GO:0010002)|cell-cell signaling (GO:0007267)|heart development (GO:0007507)|peptide hormone processing (GO:0016486)	cytoplasmic vesicle membrane (GO:0030659)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)	metal ion binding (GO:0046872)|metalloendopeptidase activity (GO:0004222)|methyltransferase activity (GO:0008168)			breast(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(11)|lung(13)|ovary(3)|prostate(1)|skin(4)|upper_aerodigestive_tract(4)|urinary_tract(4)	49	all_cancers(143;1.39e-10)|Ovarian(172;0.0339)		Epithelial(37;8.28e-34)|OV - Ovarian serous cystadenocarcinoma(80;2.72e-22)			ATTGAGAAGGTAGGGCCACTG	0.577																																					.		Atlas-SNP	.											.	ECE2	303	.	0			c.957+2T>C						PASS	.						56.0	53.0	54.0					3																	183995839		2203	4300	6503	SO:0001630	splice_region_variant	9718	exon5			AGAAGGTAGGGCC	AF428263	CCDS3255.1, CCDS33899.1, CCDS3256.2, CCDS43179.1, CCDS46969.1	3q27.1	2007-07-26			ENSG00000145194	ENSG00000145194			13275	protein-coding gene	gene with protein product		610145				11718899	Standard	NM_032331		Approved	KIAA0604, MGC2408	uc003fni.4	O60344	OTTHUMG00000150551	ENST00000402825.3:c.957+2T>C	3.37:g.183995839T>C		83.0	0.0	0		82.0	35.0	0.426829	NM_014693	A5PLK8|Q6NTG7|Q6UW36|Q8NFD7|Q96NX3|Q96NX4|Q9BRZ8	Splice_Site	SNP	ENST00000402825.3	37	CCDS3256.2	.	.	.	.	.	.	.	.	.	.	T	6.303	0.424006	0.11928	.	.	ENSG00000145194	ENST00000402825;ENST00000359140;ENST00000404464;ENST00000357474;ENST00000430587	.	.	.	4.96	1.22	0.21188	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	4.2333	0.10613	0.0:0.2167:0.1723:0.6111	rs56080981;rs62619887	.	.	.	.	-1	.	.	.	+	.	.	ECE2	185478533	0.998000	0.40836	0.167000	0.22817	0.190000	0.23558	2.513000	0.45494	0.060000	0.16281	0.459000	0.35465	.	.	.	weak		0.577	ECE2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318874.3	NM_014693	Intron
TNFSF4	7292	hgsc.bcm.edu	37	1	173155860	173155860	+	Missense_Mutation	SNP	C	C	T	rs146261831		TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr1:173155860C>T	ENST00000281834.3	-	3	483	c.347G>A	c.(346-348)aGc>aAc	p.S116N	TNFSF4_ENST00000367718.1_Missense_Mutation_p.S66N|TNFSF4_ENST00000488053.1_5'Flank	NM_003326.3	NP_003317.1	P23510	TNFL4_HUMAN	tumor necrosis factor (ligand) superfamily, member 4	116					acute inflammatory response (GO:0002526)|CD4-positive, alpha-beta T cell costimulation (GO:0035783)|cellular response to lipopolysaccharide (GO:0071222)|cellular response to nitrogen dioxide (GO:0035714)|cellular response to prostaglandin E stimulus (GO:0071380)|chemokine (C-C motif) ligand 11 production (GO:0071954)|cholesterol metabolic process (GO:0008203)|defense response to nematode (GO:0002215)|immune response (GO:0006955)|memory T cell activation (GO:0035709)|negative regulation of cytokine secretion (GO:0050710)|negative regulation of interferon-gamma production (GO:0032689)|negative regulation of interleukin-17 production (GO:0032700)|negative regulation of regulatory T cell differentiation (GO:0045590)|negative regulation of sequence-specific DNA binding transcription factor activity (GO:0043433)|negative regulation of T-helper 1 cell differentiation (GO:0045626)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of activated T cell proliferation (GO:0042104)|positive regulation of alpha-beta T cell proliferation (GO:0046641)|positive regulation of B cell activation (GO:0050871)|positive regulation of CD4-positive, alpha-beta T cell costimulation (GO:1900281)|positive regulation of CD4-positive, alpha-beta T cell differentiation (GO:0043372)|positive regulation of cell proliferation (GO:0008284)|positive regulation of immunoglobulin mediated immune response (GO:0002891)|positive regulation of immunoglobulin secretion (GO:0051024)|positive regulation of inflammatory response (GO:0050729)|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-13 production (GO:0032736)|positive regulation of interleukin-2 production (GO:0032743)|positive regulation of interleukin-4 production (GO:0032753)|positive regulation of interleukin-4-dependent isotype switching to IgE isotypes (GO:2000572)|positive regulation of interleukin-6 production (GO:0032755)|positive regulation of memory T cell activation (GO:2000568)|positive regulation of memory T cell differentiation (GO:0043382)|positive regulation of T cell cytokine production (GO:0002726)|positive regulation of T-helper 2 cell activation (GO:2000570)|positive regulation of T-helper 2 cell differentiation (GO:0045630)|positive regulation of type 2 immune response (GO:0002830)|regulation of adaptive immune response (GO:0002819)|regulation of inflammatory response (GO:0050727)|response to nitrogen dioxide (GO:0035713)|response to virus (GO:0009615)|signal transduction (GO:0007165)|T cell proliferation (GO:0042098)|T-helper 2 cell activation (GO:0035712)	cell surface (GO:0009986)|extracellular space (GO:0005615)|integral component of plasma membrane (GO:0005887)	receptor binding (GO:0005102)|tumor necrosis factor receptor superfamily binding (GO:0032813)			breast(2)|central_nervous_system(2)|endometrium(1)|large_intestine(2)|lung(3)|skin(1)|urinary_tract(1)	12						GTAATGAAGGCTAATGTTGAC	0.463																																					p.S116N		Atlas-SNP	.											.	TNFSF4	29	.	0			c.G347A						PASS	.	C	ASN/SER	0,4406		0,0,2203	98.0	101.0	100.0		347	-0.7	0.0	1	dbSNP_134	100	5,8595	4.3+/-15.6	0,5,4295	yes	missense	TNFSF4	NM_003326.3	46	0,5,6498	TT,TC,CC		0.0581,0.0,0.0384	benign	116/184	173155860	5,13001	2203	4300	6503	SO:0001583	missense	7292	exon3			TGAAGGCTAATGT	D90224	CCDS1306.1, CCDS72985.1	1q25	2008-07-31	2008-07-31		ENSG00000117586	ENSG00000117586		"""Tumor necrosis factor (ligand) superfamily"", ""CD molecules"""	11934	protein-coding gene	gene with protein product		603594	"""tax-transcriptionally activated glycoprotein 1, 34kD"""	TXGP1		1996093, 8076595	Standard	XM_005245475		Approved	OX-40L, gp34, CD252	uc001giw.3	P23510	OTTHUMG00000034838	ENST00000281834.3:c.347G>A	1.37:g.173155860C>T	ENSP00000281834:p.Ser116Asn	205.0	0.0	0		178.0	79.0	0.44382	NM_003326	Q5JZA5|Q8IV74|Q9HCN9	Missense_Mutation	SNP	ENST00000281834.3	37	CCDS1306.1	.	.	.	.	.	.	.	.	.	.	C	11.24	1.581728	0.28180	0.0	5.81E-4	ENSG00000117586	ENST00000367718;ENST00000281834;ENST00000545292	D;D	0.94613	-3.47;-3.47	5.91	-0.7	0.11273	Tumour necrosis factor (2);Tumour necrosis factor-like (1);	1.170620	0.05958	N	0.640076	T	0.81503	0.4836	L	0.41236	1.265	0.09310	N	1	B;B	0.12630	0.001;0.006	B;B	0.13407	0.009;0.009	T	0.69639	-0.5091	10	0.30078	T	0.28	-0.9441	4.6924	0.12786	0.0:0.2516:0.3912:0.3572	.	116;66	P23510;Q8IV74	TNFL4_HUMAN;.	N	66;116;66	ENSP00000356691:S66N;ENSP00000281834:S116N	ENSP00000281834:S116N	S	-	2	0	TNFSF4	171422483	0.000000	0.05858	0.001000	0.08648	0.055000	0.15305	-1.057000	0.03486	0.221000	0.20879	0.655000	0.94253	AGC	C|1.000;T|0.000	0.000	weak		0.463	TNFSF4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000084271.1		
SCAF11	9169	hgsc.bcm.edu	37	12	46321158	46321158	+	Missense_Mutation	SNP	T	T	G			TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr12:46321158T>G	ENST00000369367.3	-	11	2559	c.2326A>C	c.(2326-2328)Agc>Cgc	p.S776R	SCAF11_ENST00000550629.1_5'Flank|SCAF11_ENST00000465950.1_Missense_Mutation_p.S461R|SCAF11_ENST00000419565.2_Missense_Mutation_p.S776R|SCAF11_ENST00000549162.1_Missense_Mutation_p.S584R	NM_004719.2	NP_004710.2	Q99590	SCAFB_HUMAN	SR-related CTD-associated factor 11	776					mRNA processing (GO:0006397)|RNA splicing (GO:0008380)|RNA splicing, via transesterification reactions (GO:0000375)|spliceosomal complex assembly (GO:0000245)	nucleolus (GO:0005730)|nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)|zinc ion binding (GO:0008270)	p.S776G(1)		breast(2)|central_nervous_system(1)|endometrium(2)|kidney(8)|large_intestine(17)|lung(25)|ovary(3)|pancreas(1)|prostate(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(3)	69						TCTTTTGGGCTTTCAGATGGT	0.383																																					p.S776R		Atlas-SNP	.											SCAF11,NS,carcinoma,0,1	SCAF11	145	1	1	Substitution - Missense(1)	kidney(1)	c.A2326C						PASS	.						177.0	174.0	175.0					12																	46321158		2203	4300	6503	SO:0001583	missense	9169	exon11			TTGGGCTTTCAGA	Y11251	CCDS8748.2	12q13.11	2013-01-09	2011-01-10	2011-01-10	ENSG00000139218	ENSG00000139218		"""RING-type (C3HC4) zinc fingers"""	10784	protein-coding gene	gene with protein product		603668	"""splicing factor, arginine/serine-rich 2, interacting protein"", ""serine/arginine-rich splicing factor 2, interacting protein"""	SFRS2IP, SRSF2IP		9224939, 9447963	Standard	NM_004719		Approved	SIP1, SRRP129, CASP11	uc001rox.3	Q99590	OTTHUMG00000149930	ENST00000369367.3:c.2326A>C	12.37:g.46321158T>G	ENSP00000358374:p.Ser776Arg	117.0	0.0	0		125.0	64.0	0.512	NM_004719	A6NEU9|A6NLW5|Q8IW59	Missense_Mutation	SNP	ENST00000369367.3	37	CCDS8748.2	.	.	.	.	.	.	.	.	.	.	T	9.433	1.085940	0.20390	.	.	ENSG00000139218	ENST00000465950;ENST00000369367;ENST00000549162;ENST00000419565;ENST00000547018	T;T;T;T;T	0.49139	1.45;2.18;1.45;2.18;0.79	5.93	2.17	0.27698	.	0.432900	0.26146	N	0.026061	T	0.35653	0.0939	L	0.59436	1.845	0.09310	N	1	P;P	0.45078	0.85;0.498	B;B	0.37304	0.246;0.125	T	0.21415	-1.0246	10	0.34782	T	0.22	0.8665	5.4177	0.16384	0.1281:0.1381:0.0:0.7337	.	584;776	F8VXG7;Q99590	.;SCAFB_HUMAN	R	461;776;584;776;716	ENSP00000449812:S461R;ENSP00000358374:S776R;ENSP00000448864:S584R;ENSP00000413036:S776R;ENSP00000446746:S716R	ENSP00000358374:S776R	S	-	1	0	SCAF11	44607425	0.169000	0.23002	0.127000	0.21898	0.023000	0.10783	0.397000	0.20883	0.121000	0.18284	0.533000	0.62120	AGC	.	.	none		0.383	SCAF11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000313992.2	NM_004719	
OR2H1	26716	hgsc.bcm.edu	37	6	29429732	29429732	+	Silent	SNP	T	T	C	rs61732184	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr6:29429732T>C	ENST00000377136.1	+	4	651	c.186T>C	c.(184-186)tcT>tcC	p.S62S	OR2H1_ENST00000442615.1_Silent_p.S62S|OR2H1_ENST00000396792.2_Silent_p.S62S|OR2H1_ENST00000377133.1_Silent_p.S62S|OR2H1_ENST00000473369.1_Intron|OR2H1_ENST00000377132.1_Silent_p.S62S			Q9GZK4	OR2H1_HUMAN	olfactory receptor, family 2, subfamily H, member 1	62						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			large_intestine(5)|lung(12)	17						TTTTCCTCTCTGACCTCTCCT	0.527													T|||	174	0.0347444	0.1044	0.013	5008	,	,		20433	0.0119		0.0119	False		,,,				2504	0.0031				p.S62S		Atlas-SNP	.											.	OR2H1	38	.	0			c.T186C						PASS	.	T		301,2721		17,267,1227	138.0	135.0	136.0		186	-0.0	1.0	6	dbSNP_129	136	33,5385		0,33,2676	no	coding-synonymous	OR2H1	NM_030883.3		17,300,3903	CC,CT,TT		0.6091,9.9603,3.9573		62/317	29429732	334,8106	1511	2709	4220	SO:0001819	synonymous_variant	26716	exon3			CCTCTCTGACCTC	AF044491	CCDS4660.1	6p22.1	2014-02-19	2002-02-28		ENSG00000204688	ENSG00000204688		"""GPCR / Class A : Olfactory receptors"""	8252	protein-coding gene	gene with protein product			"""olfactory receptor, family 2, subfamily H, member 8"""	OR2H6, OR2H8			Standard	NM_030883		Approved	OR6-2	uc003nmi.3	Q9GZK4	OTTHUMG00000031050	ENST00000377136.1:c.186T>C	6.37:g.29429732T>C		231.0	0.0	0		253.0	121.0	0.478261	NM_030883	B0S7T4|O43629|O43661|O43662|Q5SUN6|Q9GZK9	Silent	SNP	ENST00000377136.1	37	CCDS4660.1																																																																																			T|0.964;C|0.036	0.036	strong		0.527	OR2H1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000194014.3		
TMEM171	134285	hgsc.bcm.edu	37	5	72424269	72424269	+	Silent	SNP	T	T	G	rs34728034	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr5:72424269T>G	ENST00000454765.2	+	3	1166	c.693T>G	c.(691-693)tcT>tcG	p.S231S	TMEM171_ENST00000287773.5_Silent_p.S231S			Q8WVE6	TM171_HUMAN	transmembrane protein 171	231						integral component of membrane (GO:0016021)				endometrium(5)|kidney(2)|large_intestine(2)|lung(4)|prostate(1)|stomach(1)	15		Lung NSC(167;0.0378)|Ovarian(174;0.0908)|Prostate(461;0.165)		OV - Ovarian serous cystadenocarcinoma(47;1.87e-54)|Lung(70;0.115)		TTCCTGAATCTTCAGCTTCTG	0.418													T|||	82	0.0163738	0.0545	0.0144	5008	,	,		17554	0.0		0.0	False		,,,				2504	0.0				p.S231S	NSCLC(112;638 2280 27369 30736)	Atlas-SNP	.											.	TMEM171	41	.	0			c.T693G						PASS	.	T	,	229,4177	138.0+/-173.8	6,217,1980	193.0	194.0	194.0		693,693	4.1	1.0	5	dbSNP_126	194	2,8598	1.2+/-3.3	0,2,4298	no	coding-synonymous,coding-synonymous	TMEM171	NM_001161342.1,NM_173490.6	,	6,219,6278	GG,GT,TT		0.0233,5.1975,1.7761	,	231/324,231/325	72424269	231,12775	2203	4300	6503	SO:0001819	synonymous_variant	134285	exon3			TGAATCTTCAGCT	BC018083	CCDS4017.1, CCDS54869.1	5q13.2	2008-02-05			ENSG00000157111	ENSG00000157111			27031	protein-coding gene	gene with protein product						12477932	Standard	NM_173490		Approved	PRP2	uc003kcm.2	Q8WVE6	OTTHUMG00000131269	ENST00000454765.2:c.693T>G	5.37:g.72424269T>G		176.0	0.0	0		187.0	95.0	0.508021	NM_173490	Q8N0S1|Q8TDT7	Silent	SNP	ENST00000454765.2	37	CCDS4017.1																																																																																			T|0.980;G|0.020	0.020	strong		0.418	TMEM171-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000254037.2	NM_173490	
MAP7D1	55700	hgsc.bcm.edu	37	1	36644874	36644874	+	Silent	SNP	G	G	A			TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr1:36644874G>A	ENST00000373151.2	+	13	2358	c.2142G>A	c.(2140-2142)gaG>gaA	p.E714E	MAP7D1_ENST00000373150.4_Silent_p.E682E|MAP7D1_ENST00000316156.4_Silent_p.E677E|MAP7D1_ENST00000373148.4_Silent_p.E251E	NM_018067.3	NP_060537.3	Q3KQU3	MA7D1_HUMAN	MAP7 domain containing 1	714					microtubule cytoskeleton organization (GO:0000226)	cytoplasm (GO:0005737)|microtubule (GO:0005874)|microtubule cytoskeleton (GO:0015630)				breast(2)|cervix(1)|endometrium(2)|large_intestine(3)|lung(3)|ovary(3)|prostate(3)|skin(1)|urinary_tract(1)	19		Myeloproliferative disorder(586;0.0393)				GTCTGGAGGAGATCATGAAGA	0.597																																					p.E714E		Atlas-SNP	.											.	MAP7D1	62	.	0			c.G2142A						PASS	.						31.0	35.0	34.0					1																	36644874		2203	4300	6503	SO:0001819	synonymous_variant	55700	exon13			GGAGGAGATCATG	AK096341	CCDS30673.1, CCDS65492.1, CCDS65493.1	1p34.3	2008-02-05	2007-02-08	2007-02-08	ENSG00000116871	ENSG00000116871			25514	protein-coding gene	gene with protein product			"""proline arginine rich coiled coil 1"", ""arginine/proline rich coiled-coil 1"""	PARCC1, RPRC1		10574461	Standard	XM_005271024		Approved	FLJ10350, FLJ39022	uc001bzz.3	Q3KQU3	OTTHUMG00000007714	ENST00000373151.2:c.2142G>A	1.37:g.36644874G>A		125.0	0.0	0		138.0	75.0	0.543478	NM_018067	D3DPS4|Q7L8J5|Q8N905|Q8TAK0|Q9HBQ2|Q9NW29|Q9ULN3	Silent	SNP	ENST00000373151.2	37	CCDS30673.1																																																																																			.	.	none		0.597	MAP7D1-009	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000382095.1	NM_018067	
TTN	7273	hgsc.bcm.edu	37	2	179429612	179429612	+	Missense_Mutation	SNP	A	A	G	rs186273940	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr2:179429612A>G	ENST00000591111.1	-	276	76548	c.76324T>C	c.(76324-76326)Tca>Cca	p.S25442P	TTN-AS1_ENST00000592689.1_RNA|TTN_ENST00000342175.6_Missense_Mutation_p.S18210P|TTN-AS1_ENST00000419746.1_RNA|TTN-AS1_ENST00000590807.1_RNA|TTN-AS1_ENST00000586831.1_RNA|TTN-AS1_ENST00000592630.1_RNA|TTN-AS1_ENST00000590932.1_RNA|TTN-AS1_ENST00000456053.1_RNA|TTN-AS1_ENST00000586707.1_RNA|TTN-AS1_ENST00000438095.1_RNA|TTN_ENST00000359218.5_Missense_Mutation_p.S18143P|TTN_ENST00000460472.2_Missense_Mutation_p.S18018P|TTN-AS1_ENST00000592600.1_RNA|TTN_ENST00000589042.1_Missense_Mutation_p.S27083P|TTN-AS1_ENST00000585451.1_RNA|TTN-AS1_ENST00000592750.1_RNA|TTN_ENST00000342992.6_Missense_Mutation_p.S24515P|TTN-AS1_ENST00000591332.1_RNA|TTN-AS1_ENST00000586452.1_RNA			Q8WZ42	TITIN_HUMAN	titin	25442	Fibronectin type-III 85. {ECO:0000255|PROSITE-ProRule:PRU00316}.				adult heart development (GO:0007512)|blood coagulation (GO:0007596)|cardiac muscle contraction (GO:0060048)|cardiac muscle fiber development (GO:0048739)|cardiac muscle hypertrophy (GO:0003300)|cardiac muscle tissue morphogenesis (GO:0055008)|cardiac myofibril assembly (GO:0055003)|detection of muscle stretch (GO:0035995)|forward locomotion (GO:0043056)|in utero embryonic development (GO:0001701)|mitotic chromosome condensation (GO:0007076)|muscle contraction (GO:0006936)|muscle filament sliding (GO:0030049)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|regulation of catalytic activity (GO:0050790)|regulation of protein kinase activity (GO:0045859)|regulation of relaxation of cardiac muscle (GO:1901897)|response to calcium ion (GO:0051592)|sarcomere organization (GO:0045214)|sarcomerogenesis (GO:0048769)|skeletal muscle myosin thick filament assembly (GO:0030241)|skeletal muscle thin filament assembly (GO:0030240)|somitogenesis (GO:0001756)|striated muscle contraction (GO:0006941)	condensed nuclear chromosome (GO:0000794)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|I band (GO:0031674)|M band (GO:0031430)|nucleus (GO:0005634)|striated muscle thin filament (GO:0005865)|Z disc (GO:0030018)	actin filament binding (GO:0051015)|actinin binding (GO:0042805)|ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|calmodulin binding (GO:0005516)|enzyme binding (GO:0019899)|identical protein binding (GO:0042802)|muscle alpha-actinin binding (GO:0051371)|protease binding (GO:0002020)|protein kinase binding (GO:0019901)|protein self-association (GO:0043621)|protein serine/threonine kinase activity (GO:0004674)|structural constituent of muscle (GO:0008307)|structural molecule activity conferring elasticity (GO:0097493)|telethonin binding (GO:0031433)			NS(24)|autonomic_ganglia(1)|breast(64)|central_nervous_system(14)|cervix(14)|endometrium(96)|haematopoietic_and_lymphoid_tissue(16)|kidney(91)|large_intestine(303)|liver(1)|lung(595)|ovary(58)|pancreas(17)|prostate(38)|skin(60)|stomach(29)|upper_aerodigestive_tract(1)|urinary_tract(26)	1448			OV - Ovarian serous cystadenocarcinoma(117;0.023)|Epithelial(96;0.0454)|all cancers(119;0.134)			TTTGAGATTGATGTCACAAAA	0.408													A|||	3	0.000599042	0.0	0.0	5008	,	,		21196	0.0		0.003	False		,,,				2504	0.0				p.S27083P		Atlas-SNP	.											.	TTN	18412	.	0			c.T81247C						PASS	.	A	PRO/SER,PRO/SER,PRO/SER,PRO/SER	0,3750		0,0,1875	77.0	73.0	74.0		54052,73543,54427,54628	4.8	1.0	2		74	6,8210		1,4,4103	yes	missense,missense,missense,missense	TTN	NM_003319.4,NM_133378.4,NM_133432.3,NM_133437.3	74,74,74,74	1,4,5978	GG,GA,AA		0.073,0.0,0.0501	possibly-damaging,possibly-damaging,possibly-damaging,possibly-damaging	18018/26927,24515/33424,18143/27052,18210/27119	179429612	6,11960	1875	4108	5983	SO:0001583	missense	7273	exon326			AGATTGATGTCAC	X90568	CCDS54421.1, CCDS54422.1, CCDS54423.1, CCDS54424.1, CCDS33337.1, CCDS59435.1, CCDS74610.1	2q31	2014-09-17	2004-02-13		ENSG00000155657	ENSG00000155657		"""Immunoglobulin superfamily / I-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"", ""Fibronectin type III domain containing"""	12403	protein-coding gene	gene with protein product		188840	"""cardiomyopathy, dilated 1G (autosomal dominant)"""	CMD1G		2129545, 10051295	Standard	NM_003319		Approved	CMPD4, FLJ32040, TMD, CMH9, LGMD2J, MYLK5	uc031rqd.1	Q8WZ42	OTTHUMG00000154448	ENST00000591111.1:c.76324T>C	2.37:g.179429612A>G	ENSP00000465570:p.Ser25442Pro	96.0	0.0	0		122.0	73.0	0.598361	NM_001267550	A6NKB1|E7EQE6|E7ET18|K7ENY1|Q10465|Q10466|Q15598|Q2XUS3|Q32Q60|Q4U1Z6|Q4ZG20|Q6NSG0|Q6PDB1|Q6PJP0|Q7KYM2|Q7KYN4|Q7KYN5|Q7LDM3|Q7Z2X3|Q8TCG8|Q8WZ42|Q8WZ51|Q8WZ52|Q8WZ53|Q8WZB3|Q92761|Q92762|Q9UD97|Q9UP84|Q9Y6L9	Missense_Mutation	SNP	ENST00000591111.1	37		3	0.0013736263736263737	0	0.0	0	0.0	0	0.0	3	0.00395778364116095	A	8.744	0.919583	0.17982	0.0	7.3E-4	ENSG00000155657	ENST00000342992;ENST00000460472;ENST00000342175;ENST00000359218;ENST00000356127	T;T;T;T	0.57907	0.37;0.37;0.37;0.37	6.02	4.85	0.62838	Fibronectin, type III (4);Peptidase C2, calpain, large subunit, domain III (1);Ribonuclease H-like (1);Immunoglobulin-like fold (1);	.	.	.	.	T	0.51907	0.1702	L	0.53617	1.68	0.44207	D	0.997039	P;P;P;P	0.42584	0.784;0.784;0.784;0.662	P;P;P;P	0.48368	0.575;0.575;0.575;0.478	T	0.55617	-0.8113	9	0.87932	D	0	.	4.0826	0.09932	0.5754:0.2427:0.0654:0.1165	.	18018;18143;18210;25442	D3DPF9;E7EQE6;E7ET18;Q8WZ42	.;.;.;TITIN_HUMAN	P	24515;18018;18210;18143;18016	ENSP00000343764:S24515P;ENSP00000434586:S18018P;ENSP00000340554:S18210P;ENSP00000352154:S18143P	ENSP00000340554:S18210P	S	-	1	0	TTN	179137858	1.000000	0.71417	0.960000	0.40013	0.993000	0.82548	1.448000	0.35112	1.063000	0.40649	0.528000	0.53228	TCA	A|0.999;G|0.001	0.001	strong		0.408	TTN-019	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000460310.1	NM_133378	
KPTN	11133	hgsc.bcm.edu	37	19	47987230	47987230	+	Missense_Mutation	SNP	C	C	T	rs142867197	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr19:47987230C>T	ENST00000338134.3	-	1	295	c.188G>A	c.(187-189)cGg>cAg	p.R63Q	NAPA-AS1_ENST00000593284.1_RNA|NAPA-AS1_ENST00000594367.1_RNA|KPTN_ENST00000595484.1_5'UTR|KPTN_ENST00000536339.1_5'UTR	NM_007059.2	NP_008990.2	Q9Y664	KPTN_HUMAN	kaptin (actin binding protein)	63					actin filament organization (GO:0007015)|cellular component movement (GO:0006928)|sensory perception of sound (GO:0007605)	actin cytoskeleton (GO:0015629)|cell projection (GO:0042995)|cytoplasm (GO:0005737)|microtubule organizing center (GO:0005815)|nucleus (GO:0005634)	actin binding (GO:0003779)			breast(1)|lung(3)|ovary(2)|pancreas(2)	8		all_cancers(25;1.55e-10)|all_epithelial(76;3.4e-08)|all_lung(116;1.73e-07)|Lung NSC(112;3.95e-07)|Ovarian(192;0.0139)|all_neural(266;0.026)|Breast(70;0.0503)		OV - Ovarian serous cystadenocarcinoma(262;0.000428)|all cancers(93;0.000631)|Epithelial(262;0.0153)|GBM - Glioblastoma multiforme(486;0.0694)		GGCCACTGGCCGGATTTTCTG	0.667											OREG0025593	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	C|||	2	0.000399361	0.0	0.0	5008	,	,		14783	0.0		0.002	False		,,,				2504	0.0				p.R63Q		Atlas-SNP	.											.	KPTN	34	.	0			c.G188A						PASS	.	C	GLN/ARG	1,3881		0,1,1940	42.0	48.0	46.0		188	4.6	1.0	19	dbSNP_134	46	13,8253		0,13,4120	yes	missense	KPTN	NM_007059.2	43	0,14,6060	TT,TC,CC		0.1573,0.0258,0.1152	possibly-damaging	63/437	47987230	14,12134	1941	4133	6074	SO:0001583	missense	11133	exon1			ACTGGCCGGATTT	AF105369	CCDS42583.1	19q13.32	2014-08-13	2001-11-28		ENSG00000118162	ENSG00000118162			6404	protein-coding gene	gene with protein product		615620	"""kaptin (actin-binding protein)"""			10099934	Standard	XM_005258467		Approved	2E4	uc002pgy.3	Q9Y664	OTTHUMG00000183443	ENST00000338134.3:c.188G>A	19.37:g.47987230C>T	ENSP00000337850:p.Arg63Gln	25.0	0.0	0	951	44.0	22.0	0.5	NM_007059	B3KN86|B4DQ76|Q96GT1	Missense_Mutation	SNP	ENST00000338134.3	37	CCDS42583.1	2	9.157509157509158E-4	0	0.0	0	0.0	0	0.0	2	0.002638522427440633	C	22.0	4.231215	0.79688	2.58E-4	0.001573	ENSG00000118162	ENST00000338134	.	.	.	4.59	4.59	0.56863	.	0.128494	0.50627	D	0.000103	T	0.57388	0.2050	L	0.56396	1.775	0.80722	D	1	B	0.30281	0.275	B	0.23716	0.048	T	0.58053	-0.7704	9	0.33940	T	0.23	-22.8261	16.3101	0.82865	0.0:1.0:0.0:0.0	.	63	Q9Y664	KPTN_HUMAN	Q	63	.	ENSP00000337850:R63Q	R	-	2	0	KPTN	52679042	1.000000	0.71417	1.000000	0.80357	0.987000	0.75469	6.799000	0.75160	2.390000	0.81377	0.313000	0.20887	CGG	C|0.998;T|0.002	0.002	strong		0.667	KPTN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466672.2		
CCDC158	339965	hgsc.bcm.edu	37	4	77255210	77255210	+	Silent	SNP	C	C	T	rs113022439	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr4:77255210C>T	ENST00000388914.3	-	18	2927	c.2775G>A	c.(2773-2775)aaG>aaA	p.K925K		NM_001042784.1	NP_001036249.1	Q5M9N0	CD158_HUMAN	coiled-coil domain containing 158	925										breast(1)|central_nervous_system(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(9)|lung(28)|ovary(3)|pancreas(1)|prostate(1)|skin(6)|stomach(1)	56						CTTCCTCTGTCTTGCTCAGAG	0.483													C|||	32	0.00638978	0.0015	0.0072	5008	,	,		17210	0.0		0.0239	False		,,,				2504	0.001				p.K925K		Atlas-SNP	.											.	CCDC158	114	.	0			c.G2775A						PASS	.	C		15,4101		0,15,2043	158.0	159.0	159.0		2775	3.8	0.6	4	dbSNP_132	159	300,8128		4,292,3918	no	coding-synonymous	CCDC158	NM_001042784.1		4,307,5961	TT,TC,CC		3.5596,0.3644,2.5112		925/1114	77255210	315,12229	2058	4214	6272	SO:0001819	synonymous_variant	339965	exon18			CTCTGTCTTGCTC	BC035224	CCDS43242.1	4q21.1	2009-04-06			ENSG00000163749	ENSG00000163749			26374	protein-coding gene	gene with protein product						12477932	Standard	NM_001042784		Approved	FLJ25770	uc003hkb.4	Q5M9N0	OTTHUMG00000160916	ENST00000388914.3:c.2775G>A	4.37:g.77255210C>T		171.0	0.0	0		177.0	93.0	0.525424	NM_001042784	Q8IYQ1|Q8N7D4|Q8N7E3	Silent	SNP	ENST00000388914.3	37	CCDS43242.1																																																																																			C|0.984;T|0.016	0.016	strong		0.483	CCDC158-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000362694.2	NM_001042784	
LPAR2	9170	hgsc.bcm.edu	37	19	19737992	19737992	+	Silent	SNP	G	G	A	rs150741448	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr19:19737992G>A	ENST00000542587.1	-	5	1004	c.102C>T	c.(100-102)gtC>gtT	p.V34V	LPAR2_ENST00000586703.1_Silent_p.V34V|LPAR2_ENST00000407877.3_Silent_p.V34V|LPAR2_ENST00000589311.1_5'Flank			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		59.0	0.0	0		63.0	29.0	0.460317	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	
VPS41	27072	hgsc.bcm.edu	37	7	38785204	38785204	+	Missense_Mutation	SNP	T	T	C			TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr7:38785204T>C	ENST00000310301.4	-	23	1990	c.1936A>G	c.(1936-1938)Atc>Gtc	p.I646V	VPS41_ENST00000395969.2_Missense_Mutation_p.I621V	NM_014396.3	NP_055211.2	P49754	VPS41_HUMAN	vacuolar protein sorting 41 homolog (S. cerevisiae)	646					Golgi vesicle transport (GO:0048193)|intracellular protein transport (GO:0006886)|vesicle-mediated transport (GO:0016192)	cytosol (GO:0005829)|early endosome (GO:0005769)|Golgi-associated vesicle (GO:0005798)|HOPS complex (GO:0030897)|late endosome (GO:0005770)|lysosomal membrane (GO:0005765)|membrane (GO:0016020)|microtubule cytoskeleton (GO:0015630)	zinc ion binding (GO:0008270)			NS(1)|breast(1)|central_nervous_system(2)|endometrium(5)|kidney(4)|large_intestine(5)|lung(17)|ovary(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(4)	44						TGTTGACAGATCTCAAGAGCC	0.328																																					p.I646V		Atlas-SNP	.											.	VPS41	102	.	0			c.A1936G						PASS	.						112.0	114.0	113.0					7																	38785204		2203	4300	6503	SO:0001583	missense	27072	exon23			GACAGATCTCAAG	U87309	CCDS5457.1, CCDS5458.2	7p14.1-p13	2009-05-08	2006-12-19		ENSG00000006715	ENSG00000006715			12713	protein-coding gene	gene with protein product		605485	"""vacuolar protein sorting 41 (yeast homolog)"", ""vacuolar protein sorting 41 (yeast)"""			9159129	Standard	NM_080631		Approved	HVSP41	uc003tgy.3	P49754	OTTHUMG00000023629	ENST00000310301.4:c.1936A>G	7.37:g.38785204T>C	ENSP00000309457:p.Ile646Val	89.0	0.0	0		101.0	44.0	0.435644	NM_014396	E9PF36|Q86TP8|Q99851|Q99852	Missense_Mutation	SNP	ENST00000310301.4	37	CCDS5457.1	.	.	.	.	.	.	.	.	.	.	T	13.62	2.290379	0.40494	.	.	ENSG00000006715	ENST00000310301;ENST00000395969	T;T	0.19105	2.17;2.17	5.35	5.35	0.76521	Tetratricopeptide-like helical (1);	0.252290	0.45126	D	0.000390	T	0.19725	0.0474	L	0.41236	1.265	0.58432	D	0.999996	B;B;B	0.06786	0.001;0.001;0.001	B;B;B	0.04013	0.001;0.001;0.001	T	0.02617	-1.1133	10	0.30078	T	0.28	-15.5727	15.6427	0.77020	0.0:0.0:0.0:1.0	.	646;621;646	B2RB94;E9PF36;P49754	.;.;VPS41_HUMAN	V	646;621	ENSP00000309457:I646V;ENSP00000379297:I621V	ENSP00000309457:I646V	I	-	1	0	VPS41	38751729	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	4.923000	0.63412	2.152000	0.67230	0.455000	0.32223	ATC	.	.	none		0.328	VPS41-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000226986.3		
RIC3	79608	hgsc.bcm.edu	37	11	8159884	8159884	+	Missense_Mutation	SNP	C	C	G	rs80168649	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr11:8159884C>G	ENST00000309737.6	-	3	361	c.362G>C	c.(361-363)gGg>gCg	p.G121A	RIC3_ENST00000425599.2_Missense_Mutation_p.G121A|RIC3_ENST00000530060.1_5'UTR|RIC3_ENST00000343202.4_Missense_Mutation_p.G121A|RIC3_ENST00000539720.1_Missense_Mutation_p.G72A|RIC3_ENST00000335425.7_Intron			Q7Z5B4	RIC3_HUMAN	RIC3 acetylcholine receptor chaperone	121					cellular protein complex assembly (GO:0043623)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|protein folding (GO:0006457)|synaptic transmission, cholinergic (GO:0007271)	endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)				breast(1)|endometrium(2)|large_intestine(2)|lung(9)|ovary(2)|pancreas(1)	17				Epithelial(150;2.89e-07)|BRCA - Breast invasive adenocarcinoma(625;0.204)		AGTTGTTTTCCCCTTTGAGAG	0.438													C|||	17	0.00339457	0.0008	0.0014	5008	,	,		16568	0.0		0.0149	False		,,,				2504	0.0				p.G121A		Atlas-SNP	.											.	RIC3	42	.	0			c.G362C						PASS	.	C	,ALA/GLY,ALA/GLY,ALA/GLY	12,4390	19.1+/-41.9	0,12,2189	224.0	215.0	218.0		,362,362,362	5.8	1.0	11	dbSNP_131	218	114,8478	60.6+/-122.4	0,114,4182	yes	intron,missense,missense,missense	RIC3	NM_001135109.1,NM_001206671.1,NM_001206672.1,NM_024557.3	,60,60,60	0,126,6371	GG,GC,CC		1.3268,0.2726,0.9697	,probably-damaging,probably-damaging,probably-damaging	,121/370,121/289,121/369	8159884	126,12868	2201	4296	6497	SO:0001583	missense	79608	exon3			GTTTTCCCCTTTG		CCDS7788.1, CCDS44533.1, CCDS55741.1, CCDS55742.1	11p15.4	2013-08-05	2013-08-05		ENSG00000166405	ENSG00000166405			30338	protein-coding gene	gene with protein product		610509	"""resistance to inhibitors of cholinesterase 3 homolog (C. elegans)"""			12821669	Standard	NM_024557		Approved	FLJ11608, PRO1385, AYST720	uc001mgd.2	Q7Z5B4	OTTHUMG00000165694	ENST00000309737.6:c.362G>C	11.37:g.8159884C>G	ENSP00000308820:p.Gly121Ala	106.0	0.0	0		113.0	50.0	0.442478	NM_001206672	B0B1U0|B2RD25|D3DQU5|Q6UX78|Q7Z5B3|Q86T94|Q8TBJ9|Q9HAH8	Missense_Mutation	SNP	ENST00000309737.6	37	CCDS55742.1	15	0.006868131868131868	1	0.0020325203252032522	0	0.0	0	0.0	14	0.018469656992084433	C	21.8	4.195192	0.78902	0.002726	0.013268	ENSG00000166405	ENST00000343202;ENST00000309737;ENST00000543346;ENST00000539720;ENST00000425599;ENST00000531450	T;T;T;T;T	0.30182	1.54;1.54;1.54;1.54;1.54	5.78	5.78	0.91487	.	0.000000	0.85682	D	0.000000	T	0.38639	0.1048	M	0.68317	2.08	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;0.998;0.999;0.999	T	0.25606	-1.0127	10	0.32370	T	0.25	.	18.1955	0.89820	0.0:1.0:0.0:0.0	.	121;121;121;121	B7Z1U4;B0B1U0;Q7Z5B4;Q7Z5B4-5	.;.;RIC3_HUMAN;.	A	121;121;121;72;121;121	ENSP00000344904:G121A;ENSP00000308820:G121A;ENSP00000443871:G72A;ENSP00000395320:G121A;ENSP00000431658:G121A	ENSP00000308820:G121A	G	-	2	0	RIC3	8116460	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	3.457000	0.53007	2.738000	0.93877	0.609000	0.83330	GGG	C|0.992;G|0.008	0.008	strong		0.438	RIC3-008	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000385900.1	NM_024557	
ABCD4	5826	hgsc.bcm.edu	37	14	74759066	74759066	+	Missense_Mutation	SNP	G	G	A	rs147795328	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr14:74759066G>A	ENST00000356924.4	-	11	1185	c.1042C>T	c.(1042-1044)Cgg>Tgg	p.R348W	AC005519.4_ENST00000554532.2_RNA|ABCD4_ENST00000557554.1_Intron|ABCD4_ENST00000298816.7_Missense_Mutation_p.R244W	NM_005050.3	NP_005041.1	O14678	ABCD4_HUMAN	ATP-binding cassette, sub-family D (ALD), member 4	348					cobalamin metabolic process (GO:0009235)|transmembrane transport (GO:0055085)	ATP-binding cassette (ABC) transporter complex (GO:0043190)|endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|peroxisome (GO:0005777)	ATP binding (GO:0005524)|ATPase activity, coupled to transmembrane movement of substances (GO:0042626)			cervix(2)|endometrium(3)|kidney(3)|large_intestine(6)|lung(5)|ovary(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(3)|urinary_tract(1)	27				BRCA - Breast invasive adenocarcinoma(234;0.00153)		AGCGTCTCCCGAAGCTGCCCA	0.562													G|||	17	0.00339457	0.0008	0.0014	5008	,	,		21281	0.001		0.001	False		,,,				2504	0.0133				p.R348W		Atlas-SNP	.											.	ABCD4	54	.	0			c.C1042T						PASS	.	G	TRP/ARG	0,4406		0,0,2203	56.0	53.0	54.0		1042	4.2	1.0	14	dbSNP_134	54	3,8597	3.0+/-9.4	0,3,4297	yes	missense	ABCD4	NM_005050.3	101	0,3,6500	AA,AG,GG		0.0349,0.0,0.0231	benign	348/607	74759066	3,13003	2203	4300	6503	SO:0001583	missense	5826	exon11			TCTCCCGAAGCTG	AF009746	CCDS9828.1	14q24	2012-03-14			ENSG00000119688	ENSG00000119688		"""ATP binding cassette transporters / subfamily D"""	68	protein-coding gene	gene with protein product		603214		PXMP1L		9266848, 9302272	Standard	NR_003256		Approved	PMP69, P70R, EST352188	uc001xpr.2	O14678	OTTHUMG00000171207	ENST00000356924.4:c.1042C>T	14.37:g.74759066G>A	ENSP00000349396:p.Arg348Trp	61.0	0.0	0		69.0	34.0	0.492754	NM_005050	A8K5L7|Q6IAQ0|Q96E75	Missense_Mutation	SNP	ENST00000356924.4	37	CCDS9828.1	2	9.157509157509158E-4	0	0.0	1	0.0027624309392265192	0	0.0	1	0.0013192612137203166	G	12.58	1.981289	0.34942	0.0	3.49E-4	ENSG00000119688	ENST00000356924;ENST00000298816;ENST00000537629	D;D	0.94457	-3.43;-3.12	5.1	4.2	0.49525	ABC transporter, transmembrane domain, type 1 (1);	0.326291	0.37437	N	0.002086	D	0.91068	0.7189	L	0.34521	1.04	0.28094	N	0.931705	P;B;P;B	0.44241	0.829;0.004;0.738;0.012	B;B;B;B	0.42798	0.398;0.007;0.394;0.007	D	0.86008	0.1499	10	0.38643	T	0.18	.	14.4627	0.67462	0.0:0.1467:0.8533:0.0	.	244;244;348;348	F8W7M4;B7Z4V6;A8K5L7;O14678	.;.;.;ABCD4_HUMAN	W	348;244;85	ENSP00000349396:R348W;ENSP00000298816:R244W	ENSP00000298816:R244W	R	-	1	2	ABCD4	73828819	1.000000	0.71417	0.998000	0.56505	0.580000	0.36256	2.853000	0.48317	1.487000	0.48415	0.655000	0.94253	CGG	G|0.999;A|0.001	0.001	strong		0.562	ABCD4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000314382.1	NM_005050	
USP19	10869	hgsc.bcm.edu	37	3	49148980	49148980	+	Missense_Mutation	SNP	A	A	G			TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr3:49148980A>G	ENST00000398888.2	-	20	3179	c.2861T>C	c.(2860-2862)aTt>aCt	p.I954T	USP19_ENST00000434032.2_Missense_Mutation_p.I1055T|USP19_ENST00000398898.2_Missense_Mutation_p.I994T|USP19_ENST00000398896.1_Missense_Mutation_p.I762T|USP19_ENST00000417901.1_Missense_Mutation_p.I1057T|USP19_ENST00000398892.3_Missense_Mutation_p.I994T|USP19_ENST00000453664.1_Missense_Mutation_p.I1045T	NM_006677.2	NP_006668.1	O94966	UBP19_HUMAN	ubiquitin specific peptidase 19	954	USP.				ER-associated ubiquitin-dependent protein catabolic process (GO:0030433)|negative regulation of skeletal muscle tissue development (GO:0048642)|positive regulation of cell cycle process (GO:0090068)|protein deubiquitination (GO:0016579)|regulation of cellular response to hypoxia (GO:1900037)|regulation of protein stability (GO:0031647)|response to endoplasmic reticulum stress (GO:0034976)|skeletal muscle atrophy (GO:0014732)	cytosol (GO:0005829)|endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)	metal ion binding (GO:0046872)|ubiquitin-specific protease activity (GO:0004843)			NS(1)|breast(3)|endometrium(5)|kidney(2)|large_intestine(10)|lung(5)|ovary(4)|prostate(2)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(2)	38				BRCA - Breast invasive adenocarcinoma(193;8.01e-05)|Kidney(197;0.00219)|KIRC - Kidney renal clear cell carcinoma(197;0.00245)		GCCAACCTCAATGGGCCCACT	0.627																																					p.I1057T		Atlas-SNP	.											.	USP19	158	.	0			c.T3170C						PASS	.						35.0	36.0	36.0					3																	49148980		1888	4115	6003	SO:0001583	missense	10869	exon21			ACCTCAATGGGCC	AB020698	CCDS43090.1, CCDS56254.1, CCDS56255.1, CCDS56256.1	3p21.31	2005-10-13	2005-08-08		ENSG00000172046	ENSG00000172046		"""Zinc fingers, MYND-type"", ""Ubiquitin-specific peptidases"""	12617	protein-coding gene	gene with protein product		614471	"""ubiquitin specific protease 19"""			12838346	Standard	NM_001199160		Approved	KIAA0891, ZMYND9	uc011bch.2	O94966	OTTHUMG00000133611	ENST00000398888.2:c.2861T>C	3.37:g.49148980A>G	ENSP00000381863:p.Ile954Thr	49.0	0.0	0		41.0	16.0	0.390244	NM_001199161	A5PKX8|A6H8U2|B4DGT3|B4DTZ0|E7EN22|E7ETS0|E9PEG8|Q3KQW4|Q641Q9|Q6NZY8|Q86XV9	Missense_Mutation	SNP	ENST00000398888.2	37	CCDS43090.1	.	.	.	.	.	.	.	.	.	.	A	2.782	-0.253241	0.05829	.	.	ENSG00000172046	ENST00000398896;ENST00000398898;ENST00000417901;ENST00000453664;ENST00000398892;ENST00000398888;ENST00000434032	T;T;T;T;T;T;T	0.18174	2.23;2.24;2.34;2.34;2.24;2.33;2.34	6.04	-9.85	0.00476	Peptidase C19, ubiquitin carboxyl-terminal hydrolase 2 (2);	1.404660	0.03866	N	0.274854	T	0.05640	0.0148	N	0.05414	-0.055	0.09310	N	1	B;B;B;B;B	0.02656	0.0;0.0;0.0;0.0;0.0	B;B;B;B;B	0.06405	0.001;0.001;0.002;0.0;0.0	T	0.24977	-1.0145	10	0.14252	T	0.57	11.2509	3.8486	0.08945	0.2931:0.3067:0.3169:0.0833	.	1055;1045;954;994;762	E9PEG8;E7EN22;O94966;B5MEG5;E7ESU0	.;.;UBP19_HUMAN;.;.	T	762;994;1057;1045;994;954;1055	ENSP00000381870:I762T;ENSP00000381872:I994T;ENSP00000395260:I1057T;ENSP00000400090:I1045T;ENSP00000381867:I994T;ENSP00000381863:I954T;ENSP00000401197:I1055T	ENSP00000381863:I954T	I	-	2	0	USP19	49123984	0.000000	0.05858	0.000000	0.03702	0.819000	0.46315	-1.946000	0.01536	-1.572000	0.01661	-0.450000	0.05554	ATT	.	.	none		0.627	USP19-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000257721.1	NM_006677	
SLCO1B1	10599	hgsc.bcm.edu	37	12	21377717	21377717	+	Silent	SNP	C	C	G	rs143812591		TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr12:21377717C>G	ENST00000256958.2	+	14	1905	c.1809C>G	c.(1807-1809)tcC>tcG	p.S603S		NM_006446.4	NP_006437.3	Q9Y6L6	SO1B1_HUMAN	solute carrier organic anion transporter family, member 1B1	603					bile acid and bile salt transport (GO:0015721)|bile acid metabolic process (GO:0008206)|organic anion transport (GO:0015711)|small molecule metabolic process (GO:0044281)|sodium-independent organic anion transport (GO:0043252)|transmembrane transport (GO:0055085)	integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)	sodium-independent organic anion transmembrane transporter activity (GO:0015347)			breast(1)|central_nervous_system(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(14)|lung(33)|ovary(3)|pancreas(1)|prostate(1)|skin(8)|upper_aerodigestive_tract(1)	70					Acetylcysteine(DB06151)|Aminohippurate(DB00345)|Atorvastatin(DB01076)|Axitinib(DB06626)|Benzylpenicillin(DB01053)|Bezafibrate(DB01393)|Cabazitaxel(DB06772)|Caspofungin(DB00520)|Conjugated Estrogens(DB00286)|Cyclosporine(DB00091)|Dabrafenib(DB08912)|Dextrothyroxine(DB00509)|Digoxin(DB00390)|Dinoprostone(DB00917)|Eltrombopag(DB06210)|Estradiol(DB00783)|Estrone(DB00655)|Ezetimibe(DB00973)|Fexofenadine(DB00950)|Fluvastatin(DB01095)|Gadoxetate(DB08884)|Gemfibrozil(DB01241)|Indinavir(DB00224)|Irinotecan(DB00762)|L-Carnitine(DB00583)|Levothyroxine(DB00451)|Liothyronine(DB00279)|Liotrix(DB01583)|Lovastatin(DB00227)|Methotrexate(DB00563)|Mycophenolate mofetil(DB00688)|Nelfinavir(DB00220)|Olmesartan(DB00275)|Ouabain(DB01092)|Pantoprazole(DB00213)|Pazopanib(DB06589)|Penicillamine(DB00859)|Pioglitazone(DB01132)|Pitavastatin(DB08860)|Pravastatin(DB00175)|Quinidine(DB00908)|Repaglinide(DB00912)|Rifampicin(DB01045)|Rilpivirine(DB08864)|Ritonavir(DB00503)|Rosiglitazone(DB00412)|Rosuvastatin(DB01098)|Saquinavir(DB01232)|SIMEPREVIR(DB06290)|Simvastatin(DB00641)|Sirolimus(DB00877)|Sumatriptan(DB00669)|Valsartan(DB00177)|Verapamil(DB00661)	TAAAGTGGTCCACCAACAACT	0.358																																					p.S603S		Atlas-SNP	.											.	SLCO1B1	151	.	0			c.C1809G						PASS	.	C		0,4406		0,0,2203	148.0	143.0	145.0		1809	-3.8	0.0	12	dbSNP_134	145	2,8598	2.2+/-6.3	0,2,4298	no	coding-synonymous	SLCO1B1	NM_006446.4		0,2,6501	GG,GC,CC		0.0233,0.0,0.0154		603/692	21377717	2,13004	2203	4300	6503	SO:0001819	synonymous_variant	10599	exon14			GTGGTCCACCAAC		CCDS8685.1	12p12	2013-05-22	2003-11-25	2003-11-26	ENSG00000134538	ENSG00000134538		"""Solute carriers"""	10959	protein-coding gene	gene with protein product		604843	"""solute carrier family 21 (organic anion transporter), member 6"""	SLC21A6		10358072	Standard	NM_006446		Approved	OATP-C, LST-1, OATP1B1	uc001req.4	Q9Y6L6	OTTHUMG00000169047	ENST00000256958.2:c.1809C>G	12.37:g.21377717C>G		82.0	0.0	0		83.0	42.0	0.506024	NM_006446	B2R7G2|Q29R64|Q9NQ37|Q9UBF3|Q9UH89	Silent	SNP	ENST00000256958.2	37	CCDS8685.1																																																																																			C|1.000;G|0.000	0.000	weak		0.358	SLCO1B1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402070.1	NM_006446	
DNAJB12	54788	hgsc.bcm.edu	37	10	74098037	74098037	+	Silent	SNP	A	A	G	rs138477026	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr10:74098037A>G	ENST00000444643.2	-	6	1088	c.756T>C	c.(754-756)ccT>ccC	p.P252P	DNAJB12_ENST00000461919.1_Silent_p.P47P|DNAJB12_ENST00000394903.2_Silent_p.P286P|DNAJB12_ENST00000338820.3_Silent_p.P286P			Q9NXW2	DJB12_HUMAN	DnaJ (Hsp40) homolog, subfamily B, member 12	252						integral component of membrane (GO:0016021)|membrane (GO:0016020)				endometrium(1)|large_intestine(2)|skin(1)	4						GGATGAGGATAGGCATCAGCT	0.582													A|||	8	0.00159744	0.0	0.0014	5008	,	,		18106	0.0		0.001	False		,,,				2504	0.0061				p.P286P		Atlas-SNP	.											.	DNAJB12	22	.	0			c.T858C						PASS	.	A	,	0,4406		0,0,2203	111.0	96.0	101.0		858,858	4.9	1.0	10	dbSNP_134	101	7,8593	5.7+/-21.5	0,7,4293	no	coding-synonymous,coding-synonymous	DNAJB12	NM_001002762.2,NM_017626.4	,	0,7,6496	GG,GA,AA		0.0814,0.0,0.0538	,	286/410,286/410	74098037	7,12999	2203	4300	6503	SO:0001819	synonymous_variant	54788	exon6			GAGGATAGGCATC	AK000034	CCDS7316.2	10q22	2011-09-02			ENSG00000148719	ENSG00000148719		"""Heat shock proteins / DNAJ (HSP40)"""	14891	protein-coding gene	gene with protein product		608376				11147971	Standard	NM_001002762		Approved	DJ10, FLJ20027	uc001jta.2	Q9NXW2	OTTHUMG00000018436	ENST00000444643.2:c.756T>C	10.37:g.74098037A>G		71.0	0.0	0		82.0	34.0	0.414634	NM_017626	B7Z7I3|Q9H6H0	Silent	SNP	ENST00000444643.2	37																																																																																				A|1.000;G|0.000	0.000	strong		0.582	DNAJB12-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000048581.2		
C1orf168	199920	hgsc.bcm.edu	37	1	57257914	57257914	+	Missense_Mutation	SNP	G	G	A			TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr1:57257914G>A	ENST00000343433.6	-	2	652	c.572C>T	c.(571-573)gCc>gTc	p.A191V	C1orf168_ENST00000484327.1_5'UTR	NM_001004303.4	NP_001004303.3	Q5VWT5	CA168_HUMAN	chromosome 1 open reading frame 168	191										NS(1)|breast(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(10)|lung(13)|ovary(3)|skin(6)|stomach(1)|urinary_tract(2)	46						AAGAGTCTGGGCTCCTTTTGT	0.468																																					p.A191V		Atlas-SNP	.											C1orf168,caecum,carcinoma,+1,1	C1orf168	102	1	0			c.C572T						PASS	.						102.0	104.0	104.0					1																	57257914		2203	4300	6503	SO:0001583	missense	199920	exon2			GTCTGGGCTCCTT	BX648439	CCDS30729.1	1p32.2	2011-02-22			ENSG00000187889	ENSG00000187889			27295	protein-coding gene	gene with protein product						14702039	Standard	NM_001004303		Approved	RP4-758N20.2, FLJ43208	uc001cym.4	Q5VWT5	OTTHUMG00000008281	ENST00000343433.6:c.572C>T	1.37:g.57257914G>A	ENSP00000345972:p.Ala191Val	80.0	0.0	0		95.0	46.0	0.484211	NM_001004303	Q63HM3|Q6ZUY6	Missense_Mutation	SNP	ENST00000343433.6	37	CCDS30729.1	.	.	.	.	.	.	.	.	.	.	G	20.2	3.949546	0.73787	.	.	ENSG00000187889	ENST00000343433	T	0.32988	1.43	4.55	1.41	0.22369	.	0.483859	0.18959	N	0.126441	T	0.18882	0.0453	L	0.32530	0.975	0.09310	N	1	P;B	0.37955	0.612;0.176	B;B	0.37692	0.256;0.067	T	0.09997	-1.0649	10	0.49607	T	0.09	0.0321	2.8636	0.05594	0.1004:0.1808:0.5323:0.1865	.	191;191	Q5VWT5-2;Q5VWT5	.;CA168_HUMAN	V	191	ENSP00000345972:A191V	ENSP00000345972:A191V	A	-	2	0	C1orf168	57030502	0.000000	0.05858	0.213000	0.23690	0.813000	0.45954	0.139000	0.16036	0.642000	0.30620	0.563000	0.77884	GCC	.	.	none		0.468	C1orf168-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000022751.2	NM_001004303	
TFAM	7019	hgsc.bcm.edu	37	10	60145363	60145363	+	Missense_Mutation	SNP	C	C	T			TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr10:60145363C>T	ENST00000487519.1	+	1	582	c.56C>T	c.(55-57)gCa>gTa	p.A19V	TFAM_ENST00000373899.3_3'UTR|TFAM_ENST00000373895.3_Missense_Mutation_p.A19V	NM_001270782.1|NM_003201.2	NP_001257711.1|NP_003192.1	Q00059	TFAM_HUMAN	transcription factor A, mitochondrial	19					DNA-dependent DNA replication (GO:0006261)|gene expression (GO:0010467)|mitochondrial respiratory chain complex assembly (GO:0033108)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of transcription from RNA polymerase I promoter (GO:0006356)|transcription from mitochondrial promoter (GO:0006390)|transcription initiation from mitochondrial promoter (GO:0006391)	mitochondrial matrix (GO:0005759)|mitochondrial nucleoid (GO:0042645)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	chromatin binding (GO:0003682)|DNA binding, bending (GO:0008301)|mitochondrial light strand promoter sense binding (GO:0070363)|poly(A) RNA binding (GO:0044822)|sequence-specific DNA binding transcription factor activity (GO:0003700)			kidney(1)|large_intestine(1)|lung(4)|prostate(1)	7						AGGTCTGGAGCAGAGCTGTGC	0.667											OREG0020196	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.A19V		Atlas-SNP	.											.	TFAM	52	.	0			c.C56T						PASS	.						75.0	62.0	66.0					10																	60145363		2201	4289	6490	SO:0001583	missense	7019	exon1			CTGGAGCAGAGCT	BC018628	CCDS7253.1, CCDS59217.1	10q21	2010-09-24			ENSG00000108064	ENSG00000108064			11741	protein-coding gene	gene with protein product		600438		TCF6, TCF6L2		7789991	Standard	NM_003201		Approved		uc001jkf.4	Q00059	OTTHUMG00000018270	ENST00000487519.1:c.56C>T	10.37:g.60145363C>T	ENSP00000420588:p.Ala19Val	78.0	0.0	0	1043	95.0	43.0	0.452632	NM_003201	A8MRB2|A9QXC6|B5BU05|Q5U0C6	Missense_Mutation	SNP	ENST00000487519.1	37	CCDS7253.1	.	.	.	.	.	.	.	.	.	.	C	9.457	1.092160	0.20471	.	.	ENSG00000108064	ENST00000487519;ENST00000373895	T;T	0.14516	2.53;2.5	4.31	1.43	0.22495	.	0.907854	0.09398	N	0.807600	T	0.09598	0.0236	L	0.32530	0.975	0.09310	N	0.999999	B;B	0.10296	0.003;0.003	B;B	0.10450	0.005;0.003	T	0.42965	-0.9420	10	0.17832	T	0.49	.	6.2181	0.20665	0.0:0.6834:0.0:0.3166	.	19;19	A8MRB2;Q00059	.;TFAM_HUMAN	V	19	ENSP00000420588:A19V;ENSP00000363002:A19V	ENSP00000363002:A19V	A	+	2	0	TFAM	59815369	0.048000	0.20356	0.198000	0.23420	0.309000	0.27889	0.110000	0.15437	0.333000	0.23563	-0.123000	0.14984	GCA	.	.	none		0.667	TFAM-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048146.1	NM_003201	
SPHKAP	80309	hgsc.bcm.edu	37	2	228884530	228884530	+	Missense_Mutation	SNP	G	G	A	rs61752225	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr2:228884530G>A	ENST00000392056.3	-	7	1086	c.1040C>T	c.(1039-1041)tCc>tTc	p.S347F	SPHKAP_ENST00000344657.5_Missense_Mutation_p.S347F	NM_001142644.1	NP_001136116.1	Q2M3C7	SPKAP_HUMAN	SPHK1 interactor, AKAP domain containing	347						extracellular vesicular exosome (GO:0070062)|mitochondrion (GO:0005739)|Z disc (GO:0030018)	protein kinase A binding (GO:0051018)			NS(5)|breast(5)|central_nervous_system(2)|endometrium(11)|haematopoietic_and_lymphoid_tissue(3)|kidney(12)|large_intestine(25)|lung(86)|ovary(6)|pancreas(1)|prostate(6)|skin(17)|stomach(1)|upper_aerodigestive_tract(4)|urinary_tract(1)	185		Renal(207;0.025)|all_hematologic(139;0.15)|all_lung(227;0.204)|Acute lymphoblastic leukemia(138;0.205)|Esophageal squamous(248;0.23)		Epithelial(121;8.17e-11)|all cancers(144;7.92e-08)|Lung(261;0.0168)|LUSC - Lung squamous cell carcinoma(224;0.0232)		ATCCATCATGGAGAAATAAGC	0.428													G|||	12	0.00239617	0.0015	0.0058	5008	,	,		11672	0.0		0.004	False		,,,				2504	0.002				p.S347F		Atlas-SNP	.											SPHKAP_ENST00000392056,NS,carcinoma,-1,4	SPHKAP	750	4	0			c.C1040T						PASS	.	G	PHE/SER,PHE/SER	1,4405	2.1+/-5.4	0,1,2202	140.0	133.0	135.0		1040,1040	3.8	0.5	2	dbSNP_129	135	40,8560	26.8+/-75.7	0,40,4260	yes	missense,missense	SPHKAP	NM_001142644.1,NM_030623.3	155,155	0,41,6462	AA,AG,GG		0.4651,0.0227,0.3152	benign,benign	347/1701,347/1672	228884530	41,12965	2203	4300	6503	SO:0001583	missense	80309	exon7			ATCATGGAGAAAT		CCDS33389.1, CCDS46537.1	2q36.3	2010-08-20			ENSG00000153820	ENSG00000153820		"""A-kinase anchor proteins"""	30619	protein-coding gene	gene with protein product	"""sphingosine kinase type 1-interacting protein"""	611646				12080051, 11214970	Standard	NM_030623		Approved	SKIP	uc002vpq.2	Q2M3C7	OTTHUMG00000153584	ENST00000392056.3:c.1040C>T	2.37:g.228884530G>A	ENSP00000375909:p.Ser347Phe	290.0	0.0	0		264.0	119.0	0.450758	NM_030623	Q68DA3|Q68DR8|Q9C0I5	Missense_Mutation	SNP	ENST00000392056.3	37	CCDS46537.1	11	0.005036630036630037	4	0.008130081300813009	3	0.008287292817679558	0	0.0	4	0.005277044854881266	G	10.13	1.267055	0.23136	2.27E-4	0.004651	ENSG00000153820	ENST00000392056;ENST00000344657	T;T	0.12984	2.63;2.63	5.78	3.84	0.44239	.	1.477610	0.03572	N	0.228681	T	0.20007	0.0481	M	0.62723	1.935	0.09310	N	1	P;P	0.42993	0.612;0.797	B;P	0.47528	0.259;0.549	T	0.25293	-1.0136	10	0.72032	D	0.01	.	10.8001	0.46483	0.0:0.1313:0.7185:0.1502	rs61752225	347;347	Q2M3C7;Q2M3C7-2	SPKAP_HUMAN;.	F	347	ENSP00000375909:S347F;ENSP00000339886:S347F	ENSP00000339886:S347F	S	-	2	0	SPHKAP	228592774	0.820000	0.29190	0.537000	0.28052	0.062000	0.15995	2.710000	0.47169	2.742000	0.94016	0.650000	0.86243	TCC	G|0.997;A|0.003	0.003	strong		0.428	SPHKAP-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000331750.1	NM_030623	
CELSR2	1952	hgsc.bcm.edu	37	1	109811522	109811522	+	Missense_Mutation	SNP	G	G	A	rs148006855	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr1:109811522G>A	ENST00000271332.3	+	19	6584	c.6523G>A	c.(6523-6525)Gac>Aac	p.D2175N		NM_001408.2	NP_001399.1	Q9HCU4	CELR2_HUMAN	cadherin, EGF LAG seven-pass G-type receptor 2	2175					cerebrospinal fluid secretion (GO:0033326)|cilium assembly (GO:0042384)|cilium movement (GO:0003341)|dendrite morphogenesis (GO:0048813)|G-protein coupled receptor signaling pathway (GO:0007186)|homophilic cell adhesion (GO:0007156)|neural plate anterior/posterior regionalization (GO:0021999)|neuron migration (GO:0001764)|neuropeptide signaling pathway (GO:0007218)|regulation of cell-cell adhesion (GO:0022407)|regulation of protein localization (GO:0032880)|regulation of transcription, DNA-templated (GO:0006355)|ventricular system development (GO:0021591)|Wnt signaling pathway (GO:0016055)	cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|G-protein coupled receptor activity (GO:0004930)			NS(1)|autonomic_ganglia(1)|breast(3)|central_nervous_system(1)|cervix(3)|endometrium(16)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(14)|lung(27)|ovary(5)|prostate(1)|skin(3)|urinary_tract(2)	82		all_epithelial(167;0.000114)|all_lung(203;0.000321)|Lung NSC(277;0.000626)|Breast(1374;0.244)		Colorectal(144;0.0296)|Lung(183;0.067)|COAD - Colon adenocarcinoma(174;0.114)|Epithelial(280;0.193)|all cancers(265;0.219)		AGTGCGCTTGGACAAAGGGAA	0.622													G|||	25	0.00499201	0.0	0.0	5008	,	,		19345	0.0		0.002	False		,,,				2504	0.0235				p.D2175N	NSCLC(158;1285 2011 34800 34852 42084)	Atlas-SNP	.											CELSR2,NS,neuroblastoma,-2,1	CELSR2	228	1	0			c.G6523A						PASS	.	G	ASN/ASP	2,4404	4.2+/-10.8	0,2,2201	71.0	76.0	74.0		6523	4.4	1.0	1	dbSNP_134	74	9,8591	7.1+/-27.0	0,9,4291	yes	missense	CELSR2	NM_001408.2	23	0,11,6492	AA,AG,GG		0.1047,0.0454,0.0846	benign	2175/2924	109811522	11,12995	2203	4300	6503	SO:0001583	missense	1952	exon19			CGCTTGGACAAAG	D87469	CCDS796.1	1p13.3	2014-08-08	2013-02-18		ENSG00000143126	ENSG00000143126		"""Cadherins / Major cadherins"", ""-"", ""GPCR / Class B : Orphans"""	3231	protein-coding gene	gene with protein product		604265	"""cadherin, EGF LAG seven-pass G-type receptor 2, flamingo (Drosophila) homolog"""	EGFL2		9693030, 10907856	Standard	NM_001408		Approved	KIAA0279, MEGF3, Flamingo1, CDHF10	uc001dxa.4	Q9HCU4	OTTHUMG00000012003	ENST00000271332.3:c.6523G>A	1.37:g.109811522G>A	ENSP00000271332:p.Asp2175Asn	157.0	0.0	0		168.0	68.0	0.404762	NM_001408	Q5T2Y7|Q92566	Missense_Mutation	SNP	ENST00000271332.3	37	CCDS796.1	1	4.578754578754579E-4	0	0.0	0	0.0	0	0.0	1	0.0013192612137203166	G	13.84	2.356070	0.41700	4.54E-4	0.001047	ENSG00000143126	ENST00000271332	T	0.10860	2.83	4.36	4.36	0.52297	Domain of unknown function DUF3497 (1);	.	.	.	.	T	0.05410	0.0143	L	0.48642	1.525	0.34853	D	0.741849	B	0.26935	0.164	B	0.28709	0.093	T	0.09443	-1.0674	9	0.52906	T	0.07	.	10.689	0.45860	0.0898:0.0:0.9102:0.0	.	2175	Q9HCU4	CELR2_HUMAN	N	2175	ENSP00000271332:D2175N	ENSP00000271332:D2175N	D	+	1	0	CELSR2	109613045	1.000000	0.71417	1.000000	0.80357	0.957000	0.61999	3.180000	0.50895	2.430000	0.82344	0.462000	0.41574	GAC	G|0.999;A|0.001	0.001	strong		0.622	CELSR2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000033200.1	NM_001408	
BRINP1	1620	hgsc.bcm.edu	37	9	121930416	121930416	+	Missense_Mutation	SNP	C	C	T	rs141766717	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr9:121930416C>T	ENST00000265922.3	-	8	1693	c.1232G>A	c.(1231-1233)cGg>cAg	p.R411Q	BRINP1_ENST00000482797.1_Intron	NM_014618.2	NP_055433.2	O60477	BRNP1_HUMAN	bone morphogenetic protein/retinoic acid inducible neural-specific 1	411					cell cycle arrest (GO:0007050)|cell death (GO:0008219)|cellular response to retinoic acid (GO:0071300)|negative regulation of cell cycle (GO:0045786)|negative regulation of mitotic cell cycle (GO:0045930)|positive regulation of neuron differentiation (GO:0045666)	cytoplasm (GO:0005737)		p.R411Q(1)									CACGCAGCTCCGCTGGCTCTC	0.597													C|||	5	0.000998403	0.0015	0.0	5008	,	,		19155	0.002		0.0	False		,,,				2504	0.001				p.R411Q		Atlas-SNP	.											DBC1,NS,carcinoma,0,2	DBC1	194	2	1	Substitution - Missense(1)	lung(1)	c.G1232A						PASS	.	C	GLN/ARG	6,4400	11.4+/-27.6	0,6,2197	20.0	18.0	19.0		1232	5.7	1.0	9	dbSNP_134	19	9,8591	7.1+/-27.0	0,9,4291	yes	missense	DBC1	NM_014618.2	43	0,15,6488	TT,TC,CC		0.1047,0.1362,0.1153	probably-damaging	411/762	121930416	15,12991	2203	4300	6503	SO:0001583	missense	1620	exon8			CAGCTCCGCTGGC	AF027734	CCDS6822.1	9q32-q33	2013-08-06	2013-08-06	2013-07-31	ENSG00000078725	ENSG00000078725			2687	protein-coding gene	gene with protein product		602865	"""deleted in bladder cancer chromosome region candidate 1"", ""deleted in bladder cancer 1"""	DBCCR1, DBC1		9175739, 10444335, 15193422	Standard	NM_014618		Approved	FAM5A	uc004bkc.2	O60477	OTTHUMG00000021020	ENST00000265922.3:c.1232G>A	9.37:g.121930416C>T	ENSP00000265922:p.Arg411Gln	90.0	0.0	0		125.0	62.0	0.496	NM_014618	Q6IPV6|Q6P1A0|Q8WU22	Missense_Mutation	SNP	ENST00000265922.3	37	CCDS6822.1	1	4.578754578754579E-4	0	0.0	0	0.0	1	0.0017482517482517483	0	0.0	C	24.4	4.525548	0.85600	0.001362	0.001047	ENSG00000078725	ENST00000373969;ENST00000265922	T	0.62364	0.03	5.69	5.69	0.88448	.	0.000000	0.85682	D	0.000000	T	0.62588	0.2440	L	0.41824	1.3	0.80722	D	1	D	0.63880	0.993	P	0.47134	0.539	T	0.63296	-0.6669	10	0.46703	T	0.11	-21.7784	19.8211	0.96595	0.0:1.0:0.0:0.0	.	411	O60477	DBC1_HUMAN	Q	411	ENSP00000265922:R411Q	ENSP00000265922:R411Q	R	-	2	0	DBC1	120970237	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	4.890000	0.63178	2.687000	0.91594	0.655000	0.94253	CGG	C|0.999;T|0.001	0.001	strong		0.597	BRINP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055440.2	NM_014618	
COL3A1	1281	hgsc.bcm.edu	37	2	189858790	189858790	+	Silent	SNP	T	T	C			TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr2:189858790T>C	ENST00000304636.3	+	17	1346	c.1176T>C	c.(1174-1176)ccT>ccC	p.P392P	COL3A1_ENST00000317840.5_Silent_p.P392P	NM_000090.3	NP_000081	P02461	CO3A1_HUMAN	collagen, type III, alpha 1	392	Triple-helical region.				aging (GO:0007568)|axon guidance (GO:0007411)|blood vessel development (GO:0001568)|cell-matrix adhesion (GO:0007160)|cellular response to amino acid stimulus (GO:0071230)|cerebral cortex development (GO:0021987)|collagen catabolic process (GO:0030574)|collagen fibril organization (GO:0030199)|digestive tract development (GO:0048565)|extracellular fibril organization (GO:0043206)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|heart development (GO:0007507)|integrin-mediated signaling pathway (GO:0007229)|negative regulation of immune response (GO:0050777)|negative regulation of neuron migration (GO:2001223)|peptide cross-linking (GO:0018149)|platelet activation (GO:0030168)|positive regulation of Rho protein signal transduction (GO:0035025)|response to cytokine (GO:0034097)|response to mechanical stimulus (GO:0009612)|response to radiation (GO:0009314)|skeletal system development (GO:0001501)|skin development (GO:0043588)|transforming growth factor beta receptor signaling pathway (GO:0007179)|wound healing (GO:0042060)	collagen type III trimer (GO:0005586)|endoplasmic reticulum lumen (GO:0005788)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)	extracellular matrix structural constituent (GO:0005201)|integrin binding (GO:0005178)|metal ion binding (GO:0046872)|platelet-derived growth factor binding (GO:0048407)			NS(2)|breast(1)|central_nervous_system(7)|cervix(1)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(17)|lung(60)|ovary(4)|pancreas(1)|prostate(5)|skin(10)|upper_aerodigestive_tract(3)|urinary_tract(3)	126			OV - Ovarian serous cystadenocarcinoma(117;0.0106)|Epithelial(96;0.141)		Collagenase(DB00048)	ATGGTAGTCCTGGTGGTAAAG	0.383																																					p.P392P		Atlas-SNP	.											.	COL3A1	292	.	0			c.T1176C						PASS	.						129.0	127.0	128.0					2																	189858790		2203	4300	6503	SO:0001819	synonymous_variant	1281	exon17			TAGTCCTGGTGGT	X15332	CCDS2297.1	2q32.2	2014-09-17	2008-06-23		ENSG00000168542	ENSG00000168542		"""Collagens"""	2201	protein-coding gene	gene with protein product		120180	"""Ehlers-Danlos syndrome type IV, autosomal dominant"""	EDS4A		2780304, 2834369	Standard	NM_000090		Approved		uc002uqj.1	P02461	OTTHUMG00000132648	ENST00000304636.3:c.1176T>C	2.37:g.189858790T>C		96.0	0.0	0		80.0	36.0	0.45	NM_000090	D2JYH5|D3DPH4|P78429|Q15112|Q16403|Q53S91|Q541P8|Q6LDB3|Q6LDJ2|Q6LDJ3|Q7KZ56|Q8N6U4|Q9UC88|Q9UC89|Q9UC90|Q9UC91|R4N3C5|V9GZI1	Silent	SNP	ENST00000304636.3	37	CCDS2297.1	.	.	.	.	.	.	.	.	.	.	T	9.959	1.222154	0.22457	.	.	ENSG00000168542	ENST00000450867	.	.	.	5.86	3.44	0.39384	.	.	.	.	.	T	0.54549	0.1865	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.46830	-0.9163	4	.	.	.	.	5.9517	0.19250	0.1242:0.1382:0.0:0.7376	.	.	.	.	R	59	.	.	W	+	1	0	COL3A1	189567035	0.989000	0.36119	1.000000	0.80357	0.974000	0.67602	0.128000	0.15810	0.540000	0.28808	0.528000	0.53228	TGG	.	.	none		0.383	COL3A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255899.3	NM_000090	
ARHGEF28	64283	hgsc.bcm.edu	37	5	73205382	73205382	+	Missense_Mutation	SNP	A	A	G	rs200976886	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr5:73205382A>G	ENST00000426542.2	+	33	4327	c.4307A>G	c.(4306-4308)gAg>gGg	p.E1436G	ARHGEF28_ENST00000513042.2_Missense_Mutation_p.E1436G|ARHGEF28_ENST00000296799.4_Missense_Mutation_p.E1123G|ARHGEF28_ENST00000287898.5_Missense_Mutation_p.E1392G|ARHGEF28_ENST00000296794.6_Missense_Mutation_p.E1436G|ARHGEF28_ENST00000437974.1_Missense_Mutation_p.E1436G|ARHGEF28_ENST00000545377.1_Missense_Mutation_p.E1436G|ARHGEF28_ENST00000512883.1_Missense_Mutation_p.E356G			Q8N1W1	ARG28_HUMAN	Rho guanine nucleotide exchange factor (GEF) 28	1436	Interaction with microtubules. {ECO:0000250}.				central nervous system neuron axonogenesis (GO:0021955)|intracellular signal transduction (GO:0035556)|neurofilament cytoskeleton organization (GO:0060052)	cytoplasm (GO:0005737)|plasma membrane (GO:0005886)	metal ion binding (GO:0046872)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)|RNA binding (GO:0003723)										CAGCATGAGGAGCTGGCCAAT	0.677													A|||	6	0.00119808	0.0	0.0014	5008	,	,		17397	0.0		0.005	False		,,,				2504	0.0				p.E1436G		Atlas-SNP	.											.	.	.	.	0			c.A4307G						PASS	.	A	GLY/GLU,GLY/GLU	0,4202		0,0,2101	10.0	11.0	11.0		4307,4307	2.7	1.0	5		11	4,8440		0,4,4218	yes	missense,missense	RGNEF	NM_001080479.2,NM_001177693.1	98,98	0,4,6319	GG,GA,AA		0.0474,0.0,0.0316	probably-damaging,probably-damaging	1436/1732,1436/1706	73205382	4,12642	2101	4222	6323	SO:0001583	missense	64283	exon34			ATGAGGAGCTGGC		CCDS47231.1, CCDS47231.2, CCDS54870.1, CCDS58957.1	5q13.2	2012-08-08			ENSG00000214944	ENSG00000214944			30322	protein-coding gene	gene with protein product		612790				9199174, 11058585	Standard	NM_001177693		Approved	RGNEF, p190RhoGEF, RIP2	uc010izf.3	Q8N1W1	OTTHUMG00000162454	ENST00000426542.2:c.4307A>G	5.37:g.73205382A>G	ENSP00000412175:p.Glu1436Gly	122.0	0.0	0		166.0	92.0	0.554217	NM_001080479	B2RXG7|B4E3K4|B5MDA3|B7ZW32|E9PC75|Q8NCM7|Q96E37|Q9H6L3|Q9H6W0	Missense_Mutation	SNP	ENST00000426542.2	37	CCDS54870.1	.	.	.	.	.	.	.	.	.	.	A	16.75	3.209869	0.58343	0.0	4.74E-4	ENSG00000214944	ENST00000296794;ENST00000545377;ENST00000513042;ENST00000287898;ENST00000437974;ENST00000426542;ENST00000296799;ENST00000512883	T;T;T;T;T;T;T;T	0.38077	1.16;1.16;1.16;1.16;1.16;1.16;1.16;1.16	5.34	2.73	0.32206	.	1.144270	0.07072	U	0.835626	T	0.62109	0.2401	M	0.81942	2.565	0.42236	D	0.991911	D;D;D;D;D	0.71674	0.996;0.998;0.997;0.997;0.998	P;D;D;D;D	0.67382	0.894;0.947;0.947;0.951;0.944	T	0.55698	-0.8100	10	0.87932	D	0	.	11.6878	0.51497	0.7192:0.2808:0.0:0.0	.	1123;1436;1436;356;1436	B5MDA3;Q8N1W1;E9PC75;D6RGZ3;Q8N1W1-4	.;RGNEF_HUMAN;.;.;.	G	1436;1436;1436;1392;1436;1436;1123;356	ENSP00000296794:E1436G;ENSP00000441913:E1436G;ENSP00000441436:E1436G;ENSP00000287898:E1392G;ENSP00000411459:E1436G;ENSP00000412175:E1436G;ENSP00000296799:E1123G;ENSP00000421081:E356G	ENSP00000287898:E1392G	E	+	2	0	RP11-428C6.1	73241138	1.000000	0.71417	1.000000	0.80357	0.282000	0.26991	4.810000	0.62598	0.841000	0.35020	0.454000	0.30748	GAG	A|0.997;G|0.003	0.003	weak		0.677	ARHGEF28-004	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000368975.1		
SIPA1L2	57568	hgsc.bcm.edu	37	1	232596859	232596859	+	Missense_Mutation	SNP	C	C	T			TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr1:232596859C>T	ENST00000366630.1	-	9	3227	c.2869G>A	c.(2869-2871)Ggg>Agg	p.G957R	SIPA1L2_ENST00000308942.4_Missense_Mutation_p.G31R|SIPA1L2_ENST00000262861.4_Missense_Mutation_p.G957R			Q9P2F8	SI1L2_HUMAN	signal-induced proliferation-associated 1 like 2	957	PDZ. {ECO:0000255|PROSITE- ProRule:PRU00143}.				regulation of small GTPase mediated signal transduction (GO:0051056)		GTPase activator activity (GO:0005096)			NS(1)|breast(5)|central_nervous_system(2)|endometrium(15)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(13)|lung(49)|ovary(2)|pancreas(1)|prostate(2)|skin(3)|upper_aerodigestive_tract(2)	103		all_cancers(173;0.00605)|Prostate(94;0.128)|all_epithelial(177;0.186)				TGGCCCAGCCCGTTCCTCCTC	0.562																																					p.G957R		Atlas-SNP	.											.	SIPA1L2	218	.	0			c.G2869A						PASS	.						129.0	137.0	135.0					1																	232596859		2130	4269	6399	SO:0001583	missense	57568	exon8			CCAGCCCGTTCCT	AB037810	CCDS41474.1	1q42.2	2008-02-05			ENSG00000116991	ENSG00000116991			23800	protein-coding gene	gene with protein product		611609					Standard	NM_020808		Approved	KIAA1389	uc001hvg.3	Q9P2F8	OTTHUMG00000037820	ENST00000366630.1:c.2869G>A	1.37:g.232596859C>T	ENSP00000355589:p.Gly957Arg	186.0	0.0	0		173.0	90.0	0.520231	NM_020808	Q2TV88|Q5VXR7|Q5VXR8|Q641Q4|Q8NA38|Q96DZ3|Q9H9F6	Missense_Mutation	SNP	ENST00000366630.1	37	CCDS41474.1	.	.	.	.	.	.	.	.	.	.	C	23.5	4.424498	0.83667	.	.	ENSG00000116991	ENST00000366630;ENST00000262861;ENST00000308942	T;T;T	0.28069	1.63;1.63;1.63	5.94	5.94	0.96194	PDZ/DHR/GLGF (3);	0.108992	0.64402	D	0.000005	T	0.55465	0.1922	L	0.59436	1.845	0.54753	D	0.999985	D;D	0.89917	1.0;0.996	D;D	0.80764	0.994;0.927	T	0.52132	-0.8616	10	0.66056	D	0.02	-32.9946	20.3594	0.98849	0.0:1.0:0.0:0.0	.	957;31	Q9P2F8;Q9P2F8-2	SI1L2_HUMAN;.	R	957;957;31	ENSP00000355589:G957R;ENSP00000262861:G957R;ENSP00000309102:G31R	ENSP00000262861:G957R	G	-	1	0	SIPA1L2	230663482	0.997000	0.39634	0.993000	0.49108	0.957000	0.61999	3.845000	0.55880	2.816000	0.96949	0.563000	0.77884	GGG	.	.	none		0.562	SIPA1L2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000092318.1	XM_045839	
POU5F1	5460	hgsc.bcm.edu	37	6	31138310	31138310	+	Missense_Mutation	SNP	C	C	T	rs41257954	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr6:31138310C>T	ENST00000259915.8	-	1	160	c.88G>A	c.(88-90)Gtt>Att	p.V30I	POU5F1_ENST00000441888.3_Intron	NM_002701.4	NP_002692.2	Q01860	PO5F1_HUMAN	POU class 5 homeobox 1	30					anatomical structure morphogenesis (GO:0009653)|blastocyst development (GO:0001824)|BMP signaling pathway involved in heart induction (GO:0003130)|cardiac cell fate determination (GO:0060913)|cell fate commitment involved in formation of primary germ layer (GO:0060795)|endodermal cell fate specification (GO:0001714)|mRNA transcription from RNA polymerase II promoter (GO:0042789)|negative regulation of gene silencing by miRNA (GO:0060965)|positive regulation of catenin import into nucleus (GO:0035413)|positive regulation of SMAD protein import into nucleus (GO:0060391)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of asymmetric cell division (GO:0009786)|regulation of gene expression (GO:0010468)|regulation of heart induction by regulation of canonical Wnt signaling pathway (GO:0090081)|regulation of methylation-dependent chromatin silencing (GO:0090308)|regulation of transcription, DNA-templated (GO:0006355)|response to wounding (GO:0009611)|somatic stem cell maintenance (GO:0035019)|transcription from RNA polymerase II promoter (GO:0006366)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	DNA binding (GO:0003677)|miRNA binding (GO:0035198)|poly(A) RNA binding (GO:0044822)|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)|transcription factor binding (GO:0008134)|transcription regulatory region DNA binding (GO:0044212)|ubiquitin protein ligase binding (GO:0031625)		EWSR1/POU5F1(10)	breast(1)|large_intestine(2)|lung(3)|ovary(2)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	13					Dopamine(DB00988)|Norepinephrine(DB00368)	CGAGGATCAACCCAGCCCGGC	0.687			T	EWSR1	sarcoma								C|||	59	0.0117812	0.0015	0.0043	5008	,	,		13351	0.0149		0.0278	False		,,,				2504	0.0112				p.V30I		Atlas-SNP	.		Dom	yes		6	6p21.31	5460	"""POU domain, class 5, transcription factor 1"""		M	.	POU5F1	25	.	0			c.G88A						PASS	.	C	ILE/VAL	10,2778		0,10,1384	4.0	5.0	5.0		88	1.9	1.0	6	dbSNP_127	5	72,4952		0,72,2440	no	missense	POU5F1	NM_002701.4	29	0,82,3824	TT,TC,CC		1.4331,0.3587,1.0497	benign	30/361	31138310	82,7730	1394	2512	3906	SO:0001583	missense	5460	exon1			GATCAACCCAGCC	Z11898	CCDS34391.1, CCDS47398.1, CCDS47398.2, CCDS75420.1	6p21.33	2011-06-20	2007-07-13		ENSG00000204531	ENSG00000204531		"""Homeoboxes / POU class"""	9221	protein-coding gene	gene with protein product		164177	"""POU domain class 5, transcription factor 1"""	OTF3		1408763	Standard	NM_002701		Approved	OCT3, Oct4, MGC22487	uc003nsv.3	Q01860	OTTHUMG00000031206	ENST00000259915.8:c.88G>A	6.37:g.31138310C>T	ENSP00000259915:p.Val30Ile	67.0	0.0	0		77.0	76.0	0.987013	NM_002701	A6NCS1|A6NLL8|D2IYK4|P31359|Q15167|Q15168|Q16422|Q5STF3|Q5STF4	Missense_Mutation	SNP	ENST00000259915.8	37	CCDS34391.1	42	0.019230769230769232	2	0.0040650406504065045	2	0.0055248618784530384	14	0.024475524475524476	24	0.0316622691292876	C	15.63	2.891065	0.52014	0.003587	0.014331	ENSG00000204531	ENST00000259915;ENST00000448657	T	0.61742	0.08	3.7	1.92	0.25849	.	0.791726	0.10706	N	0.643431	T	0.34600	0.0903	M	0.61703	1.905	0.80722	D	1	B	0.02656	0.0	B	0.01281	0.0	T	0.43163	-0.9408	10	0.66056	D	0.02	.	5.9515	0.19248	0.0:0.7594:0.0:0.2406	rs41257954	30	Q01860	PO5F1_HUMAN	I	30	ENSP00000259915:V30I	ENSP00000259915:V30I	V	-	1	0	POU5F1	31246289	0.985000	0.35326	0.998000	0.56505	0.952000	0.60782	0.124000	0.15728	0.553000	0.29044	0.549000	0.68633	GTT	C|0.974;T|0.026	0.026	strong		0.687	POU5F1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076413.4	NM_002701	
PGC	5225	hgsc.bcm.edu	37	6	41710111	41710111	+	Silent	SNP	G	G	A	rs61731757	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr6:41710111G>A	ENST00000373025.3	-	5	626	c.564C>T	c.(562-564)tcC>tcT	p.S188S	PGC_ENST00000425343.2_Silent_p.S188S	NM_002630.3	NP_002621.1	P20142	PEPC_HUMAN	progastricsin (pepsinogen C)	188					digestion (GO:0007586)|proteolysis (GO:0006508)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)	aspartic-type endopeptidase activity (GO:0004190)			endometrium(3)|kidney(1)|large_intestine(5)|lung(6)|skin(1)	16	Ovarian(28;0.0355)|Colorectal(47;0.121)		Epithelial(12;0.000132)|STAD - Stomach adenocarcinoma(11;0.000204)|Colorectal(64;0.00245)|COAD - Colon adenocarcinoma(64;0.00507)			CCTCATCCACGGACAGAGCAG	0.602													G|||	12	0.00239617	0.0	0.0043	5008	,	,		18988	0.0		0.0089	False		,,,				2504	0.0				p.S188S		Atlas-SNP	.											.	PGC	56	.	0			c.C564T						PASS	.	G	,	7,4399	12.9+/-30.5	0,7,2196	130.0	94.0	106.0		564,564	-3.7	0.0	6	dbSNP_129	106	81,8519	47.2+/-106.3	0,81,4219	no	coding-synonymous,coding-synonymous	PGC	NM_001166424.1,NM_002630.3	,	0,88,6415	AA,AG,GG		0.9419,0.1589,0.6766	,	188/316,188/389	41710111	88,12918	2203	4300	6503	SO:0001819	synonymous_variant	5225	exon5			ATCCACGGACAGA		CCDS4859.1, CCDS55000.1	6p21.1	2012-10-02			ENSG00000096088	ENSG00000096088	3.4.23.3		8890	protein-coding gene	gene with protein product		169740					Standard	NM_002630		Approved		uc003ora.2	P20142	OTTHUMG00000014683	ENST00000373025.3:c.564C>T	6.37:g.41710111G>A		116.0	0.0	0		120.0	59.0	0.491667	NM_002630	B4DVZ3|Q5T3D7|Q5T3D8	Silent	SNP	ENST00000373025.3	37	CCDS4859.1																																																																																			G|0.994;A|0.006	0.006	strong		0.602	PGC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040521.2		
SCN4A	6329	hgsc.bcm.edu	37	17	62018931	62018931	+	Missense_Mutation	SNP	G	G	A			TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr17:62018931G>A	ENST00000435607.1	-	24	4787	c.4711C>T	c.(4711-4713)Ccc>Tcc	p.P1571S	SCN4A_ENST00000578147.1_Missense_Mutation_p.P1571S	NM_000334.4	NP_000325.4	P35499	SCN4A_HUMAN	sodium channel, voltage-gated, type IV, alpha subunit	1571					membrane depolarization during action potential (GO:0086010)|muscle contraction (GO:0006936)|neuronal action potential (GO:0019228)|sodium ion transmembrane transport (GO:0035725)|sodium ion transport (GO:0006814)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|voltage-gated sodium channel complex (GO:0001518)	voltage-gated sodium channel activity (GO:0005248)			breast(4)|central_nervous_system(3)|cervix(1)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(23)|lung(40)|ovary(3)|pancreas(1)|prostate(6)|skin(4)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	101					Diclofenac(DB00586)|Flecainide(DB01195)|Propofol(DB00818)|Valproic Acid(DB00313)|Zonisamide(DB00909)	CCGATGGAGGGGTTGCCGCAG	0.577																																					p.P1571S		Atlas-SNP	.											.	SCN4A	205	.	0			c.C4711T						PASS	.						46.0	52.0	50.0					17																	62018931		2149	4263	6412	SO:0001583	missense	6329	exon24			TGGAGGGGTTGCC	U24693		17q23.3	2012-02-26	2007-01-23					"""Sodium channels"", ""Voltage-gated ion channels / Sodium channels"""	10591	protein-coding gene	gene with protein product		603967		HYKPP		1654742, 1659948, 16382098	Standard	XM_005257566		Approved	Nav1.4, HYPP, SkM1	uc002jds.1	P35499		ENST00000435607.1:c.4711C>T	17.37:g.62018931G>A	ENSP00000396320:p.Pro1571Ser	142.0	0.0	0		139.0	62.0	0.446043	NM_000334	Q15478|Q16447|Q7Z6B1	Missense_Mutation	SNP	ENST00000435607.1	37	CCDS45761.1	.	.	.	.	.	.	.	.	.	.	g	17.38	3.376136	0.61735	.	.	ENSG00000007314	ENST00000435607	D	0.98178	-4.77	3.9	3.9	0.45041	Ion transport (1);	0.000000	0.85682	D	0.000000	D	0.98210	0.9408	L	0.46670	1.46	0.58432	D	0.999998	D	0.89917	1.0	D	0.81914	0.995	D	0.98880	1.0769	10	0.62326	D	0.03	.	15.4266	0.75055	0.0:0.0:1.0:0.0	.	1571	P35499	SCN4A_HUMAN	S	1571	ENSP00000396320:P1571S	ENSP00000396320:P1571S	P	-	1	0	SCN4A	59372663	1.000000	0.71417	1.000000	0.80357	0.906000	0.53458	9.601000	0.98297	2.177000	0.69029	0.556000	0.70494	CCC	.	.	none		0.577	SCN4A-201	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding		NM_000334	
OR2J3	442186	hgsc.bcm.edu	37	6	29080386	29080386	+	Missense_Mutation	SNP	T	T	C	rs79293918	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr6:29080386T>C	ENST00000377169.1	+	1	719	c.719T>C	c.(718-720)gTg>gCg	p.V240A		NM_001005216.2	NP_001005216.2	O76001	OR2J3_HUMAN	olfactory receptor, family 2, subfamily J, member 3	240						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			endometrium(2)|large_intestine(5)|lung(13)|prostate(1)|skin(1)|upper_aerodigestive_tract(2)	24						CTTCAGAAAGTGTTTGGAACA	0.448													T|||	116	0.0231629	0.0651	0.0101	5008	,	,		22544	0.0079		0.0119	False		,,,				2504	0.0031				p.V240A		Atlas-SNP	.											.	OR2J3	53	.	0			c.T719C						PASS	.	T	ALA/VAL	185,2355		4,177,1089	118.0	123.0	121.0		719	1.6	0.9	6	dbSNP_131	121	26,5120		0,26,2547	yes	missense	OR2J3	NM_001005216.2	64	4,203,3636	CC,CT,TT		0.5052,7.2835,2.7453	possibly-damaging	240/312	29080386	211,7475	1270	2573	3843	SO:0001583	missense	442186	exon1			AGAAAGTGTTTGG		CCDS43433.1	6p22.2-p21.31	2012-08-09			ENSG00000204701	ENSG00000204701		"""GPCR / Class A : Olfactory receptors"""	8261	protein-coding gene	gene with protein product		615016					Standard	NM_001005216		Approved	OR6-6	uc011dll.2	O76001	OTTHUMG00000031092	ENST00000377169.1:c.719T>C	6.37:g.29080386T>C	ENSP00000366374:p.Val240Ala	318.0	1.0	0.00314465		345.0	152.0	0.44058	NM_001005216	B0UY52|B9EH11|Q5SUJ7|Q6IF25|Q96R15|Q9GZK5|Q9GZL4|Q9GZL5	Missense_Mutation	SNP	ENST00000377169.1	37	CCDS43433.1	54	0.024725274725274724	32	0.06504065040650407	6	0.016574585635359115	6	0.01048951048951049	10	0.013192612137203167	T	0.005	-2.139654	0.00335	0.072835	0.005052	ENSG00000204701	ENST00000377169	T	0.00009	9.47	2.78	1.63	0.23807	GPCR, rhodopsin-like superfamily (1);	.	.	.	.	T	0.00012	0.0000	N	0.00123	-2.06	0.40080	D	0.976121	B	0.09022	0.002	B	0.13407	0.009	T	0.00849	-1.1541	9	0.02654	T	1	.	3.5019	0.07676	0.0:0.4818:0.0:0.5182	.	240	O76001	OR2J3_HUMAN	A	240	ENSP00000366374:V240A	ENSP00000366374:V240A	V	+	2	0	OR2J3	29188365	0.981000	0.34729	0.937000	0.37676	0.020000	0.10135	1.790000	0.38734	1.268000	0.44264	0.358000	0.22013	GTG	T|0.981;C|0.019	0.019	strong		0.448	OR2J3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076132.2		
TRIM14	9830	hgsc.bcm.edu	37	9	100857170	100857170	+	Silent	SNP	A	A	G	rs150211153	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr9:100857170A>G	ENST00000341469.2	-	4	688	c.679T>C	c.(679-681)Ttg>Ctg	p.L227L	TRIM14_ENST00000342043.3_Silent_p.L227L|TRIM14_ENST00000375098.3_Silent_p.L227L|TRIM14_ENST00000538344.1_5'Flank	NM_014788.2	NP_055603.2	Q14142	TRI14_HUMAN	tripartite motif containing 14	227					innate immune response (GO:0045087)|negative regulation of viral transcription (GO:0032897)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)	cytoplasm (GO:0005737)|intracellular (GO:0005622)	zinc ion binding (GO:0008270)			central_nervous_system(1)|cervix(1)|endometrium(2)|kidney(1)|large_intestine(1)|lung(2)|upper_aerodigestive_tract(1)	9		Acute lymphoblastic leukemia(62;0.0559)				CGAATGTCCAATGGCGTCTGT	0.532													A|||	2	0.000399361	0.0	0.0	5008	,	,		22256	0.0		0.002	False		,,,				2504	0.0				p.L227L	Colon(14;460 597 13826 51781)	Atlas-SNP	.											.	TRIM14	24	.	0			c.T679C						PASS	.	A	,,	2,4404	4.2+/-10.8	0,2,2201	128.0	111.0	117.0		679,679,679	-0.0	0.3	9	dbSNP_134	117	11,8589	8.4+/-32.0	0,11,4289	no	coding-synonymous,coding-synonymous,coding-synonymous	TRIM14	NM_014788.2,NM_033219.1,NM_033220.1	,,	0,13,6490	GG,GA,AA		0.1279,0.0454,0.1	,,	227/443,227/443,227/443	100857170	13,12993	2203	4300	6503	SO:0001819	synonymous_variant	9830	exon4			TGTCCAATGGCGT	AF220130	CCDS6734.1	9q31.1	2011-04-20	2011-01-25		ENSG00000106785	ENSG00000106785		"""Tripartite motif containing / Tripartite motif containing"""	16283	protein-coding gene	gene with protein product		606556	"""tripartite motif-containing 14"""			11331580	Standard	XM_005252320		Approved	KIAA0129	uc004ayd.2	Q14142	OTTHUMG00000020339	ENST00000341469.2:c.679T>C	9.37:g.100857170A>G		123.0	0.0	0		113.0	57.0	0.504425	NM_033219	A8K9W0|E7EQC4|F8W956|Q548W9|Q5TBQ8|Q6ZWL7|Q9BRD8|Q9C020	Silent	SNP	ENST00000341469.2	37	CCDS6734.1																																																																																			A|0.999;G|0.001	0.001	strong		0.532	TRIM14-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053350.1	NM_014788	
CFTR	1080	hgsc.bcm.edu	37	7	117306991	117306991	+	Silent	SNP	C	C	T	rs1800135	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr7:117306991C>T	ENST00000003084.6	+	27	4404	c.4272C>T	c.(4270-4272)taC>taT	p.Y1424Y	CFTR_ENST00000454343.1_Silent_p.Y1363Y	NM_000492.3	NP_000483.3	P13569	CFTR_HUMAN	cystic fibrosis transmembrane conductance regulator (ATP-binding cassette sub-family C, member 7)	1424	ABC transporter 2. {ECO:0000255|PROSITE- ProRule:PRU00434}.				cellular response to cAMP (GO:0071320)|cellular response to hormone stimulus (GO:0032870)|chloride transmembrane transport (GO:1902476)|cholesterol biosynthetic process (GO:0006695)|cholesterol transport (GO:0030301)|intracellular pH elevation (GO:0051454)|iodide transport (GO:0015705)|lung development (GO:0030324)|membrane hyperpolarization (GO:0060081)|positive regulation of vasodilation (GO:0045909)|positive regulation of voltage-gated chloride channel activity (GO:1902943)|respiratory gaseous exchange (GO:0007585)|response to cytokine (GO:0034097)|response to drug (GO:0042493)|response to estrogen (GO:0043627)|response to peptide hormone (GO:0043434)|sperm capacitation (GO:0048240)|transepithelial chloride transport (GO:0030321)|transmembrane transport (GO:0055085)|transport (GO:0006810)|vasodilation (GO:0042311)|water transport (GO:0006833)	apical plasma membrane (GO:0016324)|basolateral plasma membrane (GO:0016323)|cell surface (GO:0009986)|chloride channel complex (GO:0034707)|cytoplasmic vesicle membrane (GO:0030659)|early endosome (GO:0005769)|extracellular vesicular exosome (GO:0070062)|microvillus (GO:0005902)|plasma membrane (GO:0005886)|protein complex (GO:0043234)	ATP binding (GO:0005524)|ATP-binding and phosphorylation-dependent chloride channel activity (GO:0005224)|bicarbonate transmembrane transporter activity (GO:0015106)|channel-conductance-controlling ATPase activity (GO:0005260)|chloride channel activity (GO:0005254)|chloride channel inhibitor activity (GO:0019869)|chloride transmembrane transporter activity (GO:0015108)|enzyme binding (GO:0019899)|PDZ domain binding (GO:0030165)			NS(1)|breast(2)|central_nervous_system(2)|cervix(1)|endometrium(5)|kidney(6)|large_intestine(15)|lung(22)|ovary(2)|pancreas(1)|prostate(3)|skin(9)	69	Lung NSC(10;0.00148)|all_lung(10;0.00171)		STAD - Stomach adenocarcinoma(10;0.000534)		Bumetanide(DB00887)|Crofelemer(DB04941)|Glyburide(DB01016)|Ibuprofen(DB01050)|Ivacaftor(DB08820)	TGCGGCAGTACGATTCCATCC	0.542									Cystic Fibrosis				C|||	21	0.00419329	0.0	0.0058	5008	,	,		17076	0.0		0.0139	False		,,,				2504	0.0031				p.Y1424Y		Atlas-SNP	.											.	CFTR	171	.	0			c.C4272T						PASS	.	C		9,4397	15.5+/-35.6	0,9,2194	59.0	51.0	54.0		4272	-9.6	0.0	7	dbSNP_89	54	58,8542	36.9+/-92.0	1,56,4243	no	coding-synonymous	CFTR	NM_000492.3		1,65,6437	TT,TC,CC		0.6744,0.2043,0.5151		1424/1481	117306991	67,12939	2203	4300	6503	SO:0001819	synonymous_variant	1080	exon27	Familial Cancer Database	CF	GCAGTACGATTCC	M28668	CCDS5773.1	7q31-q32	2014-09-17	2006-09-18		ENSG00000001626	ENSG00000001626		"""Ion channels / Chloride channels : Cystic fibrosis transmembrane conductance regulators"", ""ATP binding cassette transporters / subfamily C"""	1884	protein-coding gene	gene with protein product	"""ATP-binding cassette sub-family C, member 7"""	602421	"""cystic fibrosis transmembrane conductance regulator, ATP-binding cassette (sub-family C, member 7)"""	CF, ABCC7		2772657	Standard	XM_006715842		Approved	MRP7, ABC35, TNR-CFTR, dJ760C5.1, CFTR/MRP	uc003vjd.3	P13569	OTTHUMG00000023076	ENST00000003084.6:c.4272C>T	7.37:g.117306991C>T		218.0	1.0	0.00458716		191.0	92.0	0.481675	NM_000492	Q20BG8|Q20BH2|Q2I0A1|Q2I102	Silent	SNP	ENST00000003084.6	37	CCDS5773.1																																																																																			C|0.994;T|0.006	0.006	strong		0.542	CFTR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000059397.3	NM_000492	
SMCO3	440087	hgsc.bcm.edu	37	12	14959006	14959006	+	Missense_Mutation	SNP	T	T	G			TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr12:14959006T>G	ENST00000316048.2	-	2	681	c.609A>C	c.(607-609)aaA>aaC	p.K203N	C12orf60_ENST00000330828.2_Intron|WBP11_ENST00000261167.2_5'Flank|C12orf60_ENST00000527783.1_Intron	NM_001013698.2	NP_001013720.2	A2RU48	SMCO3_HUMAN	single-pass membrane protein with coiled-coil domains 3	203						integral component of membrane (GO:0016021)											CTGAGGCTGATTTGAACTCCA	0.403																																					p.K203N		Atlas-SNP	.											.	.	.	.	0			c.A609C						PASS	.						135.0	132.0	133.0					12																	14959006		1900	4122	6022	SO:0001583	missense	0	exon2			GGCTGATTTGAAC		CCDS41759.1	12p12.3	2013-03-11	2013-03-11	2013-03-11	ENSG00000179256	ENSG00000179256			34401	protein-coding gene	gene with protein product			"""chromosome 12 open reading frame 69"""	C12orf69			Standard	NM_001013698		Approved	LOC440087	uc001rck.1	A2RU48	OTTHUMG00000167474	ENST00000316048.2:c.609A>C	12.37:g.14959006T>G	ENSP00000381895:p.Lys203Asn	237.0	0.0	0		243.0	104.0	0.427984	NM_001013698	Q8NAI5	Missense_Mutation	SNP	ENST00000316048.2	37	CCDS41759.1	.	.	.	.	.	.	.	.	.	.	T	14.83	2.652321	0.47362	.	.	ENSG00000179256	ENST00000316048	T	0.16743	2.32	4.38	-0.586	0.11694	.	0.000000	0.41712	U	0.000829	T	0.10465	0.0256	L	0.27053	0.805	0.25005	N	0.991445	B	0.23185	0.081	B	0.25884	0.064	T	0.21042	-1.0257	10	0.72032	D	0.01	-3.6815	7.1498	0.25604	0.0:0.4745:0.0:0.5255	.	203	A2RU48	CL069_HUMAN	N	203	ENSP00000381895:K203N	ENSP00000381895:K203N	K	-	3	2	C12orf69	14850273	0.960000	0.32886	0.981000	0.43875	0.772000	0.43724	0.877000	0.28106	-0.010000	0.14271	-1.017000	0.02453	AAA	.	.	none		0.403	SMCO3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000394738.1	NM_001013698	
MYH9	4627	hgsc.bcm.edu	37	22	36691691	36691691	+	Silent	SNP	T	T	C	rs875725	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr22:36691691T>C	ENST00000216181.5	-	26	3575	c.3345A>G	c.(3343-3345)gaA>gaG	p.E1115E		NM_002473.4	NP_002464.1	P35579	MYH9_HUMAN	myosin, heavy chain 9, non-muscle	1115					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						CTTCCTGGAGTTCAGAGATCT	0.522			T	ALK	ALCL		"""Deafness, autosomal dominant 17, Epstein syndrome, Fechtner syndrome, May-Hegglin anomaly, Sebastian syndrome"""		Hereditary Macrothrombocytopenia, MYH9-associated				T|||	128	0.0255591	0.0696	0.0159	5008	,	,		20546	0.0		0.0199	False		,,,				2504	0.0051				p.E1115E		Atlas-SNP	.		Dom	yes		22	22q13.1	4627	"""myosin, heavy polypeptide 9, non-muscle"""	yes	L	.	MYH9	225	.	0			c.A3345G						PASS	.	T		346,4060	177.3+/-206.3	15,316,1872	51.0	48.0	49.0		3345	-1.8	0.9	22	dbSNP_86	49	106,8494	57.9+/-119.4	1,104,4195	no	coding-synonymous	MYH9	NM_002473.4		16,420,6067	CC,CT,TT		1.2326,7.8529,3.4753		1115/1961	36691691	452,12554	2203	4300	6503	SO:0001819	synonymous_variant	4627	exon26	Familial Cancer Database	MYHIIA syndrome, incl. Fechtner Syndrome, FTNS, and May-Hegglin Anomaly, MHA	CTGGAGTTCAGAG		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.3345A>G	22.37:g.36691691T>C		113.0	0.0	0		108.0	53.0	0.490741	NM_002473	A8K6E4|O60805|Q60FE2|Q86T83	Silent	SNP	ENST00000216181.5	37	CCDS13927.1																																																																																			T|0.965;C|0.035	0.035	strong		0.522	MYH9-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000259110.3	NM_002473	
ENPP7	339221	hgsc.bcm.edu	37	17	77710990	77710990	+	Missense_Mutation	SNP	C	C	T	rs139719997	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr17:77710990C>T	ENST00000328313.5	+	4	1398	c.1177C>T	c.(1177-1179)Cgg>Tgg	p.R393W		NM_178543.3	NP_848638.3			ectonucleotide pyrophosphatase/phosphodiesterase 7											breast(1)|central_nervous_system(2)|endometrium(3)|kidney(2)|large_intestine(3)|lung(12)|ovary(2)|prostate(6)|skin(3)	34			OV - Ovarian serous cystadenocarcinoma(97;0.016)|BRCA - Breast invasive adenocarcinoma(99;0.0224)			GCTCATGTGCCGGCTGCTGGG	0.647													C|||	7	0.00139776	0.0	0.0029	5008	,	,		18712	0.0		0.002	False		,,,				2504	0.0031				p.R393W		Atlas-SNP	.											ENPP7,NS,carcinoma,-2,1	ENPP7	63	1	0			c.C1177T						PASS	.	C	TRP/ARG	3,4403	6.2+/-15.9	0,3,2200	61.0	51.0	55.0		1177	0.8	0.7	17	dbSNP_134	55	30,8570	20.4+/-63.3	0,30,4270	yes	missense	ENPP7	NM_178543.3	101	0,33,6470	TT,TC,CC		0.3488,0.0681,0.2537	possibly-damaging	393/459	77710990	33,12973	2203	4300	6503	SO:0001583	missense	339221	exon4			ATGTGCCGGCTGC	AY230663	CCDS11763.1	17q25.3	2014-04-09			ENSG00000182156	ENSG00000182156			23764	protein-coding gene	gene with protein product	"""alkaline sphingomyelinase"""					12885774	Standard	NM_178543		Approved	alk-SMase, NPP7	uc002jxa.3	Q6UWV6	OTTHUMG00000177462	ENST00000328313.5:c.1177C>T	17.37:g.77710990C>T	ENSP00000332656:p.Arg393Trp	64.0	0.0	0		91.0	38.0	0.417582	NM_178543		Missense_Mutation	SNP	ENST00000328313.5	37	CCDS11763.1	2	9.157509157509158E-4	0	0.0	0	0.0	0	0.0	2	0.002638522427440633	C	13.24	2.177465	0.38413	6.81E-4	0.003488	ENSG00000182156	ENST00000328313	T	0.75589	-0.95	3.07	0.824	0.18818	Alkaline phosphatase-like, alpha/beta/alpha (1);Alkaline-phosphatase-like, core domain (1);	0.824992	0.10969	N	0.614092	T	0.69088	0.3072	L	0.42245	1.32	0.25279	N	0.989453	D	0.54047	0.964	P	0.48677	0.586	T	0.59043	-0.7528	10	0.72032	D	0.01	-10.5339	5.5668	0.17175	0.3222:0.4528:0.225:0.0	.	393	Q6UWV6	ENPP7_HUMAN	W	393	ENSP00000332656:R393W	ENSP00000332656:R393W	R	+	1	2	ENPP7	75325585	0.000000	0.05858	0.698000	0.30274	0.382000	0.30200	-0.066000	0.11598	0.075000	0.16796	0.561000	0.74099	CGG	C|0.997;T|0.003	0.003	strong		0.647	ENPP7-001	KNOWN	upstream_ATG|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000437038.1	NM_178543	
SPTA1	6708	hgsc.bcm.edu	37	1	158592901	158592901	+	Missense_Mutation	SNP	C	C	G	rs77877855	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr1:158592901C>G	ENST00000368147.4	-	43	6172	c.5992G>C	c.(5992-5994)Gct>Cct	p.A1998P		NM_003126.2	NP_003117.2	P02549	SPTA1_HUMAN	spectrin, alpha, erythrocytic 1	1998					actin filament capping (GO:0051693)|actin filament organization (GO:0007015)|axon guidance (GO:0007411)|hemopoiesis (GO:0030097)|lymphocyte homeostasis (GO:0002260)|plasma membrane organization (GO:0007009)|porphyrin-containing compound biosynthetic process (GO:0006779)|positive regulation of protein binding (GO:0032092)|positive regulation of T cell proliferation (GO:0042102)|regulation of cell shape (GO:0008360)	actin cytoskeleton (GO:0015629)|cuticular plate (GO:0032437)|cytosol (GO:0005829)|intrinsic component of the cytoplasmic side of the plasma membrane (GO:0031235)|spectrin (GO:0008091)|spectrin-associated cytoskeleton (GO:0014731)	actin filament binding (GO:0051015)|calcium ion binding (GO:0005509)|structural constituent of cytoskeleton (GO:0005200)			NS(3)|breast(7)|cervix(1)|endometrium(22)|kidney(9)|large_intestine(29)|liver(2)|lung(183)|ovary(5)|prostate(18)|skin(11)|soft_tissue(1)|stomach(1)|upper_aerodigestive_tract(9)|urinary_tract(6)	307	all_hematologic(112;0.0378)					TTGTGTTGAGCAGAAATCAGT	0.507													C|||	270	0.0539137	0.1407	0.0303	5008	,	,		16400	0.0		0.0229	False		,,,				2504	0.0409				p.A1998P		Atlas-SNP	.											.	SPTA1	720	.	0			c.G5992C						PASS	.	C	PRO/ALA	550,3340		26,498,1421	323.0	325.0	324.0		5992	3.9	0.4	1	dbSNP_131	324	126,8146		2,122,4012	yes	missense	SPTA1	NM_003126.2	27	28,620,5433	GG,GC,CC		1.5232,14.1388,5.5583	probably-damaging	1998/2420	158592901	676,11486	1945	4136	6081	SO:0001583	missense	6708	exon43			GTTGAGCAGAAAT	M61877	CCDS41423.1	1q21	2014-06-23	2014-06-23		ENSG00000163554	ENSG00000163554		"""EF-hand domain containing"""	11272	protein-coding gene	gene with protein product	"""elliptocytosis 2"""	182860	"""spectrin, alpha, erythrocytic 1 (elliptocytosis 2)"""				Standard	NM_003126		Approved	EL2	uc001fst.1	P02549	OTTHUMG00000019636	ENST00000368147.4:c.5992G>C	1.37:g.158592901C>G	ENSP00000357129:p.Ala1998Pro	260.0	0.0	0		221.0	100.0	0.452489	NM_003126	Q15514|Q5VYL1|Q5VYL2|Q6LDY5	Missense_Mutation	SNP	ENST00000368147.4	37	CCDS41423.1	101	0.04624542124542125	75	0.1524390243902439	10	0.027624309392265192	0	0.0	16	0.021108179419525065	C	15.33	2.800750	0.50315	0.141388	0.015232	ENSG00000163554	ENST00000368148;ENST00000368147	T;T	0.53423	0.62;0.62	4.78	3.86	0.44501	.	.	.	.	.	T	0.54175	0.1842	M	0.72118	2.19	0.36867	D	0.888732	D	0.53462	0.96	P	0.62885	0.908	T	0.60944	-0.7162	9	0.54805	T	0.06	.	13.0889	0.59156	0.1622:0.8378:0.0:0.0	.	1998	P02549	SPTA1_HUMAN	P	1998;1995	ENSP00000357130:A1998P;ENSP00000357129:A1995P	ENSP00000357129:A1995P	A	-	1	0	SPTA1	156859525	0.996000	0.38824	0.362000	0.25862	0.025000	0.11179	3.441000	0.52893	1.203000	0.43233	0.655000	0.94253	GCT	C|0.961;G|0.039	0.039	strong		0.507	SPTA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051851.3	NM_003126	
MKI67	4288	hgsc.bcm.edu	37	10	129902131	129902131	+	Missense_Mutation	SNP	T	T	C	rs146439186		TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr10:129902131T>C	ENST00000368654.3	-	13	8348	c.7973A>G	c.(7972-7974)gAa>gGa	p.E2658G	MKI67_ENST00000368653.3_Missense_Mutation_p.E2298G	NM_002417.4	NP_002408.3	P46013	KI67_HUMAN	marker of proliferation Ki-67	2658	16 X 122 AA approximate repeats.				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)				GGGTTCCTCTTCTACTGGGTT	0.517													T|||	1	0.000199681	0.0	0.0	5008	,	,		19173	0.0		0.0	False		,,,				2504	0.001				p.E2658G		Atlas-SNP	.											.	MKI67	363	.	0			c.A7973G						PASS	.	T	GLY/GLU,GLY/GLU	3,4403	6.2+/-15.9	0,3,2200	163.0	171.0	168.0		6893,7973	-7.3	0.0	10	dbSNP_134	168	18,8582	13.3+/-46.6	0,18,4282	yes	missense,missense	MKI67	NM_001145966.1,NM_002417.4	98,98	0,21,6482	CC,CT,TT		0.2093,0.0681,0.1615	possibly-damaging,possibly-damaging	2298/2897,2658/3257	129902131	21,12985	2203	4300	6503	SO:0001583	missense	4288	exon13			TCCTCTTCTACTG	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.7973A>G	10.37:g.129902131T>C	ENSP00000357643:p.Glu2658Gly	157.0	0.0	0		213.0	88.0	0.413146	NM_002417	Q5VWH2	Missense_Mutation	SNP	ENST00000368654.3	37	CCDS7659.1	.	.	.	.	.	.	.	.	.	.	T	4.259	0.047198	0.08243	6.81E-4	0.002093	ENSG00000148773	ENST00000368654;ENST00000368653;ENST00000537609	T;T	0.02216	4.39;4.39	3.68	-7.35	0.01422	.	0.726931	0.11842	N	0.524155	T	0.02156	0.0067	M	0.62723	1.935	0.09310	N	1	B;B;B	0.34290	0.11;0.11;0.447	B;B;B	0.33846	0.027;0.075;0.171	T	0.06373	-1.0830	10	0.33141	T	0.24	.	2.5101	0.04654	0.1564:0.0851:0.3995:0.3589	.	2657;2298;2658	F5H4V4;P46013-2;P46013	.;.;KI67_HUMAN	G	2658;2298;2657	ENSP00000357643:E2658G;ENSP00000357642:E2298G	ENSP00000357642:E2298G	E	-	2	0	MKI67	129792121	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-0.059000	0.11731	-4.528000	0.00044	-1.301000	0.01330	GAA	T|0.998;C|0.002	0.002	strong		0.517	MKI67-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000050999.1	NM_002417	
RFPL3	10738	hgsc.bcm.edu	37	22	32754286	32754286	+	Silent	SNP	G	G	A	rs9621426	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr22:32754286G>A	ENST00000249007.4	+	1	433	c.228G>A	c.(226-228)ctG>ctA	p.L76L	RFPL3_ENST00000382088.3_Silent_p.L47L|RFPL3_ENST00000397468.1_Silent_p.L47L|RFPL3S_ENST00000461833.1_5'Flank	NM_001098535.1	NP_001092005.1	O75679	RFPL3_HUMAN	ret finger protein-like 3	76							zinc ion binding (GO:0008270)			cervix(1)|endometrium(3)|kidney(1)|large_intestine(1)|lung(5)|ovary(1)|skin(2)|stomach(1)	15						GGGAGGATCTGCTTTGCTGTT	0.537													a|||	62	0.0123802	0.0015	0.0216	5008	,	,		19556	0.0		0.0378	False		,,,				2504	0.0072				p.L76L		Atlas-SNP	.											.	RFPL3	91	.	0			c.G228A						PASS	.	A	,	20,4386	824.5+/-416.5	0,20,2183	127.0	119.0	122.0		228,141	-0.6	0.0	22	dbSNP_119	122	264,8336	807.6+/-407.2	4,256,4040	no	coding-synonymous,coding-synonymous	RFPL3	NM_001098535.1,NM_006604.2	,	4,276,6223	AA,AG,GG		3.0698,0.4539,2.1836	,	76/318,47/289	32754286	284,12722	2203	4300	6503	SO:0001819	synonymous_variant	10738	exon1			GGATCTGCTTTGC	AJ010232	CCDS13904.1, CCDS43011.1	22q12	2006-04-25			ENSG00000128276	ENSG00000128276			9980	protein-coding gene	gene with protein product		605970				10508838	Standard	NM_006604		Approved		uc010gwn.3	O75679	OTTHUMG00000030290	ENST00000249007.4:c.228G>A	22.37:g.32754286G>A		266.0	0.0	0		271.0	137.0	0.505535	NM_001098535	A2A279|Q6IC03|Q6IC04|Q6NSX3|Q8N5R4	Silent	SNP	ENST00000249007.4	37	CCDS43011.1																																																																																			G|0.979;A|0.021	0.021	strong		0.537	RFPL3-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000075172.3	NM_006604	
BPIFB4	149954	hgsc.bcm.edu	37	20	31671575	31671575	+	Missense_Mutation	SNP	T	T	G	rs144272671	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr20:31671575T>G	ENST00000375483.3	+	3	572	c.572T>G	c.(571-573)cTc>cGc	p.L191R		NM_182519.2	NP_872325.2	P59827	BPIB4_HUMAN	BPI fold containing family B, member 4	191	Gly-rich.					cytoplasm (GO:0005737)|extracellular region (GO:0005576)	lipid binding (GO:0008289)										GGTGGCCTGCTCGGCGGAGGT	0.662													T|||	23	0.00459265	0.0	0.0	5008	,	,		15553	0.001		0.0	False		,,,				2504	0.0225				p.L191R		Atlas-SNP	.											.	.	.	.	0			c.T572G						PASS	.	T	ARG/LEU	0,4400		0,0,2200	26.0	32.0	30.0		572	3.3	1.0	20	dbSNP_134	30	17,8581		0,17,4282	yes	missense	BPIFB4	NM_182519.2	102	0,17,6482	GG,GT,TT		0.1977,0.0,0.1308	probably-damaging	191/615	31671575	17,12981	2200	4299	6499	SO:0001583	missense	149954	exon3			GCCTGCTCGGCGG	AF549190	CCDS13213.2	20q11.21	2011-08-04	2011-07-29	2011-07-29	ENSG00000186191	ENSG00000186191		"""BPI fold containing"""	16179	protein-coding gene	gene with protein product		615718	"""chromosome 20 open reading frame 186"""	C20orf186		11971875, 21787333	Standard	NM_182519		Approved	dJ726C3.5, LPLUNC4	uc010zue.2	P59827	OTTHUMG00000032235	ENST00000375483.3:c.572T>G	20.37:g.31671575T>G	ENSP00000364632:p.Leu191Arg	90.0	0.0	0		127.0	74.0	0.582677	NM_182519	Q5TDX6	Missense_Mutation	SNP	ENST00000375483.3	37	CCDS13213.2	.	.	.	.	.	.	.	.	.	.	T	13.01	2.109728	0.37242	0.0	0.001977	ENSG00000186191	ENST00000375483	T	0.01430	4.9	3.33	3.33	0.38152	.	0.672431	0.13031	N	0.419352	T	0.03695	0.0105	L	0.29908	0.895	0.36259	D	0.854418	D	0.65815	0.995	D	0.72982	0.979	T	0.57039	-0.7879	10	0.62326	D	0.03	-15.6488	8.2721	0.31851	0.0:0.0:0.0:1.0	.	191	P59827	BPIB4_HUMAN	R	191	ENSP00000364632:L191R	ENSP00000364632:L191R	L	+	2	0	BPIFB4	31135236	0.999000	0.42202	0.992000	0.48379	0.309000	0.27889	3.953000	0.56699	1.516000	0.48900	0.334000	0.21626	CTC	T|0.998;G|0.002	0.002	strong		0.662	BPIFB4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078655.5	NM_182519	
ACOXL	55289	hgsc.bcm.edu	37	2	111666368	111666368	+	Missense_Mutation	SNP	G	G	A	rs116012262	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr2:111666368G>A	ENST00000389811.4	+	11	1015	c.791G>A	c.(790-792)cGg>cAg	p.R264Q	ACOXL_ENST00000439055.1_Missense_Mutation_p.R264Q			Q9NUZ1	ACOXL_HUMAN	acyl-CoA oxidase-like	264					fatty acid beta-oxidation (GO:0006635)	peroxisome (GO:0005777)	acyl-CoA dehydrogenase activity (GO:0003995)|acyl-CoA oxidase activity (GO:0003997)			kidney(1)|large_intestine(4)|lung(10)|pancreas(1)|prostate(2)|skin(2)|urinary_tract(1)	21						CCCTCTAGCCGGAGGCAGTTT	0.527													g|||	4	0.000798722	0.0	0.0	5008	,	,		19159	0.001		0.003	False		,,,				2504	0.0				p.R264Q		Atlas-SNP	.											.	ACOXL	93	.	0			c.G791A						PASS	.		GLN/ARG	2,4404	4.2+/-10.8	0,2,2201	89.0	86.0	87.0		791	3.2	1.0	2	dbSNP_132	87	25,8575	17.9+/-57.8	0,25,4275	yes	missense	ACOXL	NM_001142807.1	43	0,27,6476	AA,AG,GG		0.2907,0.0454,0.2076	probably-damaging	264/581	111666368	27,12979	2203	4300	6503	SO:0001583	missense	55289	exon11			CTAGCCGGAGGCA		CCDS46389.1	2q13	2010-06-30	2010-04-30		ENSG00000153093	ENSG00000153093			25621	protein-coding gene	gene with protein product			"""acyl-Coenzyme A oxidase-like"""				Standard	NM_001142807		Approved	FLJ11042	uc010yxk.1	Q9NUZ1	OTTHUMG00000131257	ENST00000389811.4:c.791G>A	2.37:g.111666368G>A	ENSP00000374461:p.Arg264Gln	168.0	0.0	0		124.0	67.0	0.540323	NM_001142807	A2RRB7|B7WPB3|B7WPP7|E9PB20|Q53R27|Q53R31|Q53SC6|Q8TCE7	Missense_Mutation	SNP	ENST00000389811.4	37		2	9.157509157509158E-4	0	0.0	0	0.0	1	0.0017482517482517483	1	0.0013192612137203166	g	15.47	2.842370	0.51057	4.54E-4	0.002907	ENSG00000153093	ENST00000389811;ENST00000439055;ENST00000422487;ENST00000417074	D;D;D	0.89810	-2.57;-2.57;-2.57	5.02	3.2	0.36748	Acyl-CoA dehydrogenase/oxidase C-terminal (2);Acyl-CoA oxidase/dehydrogenase, type 1 (1);	0.339475	0.23160	N	0.051250	D	0.94122	0.8115	M	0.87097	2.86	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.97110	0.968;0.947;1.0	D	0.93087	0.6496	10	0.87932	D	0	-44.5563	9.5964	0.39576	0.1755:0.0:0.8245:0.0	.	264;264;264	E9PB20;Q9NUZ1-2;Q9NUZ1	.;.;ACOXL_HUMAN	Q	264;264;115;102	ENSP00000374461:R264Q;ENSP00000407761:R264Q;ENSP00000387832:R102Q	ENSP00000374461:R264Q	R	+	2	0	ACOXL	111382839	1.000000	0.71417	0.993000	0.49108	0.173000	0.22820	3.379000	0.52440	0.509000	0.28195	0.558000	0.71614	CGG	G|0.999;A|0.001	0.001	strong		0.527	ACOXL-001	NOVEL	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000254024.2	NM_018308	
ITGA11	22801	hgsc.bcm.edu	37	15	68653946	68653946	+	Missense_Mutation	SNP	C	C	T	rs148886354	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr15:68653946C>T	ENST00000315757.7	-	5	540	c.454G>A	c.(454-456)Gtg>Atg	p.V152M	ITGA11_ENST00000423218.2_Missense_Mutation_p.V152M|ITGA11_ENST00000562826.1_5'UTR	NM_001004439.1	NP_001004439.1	Q9UKX5	ITA11_HUMAN	integrin, alpha 11	152					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						GCTGGGGCCACGGTCTTGGAG	0.557													C|||	3	0.000599042	0.0	0.0014	5008	,	,		20919	0.001		0.001	False		,,,				2504	0.0				p.V152M		Atlas-SNP	.											.	ITGA11	110	.	0			c.G454A						PASS	.	C	MET/VAL	0,3976		0,0,1988	74.0	74.0	74.0		454	4.7	1.0	15	dbSNP_134	74	12,8308		0,12,4148	yes	missense	ITGA11	NM_001004439.1	21	0,12,6136	TT,TC,CC		0.1442,0.0,0.0976	probably-damaging	152/1189	68653946	12,12284	1988	4160	6148	SO:0001583	missense	22801	exon5			GGGCCACGGTCTT	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.454G>A	15.37:g.68653946C>T	ENSP00000327290:p.Val152Met	51.0	0.0	0		51.0	29.0	0.568627	NM_001004439	J3KQM2|Q8WYI8|Q9UKQ1	Missense_Mutation	SNP	ENST00000315757.7	37	CCDS45291.1	3	0.0013736263736263737	0	0.0	1	0.0027624309392265192	1	0.0017482517482517483	1	0.0013192612137203166	C	14.81	2.646911	0.47258	0.0	0.001442	ENSG00000137809	ENST00000315757;ENST00000423218;ENST00000537153	T;T	0.60040	0.22;0.22	4.66	4.66	0.58398	.	0.063133	0.64402	D	0.000004	T	0.52996	0.1769	M	0.61703	1.905	0.43050	D	0.994657	P;P	0.43607	0.812;0.809	B;B	0.34489	0.163;0.184	T	0.62812	-0.6775	10	0.49607	T	0.09	.	16.915	0.86149	0.0:1.0:0.0:0.0	.	152;152	A8K8T0;Q9UKX5	.;ITA11_HUMAN	M	152	ENSP00000327290:V152M;ENSP00000403392:V152M	ENSP00000327290:V152M	V	-	1	0	ITGA11	66441000	0.998000	0.40836	0.999000	0.59377	0.993000	0.82548	3.185000	0.50934	2.282000	0.76494	0.555000	0.69702	GTG	C|0.999;T|0.001	0.001	strong		0.557	ITGA11-201	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding		NM_012211	
STAB2	55576	hgsc.bcm.edu	37	12	104048446	104048446	+	Missense_Mutation	SNP	G	G	T	rs149524008	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr12:104048446G>T	ENST00000388887.2	+	13	1725	c.1521G>T	c.(1519-1521)aaG>aaT	p.K507N	RP11-341G23.2_ENST00000551905.1_RNA	NM_017564.9	NP_060034.9			stabilin 2											NS(4)|breast(7)|central_nervous_system(1)|cervix(1)|endometrium(15)|kidney(11)|large_intestine(26)|lung(77)|ovary(10)|pancreas(1)|prostate(5)|skin(14)|stomach(2)	174						CCATGGACAAGTTAGAACCCA	0.443													G|||	22	0.00439297	0.0008	0.0029	5008	,	,		21467	0.0		0.0159	False		,,,				2504	0.0031				p.K507N		Atlas-SNP	.											.	STAB2	370	.	0			c.G1521T						PASS	.	G	ASN/LYS	6,4400	14.3+/-33.2	0,6,2197	103.0	93.0	96.0		1521	0.5	0.0	12	dbSNP_134	96	85,8515	48.9+/-108.6	2,81,4217	yes	missense	STAB2	NM_017564.9	94	2,87,6414	TT,TG,GG		0.9884,0.1362,0.6997	benign	507/2552	104048446	91,12915	2203	4300	6503	SO:0001583	missense	55576	exon13			GGACAAGTTAGAA	AF160476	CCDS31888.1	12q23.3	2007-01-29				ENSG00000136011			18629	protein-coding gene	gene with protein product	"""hyaluronic acid receptor for endocytosis"""	608561				11829752, 12077138	Standard	XR_429107		Approved	DKFZP434E0321, FELL, STAB-2, HARE, FEEL-2	uc001tjw.3	Q8WWQ8	OTTHUMG00000170056	ENST00000388887.2:c.1521G>T	12.37:g.104048446G>T	ENSP00000373539:p.Lys507Asn	85.0	0.0	0		76.0	41.0	0.539474	NM_017564		Missense_Mutation	SNP	ENST00000388887.2	37	CCDS31888.1	15	0.006868131868131868	0	0.0	1	0.0027624309392265192	0	0.0	14	0.018469656992084433	G	1.712	-0.498842	0.04291	0.001362	0.009884	ENSG00000136011	ENST00000388887	T	0.63580	-0.05	5.8	0.469	0.16741	FAS1 domain (2);	0.583558	0.18587	N	0.136838	T	0.25494	0.0620	N	0.22421	0.69	0.09310	N	1	B	0.09022	0.002	B	0.11329	0.006	T	0.11421	-1.0588	10	0.24483	T	0.36	.	7.5112	0.27575	0.0643:0.4925:0.2505:0.1927	.	507	Q8WWQ8	STAB2_HUMAN	N	507	ENSP00000373539:K507N	ENSP00000373539:K507N	K	+	3	2	STAB2	102572576	0.991000	0.36638	0.000000	0.03702	0.002000	0.02628	0.356000	0.20181	-0.171000	0.10797	-0.257000	0.10917	AAG	G|0.992;T|0.008	0.008	strong		0.443	STAB2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000407089.1		
TCTN2	79867	hgsc.bcm.edu	37	12	124171538	124171538	+	Silent	SNP	C	C	G	rs149430216	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr12:124171538C>G	ENST00000303372.5	+	6	848	c.720C>G	c.(718-720)ccC>ccG	p.P240P	TCTN2_ENST00000426174.2_Silent_p.P239P	NM_001143850.2|NM_024809.4	NP_001137322.1|NP_079085.2	Q96GX1	TECT2_HUMAN	tectonic family member 2	240					cilium assembly (GO:0042384)|cilium morphogenesis (GO:0060271)|smoothened signaling pathway (GO:0007224)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|integral component of membrane (GO:0016021)|TCTN-B9D complex (GO:0036038)				breast(2)|cervix(2)|endometrium(4)|kidney(1)|large_intestine(4)|lung(12)|ovary(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	30	all_neural(191;0.101)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;0.000163)|Epithelial(86;0.000502)|all cancers(50;0.00451)		TGCAGTCCCCCCTTGCCAACA	0.572													C|||	3	0.000599042	0.0	0.0014	5008	,	,		18850	0.0		0.002	False		,,,				2504	0.0				p.P240P		Atlas-SNP	.											.	TCTN2	50	.	0			c.C720G						PASS	.	C	,	5,4401	9.9+/-24.2	0,5,2198	308.0	279.0	289.0		717,720	-4.8	0.0	12	dbSNP_134	289	55,8545	33.8+/-87.4	0,55,4245	no	coding-synonymous,coding-synonymous	TCTN2	NM_001143850.1,NM_024809.3	,	0,60,6443	GG,GC,CC		0.6395,0.1135,0.4613	,	239/697,240/698	124171538	60,12946	2203	4300	6503	SO:0001819	synonymous_variant	79867	exon6			GTCCCCCCTTGCC	AK056924	CCDS9253.1, CCDS45007.1	12q24.31	2011-04-12	2007-08-20	2007-08-20	ENSG00000168778	ENSG00000168778		"""Tectonic proteins"""	25774	protein-coding gene	gene with protein product	"""Meckel syndrome, type 8"""	613846	"""chromosome 12 open reading frame 38"""	C12orf38		21462283	Standard	NM_024809		Approved	FLJ12975, TECT2, MKS8	uc001ufp.3	Q96GX1	OTTHUMG00000168700	ENST00000303372.5:c.720C>G	12.37:g.124171538C>G		223.0	0.0	0		209.0	98.0	0.4689	NM_024809	A8K7Y8|B3KPW5|Q9H966	Silent	SNP	ENST00000303372.5	37	CCDS9253.1																																																																																			C|0.996;G|0.004	0.004	strong		0.572	TCTN2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000400652.1	NM_024809	
LRRC75A	388341	hgsc.bcm.edu	37	17	16347001	16347001	+	Silent	SNP	C	C	T	rs200702301	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr17:16347001C>T	ENST00000470794.1	-	4	963	c.936G>A	c.(934-936)cgG>cgA	p.R312R	C17orf76-AS1_ENST00000581718.1_RNA|C17orf76-AS1_ENST00000584926.1_RNA|C17orf76-AS1_ENST00000584141.1_RNA|C17orf76-AS1_ENST00000483140.1_RNA|C17orf76-AS1_ENST00000472367.1_RNA|C17orf76-AS1_ENST00000487066.1_RNA|C17orf76-AS1_ENST00000480811.1_RNA|C17orf76-AS1_ENST00000580770.1_RNA|RP11-138I1.3_ENST00000585048.1_lincRNA|C17orf76-AS1_ENST00000580180.1_RNA|C17orf76-AS1_ENST00000584177.1_RNA|C17orf76-AS1_ENST00000478103.2_RNA|C17orf76-AS1_ENST00000484836.1_RNA|C17orf76-AS1_ENST00000391079.1_RNA|FAM211A_ENST00000409083.3_3'UTR|C17orf76-AS1_ENST00000477249.2_RNA|C17orf76-AS1_ENST00000579473.1_RNA|C17orf76-AS1_ENST00000492250.1_RNA|C17orf76-AS1_ENST00000470491.2_RNA|C17orf76-AS1_ENST00000475947.2_RNA|C17orf76-AS1_ENST00000491009.1_RNA|C17orf76-AS1_ENST00000581913.1_RNA|C17orf76-AS1_ENST00000460249.1_RNA|C17orf76-AS1_ENST00000481027.1_RNA|C17orf76-AS1_ENST00000481898.1_RNA|C17orf76-AS1_ENST00000583400.2_RNA|C17orf76-AS1_ENST00000582911.1_RNA|C17orf76-AS1_ENST00000475953.1_RNA	NM_001113567.2	NP_001107039.1														lung(1)	1						CTGTCCCTTCCCGGACCTCCT	0.667													C|||	3	0.000599042	0.0008	0.0	5008	,	,		17848	0.0		0.002	False		,,,				2504	0.0				p.R312R		Atlas-SNP	.											.	FAM211A	21	.	0			c.G936A						PASS	.						28.0	33.0	31.0					17																	16347001		692	1591	2283	SO:0001819	synonymous_variant	388341	exon4			CCCTTCCCGGACC																												ENST00000470794.1:c.936G>A	17.37:g.16347001C>T		75.0	0.0	0		69.0	34.0	0.492754	NM_001113567		Silent	SNP	ENST00000470794.1	37	CCDS45620.1																																																																																			C|0.996;T|0.004	0.004	weak		0.667	FAM211A-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000130463.3		
KIAA1551	55196	hgsc.bcm.edu	37	12	32137901	32137901	+	Missense_Mutation	SNP	A	A	C	rs3759296	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr12:32137901A>C	ENST00000312561.4	+	4	4426	c.4012A>C	c.(4012-4014)Aca>Cca	p.T1338P	KIAA1551_ENST00000535596.1_Intron	NM_018169.3	NP_060639	Q9HCM1	K1551_HUMAN	KIAA1551	1338			T -> A (in dbSNP:rs3759296).					p.T1338A(1)									AAAAACAAAAACAGCTTTTTT	0.348																																					p.T1338P		Atlas-SNP	.											C12orf35,NS,carcinoma,0,1	.	.	1	1	Substitution - Missense(1)	stomach(1)	c.A4012C						PASS	.						86.0	90.0	88.0					12																	32137901		2203	4300	6503	SO:0001583	missense	55196	exon4			ACAAAAACAGCTT	AK001514	CCDS8725.2	12p11.21	2012-08-14	2012-08-14	2012-08-14	ENSG00000174718	ENSG00000174718			25559	protein-coding gene	gene with protein product			"""chromosome 12 open reading frame 35"""	C12orf35		10997877	Standard	NM_018169		Approved	FLJ20696, FLJ10652	uc001rks.3	Q9HCM1	OTTHUMG00000128501	ENST00000312561.4:c.4012A>C	12.37:g.32137901A>C	ENSP00000310338:p.Thr1338Pro	129.0	0.0	0		150.0	74.0	0.493333	NM_018169	B2RTU5|Q4KN17|Q9NVL6|Q9NWP9	Missense_Mutation	SNP	ENST00000312561.4	37	CCDS8725.2	.	.	.	.	.	.	.	.	.	.	A	10.15	1.271497	0.23221	.	.	ENSG00000174718	ENST00000312561	T	0.12465	2.68	5.3	-8.75	0.00834	.	2.186560	0.01601	N	0.022031	T	0.06280	0.0162	N	0.14661	0.345	0.80722	P	0.0	B	0.24882	0.113	B	0.23275	0.045	T	0.21690	-1.0238	8	.	.	.	.	5.0984	0.14747	0.216:0.2115:0.4686:0.1039	.	1338	Q9HCM1	CL035_HUMAN	P	1338	ENSP00000310338:T1338P	.	T	+	1	0	C12orf35	32029168	0.000000	0.05858	0.000000	0.03702	0.004000	0.04260	-2.164000	0.01275	-1.463000	0.01904	0.460000	0.39030	ACA	A|0.986;G|0.014	.	alt		0.348	KIAA1551-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250307.2	NM_018169	
SEPT1	1731	hgsc.bcm.edu	37	16	30387148	30387148	+	IGR	SNP	A	A	G			TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr16:30387148A>G	ENST00000571393.1	-	0	1589				MYLPF_ENST00000322861.7_Missense_Mutation_p.K4R			Q8WYJ6	SEPT1_HUMAN	septin 1						cell cycle (GO:0007049)|cell division (GO:0051301)	septin complex (GO:0031105)	GTP binding (GO:0005525)			breast(2)|endometrium(1)|large_intestine(3)|lung(15)|ovary(1)|skin(1)|urinary_tract(1)	24			Colorectal(24;0.193)			CAGGCACCCAAGAGGGCCAAG	0.572																																					p.K4R		Atlas-SNP	.											.	MYLPF	12	.	0			c.A11G						PASS	.						46.0	50.0	48.0					16																	30387148		2197	4300	6497	SO:0001628	intergenic_variant	29895	exon2			CACCCAAGAGGGC	AF308288	CCDS10678.1, CCDS10678.2, CCDS10678.3	16p11.2	2013-01-21		2001-09-10	ENSG00000180096	ENSG00000180096	3.1.5.1	"""Septins"""	2879	protein-coding gene	gene with protein product		612897		DIFF6		8697812	Standard	NM_052838		Approved	PNUTL3	uc002dxy.4	Q8WYJ6	OTTHUMG00000176984		16.37:g.30387148A>G		101.0	0.0	0		107.0	48.0	0.448598	NM_013292	B4DVE6|Q658T1|Q8NEZ1|Q96EL4|Q9H285	Missense_Mutation	SNP	ENST00000571393.1	37		.	.	.	.	.	.	.	.	.	.	A	11.07	1.529847	0.27387	.	.	ENSG00000180209	ENST00000322861	T	0.75154	-0.91	5.56	5.56	0.83823	.	0.000000	0.85682	D	0.000000	T	0.71324	0.3326	N	0.10809	0.05	0.58432	D	0.999999	D	0.58268	0.982	D	0.67548	0.952	T	0.68914	-0.5283	10	0.15499	T	0.54	.	14.7308	0.69379	1.0:0.0:0.0:0.0	.	4	Q96A32	MLRS_HUMAN	R	4	ENSP00000325239:K4R	ENSP00000325239:K4R	K	+	2	0	MYLPF	30294649	1.000000	0.71417	1.000000	0.80357	0.004000	0.04260	8.674000	0.91191	2.120000	0.65058	0.372000	0.22366	AAG	.	.	none		0.572	SEPT1-201	KNOWN	basic	protein_coding	protein_coding		NM_052838	
MED11	400569	hgsc.bcm.edu	37	17	4636385	4636385	+	Missense_Mutation	SNP	C	C	T			TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr17:4636385C>T	ENST00000293777.5	+	3	313	c.257C>T	c.(256-258)tCg>tTg	p.S86L	RP11-314A20.5_ENST00000570493.2_RNA|CXCL16_ENST00000576153.1_5'Flank|MED11_ENST00000575284.1_3'UTR	NM_001001683.2	NP_001001683.1	Q9P086	MED11_HUMAN	mediator complex subunit 11	86						mediator complex (GO:0016592)	RNA polymerase II transcription cofactor activity (GO:0001104)			lung(2)|ovary(2)	4						AGCTACTCTTCGAGGAAGGAC	0.557																																					p.S86L		Atlas-SNP	.											.	MED11	5	.	0			c.C257T						PASS	.						94.0	80.0	85.0					17																	4636385		2203	4300	6503	SO:0001583	missense	400569	exon3			ACTCTTCGAGGAA	AF161414	CCDS32533.1	17p13.2	2007-07-30	2007-07-30			ENSG00000161920			32687	protein-coding gene	gene with protein product		612383	"""mediator of RNA polymerase II transcription, subunit 11 homolog (S. cerevisiae)"""			15175163, 12584197	Standard	NM_001001683		Approved	HSPC296, MGC88387	uc002fyp.3	Q9P086		ENST00000293777.5:c.257C>T	17.37:g.4636385C>T	ENSP00000293777:p.Ser86Leu	149.0	0.0	0		154.0	64.0	0.415584	NM_001001683	Q6NS89	Missense_Mutation	SNP	ENST00000293777.5	37	CCDS32533.1	.	.	.	.	.	.	.	.	.	.	C	19.38	3.816690	0.70912	.	.	ENSG00000161920	ENST00000293777	.	.	.	5.74	4.74	0.60224	.	0.163543	0.37669	N	0.001992	T	0.47040	0.1424	L	0.38175	1.15	0.41743	D	0.989629	B	0.34313	0.448	B	0.29440	0.102	T	0.51631	-0.8681	9	0.66056	D	0.02	-22.7906	14.2205	0.65823	0.0:0.8492:0.1508:0.0	.	86	Q9P086	MED11_HUMAN	L	86	.	ENSP00000293777:S86L	S	+	2	0	MED11	4583134	0.999000	0.42202	0.893000	0.35052	0.967000	0.64934	4.595000	0.61048	1.365000	0.46057	0.655000	0.94253	TCG	.	.	none		0.557	MED11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000439574.1	NM_001001683	
PHF3	23469	hgsc.bcm.edu	37	6	64394121	64394121	+	Silent	SNP	A	A	G	rs35294942	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr6:64394121A>G	ENST00000262043.3	+	4	838	c.498A>G	c.(496-498)gtA>gtG	p.V166V	PHF3_ENST00000393387.1_Silent_p.V166V|PHF3_ENST00000509330.1_Silent_p.V166V			Q92576	PHF3_HUMAN	PHD finger protein 3	166					multicellular organismal development (GO:0007275)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	zinc ion binding (GO:0008270)			breast(7)|cervix(2)|endometrium(8)|kidney(7)|large_intestine(18)|lung(21)|ovary(3)|prostate(1)|skin(2)|upper_aerodigestive_tract(6)	75	all_cancers(3;0.0241)|all_epithelial(2;0.00306)|Lung NSC(77;0.121)		LUSC - Lung squamous cell carcinoma(74;0.0644)|Lung(124;0.148)			GGAAGACTGTATCTACTGCTA	0.403													A|||	45	0.00898562	0.031	0.0029	5008	,	,		17216	0.0		0.002	False		,,,				2504	0.0				p.V166V	GBM(135;136 1820 29512 34071 46235)	Atlas-SNP	.											.	PHF3	191	.	0			c.A498G						PASS	.	A		118,4288	87.8+/-126.4	2,114,2087	176.0	183.0	180.0		498	-4.4	0.5	6	dbSNP_126	180	0,8600	1.2+/-3.3	0,0,4300	no	coding-synonymous	PHF3	NM_015153.2		2,114,6387	GG,GA,AA		0.0,2.6782,0.9073		166/2040	64394121	118,12888	2203	4300	6503	SO:0001819	synonymous_variant	23469	exon3			GACTGTATCTACT	AF091622	CCDS4966.1	6q12	2013-09-24			ENSG00000118482	ENSG00000118482		"""Zinc fingers, PHD-type"""	8921	protein-coding gene	gene with protein product		607789				11856869	Standard	XM_005248701		Approved		uc003pep.1	Q92576	OTTHUMG00000014952	ENST00000262043.3:c.498A>G	6.37:g.64394121A>G		129.0	0.0	0		113.0	59.0	0.522124	NM_015153	A3KFI8|Q14CR5|Q5CZI1|Q5T1T6|Q9NQ16|Q9UI45	Silent	SNP	ENST00000262043.3	37	CCDS4966.1																																																																																			A|0.990;G|0.010	0.010	strong		0.403	PHF3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041086.2		
MTMR10	54893	hgsc.bcm.edu	37	15	31246972	31246972	+	Missense_Mutation	SNP	C	C	T	rs142149917	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr15:31246972C>T	ENST00000435680.1	-	10	1157	c.1060G>A	c.(1060-1062)Gtt>Att	p.V354I	MTMR10_ENST00000563714.1_Missense_Mutation_p.V272I|MTMR10_ENST00000314404.8_Missense_Mutation_p.V106I|RNU6-466P_ENST00000391224.1_RNA|MTMR10_ENST00000425768.1_3'UTR	NM_017762.2	NP_060232.2	Q9NXD2	MTMRA_HUMAN	myotubularin related protein 10	354	Myotubularin phosphatase. {ECO:0000255|PROSITE-ProRule:PRU00669}.						phosphatase activity (GO:0016791)			autonomic_ganglia(1)|breast(1)|endometrium(1)|kidney(2)|large_intestine(2)|ovary(1)|upper_aerodigestive_tract(1)	9		all_lung(180;2.81e-11)		all cancers(64;7.26e-15)|Epithelial(43;7.2e-11)|GBM - Glioblastoma multiforme(186;0.000158)|BRCA - Breast invasive adenocarcinoma(123;0.00426)|Lung(196;0.174)		TTACCATTAACGCATAGCTGC	0.333													C|||	19	0.00379393	0.0	0.0043	5008	,	,		17377	0.0		0.007	False		,,,				2504	0.0092				p.V354I		Atlas-SNP	.											MTMR10_ENST00000435680,NS,carcinoma,0,2	MTMR10	74	2	0			c.G1060A						PASS	.	C	ILE/VAL	7,3651		0,7,1822	83.0	75.0	77.0		1060	4.4	0.9	15	dbSNP_134	77	58,8108		0,58,4025	yes	missense	MTMR10	NM_017762.2	29	0,65,5847	TT,TC,CC		0.7103,0.1914,0.5497	benign	354/778	31246972	65,11759	1829	4083	5912	SO:0001583	missense	54893	exon10			CATTAACGCATAG	AK000320	CCDS45204.1	15q13.3	2011-06-09				ENSG00000166912		"""Protein tyrosine phosphatases / Class I Cys-based PTPs : Myotubularins"""	25999	protein-coding gene	gene with protein product						12495846	Standard	NM_017762		Approved	FLJ20313	uc001zfh.1	Q9NXD2		ENST00000435680.1:c.1060G>A	15.37:g.31246972C>T	ENSP00000402537:p.Val354Ile	76.0	0.0	0		113.0	58.0	0.513274	NM_017762	Q6P4Q6	Missense_Mutation	SNP	ENST00000435680.1	37	CCDS45204.1	6	0.0027472527472527475	0	0.0	1	0.0027624309392265192	0	0.0	5	0.006596306068601583	C	13.17	2.158574	0.38119	0.001914	0.007103	ENSG00000166912	ENST00000435680;ENST00000314404;ENST00000340566	D;D	0.89415	-2.51;-2.51	5.32	4.4	0.53042	Myotubularin phosphatase domain (1);	0.121057	0.56097	N	0.000032	T	0.79730	0.4496	M	0.65320	2	0.80722	D	1	B;B;P;P	0.37688	0.256;0.066;0.605;0.522	B;B;B;B	0.21151	0.024;0.017;0.033;0.031	T	0.80266	-0.1454	10	0.33940	T	0.23	.	13.6029	0.62031	0.0:0.9259:0.0:0.0741	.	123;272;272;354	Q0IJ45;Q9NXD2-2;A6NGL9;Q9NXD2	.;.;.;MTMRA_HUMAN	I	354;106;272	ENSP00000402537:V354I;ENSP00000313788:V106I	ENSP00000313788:V106I	V	-	1	0	MTMR10	29034264	0.990000	0.36364	0.863000	0.33907	0.849000	0.48306	2.209000	0.42806	1.249000	0.43950	0.650000	0.86243	GTT	C|0.996;T|0.004	0.004	strong		0.333	MTMR10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000430747.1	NM_017762	
TSPEAR	54084	hgsc.bcm.edu	37	21	45948342	45948342	+	Silent	SNP	C	C	T	rs201202780		TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr21:45948342C>T	ENST00000323084.4	-	6	980	c.915G>A	c.(913-915)gtG>gtA	p.V305V	TSPEAR_ENST00000397916.1_Silent_p.V237V	NM_001272037.1|NM_144991.2	NP_001258966.1|NP_659428.2	Q8WU66	TSEAR_HUMAN	thrombospondin-type laminin G domain and EAR repeats	305					sensory perception of sound (GO:0007605)	cell surface (GO:0009986)|ciliary membrane (GO:0060170)|extracellular region (GO:0005576)|stereocilium (GO:0032420)				breast(1)|central_nervous_system(6)|cervix(1)|endometrium(2)|kidney(2)|large_intestine(7)|lung(7)|ovary(1)|pancreas(1)|skin(6)|soft_tissue(1)|upper_aerodigestive_tract(2)	37						CACCTGCTAACACGGAGACCC	0.642																																					p.V305V		Atlas-SNP	.											.	TSPEAR	110	.	0			c.G915A						PASS	.						152.0	141.0	144.0					21																	45948342		2203	4300	6503	SO:0001819	synonymous_variant	54084	exon6			TGCTAACACGGAG	AJ487962	CCDS13712.1, CCDS74801.1	21q22.3	2012-10-30	2011-01-25	2011-01-25	ENSG00000175894	ENSG00000175894			1268	protein-coding gene	gene with protein product		612920	"""chromosome 21 open reading frame 29"", ""deafness, autosomal recessive 98"""	C21orf29, DFNB98		12095917, 22678063	Standard	NM_144991		Approved	MGC11251, TSP-EAR	uc002zfe.1	Q8WU66	OTTHUMG00000041215	ENST00000323084.4:c.915G>A	21.37:g.45948342C>T		56.0	0.0	0		74.0	26.0	0.351351	NM_144991		Silent	SNP	ENST00000323084.4	37	CCDS13712.1																																																																																			C|0.999;T|0.001	0.001	weak		0.642	TSPEAR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000098761.1	NM_144991	
FRMD4A	55691	hgsc.bcm.edu	37	10	13779898	13779898	+	Silent	SNP	C	C	T	rs61755072	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr10:13779898C>T	ENST00000357447.2	-	12	1073	c.705G>A	c.(703-705)ctG>ctA	p.L235L	FRMD4A_ENST00000358621.4_Silent_p.L220L|RP11-353M9.1_ENST00000449462.1_RNA|FRMD4A_ENST00000378503.1_Silent_p.L235L|FRMD4A_ENST00000342409.2_Silent_p.L251L	NM_018027.3	NP_060497.3	Q9P2Q2	FRM4A_HUMAN	FERM domain containing 4A	235	FERM. {ECO:0000255|PROSITE- ProRule:PRU00084}.				establishment of epithelial cell polarity (GO:0090162)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|tight junction (GO:0005923)				breast(4)|endometrium(9)|kidney(2)|large_intestine(11)|lung(9)|ovary(2)|pancreas(1)|prostate(2)|skin(1)	41						CTTTGTAGCTCAGGCCCAGCC	0.468													C|||	8	0.00159744	0.0008	0.0014	5008	,	,		19078	0.0		0.006	False		,,,				2504	0.0				p.L235L		Atlas-SNP	.											.	FRMD4A	108	.	0			c.G705A						PASS	.	C		9,4397	15.5+/-35.6	0,9,2194	156.0	116.0	130.0		705	1.5	1.0	10	dbSNP_129	130	90,8510	51.1+/-111.2	0,90,4210	no	coding-synonymous	FRMD4A	NM_018027.3		0,99,6404	TT,TC,CC		1.0465,0.2043,0.7612		235/1040	13779898	99,12907	2203	4300	6503	SO:0001819	synonymous_variant	55691	exon12			GTAGCTCAGGCCC	AB037715	CCDS7101.1	10p14	2004-07-15	2004-07-15	2004-07-15	ENSG00000151474	ENSG00000151474			25491	protein-coding gene	gene with protein product			"""FERM domain containing 4"""	FRMD4		10718198	Standard	NM_018027		Approved	FLJ10210, KIAA1294, bA295P9.4	uc001ims.3	Q9P2Q2	OTTHUMG00000017708	ENST00000357447.2:c.705G>A	10.37:g.13779898C>T		147.0	0.0	0		138.0	68.0	0.492754	NM_018027	A7E2Y3|Q5T377	Silent	SNP	ENST00000357447.2	37	CCDS7101.1																																																																																			C|0.994;T|0.006	0.006	strong		0.468	FRMD4A-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000046889.1	NM_018027	
SIK1	150094	hgsc.bcm.edu	37	21	44839263	44839263	+	Missense_Mutation	SNP	C	C	T	rs34987632	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr21:44839263C>T	ENST00000270162.6	-	10	1347	c.1215G>A	c.(1213-1215)atG>atA	p.M405I		NM_173354.3	NP_775490.2	P57059	SIK1_HUMAN	salt-inducible kinase 1	405					cardiac muscle cell differentiation (GO:0055007)|cell cycle (GO:0007049)|entrainment of circadian clock by photoperiod (GO:0043153)|intracellular signal transduction (GO:0035556)|negative regulation of CREB transcription factor activity (GO:0032792)|negative regulation of gluconeogenesis (GO:0045721)|negative regulation of triglyceride biosynthetic process (GO:0010868)|positive regulation of anoikis (GO:2000210)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|regulation of cell differentiation (GO:0045595)|regulation of mitotic cell cycle (GO:0007346)|regulation of myotube differentiation (GO:0010830)|regulation of sodium ion transport (GO:0002028)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	14-3-3 protein binding (GO:0071889)|ATP binding (GO:0005524)|cAMP response element binding protein binding (GO:0008140)|magnesium ion binding (GO:0000287)|protein kinase binding (GO:0019901)|protein serine/threonine kinase activity (GO:0004674)			breast(1)|central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(2)|lung(6)|ovary(1)|prostate(1)|skin(2)|testis(2)|urinary_tract(1)	21					Dabrafenib(DB08912)	GCTCACAGTCCATCTCGGCCT	0.682													C|||	7	0.00139776	0.0	0.0029	5008	,	,		16988	0.0		0.003	False		,,,				2504	0.002				p.M405I		Atlas-SNP	.											.	SIK1	65	.	0			c.G1215A						PASS	.	C	ILE/MET	8,4394	15.5+/-35.6	0,8,2193	40.0	42.0	41.0		1215	4.3	1.0	21	dbSNP_126	41	60,8540	36.9+/-92.0	0,60,4240	yes	missense	SIK1	NM_173354.3	10	0,68,6433	TT,TC,CC		0.6977,0.1817,0.523	benign	405/784	44839263	68,12934	2201	4300	6501	SO:0001583	missense	150094	exon10			ACAGTCCATCTCG	BC038504	CCDS33575.1	21q22.3	2008-12-23	2008-12-23	2008-12-23	ENSG00000142178	ENSG00000142178			11142	protein-coding gene	gene with protein product	"""myocardial SNF1-like kinase"""	605705	"""SNF1-like kinase"""	SNF1LK		7893599	Standard	NM_173354		Approved	msk	uc002zdf.2	P57059	OTTHUMG00000086874	ENST00000270162.6:c.1215G>A	21.37:g.44839263C>T	ENSP00000270162:p.Met405Ile	130.0	0.0	0		144.0	68.0	0.472222	NM_173354	A6NC84|Q5R2V5|Q6ZNL8|Q86YJ2	Missense_Mutation	SNP	ENST00000270162.6	37	CCDS33575.1	3	0.0013736263736263737	0	0.0	1	0.0027624309392265192	0	0.0	2	0.002638522427440633	C	11.67	1.707255	0.30322	0.001817	0.006977	ENSG00000142178	ENST00000270162	T	0.71222	-0.55	5.16	4.26	0.50523	.	0.469281	0.25310	N	0.031582	T	0.50531	0.1621	L	0.38838	1.175	0.29858	N	0.827879	B	0.06786	0.001	B	0.04013	0.001	T	0.52682	-0.8543	10	0.36615	T	0.2	.	10.2121	0.43147	0.0:0.9064:0.0:0.0936	rs34987632	405	P57059	SIK1_HUMAN	I	405	ENSP00000270162:M405I	ENSP00000270162:M405I	M	-	3	0	SIK1	43663691	1.000000	0.71417	0.970000	0.41538	0.589000	0.36550	2.583000	0.46094	1.140000	0.42260	0.561000	0.74099	ATG	C|0.996;T|0.004	0.004	strong		0.682	SIK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000195654.1	NM_173354	
C10orf54	64115	hgsc.bcm.edu	37	10	73533124	73533124	+	Missense_Mutation	SNP	C	C	T	rs146887444		TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr10:73533124C>T	ENST00000394957.3	-	1	131	c.73G>A	c.(73-75)Gcg>Acg	p.A25T	CDH23_ENST00000224721.6_Intron	NM_022153.1	NP_071436.1	Q9H7M9	GI24_HUMAN	chromosome 10 open reading frame 54	25					BMP signaling pathway (GO:0030509)|negative regulation of CD4-positive, alpha-beta T cell proliferation (GO:2000562)|negative regulation of T cell cytokine production (GO:0002725)|positive regulation of BMP signaling pathway (GO:0030513)|positive regulation of stem cell differentiation (GO:2000738)|stem cell differentiation (GO:0048863)	external side of plasma membrane (GO:0009897)|integral component of membrane (GO:0016021)				breast(1)|central_nervous_system(2)|endometrium(1)|lung(1)|ovary(1)|prostate(1)|skin(1)|urinary_tract(1)	9						CCTAGGGACGCAGCCAGGAAG	0.687													C|||	1	0.000199681	0.0	0.0014	5008	,	,		14034	0.0		0.0	False		,,,				2504	0.0				p.A25T		Atlas-SNP	.											.	C10orf54	29	.	0			c.G73A						PASS	.	C	,THR/ALA	1,4385		0,1,2192	13.0	17.0	16.0		,73	3.0	1.0	10	dbSNP_134	16	5,8581		0,5,4288	yes	intron,missense	CDH23,C10orf54	NM_022124.5,NM_022153.1	,58	0,6,6480	TT,TC,CC		0.0582,0.0228,0.0463	,probably-damaging	,25/312	73533124	6,12966	2193	4293	6486	SO:0001583	missense	64115	exon1			GGGACGCAGCCAG	AF193048	CCDS31218.1	10q22.1	2013-11-28			ENSG00000107738	ENSG00000107738		"""Immunoglobulin superfamily / V-set domain containing"""	30085	protein-coding gene	gene with protein product	"""stress induced secreted protein 1"""	615608				12975309	Standard	NM_022153		Approved	SISP1, GI24, B7-H5, B7H5	uc001jsd.3	Q9H7M9	OTTHUMG00000018426	ENST00000394957.3:c.73G>A	10.37:g.73533124C>T	ENSP00000378409:p.Ala25Thr	284.0	0.0	0		285.0	145.0	0.508772	NM_022153	A1L0X9|A4ZYV1|A8MVH5|Q6UXF3|Q8WUG3|Q8WYZ8	Missense_Mutation	SNP	ENST00000394957.3	37	CCDS31218.1	1|1	4.578754578754579E-4|4.578754578754579E-4	0|0	0.0|0.0	1|1	0.0027624309392265192|0.0027624309392265192	0|0	0.0|0.0	0|0	0.0|0.0	C|C	21.8|21.8	4.199161|4.199161	0.79015|0.79015	2.28E-4|2.28E-4	5.82E-4|5.82E-4	ENSG00000107738|ENSG00000107738	ENST00000394957|ENST00000263569	T|.	0.47528|.	0.84|.	3.91|3.91	3.0|3.0	0.34707|0.34707	.|.	0.571467|.	0.17287|.	N|.	0.179798|.	T|T	0.34948|0.34948	0.0915|0.0915	N|N	0.24115|0.24115	0.695|0.695	0.28462|0.28462	N|N	0.915816|0.915816	B|.	0.30482|.	0.281|.	B|.	0.29440|.	0.102|.	T|T	0.32745|0.32745	-0.9895|-0.9895	10|6	0.29301|0.87932	T|D	0.29|0	-0.9608|-0.9608	9.7011|9.7011	0.40187|0.40187	0.0:0.7891:0.2109:0.0|0.0:0.7891:0.2109:0.0	.|.	25|.	Q9H7M9|.	GI24_HUMAN|.	T|Y	25|48	ENSP00000378409:A25T|.	ENSP00000378409:A25T|ENSP00000263569:C48Y	A|C	-|-	1|2	0|0	C10orf54|C10orf54	73203130|73203130	0.018000|0.018000	0.18449|0.18449	1.000000|1.000000	0.80357|0.80357	0.974000|0.974000	0.67602|0.67602	0.381000|0.381000	0.20619|0.20619	1.226000|1.226000	0.43582|0.43582	0.455000|0.455000	0.32223|0.32223	GCG|TGC	C|0.999;T|0.001	0.001	strong		0.687	C10orf54-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048548.1	NM_022153	
AGBL1	123624	hgsc.bcm.edu	37	15	86790997	86790997	+	Missense_Mutation	SNP	G	G	A	rs149477284	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr15:86790997G>A	ENST00000441037.2	+	6	579	c.484G>A	c.(484-486)Gtg>Atg	p.V162M	AGBL1_ENST00000421325.2_Missense_Mutation_p.V162M	NM_152336.2	NP_689549.2	Q96MI9	CBPC4_HUMAN	ATP/GTP binding protein-like 1	162					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						CAACGCCTACGTGCAGATCCG	0.642													G|||	14	0.00279553	0.0	0.0029	5008	,	,		19735	0.0		0.0119	False		,,,				2504	0.0				p.V162M		Atlas-SNP	.											.	AGBL1	151	.	0			c.G484A						PASS	.	G	MET/VAL	12,4312		0,12,2150	37.0	39.0	38.0		484	1.9	0.0	15	dbSNP_134	38	103,8421		1,101,4160	yes	missense	AGBL1	NM_152336.2	21	1,113,6310	AA,AG,GG		1.2084,0.2775,0.8951	probably-damaging	162/1067	86790997	115,12733	2162	4262	6424	SO:0001583	missense	123624	exon6			GCCTACGTGCAGA	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.484G>A	15.37:g.86790997G>A	ENSP00000413001:p.Val162Met	98.0	0.0	0		115.0	58.0	0.504348	NM_152336	A1A4X5|A6NJH6|C9JHL5	Missense_Mutation	SNP	ENST00000441037.2	37	CCDS58398.1	10	0.004578754578754579	0	0.0	1	0.0027624309392265192	0	0.0	9	0.011873350923482849	G	0.010	-1.782928	0.00634	0.002775	0.012084	ENSG00000166748	ENST00000441037;ENST00000421325	T	0.33865	1.39	5.16	1.86	0.25419	Armadillo-like helical (1);Armadillo-type fold (1);	.	.	.	.	T	0.09730	0.0239	L	0.31207	0.915	0.80722	D	1	P	0.39352	0.669	B	0.20955	0.032	T	0.25082	-1.0142	9	0.05525	T	0.97	-7.5937	5.0261	0.14385	0.4866:0.0:0.5134:0.0	.	162	Q96MI9	CBPC4_HUMAN	M	191;162	ENSP00000397173:V162M	ENSP00000397173:V162M	V	+	1	0	AGBL1	84592001	0.099000	0.21834	0.007000	0.13788	0.085000	0.17905	0.616000	0.24344	0.575000	0.29434	-0.258000	0.10820	GTG	G|0.995;A|0.005	0.005	strong		0.642	AGBL1-001	KNOWN	not_organism_supported|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000314929.5	NM_152336	
AKR1B15	441282	hgsc.bcm.edu	37	7	134260595	134260595	+	Missense_Mutation	SNP	C	C	T	rs141101327	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr7:134260595C>T	ENST00000457545.2	+	8	919	c.659C>T	c.(658-660)aCg>aTg	p.T220M	AKR1B15_ENST00000423958.1_Missense_Mutation_p.T192M	NM_001080538.2	NP_001074007.2	C9JRZ8	AK1BF_HUMAN	aldo-keto reductase family 1, member B15	220							oxidoreductase activity (GO:0016491)			endometrium(1)|kidney(3)|large_intestine(2)|lung(10)|ovary(1)|urinary_tract(1)	18						CCATACCTCACGCAGGAGAAA	0.537													C|||	31	0.0061901	0.0015	0.0072	5008	,	,		18433	0.0		0.0179	False		,,,				2504	0.0061				p.T220M		Atlas-SNP	.											.	AKR1B15	105	.	0			c.C659T						PASS	.	C	MET/THR	15,4391	20.2+/-43.8	0,15,2188	152.0	118.0	129.0		659	3.0	0.7	7	dbSNP_134	129	137,8463	67.7+/-130.1	0,137,4163	no	missense	AKR1B15	NM_001080538.2	81	0,152,6351	TT,TC,CC		1.593,0.3404,1.1687	probably-damaging	220/345	134260595	152,12854	2203	4300	6503	SO:0001583	missense	441282	exon8			ACCTCACGCAGGA		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.659C>T	7.37:g.134260595C>T	ENSP00000389289:p.Thr220Met	598.0	0.0	0		616.0	220.0	0.357143	NM_001080538	C9J3V2	Missense_Mutation	SNP	ENST00000457545.2	37	CCDS47715.2	19	0.0086996336996337	1	0.0020325203252032522	2	0.0055248618784530384	0	0.0	16	0.021108179419525065	C	11.82	1.754067	0.31046	0.003404	0.01593	ENSG00000227471	ENST00000457545;ENST00000423958	T;T	0.17854	2.25;2.25	3.87	2.98	0.34508	NADP-dependent oxidoreductase domain (3);	.	.	.	.	T	0.18173	0.0436	L	0.56199	1.76	0.39942	D	0.974421	D;D	0.89917	1.0;1.0	D;D	0.97110	0.999;1.0	T	0.01810	-1.1269	9	0.72032	D	0.01	.	8.189	0.31357	0.0:0.7958:0.0:0.2042	.	192;220	C9JRZ8-2;C9JRZ8	.;AK1BF_HUMAN	M	220;192	ENSP00000389289:T220M;ENSP00000397009:T192M	ENSP00000397009:T192M	T	+	2	0	AKR1B15	133911135	0.025000	0.19082	0.699000	0.30290	0.184000	0.23303	0.640000	0.24705	0.810000	0.34279	0.537000	0.68136	ACG	C|0.991;T|0.009	0.009	strong		0.537	AKR1B15-001	PUTATIVE	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000339726.2		
KMT2C	58508	hgsc.bcm.edu	37	7	151970899	151970899	+	Silent	SNP	T	T	C	rs577540910		TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr7:151970899T>C	ENST00000262189.6	-	7	1121	c.903A>G	c.(901-903)aaA>aaG	p.K301K	KMT2C_ENST00000355193.2_Silent_p.K301K	NM_170606.2	NP_733751.2	Q8NEZ4	KMT2C_HUMAN	lysine (K)-specific methyltransferase 2C	301					histone H3-K4 methylation (GO:0051568)|intracellular signal transduction (GO:0035556)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	histone methyltransferase complex (GO:0035097)|nucleus (GO:0005634)	DNA binding (GO:0003677)|histone methyltransferase activity (H3-K4 specific) (GO:0042800)|poly(A) RNA binding (GO:0044822)|zinc ion binding (GO:0008270)										TCTGGGTACATTTCTCTTCAC	0.438													T|||	1	0.000199681	0.0	0.0	5008	,	,		26142	0.0		0.0	False		,,,				2504	0.001				p.K301K		Atlas-SNP	.											.	MLL3	1564	.	0			c.A903G						PASS	.						135.0	129.0	131.0					7																	151970899		2203	4300	6503	SO:0001819	synonymous_variant	58508	exon7			GGTACATTTCTCT	AF264750	CCDS5931.1	7q36	2013-05-09	2013-05-09	2013-05-09	ENSG00000055609	ENSG00000055609		"""Chromatin-modifying enzymes / K-methyltransferases"", ""Zinc fingers, PHD-type"""	13726	protein-coding gene	gene with protein product		606833	"""myeloid/lymphoid or mixed-lineage leukemia 3"""	MLL3		10819331	Standard	XM_005250026		Approved	KIAA1506, HALR		Q8NEZ4	OTTHUMG00000150553	ENST00000262189.6:c.903A>G	7.37:g.151970899T>C		385.0	0.0	0		360.0	23.0	0.0638889	NM_170606	Q8NC02|Q8NDF6|Q9H9P4|Q9NR13|Q9P222|Q9UDR7	Silent	SNP	ENST00000262189.6	37	CCDS5931.1																																																																																			.	.	none		0.438	KMT2C-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000318887.3		
SETD1B	23067	hgsc.bcm.edu	37	12	122248047	122248047	+	Missense_Mutation	SNP	C	C	T			TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr12:122248047C>T	ENST00000604567.1	+	6	1264	c.1196C>T	c.(1195-1197)cCg>cTg	p.P399L	SETD1B_ENST00000267197.5_Missense_Mutation_p.P399L|SETD1B_ENST00000542440.1_Missense_Mutation_p.P399L			Q9UPS6	SET1B_HUMAN	SET domain containing 1B	399	Pro-rich.				histone H3-K4 methylation (GO:0051568)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	chromosome (GO:0005694)|histone methyltransferase complex (GO:0035097)|nucleus (GO:0005634)|Set1C/COMPASS complex (GO:0048188)	histone-lysine N-methyltransferase activity (GO:0018024)|nucleotide binding (GO:0000166)|RNA binding (GO:0003723)			NS(1)|endometrium(6)|kidney(2)|prostate(2)	11						GCTTTCTCTCCGTATCAGACC	0.642																																					p.P399L		Atlas-SNP	.											.	SETD1B	105	.	0			c.C1196T						PASS	.						4.0	6.0	5.0					12																	122248047		685	1573	2258	SO:0001583	missense	23067	exon5			TCTCTCCGTATCA	AB028999	CCDS53838.1	12q24.31	2013-02-12			ENSG00000139718	ENSG00000139718		"""Chromatin-modifying enzymes / K-methyltransferases"", ""RNA binding motif (RRM) containing"""	29187	protein-coding gene	gene with protein product		611055				10470851, 17355966	Standard	NM_015048		Approved	KIAA1076, Set1B, KMT2G	uc001ubi.3	Q9UPS6	OTTHUMG00000169080	ENST00000604567.1:c.1196C>T	12.37:g.122248047C>T	ENSP00000474253:p.Pro399Leu	121.0	0.0	0		113.0	5.0	0.0442478	NM_015048	F6MFW1	Missense_Mutation	SNP	ENST00000604567.1	37		.	.	.	.	.	.	.	.	.	.	C	12.85	2.060661	0.36373	.	.	ENSG00000139718	ENST00000542440;ENST00000267197	D;D	0.94576	-3.46;-3.46	4.78	4.78	0.61160	.	.	.	.	.	D	0.96250	0.8777	L	0.60455	1.87	0.80722	D	1	D	0.89917	1.0	D	0.64506	0.926	D	0.96855	0.9628	9	0.72032	D	0.01	.	17.8068	0.88604	0.0:1.0:0.0:0.0	.	399	Q9UPS6	SET1B_HUMAN	L	399	ENSP00000442924:P399L;ENSP00000267197:P399L	ENSP00000267197:P399L	P	+	2	0	SETD1B	120732430	1.000000	0.71417	0.821000	0.32701	0.484000	0.33280	5.401000	0.66326	2.196000	0.70406	0.467000	0.42956	CCG	.	.	none		0.642	SETD1B-002	PUTATIVE	non_canonical_U12|basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000468264.1	XM_037523	
ELMOD2	255520	hgsc.bcm.edu	37	4	141464666	141464666	+	Missense_Mutation	SNP	G	G	A	rs148286208	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr4:141464666G>A	ENST00000323570.3	+	8	794	c.662G>A	c.(661-663)aGt>aAt	p.S221N		NM_153702.3	NP_714913.1	Q8IZ81	ELMD2_HUMAN	ELMO/CED-12 domain containing 2	221	ELMO. {ECO:0000255|PROSITE- ProRule:PRU00664}.				defense response to virus (GO:0051607)|phagocytosis (GO:0006909)|positive regulation of GTPase activity (GO:0043547)|regulation of defense response to virus (GO:0050688)	cytoskeleton (GO:0005856)|membrane (GO:0016020)	GTPase activator activity (GO:0005096)			endometrium(1)|kidney(1)|large_intestine(2)|lung(1)|ovary(1)|upper_aerodigestive_tract(1)	7	all_hematologic(180;0.162)					TTACTGAAGAGTGAAGCTTTG	0.338													G|||	3	0.000599042	0.0	0.0	5008	,	,		14795	0.0		0.003	False		,,,				2504	0.0				p.S221N		Atlas-SNP	.											.	ELMOD2	16	.	0			c.G662A						PASS	.	G	ASN/SER	3,4403	6.2+/-15.9	0,3,2200	114.0	114.0	114.0		662	5.3	1.0	4	dbSNP_134	114	11,8573	7.7+/-29.5	0,11,4281	yes	missense	ELMOD2	NM_153702.3	46	0,14,6481	AA,AG,GG		0.1281,0.0681,0.1078	benign	221/294	141464666	14,12976	2203	4292	6495	SO:0001583	missense	255520	exon8			TGAAGAGTGAAGC	BX648349	CCDS3752.1	4q31.1	2006-10-24	2006-01-20		ENSG00000179387	ENSG00000179387			28111	protein-coding gene	gene with protein product		610196	"""ELMO domain containing 2"""			16773575	Standard	NM_153702		Approved	MGC10084	uc003iik.3	Q8IZ81	OTTHUMG00000133417	ENST00000323570.3:c.662G>A	4.37:g.141464666G>A	ENSP00000326342:p.Ser221Asn	81.0	0.0	0		94.0	36.0	0.382979	NM_153702	B2R712|D3DNZ0	Missense_Mutation	SNP	ENST00000323570.3	37	CCDS3752.1	3	0.0013736263736263737	0	0.0	0	0.0	0	0.0	3	0.00395778364116095	G	15.68	2.905457	0.52333	6.81E-4	0.001281	ENSG00000179387	ENST00000323570	T	0.30448	1.53	6.16	5.33	0.75918	Engulfment/cell motility, ELMO (2);	0.159239	0.64402	N	0.000001	T	0.26991	0.0661	L	0.51914	1.62	0.42822	D	0.993998	B	0.17038	0.02	B	0.22601	0.04	T	0.08493	-1.0719	10	0.18276	T	0.48	-4.9602	10.0032	0.41942	0.1887:0.0:0.8113:0.0	.	221	Q8IZ81	ELMD2_HUMAN	N	221	ENSP00000326342:S221N	ENSP00000326342:S221N	S	+	2	0	ELMOD2	141684116	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	1.898000	0.39809	1.631000	0.50456	0.650000	0.86243	AGT	A|0.001;G|0.999	0.001	strong		0.338	ELMOD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257277.2	NM_153702	
SCN4A	6329	hgsc.bcm.edu	37	17	62036738	62036738	+	Missense_Mutation	SNP	C	C	T			TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr17:62036738C>T	ENST00000435607.1	-	12	1982	c.1906G>A	c.(1906-1908)Gag>Aag	p.E636K	SCN4A_ENST00000578147.1_Missense_Mutation_p.E636K	NM_000334.4	NP_000325.4	P35499	SCN4A_HUMAN	sodium channel, voltage-gated, type IV, alpha subunit	636					membrane depolarization during action potential (GO:0086010)|muscle contraction (GO:0006936)|neuronal action potential (GO:0019228)|sodium ion transmembrane transport (GO:0035725)|sodium ion transport (GO:0006814)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|voltage-gated sodium channel complex (GO:0001518)	voltage-gated sodium channel activity (GO:0005248)			breast(4)|central_nervous_system(3)|cervix(1)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(23)|lung(40)|ovary(3)|pancreas(1)|prostate(6)|skin(4)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	101					Diclofenac(DB00586)|Flecainide(DB01195)|Propofol(DB00818)|Valproic Acid(DB00313)|Zonisamide(DB00909)	TGGAAATACTCGTAGGGGTCC	0.562																																					p.E636K		Atlas-SNP	.											.	SCN4A	205	.	0			c.G1906A						PASS	.						83.0	85.0	85.0					17																	62036738		2063	4230	6293	SO:0001583	missense	6329	exon12			AATACTCGTAGGG	U24693		17q23.3	2012-02-26	2007-01-23					"""Sodium channels"", ""Voltage-gated ion channels / Sodium channels"""	10591	protein-coding gene	gene with protein product		603967		HYKPP		1654742, 1659948, 16382098	Standard	XM_005257566		Approved	Nav1.4, HYPP, SkM1	uc002jds.1	P35499		ENST00000435607.1:c.1906G>A	17.37:g.62036738C>T	ENSP00000396320:p.Glu636Lys	151.0	0.0	0		141.0	69.0	0.489362	NM_000334	Q15478|Q16447|Q7Z6B1	Missense_Mutation	SNP	ENST00000435607.1	37	CCDS45761.1	.	.	.	.	.	.	.	.	.	.	C	19.35	3.810092	0.70797	.	.	ENSG00000007314	ENST00000435607	D	0.98362	-4.89	4.74	4.74	0.60224	Ion transport (1);	0.119294	0.56097	D	0.000022	D	0.94258	0.8156	N	0.20530	0.585	0.39768	D	0.972125	B	0.30281	0.275	B	0.24541	0.054	D	0.93435	0.6789	10	0.44086	T	0.13	.	12.1023	0.53792	0.1716:0.8284:0.0:0.0	.	636	P35499	SCN4A_HUMAN	K	636	ENSP00000396320:E636K	ENSP00000396320:E636K	E	-	1	0	SCN4A	59390470	0.996000	0.38824	1.000000	0.80357	0.927000	0.56198	3.358000	0.52284	2.481000	0.83766	0.556000	0.70494	GAG	.	.	none		0.562	SCN4A-201	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding		NM_000334	
NLRP4	147945	hgsc.bcm.edu	37	19	56369914	56369914	+	Silent	SNP	C	C	T	rs113444208	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr19:56369914C>T	ENST00000301295.6	+	3	1577	c.1155C>T	c.(1153-1155)gcC>gcT	p.A385A	NLRP4_ENST00000587891.1_Silent_p.A310A|NLRP4_ENST00000346986.5_Silent_p.A385A	NM_134444.4	NP_604393.2	Q96MN2	NALP4_HUMAN	NLR family, pyrin domain containing 4	385	NACHT. {ECO:0000255|PROSITE- ProRule:PRU00136}.				inflammatory response (GO:0006954)|innate immune response (GO:0045087)|positive regulation of type I interferon production (GO:0032481)|regulation of type I interferon production (GO:0032479)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)	ATP binding (GO:0005524)			breast(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(14)|lung(3)|ovary(6)|pancreas(1)|skin(5)|stomach(1)|upper_aerodigestive_tract(8)	42		Colorectal(82;0.0002)|Ovarian(87;0.221)		GBM - Glioblastoma multiforme(193;0.0606)		CTGAGGGTGCCGAGGGCCCGA	0.557													C|||	21	0.00419329	0.0008	0.0	5008	,	,		17743	0.0		0.006	False		,,,				2504	0.0143				p.A385A		Atlas-SNP	.											.	NLRP4	331	.	0			c.C1155T						PASS	.	C		15,4391	23.3+/-48.9	0,15,2188	55.0	52.0	53.0		1155	-7.7	0.0	19	dbSNP_132	53	50,8550	31.7+/-84.0	0,50,4250	no	coding-synonymous	NLRP4	NM_134444.4		0,65,6438	TT,TC,CC		0.5814,0.3404,0.4998		385/995	56369914	65,12941	2203	4300	6503	SO:0001819	synonymous_variant	147945	exon3			GGGTGCCGAGGGC	AF479747	CCDS12936.1	19q13.43	2009-03-27	2006-12-08	2006-12-08				"""Nucleotide-binding domain and leucine rich repeat containing"""	22943	protein-coding gene	gene with protein product	"""nucleotide-binding oligomerization domain, leucine rich repeat and pyrin domain containing 4"", ""cancer/testis antigen 58"""	609645	"""NACHT, leucine rich repeat and PYD containing 4"""	NALP4		12563287, 12019269	Standard	NM_134444		Approved	PYPAF4, FLJ32126, PAN2, RNH2, CLR19.5, CT58	uc002qmd.4	Q96MN2		ENST00000301295.6:c.1155C>T	19.37:g.56369914C>T		53.0	0.0	0		73.0	33.0	0.452055	NM_134444	Q86W87|Q96AY6	Silent	SNP	ENST00000301295.6	37	CCDS12936.1																																																																																			C|0.996;T|0.004	0.004	strong		0.557	NLRP4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000457367.2	NM_134444	
RNASE1	6035	hgsc.bcm.edu	37	14	21269811	21269811	+	Missense_Mutation	SNP	T	T	A			TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr14:21269811T>A	ENST00000397967.4	-	2	923	c.417A>T	c.(415-417)gaA>gaT	p.E139D	RNASE1_ENST00000555698.1_Missense_Mutation_p.E99D|RNASE1_ENST00000340900.3_Missense_Mutation_p.E139D|RNASE1_ENST00000397970.4_Missense_Mutation_p.E139D|RNASE1_ENST00000412779.2_Missense_Mutation_p.E139D	NM_002933.4	NP_002924.1	P07998	RNAS1_HUMAN	ribonuclease, RNase A family, 1 (pancreatic)	139					RNA phosphodiester bond hydrolysis, endonucleolytic (GO:0090502)	extracellular vesicular exosome (GO:0070062)	nucleic acid binding (GO:0003676)|pancreatic ribonuclease activity (GO:0004522)			central_nervous_system(1)|large_intestine(1)|lung(1)|ovary(1)|upper_aerodigestive_tract(1)	5	all_cancers(95;0.00671)	all_lung(585;0.235)	Epithelial(56;9.21e-07)|all cancers(55;2.9e-06)	GBM - Glioblastoma multiforme(265;0.0126)	Guanidine(DB00536)|L-Aspartic Acid(DB00128)	ATGGGCTCCCTTCACAGGCCA	0.567																																					p.E139D		Atlas-SNP	.											.	RNASE1	14	.	0			c.A417T						PASS	.						151.0	132.0	138.0					14																	21269811		2203	4300	6503	SO:0001583	missense	6035	exon3			GCTCCCTTCACAG	BC005324	CCDS9559.1	14q11.2	2014-03-13			ENSG00000129538	ENSG00000129538	3.1.27.5	"""Ribonucleases, RNase A"""	10044	protein-coding gene	gene with protein product		180440		RNS1		8588814	Standard	NM_002933		Approved		uc001vyi.3	P07998	OTTHUMG00000029603	ENST00000397967.4:c.417A>T	14.37:g.21269811T>A	ENSP00000381057:p.Glu139Asp	213.0	0.0	0		194.0	105.0	0.541237	NM_198235	B2R589|D3DS06|Q16830|Q16869|Q1KHR2|Q6ICS5|Q9UCB4|Q9UCB5	Missense_Mutation	SNP	ENST00000397967.4	37	CCDS9559.1	.	.	.	.	.	.	.	.	.	.	T	12.24	1.877944	0.33162	.	.	ENSG00000129538	ENST00000397967;ENST00000340900;ENST00000412779;ENST00000555698;ENST00000397970	T;T;T;T;T	0.46063	0.88;0.88;0.88;0.88;0.88	5.21	1.28	0.21552	Ribonuclease A, domain (4);	0.527449	0.18611	N	0.136179	T	0.31888	0.0811	L	0.50333	1.59	0.30340	N	0.785825	B	0.02656	0.0	B	0.04013	0.001	T	0.21586	-1.0241	10	0.51188	T	0.08	-29.0622	5.056	0.14533	0.0:0.4831:0.3303:0.1866	.	139	P07998	RNAS1_HUMAN	D	139;139;139;99;139	ENSP00000381057:E139D;ENSP00000344193:E139D;ENSP00000399493:E139D;ENSP00000451058:E99D;ENSP00000381060:E139D	ENSP00000344193:E139D	E	-	3	2	RNASE1	20339651	0.268000	0.24133	0.971000	0.41717	0.601000	0.36947	-0.503000	0.06383	0.056000	0.16144	-0.248000	0.11899	GAA	.	.	none		0.567	RNASE1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000073791.3		
PLEKHM1	9842	hgsc.bcm.edu	37	17	43552812	43552812	+	Silent	SNP	A	A	G	rs71227520	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr17:43552812A>G	ENST00000430334.3	-	4	710	c.577T>C	c.(577-579)Ttg>Ctg	p.L193L	PLEKHM1_ENST00000421073.2_Silent_p.L104L	NM_014798.2	NP_055613.1	Q9Y4G2	PKHM1_HUMAN	pleckstrin homology domain containing, family M (with RUN domain) member 1	193					intracellular signal transduction (GO:0035556)	cytoplasm (GO:0005737)	metal ion binding (GO:0046872)			breast(1)|central_nervous_system(1)|endometrium(6)|large_intestine(1)|lung(10)|prostate(1)|skin(3)|upper_aerodigestive_tract(2)|urinary_tract(1)	26	Renal(3;0.0405)					GACAGGGCCAATGGGGTGAGC	0.552													G|||	378	0.0754792	0.034	0.1412	5008	,	,		21329	0.001		0.1819	False		,,,				2504	0.0521				p.L193L		Atlas-SNP	.											.	PLEKHM1	69	.	0			c.T577C						PASS	.						66.0	58.0	60.0					17																	43552812		2199	4249	6448	SO:0001819	synonymous_variant	9842	exon4			GGGCCAATGGGGT	X85792	CCDS32671.1	17q21.31	2013-01-11				ENSG00000225190		"""Pleckstrin homology (PH) domain containing"""	29017	protein-coding gene	gene with protein product		611466				9205841, 12820725	Standard	NM_014798		Approved	KIAA0356	uc002ija.3	Q9Y4G2		ENST00000430334.3:c.577T>C	17.37:g.43552812A>G		194.0	0.0	0		106.0	105.0	0.990566	NM_014798	Q6P2R5|Q8TEL9|Q9NPP5|Q9NYA0	Silent	SNP	ENST00000430334.3	37	CCDS32671.1																																																																																			A|0.925;G|0.075	0.075	strong		0.552	PLEKHM1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000444659.1	NM_014798	
DCLK3	85443	hgsc.bcm.edu	37	3	36779992	36779992	+	Silent	SNP	G	G	A	rs55888784	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr3:36779992G>A	ENST00000416516.2	-	2	649	c.159C>T	c.(157-159)cgC>cgT	p.R53R		NM_033403.1	NP_208382.1	Q9C098	DCLK3_HUMAN	doublecortin-like kinase 3	53						cytoplasm (GO:0005737)|nucleus (GO:0005634)	ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)			breast(3)|endometrium(3)|kidney(2)|large_intestine(11)|lung(20)|ovary(2)|pancreas(1)|prostate(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(2)	48						TCTCCCCACAGCGGTGGTCTC	0.617													G|||	44	0.00878594	0.0008	0.013	5008	,	,		16590	0.001		0.0298	False		,,,				2504	0.0031				p.R53R		Atlas-SNP	.											DCLK3,NS,carcinoma,-2,1	DCLK3	95	1	0			c.C159T						PASS	.	G		12,3870		0,12,1929	75.0	78.0	77.0		159	1.1	0.1	3	dbSNP_129	77	220,8064		4,212,3926	no	coding-synonymous	DCLK3	NM_033403.1		4,224,5855	AA,AG,GG		2.6557,0.3091,1.907		53/649	36779992	232,11934	1941	4142	6083	SO:0001819	synonymous_variant	85443	exon2			CCCACAGCGGTGG	AB051552	CCDS43064.1	3p22.3	2007-04-02	2007-04-02	2007-04-02	ENSG00000163673	ENSG00000163673			19005	protein-coding gene	gene with protein product		613167	"""doublecortin and CaM kinase-like 3"""	DCAMKL3		11214970, 16869982	Standard	NM_033403		Approved	KIAA1765, DCDC3C	uc003cgi.2	Q9C098	OTTHUMG00000155805	ENST00000416516.2:c.159C>T	3.37:g.36779992G>A		113.0	0.0	0		106.0	58.0	0.54717	NM_033403		Silent	SNP	ENST00000416516.2	37	CCDS43064.1																																																																																			G|0.982;A|0.018	0.018	strong		0.617	DCLK3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000341727.1	XM_047355	
PXK	54899	hgsc.bcm.edu	37	3	58376938	58376938	+	Silent	SNP	G	G	A	rs55962533	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr3:58376938G>A	ENST00000356151.2	+	6	640	c.531G>A	c.(529-531)gtG>gtA	p.V177V	PXK_ENST00000463280.1_Silent_p.V144V|PXK_ENST00000302779.5_Silent_p.V160V|PXK_ENST00000484288.1_Silent_p.V177V|PXK_ENST00000536660.1_Silent_p.V40V|PXK_ENST00000383715.4_Silent_p.V160V|PXK_ENST00000479241.1_Silent_p.V160V|PXK_ENST00000383716.3_Silent_p.V144V	NM_017771.3	NP_060241.2			PX domain containing serine/threonine kinase											cervix(1)|endometrium(1)|kidney(1)|large_intestine(3)|lung(10)|ovary(1)|skin(1)|urinary_tract(1)	19				BRCA - Breast invasive adenocarcinoma(55;0.000249)|KIRC - Kidney renal clear cell carcinoma(10;0.00346)|Kidney(10;0.00368)|OV - Ovarian serous cystadenocarcinoma(275;0.22)		AACGGCTAGTGTTAAGCTGGG	0.373													G|||	16	0.00319489	0.0	0.0029	5008	,	,		17947	0.0		0.0129	False		,,,				2504	0.001				p.V177V		Atlas-SNP	.											.	PXK	89	.	0			c.G531A						PASS	.	G		19,4387	26.2+/-53.5	0,19,2184	90.0	95.0	93.0		531	1.8	1.0	3	dbSNP_129	93	110,8490	59.5+/-121.1	1,108,4191	no	coding-synonymous	PXK	NM_017771.3		1,127,6375	AA,AG,GG		1.2791,0.4312,0.9918		177/579	58376938	129,12877	2203	4300	6503	SO:0001819	synonymous_variant	54899	exon6			GCTAGTGTTAAGC	AY274811	CCDS2889.1, CCDS74952.1, CCDS74954.1, CCDS74955.1	3p21.2	2008-02-05			ENSG00000168297	ENSG00000168297			23326	protein-coding gene	gene with protein product		611450					Standard	XM_005265255		Approved	FLJ20335	uc003djz.1	Q7Z7A4	OTTHUMG00000159149	ENST00000356151.2:c.531G>A	3.37:g.58376938G>A		65.0	0.0	0		68.0	36.0	0.529412	NM_017771		Silent	SNP	ENST00000356151.2	37	CCDS2889.1																																																																																			G|0.991;A|0.009	0.009	strong		0.373	PXK-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000353499.1	NM_017771	
AK2	204	hgsc.bcm.edu	37	1	33478841	33478841	+	Missense_Mutation	SNP	C	C	T	rs201817938		TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr1:33478841C>T	ENST00000373449.2	-	6	702	c.661G>A	c.(661-663)Gca>Aca	p.A221T	AK2_ENST00000480134.1_3'UTR|AK2_ENST00000467905.1_Missense_Mutation_p.A221T|AK2_ENST00000354858.6_Missense_Mutation_p.A221T|AK2_ENST00000491241.1_5'UTR|RP1-117O3.2_ENST00000427524.1_RNA|AK2_ENST00000548033.1_Missense_Mutation_p.A179T	NM_001199199.1|NM_013411.4	NP_001186128.1|NP_037543.1			adenylate kinase 2											kidney(1)|large_intestine(2)|lung(4)|skin(1)	8		Myeloproliferative disorder(586;0.0255)|all_neural(195;0.0837)				AGGATGCTTGCGAACACGACA	0.507																																					p.A221T		Atlas-SNP	.											.	AK2	27	.	0			c.G661A						PASS	.						161.0	147.0	152.0					1																	33478841		2203	4300	6503	SO:0001583	missense	204	exon6			TGCTTGCGAACAC	U84371	CCDS373.1, CCDS374.1	1p35.1	2014-09-17			ENSG00000004455	ENSG00000004455	2.7.4.3	"""Adenylate kinases"""	362	protein-coding gene	gene with protein product		103020				8843353, 6961883	Standard	NM_013411		Approved		uc001bwp.2	P54819	OTTHUMG00000004131	ENST00000373449.2:c.661G>A	1.37:g.33478841C>T	ENSP00000362548:p.Ala221Thr	157.0	0.0	0		147.0	54.0	0.367347	NM_013411		Missense_Mutation	SNP	ENST00000373449.2	37	CCDS373.1	.	.	.	.	.	.	.	.	.	.	C	14.94	2.685133	0.47991	.	.	ENSG00000004455	ENST00000373449;ENST00000548033;ENST00000467905;ENST00000354858	T;T;T;T	0.77489	-1.1;-1.1;-1.1;-1.1	5.17	4.26	0.50523	.	0.000000	0.85682	D	0.000000	T	0.66257	0.2771	N	0.24115	0.695	0.80722	D	1	B;B;B;B	0.22480	0.006;0.07;0.004;0.003	B;B;B;B	0.19148	0.003;0.024;0.001;0.002	T	0.64433	-0.6409	10	0.51188	T	0.08	-11.7289	14.769	0.69662	0.0:0.9289:0.0:0.0711	.	213;179;221;221	P54819-5;F8VY04;P54819;P54819-2	.;.;KAD2_HUMAN;.	T	221;179;221;221	ENSP00000362548:A221T;ENSP00000449003:A179T;ENSP00000447082:A221T;ENSP00000346921:A221T	ENSP00000346921:A221T	A	-	1	0	AK2	33251428	1.000000	0.71417	0.957000	0.39632	0.542000	0.35054	6.063000	0.71162	1.499000	0.48617	0.563000	0.77884	GCA	.	.	weak		0.507	AK2-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000011884.1	NM_001625	
NBPF14	25832	hgsc.bcm.edu	37	1	148009437	148009437	+	Missense_Mutation	SNP	C	C	T			TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr1:148009437C>T	ENST00000369219.1	-	16	1886	c.1870G>A	c.(1870-1872)Ggt>Agt	p.G624S				Q5TI25	NBPFE_HUMAN	neuroblastoma breakpoint family, member 14	624	NBPF 7. {ECO:0000255|PROSITE- ProRule:PRU00647}.					cytoplasm (GO:0005737)				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)					TCAAGACAACCTGAAGGAGTT	0.483																																					p.G624S		Atlas-SNP	.											.	NBPF14	107	.	0			c.G1870A						PASS	.						128.0	260.0	221.0					1																	148009437		1703	4065	5768	SO:0001583	missense	25832	exon16			GACAACCTGAAGG	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.1870G>A	1.37:g.148009437C>T	ENSP00000358221:p.Gly624Ser	172.0	0.0	0		262.0	17.0	0.0648855	NM_015383	Q5TI23|Q8IX76|Q9UJI9	Missense_Mutation	SNP	ENST00000369219.1	37		.	.	.	.	.	.	.	.	.	.	c	1.168	-0.641686	0.03531	.	.	ENSG00000122497	ENST00000369219;ENST00000434489	T	0.05382	3.45	.	.	.	DUF1220 (2);	.	.	.	.	T	0.01124	0.0037	L	0.33792	1.035	0.09310	N	1	.	.	.	.	.	.	T	0.46247	-0.9205	4	0.06625	T	0.88	.	.	.	.	.	624	Q5TI25	NBPFE_HUMAN	S	624;214	ENSP00000358221:G624S	ENSP00000358221:G624S	G	-	1	0	NBPF14	146476061	0.982000	0.34865	.	.	.	.	-1.256000	0.02869	.	.	.	.	GGT	.	.	none		0.483	NBPF14-201	KNOWN	basic|appris_principal	protein_coding	protein_coding		NM_015383	
CDC42EP1	11135	hgsc.bcm.edu	37	22	37962583	37962583	+	Missense_Mutation	SNP	G	G	A	rs61739954	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr22:37962583G>A	ENST00000249014.4	+	2	647	c.227G>A	c.(226-228)cGc>cAc	p.R76H		NM_152243.2	NP_689449.1	Q00587	BORG5_HUMAN	CDC42 effector protein (Rho GTPase binding) 1	76					positive regulation of pseudopodium assembly (GO:0031274)|regulation of cell shape (GO:0008360)|Rho protein signal transduction (GO:0007266)	actin cytoskeleton (GO:0015629)|cytoplasm (GO:0005737)|focal adhesion (GO:0005925)|Golgi apparatus (GO:0005794)|plasma membrane (GO:0005886)				endometrium(2)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(2)|lung(4)|prostate(5)	15	Melanoma(58;0.0574)					AGCACCCATCGCTCACCCCGC	0.701													G|||	69	0.013778	0.0477	0.0043	5008	,	,		14619	0.0		0.003	False		,,,				2504	0.0				p.R76H		Atlas-SNP	.											CDC42EP1,colon,carcinoma,0,1	CDC42EP1	53	1	0			c.G227A						PASS	.	G	HIS/ARG	235,4171	133.3+/-169.7	4,227,1972	31.0	31.0	31.0		227	4.7	1.0	22	dbSNP_129	31	33,8565	21.6+/-65.8	0,33,4266	yes	missense	CDC42EP1	NM_152243.2	29	4,260,6238	AA,AG,GG		0.3838,5.3336,2.0609	probably-damaging	76/392	37962583	268,12736	2203	4299	6502	SO:0001583	missense	11135	exon2			CCCATCGCTCACC	M88338	CCDS13949.1	22q13.1	2008-06-11			ENSG00000128283	ENSG00000128283			17014	protein-coding gene	gene with protein product	"""55 kDa bone marrow stromal/endothelial cell protein"", ""serum constituent protein"""	606084				1629197, 10430899	Standard	NM_152243		Approved	MSE55, CEP1, Borg5	uc003asz.4	Q00587	OTTHUMG00000150591	ENST00000249014.4:c.227G>A	22.37:g.37962583G>A	ENSP00000249014:p.Arg76His	153.0	0.0	0		135.0	59.0	0.437037	NM_152243	A8K825|Q96GN1	Missense_Mutation	SNP	ENST00000249014.4	37	CCDS13949.1	24	0.01098901098901099	23	0.046747967479674794	1	0.0027624309392265192	0	0.0	0	0.0	G	17.07	3.295024	0.60086	0.053336	0.003838	ENSG00000128283	ENST00000249014	T	0.32515	1.45	4.7	4.7	0.59300	.	0.376263	0.27331	N	0.019849	T	0.04092	0.0114	L	0.29908	0.895	0.31658	N	0.64598	D	0.58620	0.983	P	0.46208	0.507	T	0.03545	-1.1026	10	0.42905	T	0.14	-24.6436	8.6301	0.33915	0.0834:0.2361:0.6805:0.0	rs61739954	76	Q00587	BORG5_HUMAN	H	76	ENSP00000249014:R76H	ENSP00000249014:R76H	R	+	2	0	CDC42EP1	36292529	1.000000	0.71417	1.000000	0.80357	0.943000	0.58893	1.119000	0.31258	2.429000	0.82318	0.563000	0.77884	CGC	G|0.980;A|0.020	0.020	strong		0.701	CDC42EP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318993.1	NM_152243	
PLEKHG4B	153478	hgsc.bcm.edu	37	5	163099	163099	+	Missense_Mutation	SNP	C	C	T			TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr5:163099C>T	ENST00000283426.6	+	11	1894	c.1844C>T	c.(1843-1845)gCc>gTc	p.A615V		NM_052909.3	NP_443141.3	Q96PX9	PKH4B_HUMAN	pleckstrin homology domain containing, family G (with RhoGef domain) member 4B	615							Rho guanyl-nucleotide exchange factor activity (GO:0005089)			endometrium(1)|large_intestine(2)|lung(2)|prostate(3)|skin(3)	11			all cancers(22;0.0253)|Lung(60;0.113)	Kidney(1;0.119)		CCGCCCCTTGCCCAGAGCCCC	0.657																																					p.A615V		Atlas-SNP	.											.	PLEKHG4B	167	.	0			c.C1844T						PASS	.						14.0	14.0	14.0					5																	163099		2168	4267	6435	SO:0001583	missense	153478	exon11			CCCTTGCCCAGAG	BC008352	CCDS34124.1	5p15.33	2013-01-11			ENSG00000153404	ENSG00000153404		"""Pleckstrin homology (PH) domain containing"""	29399	protein-coding gene	gene with protein product						11572484	Standard	NM_052909		Approved	KIAA1909	uc003jak.2	Q96PX9	OTTHUMG00000161570	ENST00000283426.6:c.1844C>T	5.37:g.163099C>T	ENSP00000283426:p.Ala615Val	147.0	0.0	0		138.0	76.0	0.550725	NM_052909		Missense_Mutation	SNP	ENST00000283426.6	37	CCDS34124.1	.	.	.	.	.	.	.	.	.	.	C	7.808	0.715147	0.15306	.	.	ENSG00000153404	ENST00000283426	D	0.92099	-2.97	2.71	-5.43	0.02632	.	.	.	.	.	T	0.75874	0.3909	N	0.08118	0	0.09310	N	1	B	0.02656	0.0	B	0.04013	0.001	T	0.62671	-0.6805	9	0.27785	T	0.31	.	0.5644	0.00684	0.2612:0.3176:0.2217:0.1994	.	615	Q96PX9	PKH4B_HUMAN	V	615	ENSP00000283426:A615V	ENSP00000283426:A615V	A	+	2	0	PLEKHG4B	216099	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-2.238000	0.01199	-1.825000	0.01207	-0.670000	0.03821	GCC	.	.	none		0.657	PLEKHG4B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000365359.1	NM_052909	
CDHR1	92211	hgsc.bcm.edu	37	10	85978958	85978958	+	IGR	SNP	G	G	A	rs529093147	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr10:85978958G>A	ENST00000372117.3	+	0	5428				CDHR1_ENST00000332904.3_Missense_Mutation_p.E722K	NM_033100.2	NP_149091.1	Q96JP9	CDHR1_HUMAN	cadherin-related family member 1						cellular process (GO:0009987)|homophilic cell adhesion (GO:0007156)|photoreceptor cell maintenance (GO:0045494)	integral component of plasma membrane (GO:0005887)|photoreceptor outer segment membrane (GO:0042622)	calcium ion binding (GO:0005509)			breast(1)|cervix(1)|endometrium(2)|kidney(1)|large_intestine(6)|liver(1)|lung(21)|ovary(1)|prostate(1)|skin(1)	36						TCCCCACTGCGAAATTGCCTT	0.403													G|||	6	0.00119808	0.0	0.0	5008	,	,		18511	0.0		0.0	False		,,,				2504	0.0061				p.E722K		Atlas-SNP	.											CDHR1_ENST00000332904,colon,carcinoma,0,3	CDHR1	122	3	0			c.G2164A						PASS	.																																			SO:0001628	intergenic_variant	92211	exon17			CACTGCGAAATTG	AB053448	CCDS7372.1, CCDS53548.1	10q23.1	2014-01-28	2010-01-25	2010-01-25	ENSG00000148600	ENSG00000148600		"""Cadherins / Cadherin-related"""	14550	protein-coding gene	gene with protein product		609502	"""protocadherin 21"""	PCDH21		11597768	Standard	NM_001171971		Approved	KIAA1775, CORD15, RP65	uc001kcv.3	Q96JP9	OTTHUMG00000018634		10.37:g.85978958G>A		117.0	0.0	0		80.0	36.0	0.45	NM_001171971	Q69YZ8|Q8IXY5	Missense_Mutation	SNP	ENST00000372117.3	37	CCDS7372.1	.	.	.	.	.	.	.	.	.	.	G	8.654	0.898947	0.17686	.	.	ENSG00000148600	ENST00000332904	T	0.56776	0.44	2.11	1.17	0.20885	.	.	.	.	.	T	0.24392	0.0591	.	.	.	0.09310	N	1	B	0.13145	0.007	B	0.04013	0.001	T	0.24728	-1.0152	8	0.06099	T	0.92	.	6.5893	0.22638	0.0:0.6863:0.3137:0.0	.	722	Q96JP9-2	.	K	722	ENSP00000331063:E722K	ENSP00000331063:E722K	E	+	1	0	CDHR1	85968938	0.000000	0.05858	0.002000	0.10522	0.011000	0.07611	-0.065000	0.11617	0.445000	0.26639	-0.147000	0.13772	GAA	.	.	none		0.403	CDHR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049111.1	NM_033100	
SLC26A8	116369	hgsc.bcm.edu	37	6	35911856	35911856	+	Missense_Mutation	SNP	G	G	A	rs61741366	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr6:35911856G>A	ENST00000490799.1	-	20	3087	c.2734C>T	c.(2734-2736)Ccc>Tcc	p.P912S	SLC26A8_ENST00000394602.2_Missense_Mutation_p.P807S|SLC26A8_ENST00000355574.2_Missense_Mutation_p.P912S	NM_052961.3	NP_443193.1			solute carrier family 26 (anion exchanger), member 8											breast(1)|central_nervous_system(1)|cervix(2)|endometrium(2)|kidney(4)|large_intestine(6)|lung(16)|ovary(3)|prostate(6)|skin(3)|upper_aerodigestive_tract(2)	46						TTGGGGTTGGGCTCCATCTCA	0.572													G|||	13	0.00259585	0.0008	0.0043	5008	,	,		18402	0.0		0.006	False		,,,				2504	0.0031				p.P912S		Atlas-SNP	.											.	SLC26A8	95	.	0			c.C2734T						PASS	.	G	SER/PRO,SER/PRO,SER/PRO	13,4393	20.2+/-43.8	0,13,2190	179.0	156.0	164.0		2734,2734,2419	0.5	0.0	6	dbSNP_129	164	101,8499	56.0+/-117.1	1,99,4200	yes	missense,missense,missense	SLC26A8	NM_001193476.1,NM_052961.3,NM_138718.2	74,74,74	1,112,6390	AA,AG,GG		1.1744,0.2951,0.8765	probably-damaging,probably-damaging,probably-damaging	912/971,912/971,807/866	35911856	114,12892	2203	4300	6503	SO:0001583	missense	116369	exon20			GGTTGGGCTCCAT	AF331522	CCDS4813.1, CCDS4814.1	6p21	2013-07-18	2013-07-18		ENSG00000112053	ENSG00000112053		"""Solute carriers"""	14468	protein-coding gene	gene with protein product		608480	"""solute carrier family 26, member 8"""			11834742, 11829495	Standard	NM_001193476		Approved		uc003olm.3	Q96RN1	OTTHUMG00000014586	ENST00000490799.1:c.2734C>T	6.37:g.35911856G>A	ENSP00000417638:p.Pro912Ser	275.0	0.0	0		303.0	138.0	0.455446	NM_052961		Missense_Mutation	SNP	ENST00000490799.1	37	CCDS4813.1	6	0.0027472527472527475	1	0.0020325203252032522	1	0.0027624309392265192	0	0.0	4	0.005277044854881266	G	9.857	1.195367	0.22037	0.002951	0.011744	ENSG00000112053	ENST00000490799;ENST00000394602;ENST00000355574	T;T;T	0.61274	0.12;0.12;0.12	3.3	0.505	0.16953	.	0.691418	0.12766	N	0.440964	T	0.19005	0.0456	L	0.29908	0.895	0.09310	N	1	B;B;B	0.26602	0.079;0.06;0.154	B;B;B	0.28784	0.014;0.056;0.094	T	0.24083	-1.0170	10	0.24483	T	0.36	.	5.426	0.16425	0.3874:0.0:0.6126:0.0	.	912;807;494	Q96RN1;Q96RN1-2;Q96RN1-3	S26A8_HUMAN;.;.	S	912;807;912	ENSP00000417638:P912S;ENSP00000378100:P807S;ENSP00000347778:P912S	ENSP00000347778:P912S	P	-	1	0	SLC26A8	36019834	0.365000	0.25006	0.009000	0.14445	0.037000	0.13140	1.727000	0.38095	0.080000	0.16959	-0.150000	0.13652	CCC	G|0.993;A|0.007	0.007	strong		0.572	SLC26A8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040325.2		
MYO1H	283446	hgsc.bcm.edu	37	12	109838954	109838954	+	Silent	SNP	C	C	T	rs138935511	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr12:109838954C>T	ENST00000431443.2	+	5	579	c.579C>T	c.(577-579)gtC>gtT	p.V193V	MYO1H_ENST00000310903.5_Silent_p.V193V	NM_001101421.3	NP_001094891.3	Q8N1T3	MYO1H_HUMAN	myosin IH	193	Myosin motor.					myosin complex (GO:0016459)	ATP binding (GO:0005524)|motor activity (GO:0003774)			NS(1)|breast(1)|central_nervous_system(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(9)|lung(17)|prostate(2)|upper_aerodigestive_tract(3)|urinary_tract(1)	47						CCCGAGTTGTCTACCAAAACG	0.512													C|||	5	0.000998403	0.0038	0.0	5008	,	,		17341	0.0		0.0	False		,,,				2504	0.0				p.V193V		Atlas-SNP	.											.	MYO1H	98	.	0			c.C579T						PASS	.	C		3,4061		0,3,2029	69.0	72.0	71.0		579	2.5	1.0	12	dbSNP_134	71	1,8387		0,1,4193	no	coding-synonymous	MYO1H	NM_001101421.3		0,4,6222	TT,TC,CC		0.0119,0.0738,0.0321		193/1023	109838954	4,12448	2032	4194	6226	SO:0001819	synonymous_variant	283446	exon5			AGTTGTCTACCAA		CCDS53826.1	12q24.11	2011-09-27			ENSG00000174527	ENSG00000174527		"""Myosins / Myosin superfamily : Class I"""	13879	protein-coding gene	gene with protein product		614636					Standard	NM_001101421		Approved	FLJ37587	uc010sxn.1	Q8N1T3	OTTHUMG00000169252	ENST00000431443.2:c.579C>T	12.37:g.109838954C>T		89.0	0.0	0		95.0	45.0	0.473684	NM_001101421	F5H3C6	Silent	SNP	ENST00000431443.2	37																																																																																				C|0.999;T|0.001	0.001	strong		0.512	MYO1H-201	KNOWN	basic	protein_coding	protein_coding		NM_173597	
BNIP1	662	hgsc.bcm.edu	37	5	172578595	172578595	+	Intron	SNP	T	T	C	rs180928619	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr5:172578595T>C	ENST00000351486.5	+	3	208				BNIP1_ENST00000352523.6_Silent_p.I68I|BNIP1_ENST00000393770.4_Intron|BNIP1_ENST00000231668.9_Silent_p.I68I	NM_001205.2	NP_001196.2	Q12981	SEC20_HUMAN	BCL2/adenovirus E1B 19kDa interacting protein 1						apoptotic process (GO:0006915)|autophagy (GO:0006914)|endoplasmic reticulum membrane fusion (GO:0016320)|endoplasmic reticulum organization (GO:0007029)|execution phase of apoptosis (GO:0097194)|negative regulation of apoptotic process (GO:0043066)|vesicle-mediated transport (GO:0016192)	cytoplasm (GO:0005737)|endoplasmic reticulum (GO:0005783)|integral component of endoplasmic reticulum membrane (GO:0030176)|intracellular membrane-bounded organelle (GO:0043231)|mitochondrion (GO:0005739)|nuclear envelope (GO:0005635)|SNARE complex (GO:0031201)	SNAP receptor activity (GO:0005484)			breast(1)|kidney(2)|large_intestine(2)|lung(3)|ovary(1)|pancreas(1)|skin(1)	11	Renal(175;0.000159)|Lung NSC(126;0.00199)|all_lung(126;0.00351)	Medulloblastoma(196;0.0208)|all_neural(177;0.0416)	Kidney(164;3.85e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000183)			GGGCATTTATTTGGACTGCTT	0.368													T|||	2	0.000399361	0.0015	0.0	5008	,	,		16395	0.0		0.0	False		,,,				2504	0.0				p.I68I		Atlas-SNP	.											.	BNIP1	30	.	0			c.T204C						PASS	.						108.0	103.0	105.0					5																	172578595		2203	4300	6503	SO:0001627	intron_variant	662	exon3			ATTTATTTGGACT	AF083957	CCDS4384.1, CCDS4385.1, CCDS4386.1, CCDS43400.1	5q33-q34	2008-02-05	2002-08-29		ENSG00000113734	ENSG00000113734			1082	protein-coding gene	gene with protein product		603291	"""BCL2/adenovirus E1B 19kD-interacting protein 1"""			7954800, 15272311	Standard	NM_013979		Approved	Nip1, SEC20	uc003mcj.4	Q12981	OTTHUMG00000130521	ENST00000351486.5:c.178-2730T>C	5.37:g.172578595T>C		98.0	0.0	0		121.0	55.0	0.454545	NM_013979	D3DQM3|D3DQM4|D3DQM5|D3DQM6|O75622|O75623|O75624|Q6K044|Q96FG4	Silent	SNP	ENST00000351486.5	37	CCDS4384.1																																																																																			T|0.999;C|0.001	0.001	strong		0.368	BNIP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252939.1	NM_013979	
CLTCL1	8218	hgsc.bcm.edu	37	22	19213091	19213091	+	Silent	SNP	C	C	T	rs367815723		TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr22:19213091C>T	ENST00000263200.10	-	13	2085	c.2013G>A	c.(2011-2013)ctG>ctA	p.L671L	CLTCL1_ENST00000427926.1_Silent_p.L671L|CLTCL1_ENST00000353891.5_Silent_p.L671L	NM_007098.3	NP_009029.3	P53675	CLH2_HUMAN	clathrin, heavy chain-like 1	671	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)					TGTTAGCAGACAGCATGGCAT	0.532			T	?	ALCL																																p.L671L		Atlas-SNP	.		Dom	yes		22	22q11.21	8218	"""clathrin, heavy polypeptide-like 1"""		L	.	CLTCL1	115	.	0			c.G2013A						PASS	.	C	,	0,4168		0,0,2084	46.0	47.0	47.0		2013,2013	0.6	0.9	22		47	1,8459		0,1,4229	no	coding-synonymous,coding-synonymous	CLTCL1	NM_001835.3,NM_007098.3	,	0,1,6313	TT,TC,CC		0.0118,0.0,0.0079	,	671/1584,671/1641	19213091	1,12627	2084	4230	6314	SO:0001819	synonymous_variant	8218	exon13			AGCAGACAGCATG		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.2013G>A	22.37:g.19213091C>T		74.0	0.0	0		68.0	33.0	0.485294	NM_001835	B7Z7U5|Q14017|Q15808|Q15809	Silent	SNP	ENST00000263200.10	37	CCDS46662.1																																																																																			.	.	weak		0.532	CLTCL1-001	KNOWN	non_canonical_genome_sequence_error|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000316397.5	NM_007098	
GRHPR	9380	hgsc.bcm.edu	37	9	37422763	37422763	+	Missense_Mutation	SNP	C	C	T	rs147185003	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr9:37422763C>T	ENST00000318158.6	+	1	101	c.16C>T	c.(16-18)Ctc>Ttc	p.L6F	GRHPR_ENST00000493368.1_3'UTR|GRHPR_ENST00000607784.1_Missense_Mutation_p.L6F	NM_012203.1	NP_036335.1	Q9UBQ7	GRHPR_HUMAN	glyoxylate reductase/hydroxypyruvate reductase	6					cellular nitrogen compound metabolic process (GO:0034641)|dicarboxylic acid metabolic process (GO:0043648)|excretion (GO:0007588)|glyoxylate metabolic process (GO:0046487)|metabolic process (GO:0008152)|oxidation-reduction process (GO:0055114)|protein oligomerization (GO:0051259)|small molecule metabolic process (GO:0044281)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|peroxisomal matrix (GO:0005782)	carboxylic acid binding (GO:0031406)|glycerate dehydrogenase activity (GO:0008465)|glyoxylate reductase (NADP) activity (GO:0030267)|hydroxypyruvate reductase activity (GO:0016618)|NAD binding (GO:0051287)|NADPH binding (GO:0070402)|protein homodimerization activity (GO:0042803)			endometrium(2)|kidney(1)|large_intestine(1)|lung(5)|prostate(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	12				GBM - Glioblastoma multiforme(29;0.00687)		ACCGGTGCGACTCATGAAGGT	0.701													C|||	17	0.00339457	0.0	0.0	5008	,	,		11840	0.0		0.001	False		,,,				2504	0.0164				p.L6F		Atlas-SNP	.											.	GRHPR	35	.	0			c.C16T						PASS	.	C	PHE/LEU	0,4382		0,0,2191	15.0	16.0	16.0		16	4.0	0.9	9	dbSNP_134	16	15,8557		0,15,4271	yes	missense	GRHPR	NM_012203.1	22	0,15,6462	TT,TC,CC		0.175,0.0,0.1158	possibly-damaging	6/329	37422763	15,12939	2191	4286	6477	SO:0001583	missense	9380	exon1			GTGCGACTCATGA	AF134895	CCDS6609.1	9q12	2012-07-13			ENSG00000137106	ENSG00000137106	1.1.1.79, 1.1.1.81		4570	protein-coding gene	gene with protein product	"""primary hyperoxaluria type 2"""	604296		GLXR		10524214, 10484776	Standard	XM_005251631		Approved	PH2	uc003zzu.1	Q9UBQ7	OTTHUMG00000019914	ENST00000318158.6:c.16C>T	9.37:g.37422763C>T	ENSP00000313432:p.Leu6Phe	41.0	0.0	0		65.0	23.0	0.353846	NM_012203	Q5T945|Q9H3E9|Q9H636|Q9UKX1	Missense_Mutation	SNP	ENST00000318158.6	37	CCDS6609.1	2	9.157509157509158E-4	0	0.0	0	0.0	0	0.0	2	0.002638522427440633	C	17.32	3.359027	0.61403	0.0	0.00175	ENSG00000137106	ENST00000377824;ENST00000318158	D;D	0.89050	-1.61;-2.46	4.9	3.99	0.46301	.	0.629307	0.15669	N	0.250520	D	0.86117	0.5856	L	0.40543	1.245	0.35594	D	0.807311	B	0.30664	0.289	B	0.36030	0.216	D	0.86917	0.2064	10	0.40728	T	0.16	.	14.397	0.67018	0.0:0.8509:0.1491:0.0	.	6	Q9UBQ7	GRHPR_HUMAN	F	6	ENSP00000367055:L6F;ENSP00000313432:L6F	ENSP00000313432:L6F	L	+	1	0	GRHPR	37412763	0.994000	0.37717	0.871000	0.34182	0.043000	0.13939	1.025000	0.30090	1.422000	0.47177	-0.518000	0.04402	CTC	C|0.999;T|0.001	0.001	strong		0.701	GRHPR-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052442.1	NM_012203	
MOGAT1	116255	hgsc.bcm.edu	37	2	223574546	223574546	+	Silent	SNP	A	A	G	rs142300173	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr2:223574546A>G	ENST00000446656.3	+	6	945	c.945A>G	c.(943-945)aaA>aaG	p.K315K		NM_058165.2	NP_477513.2	Q96PD6	MOGT1_HUMAN	monoacylglycerol O-acyltransferase 1	315					diacylglycerol biosynthetic process (GO:0006651)|glycerol metabolic process (GO:0006071)|triglyceride biosynthetic process (GO:0019432)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)	2-acylglycerol O-acyltransferase activity (GO:0003846)|diacylglycerol O-acyltransferase activity (GO:0004144)			breast(1)|cervix(1)|endometrium(1)|lung(5)|urinary_tract(1)	9		Renal(207;0.0183)		Epithelial(121;4.13e-10)|all cancers(144;2.06e-07)|LUSC - Lung squamous cell carcinoma(224;0.00829)|Lung(261;0.0105)		AACTTAGGAAATTGTTTGAGG	0.393													A|||	17	0.00339457	0.0113	0.0029	5008	,	,		17048	0.0		0.0	False		,,,				2504	0.0				p.K315K	Ovarian(93;205 1446 2385 11581 25911)	Atlas-SNP	.											.	MOGAT1	47	.	0			c.A945G						PASS	.	A		46,3662		0,46,1808	102.0	101.0	101.0		945	-4.6	0.0	2	dbSNP_134	101	0,8196		0,0,4098	no	coding-synonymous	MOGAT1	NM_058165.2		0,46,5906	GG,GA,AA		0.0,1.2406,0.3864		315/336	223574546	46,11858	1854	4098	5952	SO:0001819	synonymous_variant	116255	exon6			TAGGAAATTGTTT	AF384163	CCDS46524.1	2q36.2	2006-10-06	2004-05-28	2004-05-28	ENSG00000124003	ENSG00000124003			18210	protein-coding gene	gene with protein product		610268	"""diacylglycerol O-acyltransferase 2 like 1"""	DGAT2L1		14970677	Standard	NM_058165		Approved	DGAT2L, MGAT1	uc010fws.1	Q96PD6	OTTHUMG00000153394	ENST00000446656.3:c.945A>G	2.37:g.223574546A>G		158.0	0.0	0		117.0	57.0	0.487179	NM_058165	Q6IEE5	Silent	SNP	ENST00000446656.3	37	CCDS46524.1																																																																																			A|0.998;G|0.002	0.002	strong		0.393	MOGAT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000331010.3	NM_058165	
LRIG1	26018	hgsc.bcm.edu	37	3	66431280	66431280	+	Missense_Mutation	SNP	C	C	T	rs9877201	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr3:66431280C>T	ENST00000273261.3	-	18	3300	c.2776G>A	c.(2776-2778)Ggt>Agt	p.G926S	LRIG1_ENST00000496559.2_5'UTR|SLC25A26_ENST00000536651.1_3'UTR|LRIG1_ENST00000383703.3_Missense_Mutation_p.G903S	NM_015541.2	NP_056356.2	Q96JA1	LRIG1_HUMAN	leucine-rich repeats and immunoglobulin-like domains 1	926			G -> S (in dbSNP:rs9877201).		innervation (GO:0060384)|otolith morphogenesis (GO:0032474)|sensory perception of sound (GO:0007605)	integral component of membrane (GO:0016021)				NS(2)|breast(2)|cervix(1)|endometrium(3)|kidney(2)|large_intestine(7)|lung(12)|ovary(3)|prostate(1)|skin(4)|stomach(4)|urinary_tract(1)	42		Lung NSC(201;0.0101)		BRCA - Breast invasive adenocarcinoma(55;0.00047)		ACCCGGCCACCGTGTTCTGAA	0.597													C|||	554	0.110623	0.3873	0.0346	5008	,	,		18811	0.0		0.0179	False		,,,				2504	0.0				p.G926S		Atlas-SNP	.											LRIG1,NS,carcinoma,0,1	LRIG1	138	1	0			c.G2776A						PASS	.	C	SER/GLY	1492,2914	473.5+/-356.7	259,974,970	49.0	52.0	51.0		2776	-3.4	0.0	3	dbSNP_119	51	84,8516	48.9+/-108.6	1,82,4217	yes	missense	LRIG1	NM_015541.2	56	260,1056,5187	TT,TC,CC		0.9767,33.8629,12.1175	benign	926/1094	66431280	1576,11430	2203	4300	6503	SO:0001583	missense	26018	exon18			GGCCACCGTGTTC	AB050468	CCDS33783.1	3p14	2013-01-14			ENSG00000144749	ENSG00000144749		"""Immunoglobulin superfamily / I-set domain containing"""	17360	protein-coding gene	gene with protein product	"""ortholog of mouse integral membrane glycoprotein LIG-1"", ""leucine-rich repeat protein LRIG1"""	608868				11414704, 12234026	Standard	NM_015541		Approved	LIG-1, DKFZP586O1624, LIG1	uc003dmx.3	Q96JA1	OTTHUMG00000158727	ENST00000273261.3:c.2776G>A	3.37:g.66431280C>T	ENSP00000273261:p.Gly926Ser	69.0	0.0	0		81.0	40.0	0.493827	NM_015541	Q6IQ51|Q96CF9|Q9BYB8|Q9UFI4	Missense_Mutation	SNP	ENST00000273261.3	37	CCDS33783.1	210	0.09615384615384616	187	0.3800813008130081	8	0.022099447513812154	0	0.0	15	0.01978891820580475	C	10.82	1.457361	0.26161	0.338629	0.009767	ENSG00000144749	ENST00000273261;ENST00000383703;ENST00000383702	T;T	0.69040	-0.18;-0.37	5.34	-3.41	0.04839	.	0.402609	0.28016	N	0.016939	T	0.00012	0.0000	N	0.02315	-0.6	0.80722	P	0.0	B;B;B	0.24651	0.012;0.108;0.007	B;B;B	0.15870	0.014;0.014;0.002	T	0.38908	-0.9639	9	0.18710	T	0.47	.	8.9885	0.36008	0.145:0.5962:0.0:0.2587	rs9877201;rs52813156;rs59347115;rs9877201	903;926;926	Q96JA1-2;Q5XWD3;Q96JA1	.;.;LRIG1_HUMAN	S	926;903;829	ENSP00000273261:G926S;ENSP00000373208:G903S	ENSP00000273261:G926S	G	-	1	0	LRIG1	66513970	0.000000	0.05858	0.002000	0.10522	0.003000	0.03518	-0.284000	0.08422	-0.442000	0.07190	-0.794000	0.03295	GGT	C|0.879;T|0.121	0.121	strong		0.597	LRIG1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000351930.1	NM_015541	
UBXN11	91544	hgsc.bcm.edu	37	1	26608867	26608867	+	Missense_Mutation	SNP	C	C	A	rs193142354		TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr1:26608867C>A	ENST00000374222.1	-	16	1950	c.1486G>T	c.(1486-1488)Ggt>Tgt	p.G496C	UBXN11_ENST00000374217.2_Missense_Mutation_p.G463C|UBXN11_ENST00000357089.4_Missense_Mutation_p.G463C|UBXN11_ENST00000374221.3_Missense_Mutation_p.G496C|UBXN11_ENST00000314675.7_Missense_Mutation_p.G376C|UBXN11_ENST00000374223.1_Missense_Mutation_p.G253C			Q5T124	UBX11_HUMAN	UBX domain protein 11	496	3 X 8 AA tandem repeats of P-G-P-G-P-G-P- S.|Pro-rich.		Missing.			cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)		p.G490_P515delGPGPSPGPGPGPSPGPGPGPSPCPGP(1)		endometrium(3)|kidney(2)|large_intestine(4)|lung(6)|ovary(2)|prostate(3)|upper_aerodigestive_tract(3)	23						ggaccgggaccgggactgggg	0.721																																					p.G496C		Atlas-SNP	.											UBXN11,colon,carcinoma,0,2	UBXN11	54	2	1	Deletion - In frame(1)	ovary(1)	c.G1486T						PASS	.						25.0	29.0	28.0					1																	26608867		1765	4016	5781	SO:0001583	missense	91544	exon16			CGGGACCGGGACT	AF521017	CCDS41286.1, CCDS41287.1, CCDS41288.1	1p36.11	2008-07-25	2008-07-25	2008-07-25	ENSG00000158062	ENSG00000158062		"""UBX domain containing"""	30600	protein-coding gene	gene with protein product	"""socius"""	609151	"""UBX domain containing 5"""	UBXD5		11940653	Standard	NM_183008		Approved	SOC, SOCI	uc001blw.3	Q5T124	OTTHUMG00000003382	ENST00000374222.1:c.1486G>T	1.37:g.26608867C>A	ENSP00000363339:p.Gly496Cys	24.0	0.0	0		36.0	8.0	0.222222	NM_183008	D3DPK6|Q5T117|Q5T120|Q5T125|Q5T126|Q5T129|Q5T131|Q5T133|Q63HM6|Q71RB3|Q8IY27|Q8N1L6|Q8N9M4|Q8NA18|Q8NFE3|Q8NFE4|Q8NFE6	Missense_Mutation	SNP	ENST00000374222.1	37	CCDS41288.1	261	0.11950549450549451	72	0.14634146341463414	35	0.09668508287292818	16	0.027972027972027972	138	0.1820580474934037	A	8.132	0.783217	0.16189	.	.	ENSG00000158062	ENST00000314675;ENST00000374223;ENST00000357089;ENST00000374221;ENST00000374222;ENST00000374217	T;T;T;T;T;T	0.23950	1.88;1.96;2.3;2.24;2.24;2.3	.	.	.	.	.	.	.	.	T	0.00073	0.0002	N	0.22421	0.69	0.58432	P	2.9999999999752447E-6	D;D;D;D	0.76494	0.999;0.999;0.999;0.998	D;D;D;P	0.65323	0.934;0.934;0.934;0.861	T	0.12578	-1.0542	7	0.66056	D	0.02	.	6.1326	0.20213	0.0:0.6805:0.3194:0.0	.	463;458;376;496	Q5T124-2;Q5T124-4;Q5T124-3;Q5T124	.;.;.;UBX11_HUMAN	C	376;253;463;496;496;463	ENSP00000324721:G376C;ENSP00000363340:G253C;ENSP00000349601:G463C;ENSP00000363338:G496C;ENSP00000363339:G496C;ENSP00000363334:G463C	ENSP00000324721:G376C	G	-	1	0	UBXN11	26481454	0.000000	0.05858	0.121000	0.21740	0.128000	0.20619	-1.193000	0.03049	0.392000	0.25172	0.391000	0.25812	GGT	C|0.880;A|0.120	0.120	strong		0.721	UBXN11-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000009500.1	NM_145345	
SKIV2L2	23517	hgsc.bcm.edu	37	5	54674963	54674963	+	Silent	SNP	T	T	C	rs139182599	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr5:54674963T>C	ENST00000230640.5	+	18	2246	c.1992T>C	c.(1990-1992)aaT>aaC	p.N664N	SKIV2L2_ENST00000545714.1_Silent_p.N563N	NM_015360.4	NP_056175.3	P42285	SK2L2_HUMAN	superkiller viralicidic activity 2-like 2 (S. cerevisiae)	664					maturation of 5.8S rRNA (GO:0000460)|mRNA splicing, via spliceosome (GO:0000398)	catalytic step 2 spliceosome (GO:0071013)|nucleus (GO:0005634)	ATP binding (GO:0005524)|helicase activity (GO:0004386)|poly(A) RNA binding (GO:0044822)			NS(2)|endometrium(7)|haematopoietic_and_lymphoid_tissue(2)|kidney(4)|large_intestine(5)|lung(12)|ovary(1)|prostate(4)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	41		Lung NSC(810;0.000744)|Breast(144;0.181)|Prostate(74;0.194)				AGGTAAAGAATGAAGGAGATG	0.308													T|||	6	0.00119808	0.0	0.0	5008	,	,		15869	0.0		0.005	False		,,,				2504	0.001				p.N664N	Melanoma(2;92 134 23744 29976 33782)	Atlas-SNP	.											.	SKIV2L2	104	.	0			c.T1992C						PASS	.	T		6,4400	11.4+/-27.6	0,6,2197	46.0	51.0	50.0		1992	5.6	1.0	5	dbSNP_134	50	42,8552	26.8+/-75.7	0,42,4255	no	coding-synonymous	SKIV2L2	NM_015360.4		0,48,6452	CC,CT,TT		0.4887,0.1362,0.3692		664/1043	54674963	48,12952	2203	4297	6500	SO:0001819	synonymous_variant	23517	exon18			AAAGAATGAAGGA	D29641	CCDS3967.1	5q11.2	2008-11-25	2005-02-18	2005-02-18	ENSG00000039123	ENSG00000039123			18734	protein-coding gene	gene with protein product	"""functional spliceosome-associated protein 118"""		"""KIAA0052"""	KIAA0052			Standard	NM_015360		Approved	Mtr4, Dob1, fSAP118	uc003jpy.4	P42285	OTTHUMG00000097019	ENST00000230640.5:c.1992T>C	5.37:g.54674963T>C		11.0	0.0	0		9.0	8.0	0.888889	NM_015360	Q2M386|Q6MZZ8|Q6P170|Q8N5R0|Q8TAG2	Silent	SNP	ENST00000230640.5	37	CCDS3967.1																																																																																			T|0.997;C|0.003	0.003	strong		0.308	SKIV2L2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000214108.1		
RNASE3	6037	hgsc.bcm.edu	37	14	21359987	21359987	+	Missense_Mutation	SNP	C	C	G	rs202232277		TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr14:21359987C>G	ENST00000304639.3	+	2	200	c.142C>G	c.(142-144)Cct>Gct	p.P48A		NM_002935.2	NP_002926.2	P12724	ECP_HUMAN	ribonuclease, RNase A family, 3	48	Required for nearly all of the bactericidal activity; partially involved in LPS-binding and bacterial membrane depolarization.				antibacterial humoral response (GO:0019731)|defense response to Gram-positive bacterium (GO:0050830)|innate immune response in mucosa (GO:0002227)|RNA catabolic process (GO:0006401)|RNA phosphodiester bond hydrolysis (GO:0090501)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)	endonuclease activity (GO:0004519)|nucleic acid binding (GO:0003676)|ribonuclease activity (GO:0004540)			endometrium(1)|large_intestine(1)|lung(6)|ovary(1)	9	all_cancers(95;0.00453)		OV - Ovarian serous cystadenocarcinoma(11;6.3e-09)|Epithelial(56;1.42e-07)|all cancers(55;5.48e-07)	GBM - Glioblastoma multiforme(265;0.0187)	Pranlukast(DB01411)	TCTGAACCCCCCTCGATGCAC	0.478																																					p.P48A		Atlas-SNP	.											.	RNASE3	24	.	0			c.C142G						PASS	.	C	ALA/PRO	0,4382		0,0,2191	111.0	117.0	115.0		142	-4.0	0.0	14		115	1,8599	1.2+/-3.3	0,1,4299	yes	missense	RNASE3	NM_002935.2	27	0,1,6490	GG,GC,CC		0.0116,0.0,0.0077	benign	48/161	21359987	1,12981	2191	4300	6491	SO:0001583	missense	6037	exon2			AACCCCCCTCGAT	X55990	CCDS9560.1	14q11.2	2014-03-13	2010-05-07		ENSG00000169397	ENSG00000169397	3.1.27.-	"""Ribonucleases, RNase A"""	10046	protein-coding gene	gene with protein product	"""eosinophil cationic protein"""	131398		RNS3		1577491	Standard	NM_002935		Approved	ECP	uc001vyj.3	P12724	OTTHUMG00000029604	ENST00000304639.3:c.142C>G	14.37:g.21359987C>G	ENSP00000302324:p.Pro48Ala	147.0	0.0	0		132.0	64.0	0.484848	NM_002935	Q4VBC1|Q8WTP7|Q8WZ62|Q9GZN9	Missense_Mutation	SNP	ENST00000304639.3	37	CCDS9560.1	.	.	.	.	.	.	.	.	.	.	c	0.010	-1.759799	0.00657	0.0	1.16E-4	ENSG00000169397	ENST00000304639	T	0.72051	-0.62	2.56	-3.95	0.04118	Ribonuclease A, domain (4);	1.415800	0.04852	U	0.442561	T	0.55401	0.1918	L	0.53249	1.67	0.09310	N	1	B	0.22983	0.078	B	0.17433	0.018	T	0.30621	-0.9972	10	0.09590	T	0.72	.	1.8936	0.03253	0.4903:0.2296:0.1619:0.1183	.	48	P12724	ECP_HUMAN	A	48	ENSP00000302324:P48A	ENSP00000302324:P48A	P	+	1	0	RNASE3	20429827	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-5.611000	0.00110	-0.998000	0.03446	-0.415000	0.06103	CCT	C|0.999;G|0.001	0.001	weak		0.478	RNASE3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000073795.2	NM_002935	
MUC2	4583	hgsc.bcm.edu	37	11	1093054	1093054	+	Missense_Mutation	SNP	C	C	G			TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr11:1093054C>G	ENST00000441003.2	+	30	4900	c.4873C>G	c.(4873-4875)Cag>Gag	p.Q1625E	MUC2_ENST00000333592.6_5'Flank|MUC2_ENST00000361558.6_Intron|MUC2_ENST00000359061.5_Intron	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)				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)	cactggcacacagaccccaac	0.637																																					p.Q1625E		Atlas-SNP	.											.	MUC2	614	.	0			c.C4873G						PASS	.						130.0	168.0	155.0					11																	1093054		1880	3616	5496	SO:0001583	missense	4583	exon30			GGCACACAGACCC	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.4873C>G	11.37:g.1093054C>G	ENSP00000415183:p.Gln1625Glu	49.0	0.0	0		46.0	4.0	0.0869565	NM_002457	Q14878	Missense_Mutation	SNP	ENST00000441003.2	37		.	.	.	.	.	.	.	.	.	.	C	0.029	-1.348877	0.01266	.	.	ENSG00000198788	ENST00000441003	T	0.11277	2.79	1.61	-3.22	0.05125	.	.	.	.	.	T	0.02888	0.0086	.	.	.	0.09310	N	1	B	0.12013	0.005	B	0.06405	0.002	T	0.35450	-0.9788	8	0.02654	T	1	.	0.7509	0.00990	0.2924:0.2671:0.2831:0.1573	.	1625	E7EUV1	.	E	1625	ENSP00000415183:Q1625E	ENSP00000415183:Q1625E	Q	+	1	0	MUC2	1083054	0.000000	0.05858	0.000000	0.03702	0.080000	0.17528	-0.356000	0.07661	-2.888000	0.00316	0.121000	0.15741	CAG	.	.	none		0.637	MUC2-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000345894.2	NM_002457	
METTL7A	25840	hgsc.bcm.edu	37	12	51319238	51319238	+	Silent	SNP	T	T	C			TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr12:51319238T>C	ENST00000548553.1	+	2	1398	c.417T>C	c.(415-417)gaT>gaC	p.D139D	METTL7A_ENST00000332160.4_Silent_p.D139D			Q9H8H3	MET7A_HUMAN	methyltransferase like 7A	139						endoplasmic reticulum (GO:0005783)|extracellular vesicular exosome (GO:0070062)|lipid particle (GO:0005811)|membrane (GO:0016020)	methyltransferase activity (GO:0008168)			endometrium(1)|large_intestine(4)|lung(4)|upper_aerodigestive_tract(1)	10						GCTCTGTGGATGTGGTGGTCT	0.567																																					p.D139D		Atlas-SNP	.											.	METTL7A	19	.	0			c.T417C						PASS	.						74.0	65.0	68.0					12																	51319238		2203	4300	6503	SO:0001819	synonymous_variant	25840	exon1			TGTGGATGTGGTG		CCDS8804.1	12q13.12	2013-06-20			ENSG00000185432	ENSG00000185432			24550	protein-coding gene	gene with protein product						12975309	Standard	XM_006719332		Approved	DKFZP586A0522	uc001rxb.3	Q9H8H3	OTTHUMG00000169484	ENST00000548553.1:c.417T>C	12.37:g.51319238T>C		103.0	0.0	0		96.0	50.0	0.520833	NM_014033	Q9H7R3|Q9UHZ7|Q9Y422	Silent	SNP	ENST00000548553.1	37	CCDS8804.1																																																																																			.	.	none		0.567	METTL7A-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000404294.2	NM_014033	
MVB12A	93343	hgsc.bcm.edu	37	19	17534540	17534540	+	Missense_Mutation	SNP	G	G	T	rs147706400	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr19:17534540G>T	ENST00000317040.7	+	6	1627	c.572G>T	c.(571-573)gGc>gTc	p.G191V	MVB12A_ENST00000543795.1_Missense_Mutation_p.G191V|MVB12A_ENST00000529939.1_Missense_Mutation_p.G191V|MVB12A_ENST00000392702.2_Missense_Mutation_p.G151V|MVB12A_ENST00000528515.1_Missense_Mutation_p.A149S|CTD-2521M24.6_ENST00000593957.1_RNA			Q96EY5	MB12A_HUMAN	multivesicular body subunit 12A	191					protein transport (GO:0015031)|regulation of epidermal growth factor receptor signaling pathway (GO:0042058)|ubiquitin-dependent protein catabolic process via the multivesicular body sorting pathway (GO:0043162)	aggresome (GO:0016235)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|ESCRT I complex (GO:0000813)|extracellular vesicular exosome (GO:0070062)|intracellular membrane-bounded organelle (GO:0043231)|nucleus (GO:0005634)|vesicle (GO:0031982)	lipid binding (GO:0008289)|ubiquitin binding (GO:0043130)										TCAAGGCTGGGCTCTCGGGCA	0.622													G|||	4	0.000798722	0.0008	0.0014	5008	,	,		15707	0.0		0.001	False		,,,				2504	0.001				p.G191V		Atlas-SNP	.											.	.	.	.	0			c.G572T						PASS	.	G	VAL/GLY	3,4403		0,3,2200	56.0	56.0	56.0		572	5.1	1.0	19	dbSNP_134	56	7,8593		0,7,4293	yes	missense	FAM125A	NM_138401.2	109	0,10,6493	TT,TG,GG		0.0814,0.0681,0.0769	possibly-damaging	191/274	17534540	10,12996	2203	4300	6503	SO:0001583	missense	93343	exon6			GGCTGGGCTCTCG	BC011840	CCDS12359.1	19p13.11	2013-10-11	2012-12-03	2012-12-03	ENSG00000141971	ENSG00000141971			25153	protein-coding gene	gene with protein product			"""family with sequence similarity 125, member A"""	FAM125A		18005716, 20654576, 22232651	Standard	NM_138401		Approved	FLJ32495	uc002ngo.1	Q96EY5	OTTHUMG00000166252	ENST00000317040.7:c.572G>T	19.37:g.17534540G>T	ENSP00000324810:p.Gly191Val	86.0	0.0	0		65.0	37.0	0.569231	NM_138401	Q96I18	Missense_Mutation	SNP	ENST00000317040.7	37	CCDS12359.1	1|1	4.578754578754579E-4|4.578754578754579E-4	0|0	0.0|0.0	1|1	0.0027624309392265192|0.0027624309392265192	0|0	0.0|0.0	0|0	0.0|0.0	.|.	10.70|10.70	1.424914|1.424914	0.25639|0.25639	6.81E-4|6.81E-4	8.14E-4|8.14E-4	ENSG00000141971|ENSG00000141971	ENST00000528515|ENST00000528911;ENST00000528604;ENST00000317040;ENST00000392702;ENST00000529939;ENST00000543795	.|T;T;T;T;T	.|0.44482	.|0.94;0.96;1.02;0.92;0.96	5.1|5.1	5.1|5.1	0.69264|0.69264	.|.	.|0.319630	.|0.37483	.|N	.|0.002062	T|T	0.36441|0.36441	0.0967|0.0967	L|L	0.44542|0.44542	1.39|1.39	0.58432|0.58432	D|D	0.999998|0.999998	.|P	.|0.37914	.|0.611	.|B	.|0.35114	.|0.196	T|T	0.34601|0.34601	-0.9822|-0.9822	6|10	0.54805|0.66056	T|D	0.06|0.02	-28.1606|-28.1606	14.0584|14.0584	0.64784|0.64784	0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0	.|.	.|191	.|Q96EY5	.|F125A_HUMAN	S|V	149|99;52;191;151;191;191	.|ENSP00000433280:G99V;ENSP00000324810:G191V;ENSP00000376466:G151V;ENSP00000432526:G191V;ENSP00000444653:G191V	ENSP00000433677:A149S|ENSP00000324810:G191V	A|G	+|+	1|2	0|0	FAM125A|FAM125A	17395540|17395540	0.998000|0.998000	0.40836|0.40836	0.978000|0.978000	0.43139|0.43139	0.183000|0.183000	0.23260|0.23260	4.163000|4.163000	0.58183|0.58183	2.371000|2.371000	0.80710|0.80710	0.558000|0.558000	0.71614|0.71614	GCT|GGC	G|0.999;T|0.001	0.001	strong		0.622	MVB12A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000388723.2	NM_138401	
USP34	9736	hgsc.bcm.edu	37	2	61450409	61450409	+	Missense_Mutation	SNP	C	C	G			TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr2:61450409C>G	ENST00000398571.2	-	63	7694	c.7618G>C	c.(7618-7620)Gac>Cac	p.D2540H	USP34_ENST00000472689.1_5'Flank	NM_014709.3	NP_055524.3	Q70CQ2	UBP34_HUMAN	ubiquitin specific peptidase 34	2540					positive regulation of canonical Wnt signaling pathway (GO:0090263)|protein deubiquitination (GO:0016579)|protein K48-linked deubiquitination (GO:0071108)|ubiquitin-dependent protein catabolic process (GO:0006511)|Wnt signaling pathway (GO:0016055)		cysteine-type endopeptidase activity (GO:0004197)|ubiquitin thiolesterase activity (GO:0004221)|ubiquitin-specific protease activity (GO:0004843)			autonomic_ganglia(1)|breast(14)|cervix(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(10)|large_intestine(24)|lung(52)|ovary(8)|prostate(10)|skin(6)|urinary_tract(2)	138			Epithelial(17;0.229)			GCTGCCATGTCAGTCTGTGAT	0.308																																					p.D2540H		Atlas-SNP	.											USP34,NS,carcinoma,+2,1	USP34	334	1	0			c.G7618C						PASS	.						137.0	128.0	131.0					2																	61450409		1847	4096	5943	SO:0001583	missense	9736	exon63			CCATGTCAGTCTG	AB011142	CCDS42686.1	2p16.1-p15	2005-08-08	2005-08-08		ENSG00000115464	ENSG00000115464		"""Ubiquitin-specific peptidases"""	20066	protein-coding gene	gene with protein product		615295	"""ubiquitin specific protease 34"""			12838346	Standard	NM_014709		Approved	KIAA0570, KIAA0729	uc002sbe.3	Q70CQ2	OTTHUMG00000152265	ENST00000398571.2:c.7618G>C	2.37:g.61450409C>G	ENSP00000381577:p.Asp2540His	90.0	0.0	0		78.0	5.0	0.0641026	NM_014709	A8MWD0|B3KWU9|O60316|O94834|Q3B777|Q6P6C9|Q7L8P6|Q8N3T9|Q8TBW2|Q9UGA1	Missense_Mutation	SNP	ENST00000398571.2	37	CCDS42686.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	25.5|25.5	4.646274|4.646274	0.87958|0.87958	.|.	.|.	ENSG00000115464|ENSG00000115464	ENST00000263989;ENST00000398569;ENST00000398571|ENST00000411912	T|.	0.11169|.	2.8|.	5.72|5.72	5.72|5.72	0.89469|0.89469	Armadillo-type fold (1);|.	0.000000|.	0.85682|.	D|.	0.000000|.	T|.	0.74473|.	0.3721|.	L|L	0.61218|0.61218	1.895|1.895	0.80722|0.80722	D|D	1|1	D|.	0.69078|.	0.997|.	D|.	0.71870|.	0.975|.	T|.	0.71062|.	-0.4701|.	10|.	0.72032|.	D|.	0.01|.	.|.	19.8938|19.8938	0.96942|0.96942	0.0:1.0:0.0:0.0|0.0:1.0:0.0:0.0	.|.	2540|.	Q70CQ2|.	UBP34_HUMAN|.	H|S	2388;2388;2540|299	ENSP00000381577:D2540H|.	ENSP00000263989:D2388H|.	D|X	-|-	1|2	0|2	USP34|USP34	61303913|61303913	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.946000|0.946000	0.59487|0.59487	7.348000|7.348000	0.79366|0.79366	2.703000|2.703000	0.92315|0.92315	0.460000|0.460000	0.39030|0.39030	GAC|TGA	.	.	none		0.308	USP34-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000325650.4		
IL1RL2	8808	hgsc.bcm.edu	37	2	102851470	102851470	+	Missense_Mutation	SNP	G	G	A	rs75091099	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr2:102851470G>A	ENST00000264257.2	+	11	1537	c.1411G>A	c.(1411-1413)Gcg>Acg	p.A471T	IL1RL2_ENST00000539491.1_Missense_Mutation_p.A471T|IL1RL2_ENST00000441515.2_Missense_Mutation_p.A353T|IL1RL2_ENST00000481806.1_3'UTR	NM_003854.2	NP_003845.2	Q9HB29	ILRL2_HUMAN	interleukin 1 receptor-like 2	471	TIR. {ECO:0000255|PROSITE- ProRule:PRU00204}.				cellular defense response (GO:0006968)|cytokine-mediated signaling pathway (GO:0019221)|positive regulation of interleukin-6 production (GO:0032755)|positive regulation of T cell differentiation (GO:0045582)|regulation of inflammatory response (GO:0050727)|signal transduction (GO:0007165)	integral component of plasma membrane (GO:0005887)	interleukin-1 receptor activity (GO:0004908)|interleukin-1, Type I, activating receptor activity (GO:0004909)			breast(1)|cervix(1)|endometrium(5)|large_intestine(6)|liver(2)|lung(8)|ovary(2)|prostate(1)	26						AGAACAAATCGCGGTCTACAG	0.488													G|||	144	0.028754	0.0	0.0072	5008	,	,		19953	0.0724		0.006	False		,,,				2504	0.0613				p.A471T		Atlas-SNP	.											IL1RL2,NS,carcinoma,-1,1	IL1RL2	118	1	0			c.G1411A						PASS	.	G	THR/ALA	9,4397	15.5+/-35.6	0,9,2194	132.0	120.0	124.0		1411	3.4	0.2	2	dbSNP_132	124	38,8562	25.1+/-72.6	0,38,4262	yes	missense	IL1RL2	NM_003854.2	58	0,47,6456	AA,AG,GG		0.4419,0.2043,0.3614	possibly-damaging	471/576	102851470	47,12959	2203	4300	6503	SO:0001583	missense	8808	exon11			CAAATCGCGGTCT	U49065	CCDS2056.1	2q12	2013-01-14			ENSG00000115598	ENSG00000115598		"""Interleukins and interleukin receptors"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	5999	protein-coding gene	gene with protein product		604512				8898719, 10191101, 11466363	Standard	NM_003854		Approved	IL1R-rp2, IL1RRP2	uc002tbs.3	Q9HB29	OTTHUMG00000130776	ENST00000264257.2:c.1411G>A	2.37:g.102851470G>A	ENSP00000264257:p.Ala471Thr	155.0	0.0	0		160.0	73.0	0.45625	NM_003854	A4FU63|Q13525|Q45H74|Q53TU8|Q587I8	Missense_Mutation	SNP	ENST00000264257.2	37	CCDS2056.1	49	0.022435897435897436	0	0.0	3	0.008287292817679558	42	0.07342657342657342	4	0.005277044854881266	G	17.94	3.510555	0.64522	0.002043	0.004419	ENSG00000115598	ENST00000264257;ENST00000441515;ENST00000539491	T;T;T	0.11712	2.75;2.75;2.75	5.43	3.4	0.38934	Toll/interleukin-1 receptor homology (TIR) domain (4);	0.467616	0.23395	N	0.048647	T	0.01353	0.0044	M	0.69823	2.125	0.32198	N	0.57825	P;D	0.54047	0.924;0.964	P;P	0.48921	0.495;0.595	T	0.04115	-1.0976	10	0.59425	D	0.04	.	12.4276	0.55556	0.1128:0.0:0.8872:0.0	.	353;471	A4FU63;Q9HB29	.;ILRL2_HUMAN	T	471;353;471	ENSP00000264257:A471T;ENSP00000413348:A353T;ENSP00000442184:A471T	ENSP00000264257:A471T	A	+	1	0	IL1RL2	102217902	0.568000	0.26635	0.238000	0.24106	0.767000	0.43475	3.205000	0.51090	1.140000	0.42260	0.591000	0.81541	GCG	G|0.991;A|0.009	0.009	strong		0.488	IL1RL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253290.1	NM_003854	
EHMT2	10919	hgsc.bcm.edu	37	6	31851172	31851172	+	Silent	SNP	G	G	A	rs148424397	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr6:31851172G>A	ENST00000375537.4	-	23	2967	c.2961C>T	c.(2959-2961)tgC>tgT	p.C987C	EHMT2_ENST00000375530.4_Silent_p.C953C|EHMT2_ENST00000395728.3_Silent_p.C1044C|EHMT2-AS1_ENST00000434689.1_RNA|EHMT2_ENST00000480912.1_5'UTR|EHMT2_ENST00000375528.4_Silent_p.C1010C	NM_006709.3	NP_006700.3	Q96KQ7	EHMT2_HUMAN	euchromatic histone-lysine N-methyltransferase 2	987	Pre-SET. {ECO:0000255|PROSITE- ProRule:PRU00157}.				DNA methylation (GO:0006306)|DNA methylation on cytosine within a CG sequence (GO:0010424)|fertilization (GO:0009566)|histone methylation (GO:0016571)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|organ growth (GO:0035265)|peptidyl-lysine dimethylation (GO:0018027)|regulation of DNA replication (GO:0006275)|spermatid development (GO:0007286)|synaptonemal complex assembly (GO:0007130)	chromosome (GO:0005694)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	C2H2 zinc finger domain binding (GO:0070742)|histone methyltransferase activity (H3-K27 specific) (GO:0046976)|histone methyltransferase activity (H3-K9 specific) (GO:0046974)|histone-lysine N-methyltransferase activity (GO:0018024)|p53 binding (GO:0002039)|protein-lysine N-methyltransferase activity (GO:0016279)|zinc ion binding (GO:0008270)			central_nervous_system(1)|cervix(2)|kidney(2)|large_intestine(3)|lung(6)|ovary(2)|prostate(4)|upper_aerodigestive_tract(1)	21						TGAGCTGGCCGCACAGGCAGT	0.632													G|||	6	0.00119808	0.0	0.0043	5008	,	,		20855	0.0		0.003	False		,,,				2504	0.0				p.C987C		Atlas-SNP	.											.	EHMT2	45	.	0			c.C2961T						PASS	.	G	,	0,3018		0,0,1509	51.0	39.0	43.0		2961,2859	-9.0	0.7	6	dbSNP_134	43	8,5410		0,8,2701	yes	coding-synonymous,coding-synonymous	EHMT2	NM_006709.3,NM_025256.5	,	0,8,4210	AA,AG,GG		0.1477,0.0,0.0948	,	987/1211,953/1177	31851172	8,8428	1509	2709	4218	SO:0001819	synonymous_variant	10919	exon23			CTGGCCGCACAGG	AF134726	CCDS4725.1, CCDS4726.1, CCDS75425.1	6p21.3	2013-01-10	2004-03-22	2005-06-09	ENSG00000204371	ENSG00000204371	2.1.1.43	"""Chromatin-modifying enzymes / K-methyltransferases"", ""Ankyrin repeat domain containing"""	14129	protein-coding gene	gene with protein product		604599	"""chromosome 6 open reading frame 30"", ""HLA-B associated transcript 8"""	C6orf30, BAT8		8457211, 11316813	Standard	XM_005274833		Approved	G9A, Em:AF134726.3, NG36/G9a, KMT1C	uc003nxz.1	Q96KQ7	OTTHUMG00000031180	ENST00000375537.4:c.2961C>T	6.37:g.31851172G>A		252.0	0.0	0		269.0	145.0	0.539033	NM_006709	B0UZY2|Q14349|Q5JP83|Q5JQ92|Q5JQA1|Q5JQG3|Q6PK06|Q96MH5|Q96QD0|Q9UQL8|Q9Y331	Silent	SNP	ENST00000375537.4	37	CCDS4725.1																																																																																			G|0.999;A|0.001	0.001	strong		0.632	EHMT2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000076355.5	NM_006709	
DOT1L	84444	hgsc.bcm.edu	37	19	2222327	2222327	+	Silent	SNP	G	G	A	rs373960110		TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr19:2222327G>A	ENST00000398665.3	+	24	3195	c.3159G>A	c.(3157-3159)gcG>gcA	p.A1053A		NM_032482.2	NP_115871.1	Q8TEK3	DOT1L_HUMAN	DOT1-like histone H3K79 methyltransferase	1053					histone lysine methylation (GO:0034968)|regulation of JAK-STAT cascade (GO:0046425)|regulation of transcription regulatory region DNA binding (GO:2000677)	nucleus (GO:0005634)	DNA binding (GO:0003677)|histone-lysine N-methyltransferase activity (GO:0018024)|transcription factor binding (GO:0008134)			NS(1)|breast(1)|cervix(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(3)|lung(14)|ovary(2)|pancreas(2)|prostate(1)|upper_aerodigestive_tract(2)|urinary_tract(9)	42		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)		CCACTGGTGCGGGCAGTGCCA	0.662																																					p.A1053A		Atlas-SNP	.											.	DOT1L	205	.	0			c.G3159A						PASS	.	G		0,4246		0,0,2123	26.0	32.0	30.0		3159	-8.4	0.0	19		30	1,8471		0,1,4235	no	coding-synonymous	DOT1L	NM_032482.2		0,1,6358	AA,AG,GG		0.0118,0.0,0.0079		1053/1538	2222327	1,12717	2123	4236	6359	SO:0001819	synonymous_variant	84444	exon24			TGGTGCGGGCAGT	AF509504	CCDS42460.1	19p13.3	2013-05-21	2013-05-21		ENSG00000104885	ENSG00000104885	2.1.1.43	"""Chromatin-modifying enzymes / K-methyltransferases"""	24948	protein-coding gene	gene with protein product	"""histone methyltransferase DOT1L"""	607375	"""DOT1-like, histone H3 methyltransferase (S. cerevisiae)"""			11347906, 12123582	Standard	NM_032482		Approved	KIAA1814, DOT1, KMT4	uc002lvb.4	Q8TEK3	OTTHUMG00000150431	ENST00000398665.3:c.3159G>A	19.37:g.2222327G>A		127.0	0.0	0		132.0	80.0	0.606061	NM_032482	O60379|Q96JL1	Silent	SNP	ENST00000398665.3	37	CCDS42460.1	.	.	.	.	.	.	.	.	.	.	G	0.204	-1.042205	0.01997	0.0	1.18E-4	ENSG00000104885	ENST00000440640	.	.	.	4.21	-8.42	0.00957	.	.	.	.	.	T	0.14657	0.0354	.	.	.	0.09310	N	0.999999	.	.	.	.	.	.	T	0.19257	-1.0311	4	.	.	.	-2.2	0.8379	0.01143	0.3872:0.2217:0.212:0.1791	.	.	.	.	Q	840	.	.	R	+	2	0	DOT1L	2173327	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-0.688000	0.05150	-1.857000	0.01159	-0.379000	0.06801	CGG	.	.	weak		0.662	DOT1L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318066.1	NM_032482	
PSORS1C1	170679	hgsc.bcm.edu	37	6	31084191	31084191	+	Intron	SNP	T	T	C	rs33941312	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr6:31084191T>C	ENST00000259881.9	+	1	61				PSORS1C1_ENST00000467107.1_3'UTR|CDSN_ENST00000376288.2_Missense_Mutation_p.S401G	NM_014068.2	NP_054787.2	Q9UIG5	PS1C1_HUMAN	psoriasis susceptibility 1 candidate 1											kidney(1)|ovary(2)|prostate(1)|skin(1)	5						ATGCTAGAACTGCTGGGGACT	0.647													T|||	60	0.0119808	0.0008	0.0058	5008	,	,		15616	0.0149		0.0288	False		,,,				2504	0.0112				p.S401G		Atlas-SNP	.											.	CDSN	48	.	0			c.A1201G						PASS	.	T	GLY/SER,	18,4382		0,18,2182	36.0	42.0	40.0		1201,	3.7	0.3	6	dbSNP_126	40	169,8425		3,163,4131	yes	missense,intron	CDSN,PSORS1C1	NM_001264.4,NM_014068.2	56,	3,181,6313	CC,CT,TT		1.9665,0.4091,1.4391	possibly-damaging,	401/530,	31084191	187,12807	2200	4297	6497	SO:0001627	intron_variant	1041	exon2			TAGAACTGCTGGG	AB031479	CCDS34390.1	6p21.3	2014-01-28	2003-06-12		ENSG00000204540	ENSG00000204540			17202	protein-coding gene	gene with protein product		613525	"""chromosome 6 open reading frame 16"""	C6orf16			Standard	NM_014068		Approved	SEEK1	uc003nsl.2	Q9UIG5	OTTHUMG00000031077	ENST00000259881.9:c.-229+1523T>C	6.37:g.31084191T>C		38.0	0.0	0		35.0	35.0	1	NM_001264	B0V083|Q5ST21|Q86WJ8|Q86WJ9|Q96QC3	Missense_Mutation	SNP	ENST00000259881.9	37	CCDS34390.1	40	0.018315018315018316	0	0.0	2	0.0055248618784530384	14	0.024475524475524476	24	0.0316622691292876	T	9.761	1.170009	0.21621	0.004091	0.019665	ENSG00000204539	ENST00000376288	T	0.08807	3.05	3.74	3.74	0.42951	.	0.140133	0.32901	N	0.005510	T	0.06690	0.0171	N	0.24115	0.695	0.09310	N	0.999995	P	0.49696	0.927	D	0.67725	0.953	T	0.14755	-1.0461	10	0.52906	T	0.07	-3.9289	8.9816	0.35968	0.0:0.0:0.0:1.0	rs33941312	401	Q15517	CDSN_HUMAN	G	401	ENSP00000365465:S401G	ENSP00000365465:S401G	S	-	1	0	CDSN	31192170	0.006000	0.16342	0.252000	0.24328	0.287000	0.27160	-0.141000	0.10327	1.683000	0.51011	0.386000	0.25728	AGT	T|0.985;C|0.015	0.015	strong		0.647	PSORS1C1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076110.3	NM_014068	
TP53BP1	7158	hgsc.bcm.edu	37	15	43712823	43712823	+	Missense_Mutation	SNP	C	C	T	rs28903077	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr15:43712823C>T	ENST00000263801.3	-	21	4598	c.4346G>A	c.(4345-4347)cGa>cAa	p.R1449Q	TP53BP1_ENST00000382044.4_Missense_Mutation_p.R1454Q|TP53BP1_ENST00000450115.2_Missense_Mutation_p.R1454Q|TP53BP1_ENST00000382039.3_Missense_Mutation_p.R1404Q	NM_005657.2	NP_005648.1	Q12888	TP53B_HUMAN	tumor protein p53 binding protein 1	1449					cellular response to DNA damage stimulus (GO:0006974)|DNA repair (GO:0006281)|double-strand break repair (GO:0006302)|double-strand break repair via homologous recombination (GO:0000724)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|transcription from RNA polymerase II promoter (GO:0006366)	cytoplasm (GO:0005737)|kinetochore (GO:0000776)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|replication fork (GO:0005657)	damaged DNA binding (GO:0003684)|methylated histone binding (GO:0035064)|p53 binding (GO:0002039)|RNA polymerase II activating transcription factor binding (GO:0001102)|RNA polymerase II transcription cofactor activity (GO:0001104)|telomeric DNA binding (GO:0042162)			breast(4)|endometrium(5)|kidney(7)|large_intestine(22)|lung(13)|ovary(4)|pancreas(2)|prostate(1)|skin(10)|upper_aerodigestive_tract(1)|urinary_tract(3)	72		all_cancers(109;6.94e-11)|all_epithelial(112;2.69e-09)|Lung NSC(122;7.86e-07)|all_lung(180;7.84e-06)|Melanoma(134;0.0728)		GBM - Glioblastoma multiforme(94;1.59e-06)		CACATCTGTTCGTCTGGTGGA	0.552								Other conserved DNA damage response genes					C|||	2	0.000399361	0.0	0.0	5008	,	,		18672	0.0		0.002	False		,,,				2504	0.0				p.R1454Q		Atlas-SNP	.											.	TP53BP1	157	.	0			c.G4361A						PASS	.	C	GLN/ARG,GLN/ARG,GLN/ARG	0,4402		0,0,2201	66.0	64.0	64.0		4361,4361,4346	5.4	0.4	15	dbSNP_125	64	17,8579	11.9+/-42.8	0,17,4281	yes	missense,missense,missense	TP53BP1	NM_001141979.1,NM_001141980.1,NM_005657.2	43,43,43	0,17,6482	TT,TC,CC		0.1978,0.0,0.1308	probably-damaging,probably-damaging,probably-damaging	1454/1976,1454/1978,1449/1973	43712823	17,12981	2201	4298	6499	SO:0001583	missense	7158	exon21			TCTGTTCGTCTGG	U09477	CCDS10096.1, CCDS45250.1, CCDS45251.1	15q15-q21	2007-08-02	2007-08-02		ENSG00000067369	ENSG00000067369			11999	protein-coding gene	gene with protein product		605230	"""tumor protein p53-binding protein, 1"""			8016121, 9748285	Standard	NM_005657		Approved	53BP1, p202	uc001zrr.4	Q12888	OTTHUMG00000059757	ENST00000263801.3:c.4346G>A	15.37:g.43712823C>T	ENSP00000263801:p.Arg1449Gln	86.0	0.0	0		89.0	47.0	0.52809	NM_001141980	F8VY86|Q2M1Z7|Q4LE46|Q5FWZ3|Q7Z3U4	Missense_Mutation	SNP	ENST00000263801.3	37	CCDS10096.1	2	9.157509157509158E-4	0	0.0	0	0.0	0	0.0	2	0.002638522427440633	C	18.64	3.666759	0.67814	0.0	0.001978	ENSG00000067369	ENST00000263801;ENST00000382044;ENST00000382039;ENST00000450115	T;T;T;T	0.04194	3.68;3.68;3.73;3.68	5.45	5.45	0.79879	.	0.347316	0.27735	N	0.018061	T	0.11239	0.0274	L	0.29908	0.895	0.09310	N	1	D;D;D;D	0.76494	0.999;0.998;0.999;0.999	D;D;D;D	0.72625	0.978;0.945;0.975;0.975	T	0.33574	-0.9863	10	0.21014	T	0.42	-8.3136	14.178	0.65555	0.159:0.8409:0.0:0.0	rs28903077;rs28903077	1454;1449;1454;1454	B7Z3E7;Q12888;Q12888-2;F8VY86	.;TP53B_HUMAN;.;.	Q	1449;1454;1404;1454	ENSP00000263801:R1449Q;ENSP00000371475:R1454Q;ENSP00000371470:R1404Q;ENSP00000393497:R1454Q	ENSP00000263801:R1449Q	R	-	2	0	TP53BP1	41500115	0.970000	0.33590	0.397000	0.26308	0.982000	0.71751	4.145000	0.58065	2.717000	0.92951	0.585000	0.79938	CGA	C|0.998;T|0.002	0.002	strong		0.552	TP53BP1-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000132897.3		
SHROOM3	57619	hgsc.bcm.edu	37	4	77661017	77661017	+	Missense_Mutation	SNP	A	A	C	rs76656494	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr4:77661017A>C	ENST00000296043.6	+	5	2644	c.1691A>C	c.(1690-1692)gAa>gCa	p.E564A		NM_020859.3	NP_065910.3	Q8TF72	SHRM3_HUMAN	shroom family member 3	564					actin cytoskeleton organization (GO:0030036)|apical protein localization (GO:0045176)|cell morphogenesis (GO:0000902)|cellular pigment accumulation (GO:0043482)|columnar/cuboidal epithelial cell development (GO:0002066)|neural tube closure (GO:0001843)|pattern specification process (GO:0007389)|regulation of cell shape (GO:0008360)	adherens junction (GO:0005912)|apical junction complex (GO:0043296)|apical plasma membrane (GO:0016324)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|microtubule (GO:0005874)				NS(3)|breast(1)|central_nervous_system(1)|cervix(1)|endometrium(10)|kidney(2)|large_intestine(6)|lung(29)|ovary(1)|skin(5)|upper_aerodigestive_tract(1)	60			Lung(101;0.0903)			TCAGTGCCTGAAAATGAGGAG	0.502													A|||	33	0.00658946	0.0	0.013	5008	,	,		21550	0.0		0.0229	False		,,,				2504	0.001				p.E564A		Atlas-SNP	.											.	SHROOM3	134	.	0			c.A1691C						PASS	.	A	ALA/GLU	14,4392	22.3+/-47.3	0,14,2189	168.0	168.0	168.0		1691	4.4	1.0	4	dbSNP_131	168	145,8455	70.7+/-133.2	2,141,4157	yes	missense	SHROOM3	NM_020859.3	107	2,155,6346	CC,CA,AA		1.686,0.3177,1.2225	probably-damaging	564/1997	77661017	159,12847	2203	4300	6503	SO:0001583	missense	57619	exon5			TGCCTGAAAATGA	AB055660	CCDS3579.2	4q21.1	2009-11-25			ENSG00000138771	ENSG00000138771			30422	protein-coding gene	gene with protein product		604570				10589677, 16615870	Standard	NM_020859		Approved	ShrmL, SHRM, KIAA1481, APXL3	uc011cbx.2	Q8TF72	OTTHUMG00000157075	ENST00000296043.6:c.1691A>C	4.37:g.77661017A>C	ENSP00000296043:p.Glu564Ala	58.0	0.0	0		62.0	28.0	0.451613	NM_020859	Q5QTQ3|Q6ZRW3|Q96IR9|Q9P247	Missense_Mutation	SNP	ENST00000296043.6	37	CCDS3579.2	23	0.010531135531135532	1	0.0020325203252032522	5	0.013812154696132596	0	0.0	17	0.022427440633245383	A	15.10	2.733513	0.48939	0.003177	0.01686	ENSG00000138771	ENST00000296043	T	0.26660	1.72	5.59	4.39	0.52855	.	0.093877	0.44902	D	0.000410	T	0.31009	0.0783	M	0.71581	2.175	0.35431	D	0.794093	D;P;P	0.76494	0.999;0.89;0.8	D;B;B	0.65987	0.94;0.382;0.153	T	0.57688	-0.7768	10	0.72032	D	0.01	-7.8779	12.7677	0.57401	0.8629:0.1371:0.0:0.0	.	388;564;342	B4E244;Q8TF72;B3KY47	.;SHRM3_HUMAN;.	A	564	ENSP00000296043:E564A	ENSP00000296043:E564A	E	+	2	0	SHROOM3	77880041	1.000000	0.71417	1.000000	0.80357	0.414000	0.31173	1.907000	0.39897	0.925000	0.37094	0.460000	0.39030	GAA	A|0.988;C|0.012	0.012	strong		0.502	SHROOM3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252408.2	NM_020859	
EFCAB5	374786	hgsc.bcm.edu	37	17	28407861	28407861	+	Silent	SNP	G	G	A	rs147629201	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr17:28407861G>A	ENST00000394835.3	+	17	3480	c.3288G>A	c.(3286-3288)aaG>aaA	p.K1096K	EFCAB5_ENST00000320856.5_Silent_p.K972K|EFCAB5_ENST00000394832.2_Intron	NM_198529.3	NP_940931	A4FU69	EFCB5_HUMAN	EF-hand calcium binding domain 5	1096							calcium ion binding (GO:0005509)			breast(7)|endometrium(2)|kidney(4)|large_intestine(11)|lung(14)|ovary(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	43						CCCGTAATAAGCATGATTATA	0.448													G|||	50	0.00998403	0.0348	0.0029	5008	,	,		19986	0.0		0.002	False		,,,				2504	0.0				p.K1096K		Atlas-SNP	.											.	EFCAB5	122	.	0			c.G3288A						PASS	.	G		73,3703		0,73,1815	82.0	78.0	79.0		3288	4.1	0.1	17	dbSNP_134	79	10,8210		0,10,4100	no	coding-synonymous	EFCAB5	NM_198529.3		0,83,5915	AA,AG,GG		0.1217,1.9333,0.6919		1096/1504	28407861	83,11913	1888	4110	5998	SO:0001819	synonymous_variant	374786	exon17			TAATAAGCATGAT	AL833911	CCDS11254.2, CCDS54103.1	17q11.2	2013-01-10			ENSG00000176927	ENSG00000176927		"""EF-hand domain containing"""	24801	protein-coding gene	gene with protein product							Standard	NM_198529		Approved	FLJ46247	uc002het.3	A4FU69	OTTHUMG00000132753	ENST00000394835.3:c.3288G>A	17.37:g.28407861G>A		125.0	0.0	0		138.0	64.0	0.463768	NM_198529	B2RPN0|B4DS75|B4DZR5|F5GYL2|Q0VD68|Q6ZRM6|Q8NDG9	Silent	SNP	ENST00000394835.3	37	CCDS11254.2																																																																																			G|0.990;A|0.010	0.010	strong		0.448	EFCAB5-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256120.4	NM_198529	
ATP12A	479	hgsc.bcm.edu	37	13	25272807	25272807	+	Silent	SNP	C	C	T	rs148844496	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr13:25272807C>T	ENST00000381946.3	+	12	1691	c.1524C>T	c.(1522-1524)caC>caT	p.H508H	ATP12A_ENST00000218548.6_Silent_p.H514H			P54707	AT12A_HUMAN	ATPase, H+/K+ transporting, nongastric, alpha polypeptide	508					ATP biosynthetic process (GO:0006754)|ion transmembrane transport (GO:0034220)|potassium ion homeostasis (GO:0055075)|regulation of pH (GO:0006885)|transmembrane transport (GO:0055085)	basolateral plasma membrane (GO:0016323)|hydrogen:potassium-exchanging ATPase complex (GO:0005889)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|hydrogen:potassium-exchanging ATPase activity (GO:0008900)|metal ion binding (GO:0046872)			breast(6)|central_nervous_system(4)|endometrium(3)|kidney(5)|large_intestine(23)|lung(23)|ovary(2)|pancreas(1)|prostate(2)|skin(5)	74		Lung SC(185;0.0225)|Breast(139;0.077)		all cancers(112;0.0307)|Epithelial(112;0.086)|OV - Ovarian serous cystadenocarcinoma(117;0.228)		TCTCCATCCACGAGATGGATG	0.517																																					p.H514H	Pancreas(156;1582 1935 18898 22665 26498)	Atlas-SNP	.											.	ATP12A	172	.	0			c.C1542T						PASS	.	C	,	0,4406		0,0,2203	56.0	50.0	52.0		1542,1524	-2.1	0.0	13	dbSNP_134	52	6,8594	4.3+/-15.6	0,6,4294	no	coding-synonymous,coding-synonymous	ATP12A	NM_001185085.1,NM_001676.5	,	0,6,6497	TT,TC,CC		0.0698,0.0,0.0461	,	514/1046,508/1040	25272807	6,13000	2203	4300	6503	SO:0001819	synonymous_variant	479	exon12			CATCCACGAGATG	L42558	CCDS31948.1, CCDS53858.1	13q11-q12.1	2010-04-20	2002-02-25		ENSG00000075673	ENSG00000075673	3.6.3.10	"""ATPases / P-type"""	13816	protein-coding gene	gene with protein product	"""ATPase, Na+K+ transporting, alpha-1 polypeptide-like"", ""potassium-transporting ATPase alpha chain 2"", ""proton pump"", ""non-gastric H(+)/K(+) ATPase alpha subunit"", ""sodium/potassium ATPase, alpha polypeptide-like"""	182360	"""ATPase, Na+/K+ transporting, alpha polypeptide-like 1"""	ATP1AL1		8838794, 2842249	Standard	NM_001676		Approved		uc010aaa.3	P54707	OTTHUMG00000016588	ENST00000381946.3:c.1524C>T	13.37:g.25272807C>T		33.0	0.0	0		43.0	22.0	0.511628	NM_001185085	Q13816|Q13817|Q16734|Q5W035|Q8N5U2	Silent	SNP	ENST00000381946.3	37	CCDS31948.1																																																																																			C|0.999;T|0.001	0.001	strong		0.517	ATP12A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044199.1	NM_001676	
PRR27	401137	hgsc.bcm.edu	37	4	71024463	71024463	+	Missense_Mutation	SNP	G	G	C	rs142405912	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr4:71024463G>C	ENST00000344526.5	+	3	683	c.494G>C	c.(493-495)gGa>gCa	p.G165A	C4orf40_ENST00000502294.1_Missense_Mutation_p.G165A|C4orf40_ENST00000502441.2_3'UTR	NM_214711.3	NP_999876.2	Q6MZM9	PRR27_HUMAN		165	Ala/Pro-rich.					extracellular vesicular exosome (GO:0070062)				breast(2)|central_nervous_system(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(1)|lung(3)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	12						GCACCTGTTGGAGCTGAGCCT	0.632													G|||	26	0.00519169	0.0038	0.0043	5008	,	,		16092	0.001		0.0139	False		,,,				2504	0.0031				p.G165A		Atlas-SNP	.											.	C4orf40	19	.	0			c.G494C						PASS	.	G	ALA/GLY	8,4398		0,8,2195	29.0	30.0	30.0		494	1.3	0.0	4	dbSNP_134	30	114,8482		2,110,4186	no	missense	C4orf40	NM_214711.3	60	2,118,6381	CC,CG,GG		1.3262,0.1816,0.9383	benign	165/220	71024463	122,12880	2203	4298	6501	SO:0001583	missense	401137	exon3			CTGTTGGAGCTGA																												ENST00000344526.5:c.494G>C	4.37:g.71024463G>C	ENSP00000343172:p.Gly165Ala	135.0	0.0	0		107.0	9.0	0.0841122	NM_214711	A8MXP0|Q6MZR6	Missense_Mutation	SNP	ENST00000344526.5	37	CCDS3535.1	12	0.005494505494505495	0	0.0	2	0.0055248618784530384	0	0.0	10	0.013192612137203167	G	6.439	0.449185	0.12223	0.001816	0.013262	ENSG00000187533	ENST00000502294;ENST00000344526	T;T	0.29917	1.55;1.55	4.43	1.28	0.21552	.	.	.	.	.	T	0.05318	0.0141	N	0.01874	-0.695	0.09310	N	1	B	0.11235	0.004	B	0.06405	0.002	T	0.33343	-0.9872	9	0.02654	T	1	0.4193	1.7036	0.02877	0.1887:0.2762:0.391:0.1441	.	165	Q6MZM9	CD040_HUMAN	A	165	ENSP00000426249:G165A;ENSP00000343172:G165A	ENSP00000343172:G165A	G	+	2	0	C4orf40	71059052	0.000000	0.05858	0.000000	0.03702	0.008000	0.06430	-0.053000	0.11846	-0.013000	0.14199	-0.241000	0.12123	GGA	G|0.993;C|0.007	0.007	strong		0.632	C4orf40-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251558.1		
SLIT3	6586	hgsc.bcm.edu	37	5	168114030	168114030	+	Missense_Mutation	SNP	C	C	T	rs148887706	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr5:168114030C>T	ENST00000519560.1	-	30	3687	c.3268G>A	c.(3268-3270)Gtg>Atg	p.V1090M	SLIT3_ENST00000404867.3_Missense_Mutation_p.V1090M|SLIT3_ENST00000332966.8_Missense_Mutation_p.V1097M	NM_001271946.1|NM_003062.2	NP_001258875.1|NP_003053	O75094	SLIT3_HUMAN	slit homolog 3 (Drosophila)	1090	EGF-like 5. {ECO:0000255|PROSITE- ProRule:PRU00076}.				apoptotic process involved in luteolysis (GO:0061364)|axon extension involved in axon guidance (GO:0048846)|axon guidance (GO:0007411)|cellular response to hormone stimulus (GO:0032870)|negative chemotaxis (GO:0050919)|negative regulation of cell growth (GO:0030308)|negative regulation of cell proliferation (GO:0008285)|negative regulation of chemokine-mediated signaling pathway (GO:0070100)|negative regulation of gene expression (GO:0010629)|organ morphogenesis (GO:0009887)|response to cortisol (GO:0051414)|Roundabout signaling pathway (GO:0035385)	extracellular space (GO:0005615)|mitochondrion (GO:0005739)	calcium ion binding (GO:0005509)|Roundabout binding (GO:0048495)			endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(15)|liver(2)|lung(48)|ovary(4)|prostate(7)|skin(6)|upper_aerodigestive_tract(3)|urinary_tract(1)	100	Renal(175;0.000159)|Lung NSC(126;0.0174)|all_lung(126;0.0392)	Medulloblastoma(196;0.0399)|all_neural(177;0.0966)	Kidney(164;7.53e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000525)			ATTGTGTCCACGCACTGGGCC	0.622													c|||	4	0.000798722	0.0	0.0043	5008	,	,		20234	0.0		0.0	False		,,,				2504	0.001				p.V1097M	Ovarian(29;311 847 10864 17279 24903)	Atlas-SNP	.											.	SLIT3	224	.	0			c.G3289A						PASS	.	T	MET/VAL	1,4405	2.1+/-5.4	0,1,2202	75.0	68.0	70.0		3268	0.6	0.9	5	dbSNP_134	70	1,8599	1.2+/-3.3	0,1,4299	yes	missense	SLIT3	NM_003062.2	21	0,2,6501	TT,TC,CC		0.0116,0.0227,0.0154	possibly-damaging	1090/1524	168114030	2,13004	2203	4300	6503	SO:0001583	missense	6586	exon30			TGTCCACGCACTG	AB011538	CCDS4369.1, CCDS64311.1	5q35	2008-07-18	2001-11-28		ENSG00000184347	ENSG00000184347			11087	protein-coding gene	gene with protein product		603745	"""slit (Drosophila) homolog 3"""	SLIL2		9693030, 9813312	Standard	NM_001271946		Approved	slit2, MEGF5, SLIT1, Slit-3	uc010jjg.4	O75094	OTTHUMG00000130409	ENST00000519560.1:c.3268G>A	5.37:g.168114030C>T	ENSP00000430333:p.Val1090Met	308.0	0.0	0		326.0	165.0	0.506135	NM_001271946	A6H8U9|J3KNP3|O95804|Q9UFH5	Missense_Mutation	SNP	ENST00000519560.1	37	CCDS4369.1	0	0.0	0	0.0	0	0.0	0	0.0	0	0.0	c	2.527	-0.309415	0.05458	2.27E-4	1.16E-4	ENSG00000184347	ENST00000519560;ENST00000332966;ENST00000404867	D;D;D	0.95103	-3.61;-3.61;-3.61	4.59	0.628	0.17681	EGF-like calcium-binding, conserved site (1);EGF (1);EGF-like calcium-binding (1);Epidermal growth factor-like, type 3 (1);	0.373727	0.29707	N	0.011409	D	0.92264	0.7546	M	0.76574	2.34	0.38397	D	0.945565	P	0.43352	0.804	B	0.42163	0.378	D	0.87702	0.2561	10	0.42905	T	0.14	.	7.0594	0.25117	0.1166:0.6:0.0:0.2834	.	1090	O75094	SLIT3_HUMAN	M	1090;1097;1090	ENSP00000430333:V1090M;ENSP00000332164:V1097M;ENSP00000384890:V1090M	ENSP00000332164:V1097M	V	-	1	0	SLIT3	168046608	0.000000	0.05858	0.949000	0.38748	0.003000	0.03518	-0.190000	0.09615	-0.086000	0.12550	-4.011000	0.00013	GTG	C|1.000;T|0.000	0.000	strong		0.622	SLIT3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252792.4	NM_003062	
PHLDB3	653583	hgsc.bcm.edu	37	19	43990438	43990438	+	Missense_Mutation	SNP	G	G	A	rs201337364		TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr19:43990438G>A	ENST00000292140.5	-	13	1825	c.1465C>T	c.(1465-1467)Cct>Tct	p.P489S		NM_198850.3	NP_942147.3	Q6NSJ2	PHLB3_HUMAN	pleckstrin homology-like domain, family B, member 3	489							enzyme binding (GO:0019899)			breast(1)|central_nervous_system(1)|lung(5)	7		Prostate(69;0.0153)				GGAACAGCAGGGCCTGAGGAA	0.582																																					p.P489S		Atlas-SNP	.											.	PHLDB3	30	.	0			c.C1465T						PASS	.	G	SER/PRO	0,4164		0,0,2082	53.0	68.0	63.0		1465	-2.1	0.0	19		63	4,8378		0,4,4187	yes	missense	PHLDB3	NM_198850.3	74	0,4,6269	AA,AG,GG		0.0477,0.0,0.0319	possibly-damaging	489/641	43990438	4,12542	2082	4191	6273	SO:0001583	missense	653583	exon13			CAGCAGGGCCTGA		CCDS12621.2	19q13.31	2013-01-10			ENSG00000176531	ENSG00000176531		"""Pleckstrin homology (PH) domain containing"""	30499	protein-coding gene	gene with protein product							Standard	NM_198850		Approved	FLJ40193	uc002own.4	Q6NSJ2	OTTHUMG00000150693	ENST00000292140.5:c.1465C>T	19.37:g.43990438G>A	ENSP00000292140:p.Pro489Ser	38.0	0.0	0		30.0	15.0	0.5	NM_198850	Q8N7Z4	Missense_Mutation	SNP	ENST00000292140.5	37	CCDS12621.2	.	.	.	.	.	.	.	.	.	.	G	6.513	0.462872	0.12402	0.0	4.77E-4	ENSG00000176531	ENST00000292140	T	0.45276	0.9	4.29	-2.07	0.07276	.	2.063540	0.02567	N	0.097370	T	0.27419	0.0673	L	0.29908	0.895	0.09310	N	1	B;B	0.14438	0.006;0.01	B;B	0.10450	0.005;0.003	T	0.07616	-1.0763	10	0.17369	T	0.5	.	3.9887	0.09527	0.4359:0.1828:0.3813:0.0	.	193;489	B2RXH3;Q6NSJ2	.;PHLB3_HUMAN	S	489	ENSP00000292140:P489S	ENSP00000292140:P489S	P	-	1	0	PHLDB3	48682278	0.668000	0.27493	0.028000	0.17463	0.253000	0.25986	0.582000	0.23834	-0.045000	0.13468	-0.385000	0.06624	CCT	.	.	weak		0.582	PHLDB3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000319643.2		
SNX29	92017	hgsc.bcm.edu	37	16	12145791	12145791	+	Missense_Mutation	SNP	G	G	C	rs118191509	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr16:12145791G>C	ENST00000566228.1	+	8	905	c.836G>C	c.(835-837)gGg>gCg	p.G279A	SNX29_ENST00000306030.3_5'Flank|SNX29_ENST00000323433.4_5'Flank	NM_032167.3	NP_115543.3	Q8TEQ0	SNX29_HUMAN	sorting nexin 29	279						extracellular vesicular exosome (GO:0070062)	phosphatidylinositol binding (GO:0035091)			endometrium(1)|large_intestine(1)|lung(3)|ovary(1)|prostate(1)	7						CAGAACTCTGGGGACGTGTTT	0.473													G|||	34	0.00678914	0.0008	0.0014	5008	,	,		17949	0.001		0.0229	False		,,,				2504	0.0082				p.G279A		Atlas-SNP	.											.	SNX29	60	.	0			c.G836C						PASS	.	G	ALA/GLY	29,4365	32.6+/-62.9	0,29,2168	73.0	82.0	79.0		836	4.8	0.2	16	dbSNP_132	79	247,8353	96.6+/-158.3	3,241,4056	no	missense	SNX29	NM_032167.3	60	3,270,6224	CC,CG,GG		2.8721,0.66,2.1241	benign	279/376	12145791	276,12718	2197	4300	6497	SO:0001583	missense	92017	exon8			ACTCTGGGGACGT	AK074072	CCDS10553.2	16p13.13-p13.12	2011-08-16			ENSG00000048471	ENSG00000048471		"""Sorting nexins"""	30542	protein-coding gene	gene with protein product			"""RUN domain containing 2A"""	RUNDC2A		16782399	Standard	XM_005255682		Approved	FLJ12363	uc002dby.5	Q8TEQ0		ENST00000566228.1:c.836G>C	16.37:g.12145791G>C	ENSP00000456480:p.Gly279Ala	504.0	0.0	0		499.0	217.0	0.43487	NM_032167	B5MDW2|Q8N2X2|Q9HA26	Missense_Mutation	SNP	ENST00000566228.1	37	CCDS10553.2	21	0.009615384615384616	0	0.0	0	0.0	0	0.0	21	0.027704485488126648	G	4.332	0.060912	0.08339	0.0066	0.028721	ENSG00000140660	ENST00000268271	.	.	.	5.78	4.82	0.62117	.	0.280809	0.33235	N	0.005122	T	0.24547	0.0595	L	0.29908	0.895	0.80722	D	1	.	.	.	.	.	.	T	0.18147	-1.0346	7	0.07175	T	0.84	-11.8625	14.9466	0.71035	0.0:0.2704:0.7296:0.0	.	.	.	.	A	279	.	ENSP00000268271:G279A	G	+	2	0	RUNDC2A	12053292	1.000000	0.71417	0.231000	0.23993	0.455000	0.32408	3.912000	0.56386	1.447000	0.47661	0.313000	0.20887	GGG	G|0.983;C|0.017	0.017	strong		0.473	SNX29-005	PUTATIVE	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000422622.1		
HLA-A	3105	hgsc.bcm.edu	37	6	29911227	29911227	+	Nonsense_Mutation	SNP	G	G	T	rs1059537	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr6:29911227G>T	ENST00000396634.1	+	5	867	c.526G>T	c.(526-528)Gag>Tag	p.E176*	HLA-A_ENST00000376806.5_Nonsense_Mutation_p.E176*|HLA-A_ENST00000376802.2_Nonsense_Mutation_p.E176*|HLA-A_ENST00000376809.5_Nonsense_Mutation_p.E176*			P16189	1A31_HUMAN	major histocompatibility complex, class I, A	176	Alpha-2.				antigen processing and presentation of exogenous peptide antigen via MHC class I (GO:0042590)|antigen processing and presentation of exogenous peptide antigen via MHC class I, TAP-dependent (GO:0002479)|antigen processing and presentation of exogenous peptide antigen via MHC class I, TAP-independent (GO:0002480)|antigen processing and presentation of peptide antigen via MHC class I (GO:0002474)|cytokine-mediated signaling pathway (GO:0019221)|interferon-gamma-mediated signaling pathway (GO:0060333)|positive regulation of T cell mediated cytotoxicity (GO:0001916)|regulation of immune response (GO:0050776)|type I interferon signaling pathway (GO:0060337)|viral process (GO:0016032)	cell surface (GO:0009986)|early endosome membrane (GO:0031901)|endoplasmic reticulum (GO:0005783)|ER to Golgi transport vesicle membrane (GO:0012507)|Golgi apparatus (GO:0005794)|Golgi membrane (GO:0000139)|integral component of lumenal side of endoplasmic reticulum membrane (GO:0071556)|MHC class I protein complex (GO:0042612)|phagocytic vesicle membrane (GO:0030670)|plasma membrane (GO:0005886)	beta-2-microglobulin binding (GO:0030881)|peptide antigen binding (GO:0042605)|TAP binding (GO:0046977)			central_nervous_system(2)|cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(3)|lung(10)|ovary(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(5)|urinary_tract(2)	30						GGCGGCCCATGAGGCGGAGCA	0.647									Osteosarcoma, Familial Clustering of;Naso-/Oropharyngeal/Laryngeal Cancer, Familial Clustering of;Melanoma, Familial Clustering of;Lichen Sclerosis et Atrophicus, Familial Clustering of	Multiple Myeloma(9;0.094)			g|||	141	0.028155	0.0741	0.013	5008	,	,		12195	0.0149		0.0109	False		,,,				2504	0.0082				p.E176X		Atlas-SNP	.											.	HLA-A	89	.	0			c.G526T						PASS	.						37.0	29.0	31.0					6																	29911227		1506	2704	4210	SO:0001587	stop_gained	3105	exon3	Familial Cancer Database	Familial Osteogenic Sarcoma;incl.: Familial Head and Neck Cancer; ;Lichen Sclerosis, Familial	GCCCATGAGGCGG	D32129	CCDS34373.1	6p21.3	2013-01-11			ENSG00000206503	ENSG00000206503		"""Histocompatibility complex"", ""Immunoglobulin superfamily / C1-set domain containing"""	4931	protein-coding gene	gene with protein product		142800				8838351	Standard	NM_001242758		Approved		uc003nol.3	P01891	OTTHUMG00000130501	ENST00000396634.1:c.526G>T	6.37:g.29911227G>T	ENSP00000379873:p.Glu176*	192.0	0.0	0		220.0	94.0	0.427273	NM_001242758	O62924|O98009|O98137|Q8MHM1|Q9TPQ3|Q9TQ24|Q9UQU6|Q9UQU7	Nonsense_Mutation	SNP	ENST00000396634.1	37	CCDS34373.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	35|35	5.554389|5.554389	0.96501|0.96501	.|.	.|.	ENSG00000206503|ENSG00000206503	ENST00000396634;ENST00000376806;ENST00000376809;ENST00000376802|ENST00000355767	.|.	.|.	.|.	3.78|3.78	-0.78|-0.78	0.10969|0.10969	.|.	17.376800|.	0.00944|.	U|.	0.002869|.	.|T	.|0.45175	.|0.1329	.|.	.|.	.|.	0.80722|0.80722	A|A	1|1	.|.	.|.	.|.	.|.	.|.	.|.	.|T	.|0.53287	.|-0.8460	.|4	0.59425|0.87932	D|D	0.04|0	.|.	11.7413|11.7413	0.51794|0.51794	0.0:0.0:0.4323:0.5677|0.0:0.0:0.4323:0.5677	rs1059537;rs41560012|rs1059537;rs41560012	.|.	.|.	.|.	X|I	176|150	.|.	ENSP00000365998:E176X|ENSP00000348012:M150I	E|M	+|+	1|3	0|0	HLA-A|HLA-A	30019206|30019206	0.268000|0.268000	0.24133|0.24133	0.000000|0.000000	0.03702|0.03702	0.001000|0.001000	0.01503|0.01503	1.211000|1.211000	0.32382|0.32382	0.028000|0.028000	0.15324|0.15324	-0.335000|-0.335000	0.08231|0.08231	GAG|ATG	C|0.002;G|0.992;T|0.006	0.006	strong		0.647	HLA-A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252909.1	NM_002116	
FAM90A1	55138	hgsc.bcm.edu	37	12	8377348	8377348	+	Silent	SNP	T	T	C	rs199649765		TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr12:8377348T>C	ENST00000538603.1	-	4	639	c.81A>G	c.(79-81)ccA>ccG	p.P27P	FAM90A1_ENST00000307435.6_Silent_p.P27P	NM_018088.3	NP_060558.3	Q86YD7	F90A1_HUMAN	family with sequence similarity 90, member A1	27							nucleic acid binding (GO:0003676)|zinc ion binding (GO:0008270)			endometrium(2)|large_intestine(4)|lung(11)|ovary(1)|prostate(1)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)	25				Kidney(36;0.0866)		TTGGCCCAACTGGGGCCCTCC	0.642																																					p.P27P		Atlas-SNP	.											FAM90A1,NS,neuroblastoma,0,1	FAM90A1	68	1	0			c.A81G						scavenged	.						12.0	16.0	15.0					12																	8377348		2192	4271	6463	SO:0001819	synonymous_variant	55138	exon4			CCCAACTGGGGCC	AK001270	CCDS31738.1	12p13.31	2011-08-31		2005-11-20	ENSG00000171847	ENSG00000171847			25526	protein-coding gene	gene with protein product		613041					Standard	NM_018088		Approved	FLJ10408	uc001qui.2	Q86YD7	OTTHUMG00000168641	ENST00000538603.1:c.81A>G	12.37:g.8377348T>C		12.0	0.0	0		41.0	13.0	0.317073	NM_018088	D3DUU9|Q9NVZ6	Silent	SNP	ENST00000538603.1	37	CCDS31738.1																																																																																			.	.	weak		0.642	FAM90A1-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000400468.1	NM_018088	
TCTN2	79867	hgsc.bcm.edu	37	12	124172643	124172643	+	Silent	SNP	C	C	T	rs144567556	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr12:124172643C>T	ENST00000303372.5	+	7	938	c.810C>T	c.(808-810)gaC>gaT	p.D270D	TCTN2_ENST00000426174.2_Silent_p.D269D	NM_001143850.2|NM_024809.4	NP_001137322.1|NP_079085.2	Q96GX1	TECT2_HUMAN	tectonic family member 2	270					cilium assembly (GO:0042384)|cilium morphogenesis (GO:0060271)|smoothened signaling pathway (GO:0007224)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|integral component of membrane (GO:0016021)|TCTN-B9D complex (GO:0036038)				breast(2)|cervix(2)|endometrium(4)|kidney(1)|large_intestine(4)|lung(12)|ovary(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	30	all_neural(191;0.101)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;0.000163)|Epithelial(86;0.000502)|all cancers(50;0.00451)		TGGATACTGACGCAAAAGACT	0.368													c|||	8	0.00159744	0.0	0.0043	5008	,	,		20396	0.0		0.005	False		,,,				2504	0.0				p.D270D		Atlas-SNP	.											.	TCTN2	50	.	0			c.C810T						PASS	.		,	6,4400	11.4+/-27.6	0,6,2197	133.0	137.0	136.0		807,810	-11.2	0.0	12	dbSNP_134	136	64,8536	38.3+/-94.2	0,64,4236	no	coding-synonymous,coding-synonymous	TCTN2	NM_001143850.1,NM_024809.3	,	0,70,6433	TT,TC,CC		0.7442,0.1362,0.5382	,	269/697,270/698	124172643	70,12936	2203	4300	6503	SO:0001819	synonymous_variant	79867	exon7			TACTGACGCAAAA	AK056924	CCDS9253.1, CCDS45007.1	12q24.31	2011-04-12	2007-08-20	2007-08-20	ENSG00000168778	ENSG00000168778		"""Tectonic proteins"""	25774	protein-coding gene	gene with protein product	"""Meckel syndrome, type 8"""	613846	"""chromosome 12 open reading frame 38"""	C12orf38		21462283	Standard	NM_024809		Approved	FLJ12975, TECT2, MKS8	uc001ufp.3	Q96GX1	OTTHUMG00000168700	ENST00000303372.5:c.810C>T	12.37:g.124172643C>T		113.0	0.0	0		121.0	43.0	0.355372	NM_024809	A8K7Y8|B3KPW5|Q9H966	Silent	SNP	ENST00000303372.5	37	CCDS9253.1																																																																																			C|0.994;T|0.006	0.006	strong		0.368	TCTN2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000400652.1	NM_024809	
HOMEZ	57594	hgsc.bcm.edu	37	14	23744844	23744844	+	Silent	SNP	C	C	T			TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr14:23744844C>T	ENST00000357460.5	-	2	1757	c.1593G>A	c.(1591-1593)gaG>gaA	p.E531E	HOMEZ_ENST00000561013.1_Silent_p.E533E|HOMEZ_ENST00000431326.2_Silent_p.E533E	NM_020834.2	NP_065885.2	Q8IX15	HOMEZ_HUMAN	homeobox and leucine zipper encoding	531	Glu-rich.				regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleolus (GO:0005730)|nucleus (GO:0005634)	DNA binding (GO:0003677)			endometrium(5)|lung(7)	12	all_cancers(95;5.54e-06)			GBM - Glioblastoma multiforme(265;0.00643)		cctcctcctcctcttcctcat	0.493																																					p.E531E		Atlas-SNP	.											.	HOMEZ	80	.	0			c.G1593A						PASS	.						37.0	36.0	36.0					14																	23744844		2196	4286	6482	SO:0001819	synonymous_variant	57594	exon2			CTCCTCCTCTTCC	AB037864	CCDS45085.1	14q11.2	2011-06-20	2007-02-15	2007-02-15		ENSG00000215271		"""Homeoboxes / ZF class"""	20164	protein-coding gene	gene with protein product		608119	"""KIAA1443"""	KIAA1443		12925734	Standard	NM_020834		Approved		uc001wja.2	Q8IX15		ENST00000357460.5:c.1593G>A	14.37:g.23744844C>T		107.0	0.0	0		117.0	7.0	0.0598291	NM_020834	A1L445|B4DZ80|F8WCA3|Q6P049|Q86XB6|Q9P2A5	Silent	SNP	ENST00000357460.5	37	CCDS45085.1																																																																																			.	.	none		0.493	HOMEZ-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000416939.2	NM_020834	
HELZ	9931	hgsc.bcm.edu	37	17	65199433	65199433	+	Splice_Site	SNP	A	A	G			TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr17:65199433A>G	ENST00000358691.5	-	6	539		c.e6+1		HELZ_ENST00000580168.1_Splice_Site|HELZ_ENST00000580662.1_Splice_Site	NM_014877.3	NP_055692	P42694	HELZ_HUMAN	helicase with zinc finger							membrane (GO:0016020)|nucleus (GO:0005634)	ATP binding (GO:0005524)|helicase activity (GO:0004386)|metal ion binding (GO:0046872)|poly(A) RNA binding (GO:0044822)			NS(1)|breast(5)|endometrium(9)|kidney(3)|large_intestine(11)|liver(1)|lung(24)|ovary(1)|pancreas(1)|prostate(1)|skin(8)|upper_aerodigestive_tract(2)|urinary_tract(2)	69	all_cancers(12;1.24e-11)|Breast(2;1.05e-17)|all_epithelial(3;3.87e-13)					TTATCAACATACCAGGGACTC	0.398																																					.		Atlas-SNP	.											.	HELZ	160	.	0			c.372+2T>C						PASS	.						100.0	99.0	99.0					17																	65199433		1898	4122	6020	SO:0001630	splice_region_variant	9931	exon7			CAACATACCAGGG	D29677	CCDS42374.1	17q24.2	2013-01-18			ENSG00000198265	ENSG00000198265		"""Zinc fingers, CCCH-type domain containing"""	16878	protein-coding gene	gene with protein product	"""down-regulated in human cancers"""	606699				10471385, 12691822	Standard	NM_014877		Approved	KIAA0054, HUMORF5, DHRC	uc002jfx.4	P42694	OTTHUMG00000179555	ENST00000358691.5:c.372+1T>C	17.37:g.65199433A>G		76.0	0.0	0		87.0	5.0	0.0574713	NM_014877	I6L9H4	Splice_Site	SNP	ENST00000358691.5	37	CCDS42374.1	.	.	.	.	.	.	.	.	.	.	A	22.2	4.255640	0.80135	.	.	ENSG00000198265	ENST00000358691;ENST00000417253	.	.	.	6.06	6.06	0.98353	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	14.8543	0.70323	1.0:0.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	-	.	.	HELZ	62629895	1.000000	0.71417	0.999000	0.59377	0.946000	0.59487	6.429000	0.73387	2.323000	0.78572	0.528000	0.53228	.	.	.	none		0.398	HELZ-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000447068.1	NM_014877	Intron
CDC25C	995	hgsc.bcm.edu	37	5	137621421	137621421	+	Missense_Mutation	SNP	C	C	T	rs139145068	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr5:137621421C>T	ENST00000323760.6	-	14	1660	c.1382G>A	c.(1381-1383)cGg>cAg	p.R461Q	CDC25C_ENST00000415130.2_Missense_Mutation_p.R388Q|CDC25C_ENST00000513970.1_Missense_Mutation_p.R461Q|CDC25C_ENST00000348983.3_Missense_Mutation_p.R388Q|CDC25C_ENST00000357274.3_Missense_Mutation_p.R418Q|CDC25C_ENST00000514555.1_Missense_Mutation_p.R431Q|CDC25C_ENST00000356505.3_Missense_Mutation_p.R431Q	NM_001790.3	NP_001781.2	P30307	MPIP3_HUMAN	cell division cycle 25C	461					cell proliferation (GO:0008283)|DNA replication (GO:0006260)|G2/M transition of mitotic cell cycle (GO:0000086)|mitotic cell cycle (GO:0000278)|mitotic nuclear division (GO:0007067)|peptidyl-tyrosine dephosphorylation (GO:0035335)|regulation of cell cycle (GO:0051726)|regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0000079)|regulation of mitosis (GO:0007088)|spermatogenesis (GO:0007283)|viral process (GO:0016032)	cytosol (GO:0005829)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)	protein kinase binding (GO:0019901)|protein tyrosine phosphatase activity (GO:0004725)|WW domain binding (GO:0050699)	p.R461Q(1)		endometrium(2)|kidney(3)|large_intestine(5)|lung(5)|skin(1)	16			KIRC - Kidney renal clear cell carcinoma(527;0.004)|Kidney(363;0.00592)			AATCTGCTCCCGCAGCTGCCG	0.542													C|||	7	0.00139776	0.0	0.0043	5008	,	,		18171	0.0		0.001	False		,,,				2504	0.0031				p.R461Q		Atlas-SNP	.											CDC25C,NS,carcinoma,0,1	CDC25C	37	1	1	Substitution - Missense(1)	lung(1)	c.G1382A						PASS	.	C	GLN/ARG,GLN/ARG	5,4401	8.1+/-20.4	0,5,2198	92.0	83.0	86.0		1382,1163	-0.7	0.3	5	dbSNP_134	86	41,8559	27.9+/-77.7	0,41,4259	yes	missense,missense	CDC25C	NM_001790.3,NM_022809.2	43,43	0,46,6457	TT,TC,CC		0.4767,0.1135,0.3537	benign,benign	461/474,388/401	137621421	46,12960	2203	4300	6503	SO:0001583	missense	995	exon14			TGCTCCCGCAGCT	M34065	CCDS4202.1, CCDS4203.1	5q31	2013-01-17	2013-01-17		ENSG00000158402	ENSG00000158402		"""Protein tyrosine phosphatases / Class III Cys-based PTPs"", ""Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"""	1727	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 60"""	157680	"""cell division cycle 25C"", ""cell division cycle 25 homolog C (S. cerevisiae)"", ""cell division cycle 25 homolog C (S. pombe)"""	CDC25		1703321	Standard	XM_005272145		Approved	PPP1R60	uc003lcp.1	P30307	OTTHUMG00000129203	ENST00000323760.6:c.1382G>A	5.37:g.137621421C>T	ENSP00000321656:p.Arg461Gln	155.0	0.0	0		142.0	82.0	0.577465	NM_001790	D3DQB8|Q96PL3|Q9H168|Q9H2E8|Q9H2E9|Q9H2F1	Missense_Mutation	SNP	ENST00000323760.6	37	CCDS4202.1	3	0.0013736263736263737	0	0.0	2	0.0055248618784530384	0	0.0	1	0.0013192612137203166	C	12.41	1.928653	0.34002	0.001135	0.004767	ENSG00000158402	ENST00000323760;ENST00000356505;ENST00000357274;ENST00000348983;ENST00000415130;ENST00000513970;ENST00000534892;ENST00000514555	T;T;T;T;T;T;T	0.27256	2.26;2.28;1.68;1.68;1.68;2.26;2.28	5.08	-0.722	0.11184	.	0.630192	0.14121	N	0.340066	T	0.10895	0.0266	N	0.22421	0.69	0.19575	N	0.999965	B;B;B;B	0.20261	0.043;0.024;0.03;0.014	B;B;B;B	0.10450	0.005;0.003;0.005;0.002	T	0.17776	-1.0358	10	0.38643	T	0.18	0.8534	10.1514	0.42796	0.0:0.4294:0.0:0.5706	.	478;431;388;461	G3V1P6;P30307-2;P30307-4;P30307	.;.;.;MPIP3_HUMAN	Q	461;431;418;388;388;461;478;431	ENSP00000321656:R461Q;ENSP00000348898:R431Q;ENSP00000349821:R418Q;ENSP00000345205:R388Q;ENSP00000392631:R388Q;ENSP00000424795:R461Q;ENSP00000425470:R431Q	ENSP00000321656:R461Q	R	-	2	0	CDC25C	137649320	0.009000	0.17119	0.268000	0.24571	0.929000	0.56500	-0.472000	0.06623	-0.288000	0.09051	0.655000	0.94253	CGG	C|0.997;T|0.003	0.003	strong		0.542	CDC25C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251280.1		
PREPL	9581	hgsc.bcm.edu	37	2	44566479	44566479	+	Missense_Mutation	SNP	G	G	T			TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr2:44566479G>T	ENST00000409936.1	-	7	1213	c.776C>A	c.(775-777)aCa>aAa	p.T259K	PREPL_ENST00000378520.3_Missense_Mutation_p.T259K|PREPL_ENST00000409272.1_Missense_Mutation_p.T259K|PREPL_ENST00000260648.6_Missense_Mutation_p.T259K|PREPL_ENST00000409411.1_Missense_Mutation_p.T170K|PREPL_ENST00000541738.1_Missense_Mutation_p.T170K|PREPL_ENST00000410081.1_Missense_Mutation_p.T259K|PREPL_ENST00000378511.3_Missense_Mutation_p.T259K|PREPL_ENST00000409957.1_Missense_Mutation_p.T170K	NM_001171606.1	NP_001165077.1	Q4J6C6	PPCEL_HUMAN	prolyl endopeptidase-like	259						cytoskeleton (GO:0005856)|Golgi apparatus (GO:0005794)	serine-type endopeptidase activity (GO:0004252)|serine-type exopeptidase activity (GO:0070008)			breast(1)|endometrium(4)|kidney(2)|large_intestine(3)|lung(19)|ovary(1)|prostate(1)|skin(2)	33		all_hematologic(82;0.151)|Acute lymphoblastic leukemia(82;0.175)				ACTGTCTTTTGTAAGATAAAG	0.408																																					p.T259K		Atlas-SNP	.											.	PREPL	69	.	0			c.C776A						PASS	.						60.0	58.0	59.0					2																	44566479		2203	4300	6503	SO:0001583	missense	9581	exon7			TCTTTTGTAAGAT	AB007896	CCDS33190.1, CCDS42675.1, CCDS42676.1, CCDS54353.1	2p22.1	2008-02-05			ENSG00000138078	ENSG00000138078			30228	protein-coding gene	gene with protein product		609557				11524703	Standard	NM_006036		Approved	KIAA0436	uc002ruk.2	Q4J6C6	OTTHUMG00000152791	ENST00000409936.1:c.776C>A	2.37:g.44566479G>T	ENSP00000386543:p.Thr259Lys	109.0	0.0	0		120.0	60.0	0.5	NM_001171603	A7E2X6|D6W5A3|O43163|Q4J6C3|Q4J6C4|Q4ZG39|Q6ZMW7|Q96DW7	Missense_Mutation	SNP	ENST00000409936.1	37	CCDS33190.1	.	.	.	.	.	.	.	.	.	.	G	23.9	4.475698	0.84640	.	.	ENSG00000138078	ENST00000541738;ENST00000409411;ENST00000409957;ENST00000409936;ENST00000260648;ENST00000409272;ENST00000410081;ENST00000378520;ENST00000378511	T;T;T;T;T;T;T;T;T	0.48522	0.81;0.81;0.81;0.81;0.81;0.81;0.81;0.81;0.81	5.37	5.37	0.77165	Peptidase S9A/B/C, oligopeptidase, N-terminal beta-propeller (2);	0.055903	0.64402	D	0.000001	T	0.66336	0.2779	L	0.55481	1.735	0.52501	D	0.999955	D;D;D	0.89917	0.996;1.0;0.999	D;D;D	0.77557	0.99;0.983;0.984	T	0.68603	-0.5365	10	0.87932	D	0	-16.2408	19.0981	0.93263	0.0:0.0:1.0:0.0	.	259;259;259	Q4J6C6-3;Q4J6C6-2;Q4J6C6	.;.;PPCEL_HUMAN	K	170;170;170;259;259;259;259;259;259	ENSP00000439626:T170K;ENSP00000387095:T170K;ENSP00000387241:T170K;ENSP00000386543:T259K;ENSP00000260648:T259K;ENSP00000386909:T259K;ENSP00000386509:T259K;ENSP00000367781:T259K;ENSP00000367772:T259K	ENSP00000260648:T259K	T	-	2	0	PREPL	44419983	1.000000	0.71417	1.000000	0.80357	0.985000	0.73830	6.733000	0.74796	2.491000	0.84063	0.585000	0.79938	ACA	.	.	none		0.408	PREPL-008	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000327900.1	NM_006036	
OR5AR1	219493	hgsc.bcm.edu	37	11	56431618	56431618	+	Silent	SNP	C	C	T	rs77272836	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr11:56431618C>T	ENST00000302969.2	+	1	481	c.457C>T	c.(457-459)Cta>Tta	p.L153L		NM_001004730.1	NP_001004730.1	Q8NGP9	O5AR1_HUMAN	olfactory receptor, family 5, subfamily AR, member 1 (gene/pseudogene)	153						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)	p.L153I(1)		NS(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(1)|lung(12)|prostate(1)|skin(3)|stomach(1)	26						CCTGGCTGGTCTAGTGAGTTT	0.502													C|||	18	0.00359425	0.0008	0.0058	5008	,	,		21429	0.0		0.0129	False		,,,				2504	0.0				p.L153L		Atlas-SNP	.											OR5AR1,NS,carcinoma,0,1	OR5AR1	68	1	1	Substitution - Missense(1)	lung(1)	c.C457T						scavenged	.	C		14,4388	21.2+/-45.6	0,14,2187	204.0	181.0	189.0		457	4.0	1.0	11	dbSNP_132	189	100,8492	55.6+/-116.7	2,96,4198	no	coding-synonymous	OR5AR1	NM_001004730.1		2,110,6385	TT,TC,CC		1.1639,0.318,0.8773		153/311	56431618	114,12880	2201	4296	6497	SO:0001819	synonymous_variant	219493	exon1			GCTGGTCTAGTGA	AB065740	CCDS31535.1	11q11	2013-10-10	2013-10-10		ENSG00000172459	ENSG00000172459		"""GPCR / Class A : Olfactory receptors"""	15260	protein-coding gene	gene with protein product			"""olfactory receptor, family 5, subfamily AR, member 1"""				Standard	NM_001004730		Approved		uc010rjm.2	Q8NGP9	OTTHUMG00000154213	ENST00000302969.2:c.457C>T	11.37:g.56431618C>T		180.0	1.0	0.00555556		209.0	102.0	0.488038	NM_001004730	Q6IF61	Silent	SNP	ENST00000302969.2	37	CCDS31535.1																																																																																			C|0.990;T|0.010	0.010	strong		0.502	OR5AR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000334434.1	NM_001004730	
APBA3	9546	hgsc.bcm.edu	37	19	3760027	3760027	+	Missense_Mutation	SNP	G	G	A	rs11556574	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr19:3760027G>A	ENST00000316757.3	-	2	436	c.236C>T	c.(235-237)gCc>gTc	p.A79V	MRPL54_ENST00000330133.4_5'Flank	NM_004886.3	NP_004877.1	O96018	APBA3_HUMAN	amyloid beta (A4) precursor protein-binding, family A, member 3	79					in utero embryonic development (GO:0001701)|negative regulation of catalytic activity (GO:0043086)|protein transport (GO:0015031)|regulation of gene expression (GO:0010468)|synaptic transmission (GO:0007268)	perinuclear region of cytoplasm (GO:0048471)	beta-amyloid binding (GO:0001540)|enzyme binding (GO:0019899)|enzyme inhibitor activity (GO:0004857)			endometrium(1)|large_intestine(1)|skin(1)	3		Hepatocellular(1079;0.137)		UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|BRCA - Breast invasive adenocarcinoma(158;0.00467)|STAD - Stomach adenocarcinoma(1328;0.18)		GGGACAGGGGGCTCCACCTGG	0.627													G|||	15	0.00299521	0.0008	0.0	5008	,	,		16690	0.0		0.0129	False		,,,				2504	0.001				p.A79V		Atlas-SNP	.											.	APBA3	28	.	0			c.C236T						PASS	.	G	VAL/ALA	7,4399	12.9+/-30.5	0,7,2196	39.0	42.0	41.0		236	-0.5	0.0	19	dbSNP_120	41	97,8503	51.9+/-112.3	0,97,4203	yes	missense	APBA3	NM_004886.3	64	0,104,6399	AA,AG,GG		1.1279,0.1589,0.7996	benign	79/576	3760027	104,12902	2203	4300	6503	SO:0001583	missense	9546	exon2			CAGGGGGCTCCAC	AB021638	CCDS12110.1	19p13.3	2008-07-18	2008-07-18			ENSG00000011132			580	protein-coding gene	gene with protein product	"""X11-like 2"""	604262				10049767	Standard	NM_004886		Approved	X11L2, mint3	uc002lyp.1	O96018		ENST00000316757.3:c.236C>T	19.37:g.3760027G>A	ENSP00000315136:p.Ala79Val	75.0	0.0	0		87.0	42.0	0.482759	NM_004886	O60483|Q9UPZ2	Missense_Mutation	SNP	ENST00000316757.3	37	CCDS12110.1	11	0.005036630036630037	1	0.0020325203252032522	0	0.0	0	0.0	10	0.013192612137203167	G	4.003	-0.002070	0.07819	0.001589	0.011279	ENSG00000011132	ENST00000316757	T	0.43688	0.94	4.73	-0.517	0.11947	.	1.883730	0.03191	N	0.173342	T	0.20495	0.0493	N	0.24115	0.695	0.09310	N	1	B	0.13594	0.008	B	0.14578	0.011	T	0.15607	-1.0431	10	0.33940	T	0.23	.	3.9246	0.09257	0.0925:0.2707:0.4794:0.1574	rs11556574	79	O96018	APBA3_HUMAN	V	79	ENSP00000315136:A79V	ENSP00000315136:A79V	A	-	2	0	APBA3	3711027	0.001000	0.12720	0.043000	0.18650	0.078000	0.17371	0.002000	0.13061	0.389000	0.25086	0.561000	0.74099	GCC	G|0.993;A|0.007	0.007	strong		0.627	APBA3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000453634.2		
KDR	3791	hgsc.bcm.edu	37	4	55972974	55972974	+	Missense_Mutation	SNP	T	T	A	rs1870377	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr4:55972974T>A	ENST00000263923.4	-	11	1711	c.1416A>T	c.(1414-1416)caA>caT	p.Q472H		NM_002253.2	NP_002244.1	P35968	VGFR2_HUMAN	kinase insert domain receptor (a type III receptor tyrosine kinase)	472	Ig-like C2-type 5.		Q -> H (in dbSNP:rs1870377). {ECO:0000269|PubMed:15489334, ECO:0000269|PubMed:17344846}.		angiogenesis (GO:0001525)|branching morphogenesis of an epithelial tube (GO:0048754)|calcium ion homeostasis (GO:0055074)|calcium-mediated signaling using intracellular calcium source (GO:0035584)|cell fate commitment (GO:0045165)|cell maturation (GO:0048469)|cell migration involved in sprouting angiogenesis (GO:0002042)|cellular response to vascular endothelial growth factor stimulus (GO:0035924)|embryonic hemopoiesis (GO:0035162)|endothelial cell differentiation (GO:0045446)|endothelium development (GO:0003158)|extracellular matrix organization (GO:0030198)|lung alveolus development (GO:0048286)|lymph vessel development (GO:0001945)|negative regulation of apoptotic process (GO:0043066)|negative regulation of endothelial cell apoptotic process (GO:2000352)|ovarian follicle development (GO:0001541)|peptidyl-tyrosine autophosphorylation (GO:0038083)|peptidyl-tyrosine phosphorylation (GO:0018108)|positive regulation of angiogenesis (GO:0045766)|positive regulation of cell migration (GO:0030335)|positive regulation of cell proliferation (GO:0008284)|positive regulation of endothelial cell migration (GO:0010595)|positive regulation of endothelial cell proliferation (GO:0001938)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of focal adhesion assembly (GO:0051894)|positive regulation of MAPK cascade (GO:0043410)|positive regulation of mesenchymal cell proliferation (GO:0002053)|positive regulation of nitric-oxide synthase biosynthetic process (GO:0051770)|positive regulation of phosphatidylinositol 3-kinase signaling (GO:0014068)|positive regulation of positive chemotaxis (GO:0050927)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of vasculogenesis (GO:2001214)|protein autophosphorylation (GO:0046777)|regulation of cell shape (GO:0008360)|signal transduction by phosphorylation (GO:0023014)|surfactant homeostasis (GO:0043129)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)|vascular endothelial growth factor receptor signaling pathway (GO:0048010)|vascular endothelial growth factor signaling pathway (GO:0038084)|vasculogenesis (GO:0001570)|viral process (GO:0016032)	cell junction (GO:0030054)|cytoplasmic vesicle (GO:0031410)|early endosome (GO:0005769)|endosome (GO:0005768)|external side of plasma membrane (GO:0009897)|extracellular region (GO:0005576)|Golgi apparatus (GO:0005794)|integral component of plasma membrane (GO:0005887)|membrane raft (GO:0045121)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|sorting endosome (GO:0097443)	ATP binding (GO:0005524)|growth factor binding (GO:0019838)|Hsp90 protein binding (GO:0051879)|integrin binding (GO:0005178)|protein tyrosine kinase activity (GO:0004713)|receptor signaling protein tyrosine kinase activity (GO:0004716)|transmembrane receptor protein tyrosine kinase activity (GO:0004714)|vascular endothelial growth factor binding (GO:0038085)|vascular endothelial growth factor-activated receptor activity (GO:0005021)	p.Q472H(1)		NS(1)|breast(3)|central_nervous_system(4)|endometrium(2)|haematopoietic_and_lymphoid_tissue(6)|kidney(8)|large_intestine(16)|lung(71)|ovary(2)|prostate(2)|skin(10)|soft_tissue(4)|stomach(3)|upper_aerodigestive_tract(1)|urinary_tract(2)	135	all_cancers(7;0.0255)|all_lung(4;0.00175)|Lung NSC(11;0.00384)|all_epithelial(27;0.034)|Glioma(25;0.08)|all_neural(26;0.101)		Epithelial(7;0.189)		Axitinib(DB06626)|Cabozantinib(DB08875)|Pazopanib(DB06589)|Ponatinib(DB08901)|Regorafenib(DB08896)|Sorafenib(DB00398)|Sunitinib(DB01268)	CTGAGACAGCTTGGCTATAAG	0.343			Mis		"""NSCLC, angiosarcoma"""					TSP Lung(20;0.16)			T|||	1061	0.211861	0.09	0.1311	5008	,	,		17888	0.4653		0.2346	False		,,,				2504	0.1493				p.Q472H		Atlas-SNP	.		Dom	yes		4	4q11-q12	3791	vascular endothelial growth factor receptor 2		E	KDR,NS,carcinoma,0,1	KDR	307	1	1	Substitution - Missense(1)	stomach(1)	c.A1416T	GRCh37	CM074306	KDR	M	rs1870377	PASS	.	T	HIS/GLN	485,3921	221.0+/-238.3	28,429,1746	79.0	82.0	81.0		1416	-1.8	0.0	4	dbSNP_92	81	2037,6563	353.6+/-329.2	246,1545,2509	yes	missense	KDR	NM_002253.2	24	274,1974,4255	AA,AT,TT		23.686,11.0077,19.3911	benign	472/1357	55972974	2522,10484	2203	4300	6503	SO:0001583	missense	3791	exon11			GACAGCTTGGCTA	AF035121	CCDS3497.1	4q11-q12	2013-01-29			ENSG00000128052	ENSG00000128052	2.7.10.1	"""CD molecules"", ""Immunoglobulin superfamily / V-set domain containing"", ""Immunoglobulin superfamily / I-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	6307	protein-coding gene	gene with protein product		191306				1417831	Standard	NM_002253		Approved	FLK1, VEGFR, VEGFR2, CD309	uc003has.3	P35968	OTTHUMG00000128734	ENST00000263923.4:c.1416A>T	4.37:g.55972974T>A	ENSP00000263923:p.Gln472His	170.0	0.0	0		190.0	81.0	0.426316	NM_002253	A2RRS0|B5A925|C5IFA0|O60723|Q14178	Missense_Mutation	SNP	ENST00000263923.4	37	CCDS3497.1	513	0.2348901098901099	41	0.08333333333333333	52	0.143646408839779	248	0.43356643356643354	172	0.22691292875989447	T	4.227	0.041015	0.08196	0.110077	0.23686	ENSG00000128052	ENST00000263923	T	0.76448	-1.02	5.67	-1.82	0.07857	Immunoglobulin subtype (1);Immunoglobulin-like (1);	0.974058	0.08489	N	0.938324	T	0.00012	0.0000	L	0.49350	1.555	0.80722	P	0.0	P;B	0.52692	0.955;0.003	P;B	0.56514	0.8;0.011	T	0.14699	-1.0463	9	0.25106	T	0.35	.	5.5298	0.16978	0.0:0.2646:0.2451:0.4903	rs1870377;rs52810770;rs1870377	472;472	P35968-2;P35968	.;VGFR2_HUMAN	H	472	ENSP00000263923:Q472H	ENSP00000263923:Q472H	Q	-	3	2	KDR	55667731	0.011000	0.17503	0.005000	0.12908	0.006000	0.05464	-0.046000	0.11983	-0.160000	0.11002	-0.290000	0.09829	CAA	T|0.781;A|0.219	0.219	strong		0.343	KDR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250645.1		
BCL9	607	hgsc.bcm.edu	37	1	147091689	147091689	+	Silent	SNP	G	G	A	rs61751617	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr1:147091689G>A	ENST00000234739.3	+	8	2468	c.1728G>A	c.(1726-1728)ccG>ccA	p.P576P		NM_004326.2	NP_004317.2	O00512	BCL9_HUMAN	B-cell CLL/lymphoma 9	576	Pro-rich.				canonical Wnt signaling pathway (GO:0060070)|myotube differentiation involved in skeletal muscle regeneration (GO:0014908)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|skeletal muscle cell differentiation (GO:0035914)|somatic stem cell maintenance (GO:0035019)	cis-Golgi network (GO:0005801)|Golgi apparatus (GO:0005794)|nucleus (GO:0005634)				breast(1)|large_intestine(2)|ovary(2)|skin(1)|upper_aerodigestive_tract(1)	7	all_hematologic(923;0.115)					TGGAAGGGCCGAATGTCCCCA	0.567			T	"""IGH@, IGL@"""	B-ALL								G|||	75	0.014976	0.0045	0.0303	5008	,	,		19654	0.001		0.0348	False		,,,				2504	0.0123				p.P576P		Atlas-SNP	.		Dom	yes		1	1q21	607	B-cell CLL/lymphoma 9		L	BCL9_ENST00000234739,NS,carcinoma,+1,1	BCL9	150	1	0			c.G1728A						scavenged	.	G		24,4382	31.7+/-61.6	0,24,2179	82.0	89.0	86.0		1728	-10.8	0.0	1	dbSNP_129	86	333,8267	113.1+/-173.2	7,319,3974	no	coding-synonymous	BCL9	NM_004326.2		7,343,6153	AA,AG,GG		3.8721,0.5447,2.7449		576/1427	147091689	357,12649	2203	4300	6503	SO:0001819	synonymous_variant	607	exon8			AGGGCCGAATGTC	Y13620	CCDS30833.1	1q21	2008-02-05			ENSG00000116128	ENSG00000116128			1008	protein-coding gene	gene with protein product		602597				9490669	Standard	NM_004326		Approved		uc001epq.3	O00512	OTTHUMG00000014031	ENST00000234739.3:c.1728G>A	1.37:g.147091689G>A		68.0	1.0	0.0147059		84.0	49.0	0.583333	NM_004326	Q5T489	Silent	SNP	ENST00000234739.3	37	CCDS30833.1																																																																																			G|0.973;A|0.027	0.027	strong		0.567	BCL9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000039468.1	NM_004326	
PCK2	5106	hgsc.bcm.edu	37	14	24572908	24572908	+	Missense_Mutation	SNP	G	G	A	rs149521304		TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr14:24572908G>A	ENST00000216780.4	+	10	1926	c.1658G>A	c.(1657-1659)cGg>cAg	p.R553Q	PCK2_ENST00000558096.1_Missense_Mutation_p.R387Q|PCK2_ENST00000545054.2_Missense_Mutation_p.R419Q|PCK2_ENST00000559250.1_Intron|NRL_ENST00000561028.1_Intron|PCK2_ENST00000561286.1_Missense_Mutation_p.R419Q	NM_004563.2	NP_004554.2	Q16822	PCKGM_HUMAN	phosphoenolpyruvate carboxykinase 2 (mitochondrial)	553					carbohydrate metabolic process (GO:0005975)|cellular response to glucose stimulus (GO:0071333)|gluconeogenesis (GO:0006094)|glucose metabolic process (GO:0006006)|NADH oxidation (GO:0006116)|oxaloacetate metabolic process (GO:0006107)|positive regulation of insulin secretion (GO:0032024)|pyruvate metabolic process (GO:0006090)|response to glucocorticoid (GO:0051384)|small molecule metabolic process (GO:0044281)	extracellular vesicular exosome (GO:0070062)|mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)	GTP binding (GO:0005525)|metal ion binding (GO:0046872)|phosphoenolpyruvate carboxykinase (GTP) activity (GO:0004613)|phosphoenolpyruvate carboxykinase activity (GO:0004611)			breast(2)|endometrium(2)|kidney(3)|large_intestine(3)|lung(5)|ovary(1)|prostate(1)|skin(1)	18				GBM - Glioblastoma multiforme(265;0.0184)		GAGAATGCTCGGGTGCTAGAC	0.642																																					p.R553Q		Atlas-SNP	.											.	PCK2	66	.	0			c.G1658A						PASS	.	G	GLN/ARG	0,4406		0,0,2203	68.0	74.0	72.0		1658	5.6	1.0	14	dbSNP_134	72	1,8599	1.2+/-3.3	0,1,4299	no	missense	PCK2	NM_004563.2	43	0,1,6502	AA,AG,GG		0.0116,0.0,0.0077	probably-damaging	553/641	24572908	1,13005	2203	4300	6503	SO:0001583	missense	5106	exon10			ATGCTCGGGTGCT	AK129934	CCDS9609.1, CCDS41928.1	14q12	2006-06-09			ENSG00000100889	ENSG00000100889	4.1.1.32		8725	protein-coding gene	gene with protein product		614095				8645161, 9657976	Standard	XM_005267726		Approved	PEPCK, PEPCK2	uc001wlt.3	Q16822	OTTHUMG00000028791	ENST00000216780.4:c.1658G>A	14.37:g.24572908G>A	ENSP00000216780:p.Arg553Gln	146.0	0.0	0		156.0	71.0	0.455128	NM_004563	O43253|Q86U01|Q9BV62	Missense_Mutation	SNP	ENST00000216780.4	37	CCDS9609.1	.	.	.	.	.	.	.	.	.	.	G	36	5.616065	0.96649	0.0	1.16E-4	ENSG00000100889	ENST00000216780;ENST00000545054	T;T	0.07688	3.17;3.17	5.57	5.57	0.84162	Phosphoenolpyruvate carboxykinase, C-terminal (1);	0.000000	0.85682	D	0.000000	T	0.45135	0.1327	H	0.97158	3.95	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;1.0	T	0.62196	-0.6905	10	0.87932	D	0	-9.3642	17.4188	0.87508	0.0:0.0:1.0:0.0	.	419;553	B4DW73;Q16822	.;PCKGM_HUMAN	Q	553;419	ENSP00000216780:R553Q;ENSP00000441826:R419Q	ENSP00000216780:R553Q	R	+	2	0	PCK2	23642748	1.000000	0.71417	0.999000	0.59377	0.997000	0.91878	9.869000	0.99810	2.793000	0.96121	0.655000	0.94253	CGG	G|1.000;A|0.000	0.000	weak		0.642	PCK2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000071900.3	NM_001018073	
ITPKA	3706	hgsc.bcm.edu	37	15	41793728	41793728	+	Missense_Mutation	SNP	A	A	G	rs143540732		TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr15:41793728A>G	ENST00000260386.5	+	2	610	c.557A>G	c.(556-558)tAc>tGc	p.Y186C		NM_002220.2	NP_002211.1	P23677	IP3KA_HUMAN	inositol-trisphosphate 3-kinase A	186					actin cytoskeleton organization (GO:0030036)|dendritic spine maintenance (GO:0097062)|inositol metabolic process (GO:0006020)|inositol phosphate metabolic process (GO:0043647)|positive regulation of dendritic spine morphogenesis (GO:0061003)|regulation of synaptic plasticity (GO:0048167)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)|dendritic spine (GO:0043197)	ATP binding (GO:0005524)|calmodulin-dependent protein kinase activity (GO:0004683)|inositol-1,4,5-trisphosphate 3-kinase activity (GO:0008440)	p.Y186F(1)		kidney(1)|lung(3)|skin(1)	5		all_cancers(109;1.89e-19)|all_epithelial(112;2.28e-16)|Lung NSC(122;5.34e-11)|all_lung(180;1.33e-09)|Melanoma(134;0.0179)|Ovarian(310;0.143)|Colorectal(260;0.172)		OV - Ovarian serous cystadenocarcinoma(18;7.63e-17)|GBM - Glioblastoma multiforme(113;1.34e-06)|Colorectal(105;0.0148)|BRCA - Breast invasive adenocarcinoma(123;0.113)		AAGAAGCGCTACGCCTGGGTG	0.637																																					p.Y186C		Atlas-SNP	.											ITPKA,NS,carcinoma,0,1	ITPKA	19	1	1	Substitution - Missense(1)	lung(1)	c.A557G						PASS	.	A	CYS/TYR	1,4403	2.1+/-5.4	0,1,2201	29.0	25.0	26.0		557	4.7	1.0	15	dbSNP_134	26	4,8596	3.7+/-12.6	0,4,4296	yes	missense	ITPKA	NM_002220.2	194	0,5,6497	GG,GA,AA		0.0465,0.0227,0.0384	probably-damaging	186/462	41793728	5,12999	2202	4300	6502	SO:0001583	missense	3706	exon2			AGCGCTACGCCTG	X54938	CCDS10076.1	15q15.1	2011-04-28	2011-04-28		ENSG00000137825	ENSG00000137825	2.7.1.127		6178	protein-coding gene	gene with protein product		147521	"""inositol 1,4,5-trisphosphate 3-kinase A"""			1330886, 2175886	Standard	NM_002220		Approved	IP3KA, IP3-3KA	uc001znz.3	P23677	OTTHUMG00000130343	ENST00000260386.5:c.557A>G	15.37:g.41793728A>G	ENSP00000260386:p.Tyr186Cys	70.0	0.0	0		83.0	47.0	0.566265	NM_002220	Q8TAN3	Missense_Mutation	SNP	ENST00000260386.5	37	CCDS10076.1	.	.	.	.	.	.	.	.	.	.	A	21.8	4.207364	0.79240	2.27E-4	4.65E-4	ENSG00000137825	ENST00000425927;ENST00000260386	T	0.50548	0.74	4.71	4.71	0.59529	.	0.226565	0.38837	N	0.001556	T	0.66197	0.2765	M	0.70595	2.14	0.53688	D	0.999977	D	0.89917	1.0	D	0.81914	0.995	T	0.70457	-0.4866	10	0.87932	D	0	-10.9047	12.9023	0.58133	1.0:0.0:0.0:0.0	.	186	P23677	IP3KA_HUMAN	C	81;186	ENSP00000260386:Y186C	ENSP00000260386:Y186C	Y	+	2	0	ITPKA	39581020	0.997000	0.39634	0.996000	0.52242	0.995000	0.86356	3.558000	0.53749	1.972000	0.57404	0.379000	0.24179	TAC	A|1.000;G|0.000	0.000	weak		0.637	ITPKA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252695.3	NM_002220	
UFL1	23376	hgsc.bcm.edu	37	6	96985311	96985311	+	Silent	SNP	T	T	C	rs55792562	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr6:96985311T>C	ENST00000369278.4	+	9	930	c.864T>C	c.(862-864)taT>taC	p.Y288Y		NM_015323.4	NP_056138.1	O94874	UFL1_HUMAN	UFM1-specific ligase 1	288					negative regulation of NF-kappaB transcription factor activity (GO:0032088)|negative regulation of protein ubiquitination (GO:0031397)|osteoblast differentiation (GO:0001649)|protein ufmylation (GO:0071569)|regulation of proteasomal ubiquitin-dependent protein catabolic process (GO:0032434)|response to endoplasmic reticulum stress (GO:0034976)	cytoplasm (GO:0005737)|endoplasmic reticulum (GO:0005783)|membrane (GO:0016020)|nucleus (GO:0005634)	UFM1 conjugating enzyme activity (GO:0071568)										AGAAAAGATATAAGACTACAC	0.373													T|||	65	0.0129792	0.0166	0.0259	5008	,	,		17079	0.0		0.0229	False		,,,				2504	0.002				p.Y288Y		Atlas-SNP	.											.	.	.	.	0			c.T864C						PASS	.	T		61,4345	58.1+/-94.6	0,61,2142	159.0	159.0	159.0		864	-6.8	0.9	6	dbSNP_129	159	247,8351	99.7+/-161.2	4,239,4056	no	coding-synonymous	UFL1	NM_015323.4		4,300,6198	CC,CT,TT		2.8728,1.3845,2.3685		288/795	96985311	308,12696	2203	4299	6502	SO:0001819	synonymous_variant	23376	exon9			AAGATATAAGACT	BC036379	CCDS5034.1	6q16.3	2011-08-18	2011-08-18	2011-08-18	ENSG00000014123	ENSG00000014123			23039	protein-coding gene	gene with protein product	"""novel LZAP-binding protein"", ""Regulator of CDK5RAP3 and DDRGK1"""	613372	"""KIAA0776"""	KIAA0776		20018847, 20164180, 20228063, 20531390	Standard	NM_015323		Approved	NLBP, Maxer, RCAD	uc003por.3	O94874	OTTHUMG00000015238	ENST00000369278.4:c.864T>C	6.37:g.96985311T>C		128.0	0.0	0		141.0	76.0	0.539007	NM_015323	A0PJ53|B4DJ57|C0H5X5|Q8N765|Q9NTQ0	Silent	SNP	ENST00000369278.4	37	CCDS5034.1																																																																																			T|0.978;C|0.022	0.022	strong		0.373	UFL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041557.1	NM_015323	
NHSL1	57224	hgsc.bcm.edu	37	6	138794490	138794490	+	Missense_Mutation	SNP	G	G	A	rs201780864	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr6:138794490G>A	ENST00000427025.2	-	3	1064	c.436C>T	c.(436-438)Cca>Tca	p.P146S	NHSL1_ENST00000343505.5_Missense_Mutation_p.P98S|NHSL1_ENST00000479393.2_5'UTR	NM_020464.1	NP_065197.1	Q5SYE7	NHSL1_HUMAN	NHS-like 1	146										breast(2)|endometrium(4)|kidney(1)	7						TCACAGAATGGGCTGGCGTTG	0.517													G|||	6	0.00119808	0.0	0.0014	5008	,	,		14373	0.0		0.003	False		,,,				2504	0.002				p.P146S		Atlas-SNP	.											.	NHSL1	99	.	0			c.C436T						PASS	.	G	SER/PRO,SER/PRO	3,1381		0,3,689	69.0	59.0	62.0		292,436	1.1	0.9	6		62	14,3168		0,14,1577	yes	missense,missense	NHSL1	NM_001144060.1,NM_020464.1	74,74	0,17,2266	AA,AG,GG		0.44,0.2168,0.3723	benign,benign	98/1607,146/1611	138794490	17,4549	692	1591	2283	SO:0001583	missense	57224	exon3			AGAATGGGCTGGC	AB037778	CCDS47487.1, CCDS55063.1	6q23.3	2009-02-18	2004-10-07	2004-10-07	ENSG00000135540	ENSG00000135540			21021	protein-coding gene	gene with protein product			"""chromosome 6 open reading frame 63"""	C6orf63			Standard	NM_001144060		Approved	bA43P8.1, KIAA1357	uc011edp.2	Q5SYE7	OTTHUMG00000016321	ENST00000427025.2:c.436C>T	6.37:g.138794490G>A	ENSP00000394546:p.Pro146Ser	134.0	0.0	0		167.0	79.0	0.473054	NM_020464	Q3ZCS5|Q5SYE8|Q9P2J0	Missense_Mutation	SNP	ENST00000427025.2	37	CCDS55063.1	.	.	.	.	.	.	.	.	.	.	G	8.796	0.931776	0.18131	0.002168	0.0044	ENSG00000135540	ENST00000427025;ENST00000343505;ENST00000342260;ENST00000533765	T;T	0.36878	1.23;1.75	5.13	1.12	0.20585	.	0.390782	0.29307	N	0.012534	T	0.06325	0.0163	L	0.31476	0.935	0.26206	N	0.979379	B;B;B	0.06786	0.001;0.001;0.001	B;B;B	0.08055	0.002;0.003;0.002	T	0.27502	-1.0072	10	0.18710	T	0.47	-13.1246	1.0418	0.01560	0.2696:0.1535:0.4184:0.1585	.	98;98;146	E2QRJ1;Q5SYE7-2;Q5SYE7	.;.;NHSL1_HUMAN	S	146;98;84;99	ENSP00000394546:P146S;ENSP00000344672:P98S	ENSP00000344582:P84S	P	-	1	0	NHSL1	138836183	1.000000	0.71417	0.872000	0.34217	0.369000	0.29798	0.910000	0.28571	0.668000	0.31126	-0.254000	0.11334	CCA	G|0.996;A|0.004	0.004	weak		0.517	NHSL1-001	KNOWN	not_organism_supported|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000043700.2	XM_050421	
CDK20	23552	hgsc.bcm.edu	37	9	90588970	90588970	+	Intron	SNP	C	C	A	rs28364935	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr9:90588970C>A	ENST00000325303.8	-	2	381				CDK20_ENST00000605159.1_Intron|CDK20_ENST00000375883.3_Intron|CDK20_ENST00000375871.4_Intron|CDK20_ENST00000336654.5_Missense_Mutation_p.C32F	NM_001039803.2	NP_001034892.1	Q8IZL9	CDK20_HUMAN	cyclin-dependent kinase 20						cell cycle (GO:0007049)|cell division (GO:0051301)|multicellular organismal development (GO:0007275)	cilium (GO:0005929)|cytoplasm (GO:0005737)|nucleus (GO:0005634)	ATP binding (GO:0005524)|cyclin-dependent protein serine/threonine kinase activity (GO:0004693)			skin(1)	1						AGAAGGCAGACACTGCCAGCC	0.632													.|||	371	0.0740815	0.2141	0.0447	5008	,	,		17061	0.0		0.0507	False		,,,				2504	0.0061				p.C32F		Atlas-SNP	.											.	CDK20	52	.	0			c.G95T						PASS	.	C	,,,,PHE/CYS	813,3593		77,659,1467	47.0	47.0	47.0		,,,,95	1.6	0.0	9	dbSNP_125	47	365,8235		8,349,3943	yes	intron,intron,intron,intron,missense	CDK20	NM_001039803.2,NM_001170639.1,NM_001170640.1,NM_012119.4,NM_178432.3	,,,,205	85,1008,5410	AA,AC,CC		4.2442,18.4521,9.0574	,,,,	,,,,32/339	90588970	1178,11828	2203	4300	6503	SO:0001627	intron_variant	23552	exon2			GGCAGACACTGCC	AF035013	CCDS6677.1, CCDS6678.1, CCDS35060.1, CCDS55324.1, CCDS65075.1	9q22.1	2011-11-08	2009-12-16	2009-12-16	ENSG00000156345	ENSG00000156345		"""Cyclin-dependent kinases"""	21420	protein-coding gene	gene with protein product		610076	"""cell cycle related kinase"""	CCRK		19884882	Standard	NM_178432		Approved	p42	uc004apr.3	Q8IZL9	OTTHUMG00000020161	ENST00000325303.8:c.76-20G>T	9.37:g.90588970C>A		49.0	0.0	0		64.0	32.0	0.5	NM_178432	A2A389|A2A390|B4DQX1|O95137|Q5EDC4|Q5VYW1|Q9BUF4	Missense_Mutation	SNP	ENST00000325303.8	37	CCDS35060.1	168	0.07692307692307693	104	0.21138211382113822	22	0.06077348066298342	0	0.0	42	0.055408970976253295	.	1.147	-0.647886	0.03506	0.184521	0.042442	ENSG00000156345	ENST00000336654	T	0.66815	-0.23	4.55	1.56	0.23342	.	.	.	.	.	T	0.00039	0.0001	.	.	.	0.58432	P	1.999999999946489E-6	B	0.02656	0.0	B	0.01281	0.0	T	0.06250	-1.0837	6	.	.	.	.	3.4873	0.07625	0.1726:0.5644:0.1672:0.0957	rs28364935	32	A2A390	.	F	32	ENSP00000338975:C32F	.	C	-	2	0	CDK20	89778790	0.014000	0.17966	0.002000	0.10522	0.013000	0.08279	0.096000	0.15147	0.099000	0.17552	-1.293000	0.01348	TGT	C|0.916;A|0.084	0.084	strong		0.632	CDK20-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000214996.1	NM_012119	
TRIM38	10475	hgsc.bcm.edu	37	6	25966909	25966909	+	Missense_Mutation	SNP	G	G	T	rs41266771	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr6:25966909G>T	ENST00000357085.3	+	3	635	c.159G>T	c.(157-159)agG>agT	p.R53S	TRIM38_ENST00000349458.3_Missense_Mutation_p.R53S	NM_006355.3	NP_006346.1	O00635	TRI38_HUMAN	tripartite motif containing 38	53					negative regulation of defense response to virus (GO:0050687)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|positive regulation of viral entry into host cell (GO:0046598)|positive regulation of viral genome replication (GO:0045070)|proteasome-mediated ubiquitin-dependent protein catabolic process (GO:0043161)|protein K48-linked ubiquitination (GO:0070936)|regulation of interferon-beta production (GO:0032648)|signal transduction (GO:0007165)	intracellular (GO:0005622)	signal transducer activity (GO:0004871)|zinc ion binding (GO:0008270)			breast(3)|central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(5)|lung(8)|upper_aerodigestive_tract(2)	23						AGCAACTGAGGCAGGAGACAT	0.498													G|||	11	0.00219649	0.0	0.0072	5008	,	,		20263	0.0		0.006	False		,,,				2504	0.0				p.R53S		Atlas-SNP	.											.	TRIM38	50	.	0			c.G159T						PASS	.	G	SER/ARG	7,4399	12.9+/-30.5	0,7,2196	83.0	80.0	81.0		159	-1.0	0.0	6	dbSNP_127	81	73,8527	44.0+/-102.2	0,73,4227	yes	missense	TRIM38	NM_006355.2	110	0,80,6423	TT,TG,GG		0.8488,0.1589,0.6151	benign	53/466	25966909	80,12926	2203	4300	6503	SO:0001583	missense	10475	exon3			ACTGAGGCAGGAG	U90547	CCDS4568.1	6p21.3	2011-04-20	2011-01-25	2002-06-07	ENSG00000112343	ENSG00000112343		"""Tripartite motif containing / Tripartite motif containing"", ""RING-type (C3HC4) zinc fingers"""	10059	protein-coding gene	gene with protein product			"""ring finger protein 15"", ""tripartite motif-containing 38"""	RNF15			Standard	XR_241880		Approved	RORET	uc003nfm.4	O00635	OTTHUMG00000014414	ENST00000357085.3:c.159G>T	6.37:g.25966909G>T	ENSP00000349596:p.Arg53Ser	71.0	0.0	0		78.0	33.0	0.423077	NM_006355	B2R862	Missense_Mutation	SNP	ENST00000357085.3	37	CCDS4568.1	8	0.003663003663003663	0	0.0	2	0.0055248618784530384	0	0.0	6	0.0079155672823219	g	7.501	0.652721	0.14580	0.001589	0.008488	ENSG00000112343	ENST00000540262;ENST00000349458;ENST00000357085	T;T;T	0.53423	0.62;0.62;0.62	3.88	-0.956	0.10353	Zinc finger, RING/FYVE/PHD-type (1);Zinc finger, RING-type (2);Zinc finger, C3HC4 RING-type (1);	3.891910	0.00698	N	0.000762	T	0.07007	0.0178	N	0.12502	0.225	0.09310	N	1	B;B	0.02656	0.0;0.0	B;B	0.06405	0.002;0.002	T	0.05241	-1.0897	10	0.07482	T	0.82	.	1.1526	0.01789	0.3016:0.152:0.392:0.1543	rs41266771	53;53	B2R862;O00635	.;TRI38_HUMAN	S	53	ENSP00000443976:R53S;ENSP00000230099:R53S;ENSP00000349596:R53S	ENSP00000230099:R53S	R	+	3	2	TRIM38	26074888	0.000000	0.05858	0.000000	0.03702	0.012000	0.07955	0.076000	0.14712	-0.198000	0.10333	0.585000	0.79938	AGG	G|0.995;T|0.005	0.005	strong		0.498	TRIM38-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040076.2		
MTOR	2475	hgsc.bcm.edu	37	1	11188142	11188142	+	Silent	SNP	C	C	T	rs192740864	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr1:11188142C>T	ENST00000361445.4	-	43	6028	c.5952G>A	c.(5950-5952)acG>acA	p.T1984T	MTOR_ENST00000376838.1_Silent_p.T189T	NM_004958.3	NP_004949.1	P42345	MTOR_HUMAN	mechanistic target of rapamycin (serine/threonine kinase)	1984					cell growth (GO:0016049)|cellular response to hypoxia (GO:0071456)|cellular response to nutrient levels (GO:0031669)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|germ cell development (GO:0007281)|growth (GO:0040007)|innate immune response (GO:0045087)|insulin receptor signaling pathway (GO:0008286)|negative regulation of autophagy (GO:0010507)|negative regulation of cell size (GO:0045792)|negative regulation of macroautophagy (GO:0016242)|negative regulation of NFAT protein import into nucleus (GO:0051534)|neurotrophin TRK receptor signaling pathway (GO:0048011)|peptidyl-serine phosphorylation (GO:0018105)|peptidyl-threonine phosphorylation (GO:0018107)|phosphatidylinositol-mediated signaling (GO:0048015)|phosphorylation (GO:0016310)|positive regulation of actin filament polymerization (GO:0030838)|positive regulation of endothelial cell proliferation (GO:0001938)|positive regulation of gene expression (GO:0010628)|positive regulation of lamellipodium assembly (GO:0010592)|positive regulation of lipid biosynthetic process (GO:0046889)|positive regulation of myotube differentiation (GO:0010831)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|positive regulation of protein kinase B signaling (GO:0051897)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of stress fiber assembly (GO:0051496)|positive regulation of transcription from RNA polymerase III promoter (GO:0045945)|positive regulation of translation (GO:0045727)|protein autophosphorylation (GO:0046777)|protein catabolic process (GO:0030163)|protein phosphorylation (GO:0006468)|regulation of actin cytoskeleton organization (GO:0032956)|regulation of carbohydrate utilization (GO:0043610)|regulation of fatty acid beta-oxidation (GO:0031998)|regulation of glycogen biosynthetic process (GO:0005979)|regulation of protein kinase activity (GO:0045859)|regulation of Rac GTPase activity (GO:0032314)|regulation of response to food (GO:0032095)|response to amino acid (GO:0043200)|response to nutrient (GO:0007584)|response to stress (GO:0006950)|ruffle organization (GO:0031529)|signal transduction (GO:0007165)|T cell costimulation (GO:0031295)|TOR signaling (GO:0031929)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|endomembrane system (GO:0012505)|endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|lysosomal membrane (GO:0005765)|lysosome (GO:0005764)|membrane (GO:0016020)|mitochondrial outer membrane (GO:0005741)|phosphatidylinositol 3-kinase complex (GO:0005942)|PML body (GO:0016605)|TORC1 complex (GO:0031931)|TORC2 complex (GO:0031932)	ATP binding (GO:0005524)|drug binding (GO:0008144)|kinase activity (GO:0016301)|phosphoprotein binding (GO:0051219)|protein serine/threonine kinase activity (GO:0004674)|ribosome binding (GO:0043022)|RNA polymerase III type 1 promoter DNA binding (GO:0001030)|RNA polymerase III type 2 promoter DNA binding (GO:0001031)|RNA polymerase III type 3 promoter DNA binding (GO:0001032)|TFIIIC-class transcription factor binding (GO:0001156)			breast(5)|central_nervous_system(7)|endometrium(20)|kidney(34)|large_intestine(21)|lung(43)|ovary(9)|prostate(3)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(1)	149					Everolimus(DB01590)|Pimecrolimus(DB00337)|Sirolimus(DB00877)|Temsirolimus(DB06287)	GCCGGGCTGTCGTGGTAGACT	0.522													C|||	5	0.000998403	0.0	0.0014	5008	,	,		18279	0.0		0.001	False		,,,				2504	0.0031				p.T1984T		Atlas-SNP	.											.	MTOR	327	.	0			c.G5952A						PASS	.	C		0,4406		0,0,2203	125.0	130.0	128.0		5952	-8.4	0.5	1		128	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous	MTOR	NM_004958.3		0,1,6502	TT,TC,CC		0.0116,0.0,0.0077		1984/2550	11188142	1,13005	2203	4300	6503	SO:0001819	synonymous_variant	2475	exon43			GGCTGTCGTGGTA	L34075	CCDS127.1	1p36	2014-09-17	2009-05-29	2009-05-29	ENSG00000198793	ENSG00000198793			3942	protein-coding gene	gene with protein product	"""FK506 binding protein 12-rapamycin associated protein 2"", ""rapamycin target protein"", ""FKBP12-rapamycin complex-associated protein 1"", ""FKBP-rapamycin associated protein"", ""rapamycin associated protein FRAP2"", ""dJ576K7.1 (FK506 binding protein 12-rapamycin associated protein 1)"", ""rapamycin and FKBP12 target 1"", ""mammalian target of rapamycin"""	601231	"""FK506 binding protein 12-rapamycin associated protein 1"""	FRAP, FRAP2, FRAP1		8008069, 8660990	Standard	NM_004958		Approved	RAFT1, RAPT1, FLJ44809	uc001asd.3	P42345	OTTHUMG00000002001	ENST00000361445.4:c.5952G>A	1.37:g.11188142C>T		108.0	0.0	0		98.0	48.0	0.489796	NM_004958	Q4LE76|Q5TER1|Q6LE87|Q96QG3|Q9Y4I3	Silent	SNP	ENST00000361445.4	37	CCDS127.1																																																																																			C|1.000;T|0.000	0.000	strong		0.522	MTOR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000005558.1	NM_004958	
PI4KA	5297	hgsc.bcm.edu	37	22	21065652	21065652	+	Missense_Mutation	SNP	T	T	C			TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr22:21065652T>C	ENST00000572273.1	-	51	5956	c.5726A>G	c.(5725-5727)aAg>aGg	p.K1909R	PI4KA_ENST00000414196.3_Missense_Mutation_p.K719R|PI4KA_ENST00000255882.6_Missense_Mutation_p.K1967R			P42356	PI4KA_HUMAN	phosphatidylinositol 4-kinase, catalytic, alpha	1909	PI3K/PI4K. {ECO:0000255|PROSITE- ProRule:PRU00269}.				phosphatidylinositol biosynthetic process (GO:0006661)|phosphatidylinositol-mediated signaling (GO:0048015)|phospholipid metabolic process (GO:0006644)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|Golgi-associated vesicle membrane (GO:0030660)|membrane (GO:0016020)|plasma membrane (GO:0005886)	1-phosphatidylinositol 4-kinase activity (GO:0004430)|ATP binding (GO:0005524)			breast(3)|endometrium(8)|kidney(9)|large_intestine(19)|lung(29)|ovary(1)|pancreas(1)|prostate(3)|salivary_gland(1)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)	79	all_cancers(11;7.59e-25)|all_epithelial(7;1.34e-22)|Melanoma(16;0.000465)|Ovarian(15;0.00167)|Colorectal(54;0.0332)|all_neural(72;0.142)	Lung SC(17;0.0262)	LUSC - Lung squamous cell carcinoma(15;0.000536)|Lung(15;0.0108)|Epithelial(17;0.196)			ATGACCCTTCTTGTCCAGCAT	0.597																																					p.K1967R	GBM(136;1332 1831 3115 23601 50806)	Atlas-SNP	.											PI4KA_ENST00000255882,NS,carcinoma,+1,2	PI4KA	313	2	0			c.A5900G						scavenged	.						101.0	122.0	115.0					22																	21065652		2072	4111	6183	SO:0001583	missense	5297	exon51			CCCTTCTTGTCCA	L36151	CCDS33603.1, CCDS33603.2	22q11.21	2011-05-25	2007-08-14	2007-08-02	ENSG00000241973	ENSG00000241973			8983	protein-coding gene	gene with protein product		600286		PIK4CA		7961848, 8662589	Standard	NM_002650		Approved	PI4K-ALPHA, pi4K230	uc002zsz.5	P42356	OTTHUMG00000167440	ENST00000572273.1:c.5726A>G	22.37:g.21065652T>C	ENSP00000458238:p.Lys1909Arg	375.0	2.0	0.00533333		59.0	26.0	0.440678	NM_058004	Q7Z625|Q9UPG2	Missense_Mutation	SNP	ENST00000572273.1	37		.	.	.	.	.	.	.	.	.	.	T	16.62	3.174495	0.57692	.	.	ENSG00000241973	ENST00000255882;ENST00000414196;ENST00000399213	T;T	0.81330	-1.48;-1.48	5.04	5.04	0.67666	Protein kinase-like domain (1);Phosphatidylinositol 3-/4-kinase, catalytic (4);	0.112508	0.64402	D	0.000001	T	0.71854	0.3389	L	0.28274	0.84	0.53005	D	0.999967	B;B	0.18166	0.001;0.026	B;B	0.29176	0.02;0.099	T	0.66204	-0.5982	10	0.21014	T	0.42	-24.001	15.0754	0.72074	0.0:0.0:0.0:1.0	.	300;1909	A8MTF1;P42356	.;PI4KA_HUMAN	R	1909;719;300	ENSP00000402981:K719R;ENSP00000382162:K300R	ENSP00000255882:K1909R	K	-	2	0	PI4KA	19395652	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	4.560000	0.60802	2.031000	0.59945	0.443000	0.29094	AAG	.	.	none		0.597	PI4KA-202	KNOWN	basic|appris_principal	protein_coding	protein_coding		NM_058004	
GBP6	163351	hgsc.bcm.edu	37	1	89835209	89835209	+	Missense_Mutation	SNP	G	G	A	rs75966734	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr1:89835209G>A	ENST00000370456.4	+	3	388	c.295G>A	c.(295-297)Gaa>Aaa	p.E99K	GBP6_ENST00000535065.1_Intron	NM_198460.2	NP_940862.2	Q6ZN66	GBP6_HUMAN	guanylate binding protein family, member 6	99	GB1/RHD3-type G.|GTPase domain (Globular). {ECO:0000250}.				cellular response to interferon-gamma (GO:0071346)|defense response to bacterium (GO:0042742)|immune response (GO:0006955)	extracellular vesicular exosome (GO:0070062)	GTP binding (GO:0005525)|GTPase activity (GO:0003924)			breast(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(2)|kidney(11)|large_intestine(8)|lung(10)|ovary(2)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)	42		Lung NSC(277;0.0908)		all cancers(265;0.0108)|Epithelial(280;0.0398)		TCTGGACACCGAAGGTCTGGG	0.512													G|||	26	0.00519169	0.0015	0.0014	5008	,	,		20562	0.0		0.0199	False		,,,				2504	0.0031				p.E99K		Atlas-SNP	.											.	GBP6	87	.	0			c.G295A						PASS	.	G	LYS/GLU	7,4399	12.9+/-30.5	0,7,2196	81.0	75.0	77.0		295	4.6	0.9	1	dbSNP_132	77	74,8526	44.5+/-102.8	0,74,4226	yes	missense	GBP6	NM_198460.2	56	0,81,6422	AA,AG,GG		0.8605,0.1589,0.6228	probably-damaging	99/634	89835209	81,12925	2203	4300	6503	SO:0001583	missense	163351	exon3			GACACCGAAGGTC	BX537949	CCDS723.1	1p22	2008-02-05			ENSG00000183347	ENSG00000183347			25395	protein-coding gene	gene with protein product		612467					Standard	NM_198460		Approved	DKFZp686G0786	uc001dnf.2	Q6ZN66	OTTHUMG00000010123	ENST00000370456.4:c.295G>A	1.37:g.89835209G>A	ENSP00000359485:p.Glu99Lys	156.0	0.0	0		148.0	59.0	0.398649	NM_198460	A2RRM3|Q6ZN86|Q7Z3F0	Missense_Mutation	SNP	ENST00000370456.4	37	CCDS723.1	17	0.007783882783882784	1	0.0020325203252032522	0	0.0	0	0.0	16	0.021108179419525065	G	20.9	4.059633	0.76074	0.001589	0.008605	ENSG00000183347	ENST00000544311;ENST00000370456	T	0.64803	-0.12	4.55	4.55	0.56014	Guanylate-binding protein, N-terminal (1);	0.000000	0.85682	D	0.000000	D	0.85487	0.5708	H	0.98786	4.33	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.91319	0.5080	10	0.87932	D	0	-32.7322	14.7834	0.69784	0.0:0.0:1.0:0.0	.	99	Q6ZN66	GBP6_HUMAN	K	70;99	ENSP00000359485:E99K	ENSP00000359485:E99K	E	+	1	0	GBP6	89607797	1.000000	0.71417	0.911000	0.35937	0.426000	0.31534	6.781000	0.75068	2.079000	0.62486	0.585000	0.79938	GAA	G|0.993;A|0.007	0.007	strong		0.512	GBP6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000028001.1	NM_198460	
ZNF414	84330	hgsc.bcm.edu	37	19	8577924	8577924	+	Missense_Mutation	SNP	C	C	T			TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr19:8577924C>T	ENST00000255616.8	-	2	406	c.305G>A	c.(304-306)cGc>cAc	p.R102H	ZNF414_ENST00000393927.4_Missense_Mutation_p.R102H	NM_032370.2	NP_115746.2	Q96IQ9	ZN414_HUMAN	zinc finger protein 414	102					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			lung(2)	2						TGGAGGTGGGCGTCGTCTGGG	0.617																																					p.R102H		Atlas-SNP	.											.	ZNF414	25	.	0			c.G305A						PASS	.						7.0	5.0	6.0					19																	8577924		1959	3887	5846	SO:0001583	missense	84330	exon2			GGTGGGCGTCGTC	AK074191	CCDS12205.1, CCDS54211.1	19p13.2	2008-02-05				ENSG00000133250		"""Zinc fingers, C2H2-type"""	20630	protein-coding gene	gene with protein product							Standard	NM_032370		Approved	MGC15716, Zfp414	uc002mke.4	Q96IQ9		ENST00000255616.8:c.305G>A	19.37:g.8577924C>T	ENSP00000255616:p.Arg102His	105.0	0.0	0		83.0	54.0	0.650602	NM_032370	A8MY94	Missense_Mutation	SNP	ENST00000255616.8	37	CCDS12205.1	.	.	.	.	.	.	.	.	.	.	C	22.5	4.302311	0.81136	.	.	ENSG00000133250	ENST00000393927;ENST00000255616	T;T	0.09817	2.94;2.94	4.52	3.4	0.38934	.	0.170242	0.37304	N	0.002141	T	0.23965	0.0580	L	0.61036	1.89	0.29293	N	0.869209	D;D	0.76494	0.999;0.999	D;D	0.80764	0.994;0.991	T	0.02893	-1.1097	10	0.15499	T	0.54	-24.3645	11.0252	0.47741	0.0:0.8107:0.1893:0.0	.	102;102	Q96IQ9;A8MY94	ZN414_HUMAN;.	H	102	ENSP00000377504:R102H;ENSP00000255616:R102H	ENSP00000255616:R102H	R	-	2	0	ZNF414	8483924	0.975000	0.34042	0.995000	0.50966	0.988000	0.76386	0.720000	0.25896	2.219000	0.72066	0.655000	0.94253	CGC	.	.	none		0.617	ZNF414-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000460199.2	NM_032370	
TENM2	57451	hgsc.bcm.edu	37	5	167631599	167631599	+	Missense_Mutation	SNP	G	G	A	rs141103827	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr5:167631599G>A	ENST00000518659.1	+	19	3836	c.3797G>A	c.(3796-3798)cGa>cAa	p.R1266Q	TENM2_ENST00000403607.2_Missense_Mutation_p.R1090Q|TENM2_ENST00000545108.1_Missense_Mutation_p.R1266Q|TENM2_ENST00000519204.1_Missense_Mutation_p.R1145Q|TENM2_ENST00000520394.1_Missense_Mutation_p.R1034Q	NM_001122679.1	NP_001116151.1	Q9NT68	TEN2_HUMAN	teneurin transmembrane protein 2	1266					axon guidance (GO:0007411)|calcium-mediated signaling using intracellular calcium source (GO:0035584)|heterophilic cell-cell adhesion (GO:0007157)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of filopodium assembly (GO:0051491)|self proteolysis (GO:0097264)|signal transduction (GO:0007165)|single organismal cell-cell adhesion (GO:0016337)|transcription, DNA-templated (GO:0006351)	cell junction (GO:0030054)|cell-cell junction (GO:0005911)|dendrite (GO:0030425)|dendritic spine (GO:0043197)|endoplasmic reticulum (GO:0005783)|filopodium (GO:0030175)|Golgi apparatus (GO:0005794)|growth cone (GO:0030426)|integral component of plasma membrane (GO:0005887)|neuron projection (GO:0043005)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|PML body (GO:0016605)|postsynaptic membrane (GO:0045211)|synapse (GO:0045202)	cell adhesion molecule binding (GO:0050839)|protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)|receptor binding (GO:0005102)										TTTCCCTCTCGAAATGTGACC	0.522													g|||	25	0.00499201	0.0008	0.0014	5008	,	,		18911	0.0		0.004	False		,,,				2504	0.0194				p.R1257Q		Atlas-SNP	.											.	.	.	.	0			c.G3770A						PASS	.	G	GLN/ARG	3,3911		0,3,1954	93.0	89.0	90.0		3770	4.0	1.0	5	dbSNP_134	90	38,8266		0,38,4114	yes	missense	ODZ2	NM_001122679.1	43	0,41,6068	AA,AG,GG		0.4576,0.0766,0.3356	possibly-damaging	1257/2766	167631599	41,12177	1957	4152	6109	SO:0001583	missense	57451	exon19			CCTCTCGAAATGT	AB032953		5q35	2012-10-02	2012-10-02	2012-10-02	ENSG00000145934	ENSG00000145934			29943	protein-coding gene	gene with protein product		610119	"""odz, odd Oz/ten-m homolog 2 (Drosophila)"""	ODZ2		10625539	Standard	NM_001122679		Approved	KIAA1127, Ten-M2	uc010jjd.3	Q9NT68	OTTHUMG00000162928	ENST00000518659.1:c.3797G>A	5.37:g.167631599G>A	ENSP00000429430:p.Arg1266Gln	154.0	0.0	0		154.0	89.0	0.577922	NM_001122679	Q9ULU2	Missense_Mutation	SNP	ENST00000518659.1	37		4	0.0018315018315018315	0	0.0	0	0.0	0	0.0	4	0.005277044854881266	g	22.9	4.353549	0.82243	7.66E-4	0.004576	ENSG00000145934	ENST00000518659;ENST00000545108;ENST00000519204;ENST00000520394;ENST00000403607	D;D;D;D;D	0.90069	-2.61;-2.61;-2.61;-2.61;-2.61	4.9	4.01	0.46588	Six-bladed beta-propeller, TolB-like (1);	0.229981	0.43579	D	0.000549	T	0.77164	0.4090	N	0.08118	0	0.32750	N	0.506584	D;P;P	0.53885	0.963;0.785;0.942	P;B;B	0.46850	0.529;0.166;0.149	D	0.85392	0.1126	10	0.87932	D	0	.	15.0945	0.72223	0.0:0.1425:0.8575:0.0	.	1266;1266;1034	F5H2D1;Q9NT68;F8VNQ3	.;TEN2_HUMAN;.	Q	1266;1266;1145;1034;1090	ENSP00000429430:R1266Q;ENSP00000438635:R1266Q;ENSP00000428964:R1145Q;ENSP00000427874:R1034Q;ENSP00000384905:R1090Q	ENSP00000384905:R1090Q	R	+	2	0	ODZ2	167564177	1.000000	0.71417	0.986000	0.45419	0.986000	0.74619	5.887000	0.69751	1.025000	0.39708	0.550000	0.68814	CGA	G|0.997;A|0.003	0.003	strong		0.522	TENM2-001	KNOWN	not_organism_supported|basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000376096.1	NM_001122679	
CCDC39	339829	hgsc.bcm.edu	37	3	180359790	180359790	+	Missense_Mutation	SNP	T	T	C	rs200277460	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr3:180359790T>C	ENST00000442201.2	-	13	1984	c.1865A>G	c.(1864-1866)gAa>gGa	p.E622G	CCDC39_ENST00000273654.4_Missense_Mutation_p.E706G	NM_181426.1	NP_852091.1	Q9UFE4	CCD39_HUMAN	coiled-coil domain containing 39	622					axonemal dynein complex assembly (GO:0070286)|cilium-dependent cell motility (GO:0060285)|determination of digestive tract left/right asymmetry (GO:0071907)|determination of liver left/right asymmetry (GO:0071910)|determination of pancreatic left/right asymmetry (GO:0035469)|epithelial cilium movement involved in determination of left/right asymmetry (GO:0060287)|heart looping (GO:0001947)|lung development (GO:0030324)	axoneme (GO:0005930)|cytoskeleton (GO:0005856)				NS(1)|breast(1)|endometrium(4)|large_intestine(9)|lung(22)|ovary(6)|prostate(2)	45	all_cancers(143;9.31e-15)|Ovarian(172;0.0212)		OV - Ovarian serous cystadenocarcinoma(80;5.62e-23)|GBM - Glioblastoma multiforme(14;0.000558)			CCTTATGTTTTCCCGTTCTTG	0.378													T|||	3	0.000599042	0.0	0.0	5008	,	,		17354	0.0		0.003	False		,,,				2504	0.0				p.E622G		Atlas-SNP	.											.	CCDC39	242	.	0			c.A1865G						PASS	.	T	GLY/GLU	0,3678		0,0,1839	129.0	119.0	122.0		1865	4.9	1.0	3		122	11,8175		0,11,4082	yes	missense	CCDC39	NM_181426.1	98	0,11,5921	CC,CT,TT		0.1344,0.0,0.0927	benign	622/942	180359790	11,11853	1839	4093	5932	SO:0001583	missense	339829	exon13			ATGTTTTCCCGTT	BC047103	CCDS46964.1	3q26.33	2012-07-27			ENSG00000145075	ENSG00000145075			25244	protein-coding gene	gene with protein product		613798				21131972	Standard	NM_181426		Approved	DKFZp434A128, CILD14, FAP59	uc010hxe.3	Q9UFE4	OTTHUMG00000157857	ENST00000442201.2:c.1865A>G	3.37:g.180359790T>C	ENSP00000405708:p.Glu622Gly	205.0	0.0	0		207.0	95.0	0.458937	NM_181426	B4E2H1	Missense_Mutation	SNP	ENST00000442201.2	37	CCDS46964.1	2	9.157509157509158E-4	0	0.0	0	0.0	0	0.0	2	0.002638522427440633	T	16.10	3.028257	0.54790	0.0	0.001344	ENSG00000145075	ENST00000273654;ENST00000442201	.	.	.	4.9	4.9	0.64082	.	0.169998	0.52532	D	0.000067	T	0.26412	0.0645	N	0.08118	0	0.26248	N	0.978768	B	0.24882	0.113	B	0.26094	0.066	T	0.24154	-1.0168	9	0.48119	T	0.1	-11.3381	14.5324	0.67936	0.0:0.0:0.0:1.0	.	622	Q9UFE4	CCD39_HUMAN	G	706;622	.	ENSP00000273654:E706G	E	-	2	0	CCDC39	181842484	1.000000	0.71417	0.990000	0.47175	0.975000	0.68041	6.020000	0.70826	1.961000	0.56991	0.472000	0.43445	GAA	T|0.999;C|0.001	0.001	strong		0.378	CCDC39-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000349783.3	XM_291028	
ZNF653	115950	hgsc.bcm.edu	37	19	11598224	11598224	+	Missense_Mutation	SNP	C	C	T	rs74552618	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr19:11598224C>T	ENST00000293771.5	-	4	1190	c.1054G>A	c.(1054-1056)Gag>Aag	p.E352K	CTC-398G3.6_ENST00000585656.1_Intron	NM_138783.3	NP_620138.2	Q96CK0	ZN653_HUMAN	zinc finger protein 653	352					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)|large_intestine(2)|lung(8)|prostate(1)|skin(1)	17						GGCACCTCCTCGCCCAGTCCA	0.652													C|||	29	0.00579073	0.0015	0.0043	5008	,	,		16677	0.001		0.0129	False		,,,				2504	0.0102				p.E352K	Pancreas(83;980 1446 4542 6441 43352)	Atlas-SNP	.											.	ZNF653	48	.	0			c.G1054A						PASS	.	C	LYS/GLU	5,4401	9.9+/-24.2	0,5,2198	63.0	52.0	56.0		1054	4.1	1.0	19	dbSNP_131	56	120,8480	62.4+/-124.4	1,118,4181	yes	missense	ZNF653	NM_138783.3	56	1,123,6379	TT,TC,CC		1.3953,0.1135,0.9611	benign	352/616	11598224	125,12881	2203	4300	6503	SO:0001583	missense	115950	exon4			CCTCCTCGCCCAG	AY072704	CCDS12261.1	19p13.2	2013-01-08						"""Zinc fingers, C2H2-type"""	25196	protein-coding gene	gene with protein product		611371				12477932	Standard	NM_138783		Approved	Zip67	uc002mrz.2	Q96CK0		ENST00000293771.5:c.1054G>A	19.37:g.11598224C>T	ENSP00000293771:p.Glu352Lys	39.0	0.0	0		40.0	15.0	0.375	NM_138783	Q96AS7	Missense_Mutation	SNP	ENST00000293771.5	37	CCDS12261.1	17	0.007783882783882784	1	0.0020325203252032522	2	0.0055248618784530384	1	0.0017482517482517483	13	0.017150395778364115	C	20.3	3.959028	0.74016	0.001135	0.013953	ENSG00000161914	ENST00000293771	T	0.15487	2.42	4.14	4.14	0.48551	.	0.057370	0.64402	D	0.000002	T	0.09774	0.0240	L	0.32530	0.975	0.54753	D	0.999987	D	0.62365	0.991	P	0.47402	0.546	T	0.01819	-1.1267	10	0.87932	D	0	-13.1491	15.5534	0.76170	0.0:1.0:0.0:0.0	.	352	Q96CK0	ZN653_HUMAN	K	352	ENSP00000293771:E352K	ENSP00000293771:E352K	E	-	1	0	ZNF653	11459224	0.994000	0.37717	0.996000	0.52242	0.730000	0.41778	3.644000	0.54381	2.002000	0.58637	0.462000	0.41574	GAG	C|0.991;T|0.009	0.009	strong		0.652	ZNF653-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000458836.2	NM_138783	
PARPBP	55010	hgsc.bcm.edu	37	12	102547741	102547741	+	Missense_Mutation	SNP	G	G	A	rs114546604	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr12:102547741G>A	ENST00000358383.5	+	4	527	c.482G>A	c.(481-483)cGt>cAt	p.R161H	PARPBP_ENST00000541394.1_Missense_Mutation_p.R238H|PARPBP_ENST00000392911.2_Missense_Mutation_p.R80H|PARPBP_ENST00000378128.3_Missense_Mutation_p.R161H|PARPBP_ENST00000543784.1_Intron|PARPBP_ENST00000535811.1_Intron|PARPBP_ENST00000327680.2_Missense_Mutation_p.R80H			Q9NWS1	PARI_HUMAN	PARP1 binding protein	161					DNA repair (GO:0006281)|negative regulation of double-strand break repair via homologous recombination (GO:2000042)	chromatin (GO:0000785)|cytoplasm (GO:0005737)|nucleus (GO:0005634)	DNA binding (GO:0003677)			endometrium(1)|lung(8)|urinary_tract(2)	11						AAATACAACCGTGATAATGAA	0.353													A|||	153	0.0305511	0.0998	0.0058	5008	,	,		18353	0.0		0.006	False		,,,				2504	0.0112				p.R161H		Atlas-SNP	.											.	PARPBP	40	.	0			c.G482A						PASS	.	A	HIS/ARG	282,4124	800.4+/-415.6	15,252,1936	105.0	93.0	97.0		482	2.8	0.1	12	dbSNP_132	97	21,8577	817.4+/-406.9	0,21,4278	yes	missense	C12orf48	NM_017915.3	29	15,273,6214	AA,AG,GG		0.2442,6.4004,2.3301	benign	161/580	102547741	303,12701	2203	4299	6502	SO:0001583	missense	55010	exon4			ACAACCGTGATAA	AK000648	CCDS9090.1, CCDS9090.2	12q23.2	2013-03-14	2012-01-24	2012-01-24		ENSG00000185480			26074	protein-coding gene	gene with protein product	"""PARP-1 binding protein"""	613687	"""chromosome 12 open reading frame 48"""	C12orf48		20931645	Standard	NM_017915		Approved	FLJ20641, PARI	uc001tjf.3	Q9NWS1		ENST00000358383.5:c.482G>A	12.37:g.102547741G>A	ENSP00000351153:p.Arg161His	55.0	0.0	0		60.0	27.0	0.45	NM_017915	B4E0Y0|Q05C00|Q499L8|Q4FZA0|Q4KMW7|Q6NSC6|Q6PJA1|Q86W36	Missense_Mutation	SNP	ENST00000358383.5	37	CCDS9090.2	53	0.024267399267399268	48	0.0975609756097561	2	0.0055248618784530384	0	0.0	3	0.00395778364116095	A	2.534	-0.307796	0.05458	0.064004	0.002442	ENSG00000185480	ENST00000378128;ENST00000327680;ENST00000541394;ENST00000358383;ENST00000392911;ENST00000417507;ENST00000412715	T;T;T;T;T;T;T	0.42513	0.97;0.97;0.97;0.97;0.97;0.97;0.97	5.46	2.79	0.32731	.	0.713371	0.14523	N	0.314304	T	0.00412	0.0013	N	0.08118	0	0.09310	N	1	B;B;P;B;B;B	0.35527	0.0;0.0;0.507;0.018;0.0;0.0	B;B;B;B;B;B	0.14023	0.0;0.0;0.01;0.002;0.0;0.0	T	0.07947	-1.0746	10	0.27785	T	0.31	2.3812	5.7553	0.18170	0.7054:0.0:0.1593:0.1353	.	238;161;161;161;161;80	B4DZ31;Q9NWS1-6;Q9NWS1-7;Q9NWS1-3;Q9NWS1;Q9NWS1-2	.;.;.;.;PR1BP_HUMAN;.	H	161;80;238;161;80;128;128	ENSP00000367368:R161H;ENSP00000332915:R80H;ENSP00000440850:R238H;ENSP00000351153:R161H;ENSP00000376643:R80H;ENSP00000411313:R128H;ENSP00000393867:R128H	ENSP00000332915:R80H	R	+	2	0	C12orf48	101071871	0.919000	0.31177	0.084000	0.20598	0.049000	0.14656	1.172000	0.31908	0.371000	0.24564	-0.361000	0.07541	CGT	G|0.976;A|0.024	0.024	strong		0.353	PARPBP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000397030.2	NM_017915	
CD3EAP	10849	hgsc.bcm.edu	37	19	45911669	45911669	+	Missense_Mutation	SNP	G	G	A			TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr19:45911669G>A	ENST00000309424.3	+	3	931	c.443G>A	c.(442-444)cGg>cAg	p.R148Q	ERCC1_ENST00000588738.1_5'Flank|ERCC1_ENST00000423698.2_3'UTR|PPP1R13L_ENST00000418234.2_5'Flank|CD3EAP_ENST00000589804.1_Missense_Mutation_p.R150Q|ERCC1_ENST00000300853.3_3'UTR	NM_012099.1	NP_036231.1	O15446	RPA34_HUMAN	CD3e molecule, epsilon associated protein	148					rRNA transcription (GO:0009303)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)	chromosome (GO:0005694)|cytoplasm (GO:0005737)|DNA-directed RNA polymerase I complex (GO:0005736)|mitochondrion (GO:0005739)|nucleolus (GO:0005730)|nucleus (GO:0005634)|RNA polymerase I transcription factor complex (GO:0000120)	DNA-directed RNA polymerase activity (GO:0003899)|poly(A) RNA binding (GO:0044822)			breast(2)|endometrium(1)|large_intestine(3)|lung(2)|ovary(2)|prostate(1)	11		all_neural(266;0.224)|Ovarian(192;0.231)		OV - Ovarian serous cystadenocarcinoma(262;0.0251)		CTGAGGCCTCGGTTCTGTGCC	0.617																																					p.R148Q		Atlas-SNP	.											.	CD3EAP	27	.	0			c.G443A						PASS	.						42.0	44.0	43.0					19																	45911669		2203	4299	6502	SO:0001583	missense	10849	exon3			GGCCTCGGTTCTG	U86751	CCDS12661.1, CCDS74397.1	19q13.3	2008-02-05	2006-03-28			ENSG00000117877			24219	protein-coding gene	gene with protein product	"""CD3 epsilon associated protein"", ""antisense to ERCC 1"""	107325	"""CD3e antigen, epsilon polypeptide associated protein"""			10373416, 9426281, 15226435	Standard	XM_005258425		Approved	ASE-1, CAST, PAF49	uc002pbq.1	O15446		ENST00000309424.3:c.443G>A	19.37:g.45911669G>A	ENSP00000310966:p.Arg148Gln	54.0	0.0	0		71.0	30.0	0.422535	NM_012099	Q32N11|Q7Z5U2|Q9UPF6	Missense_Mutation	SNP	ENST00000309424.3	37	CCDS12661.1	.	.	.	.	.	.	.	.	.	.	G	32	5.145864	0.94603	.	.	ENSG00000117877	ENST00000309424	T	0.54279	0.58	5.27	5.27	0.74061	.	0.000000	0.64402	D	0.000003	T	0.70228	0.3200	M	0.66939	2.045	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.91635	0.998;0.999	T	0.73275	-0.4034	10	0.87932	D	0	-21.8983	14.3879	0.66958	0.0:0.0:1.0:0.0	.	150;148	O15446-2;O15446	.;RPA34_HUMAN	Q	148	ENSP00000310966:R148Q	ENSP00000310966:R148Q	R	+	2	0	CD3EAP	50603509	0.998000	0.40836	1.000000	0.80357	0.971000	0.66376	5.734000	0.68580	2.463000	0.83235	0.561000	0.74099	CGG	.	.	none		0.617	CD3EAP-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000459538.1	NM_012099	
F12	2161	hgsc.bcm.edu	37	5	176831085	176831085	+	Missense_Mutation	SNP	G	G	A	rs2230939	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr5:176831085G>A	ENST00000253496.3	-	10	1073	c.1025C>T	c.(1024-1026)cCg>cTg	p.P342L	F12_ENST00000514943.1_5'Flank	NM_000505.3	NP_000496.2	P00748	FA12_HUMAN	coagulation factor XII (Hageman factor)	342	Pro-rich.		P -> Q (in dbSNP:rs2230939).		blood coagulation (GO:0007596)|blood coagulation, intrinsic pathway (GO:0007597)|Factor XII activation (GO:0002542)|fibrinolysis (GO:0042730)|innate immune response (GO:0045087)|plasma kallikrein-kinin cascade (GO:0002353)|positive regulation of blood coagulation (GO:0030194)|positive regulation of fibrinolysis (GO:0051919)|positive regulation of plasminogen activation (GO:0010756)|protein autoprocessing (GO:0016540)|protein processing (GO:0016485)|response to misfolded protein (GO:0051788)|zymogen activation (GO:0031638)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|plasma membrane (GO:0005886)	misfolded protein binding (GO:0051787)|serine-type aminopeptidase activity (GO:0070009)|serine-type endopeptidase activity (GO:0004252)			central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(2)|lung(5)|skin(1)|urinary_tract(1)	12	all_cancers(89;2.04e-05)|Renal(175;0.000269)|Lung NSC(126;0.000832)|all_lung(126;0.00152)	all_neural(177;0.00409)|Medulloblastoma(196;0.00498)|all_hematologic(541;0.21)	Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)		Ethanolamine Oleate(DB06689)	CCGCTTCGCCGGCAAGGCTGT	0.721									Hereditary Angioedema		OREG0017088	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	G|||	4	0.000798722	0.0008	0.0014	5008	,	,		12509	0.0		0.002	False		,,,				2504	0.0				p.P342L		Atlas-SNP	.											.	F12	35	.	0			c.C1025T						PASS	.	G	LEU/PRO	0,4194		0,0,2097	9.0	12.0	11.0		1025	-5.3	0.0	5	dbSNP_98	11	13,8427		0,13,4207	yes	missense	F12	NM_000505.3	98	0,13,6304	AA,AG,GG		0.154,0.0,0.1029	benign	342/616	176831085	13,12621	2097	4220	6317	SO:0001583	missense	2161	exon10	Familial Cancer Database	HAE, type I-III, Hereditary Angioneurotic Edema, HANE,	TTCGCCGGCAAGG	M31315	CCDS34302.1	5q35.3	2014-09-17			ENSG00000131187	ENSG00000131187	3.4.21.38		3530	protein-coding gene	gene with protein product		610619					Standard	NM_000505		Approved		uc003mgo.4	P00748	OTTHUMG00000163403	ENST00000253496.3:c.1025C>T	5.37:g.176831085G>A	ENSP00000253496:p.Pro342Leu	5.0	0.0	0	1934	15.0	11.0	0.733333	NM_000505	P78339	Missense_Mutation	SNP	ENST00000253496.3	37	CCDS34302.1	3	0.0013736263736263737	0	0.0	1	0.0027624309392265192	0	0.0	2	0.002638522427440633	G	9.062	0.994618	0.19043	0.0	0.00154	ENSG00000131187	ENST00000253496	D	0.88975	-2.45	4.9	-5.28	0.02755	.	3.606630	0.00899	N	0.002331	T	0.76898	0.4052	L	0.29908	0.895	0.09310	N	0.999996	B	0.06786	0.001	B	0.04013	0.001	T	0.65776	-0.6086	10	0.10902	T	0.67	.	0.9191	0.01311	0.1778:0.1964:0.325:0.3008	.	342	P00748	FA12_HUMAN	L	342	ENSP00000253496:P342L	ENSP00000253496:P342L	P	-	2	0	F12	176763691	0.000000	0.05858	0.000000	0.03702	0.002000	0.02628	-3.303000	0.00519	-1.202000	0.02655	-0.367000	0.07326	CCG	T|0.005;G|0.993;A|0.001	0.001	strong		0.721	F12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000373217.1		
TAS1R2	80834	hgsc.bcm.edu	37	1	19180860	19180860	+	Silent	SNP	G	G	A	rs528216046		TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr1:19180860G>A	ENST00000375371.3	-	3	1125	c.1104C>T	c.(1102-1104)aaC>aaT	p.N368N	RP13-279N23.2_ENST00000494072.3_3'UTR	NM_152232.2	NP_689418.2	Q8TE23	TS1R2_HUMAN	taste receptor, type 1, member 2	368					detection of chemical stimulus involved in sensory perception of sweet taste (GO:0001582)|G-protein coupled receptor signaling pathway (GO:0007186)|positive regulation of cytokinesis (GO:0032467)|sensory perception of sweet taste (GO:0050916)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	protein heterodimerization activity (GO:0046982)|taste receptor activity (GO:0008527)			NS(1)|breast(1)|central_nervous_system(1)|endometrium(5)|kidney(4)|large_intestine(10)|lung(14)|ovary(1)|pancreas(3)|prostate(1)|skin(3)|stomach(1)	45		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;0.00466)|BRCA - Breast invasive adenocarcinoma(304;3.56e-05)|Kidney(64;0.000177)|KIRC - Kidney renal clear cell carcinoma(64;0.00262)|STAD - Stomach adenocarcinoma(196;0.00644)|READ - Rectum adenocarcinoma(331;0.0649)	Aspartame(DB00168)	ACAAGGTGGCGTTCAGGCAGT	0.622																																					p.N368N		Atlas-SNP	.											.	TAS1R2	134	.	0			c.C1104T						PASS	.						128.0	114.0	119.0					1																	19180860		2203	4300	6503	SO:0001819	synonymous_variant	80834	exon3			GGTGGCGTTCAGG		CCDS187.1	1p36.13	2012-08-22	2003-03-07		ENSG00000179002	ENSG00000179002		"""Taste receptors / Type 1"", ""GPCR / Unclassified : Taste receptors"""	14905	protein-coding gene	gene with protein product		606226	"""G protein-coupled receptor 71"""	GPR71			Standard	NM_152232		Approved	T1R2, TR2	uc001bba.1	Q8TE23	OTTHUMG00000002442	ENST00000375371.3:c.1104C>T	1.37:g.19180860G>A		170.0	0.0	0		155.0	76.0	0.490323	NM_152232	Q5TZ19	Silent	SNP	ENST00000375371.3	37	CCDS187.1																																																																																			.	.	none		0.622	TAS1R2-001	NOVEL	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000006953.1		
GABRG3	2567	hgsc.bcm.edu	37	15	27725917	27725917	+	Silent	SNP	C	C	T	rs77771286	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr15:27725917C>T	ENST00000333743.6	+	6	950	c.696C>T	c.(694-696)atC>atT	p.I232I	RP11-100M12.3_ENST00000556642.1_RNA|GABRG3_ENST00000555083.1_Silent_p.I232I	NM_033223.4	NP_150092.2	Q99928	GBRG3_HUMAN	gamma-aminobutyric acid (GABA) A receptor, gamma 3	232					gamma-aminobutyric acid signaling pathway (GO:0007214)|ion transmembrane transport (GO:0034220)|synaptic transmission (GO:0007268)|transmembrane transport (GO:0055085)	cell junction (GO:0030054)|chloride channel complex (GO:0034707)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)	chloride channel activity (GO:0005254)|extracellular ligand-gated ion channel activity (GO:0005230)|GABA-A receptor activity (GO:0004890)			breast(1)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(7)|lung(23)|skin(1)|upper_aerodigestive_tract(4)	42		all_lung(180;4.58e-12)|Breast(32;0.000625)|Colorectal(260;0.235)		all cancers(64;3.15e-07)|Epithelial(43;1.17e-06)|BRCA - Breast invasive adenocarcinoma(123;0.0261)	Acamprosate(DB00659)|Adinazolam(DB00546)|Alprazolam(DB00404)|Amoxapine(DB00543)|Bromazepam(DB01558)|Butabarbital(DB00237)|Butalbital(DB00241)|Chlordiazepoxide(DB00475)|Cinolazepam(DB01594)|Clobazam(DB00349)|Clonazepam(DB01068)|Clorazepate(DB00628)|Clotiazepam(DB01559)|Desflurane(DB01189)|Diazepam(DB00829)|Enflurane(DB00228)|Ergoloid mesylate(DB01049)|Estazolam(DB01215)|Eszopiclone(DB00402)|Ethchlorvynol(DB00189)|Etomidate(DB00292)|Fludiazepam(DB01567)|Flumazenil(DB01205)|Flurazepam(DB00690)|Glutethimide(DB01437)|Halazepam(DB00801)|Halothane(DB01159)|Isoflurane(DB00753)|Lorazepam(DB00186)|Meprobamate(DB00371)|Methoxyflurane(DB01028)|Methyprylon(DB01107)|Midazolam(DB00683)|Nitrazepam(DB01595)|Olanzapine(DB00334)|Oxazepam(DB00842)|Pentobarbital(DB00312)|Prazepam(DB01588)|Primidone(DB00794)|Propofol(DB00818)|Quazepam(DB01589)|Sevoflurane(DB01236)|Talbutal(DB00306)|Temazepam(DB00231)|Topiramate(DB00273)|Triazolam(DB00897)	CCACAGAAATCGTGACAACGT	0.443													C|||	13	0.00259585	0.0	0.0029	5008	,	,		15354	0.0		0.008	False		,,,				2504	0.0031				p.I232I	NSCLC(114;800 1656 7410 37729 45293)	Atlas-SNP	.											.	GABRG3	115	.	0			c.C696T						PASS	.	C		7,3769		0,7,1881	54.0	54.0	54.0		696	-4.5	0.2	15	dbSNP_131	54	84,8170		1,82,4044	no	coding-synonymous	GABRG3	NM_033223.4		1,89,5925	TT,TC,CC		1.0177,0.1854,0.7564		232/468	27725917	91,11939	1888	4127	6015	SO:0001819	synonymous_variant	2567	exon6			AGAAATCGTGACA		CCDS45195.1, CCDS59251.1	15q12	2012-06-22			ENSG00000182256	ENSG00000182256		"""GABA receptors"", ""Ligand-gated ion channels / GABA(A) receptors"""	4088	protein-coding gene	gene with protein product	"""GABA(G) receptor, gamma 3"""	600233				7601451	Standard	NM_033223		Approved		uc001zbg.2	Q99928	OTTHUMG00000044462	ENST00000333743.6:c.696C>T	15.37:g.27725917C>T		45.0	0.0	0		54.0	24.0	0.444444	NM_001270873	G3V594|Q9HD46|Q9NYT2	Silent	SNP	ENST00000333743.6	37	CCDS45195.1																																																																																			C|0.994;T|0.006	0.006	strong		0.443	GABRG3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000103584.2		
NBEAL1	65065	hgsc.bcm.edu	37	2	204058557	204058557	+	Missense_Mutation	SNP	C	C	G	rs114408639	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr2:204058557C>G	ENST00000449802.1	+	46	7207	c.6874C>G	c.(6874-6876)Cag>Gag	p.Q2292E		NM_001114132.1	NP_001107604.1	Q6ZS30	NBEL1_HUMAN	neurobeachin-like 1	2292										NS(1)|breast(3)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(8)|liver(1)|lung(8)|ovary(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	37						AGAAGCAGTGCAGAAGCCAAC	0.348													C|||	8	0.00159744	0.0	0.0	5008	,	,		15075	0.0		0.006	False		,,,				2504	0.002				p.Q2292E		Atlas-SNP	.											.	NBEAL1	266	.	0			c.C6874G						PASS	.	C	GLU/GLN	3,3747		0,3,1872	156.0	155.0	155.0		6874	5.4	1.0	2	dbSNP_132	155	81,8123		0,81,4021	yes	missense	NBEAL1	NM_001114132.1	29	0,84,5893	GG,GC,CC		0.9873,0.08,0.7027	benign	2292/2695	204058557	84,11870	1875	4102	5977	SO:0001583	missense	65065	exon46			GCAGTGCAGAAGC	AY172970	CCDS46495.1	2q33	2013-01-10			ENSG00000144426	ENSG00000144426		"""WD repeat domain containing"""	20681	protein-coding gene	gene with protein product		609816	"""amyotrophic lateral sclerosis 2 (juvenile) chromosome region, candidate 17"", ""amyotrophic lateral sclerosis 2 (juvenile) chromosome region, candidate 16"""	ALS2CR17, ALS2CR16		15193433	Standard	NM_001114132		Approved	MGC164581	uc002uzt.3	Q6ZS30	OTTHUMG00000154129	ENST00000449802.1:c.6874C>G	2.37:g.204058557C>G	ENSP00000399903:p.Gln2292Glu	101.0	0.0	0		95.0	45.0	0.473684	NM_001114132	A6NHD5|Q6Y876|Q6ZP36|Q6ZQY5|Q8N8R4|Q96Q30|Q96Q31	Missense_Mutation	SNP	ENST00000449802.1	37	CCDS46495.1	4	0.0018315018315018315	0	0.0	0	0.0	0	0.0	4	0.005277044854881266	C	13.17	2.158032	0.38119	8.0E-4	0.009873	ENSG00000144426	ENST00000449802;ENST00000414576	T;T	0.52526	0.66;1.25	5.43	5.43	0.79202	.	0.155623	0.40818	U	0.001008	T	0.34279	0.0892	L	0.54323	1.7	0.30447	N	0.775613	B	0.27450	0.179	B	0.27170	0.077	T	0.37979	-0.9682	10	0.27785	T	0.31	.	12.2442	0.54560	0.0:0.9212:0.0:0.0788	.	2292	Q6ZS30	NBEL1_HUMAN	E	2292;307	ENSP00000399903:Q2292E;ENSP00000388466:Q307E	ENSP00000388466:Q307E	Q	+	1	0	NBEAL1	203766802	1.000000	0.71417	0.957000	0.39632	0.991000	0.79684	4.345000	0.59360	2.550000	0.86006	0.650000	0.86243	CAG	C|0.997;G|0.003	0.003	strong		0.348	NBEAL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000333982.4		
GNB5	10681	hgsc.bcm.edu	37	15	52446260	52446260	+	Silent	SNP	C	C	T	rs35581121	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr15:52446260C>T	ENST00000261837.7	-	4	317	c.252G>A	c.(250-252)gcG>gcA	p.A84A	GNB5_ENST00000358784.7_Silent_p.A42A|GNB5_ENST00000396335.4_Silent_p.A42A|GNB5_ENST00000560116.1_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		45.0	0.0	0		51.0	28.0	0.54902	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		
UMODL1	89766	hgsc.bcm.edu	37	21	43531085	43531085	+	Missense_Mutation	SNP	A	A	T	rs139776068	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr21:43531085A>T	ENST00000408910.2	+	11	1753	c.1753A>T	c.(1753-1755)Aac>Tac	p.N585Y	UMODL1_ENST00000400427.1_Missense_Mutation_p.N513Y|C21orf128_ENST00000329015.2_5'Flank|UMODL1_ENST00000400424.2_Missense_Mutation_p.N513Y|UMODL1_ENST00000408989.2_Missense_Mutation_p.N585Y	NM_001004416.2	NP_001004416	Q5DID0	UROL1_HUMAN	uromodulin-like 1	585					adipose tissue development (GO:0060612)|cellular response to gonadotropin-releasing hormone (GO:0097211)|multicellular organismal reproductive process (GO:0048609)|regulation of apoptotic process (GO:0042981)|regulation of gene expression (GO:0010468)|regulation of ovarian follicle development (GO:2000354)|single fertilization (GO:0007338)	cytoplasm (GO:0005737)|external side of plasma membrane (GO:0009897)|extracellular space (GO:0005615)|integral component of membrane (GO:0016021)	calcium ion binding (GO:0005509)|peptidase inhibitor activity (GO:0030414)			breast(2)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(3)|kidney(2)|large_intestine(5)|lung(22)|ovary(2)|prostate(3)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)	47						CGGCCTAGAGAACTTCACCTT	0.662													A|||	27	0.00539137	0.0197	0.0014	5008	,	,		15612	0.0		0.0	False		,,,				2504	0.0				p.N585Y	Pancreas(122;680 807 13940 14411 22888 25505 31742 36028 36332 38435)	Atlas-SNP	.											.	UMODL1	186	.	0			c.A1753T						PASS	.	A	TYR/ASN,TYR/ASN,TYR/ASN,TYR/ASN	72,4004		0,72,1966	30.0	38.0	35.0		1753,1537,1537,1753	2.6	0.2	21	dbSNP_134	35	0,8368		0,0,4184	yes	missense,missense,missense,missense	UMODL1	NM_001004416.2,NM_001199527.1,NM_001199528.2,NM_173568.3	143,143,143,143	0,72,6150	TT,TA,AA		0.0,1.7664,0.5786	possibly-damaging,possibly-damaging,possibly-damaging,possibly-damaging	585/1319,513/1375,513/1247,585/1447	43531085	72,12372	2038	4184	6222	SO:0001583	missense	89766	exon11			CTAGAGAACTTCA		CCDS42935.1, CCDS42936.1, CCDS56214.1, CCDS56215.1	21q22.3	2008-07-04			ENSG00000177398	ENSG00000177398			12560	protein-coding gene	gene with protein product	"""olfactorin"""	613859				16026467	Standard	NM_173568		Approved		uc002zag.1	Q5DID0	OTTHUMG00000086788	ENST00000408910.2:c.1753A>T	21.37:g.43531085A>T	ENSP00000386147:p.Asn585Tyr	180.0	0.0	0		193.0	94.0	0.487047	NM_173568	C9JCE6|Q5DIC9|Q6LA40|Q6LA41|Q8N216	Missense_Mutation	SNP	ENST00000408910.2	37	CCDS42936.1	17	0.007783882783882784	16	0.032520325203252036	1	0.0027624309392265192	0	0.0	0	0.0	A	12.14	1.849160	0.32699	0.017664	0.0	ENSG00000177398	ENST00000400427;ENST00000400424;ENST00000408989;ENST00000408910	T;T;T;T	0.72167	-0.63;-0.61;-0.63;-0.61	3.83	2.64	0.31445	.	0.534882	0.15278	N	0.270826	T	0.39572	0.1083	N	0.19112	0.55	0.21527	N	0.999656	D;P	0.64830	0.994;0.947	P;P	0.56751	0.805;0.453	T	0.43294	-0.9400	10	0.87932	D	0	-7.3138	3.9168	0.09227	0.6689:0.2198:0.1113:0.0	.	585;585	Q5DID0-2;Q5DID0	.;UROL1_HUMAN	Y	513;513;585;585	ENSP00000383279:N513Y;ENSP00000383276:N513Y;ENSP00000386126:N585Y;ENSP00000386147:N585Y	ENSP00000383276:N513Y	N	+	1	0	UMODL1	42404154	0.482000	0.25948	0.191000	0.23289	0.007000	0.05969	0.802000	0.27069	0.780000	0.33566	0.533000	0.62120	AAC	A|0.992;T|0.008	0.008	strong		0.662	UMODL1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000195292.2		
B3GNT6	192134	hgsc.bcm.edu	37	11	76751608	76751608	+	Missense_Mutation	SNP	C	C	T			TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr11:76751608C>T	ENST00000533140.1	+	2	1151	c.1013C>T	c.(1012-1014)cCt>cTt	p.P338L	B3GNT6_ENST00000421061.1_Missense_Mutation_p.P216L|B3GNT6_ENST00000354301.5_Missense_Mutation_p.P337L			O43505	B3GN1_HUMAN	UDP-GlcNAc:betaGal beta-1,3-N-acetylglucosaminyltransferase 6 (core 3 synthase)	357					axon guidance (GO:0007411)|carbohydrate metabolic process (GO:0005975)|glycosaminoglycan metabolic process (GO:0030203)|keratan sulfate biosynthetic process (GO:0018146)|keratan sulfate metabolic process (GO:0042339)|poly-N-acetyllactosamine biosynthetic process (GO:0030311)|protein glycosylation (GO:0006486)|small molecule metabolic process (GO:0044281)	extracellular vesicular exosome (GO:0070062)|Golgi membrane (GO:0000139)|integral component of Golgi membrane (GO:0030173)	N-acetyllactosaminide beta-1,3-N-acetylglucosaminyltransferase activity (GO:0008532)			central_nervous_system(1)|kidney(2)|lung(4)|prostate(1)	8						TGCAGCTTGCCTGGCGCACAG	0.667																																					p.P337L		Atlas-SNP	.											.	B3GNT6	27	.	0			c.C1010T						PASS	.						12.0	12.0	12.0					11																	76751608		2111	4199	6310	SO:0001583	missense	192134	exon5			GCTTGCCTGGCGC	AB073740	CCDS53681.1	11q13.4	2013-02-19			ENSG00000198488	ENSG00000198488		"""Beta 3-glycosyltransferases"""	24141	protein-coding gene	gene with protein product		615315				11821425	Standard	NM_138706		Approved	B3Gn-T6	uc021qnp.1	Q6ZMB0		ENST00000533140.1:c.1013C>T	11.37:g.76751608C>T	ENSP00000435352:p.Pro338Leu	11.0	0.0	0		17.0	8.0	0.470588	NM_138706	Q4TTN0	Missense_Mutation	SNP	ENST00000533140.1	37	CCDS53681.1	.	.	.	.	.	.	.	.	.	.	C	18.27	3.586243	0.66105	.	.	ENSG00000198488	ENST00000533140;ENST00000354301;ENST00000421061	T;T;T	0.60672	1.5;0.17;2.66	2.9	2.9	0.33743	.	0.066129	0.64402	U	0.000007	T	0.76248	0.3961	M	0.86502	2.82	0.52501	D	0.999958	D	0.89917	1.0	D	0.97110	1.0	T	0.79522	-0.1769	10	0.51188	T	0.08	.	12.0142	0.53305	0.0:1.0:0.0:0.0	.	337	Q6ZMB0	B3GN6_HUMAN	L	338;337;216	ENSP00000435352:P338L;ENSP00000346256:P337L;ENSP00000403463:P216L	ENSP00000346256:P337L	P	+	2	0	B3GNT6	76429256	0.000000	0.05858	0.920000	0.36463	0.642000	0.38348	0.234000	0.17930	1.908000	0.55244	0.462000	0.41574	CCT	.	.	none		0.667	B3GNT6-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000382740.2	NM_138706	
WDR16	146845	hgsc.bcm.edu	37	17	9511492	9511492	+	Silent	SNP	C	C	T	rs146548028		TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr17:9511492C>T	ENST00000352665.5	+	7	879	c.810C>T	c.(808-810)gcC>gcT	p.A270A	WDR16_ENST00000299764.5_Silent_p.A280A|WDR16_ENST00000396219.3_Silent_p.A202A	NM_145054.4	NP_659491.4			WD repeat domain 16									p.A270A(1)		NS(1)|breast(1)|central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(7)|lung(11)|ovary(1)|prostate(2)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)	31						GCTCTGGAGCCGGACTGCTGG	0.507													c|||	1	0.000199681	0.0	0.0	5008	,	,		14489	0.0		0.001	False		,,,				2504	0.0				p.A270A		Atlas-SNP	.											WDR16,NS,carcinoma,0,1	WDR16	67	1	1	Substitution - coding silent(1)	endometrium(1)	c.C810T						PASS	.		,	1,4405	2.1+/-5.4	0,1,2202	76.0	76.0	76.0		606,810	-10.8	0.7	17	dbSNP_134	76	3,8597	3.0+/-9.4	0,3,4297	no	coding-synonymous,coding-synonymous	WDR16	NM_001080556.1,NM_145054.4	,	0,4,6499	TT,TC,CC		0.0349,0.0227,0.0308	,	202/553,270/621	9511492	4,13002	2203	4300	6503	SO:0001819	synonymous_variant	146845	exon7			TGGAGCCGGACTG	AB065281	CCDS11149.2, CCDS42262.1	17p13.1	2014-08-01			ENSG00000166596	ENSG00000166596		"""WD repeat domain containing"""	16053	protein-coding gene	gene with protein product	"""WD40-repeat protein upregulated in HCC"""	609804				15967112	Standard	NM_001080556		Approved	WDRPUH, FLJ37528	uc002gly.3	Q8N1V2	OTTHUMG00000150149	ENST00000352665.5:c.810C>T	17.37:g.9511492C>T		134.0	0.0	0		171.0	90.0	0.526316	NM_145054		Silent	SNP	ENST00000352665.5	37	CCDS11149.2																																																																																			C|0.999;T|0.001	0.001	strong		0.507	WDR16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000316569.2	NM_145054	
RIN1	9610	hgsc.bcm.edu	37	11	66099992	66099992	+	Missense_Mutation	SNP	G	G	A	rs139103405	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr11:66099992G>A	ENST00000311320.4	-	10	2233	c.2107C>T	c.(2107-2109)Cgg>Tgg	p.R703W	RP11-867G23.12_ENST00000526655.1_RNA|RIN1_ENST00000530056.1_Missense_Mutation_p.R537W|RIN1_ENST00000524804.1_5'Flank|RIN1_ENST00000424433.2_Intron	NM_004292.2	NP_004283.2	Q13671	RIN1_HUMAN	Ras and Rab interactor 1	703	Ras and 14-3-3 protein binding region.|Ras-associating. {ECO:0000255|PROSITE- ProRule:PRU00166}.				associative learning (GO:0008306)|endocytosis (GO:0006897)|memory (GO:0007613)|negative regulation of synaptic plasticity (GO:0031914)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|dendrite (GO:0030425)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)	GTPase activator activity (GO:0005096)			breast(1)|central_nervous_system(3)|haematopoietic_and_lymphoid_tissue(1)|lung(8)|ovary(1)	14						CACTCCGCCCGGCGGTAGACG	0.672																																					p.R703W		Atlas-SNP	.											.	RIN1	64	.	0			c.C2107T						PASS	.	G	TRP/ARG	0,4400		0,0,2200	73.0	84.0	80.0		2107	4.0	1.0	11	dbSNP_134	80	4,8586	3.7+/-12.6	0,4,4291	no	missense	RIN1	NM_004292.2	101	0,4,6491	AA,AG,GG		0.0466,0.0,0.0308	probably-damaging	703/784	66099992	4,12986	2200	4295	6495	SO:0001583	missense	9610	exon10			CCGCCCGGCGGTA	L36463	CCDS31614.1	11q13.2	2005-09-18				ENSG00000174791			18749	protein-coding gene	gene with protein product		605965				9144171, 1849280	Standard	NM_004292		Approved		uc001ohn.1	Q13671		ENST00000311320.4:c.2107C>T	11.37:g.66099992G>A	ENSP00000310406:p.Arg703Trp	79.0	0.0	0		106.0	50.0	0.471698	NM_004292	O15010|Q00427|Q96CC8	Missense_Mutation	SNP	ENST00000311320.4	37	CCDS31614.1	.	.	.	.	.	.	.	.	.	.	G	17.69	3.451461	0.63290	0.0	4.66E-4	ENSG00000174791	ENST00000311320;ENST00000530056	T;T	0.19394	2.15;2.15	4.93	4.0	0.46444	Ras-association (3);	0.682458	0.13161	N	0.409069	T	0.39009	0.1062	M	0.61703	1.905	0.80722	D	1	D;D;D	0.76494	0.996;0.999;0.99	P;P;P	0.60609	0.849;0.877;0.571	T	0.12967	-1.0527	10	0.87932	D	0	-13.1701	10.7254	0.46066	0.0:0.0:0.7956:0.2044	.	537;334;703	E9PNR2;B4DW96;Q13671	.;.;RIN1_HUMAN	W	703;537	ENSP00000310406:R703W;ENSP00000432798:R537W	ENSP00000310406:R703W	R	-	1	2	RIN1	65856568	0.999000	0.42202	0.998000	0.56505	0.382000	0.30200	3.479000	0.53165	1.166000	0.42689	0.462000	0.41574	CGG	G|0.999;A|0.001	0.001	strong		0.672	RIN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000392980.2	NM_004292	
NOC2L	26155	hgsc.bcm.edu	37	1	880502	880502	+	Missense_Mutation	SNP	C	C	T	rs74047418	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr1:880502C>T	ENST00000327044.6	-	18	2127	c.2078G>A	c.(2077-2079)cGg>cAg	p.R693Q		NM_015658.3	NP_056473	Q9Y3T9	NOC2L_HUMAN	nucleolar complex associated 2 homolog (S. cerevisiae)	693	Asp/Glu-rich (acidic).				apoptotic process (GO:0006915)|cellular response to UV (GO:0034644)|chromatin assembly (GO:0031497)|negative regulation of B cell apoptotic process (GO:0002903)|negative regulation of histone acetylation (GO:0035067)|negative regulation of intrinsic apoptotic signaling pathway (GO:2001243)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|nucleolus to nucleoplasm transport (GO:0032066)|transcription, DNA-templated (GO:0006351)	nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	chromatin binding (GO:0003682)|histone binding (GO:0042393)|nucleosome binding (GO:0031491)|poly(A) RNA binding (GO:0044822)|repressing transcription factor binding (GO:0070491)|transcription corepressor activity (GO:0003714)			endometrium(2)|kidney(1)|large_intestine(2)|lung(6)|ovary(2)|skin(2)|urinary_tract(1)	16	all_cancers(77;0.00164)|all_epithelial(69;0.000959)|all_lung(157;0.00963)|Lung NSC(156;0.0232)|Ovarian(185;0.0634)	all_epithelial(116;8.75e-19)|all_lung(118;2.3e-08)|Lung NSC(185;2.38e-06)|Renal(390;0.00183)|Breast(487;0.00354)|Hepatocellular(190;0.00826)|Myeloproliferative disorder(586;0.0122)|Ovarian(437;0.0308)|Lung SC(97;0.128)		UCEC - Uterine corpus endometrioid carcinoma (11;0.00459)|Epithelial(90;1.86e-38)|OV - Ovarian serous cystadenocarcinoma(86;6.08e-23)|Colorectal(212;0.000161)|COAD - Colon adenocarcinoma(227;0.000194)|BRCA - Breast invasive adenocarcinoma(365;0.000475)|Kidney(185;0.00231)|STAD - Stomach adenocarcinoma(132;0.00644)|KIRC - Kidney renal clear cell carcinoma(229;0.0344)|Lung(427;0.2)		caccccATGCCGAGTGCTCAG	0.607													c|||	6	0.00119808	0.003	0.0014	5008	,	,		17544	0.0		0.001	False		,,,				2504	0.0				p.R693Q		Atlas-SNP	.											.	NOC2L	42	.	0			c.G2078A						PASS	.	C	GLN/ARG	9,4395	15.5+/-35.6	0,9,2193	88.0	81.0	84.0		2078	-6.8	0.0	1	dbSNP_130	84	15,8585	9.8+/-36.6	0,15,4285	yes	missense	NOC2L	NM_015658.3	43	0,24,6478	TT,TC,CC		0.1744,0.2044,0.1846	possibly-damaging	693/750	880502	24,12980	2202	4300	6502	SO:0001583	missense	26155	exon18			CCATGCCGAGTGC	AL050019	CCDS3.1	1p36.33	2014-06-12			ENSG00000188976	ENSG00000188976			24517	protein-coding gene	gene with protein product	"""novel INHAT repressor"", ""protein phosphatase 1, regulatory subunit 12"""	610770					Standard	NM_015658		Approved	DKFZP564C186, NET7, NET15, NIR, PPP1R112	uc001abz.4	Q9Y3T9	OTTHUMG00000040720	ENST00000327044.6:c.2078G>A	1.37:g.880502C>T	ENSP00000317992:p.Arg693Gln	99.0	0.0	0		101.0	52.0	0.514852	NM_015658	Q5SVA3|Q9BTN6	Missense_Mutation	SNP	ENST00000327044.6	37	CCDS3.1	5	0.0022893772893772895	3	0.006097560975609756	1	0.0027624309392265192	0	0.0	1	0.0013192612137203166	C	4.022	0.001552	0.07819	0.002044	0.001744	ENSG00000188976	ENST00000327044	T	0.22134	1.97	3.39	-6.79	0.01715	Armadillo-type fold (1);	2.092900	0.02013	N	0.047121	T	0.06735	0.0172	N	0.22421	0.69	0.09310	N	1	B;B;B	0.12630	0.005;0.005;0.006	B;B;B	0.04013	0.001;0.001;0.001	T	0.28996	-1.0026	10	0.11485	T	0.65	0.8905	0.9663	0.01406	0.221:0.1346:0.2196:0.4248	.	693;693;460	B3KNC3;Q9Y3T9;Q9H9J5	.;NOC2L_HUMAN;.	Q	693	ENSP00000317992:R693Q	ENSP00000317992:R693Q	R	-	2	0	NOC2L	870365	0.000000	0.05858	0.000000	0.03702	0.007000	0.05969	-2.544000	0.00933	-2.506000	0.00507	0.448000	0.29417	CGG	C|0.998;T|0.002	0.002	strong		0.607	NOC2L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000097869.1	NM_015658	
ATE1	11101	hgsc.bcm.edu	37	10	123662023	123662023	+	Missense_Mutation	SNP	G	G	T			TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr10:123662023G>T	ENST00000224652.6	-	6	781	c.696C>A	c.(694-696)ttC>ttA	p.F232L	ATE1_ENST00000540606.1_Missense_Mutation_p.F225L|ATE1_ENST00000535655.1_Intron|ATE1_ENST00000481784.1_5'UTR|ATE1_ENST00000369043.3_Missense_Mutation_p.F232L|ATE1_ENST00000543447.1_Missense_Mutation_p.F117L|ATE1_ENST00000369040.3_Missense_Mutation_p.F136L	NM_001001976.1	NP_001001976.1	O95260	ATE1_HUMAN	arginyltransferase 1	232					protein arginylation (GO:0016598)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	arginyltransferase activity (GO:0004057)			endometrium(2)|kidney(2)|large_intestine(2)|lung(6)|upper_aerodigestive_tract(1)|urinary_tract(1)	14		all_neural(114;0.061)|Lung NSC(174;0.095)|all_lung(145;0.124)|Breast(234;0.212)				CTTGAGCCTGGAAACCCTCAA	0.423																																					p.F232L		Atlas-SNP	.											.	ATE1	67	.	0			c.C696A						PASS	.						162.0	146.0	151.0					10																	123662023		2203	4300	6503	SO:0001583	missense	11101	exon6			AGCCTGGAAACCC	AF079098	CCDS31299.1, CCDS31300.1, CCDS73211.1, CCDS73212.1, CCDS73213.1	10q26	2013-05-08			ENSG00000107669	ENSG00000107669	2.3.2.8		782	protein-coding gene	gene with protein product		607103				16002466, 16943202	Standard	XM_005269458		Approved		uc001lfq.3	O95260	OTTHUMG00000019178	ENST00000224652.6:c.696C>A	10.37:g.123662023G>T	ENSP00000224652:p.Phe232Leu	158.0	0.0	0		166.0	77.0	0.463855	NM_001001976	O95261|Q5SQQ3|Q8WW04	Missense_Mutation	SNP	ENST00000224652.6	37	CCDS31300.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	0.679|0.679	-0.798913|-0.798913	0.02841|0.02841	.|.	.|.	ENSG00000107669|ENSG00000107669	ENST00000369043;ENST00000224652;ENST00000369040;ENST00000540606;ENST00000543447|ENST00000423243	.|.	.|.	.|.	4.58|4.58	3.66|3.66	0.41972|0.41972	.|.	0.913149|.	0.09305|.	N|.	0.820356|.	T|T	0.33644|0.33644	0.0870|0.0870	L|L	0.36672|0.36672	1.1|1.1	0.09310|0.09310	N|N	1|1	B;B;B;B|.	0.02656|.	0.0;0.0;0.0;0.0|.	B;B;B;B|.	0.09377|.	0.004;0.001;0.002;0.001|.	T|T	0.20371|0.20371	-1.0277|-1.0277	9|5	0.23891|.	T|.	0.37|.	-7.5611|-7.5611	5.5146|5.5146	0.16900|0.16900	0.124:0.3975:0.4785:0.0|0.124:0.3975:0.4785:0.0	.|.	225;136;232;232|.	F5GXE4;B4E107;O95260;O95260-2|.	.;.;ATE1_HUMAN;.|.	L|T	232;232;136;225;117|229	.|.	ENSP00000224652:F232L|.	F|P	-|-	3|1	2|0	ATE1|ATE1	123652013|123652013	0.152000|0.152000	0.22762|0.22762	0.920000|0.920000	0.36463|0.36463	0.774000|0.774000	0.43823|0.43823	0.524000|0.524000	0.22940|0.22940	1.128000|1.128000	0.42052|0.42052	0.557000|0.557000	0.71058|0.71058	TTC|CCA	.	.	none		0.423	ATE1-201	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding		NM_001001976	
MYO1H	283446	hgsc.bcm.edu	37	12	109826535	109826535	+	Silent	SNP	G	G	A	rs61742038	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr12:109826535G>A	ENST00000431443.2	+	1	12	c.12G>A	c.(10-12)gcG>gcA	p.A4A	MYO1H_ENST00000310903.5_Silent_p.A4A	NM_001101421.3	NP_001094891.3	Q8N1T3	MYO1H_HUMAN	myosin IH	4						myosin complex (GO:0016459)	ATP binding (GO:0005524)|motor activity (GO:0003774)			NS(1)|breast(1)|central_nervous_system(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(9)|lung(17)|prostate(2)|upper_aerodigestive_tract(3)|urinary_tract(1)	47						TGGAAGGGGCGCTGACTGCCC	0.502													G|||	341	0.0680911	0.2474	0.0187	5008	,	,		18985	0.0		0.001	False		,,,				2504	0.0				p.A4A		Atlas-SNP	.											.	MYO1H	98	.	0			c.G12A						PASS	.	G		777,3405		61,655,1375	144.0	156.0	152.0		12	-2.6	0.8	12	dbSNP_129	152	12,8460		0,12,4224	no	coding-synonymous	MYO1H	NM_001101421.3		61,667,5599	AA,AG,GG		0.1416,18.5796,6.2352		4/1023	109826535	789,11865	2091	4236	6327	SO:0001819	synonymous_variant	283446	exon1			AGGGGCGCTGACT		CCDS53826.1	12q24.11	2011-09-27			ENSG00000174527	ENSG00000174527		"""Myosins / Myosin superfamily : Class I"""	13879	protein-coding gene	gene with protein product		614636					Standard	NM_001101421		Approved	FLJ37587	uc010sxn.1	Q8N1T3	OTTHUMG00000169252	ENST00000431443.2:c.12G>A	12.37:g.109826535G>A		132.0	0.0	0		172.0	85.0	0.494186	NM_001101421	F5H3C6	Silent	SNP	ENST00000431443.2	37																																																																																				G|0.947;A|0.053	0.053	strong		0.502	MYO1H-201	KNOWN	basic	protein_coding	protein_coding		NM_173597	
HPS3	84343	hgsc.bcm.edu	37	3	148858267	148858267	+	Missense_Mutation	SNP	A	A	G	rs199722122		TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr3:148858267A>G	ENST00000296051.2	+	2	834	c.694A>G	c.(694-696)Ata>Gta	p.I232V	HPS3_ENST00000460120.1_Intron	NM_032383.3	NP_115759.2	Q969F9	HPS3_HUMAN	Hermansky-Pudlak syndrome 3	232					organelle organization (GO:0006996)|pigmentation (GO:0043473)	BLOC-2 complex (GO:0031084)				breast(2)|endometrium(2)|kidney(1)|large_intestine(7)|lung(12)|ovary(5)|prostate(1)|skin(1)|upper_aerodigestive_tract(3)	34			LUSC - Lung squamous cell carcinoma(72;0.0473)|Lung(72;0.0607)			CAACAATCGAATAAGACGGAC	0.393									Hermansky-Pudlak syndrome																												p.I232V		Atlas-SNP	.											.	HPS3	104	.	0			c.A694G						PASS	.						82.0	80.0	81.0					3																	148858267		2168	4282	6450	SO:0001583	missense	84343	exon2	Familial Cancer Database	HPS, HPS1-8	AATCGAATAAGAC	AY033141	CCDS3140.1	3q24	2014-06-18			ENSG00000163755	ENSG00000163755			15597	protein-coding gene	gene with protein product		606118				11455388	Standard	NM_032383		Approved	SUTAL	uc003ewu.1	Q969F9	OTTHUMG00000159548	ENST00000296051.2:c.694A>G	3.37:g.148858267A>G	ENSP00000296051:p.Ile232Val	125.0	0.0	0		133.0	79.0	0.593985	NM_032383	A8K6G6|Q8WTV6|Q96AP1|Q96MR3|Q9H608	Missense_Mutation	SNP	ENST00000296051.2	37	CCDS3140.1	.	.	.	.	.	.	.	.	.	.	A	5.521	0.281147	0.10458	.	.	ENSG00000163755	ENST00000296051	T	0.62498	0.02	5.46	-7.86	0.01187	.	2.003110	0.01674	N	0.025777	T	0.28962	0.0719	N	0.01352	-0.895	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.30119	-0.9989	10	0.28530	T	0.3	2.052	7.5676	0.27887	0.0972:0.071:0.7585:0.0733	.	232	Q969F9	HPS3_HUMAN	V	232	ENSP00000296051:I232V	ENSP00000296051:I232V	I	+	1	0	HPS3	150340957	0.000000	0.05858	0.000000	0.03702	0.008000	0.06430	-0.081000	0.11321	-2.013000	0.00949	-0.263000	0.10527	ATA	A|0.999;G|0.001	0.001	weak		0.393	HPS3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000356151.1	NM_032383	
NFKB1	4790	hgsc.bcm.edu	37	4	103505961	103505961	+	Silent	SNP	C	C	T	rs4648039	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr4:103505961C>T	ENST00000505458.1	+	11	1324	c.1047C>T	c.(1045-1047)taC>taT	p.Y349Y	NFKB1_ENST00000394820.4_Silent_p.Y349Y|NFKB1_ENST00000600343.1_Silent_p.Y169Y|NFKB1_ENST00000226574.4_Silent_p.Y350Y			P19838	NFKB1_HUMAN	nuclear factor of kappa light polypeptide gene enhancer in B-cells 1	349	RHD. {ECO:0000255|PROSITE- ProRule:PRU00265}.				apoptotic process (GO:0006915)|cellular response to interleukin-1 (GO:0071347)|cellular response to interleukin-6 (GO:0071354)|cellular response to lipopolysaccharide (GO:0071222)|cellular response to mechanical stimulus (GO:0071260)|cellular response to nicotine (GO:0071316)|cellular response to peptide hormone stimulus (GO:0071375)|Fc-epsilon receptor signaling pathway (GO:0038095)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|membrane protein intracellular domain proteolysis (GO:0031293)|MyD88-dependent toll-like receptor signaling pathway (GO:0002755)|MyD88-independent toll-like receptor signaling pathway (GO:0002756)|negative regulation of apoptotic process (GO:0043066)|negative regulation of calcidiol 1-monooxygenase activity (GO:0010956)|negative regulation of cellular protein metabolic process (GO:0032269)|negative regulation of cholesterol transport (GO:0032375)|negative regulation of cytokine production (GO:0001818)|negative regulation of inflammatory response (GO:0050728)|negative regulation of interleukin-12 biosynthetic process (GO:0045083)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of vitamin D biosynthetic process (GO:0010957)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of canonical Wnt signaling pathway (GO:0090263)|positive regulation of hyaluronan biosynthetic process (GO:1900127)|positive regulation of lipid storage (GO:0010884)|positive regulation of macrophage derived foam cell differentiation (GO:0010744)|positive regulation of miRNA metabolic process (GO:2000630)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|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)|response to copper ion (GO:0046688)|response to oxidative stress (GO:0006979)|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)|transcription from RNA polymerase II promoter (GO:0006366)|TRIF-dependent toll-like receptor signaling pathway (GO:0035666)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|I-kappaB/NF-kappaB complex (GO:0033256)|mitochondrion (GO:0005739)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	double-stranded DNA binding (GO:0003690)|nucleic acid binding transcription factor activity (GO:0001071)|regulatory region DNA binding (GO:0000975)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription factor binding (GO:0008134)|transcription regulatory region DNA binding (GO:0044212)|transcription regulatory region sequence-specific DNA binding (GO:0000976)			biliary_tract(1)|breast(4)|endometrium(2)|large_intestine(6)|lung(7)|ovary(2)|skin(4)|upper_aerodigestive_tract(1)	27		Hepatocellular(203;0.217)		OV - Ovarian serous cystadenocarcinoma(123;6.59e-08)	Acetylsalicylic acid(DB00945)|Pranlukast(DB01411)|Thalidomide(DB01041)|Triflusal(DB08814)	CTTTCCTCTACTATCCTGAAA	0.303													C|||	26	0.00519169	0.0	0.0014	5008	,	,		18222	0.0		0.0219	False		,,,				2504	0.0031				p.Y350Y		Atlas-SNP	.											.	NFKB1	78	.	0			c.C1050T						PASS	.	C	,	27,4379	33.5+/-64.1	0,27,2176	55.0	57.0	56.0		1047,1050	4.0	1.0	4	dbSNP_111	56	211,8389	89.7+/-151.9	2,207,4091	no	coding-synonymous,coding-synonymous	NFKB1	NM_001165412.1,NM_003998.3	,	2,234,6267	TT,TC,CC		2.4535,0.6128,1.8299	,	349/969,350/970	103505961	238,12768	2203	4300	6503	SO:0001819	synonymous_variant	4790	exon11			CCTCTACTATCCT	M58603	CCDS3657.1, CCDS54783.1	4q24	2013-01-10	2008-07-28		ENSG00000109320	ENSG00000109320		"""Ankyrin repeat domain containing"""	7794	protein-coding gene	gene with protein product		164011				1992489	Standard	NM_003998		Approved	KBF1, p105, NFKB-p50, p50, NF-kappaB, NFkappaB, NF-kB1	uc011cep.2	P19838	OTTHUMG00000161080	ENST00000505458.1:c.1047C>T	4.37:g.103505961C>T		106.0	0.0	0		134.0	70.0	0.522388	NM_003998	A8K5Y5|B3KVE8|Q68D84|Q86V43|Q8N4X7|Q9NZC0	Silent	SNP	ENST00000505458.1	37	CCDS54783.1																																																																																			C|0.983;T|0.017	0.017	strong		0.303	NFKB1-003	KNOWN	alternative_5_UTR|non_canonical_polymorphism|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000363411.1		
TRIM15	89870	hgsc.bcm.edu	37	6	30131527	30131527	+	Silent	SNP	G	G	T	rs11961941	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr6:30131527G>T	ENST00000376694.4	+	1	535	c.66G>T	c.(64-66)ccG>ccT	p.P22P	TRIM10_ENST00000449742.2_5'Flank|TRIM15_ENST00000376688.1_Silent_p.P22P|TRIM10_ENST00000376704.3_5'Flank	NM_033229.2	NP_150232.2	Q9C019	TRI15_HUMAN	tripartite motif containing 15	22					innate immune response (GO:0045087)|mesodermal cell fate determination (GO:0007500)|negative regulation of intracellular transport of viral material (GO:1901253)|negative regulation of viral release from host cell (GO:1902187)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of RIG-I signaling pathway (GO:1900246)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|positive regulation of type I interferon production (GO:0032481)	intracellular (GO:0005622)	zinc ion binding (GO:0008270)			large_intestine(2)|lung(8)|prostate(2)|skin(1)|urinary_tract(1)	14						GTGCGGGGCCGCTGGAGGATG	0.677													G|||	137	0.0273562	0.0688	0.0144	5008	,	,		16858	0.0139		0.0139	False		,,,				2504	0.0082				p.P22P		Atlas-SNP	.											.	TRIM15	34	.	0			c.G66T						PASS	.	G		195,2827		5,185,1321	55.0	48.0	50.0		66	3.1	0.4	6	dbSNP_120	50	74,5342		0,74,2634	no	coding-synonymous	TRIM15	NM_033229.2		5,259,3955	TT,TG,GG		1.3663,6.4527,3.188		22/466	30131527	269,8169	1511	2708	4219	SO:0001819	synonymous_variant	89870	exon1			GGGGCCGCTGGAG	AF220132, U34249	CCDS4677.1	6p21.33	2013-01-09	2011-01-25		ENSG00000204610	ENSG00000204610		"""Tripartite motif containing / Tripartite motif containing"", ""RING-type (C3HC4) zinc fingers"""	16284	protein-coding gene	gene with protein product			"""zinc finger protein 178"", ""tripartite motif-containing 15"""	ZNF178		11331580, 8304341, 8812418	Standard	NM_033229		Approved	ZNFB7, RNF93	uc010jrx.3	Q9C019	OTTHUMG00000031031	ENST00000376694.4:c.66G>T	6.37:g.30131527G>T		100.0	0.0	0		105.0	45.0	0.428571	NM_033229	A2BEC9|O95604|Q8IUX9|Q9C018	Silent	SNP	ENST00000376694.4	37	CCDS4677.1																																																																																			G|0.964;T|0.036	0.036	strong		0.677	TRIM15-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076026.2	NM_033229	
ZNF646	9726	hgsc.bcm.edu	37	16	31090269	31090269	+	Missense_Mutation	SNP	C	C	T	rs75586809	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr16:31090269C>T	ENST00000394979.2	+	1	3047	c.2624C>T	c.(2623-2625)gCg>gTg	p.A875V	ZNF646_ENST00000300850.5_Missense_Mutation_p.A875V			O15015	ZN646_HUMAN	zinc finger protein 646	875					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(4)|cervix(2)|endometrium(8)|kidney(4)|large_intestine(1)|lung(21)|ovary(1)|prostate(4)|skin(3)	49						CCTGGGGAGGCGACCTCAGCA	0.642													C|||	24	0.00479233	0.0008	0.0115	5008	,	,		21323	0.0		0.0139	False		,,,				2504	0.001				p.A875V		Atlas-SNP	.											ZNF646,NS,haematopoietic_neoplasm,0,1	ZNF646	133	1	0			c.C2624T						PASS	.	C	VAL/ALA	20,4374	26.2+/-53.5	0,20,2177	51.0	54.0	53.0		2624	2.0	0.3	16	dbSNP_131	53	149,8451	71.3+/-133.9	1,147,4152	yes	missense	ZNF646	NM_014699.3	64	1,167,6329	TT,TC,CC		1.7326,0.4552,1.3006	benign	875/1833	31090269	169,12825	2197	4300	6497	SO:0001583	missense	9726	exon2			GGGAGGCGACCTC	AB002294	CCDS10702.1	16p11.2	2013-01-08			ENSG00000167395	ENSG00000167395		"""Zinc fingers, C2H2-type"""	29004	protein-coding gene	gene with protein product							Standard	NM_014699		Approved	KIAA0296	uc002eap.3	O15015	OTTHUMG00000047355	ENST00000394979.2:c.2624C>T	16.37:g.31090269C>T	ENSP00000378429:p.Ala875Val	73.0	0.0	0		92.0	38.0	0.413043	NM_014699	Q8IVD8	Missense_Mutation	SNP	ENST00000394979.2	37		14	0.00641025641025641	0	0.0	4	0.011049723756906077	0	0.0	10	0.013192612137203167	C	10.60	1.394311	0.25205	0.004552	0.017326	ENSG00000167395	ENST00000300850;ENST00000394979	T;T	0.09538	2.97;2.99	5.1	2.01	0.26516	.	.	.	.	.	T	0.02533	0.0077	N	0.19112	0.55	0.21762	N	0.999553	B	0.24768	0.111	B	0.17722	0.019	T	0.44757	-0.9307	9	0.09590	T	0.72	-4.0386	7.7886	0.29106	0.0:0.6518:0.0:0.3482	.	875	O15015-2	.	V	875	ENSP00000300850:A875V;ENSP00000378429:A875V	ENSP00000300850:A875V	A	+	2	0	ZNF646	30997770	0.000000	0.05858	0.330000	0.25442	0.849000	0.48306	-1.042000	0.03539	0.163000	0.19507	0.563000	0.77884	GCG	C|0.989;T|0.011	0.011	strong		0.642	ZNF646-003	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000108510.2	NM_014699	
TLN1	7094	hgsc.bcm.edu	37	9	35708425	35708425	+	Silent	SNP	T	T	C	rs35461988	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr9:35708425T>C	ENST00000314888.9	-	34	4736	c.4383A>G	c.(4381-4383)ctA>ctG	p.L1461L	TLN1_ENST00000540444.1_Silent_p.L1461L|TLN1_ENST00000464379.1_5'Flank	NM_006289.3	NP_006280.3	Q9Y490	TLN1_HUMAN	talin 1	1461	Interaction with SYNM.				activation of signaling protein activity involved in unfolded protein response (GO:0006987)|axon guidance (GO:0007411)|blood coagulation (GO:0007596)|cell-cell junction assembly (GO:0007043)|cell-substrate junction assembly (GO:0007044)|cellular component movement (GO:0006928)|cellular protein metabolic process (GO:0044267)|cortical actin cytoskeleton organization (GO:0030866)|cytoskeletal anchoring at plasma membrane (GO:0007016)|endoplasmic reticulum unfolded protein response (GO:0030968)|muscle contraction (GO:0006936)|platelet activation (GO:0030168)|platelet aggregation (GO:0070527)|platelet degranulation (GO:0002576)	actin cytoskeleton (GO:0015629)|cell-cell junction (GO:0005911)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|microtubule organizing center (GO:0005815)|plasma membrane (GO:0005886)|ruffle (GO:0001726)	integrin binding (GO:0005178)|LIM domain binding (GO:0030274)|structural constituent of cytoskeleton (GO:0005200)|vinculin binding (GO:0017166)			NS(2)|breast(8)|central_nervous_system(2)|endometrium(10)|kidney(5)|large_intestine(9)|lung(32)|ovary(3)|prostate(5)|skin(3)|upper_aerodigestive_tract(6)	85	all_epithelial(49;0.167)		Lung(28;0.00276)|LUSC - Lung squamous cell carcinoma(32;0.00418)|STAD - Stomach adenocarcinoma(86;0.194)			TGGGCTCCACTAGCCCTTGCT	0.562													T|||	40	0.00798722	0.0008	0.013	5008	,	,		19074	0.0		0.0288	False		,,,				2504	0.001				p.L1461L		Atlas-SNP	.											.	TLN1	185	.	0			c.A4383G						PASS	.	T		28,4378	35.2+/-66.4	0,28,2175	79.0	72.0	75.0		4383	0.9	1.0	9	dbSNP_126	75	302,8298	109.8+/-170.3	2,298,4000	no	coding-synonymous	TLN1	NM_006289.3		2,326,6175	CC,CT,TT		3.5116,0.6355,2.5373		1461/2542	35708425	330,12676	2203	4300	6503	SO:0001819	synonymous_variant	7094	exon34			CTCCACTAGCCCT	AB028950	CCDS35009.1	9p23-p21	2008-02-05			ENSG00000137076	ENSG00000137076			11845	protein-coding gene	gene with protein product		186745		TLN		7635475, 10610730	Standard	NM_006289		Approved	ILWEQ	uc003zxt.2	Q9Y490	OTTHUMG00000019874	ENST00000314888.9:c.4383A>G	9.37:g.35708425T>C		61.0	0.0	0		48.0	20.0	0.416667	NM_006289	A6NMY0|Q86YD0|Q9NZQ2|Q9UHH8|Q9UPX3	Silent	SNP	ENST00000314888.9	37	CCDS35009.1																																																																																			T|0.978;C|0.022	0.022	strong		0.562	TLN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052353.2	NM_006289	
MYBBP1A	10514	hgsc.bcm.edu	37	17	4452638	4452638	+	Silent	SNP	C	C	T			TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr17:4452638C>T	ENST00000254718.4	-	10	1725	c.1419G>A	c.(1417-1419)gaG>gaA	p.E473E	MYBBP1A_ENST00000381556.2_Silent_p.E473E			Q9BQG0	MBB1A_HUMAN	MYB binding protein (P160) 1a	473	Interaction with MYB. {ECO:0000250}.				cellular response to glucose starvation (GO:0042149)|intrinsic apoptotic signaling pathway by p53 class mediator (GO:0072332)|negative regulation of transcription, DNA-templated (GO:0045892)|nucleocytoplasmic transport (GO:0006913)|osteoblast differentiation (GO:0001649)|positive regulation of cell cycle arrest (GO:0071158)|regulation of transcription, DNA-templated (GO:0006355)|respiratory electron transport chain (GO:0022904)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|intracellular membrane-bounded organelle (GO:0043231)|membrane (GO:0016020)|NLS-dependent protein nuclear import complex (GO:0042564)|nucleolus (GO:0005730)|nucleus (GO:0005634)	DNA-directed DNA polymerase activity (GO:0003887)|poly(A) RNA binding (GO:0044822)|sequence-specific DNA binding (GO:0043565)|transcription factor binding (GO:0008134)			breast(1)|endometrium(1)|kidney(1)|large_intestine(6)|lung(7)|ovary(3)|prostate(2)|skin(2)|stomach(1)	24						TGGCCACCTGCTCAGTCAAGG	0.592																																					p.E473E		Atlas-SNP	.											.	MYBBP1A	69	.	0			c.G1419A						PASS	.						87.0	59.0	69.0					17																	4452638		2203	4300	6503	SO:0001819	synonymous_variant	10514	exon10			CACCTGCTCAGTC	AF147709	CCDS11046.1, CCDS42238.1	17p13.3	2008-07-18			ENSG00000132382	ENSG00000132382			7546	protein-coding gene	gene with protein product	"""p53-activated protein-2"""	604885				10644447	Standard	NM_014520		Approved	P160, PAP2, FLJ37886	uc002fxz.4	Q9BQG0	OTTHUMG00000090747	ENST00000254718.4:c.1419G>A	17.37:g.4452638C>T		30.0	0.0	0		35.0	19.0	0.542857	NM_014520	Q86VM3|Q9BW49|Q9P0V5|Q9UF99	Silent	SNP	ENST00000254718.4	37	CCDS11046.1																																																																																			.	.	none		0.592	MYBBP1A-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000207488.2	NM_014520	
A1CF	29974	hgsc.bcm.edu	37	10	52601702	52601702	+	Silent	SNP	A	A	G	rs141891504		TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr10:52601702A>G	ENST00000373993.1	-	3	329	c.285T>C	c.(283-285)aaT>aaC	p.N95N	A1CF_ENST00000395495.1_Silent_p.N95N|A1CF_ENST00000282641.2_Silent_p.N95N|A1CF_ENST00000374001.2_Silent_p.N95N|A1CF_ENST00000373995.3_Silent_p.N103N|A1CF_ENST00000395489.2_Silent_p.N88N|A1CF_ENST00000373997.3_Silent_p.N95N			Q9NQ94	A1CF_HUMAN	APOBEC1 complementation factor	95	RRM 1. {ECO:0000255|PROSITE- ProRule:PRU00176}.				cytidine to uridine editing (GO:0016554)|gene expression (GO:0010467)|mRNA modification (GO:0016556)|mRNA processing (GO:0006397)|protein stabilization (GO:0050821)	apolipoprotein B mRNA editing enzyme complex (GO:0030895)|cytoplasm (GO:0005737)|endoplasmic reticulum (GO:0005783)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	nucleotide binding (GO:0000166)|RNA binding (GO:0003723)|single-stranded RNA binding (GO:0003727)			NS(1)|breast(1)|central_nervous_system(1)|kidney(3)|large_intestine(4)|lung(14)|prostate(2)|skin(3)	29						CATATCCTCTATTGTTGCCAT	0.303													A|||	1	0.000199681	0.0	0.0	5008	,	,		19096	0.0		0.001	False		,,,				2504	0.0				p.N103N		Atlas-SNP	.											.	A1CF	190	.	0			c.T309C						PASS	.	A	,,,,,	2,4402	2.1+/-5.4	0,2,2200	141.0	135.0	137.0		285,309,309,285,285,309	0.4	1.0	10	dbSNP_134	137	14,8584	10.5+/-38.8	0,14,4285	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	A1CF	NM_001198818.1,NM_001198819.1,NM_001198820.1,NM_014576.3,NM_138932.2,NM_138933.2	,,,,,	0,16,6485	GG,GA,AA		0.1628,0.0454,0.1231	,,,,,	95/587,103/603,103/595,95/587,95/595,103/595	52601702	16,12986	2202	4299	6501	SO:0001819	synonymous_variant	29974	exon6			TCCTCTATTGTTG	AF271790	CCDS7241.1, CCDS7242.1, CCDS7243.1, CCDS73133.1	10q21.1	2013-02-12			ENSG00000148584	ENSG00000148584		"""RNA binding motif (RRM) containing"""	24086	protein-coding gene	gene with protein product						11815617, 11072063	Standard	NM_014576		Approved	ACF, ASP, ACF64, ACF65, APOBEC1CF	uc001jjj.3	Q9NQ94	OTTHUMG00000018240	ENST00000373993.1:c.285T>C	10.37:g.52601702A>G		75.0	0.0	0		77.0	32.0	0.415584	NM_001198820	A1L4F2|A8K7G7|B7ZM14|Q5SZQ0|Q9NQ93|Q9NQX8|Q9NQX9|Q9NXC9|Q9NZD3	Silent	SNP	ENST00000373993.1	37	CCDS7242.1																																																																																			A|0.999;G|0.001	0.001	strong		0.303	A1CF-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000048086.2	NM_014576	
APBA2	321	hgsc.bcm.edu	37	15	29390715	29390715	+	Missense_Mutation	SNP	C	C	T	rs371370074	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr15:29390715C>T	ENST00000558402.1	+	10	1873	c.1274C>T	c.(1273-1275)aCg>aTg	p.T425M	APBA2_ENST00000561069.1_Missense_Mutation_p.T425M|APBA2_ENST00000411764.1_Missense_Mutation_p.T413M|APBA2_ENST00000558259.1_Missense_Mutation_p.T425M|APBA2_ENST00000558330.1_Missense_Mutation_p.T413M			Q99767	APBA2_HUMAN	amyloid beta (A4) precursor protein-binding, family A, member 2	425	PID. {ECO:0000255|PROSITE- ProRule:PRU00148}.				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)		GATGCCCAGACGCTGACGGAA	0.423													C|||	2	0.000399361	0.0	0.0	5008	,	,		19432	0.002		0.0	False		,,,				2504	0.0				p.T425M		Atlas-SNP	.											.	APBA2	132	.	0			c.C1274T						PASS	.	C	MET/THR,MET/THR	0,4406		0,0,2203	110.0	106.0	108.0		1238,1274	4.0	0.8	15		108	1,8599	1.2+/-3.3	0,1,4299	no	missense,missense	APBA2	NM_001130414.1,NM_005503.3	81,81	0,1,6502	TT,TC,CC		0.0116,0.0,0.0077	possibly-damaging,possibly-damaging	413/738,425/750	29390715	1,13005	2203	4300	6503	SO:0001583	missense	321	exon8			CCCAGACGCTGAC	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.1274C>T	15.37:g.29390715C>T	ENSP00000453293:p.Thr425Met	70.0	0.0	0		67.0	27.0	0.402985	NM_005503	E9PGI4|O60571|Q5XKC0	Missense_Mutation	SNP	ENST00000558402.1	37	CCDS10022.1	.	.	.	.	.	.	.	.	.	.	C	14.19	2.461454	0.43736	0.0	1.16E-4	ENSG00000034053	ENST00000411764;ENST00000219865;ENST00000382938	T	0.55760	0.5	4.93	4.02	0.46733	Phosphotyrosine interaction domain (3);Pleckstrin homology-type (1);	0.184551	0.45361	N	0.000369	T	0.51550	0.1681	N	0.14661	0.345	0.58432	D	0.999997	P;P;D;P	0.67145	0.637;0.66;0.996;0.462	B;B;P;B	0.61397	0.269;0.389;0.888;0.244	T	0.58457	-0.7633	10	0.87932	D	0	.	12.3957	0.55382	0.0:0.9183:0.0:0.0817	.	413;117;413;425	Q5XKC0;Q6ZVB1;E9PGI4;Q99767	.;.;.;APBA2_HUMAN	M	413;425;117	ENSP00000409312:T413M	ENSP00000219865:T425M	T	+	2	0	APBA2	27178007	1.000000	0.71417	0.776000	0.31678	0.297000	0.27493	4.750000	0.62162	1.177000	0.42855	0.655000	0.94253	ACG	.	.	weak		0.423	APBA2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251362.3	NM_005503	
DTNB	1838	hgsc.bcm.edu	37	2	25754393	25754393	+	Missense_Mutation	SNP	T	T	C	rs199811406		TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr2:25754393T>C	ENST00000406818.3	-	9	1199	c.950A>G	c.(949-951)cAt>cGt	p.H317R	DTNB_ENST00000496972.2_Missense_Mutation_p.H260R|DTNB_ENST00000407186.1_Missense_Mutation_p.H317R|DTNB_ENST00000407038.3_Missense_Mutation_p.H317R|DTNB_ENST00000405222.1_Missense_Mutation_p.H317R|DTNB_ENST00000545439.1_Missense_Mutation_p.H113R|DTNB_ENST00000404103.3_Missense_Mutation_p.H317R|DTNB_ENST00000288642.8_Missense_Mutation_p.H317R|DTNB_ENST00000407661.3_Missense_Mutation_p.H317R	NM_001256303.1|NM_021907.4	NP_001243232.1|NP_068707.1	O60941	DTNB_HUMAN	dystrobrevin, beta	317						cytoplasm (GO:0005737)|synapse (GO:0045202)	calcium ion binding (GO:0005509)|zinc ion binding (GO:0008270)			endometrium(1)|large_intestine(3)|lung(4)|ovary(2)|upper_aerodigestive_tract(1)	11	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)					AAAAACAGGATGCGGGGGTTC	0.463																																					p.H317R		Atlas-SNP	.											.	DTNB	43	.	0			c.A950G						PASS	.	T	ARG/HIS,ARG/HIS,ARG/HIS,ARG/HIS,ARG/HIS	2,3750		0,2,1874	142.0	141.0	141.0		950,950,950,950,950	5.2	1.0	2		141	2,8196		0,2,4097	yes	missense,missense,missense,missense,missense	DTNB	NM_021907.3,NM_033147.2,NM_033148.2,NM_183360.1,NM_183361.1	29,29,29,29,29	0,4,5971	CC,CT,TT		0.0244,0.0533,0.0335	possibly-damaging,possibly-damaging,possibly-damaging,possibly-damaging,possibly-damaging	317/628,317/598,317/568,317/610,317/561	25754393	4,11946	1876	4099	5975	SO:0001583	missense	1838	exon9			ACAGGATGCGGGG	AF022728	CCDS46233.1, CCDS46234.1, CCDS46235.1, CCDS46236.1, CCDS46237.1, CCDS58702.1, CCDS74496.1	2p23.2	2008-05-15			ENSG00000138101	ENSG00000138101			3058	protein-coding gene	gene with protein product		602415				9419360	Standard	NM_021907		Approved		uc002rgh.4	O60941	OTTHUMG00000152129	ENST00000406818.3:c.950A>G	2.37:g.25754393T>C	ENSP00000384084:p.His317Arg	139.0	0.0	0		126.0	63.0	0.5	NM_021907	B7Z733|F5GZG4|G5E9F6|O43782|O60881|O75538|Q86VR4|Q96AW0|Q9UE14|Q9UE15|Q9UE16	Missense_Mutation	SNP	ENST00000406818.3	37	CCDS46237.1	.	.	.	.	.	.	.	.	.	.	T	14.61	2.586513	0.46110	5.33E-4	2.44E-4	ENSG00000138101	ENST00000496972;ENST00000406818;ENST00000404103;ENST00000407661;ENST00000407038;ENST00000405222;ENST00000407186;ENST00000288642;ENST00000545439;ENST00000535791	T;T;T;T;T;T;T;T;T	0.44083	2.28;2.28;2.28;2.28;2.31;2.31;2.31;2.28;0.93	5.15	5.15	0.70609	.	0.094216	0.64402	D	0.000001	T	0.46521	0.1397	M	0.80847	2.515	0.53005	D	0.99996	B;B;B;B;B;B;B;B;B;B;B;B	0.09022	0.001;0.001;0.002;0.002;0.001;0.001;0.0;0.001;0.0;0.002;0.002;0.001	B;B;B;B;B;B;B;B;B;B;B;B	0.17722	0.005;0.003;0.007;0.019;0.003;0.005;0.001;0.003;0.012;0.012;0.018;0.005	T	0.43523	-0.9386	10	0.34782	T	0.22	-16.4358	12.9424	0.58352	0.0:0.0:0.0:1.0	.	317;113;260;317;317;260;317;317;317;317;317;317	E7EVB6;B7Z202;F5GZG4;O60941-3;B7Z6A9;B7Z733;E9PEY4;Q96AW0;O60941-2;O60941-4;G5E9F6;O60941	.;.;.;.;.;.;.;.;.;.;.;DTNB_HUMAN	R	260;317;317;317;317;317;317;317;113;170	ENSP00000444463:H260R;ENSP00000384084:H317R;ENSP00000385482:H317R;ENSP00000385193:H317R;ENSP00000384767:H317R;ENSP00000384787:H317R;ENSP00000385784:H317R;ENSP00000288642:H317R;ENSP00000444961:H113R	ENSP00000288642:H317R	H	-	2	0	DTNB	25607897	1.000000	0.71417	0.997000	0.53966	0.996000	0.88848	5.025000	0.64097	1.930000	0.55929	0.383000	0.25322	CAT	.	.	weak		0.463	DTNB-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000325361.1	NM_033147	
ACP7	390928	hgsc.bcm.edu	37	19	39589191	39589191	+	Missense_Mutation	SNP	T	T	A	rs566749338		TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr19:39589191T>A	ENST00000331256.5	+	3	489	c.215T>A	c.(214-216)cTc>cAc	p.L72H	PAPL_ENST00000594229.1_Missense_Mutation_p.L72H	NM_001004318.2	NP_001004318.2	Q6ZNF0	PAPL_HUMAN		72						extracellular region (GO:0005576)	acid phosphatase activity (GO:0003993)|metal ion binding (GO:0046872)										CCCCTGCCCCTCCGCGCCCAG	0.642													t|||	1	0.000199681	0.0	0.0	5008	,	,		13097	0.0		0.001	False		,,,				2504	0.0				p.L72H		Atlas-SNP	.											.	.	.	.	0			c.T215A						PASS	.						35.0	33.0	34.0					19																	39589191		2203	4300	6503	SO:0001583	missense	0	exon3			TGCCCCTCCGCGC																												ENST00000331256.5:c.215T>A	19.37:g.39589191T>A	ENSP00000327557:p.Leu72His	48.0	0.0	0		41.0	25.0	0.609756	NM_001004318	B2RN68	Missense_Mutation	SNP	ENST00000331256.5	37	CCDS33018.1	.	.	.	.	.	.	.	.	.	.	T	1.006	-0.689462	0.03328	.	.	ENSG00000183760	ENST00000331256	D	0.82711	-1.64	5.2	4.19	0.49359	Purple acid phosphatase-like, N-terminal (1);Purple acid phosphatase, N-terminal (1);	0.743246	0.12988	N	0.422733	T	0.73273	0.3566	L	0.39245	1.2	0.09310	N	1	B	0.12013	0.005	B	0.12156	0.007	T	0.56613	-0.7950	10	0.14252	T	0.57	-12.7226	8.4714	0.32988	0.0:0.0927:0.0:0.9073	.	72	Q6ZNF0	PAPL_HUMAN	H	72	ENSP00000327557:L72H	ENSP00000327557:L72H	L	+	2	0	AC011443.1	44281031	0.001000	0.12720	0.249000	0.24280	0.063000	0.16089	0.986000	0.29590	1.956000	0.56807	0.533000	0.62120	CTC	.	.	none		0.642	PAPL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000463810.1		
FAM13B	51306	hgsc.bcm.edu	37	5	137354665	137354665	+	Missense_Mutation	SNP	C	C	T	rs79543971	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr5:137354665C>T	ENST00000033079.3	-	3	587	c.136G>A	c.(136-138)Gtg>Atg	p.V46M	FAM13B_ENST00000420893.2_Missense_Mutation_p.V46M|FAM13B_ENST00000425075.2_Intron	NM_016603.2	NP_057687.2	Q9NYF5	FA13B_HUMAN	family with sequence similarity 13, member B	46	Rho-GAP. {ECO:0000255|PROSITE- ProRule:PRU00172}.				regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)	GTPase activator activity (GO:0005096)			endometrium(4)|kidney(2)|lung(5)	11						ATATAGTCCACAACGTGGCGG	0.393													C|||	2	0.000399361	0.0	0.0	5008	,	,		19229	0.0		0.002	False		,,,				2504	0.0				p.V46M		Atlas-SNP	.											.	FAM13B	46	.	0			c.G136A						PASS	.	C	MET/VAL,,MET/VAL	3,4403	4.2+/-10.8	0,3,2200	92.0	88.0	89.0		136,,136	6.1	1.0	5	dbSNP_131	89	16,8584	11.9+/-42.8	0,16,4284	yes	missense,intron,missense	FAM13B	NM_001101800.1,NM_001101801.1,NM_016603.2	21,,21	0,19,6484	TT,TC,CC		0.186,0.0681,0.1461	probably-damaging,,probably-damaging	46/888,,46/916	137354665	19,12987	2203	4300	6503	SO:0001583	missense	51306	exon3			AGTCCACAACGTG	AF251038	CCDS4195.1, CCDS47269.1, CCDS47270.1	5q31	2011-09-07	2009-01-20	2009-01-20	ENSG00000031003	ENSG00000031003		"""Rho GTPase activating proteins"""	1335	protein-coding gene	gene with protein product		609371	"""chromosome 5 open reading frame 5"", ""family with sequence similarity 13, member B1"""	C5orf5, FAM13B1		11087669, 11161817	Standard	NM_016603		Approved	N61, KHCHP, ARHGAP49	uc003lbz.2	Q9NYF5	OTTHUMG00000129202	ENST00000033079.3:c.136G>A	5.37:g.137354665C>T	ENSP00000033079:p.Val46Met	159.0	0.0	0		153.0	82.0	0.535948	NM_001101800	D3DQB5|G3V0H9|Q3ZCR0|Q6PGQ2|Q9P0I7	Missense_Mutation	SNP	ENST00000033079.3	37	CCDS4195.1	2	9.157509157509158E-4	0	0.0	0	0.0	0	0.0	2	0.002638522427440633	C	27.0	4.793716	0.90453	6.81E-4	0.00186	ENSG00000031003	ENST00000033079;ENST00000420893;ENST00000514310;ENST00000502471;ENST00000509596;ENST00000508403;ENST00000505961	T;T;T;T;T;T;T	0.46819	1.88;1.88;1.88;1.88;1.88;0.86;0.86	6.08	6.08	0.98989	Rho GTPase-activating protein domain (4);Rho GTPase activation protein (1);	0.000000	0.85682	D	0.000000	T	0.72534	0.3472	M	0.78049	2.395	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.91635	0.999;0.999	T	0.73275	-0.4034	10	0.87932	D	0	-7.2121	20.6634	0.99662	0.0:1.0:0.0:0.0	.	46;46	Q9NYF5-2;Q9NYF5	.;FA13B_HUMAN	M	46	ENSP00000033079:V46M;ENSP00000388521:V46M;ENSP00000425326:V46M;ENSP00000424785:V46M;ENSP00000422311:V46M;ENSP00000426863:V46M;ENSP00000422673:V46M	ENSP00000033079:V46M	V	-	1	0	FAM13B	137382564	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	7.120000	0.77153	2.894000	0.99253	0.655000	0.94253	GTG	C|0.999;T|0.001	0.001	strong		0.393	FAM13B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251279.1		
CSMD3	114788	hgsc.bcm.edu	37	8	113395826	113395826	+	Missense_Mutation	SNP	T	T	C			TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr8:113395826T>C	ENST00000297405.5	-	37	6245	c.6001A>G	c.(6001-6003)Aac>Gac	p.N2001D	CSMD3_ENST00000352409.3_Missense_Mutation_p.N1931D|CSMD3_ENST00000343508.3_Missense_Mutation_p.N1961D|CSMD3_ENST00000455883.2_Missense_Mutation_p.N1897D	NM_198123.1	NP_937756.1	Q7Z407	CSMD3_HUMAN	CUB and Sushi multiple domains 3	2001	CUB 11. {ECO:0000255|PROSITE- ProRule:PRU00059}.					integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				breast(7)|central_nervous_system(6)|endometrium(44)|haematopoietic_and_lymphoid_tissue(8)|kidney(36)|large_intestine(72)|liver(5)|lung(389)|ovary(24)|prostate(6)|skin(23)|upper_aerodigestive_tract(19)|urinary_tract(7)	646						GGAGCATTGTTGTCTCCCCCA	0.323										HNSCC(6;0.00088)|TCGA Ovarian(7;0.080)																											p.N2001D		Atlas-SNP	.											.	CSMD3	2325	.	0			c.A6001G						PASS	.						84.0	82.0	83.0					8																	113395826		2203	4300	6503	SO:0001583	missense	114788	exon37			CATTGTTGTCTCC	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.6001A>G	8.37:g.113395826T>C	ENSP00000297405:p.Asn2001Asp	173.0	0.0	0		200.0	102.0	0.51	NM_198123	Q96PZ3	Missense_Mutation	SNP	ENST00000297405.5	37	CCDS6315.1	.	.	.	.	.	.	.	.	.	.	T	18.08	3.543166	0.65198	.	.	ENSG00000164796	ENST00000343508;ENST00000297405;ENST00000339701;ENST00000455883;ENST00000352409	T;T;T;T;T	0.17054	2.3;2.3;2.3;2.3;2.3	4.42	4.42	0.53409	CUB (5);	0.269490	0.36409	N	0.002617	T	0.19046	0.0457	N	0.15975	0.35	0.39770	D	0.972152	P;B;D	0.60575	0.913;0.083;0.988	B;B;P	0.61201	0.431;0.174;0.885	T	0.07328	-1.0778	10	0.10636	T	0.68	.	14.1168	0.65159	0.0:0.0:0.0:1.0	.	1897;2001;1961	Q7Z407-3;Q7Z407;Q7Z407-2	.;CSMD3_HUMAN;.	D	1961;2001;1271;1897;1931	ENSP00000345799:N1961D;ENSP00000297405:N2001D;ENSP00000341558:N1271D;ENSP00000412263:N1897D;ENSP00000343124:N1931D	ENSP00000297405:N2001D	N	-	1	0	CSMD3	113465002	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	4.040000	0.57333	1.975000	0.57531	0.383000	0.25322	AAC	.	.	none		0.323	CSMD3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347141.1	NM_052900	
JAK2	3717	hgsc.bcm.edu	37	9	5065003	5065003	+	Missense_Mutation	SNP	C	C	G	rs2230723	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr9:5065003C>G	ENST00000381652.3	+	9	1671	c.1177C>G	c.(1177-1179)Ctt>Gtt	p.L393V	JAK2_ENST00000544510.1_Missense_Mutation_p.L244V|JAK2_ENST00000539801.1_Missense_Mutation_p.L393V	NM_004972.3	NP_004963.1	O60674	JAK2_HUMAN	Janus kinase 2	393			L -> V (in dbSNP:rs2230723). {ECO:0000269|PubMed:17344846}.		actin filament polymerization (GO:0030041)|activation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0006919)|activation of cysteine-type endopeptidase activity involved in apoptotic signaling pathway (GO:0097296)|activation of JAK2 kinase activity (GO:0042977)|activation of MAPKK activity (GO:0000186)|apoptotic process (GO:0006915)|axon regeneration (GO:0031103)|blood coagulation (GO:0007596)|cell differentiation (GO:0030154)|cellular component movement (GO:0006928)|cytokine-mediated signaling pathway (GO:0019221)|enzyme linked receptor protein signaling pathway (GO:0007167)|erythrocyte differentiation (GO:0030218)|extrinsic apoptotic signaling pathway (GO:0097191)|G-protein coupled receptor signaling pathway (GO:0007186)|growth hormone receptor signaling pathway (GO:0060396)|histone H3-Y41 phosphorylation (GO:0035409)|hormone-mediated signaling pathway (GO:0009755)|host programmed cell death induced by symbiont (GO:0034050)|interferon-gamma-mediated signaling pathway (GO:0060333)|interleukin-12-mediated signaling pathway (GO:0035722)|intracellular signal transduction (GO:0035556)|intrinsic apoptotic signaling pathway in response to oxidative stress (GO:0008631)|JAK-STAT cascade (GO:0007259)|JAK-STAT cascade involved in growth hormone signaling pathway (GO:0060397)|mammary gland epithelium development (GO:0061180)|mesoderm development (GO:0007498)|mineralocorticoid receptor signaling pathway (GO:0031959)|negative regulation of cell proliferation (GO:0008285)|negative regulation of cell-cell adhesion (GO:0022408)|negative regulation of DNA binding (GO:0043392)|negative regulation of heart contraction (GO:0045822)|negative regulation of neuron apoptotic process (GO:0043524)|peptidyl-tyrosine phosphorylation (GO:0018108)|platelet-derived growth factor receptor signaling pathway (GO:0048008)|positive regulation of apoptotic process (GO:0043065)|positive regulation of apoptotic signaling pathway (GO:2001235)|positive regulation of cell activation (GO:0050867)|positive regulation of cell differentiation (GO:0045597)|positive regulation of cell migration (GO:0030335)|positive regulation of cell proliferation (GO:0008284)|positive regulation of cell-substrate adhesion (GO:0010811)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|positive regulation of DNA binding (GO:0043388)|positive regulation of growth hormone receptor signaling pathway (GO:0060399)|positive regulation of inflammatory response (GO:0050729)|positive regulation of insulin secretion (GO:0032024)|positive regulation of interleukin-1 beta production (GO:0032731)|positive regulation of nitric oxide biosynthetic process (GO:0045429)|positive regulation of nitric-oxide synthase biosynthetic process (GO:0051770)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|positive regulation of phosphatidylinositol 3-kinase signaling (GO:0014068)|positive regulation of phosphoprotein phosphatase activity (GO:0032516)|positive regulation of protein import into nucleus, translocation (GO:0033160)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|positive regulation of tumor necrosis factor production (GO:0032760)|positive regulation of tyrosine phosphorylation of Stat3 protein (GO:0042517)|positive regulation of tyrosine phosphorylation of Stat5 protein (GO:0042523)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|regulation of inflammatory response (GO:0050727)|regulation of interferon-gamma-mediated signaling pathway (GO:0060334)|response to antibiotic (GO:0046677)|response to hydroperoxide (GO:0033194)|response to interleukin-12 (GO:0070671)|response to lipopolysaccharide (GO:0032496)|response to tumor necrosis factor (GO:0034612)|signal transduction (GO:0007165)|STAT protein import into nucleus (GO:0007262)|tumor necrosis factor-mediated signaling pathway (GO:0033209)|tyrosine phosphorylation of STAT protein (GO:0007260)|tyrosine phosphorylation of Stat1 protein (GO:0042508)|tyrosine phosphorylation of Stat3 protein (GO:0042503)|tyrosine phosphorylation of Stat5 protein (GO:0042506)	caveola (GO:0005901)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|endosome lumen (GO:0031904)|membrane raft (GO:0045121)|nuclear matrix (GO:0016363)|nucleus (GO:0005634)	ATP binding (GO:0005524)|growth hormone receptor binding (GO:0005131)|heme binding (GO:0020037)|histone binding (GO:0042393)|histone kinase activity (H3-Y41 specific) (GO:0035401)|interleukin-12 receptor binding (GO:0005143)|non-membrane spanning protein tyrosine kinase activity (GO:0004715)|protein kinase activity (GO:0004672)|protein kinase binding (GO:0019901)|protein tyrosine kinase activity (GO:0004713)|receptor binding (GO:0005102)|SH2 domain binding (GO:0042169)		BCR/JAK2(6)|SSBP2/JAK2(4)|SEC31A/JAK2(4)|ETV6/JAK2(11)|PCM1/JAK2(30)|PAX5/JAK2(18)	breast(5)|endometrium(4)|haematopoietic_and_lymphoid_tissue(32944)|kidney(4)|large_intestine(10)|liver(1)|lung(20)|ovary(3)|prostate(4)|skin(2)|urinary_tract(1)	32998	all_hematologic(13;0.137)	Acute lymphoblastic leukemia(23;0.0198)|Breast(48;0.147)		GBM - Glioblastoma multiforme(50;0.0237)|Lung(218;0.133)	Ruxolitinib(DB08877)|Tofacitinib(DB08895)	TCCAGCCGTGCTTGAAAATAT	0.343		1	"""T, Mis, O"""	"""ETV6, PCM1, BCR"""	"""ALL, AML, MPD,  CML"""				Polycythemia Vera, Familial				C|||	60	0.0119808	0.0272	0.0202	5008	,	,		17562	0.0		0.0099	False		,,,				2504	0.0				p.L393V		Atlas-SNP	.		Dom	yes		9	9p24	3717	Janus kinase 2		L	.	JAK2	35466	.	0			c.C1177G						PASS	.	C	VAL/LEU	132,4274	94.8+/-133.5	4,124,2075	74.0	71.0	72.0		1177	5.2	0.9	9	dbSNP_98	72	52,8548	33.3+/-86.6	0,52,4248	yes	missense	JAK2	NM_004972.3	32	4,176,6323	GG,GC,CC		0.6047,2.9959,1.4147	benign	393/1133	5065003	184,12822	2203	4300	6503	SO:0001583	missense	3717	exon9	Familial Cancer Database		GCCGTGCTTGAAA		CCDS6457.1	9p24	2014-09-17	2009-04-23		ENSG00000096968	ENSG00000096968	2.7.10.1	"""SH2 domain containing"""	6192	protein-coding gene	gene with protein product		147796				1848670	Standard	NM_004972		Approved	JTK10	uc003ziw.3	O60674	OTTHUMG00000019490	ENST00000381652.3:c.1177C>G	9.37:g.5065003C>G	ENSP00000371067:p.Leu393Val	63.0	0.0	0		73.0	26.0	0.356164	NM_004972	O14636|O75297	Missense_Mutation	SNP	ENST00000381652.3	37	CCDS6457.1	29	0.013278388278388278	20	0.04065040650406504	7	0.019337016574585635	0	0.0	2	0.002638522427440633	C	7.763	0.705753	0.15172	0.029959	0.006047	ENSG00000096968	ENST00000539801;ENST00000381652;ENST00000544510	T;T;T	0.59083	0.29;0.29;0.29	5.15	5.15	0.70609	.	0.221618	0.39020	N	0.001490	T	0.10809	0.0264	N	0.17764	0.52	0.53005	D	0.999966	B	0.29612	0.251	B	0.23150	0.044	T	0.08330	-1.0727	10	0.08599	T	0.76	-14.3001	12.0387	0.53440	0.0:0.9205:0.0:0.0795	rs2230723;rs35844880	393	O60674	JAK2_HUMAN	V	393;393;244	ENSP00000440387:L393V;ENSP00000371067:L393V;ENSP00000443103:L244V	ENSP00000371067:L393V	L	+	1	0	JAK2	5055003	0.633000	0.27181	0.933000	0.37362	0.824000	0.46624	1.199000	0.32235	2.412000	0.81896	0.313000	0.20887	CTT	C|0.986;G|0.014	0.014	strong		0.343	JAK2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051609.1		
DSCAML1	57453	hgsc.bcm.edu	37	11	117309603	117309603	+	Missense_Mutation	SNP	C	C	T			TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr11:117309603C>T	ENST00000321322.6	-	24	4422	c.4421G>A	c.(4420-4422)cGa>cAa	p.R1474Q	DSCAML1_ENST00000527706.1_Missense_Mutation_p.R1204Q	NM_020693.2	NP_065744.2	Q8TD84	DSCL1_HUMAN	Down syndrome cell adhesion molecule like 1	1414	Fibronectin type-III 5. {ECO:0000255|PROSITE-ProRule:PRU00316}.				axonogenesis (GO:0007409)|brain development (GO:0007420)|cell fate determination (GO:0001709)|central nervous system development (GO:0007417)|dendrite self-avoidance (GO:0070593)|dorsal/ventral pattern formation (GO:0009953)|embryonic skeletal system morphogenesis (GO:0048704)|homophilic cell adhesion (GO:0007156)|negative regulation of cell adhesion (GO:0007162)	cell surface (GO:0009986)|extracellular space (GO:0005615)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	protein homodimerization activity (GO:0042803)			breast(3)|cervix(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(3)|kidney(7)|large_intestine(24)|lung(49)|ovary(6)|pancreas(1)|prostate(2)|skin(3)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	110	all_hematologic(175;0.0487)	Breast(348;0.0424)|Medulloblastoma(222;0.0523)|all_hematologic(192;0.232)		BRCA - Breast invasive adenocarcinoma(274;9.12e-06)|Epithelial(105;0.00172)		CTCCTCACCTCGGATGGAGCT	0.607																																					p.R1474Q		Atlas-SNP	.											.	DSCAML1	286	.	0			c.G4421A						PASS	.						44.0	42.0	43.0					11																	117309603		2201	4296	6497	SO:0001583	missense	57453	exon24			TCACCTCGGATGG		CCDS8384.1	11q22.2-q22.3	2013-02-11			ENSG00000177103	ENSG00000177103		"""Immunoglobulin superfamily / I-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"", ""Fibronectin type III domain containing"""	14656	protein-coding gene	gene with protein product		611782				11453658	Standard	NM_020693		Approved	KIAA1132	uc001prh.1	Q8TD84	OTTHUMG00000167071	ENST00000321322.6:c.4421G>A	11.37:g.117309603C>T	ENSP00000315465:p.Arg1474Gln	68.0	0.0	0		39.0	21.0	0.538462	NM_020693	Q76MU9|Q8IZY3|Q8IZY4|Q8WXU7|Q9ULT7	Missense_Mutation	SNP	ENST00000321322.6	37	CCDS8384.1	.	.	.	.	.	.	.	.	.	.	C	32	5.182083	0.94885	.	.	ENSG00000177103	ENST00000527706;ENST00000321322;ENST00000446508	T;T	0.56611	0.45;0.45	4.8	4.8	0.61643	Fibronectin, type III (4);Immunoglobulin-like fold (1);	.	.	.	.	T	0.57975	0.2090	N	0.14661	0.345	0.80722	D	1	D	0.89917	1.0	D	0.87578	0.998	T	0.63435	-0.6638	9	0.48119	T	0.1	.	18.0562	0.89365	0.0:1.0:0.0:0.0	.	1414	Q8TD84	DSCL1_HUMAN	Q	1204;1474;1181	ENSP00000434335:R1204Q;ENSP00000315465:R1474Q	ENSP00000315465:R1474Q	R	-	2	0	DSCAML1	116814813	1.000000	0.71417	1.000000	0.80357	0.831000	0.47069	7.635000	0.83286	2.503000	0.84419	0.561000	0.74099	CGA	.	.	none		0.607	DSCAML1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000392907.2	NM_020693	
FBN3	84467	hgsc.bcm.edu	37	19	8203392	8203392	+	Missense_Mutation	SNP	G	G	C	rs61729623	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr19:8203392G>C	ENST00000600128.1	-	9	1336	c.922C>G	c.(922-924)Ctc>Gtc	p.L308V	FBN3_ENST00000270509.2_Missense_Mutation_p.L308V|FBN3_ENST00000601739.1_Missense_Mutation_p.L308V			Q75N90	FBN3_HUMAN	fibrillin 3	308	TB 2.					proteinaceous extracellular matrix (GO:0005578)	calcium ion binding (GO:0005509)|extracellular matrix structural constituent (GO:0005201)			NS(1)|breast(9)|central_nervous_system(2)|cervix(1)|endometrium(11)|haematopoietic_and_lymphoid_tissue(2)|kidney(8)|large_intestine(15)|lung(53)|ovary(7)|pancreas(2)|prostate(3)|skin(10)|stomach(1)|upper_aerodigestive_tract(5)|urinary_tract(2)	132						TGGCCGGCGAGGTCTCCAGCA	0.652													g|||	14	0.00279553	0.0015	0.0014	5008	,	,		15853	0.0		0.008	False		,,,				2504	0.0031				p.L308V		Atlas-SNP	.											.	FBN3	300	.	0			c.C922G						PASS	.		VAL/LEU	9,4393		0,9,2192	24.0	26.0	25.0		922	1.7	0.0	19	dbSNP_129	25	90,8510		0,90,4210	yes	missense	FBN3	NM_032447.3	32	0,99,6402	CC,CG,GG		1.0465,0.2045,0.7614	probably-damaging	308/2810	8203392	99,12903	2201	4300	6501	SO:0001583	missense	84467	exon8			CGGCGAGGTCTCC		CCDS12196.1	19p13	2008-02-05							18794	protein-coding gene	gene with protein product		608529					Standard	NM_032447		Approved		uc002mjf.3	Q75N90		ENST00000600128.1:c.922C>G	19.37:g.8203392G>C	ENSP00000470498:p.Leu308Val	99.0	0.0	0		79.0	37.0	0.468354	NM_032447	Q75N91|Q75N92|Q75N93|Q86SJ5|Q96JP8	Missense_Mutation	SNP	ENST00000600128.1	37	CCDS12196.1	9	0.004120879120879121	1	0.0020325203252032522	1	0.0027624309392265192	0	0.0	7	0.009234828496042216	g	10.79	1.450741	0.26074	0.002045	0.010465	ENSG00000142449	ENST00000270509	D	0.94828	-3.53	4.06	1.72	0.24424	Matrix fibril-associated (3);TGF-beta binding (1);	0.090982	0.45867	N	0.000325	D	0.87826	0.6275	M	0.65498	2.005	0.25192	N	0.990126	P	0.35192	0.489	B	0.30179	0.112	T	0.77624	-0.2518	10	0.20519	T	0.43	.	9.7313	0.40363	0.0:0.1538:0.6867:0.1595	rs61729623	308	Q75N90	FBN3_HUMAN	V	308	ENSP00000270509:L308V	ENSP00000270509:L308V	L	-	1	0	FBN3	8109392	0.994000	0.37717	0.001000	0.08648	0.000000	0.00434	1.255000	0.32909	0.235000	0.21160	-0.313000	0.08912	CTC	G|0.983;C|0.017	0.017	strong		0.652	FBN3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000461428.2	NM_032447	
ATF7IP	55729	hgsc.bcm.edu	37	12	14577524	14577524	+	Silent	SNP	C	C	T	rs146972131		TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr12:14577524C>T	ENST00000540793.1	+	1	830	c.675C>T	c.(673-675)gcC>gcT	p.A225A	ATF7IP_ENST00000261168.4_Silent_p.A225A|ATF7IP_ENST00000536444.1_Silent_p.A225A|ATF7IP_ENST00000544627.1_Silent_p.A233A|ATF7IP_ENST00000543189.1_Silent_p.A225A|ATF7IP_ENST00000541654.1_3'UTR			Q6VMQ6	MCAF1_HUMAN	activating transcription factor 7 interacting protein	225					DNA methylation (GO:0006306)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of RNA polymerase II transcriptional preinitiation complex assembly (GO:0045898)|transcription, DNA-templated (GO:0006351)|viral process (GO:0016032)	nucleus (GO:0005634)				cervix(1)|endometrium(7)|kidney(5)|large_intestine(10)|liver(2)|lung(22)|ovary(1)|prostate(4)|skin(1)|urinary_tract(1)	54						GTGATTGTGCCGCTGATGATA	0.517																																					p.A225A		Atlas-SNP	.											.	ATF7IP	136	.	0			c.C675T						PASS	.	C		0,4406		0,0,2203	127.0	115.0	119.0		675	-0.9	0.0	12	dbSNP_134	119	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous	ATF7IP	NM_018179.3		0,1,6502	TT,TC,CC		0.0116,0.0,0.0077		225/1271	14577524	1,13005	2203	4300	6503	SO:0001819	synonymous_variant	55729	exon2			TTGTGCCGCTGAT	AJ242978	CCDS8663.1, CCDS66326.1, CCDS66327.1, CCDS73449.1	12p13.1	2005-11-18				ENSG00000171681			20092	protein-coding gene	gene with protein product		613644				10976766, 10777215	Standard	XM_005253424		Approved	FLJ10688, p621	uc001rbw.3	Q6VMQ6		ENST00000540793.1:c.675C>T	12.37:g.14577524C>T		270.0	1.0	0.0037037		280.0	135.0	0.482143	NM_018179	F5GX74|G3V1U0|Q4G0T9|Q6P3T3|Q86XW5|Q9NVJ9|Q9NWC2|Q9Y4X8	Silent	SNP	ENST00000540793.1	37	CCDS8663.1																																																																																			C|1.000;T|0.000	0.000	weak		0.517	ATF7IP-024	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000401400.1	NM_018179	
FMN2	56776	hgsc.bcm.edu	37	1	240371502	240371502	+	Silent	SNP	C	C	T	rs200984130		TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr1:240371502C>T	ENST00000319653.9	+	5	3620	c.3390C>T	c.(3388-3390)ccC>ccT	p.P1130P		NM_020066.4	NP_064450.3	Q9NZ56	FMN2_HUMAN	formin 2	1130	FH1.|Pro-rich.				cellular response to DNA damage stimulus (GO:0006974)|cellular response to hypoxia (GO:0071456)|establishment of meiotic spindle localization (GO:0051295)|formin-nucleated actin cable assembly (GO:0070649)|homologous chromosome movement towards spindle pole involved in homologous chromosome segregation (GO:0051758)|intracellular signal transduction (GO:0035556)|intracellular transport (GO:0046907)|multicellular organismal development (GO:0007275)|negative regulation of apoptotic process (GO:0043066)|negative regulation of protein catabolic process (GO:0042177)|oogenesis (GO:0048477)|polar body extrusion after meiotic divisions (GO:0040038)|protein transport (GO:0015031)|vesicle-mediated transport (GO:0016192)	cell cortex (GO:0005938)|cytoplasmic vesicle membrane (GO:0030659)|cytosol (GO:0005829)|endoplasmic reticulum membrane (GO:0005789)|microvillus (GO:0005902)|nucleolus (GO:0005730)|plasma membrane (GO:0005886)|spindle (GO:0005819)	actin binding (GO:0003779)			NS(1)|breast(7)|central_nervous_system(6)|cervix(1)|endometrium(14)|haematopoietic_and_lymphoid_tissue(1)|kidney(10)|large_intestine(13)|lung(87)|ovary(6)|pancreas(3)|prostate(12)|skin(7)|stomach(2)|upper_aerodigestive_tract(6)|urinary_tract(2)	178	Ovarian(103;0.127)	all_cancers(173;0.013)	OV - Ovarian serous cystadenocarcinoma(106;0.0106)			CGGGCATACCCCCTCCTCCCC	0.721																																					p.P1130P		Atlas-SNP	.											.	FMN2	451	.	0			c.C3390T						PASS	.						7.0	8.0	8.0					1																	240371502		2106	4124	6230	SO:0001819	synonymous_variant	56776	exon5			CATACCCCCTCCT	AF218942	CCDS31069.2	1q43	2008-02-05			ENSG00000155816	ENSG00000155816			14074	protein-coding gene	gene with protein product		606373				10781961	Standard	NM_020066		Approved		uc010pyd.2	Q9NZ56	OTTHUMG00000039883	ENST00000319653.9:c.3390C>T	1.37:g.240371502C>T		71.0	0.0	0		82.0	6.0	0.0731707	NM_020066	B0QZA7|B4DP05|Q59GF6|Q5VU37|Q9NZ55	Silent	SNP	ENST00000319653.9	37	CCDS31069.2																																																																																			C|0.999;T|0.001	0.001	weak		0.721	FMN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000096217.2	XM_371352	
OR51B5	282763	hgsc.bcm.edu	37	11	5364493	5364493	+	Missense_Mutation	SNP	T	T	C	rs57900141	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr11:5364493T>C	ENST00000300773.2	-	1	316	c.262A>G	c.(262-264)Agg>Ggg	p.R88G	HBE1_ENST00000380237.1_Intron|AC104389.28_ENST00000415970.1_RNA|HBG2_ENST00000380252.1_Intron|HBG2_ENST00000380259.2_Intron	NM_001005567.2	NP_001005567.2	Q9H339	O51B5_HUMAN	olfactory receptor, family 51, subfamily B, member 5	88			R -> G (in dbSNP:rs57900141).		detection of chemical stimulus involved in sensory perception of smell (GO:0050911)|sensory perception of smell (GO:0007608)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			NS(1)|central_nervous_system(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(4)|lung(13)|prostate(1)|skin(5)|upper_aerodigestive_tract(2)	28		Medulloblastoma(188;0.0075)|all_neural(188;0.0572)|Breast(177;0.0675)		Epithelial(150;3.05e-09)|BRCA - Breast invasive adenocarcinoma(625;0.135)		CCAATCTCCCTGTGATCCAGC	0.562													T|||	528	0.105431	0.3306	0.0519	5008	,	,		18694	0.0		0.0497	False		,,,				2504	0.0051				p.R88G		Atlas-SNP	.											.	OR51B5	60	.	0			c.A262G						PASS	.	T	GLY/ARG	1300,3102	434.3+/-343.9	182,936,1083	42.0	42.0	42.0		262	4.8	0.9	11	dbSNP_129	42	458,8136	134.7+/-192.1	14,430,3853	yes	missense	OR51B5	NM_001005567.2	125	196,1366,4936	CC,CT,TT		5.3293,29.532,13.5272	probably-damaging	88/313	5364493	1758,11238	2201	4297	6498	SO:0001583	missense	282763	exon5			TCTCCCTGTGATC	BK004430	CCDS31378.1	11p15.4	2012-08-09			ENSG00000242180	ENSG00000242180		"""GPCR / Class A : Olfactory receptors"""	19599	protein-coding gene	gene with protein product							Standard	NM_001005567		Approved		uc001maq.2	Q9H339	OTTHUMG00000066676	ENST00000300773.2:c.262A>G	11.37:g.5364493T>C	ENSP00000300773:p.Arg88Gly	42.0	0.0	0		64.0	30.0	0.46875	NM_001005567	B2RN59	Missense_Mutation	SNP	ENST00000300773.2	37	CCDS31378.1	209	0.09569597069597069	150	0.3048780487804878	23	0.06353591160220995	0	0.0	36	0.047493403693931395	T	14.56	2.573102	0.45902	0.29532	0.053293	ENSG00000242180	ENST00000300773	T	0.37752	1.18	4.76	4.76	0.60689	GPCR, rhodopsin-like superfamily (1);	0.186059	0.26532	N	0.023845	T	0.00012	0.0000	L	0.60845	1.875	0.80722	P	0.0	D	0.89917	1.0	D	0.91635	0.999	T	0.18777	-1.0326	9	0.87932	D	0	.	9.6048	0.39626	0.0:0.0:0.1761:0.8239	rs57900141;rs61738479	88	Q9H339	O51B5_HUMAN	G	88	ENSP00000300773:R88G	ENSP00000300773:R88G	R	-	1	2	OR51B5	5321069	0.000000	0.05858	0.874000	0.34290	0.601000	0.36947	-0.007000	0.12810	2.017000	0.59298	0.529000	0.55759	AGG	T|0.879;C|0.121	0.121	strong		0.562	OR51B5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000142975.1	NM_001005567	
DENND4A	10260	hgsc.bcm.edu	37	15	65957717	65957717	+	Silent	SNP	C	C	G	rs61751113	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr15:65957717C>G	ENST00000431932.2	-	29	5401	c.5193G>C	c.(5191-5193)ccG>ccC	p.P1731P	DENND4A_ENST00000443035.3_Silent_p.P1774P	NM_005848.3	NP_005839.3	Q7Z401	MYCPP_HUMAN	DENN/MADD domain containing 4A	1731					positive regulation of Rab GTPase activity (GO:0032851)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|Rab guanyl-nucleotide exchange factor activity (GO:0017112)			breast(1)|central_nervous_system(1)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(17)|lung(11)|ovary(2)|skin(2)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(2)	51						AGGGCTGTCCCGGATCCTGAT	0.373													C|||	21	0.00419329	0.0008	0.0101	5008	,	,		16939	0.0		0.0089	False		,,,				2504	0.0041				p.P1774P		Atlas-SNP	.											.	DENND4A	217	.	0			c.G5322C						PASS	.	C	,	2,3794		0,2,1896	153.0	152.0	152.0		5322,5193	-6.4	0.9	15	dbSNP_129	152	123,8115		1,121,3997	no	coding-synonymous,coding-synonymous	DENND4A	NM_001144823.1,NM_005848.3	,	1,123,5893	GG,GC,CC		1.4931,0.0527,1.0387	,	1774/1907,1731/1864	65957717	125,11909	1898	4119	6017	SO:0001819	synonymous_variant	10260	exon30			CTGTCCCGGATCC	AF534403	CCDS45285.1, CCDS53949.1	15q22.31	2012-10-03	2006-01-27	2006-01-27				"""DENN/MADD domain containing"""	24321	protein-coding gene	gene with protein product		600382	"""c-myc promoter binding protein"""	MYCPBP		8056341, 12906859	Standard	NM_005848		Approved	IRLB	uc002api.3	Q7Z401		ENST00000431932.2:c.5193G>C	15.37:g.65957717C>G		121.0	0.0	0		123.0	69.0	0.560976	NM_001144823	E7EPL3|Q14655|Q86T77|Q8IVX2|Q8NB93	Silent	SNP	ENST00000431932.2	37	CCDS45285.1																																																																																			C|0.991;G|0.009	0.009	strong		0.373	DENND4A-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000419611.1	NM_005848	
COL13A1	1305	hgsc.bcm.edu	37	10	71640267	71640267	+	Silent	SNP	C	C	A			TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr10:71640267C>A	ENST00000398978.3	+	6	936	c.444C>A	c.(442-444)ccC>ccA	p.P148P	COL13A1_ENST00000522165.1_Silent_p.P148P|COL13A1_ENST00000354547.3_Silent_p.P148P|COL13A1_ENST00000398972.3_Silent_p.P148P|COL13A1_ENST00000398971.3_Silent_p.P148P|COL13A1_ENST00000357811.3_Silent_p.P148P|COL13A1_ENST00000398966.3_Silent_p.P148P|COL13A1_ENST00000520267.1_Intron|COL13A1_ENST00000398964.3_Intron|COL13A1_ENST00000356340.3_Silent_p.P148P|COL13A1_ENST00000398969.3_Intron|COL13A1_ENST00000398968.3_Silent_p.P148P|COL13A1_ENST00000517713.1_Silent_p.P148P|COL13A1_ENST00000398974.3_Silent_p.P136P|COL13A1_ENST00000520133.1_Intron|COL13A1_ENST00000398973.3_Silent_p.P148P	NM_001130103.1	NP_001123575.1			collagen, type XIII, alpha 1									p.P148P(1)		endometrium(5)|large_intestine(3)|lung(15)|ovary(1)|prostate(2)|skin(1)|urinary_tract(1)	28						AGGGGTCCCCCGGAGACGCTG	0.622																																					p.P148P		Atlas-SNP	.											COL13A1_ENST00000398978,NS,carcinoma,0,1	COL13A1	133	1	1	Substitution - coding silent(1)	endometrium(1)	c.C444A						PASS	.						33.0	34.0	34.0					10																	71640267		1821	4077	5898	SO:0001819	synonymous_variant	1305	exon6			GTCCCCCGGAGAC	AJ293624	CCDS44419.1, CCDS44423.1, CCDS44424.1, CCDS44425.1, CCDS44427.1, CCDS44428.1, CCDS44423.2, CCDS44424.2, CCDS44425.2, CCDS44427.2, CCDS44428.2	10q22	2013-01-16			ENSG00000197467	ENSG00000197467		"""Collagens"""	2190	protein-coding gene	gene with protein product		120350					Standard	NM_001130103		Approved		uc001jql.3	Q5TAT6	OTTHUMG00000018394	ENST00000398978.3:c.444C>A	10.37:g.71640267C>A		115.0	0.0	0		137.0	63.0	0.459854	NM_080802		Silent	SNP	ENST00000398978.3	37	CCDS44419.1																																																																																			.	.	none		0.622	COL13A1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000048468.1	NM_005203	
CACNA1H	8912	hgsc.bcm.edu	37	16	1268596	1268596	+	Silent	SNP	C	C	T	rs372529098		TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr16:1268596C>T	ENST00000348261.5	+	33	6080	c.5832C>T	c.(5830-5832)caC>caT	p.H1944H	CACNA1H_ENST00000358590.4_Silent_p.H1938H|CACNA1H_ENST00000565831.1_Silent_p.H1938H	NM_021098.2	NP_066921.2	O95180	CAC1H_HUMAN	calcium channel, voltage-dependent, T type, alpha 1H subunit	1944					aldosterone biosynthetic process (GO:0032342)|axon guidance (GO:0007411)|calcium ion import (GO:0070509)|cellular response to hormone stimulus (GO:0032870)|cellular response to potassium ion (GO:0035865)|cortisol biosynthetic process (GO:0034651)|membrane depolarization during action potential (GO:0086010)|muscle contraction (GO:0006936)|muscle organ development (GO:0007517)|myoblast fusion (GO:0007520)|positive regulation of acrosome reaction (GO:2000344)|regulation of heart contraction (GO:0008016)|regulation of membrane potential (GO:0042391)|transport (GO:0006810)	caveola (GO:0005901)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|sarcolemma (GO:0042383)|voltage-gated calcium channel complex (GO:0005891)	low voltage-gated calcium channel activity (GO:0008332)|metal ion binding (GO:0046872)|scaffold protein binding (GO:0097110)			breast(4)|endometrium(5)|kidney(2)|lung(23)	34		Hepatocellular(780;0.00369)			Amiodarone(DB01118)|Bepridil(DB01244)|Cinnarizine(DB00568)|Felodipine(DB01023)|Flunarizine(DB04841)|Isradipine(DB00270)|Nifedipine(DB01115)|Nitrendipine(DB01054)|Spironolactone(DB00421)|Zonisamide(DB00909)	CGGCGCCCCACCCCCGCCCGC	0.657																																					p.H1944H		Atlas-SNP	.											.	CACNA1H	317	.	0			c.C5832T						PASS	.	C	,	0,3962		0,0,1981	13.0	17.0	16.0		5814,5832	-2.1	0.0	16		16	2,8230		0,2,4114	no	coding-synonymous,coding-synonymous	CACNA1H	NM_001005407.1,NM_021098.2	,	0,2,6095	TT,TC,CC		0.0243,0.0,0.0164	,	1938/2348,1944/2354	1268596	2,12192	1981	4116	6097	SO:0001819	synonymous_variant	8912	exon33			GCCCCACCCCCGC	AL031703	CCDS45375.1, CCDS45376.1	16p13.3	2012-03-07	2007-02-16					"""Calcium channel subunits"", ""Voltage-gated ion channels / Calcium channels"""	1395	protein-coding gene	gene with protein product		607904				9670923, 16382099	Standard	NM_021098		Approved	Cav3.2	uc002cks.3	O95180		ENST00000348261.5:c.5832C>T	16.37:g.1268596C>T		97.0	0.0	0		103.0	45.0	0.436893	NM_021098	B5ME00|F8WFD1|O95802|Q8WWI6|Q96QI6|Q96RZ9|Q9NYY4|Q9NYY5	Silent	SNP	ENST00000348261.5	37	CCDS45375.1																																																																																			.	.	weak		0.657	CACNA1H-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000421601.1	NM_001005407	
ALK	238	hgsc.bcm.edu	37	2	29543699	29543699	+	Silent	SNP	G	G	A	rs56165377	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr2:29543699G>A	ENST00000389048.3	-	7	2370	c.1464C>T	c.(1462-1464)ggC>ggT	p.G488G	ALK_ENST00000498037.1_5'Flank|ALK_ENST00000431873.1_Intron	NM_004304.4	NP_004295.2	Q9UM73	ALK_HUMAN	anaplastic lymphoma receptor tyrosine kinase	488	MAM 2. {ECO:0000255|PROSITE- ProRule:PRU00128}.				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)	CTTGGGTCCAGCCACAGAAGC	0.532			"""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				G|||	20	0.00399361	0.0	0.0202	5008	,	,		18892	0.0		0.006	False		,,,				2504	0.0				p.G488G		Atlas-SNP	.	yes	Dom	yes	Familial neuroblastoma	2	2p23	238	anaplastic lymphoma kinase (Ki-1)		"""L, E, M"""	.	ALK	533	.	0			c.C1464T						PASS	.	G		6,4400	11.4+/-27.6	0,6,2197	189.0	167.0	175.0		1464	5.9	1.0	2	dbSNP_129	175	88,8512	49.4+/-109.1	0,88,4212	no	coding-synonymous	ALK	NM_004304.4		0,94,6409	AA,AG,GG		1.0233,0.1362,0.7227		488/1621	29543699	94,12912	2203	4300	6503	SO:0001819	synonymous_variant	238	exon7	Familial Cancer Database	Familial Neuroblastoma;CCHS, Ondine Curse, incl. Ondine-Hirschsprung Disease	GGTCCAGCCACAG	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.1464C>T	2.37:g.29543699G>A		136.0	0.0	0		149.0	85.0	0.57047	NM_004304	Q4ZFX9|Q53QQ6|Q53RZ4|Q59FI3|Q9Y4K6	Silent	SNP	ENST00000389048.3	37	CCDS33172.1																																																																																			G|0.995;A|0.005	0.005	strong		0.532	ALK-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000324994.1	NM_004304	
GABBR2	9568	hgsc.bcm.edu	37	9	101151234	101151234	+	Missense_Mutation	SNP	G	G	C			TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr9:101151234G>C	ENST00000259455.2	-	10	1890	c.1431C>G	c.(1429-1431)atC>atG	p.I477M		NM_005458.7	NP_005449.5	O75899	GABR2_HUMAN	gamma-aminobutyric acid (GABA) B receptor, 2	477					G-protein coupled receptor signaling pathway (GO:0007186)|gamma-aminobutyric acid signaling pathway (GO:0007214)|negative regulation of adenylate cyclase activity (GO:0007194)|synaptic transmission (GO:0007268)	cell junction (GO:0030054)|cytoplasm (GO:0005737)|G-protein coupled receptor heterodimeric complex (GO:0038039)|integral component of plasma membrane (GO:0005887)|neuron projection (GO:0043005)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)	G-protein coupled GABA receptor activity (GO:0004965)		NOTCH1_ENST00000277541/GABBR2(2)	breast(4)|endometrium(4)|large_intestine(12)|lung(21)|ovary(2)|skin(4)|stomach(1)|urinary_tract(1)	49		Acute lymphoblastic leukemia(62;0.0527)			Baclofen(DB00181)	GAGGTAGGGAGATCTTCCGCA	0.502																																					p.I477M		Atlas-SNP	.											.	GABBR2	126	.	0			c.C1431G						PASS	.						336.0	253.0	281.0					9																	101151234		2203	4300	6503	SO:0001583	missense	9568	exon10			TAGGGAGATCTTC	AF069755	CCDS6736.1	9q22.1-q22.3	2012-08-29	2006-02-16	2006-02-16	ENSG00000136928	ENSG00000136928		"""GABA receptors"", ""GPCR / Class C : GABA(B) receptors"""	4507	protein-coding gene	gene with protein product		607340	"""G protein-coupled receptor 51"""	GPR51		10087195	Standard	NM_005458		Approved	HG20, GABABR2, GPRC3B	uc004ays.3	O75899	OTTHUMG00000020345	ENST00000259455.2:c.1431C>G	9.37:g.101151234G>C	ENSP00000259455:p.Ile477Met	284.0	1.0	0.00352113		273.0	118.0	0.432234	NM_005458	O75974|O75975|Q5VXZ2|Q8WX04|Q9P1R2|Q9UNR1|Q9UNS9	Missense_Mutation	SNP	ENST00000259455.2	37	CCDS6736.1	.	.	.	.	.	.	.	.	.	.	G	17.48	3.399282	0.62177	.	.	ENSG00000136928	ENST00000259455	T	0.80304	-1.36	4.83	4.83	0.62350	.	0.000000	0.85682	D	0.000000	T	0.81044	0.4741	M	0.63843	1.955	0.80722	D	1	P	0.50617	0.937	P	0.49276	0.605	T	0.82902	-0.0227	10	0.87932	D	0	.	9.4371	0.38646	0.0978:0.0:0.9022:0.0	.	477	O75899	GABR2_HUMAN	M	477	ENSP00000259455:I477M	ENSP00000259455:I477M	I	-	3	3	GABBR2	100191055	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	2.035000	0.41155	2.389000	0.81357	0.655000	0.94253	ATC	.	.	none		0.502	GABBR2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053373.1		
CNGB1	1258	hgsc.bcm.edu	37	16	58001086	58001086	+	Silent	SNP	C	C	T	rs61997250	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr16:58001086C>T	ENST00000251102.8	-	2	165	c.105G>A	c.(103-105)gcG>gcA	p.A35A	CNGB1_ENST00000311183.4_Silent_p.A35A|CNGB1_ENST00000564448.1_Silent_p.A35A	NM_001297.4	NP_001288.3	Q14028	CNGB1_HUMAN	cyclic nucleotide gated channel beta 1	35	Glu-rich.				cation transport (GO:0006812)|cytosolic calcium ion homeostasis (GO:0051480)|detection of light stimulus involved in visual perception (GO:0050908)|phototransduction, visible light (GO:0007603)|potassium ion transmembrane transport (GO:0071805)|protein heterotetramerization (GO:0051290)|regulation of membrane potential (GO:0042391)|regulation of rhodopsin mediated signaling pathway (GO:0022400)|retina homeostasis (GO:0001895)|rhodopsin mediated signaling pathway (GO:0016056)|sensory perception of smell (GO:0007608)|transport (GO:0006810)|visual perception (GO:0007601)	integral component of plasma membrane (GO:0005887)|intracellular cyclic nucleotide activated cation channel complex (GO:0017071)|plasma membrane (GO:0005886)|terminal bouton (GO:0043195)|transmembrane transporter complex (GO:1902495)	cAMP binding (GO:0030552)|cGMP binding (GO:0030553)|intracellular cAMP activated cation channel activity (GO:0005222)|intracellular cGMP activated cation channel activity (GO:0005223)|ligand-gated ion channel activity (GO:0015276)|voltage-gated potassium channel activity (GO:0005249)			breast(7)|cervix(2)|endometrium(4)|kidney(2)|large_intestine(11)|liver(1)|lung(12)|ovary(1)|pancreas(1)|prostate(2)|skin(5)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(2)	54						GTTCCACCTCCGCCTCCATCT	0.647													C|||	41	0.0081869	0.0023	0.0072	5008	,	,		17304	0.0		0.0258	False		,,,				2504	0.0072				p.A35A	Colon(156;1293 1853 16336 28962 38659)	Atlas-SNP	.											.	CNGB1	105	.	0			c.G105A						PASS	.	C	,	32,3990		0,32,1979	96.0	101.0	99.0		105,105	-8.9	0.0	16	dbSNP_129	99	242,8090		4,234,3928	no	coding-synonymous,coding-synonymous	CNGB1	NM_001135639.1,NM_001297.4	,	4,266,5907	TT,TC,CC		2.9045,0.7956,2.2179	,	35/300,35/1252	58001086	274,12080	2011	4166	6177	SO:0001819	synonymous_variant	1258	exon2			CACCTCCGCCTCC	AF042498	CCDS42169.1, CCDS45495.1, CCDS67042.1	16q13	2013-02-14			ENSG00000070729	ENSG00000070729		"""Voltage-gated ion channels / Cyclic nucleotide-regulated channels"""	2151	protein-coding gene	gene with protein product	"""glutamic acid-rich protein"""	600724		CNCG2, CNCG3L		8766832, 7590744, 16382102	Standard	NM_001297		Approved	RCNC2, RCNCb, GARP, GAR1, CNGB1B, RP45	uc002emt.2	Q14028	OTTHUMG00000154810	ENST00000251102.8:c.105G>A	16.37:g.58001086C>T		93.0	0.0	0		92.0	44.0	0.478261	NM_001297	H3BN09|O43636|Q13059|Q14029|Q9UMG2	Silent	SNP	ENST00000251102.8	37	CCDS42169.1																																																																																			C|0.981;T|0.019	0.019	strong		0.647	CNGB1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000337167.2	NM_001297	
ZHX2	22882	hgsc.bcm.edu	37	8	123965193	123965193	+	Silent	SNP	C	C	T	rs111726812	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr8:123965193C>T	ENST00000314393.4	+	3	2278	c.1443C>T	c.(1441-1443)agC>agT	p.S481S		NM_014943.3	NP_055758.1	Q9Y6X8	ZHX2_HUMAN	zinc fingers and homeoboxes 2	481	Required for interaction with NFYA.				mRNA catabolic process (GO:0006402)|negative regulation of neuron differentiation (GO:0045665)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|somatic stem cell maintenance (GO:0035019)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription corepressor activity (GO:0003714)			breast(1)|central_nervous_system(1)|endometrium(7)|kidney(1)|large_intestine(10)|lung(15)|ovary(1)|prostate(1)|skin(4)|stomach(3)|urinary_tract(1)	45	Lung NSC(37;2e-09)|Ovarian(258;0.0205)|Hepatocellular(40;0.105)		STAD - Stomach adenocarcinoma(47;0.00527)			TTGCCAGGAGCGAGATCAAGA	0.567													C|||	116	0.0231629	0.0439	0.0317	5008	,	,		18163	0.0		0.0298	False		,,,				2504	0.0061				p.S481S	Esophageal Squamous(94;1056 1388 11767 13799 49639)	Atlas-SNP	.											ZHX2,caecum,carcinoma,0,1	ZHX2	106	1	0			c.C1443T						scavenged	.	C		179,4227	116.7+/-154.6	5,169,2029	88.0	82.0	84.0		1443	-8.1	0.7	8	dbSNP_132	84	278,8322	105.4+/-166.3	6,266,4028	no	coding-synonymous	ZHX2	NM_014943.3		11,435,6057	TT,TC,CC		3.2326,4.0626,3.5138		481/838	123965193	457,12549	2203	4300	6503	SO:0001819	synonymous_variant	22882	exon3			CAGGAGCGAGATC	AB020661	CCDS6336.1	8q24.13	2012-03-09	2004-01-23		ENSG00000178764	ENSG00000178764		"""Zinc fingers, C2H2-type"", ""Homeoboxes / ZF class"""	18513	protein-coding gene	gene with protein product		609185	"""zinc-fingers and homeoboxes 2"""			10048485, 12741956	Standard	XM_005250837		Approved	KIAA0854	uc003ypk.1	Q9Y6X8	OTTHUMG00000165077	ENST00000314393.4:c.1443C>T	8.37:g.123965193C>T		70.0	1.0	0.0142857		70.0	32.0	0.457143	NM_014943		Silent	SNP	ENST00000314393.4	37	CCDS6336.1																																																																																			C|0.965;T|0.035	0.035	strong		0.567	ZHX2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000381709.1	NM_014943	
TEAD3	7005	hgsc.bcm.edu	37	6	35446225	35446225	+	Missense_Mutation	SNP	A	A	G	rs144697750	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr6:35446225A>G	ENST00000402886.3	-	4	439	c.286T>C	c.(286-288)Tcc>Ccc	p.S96P	TEAD3_ENST00000338863.7_Missense_Mutation_p.S156P			Q99594	TEAD3_HUMAN	TEA domain family member 3	156					female pregnancy (GO:0007565)|gene expression (GO:0010467)|hippo signaling (GO:0035329)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription initiation from RNA polymerase II promoter (GO:0006367)	nucleoplasm (GO:0005654)|transcription factor complex (GO:0005667)	DNA binding (GO:0003677)|RNA polymerase II transcription factor binding (GO:0001085)|sequence-specific DNA binding transcription factor activity (GO:0003700)			central_nervous_system(1)|large_intestine(1)|lung(5)|ovary(1)|prostate(1)|urinary_tract(1)	10						GAGGAAGTGGAGAAGACGGCC	0.612													a|||	16	0.00319489	0.0008	0.0072	5008	,	,		17840	0.0		0.008	False		,,,				2504	0.002				p.S156P		Atlas-SNP	.											.	TEAD3	52	.	0			c.T466C						PASS	.		PRO/SER	7,4137		0,7,2065	54.0	65.0	62.0		466	3.3	1.0	6	dbSNP_134	62	49,8365		0,49,4158	yes	missense	TEAD3	NM_003214.3	74	0,56,6223	GG,GA,AA		0.5824,0.1689,0.4459	benign	156/436	35446225	56,12502	2072	4207	6279	SO:0001583	missense	7005	exon6			AAGTGGAGAAGAC	X94439	CCDS47414.1	6p21.2	2008-07-28			ENSG00000007866	ENSG00000007866			11716	protein-coding gene	gene with protein product		603170		TEAD5		9889009, 9148898	Standard	NM_003214		Approved	TEF-5, ETFR-1	uc003oku.4	Q99594	OTTHUMG00000014571	ENST00000402886.3:c.286T>C	6.37:g.35446225A>G	ENSP00000384577:p.Ser96Pro	60.0	0.0	0		76.0	34.0	0.447368	NM_003214	O95910|Q5BJG7|Q8N6Y4	Missense_Mutation	SNP	ENST00000402886.3	37		8	0.003663003663003663	0	0.0	2	0.0055248618784530384	0	0.0	6	0.0079155672823219	a	3.061	-0.193152	0.06259	0.001689	0.005824	ENSG00000007866	ENST00000338863;ENST00000402886;ENST00000373905;ENST00000433586	T;T;T	0.56275	0.48;0.47;0.91	4.46	3.26	0.37387	.	0.213980	0.41097	N	0.000949	T	0.19485	0.0468	N	0.17082	0.46	0.35183	D	0.77268	B;B;P	0.41748	0.002;0.0;0.761	B;B;P	0.45377	0.011;0.001;0.478	T	0.03473	-1.1033	10	0.09843	T	0.71	-16.0678	9.8736	0.41189	0.847:0.0:0.0:0.153	.	96;172;156	B5MCM0;Q7Z6V0;Q99594	.;.;TEAD3_HUMAN	P	156;96;172;67	ENSP00000345772:S156P;ENSP00000384577:S96P;ENSP00000416400:S67P	ENSP00000345772:S156P	S	-	1	0	TEAD3	35554203	1.000000	0.71417	0.997000	0.53966	0.915000	0.54546	2.068000	0.41471	0.826000	0.34661	0.444000	0.29173	TCC	A|0.995;G|0.005	0.005	strong		0.612	TEAD3-005	NOVEL	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000316961.2		
GALR2	8811	hgsc.bcm.edu	37	17	74072923	74072923	+	Missense_Mutation	SNP	T	T	G	rs369779116		TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr17:74072923T>G	ENST00000329003.3	+	2	665	c.575T>G	c.(574-576)tTc>tGc	p.F192C	ZACN_ENST00000334586.5_5'Flank|ZACN_ENST00000392503.2_5'Flank	NM_003857.2	NP_003848.1	O43603	GALR2_HUMAN	galanin receptor 2	192					adenylate cyclase-modulating G-protein coupled receptor signaling pathway (GO:0007188)|cell surface receptor signaling pathway (GO:0007166)|digestion (GO:0007586)|feeding behavior (GO:0007631)|learning or memory (GO:0007611)|multicellular organismal development (GO:0007275)|muscle contraction (GO:0006936)|negative regulation of adenylate cyclase activity (GO:0007194)|neuron projection development (GO:0031175)|neuropeptide signaling pathway (GO:0007218)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|positive regulation of large conductance calcium-activated potassium channel activity (GO:1902608)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|synaptic transmission (GO:0007268)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	galanin receptor activity (GO:0004966)|peptide hormone binding (GO:0017046)			cervix(1)|lung(4)|upper_aerodigestive_tract(2)|urinary_tract(1)	8						ATCTGCACCTTCGTCTTCAGC	0.692																																					p.F192C		Atlas-SNP	.											.	GALR2	17	.	0			c.T575G						PASS	.	T	CYS/PHE	1,4399		0,1,2199	45.0	31.0	36.0		575	5.0	1.0	17		36	0,8596		0,0,4298	no	missense	GALR2	NM_003857.2	205	0,1,6497	GG,GT,TT		0.0,0.0227,0.0077	probably-damaging	192/388	74072923	1,12995	2200	4298	6498	SO:0001583	missense	8811	exon2			GCACCTTCGTCTT	AF040630	CCDS11739.1	17q25.3	2012-08-08			ENSG00000182687	ENSG00000182687		"""GPCR / Class A : Galanin receptors"""	4133	protein-coding gene	gene with protein product		603691				9685625, 9832121	Standard	NM_003857		Approved	GALNR2	uc002jqm.1	O43603	OTTHUMG00000167479	ENST00000329003.3:c.575T>G	17.37:g.74072923T>G	ENSP00000329684:p.Phe192Cys	50.0	0.0	0		65.0	29.0	0.446154	NM_003857	A5JUU4|Q32MN8	Missense_Mutation	SNP	ENST00000329003.3	37	CCDS11739.1	.	.	.	.	.	.	.	.	.	.	T	26.6	4.752255	0.89753	2.27E-4	0.0	ENSG00000182687	ENST00000329003	T	0.72394	-0.65	4.97	4.97	0.65823	GPCR, rhodopsin-like superfamily (1);	0.000000	0.85682	D	0.000000	D	0.87657	0.6232	M	0.93720	3.45	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	D	0.90899	0.4767	10	0.87932	D	0	.	14.3163	0.66452	0.0:0.0:0.0:1.0	.	192	O43603	GALR2_HUMAN	C	192	ENSP00000329684:F192C	ENSP00000329684:F192C	F	+	2	0	GALR2	71584518	1.000000	0.71417	0.978000	0.43139	0.984000	0.73092	7.925000	0.87563	1.871000	0.54225	0.379000	0.24179	TTC	.	.	weak		0.692	GALR2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000394760.1		
SEC16A	9919	hgsc.bcm.edu	37	9	139347953	139347953	+	Missense_Mutation	SNP	G	G	A	rs202042941		TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr9:139347953G>A	ENST00000371706.3	-	20	5585	c.5552C>T	c.(5551-5553)cCg>cTg	p.P1851L	SEC16A_ENST00000290037.6_Missense_Mutation_p.P1851L|SEC16A_ENST00000431893.2_Missense_Mutation_p.P1851L|SEC16A_ENST00000313050.7_Missense_Mutation_p.P2029L|SEC16A_ENST00000398335.1_5'Flank			O15027	SC16A_HUMAN	SEC16 homolog A (S. cerevisiae)	1851	Pro-rich.				COPII vesicle coating (GO:0048208)|endoplasmic reticulum organization (GO:0007029)|protein transport (GO:0015031)|substantia nigra development (GO:0021762)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|Golgi membrane (GO:0000139)				breast(1)|central_nervous_system(3)|endometrium(7)|kidney(5)|large_intestine(15)|lung(14)|ovary(3)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	51		Myeloproliferative disorder(178;0.0511)		Epithelial(140;2.9e-06)|OV - Ovarian serous cystadenocarcinoma(145;5.88e-06)		CGCCTCCTGCGGCACTATCCC	0.483																																					p.P2029L		Atlas-SNP	.											.	SEC16A	249	.	0			c.C6086T						PASS	.	G	LEU/PRO	4,3968		0,4,1982	75.0	79.0	78.0		6086	2.0	0.0	9		78	6,8312		0,6,4153	yes	missense	SEC16A	NM_014866.1	98	0,10,6135	AA,AG,GG		0.0721,0.1007,0.0814	benign	2029/2358	139347953	10,12280	1986	4159	6145	SO:0001583	missense	9919	exon22			TCCTGCGGCACTA	AK074565	CCDS55351.1, CCDS75936.1	9q34.3	2007-06-20	2007-06-20	2007-06-20	ENSG00000148396	ENSG00000148396			29006	protein-coding gene	gene with protein product		612854	"""KIAA0310"""	KIAA0310		9205841	Standard	NM_014866		Approved	p250	uc004chx.3	O15027	OTTHUMG00000020932	ENST00000371706.3:c.5552C>T	9.37:g.139347953G>A	ENSP00000360771:p.Pro1851Leu	29.0	0.0	0		28.0	9.0	0.321429	NM_014866	A1YCA4|Q4G0D7|Q5SXP0|Q5SXP1|Q8N347|Q96HP1	Missense_Mutation	SNP	ENST00000371706.3	37		.	.	.	.	.	.	.	.	.	.	G	15.41	2.825603	0.50739	0.001007	7.21E-4	ENSG00000148396	ENST00000313050;ENST00000277537;ENST00000453963;ENST00000371706;ENST00000290037;ENST00000431893;ENST00000404925;ENST00000398348	T;T;T;T;T;T	0.44482	1.89;0.92;1.51;1.88;1.88;1.87	4.84	1.96	0.26148	.	0.491778	0.21508	N	0.073403	T	0.56321	0.1977	M	0.71581	2.175	0.25198	N	0.990071	D;D;P;B;P	0.76494	0.997;0.999;0.573;0.278;0.769	D;D;B;B;B	0.71870	0.926;0.975;0.213;0.035;0.106	T	0.44772	-0.9306	10	0.45353	T	0.12	-0.9711	7.4567	0.27270	0.278:0.0:0.722:0.0	.	2029;1851;1851;1419;1851	F1T0I1;O15027-5;O15027-4;A4QN19;O15027	.;.;.;.;SC16A_HUMAN	L	2029;423;751;1851;1851;1851;1419;387	ENSP00000325827:P2029L;ENSP00000277537:P423L;ENSP00000403525:P751L;ENSP00000360771:P1851L;ENSP00000290037:P1851L;ENSP00000387583:P1851L	ENSP00000277537:P423L	P	-	2	0	SEC16A	138467774	0.128000	0.22383	0.002000	0.10522	0.019000	0.09904	1.080000	0.30779	0.191000	0.20236	0.561000	0.74099	CCG	.	.	weak		0.483	SEC16A-001	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000055077.1	XM_088459	
CECR5	27440	hgsc.bcm.edu	37	22	17618937	17618937	+	Missense_Mutation	SNP	G	G	A	rs35327402	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr22:17618937G>A	ENST00000336737.4	-	8	1271	c.1246C>T	c.(1246-1248)Cgc>Tgc	p.R416C	CECR5_ENST00000155674.5_Missense_Mutation_p.R386C|CECR5_ENST00000399852.3_Missense_Mutation_p.R216C	NM_033070.2	NP_149061.1	Q9BXW7	CECR5_HUMAN	cat eye syndrome chromosome region, candidate 5	416			R -> C (in dbSNP:rs35327402).			mitochondrion (GO:0005739)				NS(1)|breast(1)|central_nervous_system(1)|endometrium(2)|large_intestine(3)|liver(1)|lung(10)|pancreas(1)|prostate(1)	21		all_epithelial(15;0.0181)|Lung NSC(13;0.109)|all_lung(157;0.132)				CCCTCCTTGCGGAAGACCAGC	0.632													G|||	15	0.00299521	0.0008	0.0043	5008	,	,		19931	0.0		0.008	False		,,,				2504	0.0031				p.R416C		Atlas-SNP	.											.	CECR5	46	.	0			c.C1246T						PASS	.	G	CYS/ARG,CYS/ARG	2,4404	4.2+/-10.8	0,2,2201	98.0	85.0	90.0		1156,1246	2.2	0.6	22	dbSNP_126	90	32,8568	21.6+/-65.8	0,32,4268	yes	missense,missense	CECR5	NM_017829.5,NM_033070.2	180,180	0,34,6469	AA,AG,GG		0.3721,0.0454,0.2614	benign,benign	386/394,416/424	17618937	34,12972	2203	4300	6503	SO:0001583	missense	27440	exon8			CCTTGCGGAAGAC	AF273270	CCDS13741.1, CCDS33595.1	22q11.2	2008-06-12			ENSG00000069998	ENSG00000069998			1843	protein-coding gene	gene with protein product						11381032	Standard	NM_017829		Approved		uc002zmf.3	Q9BXW7	OTTHUMG00000150071	ENST00000336737.4:c.1246C>T	22.37:g.17618937G>A	ENSP00000337358:p.Arg416Cys	103.0	0.0	0		113.0	64.0	0.566372	NM_033070	B2RCK5|Q9BXW8|Q9NWA8|Q9NX41	Missense_Mutation	SNP	ENST00000336737.4	37	CCDS33595.1	8	0.003663003663003663	0	0.0	2	0.0055248618784530384	0	0.0	6	0.0079155672823219	G	10.55	1.382430	0.24944	4.54E-4	0.003721	ENSG00000069998	ENST00000155674;ENST00000336737;ENST00000399852	T;T;T	0.25250	1.81;1.81;1.81	4.47	2.2	0.27929	HAD-like domain (1);	0.532262	0.21527	N	0.073110	T	0.12475	0.0303	L	0.44542	1.39	0.22112	N	0.999352	B;B;B;B	0.24426	0.103;0.015;0.014;0.023	B;B;B;B	0.18263	0.021;0.008;0.006;0.008	T	0.15321	-1.0441	10	0.59425	D	0.04	-8.9079	3.6609	0.08238	0.0871:0.1262:0.4078:0.3789	rs35327402	386;216;416;280	Q9BXW7-2;A8MYZ9;Q9BXW7;B3KVW8	.;.;CECR5_HUMAN;.	C	386;416;216	ENSP00000155674:R386C;ENSP00000337358:R416C;ENSP00000382745:R216C	ENSP00000155674:R386C	R	-	1	0	CECR5	15998937	0.000000	0.05858	0.641000	0.29422	0.811000	0.45836	-0.486000	0.06513	1.065000	0.40693	0.561000	0.74099	CGC	G|0.996;A|0.004	0.004	strong		0.632	CECR5-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000316100.1	NM_017829	
FAM129C	199786	hgsc.bcm.edu	37	19	17638144	17638144	+	Missense_Mutation	SNP	A	A	C	rs200304763	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr19:17638144A>C	ENST00000335393.4	+	2	226	c.88A>C	c.(88-90)Agc>Cgc	p.S30R	FAM129C_ENST00000300971.2_Missense_Mutation_p.S30R|FAM129C_ENST00000599124.1_5'UTR|FAM129C_ENST00000599164.1_5'UTR|FAM129C_ENST00000352727.3_Missense_Mutation_p.S30R|FAM129C_ENST00000332386.5_Missense_Mutation_p.S30R|FAM129C_ENST00000597887.1_3'UTR|FAM129C_ENST00000449408.2_5'UTR|FAM129C_ENST00000595684.1_Missense_Mutation_p.S30R|FAM129C_ENST00000601861.1_5'UTR|FAM129C_ENST00000600871.1_5'UTR	NM_173544.4	NP_775815	Q86XR2	NIBL2_HUMAN	family with sequence similarity 129, member C	30										autonomic_ganglia(1)|breast(1)|central_nervous_system(1)|endometrium(1)|large_intestine(8)|liver(2)|lung(14)|ovary(1)|skin(3)|stomach(1)	33						GGGAGACGACAGCAGCATGGG	0.692													A|||	7	0.00139776	0.0	0.0014	5008	,	,		11745	0.0		0.0	False		,,,				2504	0.0061				p.S30R		Atlas-SNP	.											.	FAM129C	110	.	0			c.A88C						PASS	.	A	ARG/SER,ARG/SER	0,4044		0,0,2022	25.0	21.0	23.0		88,88	-3.7	0.0	19		23	1,7935		0,1,3967	yes	missense,missense	FAM129C	NM_001098524.1,NM_173544.4	110,110	0,1,5989	CC,CA,AA		0.0126,0.0,0.0083	probably-damaging,probably-damaging	30/652,30/698	17638144	1,11979	2022	3968	5990	SO:0001583	missense	199786	exon2			GACGACAGCAGCA	AY254198	CCDS12362.1, CCDS42521.1	19p13.11	2008-02-05				ENSG00000167483			24130	protein-coding gene	gene with protein product	B cell novel protein 1	609967				12886250	Standard	NM_173544		Approved	FLJ39802, BCNP1	uc021uqj.1	Q86XR2		ENST00000335393.4:c.88A>C	19.37:g.17638144A>C	ENSP00000335040:p.Ser30Arg	194.0	0.0	0		208.0	89.0	0.427885	NM_001098524	B4DNU3|B4DVN7|Q7Z6H6|Q86XR3|Q86XR4|Q8TEQ3	Missense_Mutation	SNP	ENST00000335393.4	37	CCDS12362.1	5	0.0022893772893772895	4	0.008130081300813009	1	0.0027624309392265192	0	0.0	0	0.0	A	15.73	2.920339	0.52653	0.0	1.26E-4	ENSG00000167483	ENST00000335393;ENST00000332386;ENST00000352727;ENST00000300971	T;T;T;T	0.26810	1.93;2.03;1.71;1.72	3.98	-3.67	0.04476	.	0.829479	0.10133	N	0.711885	T	0.13756	0.0333	L	0.51422	1.61	0.19300	N	0.999979	B;B	0.06786	0.001;0.001	B;B	0.06405	0.002;0.002	T	0.23048	-1.0199	10	0.39692	T	0.17	.	6.6521	0.22967	0.3189:0.1624:0.5187:0.0	.	30;30	Q86XR2;Q86XR2-3	NIBL2_HUMAN;.	R	30	ENSP00000335040:S30R;ENSP00000333447:S30R;ENSP00000341067:S30R;ENSP00000300971:S30R	ENSP00000300971:S30R	S	+	1	0	FAM129C	17499144	0.004000	0.15560	0.001000	0.08648	0.023000	0.10783	-0.012000	0.12699	-0.984000	0.03507	-0.415000	0.06103	AGC	A|0.998;C|0.002	0.002	strong		0.692	FAM129C-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000464206.1	NM_173544	
MTMR8	55613	hgsc.bcm.edu	37	X	63488670	63488670	+	Missense_Mutation	SNP	G	G	T			TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chrX:63488670G>T	ENST00000374852.3	-	14	1929	c.1862C>A	c.(1861-1863)gCc>gAc	p.A621D	MTMR8_ENST00000453546.1_Intron	NM_017677.3	NP_060147.2	Q96EF0	MTMR8_HUMAN	myotubularin related protein 8	621						nucleus (GO:0005634)	protein tyrosine phosphatase activity (GO:0004725)	p.0?(2)		breast(5)|endometrium(4)|haematopoietic_and_lymphoid_tissue(3)|kidney(2)|large_intestine(8)|lung(10)|ovary(2)|skin(3)	37						GATATTTATGGCCCTAAGGCT	0.527																																					p.A621D		Atlas-SNP	.											.	MTMR8	178	.	2	Whole gene deletion(2)	ovary(1)|large_intestine(1)	c.C1862A						PASS	.						83.0	65.0	71.0					X																	63488670		2203	4300	6503	SO:0001583	missense	55613	exon14			TTTATGGCCCTAA	AK000133	CCDS14379.1	Xq11.2-q12	2013-01-11			ENSG00000102043	ENSG00000102043		"""Protein tyrosine phosphatases / Class I Cys-based PTPs : Myotubularins"""	16825	protein-coding gene	gene with protein product						11275328	Standard	NM_017677		Approved	FLJ20126	uc004dvs.3	Q96EF0	OTTHUMG00000021707	ENST00000374852.3:c.1862C>A	X.37:g.63488670G>T	ENSP00000363985:p.Ala621Asp	71.0	0.0	0		75.0	75.0	1	NM_017677	Q5JT99|Q9NXP6	Missense_Mutation	SNP	ENST00000374852.3	37	CCDS14379.1	.	.	.	.	.	.	.	.	.	.	G	12.94	2.088488	0.36855	.	.	ENSG00000102043	ENST00000374852;ENST00000247400	D	0.95272	-3.66	2.51	2.51	0.30379	.	0.460045	0.16633	U	0.205952	D	0.85969	0.5821	N	0.08118	0	0.09310	N	1	P	0.41232	0.743	B	0.40602	0.334	T	0.80162	-0.1497	10	0.87932	D	0	.	6.6727	0.23078	0.0:0.2931:0.7069:0.0	.	621	Q96EF0	MTMR8_HUMAN	D	621;507	ENSP00000363985:A621D	ENSP00000247400:A507D	A	-	2	0	MTMR8	63405395	0.859000	0.29813	0.004000	0.12327	0.057000	0.15508	1.348000	0.33987	1.541000	0.49316	0.436000	0.28706	GCC	.	.	none		0.527	MTMR8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056949.2	NM_017677	
GNAQ	2776	hgsc.bcm.edu	37	9	80537112	80537112	+	Missense_Mutation	SNP	T	T	A			TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr9:80537112T>A	ENST00000286548.4	-	2	508	c.286A>T	c.(286-288)Aca>Tca	p.T96S		NM_002072.3	NP_002063.2	P50148	GNAQ_HUMAN	guanine nucleotide binding protein (G protein), q polypeptide	96					action potential (GO:0001508)|activation of phospholipase C activity (GO:0007202)|adenylate cyclase-activating G-protein coupled receptor signaling pathway (GO:0007189)|blood coagulation (GO:0007596)|developmental pigmentation (GO:0048066)|embryonic digit morphogenesis (GO:0042733)|forebrain neuron development (GO:0021884)|glutamate receptor signaling pathway (GO:0007215)|heart development (GO:0007507)|maternal behavior (GO:0042711)|negative regulation of protein kinase activity (GO:0006469)|neuron remodeling (GO:0016322)|phospholipase C-activating dopamine receptor signaling pathway (GO:0060158)|platelet activation (GO:0030168)|positive regulation of GTPase activity (GO:0043547)|post-embryonic development (GO:0009791)|protein stabilization (GO:0050821)|regulation of catenin import into nucleus (GO:0035412)|regulation of melanocyte differentiation (GO:0045634)|skeletal system development (GO:0001501)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|heterotrimeric G-protein complex (GO:0005834)|lysosomal membrane (GO:0005765)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	G-protein beta/gamma-subunit complex binding (GO:0031683)|GTP binding (GO:0005525)|GTPase activator activity (GO:0005096)|GTPase activity (GO:0003924)|metal ion binding (GO:0046872)|signal transducer activity (GO:0004871)|type 2A serotonin receptor binding (GO:0031826)	p.T96S(1)		NS(1)|endometrium(3)|eye(229)|kidney(1)|large_intestine(4)|lung(6)|meninges(11)|ovary(1)|prostate(1)|skin(44)|upper_aerodigestive_tract(1)	302						ATCTTGAGTGTGTCCATGGCT	0.473			Mis		uveal melanoma																																p.T96S		Atlas-SNP	.		Dom	yes		9	9q21	2776	"""guanine nucleotide binding protein (G protein), q polypeptide"""		E	GNAQ,NS,carcinoma,0,2	GNAQ	384	2	1	Substitution - Missense(1)	prostate(1)	c.A286T						scavenged	.																																			SO:0001583	missense	2776	exon2			TGAGTGTGTCCAT		CCDS6658.1	9q21	2010-03-17			ENSG00000156052	ENSG00000156052			4390	protein-coding gene	gene with protein product		600998				8825633	Standard	NM_002072		Approved	G-ALPHA-q, GAQ	uc004akw.3	P50148	OTTHUMG00000020059	ENST00000286548.4:c.286A>T	9.37:g.80537112T>A	ENSP00000286548:p.Thr96Ser	148.0	0.0	0		152.0	9.0	0.0592105	NM_002072	O15108|Q13462|Q6NT27|Q92471|Q9BZB9	Missense_Mutation	SNP	ENST00000286548.4	37	CCDS6658.1	.	.	.	.	.	.	.	.	.	.	T	13.12	2.141103	0.37825	.	.	ENSG00000156052	ENST00000286548;ENST00000411677	D;D	0.87809	-2.3;-2.3	5.86	5.86	0.93980	G protein alpha subunit, helical insertion (2);	0.000000	0.85682	D	0.000000	D	0.84170	0.5413	L	0.52126	1.63	0.80722	D	1	B	0.02656	0.0	B	0.04013	0.001	T	0.79122	-0.1933	10	0.29301	T	0.29	.	16.2652	0.82574	0.0:0.0:0.0:1.0	.	96	P50148	GNAQ_HUMAN	S	96;67	ENSP00000286548:T96S;ENSP00000391501:T67S	ENSP00000286548:T96S	T	-	1	0	GNAQ	79726932	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	5.145000	0.64839	2.241000	0.73720	0.528000	0.53228	ACA	.	.	none		0.473	GNAQ-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052761.1	NM_002072	
DECR2	26063	hgsc.bcm.edu	37	16	460976	460976	+	Silent	SNP	G	G	A	rs140561403	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr16:460976G>A	ENST00000219481.5	+	7	699	c.561G>A	c.(559-561)gcG>gcA	p.A187A	DECR2_ENST00000424398.2_Silent_p.A175A|DECR2_ENST00000461947.1_3'UTR	NM_020664.3	NP_065715.1	Q9NUI1	DECR2_HUMAN	2,4-dienoyl CoA reductase 2, peroxisomal	187					unsaturated fatty acid biosynthetic process (GO:0006636)	peroxisomal membrane (GO:0005778)	2,4-dienoyl-CoA reductase (NADPH) activity (GO:0008670)|receptor binding (GO:0005102)|trans-2-enoyl-CoA reductase (NADPH) activity (GO:0019166)			central_nervous_system(1)|endometrium(3)|large_intestine(1)|lung(4)	9		Hepatocellular(16;0.00015)				GTGCAGACGCGATGACGCGGC	0.657													G|||	28	0.00559105	0.0008	0.0187	5008	,	,		16609	0.001		0.0119	False		,,,				2504	0.001				p.A187A		Atlas-SNP	.											DECR2,NS,carcinoma,+1,1	DECR2	47	1	0			c.G561A						PASS	.	G		37,4355		0,37,2159	43.0	41.0	42.0		561	-11.0	0.5	16	dbSNP_134	42	141,8453		1,139,4157	no	coding-synonymous	DECR2	NM_020664.3		1,176,6316	AA,AG,GG		1.6407,0.8424,1.3707		187/293	460976	178,12808	2196	4297	6493	SO:0001819	synonymous_variant	26063	exon7			AGACGCGATGACG	AJ293009	CCDS10409.1	16p13.3	2011-09-14			ENSG00000242612	ENSG00000242612	1.3.1.34	"""Short chain dehydrogenase/reductase superfamily / Classical SDR fold cluster 1"""	2754	protein-coding gene	gene with protein product	"""short chain dehydrogenase/reductase family 17C, member 1"""	615839				11514237, 19027726	Standard	NM_020664		Approved	PDCR, SDR17C1	uc002chb.3	Q9NUI1	OTTHUMG00000047846	ENST00000219481.5:c.561G>A	16.37:g.460976G>A		91.0	0.0	0		105.0	55.0	0.52381	NM_020664	Q6ZRS7|Q96ET0	Silent	SNP	ENST00000219481.5	37	CCDS10409.1																																																																																			G|0.988;A|0.012	0.012	strong		0.657	DECR2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000109069.4	NM_020664	
MYPN	84665	hgsc.bcm.edu	37	10	69934012	69934012	+	Silent	SNP	C	C	A	rs71584491	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr10:69934012C>A	ENST00000358913.5	+	11	2651	c.2163C>A	c.(2161-2163)gcC>gcA	p.A721A	MYPN_ENST00000540630.1_Silent_p.A721A|MYPN_ENST00000354393.2_Silent_p.A446A	NM_001256267.1|NM_032578.3	NP_001243196.1|NP_115967.2	Q86TC9	MYPN_HUMAN	myopalladin	721					sarcomere organization (GO:0045214)	I band (GO:0031674)|nucleus (GO:0005634)|Z disc (GO:0030018)	cytoskeletal protein binding (GO:0008092)|muscle alpha-actinin binding (GO:0051371)|SH3 domain binding (GO:0017124)			breast(2)|central_nervous_system(1)|endometrium(13)|kidney(6)|large_intestine(13)|liver(1)|lung(43)|ovary(3)|prostate(1)|skin(6)|upper_aerodigestive_tract(5)	94						TCAGCTTGGCCCGGCCGAAGT	0.537													C|||	215	0.0429313	0.1331	0.0173	5008	,	,		18309	0.0		0.0109	False		,,,				2504	0.0164				p.A721A		Atlas-SNP	.											.	MYPN	189	.	0			c.C2163A						PASS	.	C		458,3948	218.4+/-236.5	22,414,1767	117.0	120.0	119.0		2163	4.1	1.0	10	dbSNP_130	119	106,8494	57.2+/-118.5	0,106,4194	no	coding-synonymous	MYPN	NM_032578.2		22,520,5961	AA,AC,CC		1.2326,10.3949,4.3365		721/1321	69934012	564,12442	2203	4300	6503	SO:0001819	synonymous_variant	84665	exon11			CTTGGCCCGGCCG	AL834247	CCDS7275.1, CCDS73142.1	10q22.1	2014-09-17			ENSG00000138347	ENSG00000138347		"""Immunoglobulin superfamily / I-set domain containing"""	23246	protein-coding gene	gene with protein product	"""sarcomeric protein myopalladin, 145 kDa"""	608517				11309420, 12482578	Standard	NM_032578		Approved	MYOP	uc001jnm.5	Q86TC9	OTTHUMG00000018344	ENST00000358913.5:c.2163C>A	10.37:g.69934012C>A		150.0	0.0	0		175.0	88.0	0.502857	NM_032578	Q5VV35|Q5VV36|Q86T37|Q8N3L4|Q96K90|Q96KF5	Silent	SNP	ENST00000358913.5	37	CCDS7275.1																																																																																			C|0.956;A|0.044	0.044	strong		0.537	MYPN-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000048307.1	NM_032578	
KIAA1033	23325	hgsc.bcm.edu	37	12	105550565	105550565	+	Silent	SNP	C	C	T	rs35149056	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr12:105550565C>T	ENST00000332180.5	+	27	2907	c.2820C>T	c.(2818-2820)gcC>gcT	p.A940A		NM_015275.1	NP_056090.1			KIAA1033											breast(3)|central_nervous_system(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(8)|lung(15)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	41						GCAGCAATGCCATTAGGTATG	0.308													C|||	217	0.0433307	0.0166	0.0692	5008	,	,		14135	0.001		0.0795	False		,,,				2504	0.0675				p.A940A		Atlas-SNP	.											.	KIAA1033	83	.	0			c.C2820T						PASS	.	C		82,3618		1,80,1769	208.0	186.0	193.0		2820	4.9	1.0	12	dbSNP_126	193	613,7575		27,559,3508	no	coding-synonymous	KIAA1033	NM_015275.1		28,639,5277	TT,TC,CC		7.4866,2.2162,5.8462		940/1174	105550565	695,11193	1850	4094	5944	SO:0001819	synonymous_variant	23325	exon27			CAATGCCATTAGG	AB028956	CCDS41826.1, CCDS73514.1	12q24.11	2014-05-09				ENSG00000136051			29174	protein-coding gene	gene with protein product		615748				20376207, 20498093, 21498477	Standard	XM_005268742		Approved	SWIP	uc001tld.3	Q2M389		ENST00000332180.5:c.2820C>T	12.37:g.105550565C>T		102.0	0.0	0		96.0	39.0	0.40625	NM_015275		Silent	SNP	ENST00000332180.5	37	CCDS41826.1																																																																																			C|0.946;T|0.054	0.054	strong		0.308	KIAA1033-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000406138.4	NM_015275	
BCAS4	55653	hgsc.bcm.edu	37	20	49411689	49411689	+	Silent	SNP	G	G	T	rs117388674	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr20:49411689G>T	ENST00000358791.5	+	1	259	c.159G>T	c.(157-159)ctG>ctT	p.L53L	BCAS4_ENST00000262591.5_Silent_p.L53L|BCAS4_ENST00000371608.2_Silent_p.L53L|BCAS4_ENST00000485049.1_3'UTR|BCAS4_ENST00000609336.1_Silent_p.L23L	NM_017843.3	NP_060313.3	Q8TDM0	BCAS4_HUMAN	breast carcinoma amplified sequence 4	53						cytoplasm (GO:0005737)				large_intestine(2)|lung(2)|pancreas(1)|upper_aerodigestive_tract(1)	6						CGCTCTTCCTGACCCCCGAGC	0.736													G|||	168	0.0335463	0.0605	0.0101	5008	,	,		9022	0.0169		0.0298	False		,,,				2504	0.0348				p.L53L		Atlas-SNP	.											.	BCAS4	41	.	0			c.G159T						PASS	.	G	,,	67,2413		0,67,1173	1.0	2.0	2.0		159,159,159	1.5	1.0	20	dbSNP_132	2	106,5142		0,106,2518	no	coding-synonymous,coding-synonymous,coding-synonymous	BCAS4	NM_001010974.1,NM_017843.3,NM_198799.2	,,	0,173,3691	TT,TG,GG		2.0198,2.7016,2.2386	,,	53/159,53/212,53/204	49411689	173,7555	1240	2624	3864	SO:0001819	synonymous_variant	55653	exon1			CTTCCTGACCCCC	AK000502	CCDS13432.2, CCDS33487.1	20q13	2008-07-03			ENSG00000124243	ENSG00000124243			14367	protein-coding gene	gene with protein product		607471				12378525	Standard	NM_001010974		Approved	FLJ20495, CNOL	uc002xvq.3	Q8TDM0	OTTHUMG00000032735	ENST00000358791.5:c.159G>T	20.37:g.49411689G>T		16.0	0.0	0		22.0	12.0	0.545455	NM_198799	Q5TD52|Q5TD53|Q5TD54|Q5U5K7|Q5XKE8|Q8IXI7|Q8NEZ6|Q8TDL9|Q9NX13|Q9Y511	Silent	SNP	ENST00000358791.5	37	CCDS33487.1	80	0.03663003663003663	34	0.06910569105691057	5	0.013812154696132596	17	0.02972027972027972	24	0.0316622691292876	G	8.976	0.974160	0.18736	0.027016	0.020198	ENSG00000124243	ENST00000445038	.	.	.	4.77	1.51	0.23008	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	-21.7382	3.8781	0.09066	0.0999:0.1588:0.5791:0.1622	.	.	.	.	L	28	.	.	X	+	2	2	BCAS4	48845096	1.000000	0.71417	1.000000	0.80357	0.438000	0.31896	0.689000	0.25437	1.004000	0.39156	0.484000	0.47621	TGA	G|0.963;T|0.037	0.037	strong		0.736	BCAS4-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000079700.1	NM_017843	
OR9G1	390174	hgsc.bcm.edu	37	11	56468258	56468258	+	Missense_Mutation	SNP	C	C	T	rs78340277	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr11:56468258C>T	ENST00000312153.1	+	1	395	c.395C>T	c.(394-396)gCc>gTc	p.A132V		NM_001005213.1	NP_001005213.1	Q8NH87	OR9G1_HUMAN	olfactory receptor, family 9, subfamily G, member 1	132						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			breast(2)|kidney(1)|lung(25)|stomach(2)|upper_aerodigestive_tract(1)	31						CTGCTTTATGCCCAGGCCATG	0.498													C|||	31	0.0061901	0.0015	0.0029	5008	,	,		19708	0.0		0.0239	False		,,,				2504	0.0031				p.A132V		Atlas-SNP	.											.	.	.	.	0			c.C395T						PASS	.	C	VAL/ALA	16,4386	21.2+/-45.6	0,16,2185	186.0	171.0	176.0		395	4.4	0.8	11	dbSNP_131	176	171,8421	67.7+/-130.1	0,171,4125	yes	missense	OR9G1	NM_001005213.1	64	0,187,6310	TT,TC,CC		1.9902,0.3635,1.4391	possibly-damaging	132/306	56468258	187,12807	2201	4296	6497	SO:0001583	missense	504191	exon1			TTTATGCCCAGGC	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.395C>T	11.37:g.56468258C>T	ENSP00000309012:p.Ala132Val	315.0	0.0	0		305.0	72.0	0.236066	NM_001013358	Q6IEU9|Q8NGQ0	Missense_Mutation	SNP	ENST00000312153.1	37	CCDS31536.1	16	0.007326007326007326	1	0.0020325203252032522	1	0.0027624309392265192	0	0.0	14	0.018469656992084433	C	11.81	1.748637	0.30955	0.003635	0.019902	ENSG00000174914	ENST00000312153	T	0.01572	4.76	4.43	4.43	0.53597	GPCR, rhodopsin-like superfamily (1);	0.696787	0.13040	N	0.418614	T	0.00998	0.0033	L	0.31120	0.905	0.09310	N	1	B	0.02656	0.0	B	0.10450	0.005	T	0.40117	-0.9580	10	0.66056	D	0.02	-6.4294	10.827	0.46638	0.0:0.9106:0.0:0.0894	.	132	Q8NH87	OR9G1_HUMAN	V	132	ENSP00000309012:A132V	ENSP00000309012:A132V	A	+	2	0	OR9G1	56224834	0.000000	0.05858	0.813000	0.32504	0.681000	0.39784	-0.197000	0.09518	2.430000	0.82344	0.585000	0.79938	GCC	C|0.987;T|0.013	0.013	strong		0.498	OR9G1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000393253.1	NM_001005213	
ICE2	79664	hgsc.bcm.edu	37	15	60747576	60747576	+	Silent	SNP	G	G	A	rs61753854	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr15:60747576G>A	ENST00000261520.4	-	7	966	c.732C>T	c.(730-732)gaC>gaT	p.D244D	NARG2_ENST00000561114.1_Silent_p.D244D|NARG2_ENST00000439632.1_Silent_p.D107D	NM_024611.4	NP_078887.2														breast(1)|central_nervous_system(1)|endometrium(7)|kidney(3)|large_intestine(2)|lung(10)|ovary(1)|prostate(1)|skin(4)|upper_aerodigestive_tract(2)	32						TAGCTATATCGTCCTTTGACA	0.328													G|||	16	0.00319489	0.0	0.0014	5008	,	,		18300	0.0		0.002	False		,,,				2504	0.0133				p.D244D		Atlas-SNP	.											NARG2,NS,carcinoma,0,1	NARG2	82	1	0			c.C732T						PASS	.	G	,	2,4402	2.1+/-5.4	0,2,2200	193.0	175.0	181.0		321,732	-2.8	0.0	15	dbSNP_129	181	19,8581	13.3+/-46.6	0,19,4281	no	coding-synonymous,coding-synonymous	NARG2	NM_001018089.1,NM_024611.4	,	0,21,6481	AA,AG,GG		0.2209,0.0454,0.1615	,	107/846,244/983	60747576	21,12983	2202	4300	6502	SO:0001819	synonymous_variant	79664	exon7			TATATCGTCCTTT																												ENST00000261520.4:c.732C>T	15.37:g.60747576G>A		113.0	0.0	0		122.0	59.0	0.483607	NM_024611		Silent	SNP	ENST00000261520.4	37	CCDS10176.1																																																																																			G|0.998;A|0.002	0.002	strong		0.328	NARG2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256136.1		
PCNT	5116	hgsc.bcm.edu	37	21	47847547	47847547	+	Silent	SNP	C	C	T	rs150882711	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr21:47847547C>T	ENST00000359568.5	+	34	7439	c.7332C>T	c.(7330-7332)acC>acT	p.T2444T	PCNT_ENST00000480896.1_3'UTR	NM_006031.5	NP_006022.3	O95613	PCNT_HUMAN	pericentrin	2444					brain morphogenesis (GO:0048854)|cerebellar cortex morphogenesis (GO:0021696)|cilium assembly (GO:0042384)|G2/M transition of mitotic cell cycle (GO:0000086)|in utero embryonic development (GO:0001701)|limb morphogenesis (GO:0035108)|microtubule cytoskeleton organization (GO:0000226)|mitotic cell cycle (GO:0000278)|multicellular organism growth (GO:0035264)|negative regulation of apoptotic process (GO:0043066)|neural precursor cell proliferation (GO:0061351)|neuron migration (GO:0001764)|olfactory bulb development (GO:0021772)|positive regulation of intracellular protein transport (GO:0090316)|spindle organization (GO:0007051)	centriolar satellite (GO:0034451)|centriole (GO:0005814)|centrosome (GO:0005813)|ciliary basal body (GO:0036064)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|intercellular bridge (GO:0045171)|membrane (GO:0016020)|microtubule (GO:0005874)|motile cilium (GO:0031514)|pericentriolar material (GO:0000242)				NS(1)|breast(5)|central_nervous_system(2)|cervix(1)|endometrium(11)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(15)|liver(2)|lung(41)|ovary(5)|pancreas(3)|prostate(3)|skin(5)|upper_aerodigestive_tract(2)|urinary_tract(2)	104	Breast(49;0.112)					AAGTGCCCACCGCGTGCCCCG	0.557													C|||	2	0.000399361	0.0	0.0	5008	,	,		21792	0.0		0.002	False		,,,				2504	0.0				p.T2444T		Atlas-SNP	.											.	PCNT	283	.	0			c.C7332T						PASS	.	C		3,4403	6.2+/-15.9	0,3,2200	68.0	70.0	70.0		7332	-4.9	0.0	21	dbSNP_134	70	8,8592	6.4+/-24.3	0,8,4292	no	coding-synonymous	PCNT	NM_006031.5		0,11,6492	TT,TC,CC		0.093,0.0681,0.0846		2444/3337	47847547	11,12995	2203	4300	6503	SO:0001819	synonymous_variant	5116	exon34			GCCCACCGCGTGC	AB007862	CCDS33592.1	21q22.3	2014-02-20	2008-01-30	2005-11-03	ENSG00000160299	ENSG00000160299			16068	protein-coding gene	gene with protein product	"""kendrin"", ""Seckel syndrome 4"""	605925	"""pericentrin 2 (kendrin)"""	PCNT2		8812505, 9455477	Standard	NM_006031		Approved	KEN, KIAA0402, PCN, PCNTB, SCKL4	uc002zji.4	O95613	OTTHUMG00000090665	ENST00000359568.5:c.7332C>T	21.37:g.47847547C>T		71.0	0.0	0		48.0	20.0	0.416667	NM_006031	O43152|Q7Z7C9	Silent	SNP	ENST00000359568.5	37	CCDS33592.1																																																																																			C|0.999;T|0.001	0.001	strong		0.557	PCNT-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207336.1	NM_006031	
FAT1	2195	hgsc.bcm.edu	37	4	187518874	187518874	+	Silent	SNP	G	G	A	rs116628547	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr4:187518874G>A	ENST00000441802.2	-	24	12539	c.12330C>T	c.(12328-12330)ggC>ggT	p.G4110G	FAT1_ENST00000512347.1_5'Flank	NM_005245.3	NP_005236.2	Q14517	FAT1_HUMAN	FAT atypical cadherin 1	4110	EGF-like 4. {ECO:0000255|PROSITE- ProRule:PRU00076}.				actin filament organization (GO:0007015)|anatomical structure morphogenesis (GO:0009653)|cell adhesion (GO:0007155)|cell migration (GO:0016477)|cell-cell signaling (GO:0007267)|establishment or maintenance of cell polarity (GO:0007163)|homophilic cell adhesion (GO:0007156)|single organismal cell-cell adhesion (GO:0016337)	cell-cell junction (GO:0005911)|extracellular vesicular exosome (GO:0070062)|filopodium (GO:0030175)|focal adhesion (GO:0005925)|integral component of plasma membrane (GO:0005887)|lamellipodium (GO:0030027)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			NS(1)|breast(3)|central_nervous_system(3)|endometrium(38)|haematopoietic_and_lymphoid_tissue(2)|kidney(12)|large_intestine(33)|lung(88)|ovary(13)|pancreas(2)|prostate(16)|skin(2)|upper_aerodigestive_tract(11)|urinary_tract(4)	228						GACAAACGGCGCCATCCAAAC	0.418										HNSCC(5;0.00058)			G|||	15	0.00299521	0.0008	0.0014	5008	,	,		18073	0.0		0.008	False		,,,				2504	0.0051				p.G4110G	Colon(197;1040 2055 4143 4984 49344)	Atlas-SNP	.											.	FAT1	500	.	0			c.C12330T						PASS	.	G		7,3819		0,7,1906	74.0	66.0	68.0		12330	-3.1	1.0	4	dbSNP_132	68	51,8225		0,51,4087	no	coding-synonymous	FAT1	NM_005245.3		0,58,5993	AA,AG,GG		0.6162,0.183,0.4793		4110/4589	187518874	58,12044	1913	4138	6051	SO:0001819	synonymous_variant	2195	exon24			AACGGCGCCATCC	X87241	CCDS47177.1	4q35.2	2013-05-31	2013-05-31	2008-10-30	ENSG00000083857	ENSG00000083857		"""Cadherins / Cadherin-related"""	3595	protein-coding gene	gene with protein product	"""cadherin-related family member 8"""	600976	"""FAT tumor suppressor (Drosophila) homolog"", ""FAT tumor suppressor homolog 1 (Drosophila)"""	FAT		8586420	Standard	XM_005262834		Approved	CDHF7, CDHR8	uc003izf.3	Q14517	OTTHUMG00000160320	ENST00000441802.2:c.12330C>T	4.37:g.187518874G>A		158.0	0.0	0		147.0	81.0	0.55102	NM_005245		Silent	SNP	ENST00000441802.2	37	CCDS47177.1																																																																																			G|0.995;A|0.005	0.005	strong		0.418	FAT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000360209.3	NM_005245	
SRRM1	10250	hgsc.bcm.edu	37	1	24995933	24995933	+	Missense_Mutation	SNP	C	C	T	rs149689871		TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr1:24995933C>T	ENST00000323848.9	+	14	2374	c.2059C>T	c.(2059-2061)Cgg>Tgg	p.R687W	SRRM1_ENST00000479034.1_3'UTR|SRRM1_ENST00000374389.4_Missense_Mutation_p.R696W|snoU13_ENST00000459464.1_RNA|SRRM1_ENST00000447431.2_Missense_Mutation_p.R699W	NM_005839.3	NP_005830.2	Q8IYB3	SRRM1_HUMAN	serine/arginine repetitive matrix 1	687	Arg-rich.|Necessary for speckles and matrix localization.|Pro-rich.|Ser-rich.				gene expression (GO:0010467)|mRNA 3'-end processing (GO:0031124)|mRNA export from nucleus (GO:0006406)|mRNA splicing, via spliceosome (GO:0000398)|RNA splicing (GO:0008380)|RNA splicing, via transesterification reactions (GO:0000375)|termination of RNA polymerase II transcription (GO:0006369)|transcription from RNA polymerase II promoter (GO:0006366)	catalytic step 2 spliceosome (GO:0071013)|cytosol (GO:0005829)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	DNA binding (GO:0003677)|poly(A) RNA binding (GO:0044822)			breast(1)|central_nervous_system(3)|endometrium(3)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(12)|lung(9)|ovary(2)|prostate(1)|urinary_tract(2)	36		Colorectal(325;3.46e-05)|Renal(390;0.0007)|Lung NSC(340;0.000946)|all_lung(284;0.00125)|Ovarian(437;0.00764)|Breast(348;0.0148)|Myeloproliferative disorder(586;0.0255)|all_neural(195;0.19)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0422)|OV - Ovarian serous cystadenocarcinoma(117;1.01e-24)|Colorectal(126;5.95e-08)|COAD - Colon adenocarcinoma(152;3.24e-06)|GBM - Glioblastoma multiforme(114;0.000148)|BRCA - Breast invasive adenocarcinoma(304;0.00177)|KIRC - Kidney renal clear cell carcinoma(1967;0.00348)|STAD - Stomach adenocarcinoma(196;0.00483)|READ - Rectum adenocarcinoma(331;0.0649)|Lung(427;0.138)		GCCCTCACCACGGCCTCGAGC	0.582																																					p.R687W	Ovarian(68;897 1494 3282 17478)	Atlas-SNP	.											.	SRRM1	81	.	0			c.C2059T						PASS	.	C	TRP/ARG	0,4406		0,0,2203	73.0	68.0	70.0		2059	5.8	1.0	1	dbSNP_134	70	1,8599	1.2+/-3.3	0,1,4299	yes	missense	SRRM1	NM_005839.3	101	0,1,6502	TT,TC,CC		0.0116,0.0,0.0077	probably-damaging	687/905	24995933	1,13005	2203	4300	6503	SO:0001583	missense	10250	exon14			TCACCACGGCCTC	AF048977	CCDS255.1	1p36	2010-04-22			ENSG00000133226	ENSG00000133226			16638	protein-coding gene	gene with protein product	"""Ser/Arg-related nuclear matrix protein"", ""plenty of prolines 101-like"""	605975				9531537	Standard	NM_005839		Approved	SRM160, POP101, MGC39488	uc001bjm.3	Q8IYB3	OTTHUMG00000003320	ENST00000323848.9:c.2059C>T	1.37:g.24995933C>T	ENSP00000326261:p.Arg687Trp	115.0	0.0	0		120.0	55.0	0.458333	NM_005839	O60585|Q5VVN4	Missense_Mutation	SNP	ENST00000323848.9	37	CCDS255.1	.	.	.	.	.	.	.	.	.	.	C	18.70	3.681006	0.68042	0.0	1.16E-4	ENSG00000133226	ENST00000323848;ENST00000447431;ENST00000374389	T;T;T	0.37752	1.18;1.18;1.18	5.75	5.75	0.90469	.	0.000000	0.56097	D	0.000035	T	0.43433	0.1247	N	0.08118	0	0.80722	D	1	D;D	0.76494	0.999;0.993	D;B	0.74348	0.983;0.265	T	0.55244	-0.8171	10	0.72032	D	0.01	-1.1771	19.9382	0.97149	0.0:1.0:0.0:0.0	.	699;687	E9PCT1;Q8IYB3	.;SRRM1_HUMAN	W	687;699;696	ENSP00000326261:R687W;ENSP00000391430:R699W;ENSP00000363510:R696W	ENSP00000326261:R687W	R	+	1	2	SRRM1	24868520	0.999000	0.42202	0.999000	0.59377	0.987000	0.75469	3.471000	0.53107	2.720000	0.93068	0.563000	0.77884	CGG	C|1.000;T|0.000	0.000	weak		0.582	SRRM1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000009292.2	NM_005839	
HERC5	51191	hgsc.bcm.edu	37	4	89380540	89380540	+	Missense_Mutation	SNP	A	A	G	rs75070724	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr4:89380540A>G	ENST00000264350.3	+	2	461	c.308A>G	c.(307-309)gAc>gGc	p.D103G	HERC5_ENST00000508695.1_3'UTR	NM_016323.3	NP_057407.2	Q9UII4	HERC5_HUMAN	HECT and RLD domain containing E3 ubiquitin protein ligase 5	103					cytokine-mediated signaling pathway (GO:0019221)|defense response to virus (GO:0051607)|innate immune response (GO:0045087)|ISG15-protein conjugation (GO:0032020)|negative regulation of type I interferon production (GO:0032480)|protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:0042787)|regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0000079)|regulation of defense response to virus (GO:0050688)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleus (GO:0005634)	ISG15 ligase activity (GO:0042296)|poly(A) RNA binding (GO:0044822)|ubiquitin-protein transferase activity (GO:0004842)			NS(2)|breast(3)|cervix(1)|endometrium(5)|kidney(3)|large_intestine(11)|liver(2)|lung(17)|ovary(4)|prostate(1)|skin(4)	53		Hepatocellular(203;0.114)		OV - Ovarian serous cystadenocarcinoma(123;0.000209)		CATTCCGTGGACCAAGGAGCA	0.368													a|||	6	0.00119808	0.0	0.0014	5008	,	,		15874	0.0		0.005	False		,,,				2504	0.0				p.D103G	Esophageal Squamous(39;887 1012 34045 50514)	Atlas-SNP	.											.	HERC5	114	.	0			c.A308G						PASS	.	A	GLY/ASP	4,4402	8.1+/-20.4	0,4,2199	133.0	127.0	129.0		308	2.4	1.0	4	dbSNP_131	129	24,8576	17.3+/-56.4	0,24,4276	yes	missense	HERC5	NM_016323.2	94	0,28,6475	GG,GA,AA		0.2791,0.0908,0.2153	benign	103/1025	89380540	28,12978	2203	4300	6503	SO:0001583	missense	51191	exon2			CCGTGGACCAAGG	AB027289	CCDS3630.1	4q22.1-q23	2012-02-23	2012-02-23		ENSG00000138646	ENSG00000138646			24368	protein-coding gene	gene with protein product		608242	"""hect domain and RLD 5"""			10581175	Standard	NM_016323		Approved	CEB1	uc003hrt.4	Q9UII4	OTTHUMG00000130953	ENST00000264350.3:c.308A>G	4.37:g.89380540A>G	ENSP00000264350:p.Asp103Gly	483.0	0.0	0		490.0	258.0	0.526531	NM_016323	B2RTQ1|Q69G20	Missense_Mutation	SNP	ENST00000264350.3	37	CCDS3630.1	4	0.0018315018315018315	0	0.0	0	0.0	0	0.0	4	0.005277044854881266	a	10.19	1.281261	0.23392	9.08E-4	0.002791	ENSG00000138646	ENST00000264350	T	0.80123	-1.34	3.62	2.4	0.29515	Regulator of chromosome condensation/beta-lactamase-inhibitor protein II (2);	0.115379	0.34088	N	0.004267	T	0.59528	0.2200	N	0.25890	0.77	0.80722	D	1	B	0.06786	0.001	B	0.06405	0.002	T	0.60037	-0.7341	10	0.59425	D	0.04	.	8.5302	0.33329	0.8048:0.1952:0.0:0.0	.	103	Q9UII4	HERC5_HUMAN	G	103	ENSP00000264350:D103G	ENSP00000264350:D103G	D	+	2	0	HERC5	89599563	1.000000	0.71417	1.000000	0.80357	0.667000	0.39255	2.018000	0.40991	0.730000	0.32425	0.529000	0.55759	GAC	A|0.998;G|0.002	0.002	strong		0.368	HERC5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253554.2	NM_016323	
SEC14L5	9717	hgsc.bcm.edu	37	16	5046919	5046919	+	Missense_Mutation	SNP	C	C	T	rs199609540	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr16:5046919C>T	ENST00000251170.7	+	8	1024	c.844C>T	c.(844-846)Cgg>Tgg	p.R282W		NM_014692.1	NP_055507.1	O43304	S14L5_HUMAN	SEC14-like 5 (S. cerevisiae)	282						integral component of membrane (GO:0016021)|intracellular (GO:0005622)	transporter activity (GO:0005215)			NS(1)|breast(2)|central_nervous_system(1)|cervix(1)|endometrium(4)|kidney(2)|large_intestine(7)|lung(9)|ovary(1)|skin(1)	29						GGACAAGGCCCGGGAAATGCT	0.567													C|||	2	0.000399361	0.0	0.0	5008	,	,		17171	0.001		0.001	False		,,,				2504	0.0				p.R282W		Atlas-SNP	.											SEC14L5,NS,lymphoid_neoplasm,0,1	SEC14L5	79	1	0			c.C844T						scavenged	.	C	TRP/ARG	3,3813		0,3,1905	55.0	54.0	54.0		844	3.5	1.0	16		54	8,8228		0,8,4110	yes	missense	SEC14L5	NM_014692.1	101	0,11,6015	TT,TC,CC		0.0971,0.0786,0.0913	benign	282/697	5046919	11,12041	1908	4118	6026	SO:0001583	missense	9717	exon8			AAGGCCCGGGAAA	AB007880	CCDS45403.1	16p13.3	2008-02-05				ENSG00000103184			29032	protein-coding gene	gene with protein product						9455477	Standard	NM_014692		Approved	KIAA0420, PRELID4B	uc002cye.2	O43304		ENST00000251170.7:c.844C>T	16.37:g.5046919C>T	ENSP00000251170:p.Arg282Trp	161.0	1.0	0.00621118		137.0	65.0	0.474453	NM_014692		Missense_Mutation	SNP	ENST00000251170.7	37	CCDS45403.1	.	.	.	.	.	.	.	.	.	.	C	15.06	2.719825	0.48728	7.86E-4	9.71E-4	ENSG00000103184	ENST00000251170	D	0.85556	-2.0	4.51	3.48	0.39840	Phosphatidylinositol transfer protein-like, N-terminal (1);Cellular retinaldehyde-binding/triple function, N-terminal (1);	0.464358	0.19561	N	0.111327	D	0.84853	0.5564	M	0.80616	2.505	0.46654	D	0.999142	B	0.31054	0.306	B	0.30782	0.12	D	0.86408	0.1746	10	0.62326	D	0.03	-6.5997	12.6573	0.56793	0.2671:0.7329:0.0:0.0	.	282	O43304	S14L5_HUMAN	W	282	ENSP00000251170:R282W	ENSP00000251170:R282W	R	+	1	2	SEC14L5	4986920	0.598000	0.26882	1.000000	0.80357	0.994000	0.84299	0.860000	0.27871	2.492000	0.84095	0.491000	0.48974	CGG	C|0.996;T|0.004	0.004	strong		0.567	SEC14L5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000434379.1		
OBSCN	84033	hgsc.bcm.edu	37	1	228537608	228537608	+	Missense_Mutation	SNP	G	G	A	rs375733623		TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr1:228537608G>A	ENST00000422127.1	+	76	18210	c.18166G>A	c.(18166-18168)Gtg>Atg	p.V6056M	OBSCN_ENST00000366709.4_Missense_Mutation_p.V3175M|OBSCN_ENST00000570156.2_Missense_Mutation_p.V7013M|OBSCN_ENST00000366707.4_Missense_Mutation_p.V3690M|OBSCN_ENST00000284548.11_Missense_Mutation_p.V6056M	NM_001098623.2	NP_001092093.2	Q5VST9	OBSCN_HUMAN	obscurin, cytoskeletal calmodulin and titin-interacting RhoGEF	6056	Ig-like 52.				apoptotic signaling pathway (GO:0097190)|multicellular organismal development (GO:0007275)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of apoptotic process (GO:0043065)|protein localization to M-band (GO:0036309)|regulation of small GTPase mediated signal transduction (GO:0051056)|sarcomere organization (GO:0045214)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)|M band (GO:0031430)|myofibril (GO:0030016)|Z disc (GO:0030018)	ankyrin binding (GO:0030506)|ATP binding (GO:0005524)|metal ion binding (GO:0046872)|protein serine/threonine kinase activity (GO:0004674)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)|structural constituent of muscle (GO:0008307)|titin binding (GO:0031432)			NS(2)|breast(7)|central_nervous_system(5)|cervix(2)|endometrium(30)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(37)|lung(89)|ovary(8)|pancreas(3)|prostate(13)|skin(6)|stomach(11)|upper_aerodigestive_tract(2)|urinary_tract(3)	223		Prostate(94;0.0405)				AGCAGTGCAGGTGGACCCCCA	0.632																																					p.V7013M		Atlas-SNP	.											.	OBSCN	2142	.	0			c.G21037A						PASS	.	G	MET/VAL,MET/VAL	0,4170		0,0,2085	32.0	39.0	36.0		18166,18166	5.4	1.0	1		36	1,8301		0,1,4150	no	missense,missense	OBSCN	NM_001098623.1,NM_052843.2	21,21	0,1,6235	AA,AG,GG		0.012,0.0,0.0080	probably-damaging,probably-damaging	6056/7969,6056/6621	228537608	1,12471	2085	4151	6236	SO:0001583	missense	84033	exon87			GTGCAGGTGGACC	AJ002535	CCDS1570.2, CCDS58065.1, CCDS59204.1	1q42	2014-09-17			ENSG00000154358	ENSG00000154358		"""Rho guanine nucleotide exchange factors"", ""Immunoglobulin superfamily / I-set domain containing"", ""Fibronectin type III domain containing"""	15719	protein-coding gene	gene with protein product		608616				11448995, 11814696	Standard	NM_001098623		Approved	KIAA1556, UNC89, KIAA1639, ARHGEF30	uc001hsq.2	Q5VST9	OTTHUMG00000039772	ENST00000422127.1:c.18166G>A	1.37:g.228537608G>A	ENSP00000409493:p.Val6056Met	78.0	0.0	0		106.0	59.0	0.556604	NM_001271223	Q2A664|Q5T7G8|Q5T7G9|Q5VSU2|Q86YC7|Q8NHN0|Q8NHN1|Q8NHN2|Q8NHN3|Q8NHN4|Q8NHN5|Q8NHN6|Q8NHN7|Q8NHN8|Q8NHN9|Q96AA2|Q9HCD3|Q9HCL6	Missense_Mutation	SNP	ENST00000422127.1	37	CCDS58065.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	33|33	5.205199|5.205199	0.95033|0.95033	0.0|0.0	1.2E-4|1.2E-4	ENSG00000154358|ENSG00000154358	ENST00000441106|ENST00000284548;ENST00000422127;ENST00000366707;ENST00000366709	.|T;T;T;T	.|0.67345	.|-0.26;-0.26;-0.26;-0.26	5.39|5.39	5.39|5.39	0.77823|0.77823	.|Immunoglobulin I-set (1);Immunoglobulin subtype 2 (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	.|0.168788	.|0.38837	.|N	.|0.001548	T|T	0.68686|0.68686	0.3028|0.3028	N|N	0.10945|0.10945	0.07|0.07	0.48571|0.48571	D|D	0.999676|0.999676	.|D;D	.|0.89917	.|1.0;1.0	.|D;D	.|0.77004	.|0.989;0.98	T|T	0.72520|0.72520	-0.4268|-0.4268	5|10	.|0.39692	.|T	.|0.17	.|.	19.1538|19.1538	0.93502|0.93502	0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0	.|.	.|6056;6056	.|Q5VST9;Q5VST9-3	.|OBSCN_HUMAN;.	D|M	672|6056;6056;3690;3175	.|ENSP00000284548:V6056M;ENSP00000409493:V6056M;ENSP00000355668:V3690M;ENSP00000355670:V3175M	.|ENSP00000284548:V6056M	G|V	+|+	2|1	0|0	OBSCN|OBSCN	226604231|226604231	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.810000|0.810000	0.45777|0.45777	7.813000|7.813000	0.86123|0.86123	2.517000|2.517000	0.84864|0.84864	0.491000|0.491000	0.48974|0.48974	GGT|GTG	.	.	none		0.632	OBSCN-204	KNOWN	basic|CCDS	protein_coding	protein_coding		NM_052843	
FAM90A1	55138	hgsc.bcm.edu	37	12	8377415	8377415	+	Missense_Mutation	SNP	C	C	T	rs200454993		TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr12:8377415C>T	ENST00000538603.1	-	4	572	c.14G>A	c.(13-15)cGt>cAt	p.R5H	FAM90A1_ENST00000307435.6_Missense_Mutation_p.R5H	NM_018088.3	NP_060558.3	Q86YD7	F90A1_HUMAN	family with sequence similarity 90, member A1	5							nucleic acid binding (GO:0003676)|zinc ion binding (GO:0008270)	p.R5H(1)		endometrium(2)|large_intestine(4)|lung(11)|ovary(1)|prostate(1)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)	25				Kidney(36;0.0866)		TTTGGGGTCACGACGTGCCAT	0.577													.|||	28	0.00559105	0.0045	0.0072	5008	,	,		14884	0.005		0.008	False		,,,				2504	0.0041				p.R5H		Atlas-SNP	.											FAM90A1,NS,carcinoma,0,2	FAM90A1	68	2	1	Substitution - Missense(1)	stomach(1)	c.G14A						scavenged	.						47.0	53.0	51.0					12																	8377415		2203	4300	6503	SO:0001583	missense	55138	exon4			GGGTCACGACGTG	AK001270	CCDS31738.1	12p13.31	2011-08-31		2005-11-20	ENSG00000171847	ENSG00000171847			25526	protein-coding gene	gene with protein product		613041					Standard	NM_018088		Approved	FLJ10408	uc001qui.2	Q86YD7	OTTHUMG00000168641	ENST00000538603.1:c.14G>A	12.37:g.8377415C>T	ENSP00000445418:p.Arg5His	20.0	0.0	0		41.0	7.0	0.170732	NM_018088	D3DUU9|Q9NVZ6	Missense_Mutation	SNP	ENST00000538603.1	37	CCDS31738.1	.	.	.	.	.	.	.	.	.	.	.	5.040	0.193071	0.09599	.	.	ENSG00000171847	ENST00000307435;ENST00000538603;ENST00000442295	T;T	0.14022	2.54;2.54	0.408	-0.719	0.11201	.	.	.	.	.	T	0.05593	0.0147	N	0.11427	0.14	0.09310	N	1	B	0.15719	0.014	B	0.14023	0.01	T	0.44065	-0.9352	8	0.17832	T	0.49	1.8103	.	.	.	.	5	Q86YD7	F90A1_HUMAN	H	5	ENSP00000307798:R5H;ENSP00000445418:R5H	ENSP00000307798:R5H	R	-	2	0	FAM90A1	8268682	0.006000	0.16342	0.000000	0.03702	0.014000	0.08584	0.250000	0.18235	-0.410000	0.07542	0.196000	0.17591	CGT	.	.	weak		0.577	FAM90A1-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000400468.1	NM_018088	
SSTR4	6754	hgsc.bcm.edu	37	20	23016819	23016819	+	Silent	SNP	C	C	T	rs141700474	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr20:23016819C>T	ENST00000255008.3	+	1	763	c.699C>T	c.(697-699)ctC>ctT	p.L233L	RP4-753D10.3_ENST00000440921.1_RNA	NM_001052.2	NP_001043.2	P31391	SSR4_HUMAN	somatostatin receptor 4	233					arachidonic acid metabolic process (GO:0019369)|cell migration (GO:0016477)|cellular response to glucocorticoid stimulus (GO:0071385)|forebrain development (GO:0030900)|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 cAMP metabolic process (GO:0030815)|negative regulation of cell proliferation (GO:0008285)|positive regulation of MAPK cascade (GO:0043410)	cytoplasm (GO:0005737)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	somatostatin receptor activity (GO:0004994)			breast(1)|central_nervous_system(2)|endometrium(6)|kidney(1)|large_intestine(4)|lung(16)|ovary(1)|upper_aerodigestive_tract(1)	32	Colorectal(13;0.0518)|Lung NSC(19;0.0542)|all_lung(19;0.118)					GCTACCTGCTCATCGTGGGCA	0.657													C|||	34	0.00678914	0.0113	0.0072	5008	,	,		17179	0.0		0.006	False		,,,				2504	0.0082				p.L233L	Esophageal Squamous(15;850 1104 16640)	Atlas-SNP	.											.	SSTR4	83	.	0			c.C699T						PASS	.	C		50,4310		0,50,2130	78.0	85.0	83.0		699	-1.4	0.5	20	dbSNP_134	83	81,8495		0,81,4207	no	coding-synonymous	SSTR4	NM_001052.2		0,131,6337	TT,TC,CC		0.9445,1.1468,1.0127		233/389	23016819	131,12805	2180	4288	6468	SO:0001819	synonymous_variant	6754	exon1			CCTGCTCATCGTG		CCDS42856.1	20p11.21	2014-07-11			ENSG00000132671	ENSG00000132671		"""GPCR / Class A : Somatostatin receptors"""	11333	protein-coding gene	gene with protein product		182454				8483934	Standard	NM_001052		Approved		uc002wsr.2	P31391	OTTHUMG00000032054	ENST00000255008.3:c.699C>T	20.37:g.23016819C>T		40.0	0.0	0		59.0	24.0	0.40678	NM_001052	Q17RM1|Q17RM3|Q9UIY1	Silent	SNP	ENST00000255008.3	37	CCDS42856.1																																																																																			C|0.993;T|0.007	0.007	strong		0.657	SSTR4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078308.1		
PTCH2	8643	hgsc.bcm.edu	37	1	45292926	45292926	+	Silent	SNP	C	C	G	rs111471526	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr1:45292926C>G	ENST00000372192.3	-	16	2557	c.2427G>C	c.(2425-2427)tcG>tcC	p.S809S	PTCH2_ENST00000447098.2_Silent_p.S809S	NM_003738.4	NP_003729.3	Q9Y6C5	PTC2_HUMAN	patched 2	809					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)					CATTGCGGTACGAGTGGCGGG	0.627									Basal Cell Nevus syndrome				C|||	34	0.00678914	0.0008	0.0086	5008	,	,		17933	0.0		0.0249	False		,,,				2504	0.002				p.S809S		Atlas-SNP	.											.	PTCH2	96	.	0			c.G2427C						PASS	.	C	,	10,4396	16.8+/-37.8	0,10,2193	69.0	77.0	74.0		2427,2427	-9.9	0.8	1	dbSNP_132	74	153,8447	74.8+/-137.4	3,147,4150	no	coding-synonymous,coding-synonymous	PTCH2	NM_001166292.1,NM_003738.4	,	3,157,6343	GG,GC,CC		1.7791,0.227,1.2533	,	809/1147,809/1204	45292926	163,12843	2203	4300	6503	SO:0001819	synonymous_variant	8643	exon16	Familial Cancer Database	Gorlin syndrome, Gorlin-Golz syndrome, Naevoid Basal Cell Carcinoma syndrome, NBCCS	GCGGTACGAGTGG	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.2427G>C	1.37:g.45292926C>G		87.0	0.0	0		92.0	37.0	0.402174	NM_001166292	O95341|O95856|Q53Z57|Q5QP87|Q6UX14	Silent	SNP	ENST00000372192.3	37	CCDS516.1																																																																																			C|0.988;G|0.012	0.012	strong		0.627	PTCH2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000023428.4	NM_003738	
FAM214A	56204	hgsc.bcm.edu	37	15	52905882	52905882	+	Silent	SNP	G	G	A			TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr15:52905882G>A	ENST00000261844.7	-	3	341	c.189C>T	c.(187-189)gaC>gaT	p.D63D	FAM214A_ENST00000546305.2_Silent_p.D70D	NM_019600.2	NP_062546.2	Q32MH5	F214A_HUMAN	family with sequence similarity 214, member A	63																	GGGCCAGCTTGTCACTACATT	0.368																																					p.D63D		Atlas-SNP	.											.	.	.	.	0			c.C189T						PASS	.						125.0	117.0	119.0					15																	52905882		1915	4142	6057	SO:0001819	synonymous_variant	56204	exon3			CAGCTTGTCACTA	AB037791	CCDS45263.1, CCDS66773.1	15q21.2-q21.3	2011-12-01	2011-12-01	2011-12-01	ENSG00000047346	ENSG00000047346			25609	protein-coding gene	gene with protein product			"""KIAA1370"""	KIAA1370		10718198	Standard	XM_005254547		Approved	FLJ10980	uc002acg.4	Q32MH5		ENST00000261844.7:c.189C>T	15.37:g.52905882G>A		74.0	0.0	0		97.0	32.0	0.329897	NM_019600	A8KA52|B4DEP5|B4DF40|F5H8G0|Q32MH6|Q4G0R7|Q5XJ16|Q6PDA3|Q9NV24|Q9P2H7	Silent	SNP	ENST00000261844.7	37	CCDS45263.1																																																																																			.	.	none		0.368	FAM214A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000419914.1	NM_019600	
OR10A6	390093	hgsc.bcm.edu	37	11	7949707	7949707	+	Missense_Mutation	SNP	A	A	G	rs111488559	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr11:7949707A>G	ENST00000309838.2	-	1	502	c.503T>C	c.(502-504)tTt>tCt	p.F168S		NM_001004461.1	NP_001004461.1	Q8NH74	O10A6_HUMAN	olfactory receptor, family 10, subfamily A, member 6	168						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			breast(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(9)|lung(5)|ovary(1)|prostate(1)|skin(3)|urinary_tract(1)	22				Epithelial(150;1.38e-07)|BRCA - Breast invasive adenocarcinoma(625;0.189)		AAGGCCACAAAAGGGAAAACT	0.328													A|||	92	0.0183706	0.0015	0.0648	5008	,	,		19130	0.0		0.0258	False		,,,				2504	0.0194				p.F168S		Atlas-SNP	.											.	OR10A6	49	.	0			c.T503C						PASS	.	A	SER/PHE	43,4359	41.6+/-74.8	0,43,2158	41.0	44.0	43.0		503	3.2	1.0	11	dbSNP_132	43	338,8252	113.1+/-173.2	14,310,3971	yes	missense	OR10A6	NM_001004461.1	155	14,353,6129	GG,GA,AA		3.9348,0.9768,2.9326	possibly-damaging	168/315	7949707	381,12611	2201	4295	6496	SO:0001583	missense	390093	exon1			CCACAAAAGGGAA	AB065515	CCDS31420.1	11p15.4	2012-08-09			ENSG00000175393	ENSG00000175393		"""GPCR / Class A : Olfactory receptors"""	15132	protein-coding gene	gene with protein product							Standard	NM_001004461		Approved		uc010rbh.2	Q8NH74	OTTHUMG00000165671	ENST00000309838.2:c.503T>C	11.37:g.7949707A>G	ENSP00000312470:p.Phe168Ser	160.0	0.0	0		136.0	63.0	0.463235	NM_001004461	Q6IF59	Missense_Mutation	SNP	ENST00000309838.2	37	CCDS31420.1	34	0.015567765567765568	2	0.0040650406504065045	16	0.04419889502762431	0	0.0	16	0.021108179419525065	A	12.07	1.828003	0.32329	0.009768	0.039348	ENSG00000175393	ENST00000309838	T	0.00193	8.58	4.41	3.24	0.37175	GPCR, rhodopsin-like superfamily (1);	0.000000	0.44688	D	0.000440	T	0.00178	0.0005	H	0.94183	3.505	0.28076	N	0.93237	D	0.57899	0.981	P	0.58077	0.832	T	0.17018	-1.0383	10	0.87932	D	0	.	7.0241	0.24930	0.615:0.0:0.0:0.3849	.	168	Q8NH74	O10A6_HUMAN	S	168	ENSP00000312470:F168S	ENSP00000312470:F168S	F	-	2	0	OR10A6	7906283	0.999000	0.42202	0.997000	0.53966	0.171000	0.22731	1.052000	0.30429	0.792000	0.33850	0.533000	0.62120	TTT	A|0.976;G|0.024	0.024	strong		0.328	OR10A6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000385703.1	NM_001004461	
ERCC1	2067	hgsc.bcm.edu	37	19	45922389	45922389	+	Missense_Mutation	SNP	G	G	C			TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr19:45922389G>C	ENST00000300853.3	-	5	1083	c.492C>G	c.(490-492)ttC>ttG	p.F164L	ERCC1_ENST00000591636.1_Missense_Mutation_p.F164L|ERCC1_ENST00000423698.2_Missense_Mutation_p.F92L|ERCC1_ENST00000340192.7_Missense_Mutation_p.F164L|ERCC1_ENST00000589165.1_Missense_Mutation_p.F164L|ERCC1_ENST00000013807.5_Missense_Mutation_p.F164L	NM_001983.3	NP_001974.1	P07992	ERCC1_HUMAN	excision repair cross-complementation group 1	164					cell proliferation (GO:0008283)|chromosome organization (GO:0051276)|DNA catabolic process, endonucleolytic (GO:0000737)|DNA recombination (GO:0006310)|DNA repair (GO:0006281)|double-strand break repair (GO:0006302)|embryonic organ development (GO:0048568)|interstrand cross-link repair (GO:0036297)|isotype switching (GO:0045190)|male gonad development (GO:0008584)|mitotic recombination (GO:0006312)|multicellular organism growth (GO:0035264)|multicellular organismal aging (GO:0010259)|negative regulation of telomere maintenance (GO:0032205)|nucleotide-excision repair (GO:0006289)|nucleotide-excision repair, DNA damage removal (GO:0000718)|nucleotide-excision repair, DNA incision, 3'-to lesion (GO:0006295)|nucleotide-excision repair, DNA incision, 5'-to lesion (GO:0006296)|oogenesis (GO:0048477)|post-embryonic hemopoiesis (GO:0035166)|pyrimidine dimer repair by nucleotide-excision repair (GO:0000720)|replicative cell aging (GO:0001302)|response to nutrient (GO:0007584)|response to oxidative stress (GO:0006979)|response to sucrose (GO:0009744)|response to X-ray (GO:0010165)|spermatogenesis (GO:0007283)|syncytium formation (GO:0006949)|transcription-coupled nucleotide-excision repair (GO:0006283)|UV protection (GO:0009650)	cytoplasm (GO:0005737)|nuclear chromosome, telomeric region (GO:0000784)|nucleoplasm (GO:0005654)|nucleotide-excision repair complex (GO:0000109)|nucleus (GO:0005634)|transcription factor TFIID complex (GO:0005669)	damaged DNA binding (GO:0003684)|endonuclease activity (GO:0004519)|protein C-terminus binding (GO:0008022)|protein domain specific binding (GO:0019904)|single-stranded DNA binding (GO:0003697)			central_nervous_system(1)|endometrium(4)|kidney(1)|large_intestine(4)|lung(2)|ovary(2)|skin(1)	15		Ovarian(192;0.051)|all_neural(266;0.112)		OV - Ovarian serous cystadenocarcinoma(262;0.0247)		CCCGCAAGGCGAAGTTCTTCC	0.627								Nucleotide excision repair (NER)																													p.F164L		Atlas-SNP	.											.	ERCC1	46	.	0			c.C492G						PASS	.						68.0	55.0	59.0					19																	45922389		2202	4299	6501	SO:0001583	missense	2067	exon5			CAAGGCGAAGTTC		CCDS12662.1, CCDS12663.1, CCDS54279.1	19q13.32	2014-03-07	2014-03-07			ENSG00000012061			3433	protein-coding gene	gene with protein product		126380	"""excision repair cross-complementing rodent repair deficiency, complementation group 1 (includes overlapping antisense sequence)"""			6462228	Standard	NM_001983		Approved	RAD10	uc002pbs.2	P07992		ENST00000300853.3:c.492C>G	19.37:g.45922389G>C	ENSP00000300853:p.Phe164Leu	52.0	0.0	0		47.0	27.0	0.574468	NM_001983	B2RC01|B3KRR0|Q7Z7F5|Q96S40	Missense_Mutation	SNP	ENST00000300853.3	37	CCDS12662.1	.	.	.	.	.	.	.	.	.	.	G	17.89	3.499600	0.64298	.	.	ENSG00000012061	ENST00000300853;ENST00000340192;ENST00000423698;ENST00000013807	T;T;T;T	0.44482	0.94;0.92;0.95;0.92	4.71	1.33	0.21861	Restriction endonuclease, type II-like (1);	0.170692	0.51477	D	0.000090	T	0.47154	0.1430	M	0.74258	2.255	0.48040	D	0.999578	D;D;P;P	0.60575	0.984;0.988;0.898;0.95	P;B;B;B	0.50537	0.643;0.441;0.344;0.426	T	0.47699	-0.9097	10	0.72032	D	0.01	-17.7424	7.097	0.25315	0.3011:0.0:0.6989:0.0	.	164;92;164;164	Q7Z7F5;B3KRR0;Q96S40;P07992	.;.;.;ERCC1_HUMAN	L	164;164;92;164	ENSP00000300853:F164L;ENSP00000345203:F164L;ENSP00000394875:F92L;ENSP00000013807:F164L	ENSP00000013807:F164L	F	-	3	2	ERCC1	50614229	1.000000	0.71417	0.995000	0.50966	0.977000	0.68977	0.770000	0.26618	0.418000	0.25898	0.462000	0.41574	TTC	.	.	none		0.627	ERCC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000459542.1	NM_001983	
OSBPL7	114881	hgsc.bcm.edu	37	17	45886796	45886796	+	Missense_Mutation	SNP	A	A	C			TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr17:45886796A>C	ENST00000007414.3	-	19	2120	c.1929T>G	c.(1927-1929)aaT>aaG	p.N643K	OSBPL7_ENST00000392507.3_Missense_Mutation_p.N643K	NM_145798.2	NP_665741.1	Q9BZF2	OSBL7_HUMAN	oxysterol binding protein-like 7	643					cellular response to cholesterol (GO:0071397)|lipid transport (GO:0006869)|positive regulation of proteasomal protein catabolic process (GO:1901800)	autophagic vacuole (GO:0005776)|cytosol (GO:0005829)|perinuclear endoplasmic reticulum (GO:0097038)|plasma membrane (GO:0005886)	cholesterol binding (GO:0015485)			autonomic_ganglia(1)|endometrium(6)|kidney(2)|large_intestine(5)|liver(2)|lung(13)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	32						CACTCAGGACATTGTGAATGC	0.547																																					p.N643K		Atlas-SNP	.											.	OSBPL7	65	.	0			c.T1929G						PASS	.						134.0	98.0	110.0					17																	45886796		2203	4300	6503	SO:0001583	missense	114881	exon19			CAGGACATTGTGA	AF392446	CCDS11515.1	17q21	2013-01-10				ENSG00000006025		"""Oxysterol binding proteins"", ""Pleckstrin homology (PH) domain containing"""	16387	protein-coding gene	gene with protein product		606735				14593528, 11735225	Standard	NM_145798		Approved	ORP7, MGC71150	uc002ilx.1	Q9BZF2		ENST00000007414.3:c.1929T>G	17.37:g.45886796A>C	ENSP00000007414:p.Asn643Lys	76.0	0.0	0		86.0	39.0	0.453488	NM_145798	D3DTT6|Q6PIV6	Missense_Mutation	SNP	ENST00000007414.3	37	CCDS11515.1	.	.	.	.	.	.	.	.	.	.	A	17.75	3.467556	0.63625	.	.	ENSG00000006025	ENST00000007414;ENST00000392507	T;T	0.44881	0.91;0.91	4.91	3.89	0.44902	.	0.043933	0.85682	D	0.000000	T	0.73450	0.3588	H	0.96460	3.825	0.54753	D	0.999983	D	0.89917	1.0	D	0.87578	0.998	T	0.80894	-0.1178	10	0.87932	D	0	-37.8662	12.0721	0.53622	0.087:0.0:0.913:0.0	.	643	Q9BZF2	OSBL7_HUMAN	K	643	ENSP00000007414:N643K;ENSP00000376295:N643K	ENSP00000007414:N643K	N	-	3	2	OSBPL7	43241795	1.000000	0.71417	1.000000	0.80357	0.825000	0.46686	2.907000	0.48743	1.045000	0.40225	-0.337000	0.08149	AAT	.	.	none		0.547	OSBPL7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000441367.1	NM_017731	
RERG	85004	hgsc.bcm.edu	37	12	15262273	15262273	+	Missense_Mutation	SNP	T	T	A			TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr12:15262273T>A	ENST00000256953.2	-	5	707	c.371A>T	c.(370-372)cAc>cTc	p.H124L	RERG_ENST00000536465.1_Missense_Mutation_p.H124L|RERG_ENST00000538313.1_Missense_Mutation_p.H124L|RERG_ENST00000546331.1_Missense_Mutation_p.H105L	NM_032918.2	NP_116307.1	Q96A58	RERG_HUMAN	RAS-like, estrogen-regulated, growth inhibitor	124					negative regulation of cell growth (GO:0030308)|negative regulation of cell proliferation (GO:0008285)|response to hormone (GO:0009725)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)|membrane (GO:0016020)|nucleus (GO:0005634)	estrogen receptor binding (GO:0030331)|GDP binding (GO:0019003)|GTP binding (GO:0005525)|GTPase activity (GO:0003924)			NS(1)|endometrium(1)|kidney(2)|large_intestine(3)|lung(6)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)	16						CTGCCTGGAGTGGTCCAAGTC	0.473																																					p.H124L		Atlas-SNP	.											.	RERG	30	.	0			c.A371T						PASS	.						236.0	211.0	219.0					12																	15262273		2203	4300	6503	SO:0001583	missense	85004	exon5			CTGGAGTGGTCCA	AF339750	CCDS8673.1, CCDS53753.1	12p13.1	2014-05-09			ENSG00000134533	ENSG00000134533			15980	protein-coding gene	gene with protein product		612664				11533059	Standard	NM_032918		Approved	MGC15754	uc001rct.3	Q96A58	OTTHUMG00000168745	ENST00000256953.2:c.371A>T	12.37:g.15262273T>A	ENSP00000256953:p.His124Leu	236.0	0.0	0		219.0	99.0	0.452055	NM_032918	B2R9R0|B4DI02	Missense_Mutation	SNP	ENST00000256953.2	37	CCDS8673.1	.	.	.	.	.	.	.	.	.	.	T	19.26	3.792870	0.70452	.	.	ENSG00000134533	ENST00000256953;ENST00000538313;ENST00000536465;ENST00000546331	T;T;T;T	0.79940	-1.32;-1.32;-1.32;-1.32	5.33	5.33	0.75918	Small GTP-binding protein domain (1);	0.000000	0.85682	D	0.000000	T	0.74898	0.3777	L	0.45744	1.44	0.80722	D	1	B;B	0.26400	0.148;0.012	B;B	0.20577	0.03;0.018	T	0.72679	-0.4220	10	0.44086	T	0.13	.	14.4198	0.67175	0.0:0.0:0.0:1.0	.	105;124	B4DI02;Q96A58	.;RERG_HUMAN	L	124;124;124;105	ENSP00000256953:H124L;ENSP00000441505:H124L;ENSP00000438280:H124L;ENSP00000444485:H105L	ENSP00000256953:H124L	H	-	2	0	RERG	15153540	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	7.992000	0.88273	2.145000	0.66743	0.533000	0.62120	CAC	.	.	none		0.473	RERG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000400882.1	NM_032918	
CHD7	55636	hgsc.bcm.edu	37	8	61767070	61767070	+	Silent	SNP	G	G	A	rs61733338	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr8:61767070G>A	ENST00000423902.2	+	32	7403	c.6924G>A	c.(6922-6924)tcG>tcA	p.S2308S	CHD7_ENST00000524602.1_Intron	NM_017780.3	NP_060250.2	Q9P2D1	CHD7_HUMAN	chromodomain helicase DNA binding protein 7	2308					adult heart development (GO:0007512)|adult walking behavior (GO:0007628)|artery morphogenesis (GO:0048844)|blood circulation (GO:0008015)|central nervous system development (GO:0007417)|chromatin modification (GO:0016568)|cognition (GO:0050890)|cranial nerve development (GO:0021545)|embryonic hindlimb morphogenesis (GO:0035116)|epithelium development (GO:0060429)|face development (GO:0060324)|female genitalia development (GO:0030540)|genitalia development (GO:0048806)|heart morphogenesis (GO:0003007)|in utero embryonic development (GO:0001701)|inner ear morphogenesis (GO:0042472)|limb development (GO:0060173)|nose development (GO:0043584)|olfactory behavior (GO:0042048)|olfactory bulb development (GO:0021772)|olfactory nerve development (GO:0021553)|palate development (GO:0060021)|positive regulation of multicellular organism growth (GO:0040018)|regulation of growth hormone secretion (GO:0060123)|regulation of neurogenesis (GO:0050767)|regulation of transcription, DNA-templated (GO:0006355)|retina development in camera-type eye (GO:0060041)|rRNA processing (GO:0006364)|semicircular canal morphogenesis (GO:0048752)|sensory perception of sound (GO:0007605)|skeletal system development (GO:0001501)|T cell differentiation (GO:0030217)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	ATP binding (GO:0005524)|chromatin binding (GO:0003682)|DNA binding (GO:0003677)|helicase activity (GO:0004386)	p.S2308S(2)		NS(1)|breast(6)|central_nervous_system(8)|cervix(2)|endometrium(16)|haematopoietic_and_lymphoid_tissue(1)|kidney(9)|large_intestine(16)|lung(49)|ovary(4)|pancreas(2)|prostate(4)|skin(2)|urinary_tract(3)	123		all_cancers(86;0.2)|all_lung(136;0.0402)|Lung NSC(129;0.0459)|all_epithelial(80;0.0477)	BRCA - Breast invasive adenocarcinoma(89;0.143)			TTGCCTTCTCGTTTTGGCCTA	0.423													G|||	12	0.00239617	0.0091	0.0	5008	,	,		19366	0.0		0.0	False		,,,				2504	0.0				p.S2308S		Atlas-SNP	.											CHD7_ENST00000423902,NS,carcinoma,0,2	CHD7	534	2	2	Substitution - coding silent(2)	prostate(2)	c.G6924A						PASS	.	G		22,3776		0,22,1877	220.0	199.0	206.0		6924	-4.3	1.0	8	dbSNP_129	206	0,8224		0,0,4112	no	coding-synonymous	CHD7	NM_017780.3		0,22,5989	AA,AG,GG		0.0,0.5793,0.183		2308/2998	61767070	22,12000	1899	4112	6011	SO:0001819	synonymous_variant	55636	exon32			CTTCTCGTTTTGG	AB037837	CCDS47865.1	8q12.2	2014-09-17				ENSG00000171316			20626	protein-coding gene	gene with protein product		608892	"""CHARGE association"""	CRG		15300250, 18834967	Standard	NM_017780		Approved	KIAA1416, FLJ20357, FLJ20361	uc003xue.3	Q9P2D1		ENST00000423902.2:c.6924G>A	8.37:g.61767070G>A		76.0	0.0	0		90.0	37.0	0.411111	NM_017780	D0VBA5|E9PNZ2|Q05DI5|Q2TAN4|Q66K35|Q7Z6C0|Q7Z7Q2|Q9NXA0|Q9NXA3	Silent	SNP	ENST00000423902.2	37	CCDS47865.1																																																																																			G|0.997;A|0.003	0.003	strong		0.423	CHD7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000383468.2	XM_098762	
PDE6B	5158	hgsc.bcm.edu	37	4	663878	663878	+	Silent	SNP	A	A	G	rs137864502		TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr4:663878A>G	ENST00000496514.1	+	22	2568	c.2547A>G	c.(2545-2547)tcA>tcG	p.S849S	ATP5I_ENST00000506525.1_5'Flank|PDE6B_ENST00000429163.2_Silent_p.S570S|PDE6B_ENST00000255622.6_Silent_p.S848S			P35913	PDE6B_HUMAN	phosphodiesterase 6B, cGMP-specific, rod, beta	849					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)			NS(1)|breast(3)|cervix(1)|endometrium(2)|kidney(2)|large_intestine(5)|lung(11)|ovary(2)|prostate(2)|urinary_tract(1)	30					Caffeine(DB00201)	CCAAGTCTTCAACCTGCTGTA	0.527																																					p.S849S	GBM(71;463 1194 9848 25922 46834)	Atlas-SNP	.											.	PDE6B	80	.	0			c.A2547G						PASS	.	A	,,	1,4405	2.1+/-5.4	0,1,2202	165.0	163.0	164.0		2547,2544,1710	-8.7	0.5	4	dbSNP_134	164	0,8600		0,0,4300	no	coding-synonymous,coding-synonymous,coding-synonymous	PDE6B	NM_000283.3,NM_001145291.1,NM_001145292.1	,,	0,1,6502	GG,GA,AA		0.0,0.0227,0.0077	,,	849/855,848/854,570/576	663878	1,13005	2203	4300	6503	SO:0001819	synonymous_variant	5158	exon22			GTCTTCAACCTGC	BC000249	CCDS33932.1, CCDS46993.1, CCDS54703.1	4p16.3	2014-01-28	2008-07-31		ENSG00000133256	ENSG00000133256	3.1.4.17	"""Phosphodiesterases"""	8786	protein-coding gene	gene with protein product	"""congenital stationary night blindness 3, autosomal dominant"""	180072		PDEB		1313787	Standard	NM_001145292		Approved	CSNB3, rd1, RP40, CSNBAD2	uc003gap.3	P35913	OTTHUMG00000159909	ENST00000496514.1:c.2547A>G	4.37:g.663878A>G		150.0	0.0	0		111.0	60.0	0.540541	NM_000283	B7Z9T9|E7ETT3|Q53XN5|Q9BWH5|Q9UD49	Silent	SNP	ENST00000496514.1	37	CCDS33932.1																																																																																			A|1.000;G|0.000	0.000	weak		0.527	PDE6B-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000358109.1	NM_000283	
HIST1H1B	3009	hgsc.bcm.edu	37	6	27834877	27834877	+	Missense_Mutation	SNP	T	T	C	rs11970638	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr6:27834877T>C	ENST00000331442.3	-	1	482	c.431A>G	c.(430-432)aAg>aGg	p.K144R		NM_005322.2	NP_005313.1	P16401	H15_HUMAN	histone cluster 1, H1b	144			K -> R (in dbSNP:rs11970638).		chromatin organization (GO:0006325)|establishment of protein localization to chromatin (GO:0071169)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|nucleosome assembly (GO:0006334)|positive regulation of cell growth (GO:0030307)|positive regulation of histone H3-K9 methylation (GO:0051574)|protein stabilization (GO:0050821)	extracellular vesicular exosome (GO:0070062)|nuclear chromatin (GO:0000790)|nuclear heterochromatin (GO:0005720)|nucleosome (GO:0000786)	chromatin DNA binding (GO:0031490)|histone deacetylase binding (GO:0042826)|poly(A) RNA binding (GO:0044822)			endometrium(1)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(5)|lung(12)|prostate(2)|upper_aerodigestive_tract(2)	24						CCCTGCAGCCTTCTTGGCCTT	0.617													T|||	136	0.0271565	0.0802	0.0144	5008	,	,		15536	0.005		0.0119	False		,,,				2504	0.0031				p.K144R		Atlas-SNP	.											.	HIST1H1B	54	.	0			c.A431G						PASS	.	T	ARG/LYS	380,4026		14,352,1837	95.0	111.0	106.0		431	5.2	0.9	6	dbSNP_120	106	51,8547		1,49,4249	yes	missense	HIST1H1B	NM_005322.2	26	15,401,6086	CC,CT,TT		0.5932,8.6246,3.3144	probably-damaging	144/227	27834877	431,12573	2203	4299	6502	SO:0001583	missense	3009	exon1			GCAGCCTTCTTGG	AF531304	CCDS4635.1	6p22.1	2012-05-04	2006-10-11	2003-02-14	ENSG00000184357	ENSG00000184357		"""Histones / Replication-dependent"""	4719	protein-coding gene	gene with protein product		142711	"""H1 histone family, member 5"", ""histone 1, H1b"""	H1F5		9031620, 9119399, 12408966	Standard	NM_005322		Approved	H1.5, H1b, H1s-3	uc003njx.3	P16401	OTTHUMG00000016139	ENST00000331442.3:c.431A>G	6.37:g.27834877T>C	ENSP00000330074:p.Lys144Arg	106.0	0.0	0		111.0	48.0	0.432432	NM_005322	Q14529|Q3MJ42	Missense_Mutation	SNP	ENST00000331442.3	37	CCDS4635.1	61	0.027930402930402932	40	0.08130081300813008	8	0.022099447513812154	4	0.006993006993006993	9	0.011873350923482849	T	15.08	2.726408	0.48833	0.086246	0.005932	ENSG00000184357	ENST00000331442	T	0.24538	1.85	5.19	5.19	0.71726	.	0.587579	0.17333	N	0.178040	T	0.20577	0.0495	N	0.08118	0	0.80722	D	1	D	0.63880	0.993	D	0.72625	0.978	T	0.29088	-1.0023	10	0.51188	T	0.08	-5.6028	14.5461	0.68032	0.0:0.0:0.0:1.0	rs11970638;rs11970638	144	P16401	H15_HUMAN	R	144	ENSP00000330074:K144R	ENSP00000330074:K144R	K	-	2	0	HIST1H1B	27942856	1.000000	0.71417	0.944000	0.38274	0.103000	0.19146	3.084000	0.50143	2.103000	0.63969	0.533000	0.62120	AAG	T|0.968;C|0.032	0.032	strong		0.617	HIST1H1B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000043371.1	NM_005322	
POLR1E	64425	hgsc.bcm.edu	37	9	37501752	37501752	+	Silent	SNP	T	T	C	rs17412622	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr9:37501752T>C	ENST00000377798.4	+	11	1124	c.1011T>C	c.(1009-1011)acT>acC	p.T337T	POLR1E_ENST00000377792.3_Silent_p.T399T|POLR1E_ENST00000442009.2_Silent_p.T267T	NM_022490.1	NP_071935.1	O15160	RPAC1_HUMAN	polymerase (RNA) I polypeptide E, 53kDa	0					gene expression (GO:0010467)|innate immune response (GO:0045087)|positive regulation of type I interferon production (GO:0032481)|termination of RNA polymerase I transcription (GO:0006363)|termination of RNA polymerase III transcription (GO:0006386)|transcription elongation from RNA polymerase I promoter (GO:0006362)|transcription elongation from RNA polymerase III promoter (GO:0006385)|transcription from RNA polymerase I promoter (GO:0006360)|transcription from RNA polymerase III promoter (GO:0006383)|transcription initiation from RNA polymerase I promoter (GO:0006361)	cytosol (GO:0005829)|DNA-directed RNA polymerase I complex (GO:0005736)|DNA-directed RNA polymerase III complex (GO:0005666)|nucleoplasm (GO:0005654)	DNA binding (GO:0003677)|DNA-directed RNA polymerase activity (GO:0003899)			autonomic_ganglia(1)|endometrium(1)|kidney(2)|large_intestine(3)|lung(1)|ovary(1)|prostate(1)|skin(1)|stomach(1)	12				GBM - Glioblastoma multiforme(29;0.00851)|Lung(182;0.229)		CGAAGATTACTGCATATGTGA	0.388													T|||	112	0.0223642	0.003	0.036	5008	,	,		23063	0.0		0.0676	False		,,,				2504	0.0153				p.T337T	Ovarian(116;843 1620 18506 32459 34463)	Atlas-SNP	.											.	POLR1E	28	.	0			c.T1011C						PASS	.	T		77,4329	67.6+/-105.2	1,75,2127	148.0	135.0	139.0		1011	-11.6	0.0	9	dbSNP_123	139	659,7941	167.1+/-218.9	23,613,3664	no	coding-synonymous	POLR1E	NM_022490.1		24,688,5791	CC,CT,TT		7.6628,1.7476,5.6589		337/420	37501752	736,12270	2203	4300	6503	SO:0001819	synonymous_variant	64425	exon11			GATTACTGCATAT	AK091294	CCDS6611.1	9p13.1	2013-01-21	2006-03-09	2006-03-09	ENSG00000137054	ENSG00000137054		"""RNA polymerase subunits"""	17631	protein-coding gene	gene with protein product	"""RNA polymerase I associated factor 53"""		"""polymerase (RNA) I associated factor 1"""	PRAF1		8641287	Standard	XM_005251547		Approved	FLJ13390, PAF53, FLJ13970	uc003zzy.1	Q9GZS1	OTTHUMG00000019920	ENST00000377798.4:c.1011T>C	9.37:g.37501752T>C		132.0	0.0	0		114.0	63.0	0.552632	NM_022490	O75395|Q5JTE3	Silent	SNP	ENST00000377798.4	37	CCDS6611.1																																																																																			T|0.952;C|0.048	0.048	strong		0.388	POLR1E-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052464.1	NM_022490	
ARHGAP11B	89839	hgsc.bcm.edu	37	15	30927750	30927750	+	Missense_Mutation	SNP	G	G	A			TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr15:30927750G>A	ENST00000428041.2	+	6	866	c.721G>A	c.(721-723)Gtg>Atg	p.V241M		NM_001039841.1	NP_001034930.1	Q3KRB8	RHGBB_HUMAN	Rho GTPase activating protein 11B	241	Rho-GAP. {ECO:0000255|PROSITE- ProRule:PRU00172}.				regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)	GTPase activator activity (GO:0005096)			endometrium(2)|kidney(1)|large_intestine(3)|lung(1)|prostate(1)	8		all_lung(180;2.71e-09)|Breast(32;0.00116)		all cancers(64;1.9e-15)|Epithelial(43;3.59e-12)|GBM - Glioblastoma multiforme(186;9e-05)|BRCA - Breast invasive adenocarcinoma(123;0.00177)|Lung(196;0.153)		GATGGTCTCTGTGCTACTCCA	0.413																																					p.V241M		Atlas-SNP	.											ARHGAP11B,colon,carcinoma,-2,1	ARHGAP11B	14	1	0			c.G721A						PASS	.						150.0	150.0	150.0					15																	30927750		2202	4298	6500	SO:0001583	missense	89839	exon6			GTCTCTGTGCTAC	BC105788	CCDS32185.1	15q13.2	2011-07-13				ENSG00000187951		"""Rho GTPase activating proteins"""	15782	protein-coding gene	gene with protein product	"""GAP (1-8)"""		"""family with sequence similarity 7, member B1"""	FAM7B1		11829490	Standard	NM_001039841		Approved	B'-T	uc001zet.1	Q3KRB8		ENST00000428041.2:c.721G>A	15.37:g.30927750G>A	ENSP00000392760:p.Val241Met	250.0	0.0	0		252.0	97.0	0.384921	NM_001039841		Missense_Mutation	SNP	ENST00000428041.2	37	CCDS32185.1	.	.	.	.	.	.	.	.	.	.	.	5.293	0.239371	0.10023	.	.	ENSG00000187951	ENST00000428041	T	0.10763	2.84	1.49	1.49	0.22878	Rho GTPase-activating protein domain (1);	.	.	.	.	T	0.04407	0.0121	N	0.14661	0.345	0.18873	N	0.999987	P	0.43857	0.819	B	0.28991	0.097	T	0.35699	-0.9778	9	0.44086	T	0.13	.	6.461	0.21956	0.0:0.0:1.0:0.0	.	241	Q3KRB8	RHGBB_HUMAN	M	241	ENSP00000392760:V241M	ENSP00000392760:V241M	V	+	1	0	ARHGAP11B	28715042	1.000000	0.71417	1.000000	0.80357	0.324000	0.28378	1.574000	0.36482	1.121000	0.41925	0.162000	0.16502	GTG	.	.	none		0.413	ARHGAP11B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000430729.1	NM_001039841	
SMIM11	54065	hgsc.bcm.edu	37	21	35757915	35757915	+	Missense_Mutation	SNP	A	A	G	rs34016792	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr21:35757915A>G	ENST00000399295.2	+	3	522	c.152A>G	c.(151-153)aAg>aGg	p.K51R	SMIM11_ENST00000481710.1_3'UTR|SMIM11_ENST00000399292.3_Missense_Mutation_p.K51R|SMIM11_ENST00000399299.1_Intron			P58511	SIM11_HUMAN	small integral membrane protein 11	51			K -> R (in dbSNP:rs34016792).			integral component of membrane (GO:0016021)											GAAAGGAAGAAGCAATCAGAG	0.433													A|||	81	0.0161741	0.0113	0.0231	5008	,	,		20372	0.002		0.0129	False		,,,				2504	0.0358				p.K51R		Atlas-SNP	.											.	.	.	.	0			c.A152G						PASS	.	A	ARG/LYS	67,4339	61.1+/-98.1	0,67,2136	51.0	47.0	49.0		152	-3.9	0.0	21	dbSNP_126	49	269,8331	100.1+/-161.6	4,261,4035	yes	missense	FAM165B	NM_058182.4	26	4,328,6171	GG,GA,AA		3.1279,1.5207,2.5834	benign	51/59	35757915	336,12670	2203	4300	6503	SO:0001583	missense	54065	exon3			GGAAGAAGCAATC	BC015596	CCDS33550.1	21q22.12	2012-12-03	2012-12-03	2012-12-03	ENSG00000205670	ENSG00000205670			1293	protein-coding gene	gene with protein product			"""chromosome 21 open reading frame 51"", ""family with sequence similarity 165, member B"""	C21orf51, FAM165B			Standard	NM_058182		Approved		uc002ytu.4	P58511	OTTHUMG00000086193	ENST00000399295.2:c.152A>G	21.37:g.35757915A>G	ENSP00000382234:p.Lys51Arg	112.0	0.0	0		95.0	45.0	0.473684	NM_058182		Missense_Mutation	SNP	ENST00000399295.2	37	CCDS33550.1	26	0.011904761904761904	4	0.008130081300813009	12	0.03314917127071823	1	0.0017482517482517483	9	0.011873350923482849	A	10.26	1.300114	0.23650	0.015207	0.031279	ENSG00000205670	ENST00000399292;ENST00000399295	T;T	0.36520	1.25;1.25	5.64	-3.86	0.04230	.	.	.	.	.	T	0.04679	0.0127	.	.	.	0.09310	N	1	B	0.02656	0.0	B	0.04013	0.001	T	0.23691	-1.0181	8	0.15952	T	0.53	.	2.0315	0.03530	0.3294:0.3538:0.2024:0.1144	rs34016792	51	P58511	F165B_HUMAN	R	51	ENSP00000382231:K51R;ENSP00000382234:K51R	ENSP00000382231:K51R	K	+	2	0	FAM165B	34679785	0.000000	0.05858	0.000000	0.03702	0.143000	0.21401	0.555000	0.23422	-0.979000	0.03529	-0.371000	0.07208	AAG	A|0.979;G|0.021	0.021	strong		0.433	SMIM11-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000194078.1	NM_058182	
DOK2	9046	hgsc.bcm.edu	37	8	21767042	21767042	+	Missense_Mutation	SNP	C	C	T	rs372534431		TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr8:21767042C>T	ENST00000276420.4	-	5	1277	c.1019G>A	c.(1018-1020)cGa>cAa	p.R340Q	DOK2_ENST00000544659.1_Missense_Mutation_p.R186Q	NM_003974.2	NP_003965.2	O60496	DOK2_HUMAN	docking protein 2, 56kDa	340	Pro-rich.				blood coagulation (GO:0007596)|cell surface receptor signaling pathway (GO:0007166)|leukocyte migration (GO:0050900)|Ras protein signal transduction (GO:0007265)|signal transduction (GO:0007165)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)	cytosol (GO:0005829)	receptor signaling protein activity (GO:0005057)			NS(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(3)|large_intestine(1)|lung(9)|ovary(2)|prostate(3)|skin(1)	26				Colorectal(74;0.0145)|COAD - Colon adenocarcinoma(73;0.0608)		GTGGTCAGGTCGAGGGGGCAG	0.642																																					p.R340Q		Atlas-SNP	.											.	DOK2	51	.	0			c.G1019A						PASS	.	C	GLN/ARG	1,4405	2.1+/-5.4	0,1,2202	54.0	51.0	52.0		1019	-7.8	0.0	8		52	0,8600		0,0,4300	no	missense	DOK2	NM_003974.2	43	0,1,6502	TT,TC,CC		0.0,0.0227,0.0077	benign	340/413	21767042	1,13005	2203	4300	6503	SO:0001583	missense	9046	exon5			TCAGGTCGAGGGG	AF034970	CCDS6016.1	8p21.3	2008-08-07	2002-08-29		ENSG00000147443	ENSG00000147443			2991	protein-coding gene	gene with protein product		604997	"""docking protein 2, 56kD"""			9478921, 14645010	Standard	NM_003974		Approved	p56dok-2, Dok-2	uc003wzy.1	O60496	OTTHUMG00000131075	ENST00000276420.4:c.1019G>A	8.37:g.21767042C>T	ENSP00000276420:p.Arg340Gln	100.0	0.0	0		94.0	40.0	0.425532	NM_003974	Q8N5A4	Missense_Mutation	SNP	ENST00000276420.4	37	CCDS6016.1	.	.	.	.	.	.	.	.	.	.	C	6.665	0.491294	0.12702	2.27E-4	0.0	ENSG00000147443	ENST00000276420;ENST00000544659	T;T	0.31247	1.91;1.5	5.42	-7.8	0.01214	.	2.171590	0.01745	N	0.029603	T	0.15522	0.0374	L	0.27053	0.805	0.09310	N	1	B;B	0.10296	0.003;0.003	B;B	0.04013	0.001;0.001	T	0.10823	-1.0613	10	0.27785	T	0.31	.	0.8219	0.01113	0.2645:0.1123:0.2445:0.3787	.	340;340	O60496;A8K7W1	DOK2_HUMAN;.	Q	340;186	ENSP00000276420:R340Q;ENSP00000443602:R186Q	ENSP00000276420:R340Q	R	-	2	0	DOK2	21822988	0.000000	0.05858	0.000000	0.03702	0.003000	0.03518	-0.338000	0.07842	-1.129000	0.02918	-0.345000	0.07892	CGA	.	.	weak		0.642	DOK2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253735.3	NM_003974	
ST6GALNAC6	30815	hgsc.bcm.edu	37	9	130656800	130656800	+	Silent	SNP	G	G	A	rs11552227	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr9:130656800G>A	ENST00000373146.1	-	4	467	c.288C>T	c.(286-288)ctC>ctT	p.L96L	ST6GALNAC6_ENST00000291839.5_Silent_p.L96L|ST6GALNAC6_ENST00000542456.1_Missense_Mutation_p.S32L|ST6GALNAC6_ENST00000373141.1_Silent_p.L62L|ST6GALNAC6_ENST00000485320.1_5'UTR|ST6GALNAC6_ENST00000373144.3_Silent_p.L62L|ST6GALNAC6_ENST00000373142.1_Silent_p.L96L			Q969X2	SIA7F_HUMAN	ST6 (alpha-N-acetyl-neuraminyl-2,3-beta-galactosyl-1,3)-N-acetylgalactosaminide alpha-2,6-sialyltransferase 6	96					cell-cell recognition (GO:0009988)|ganglioside biosynthetic process (GO:0001574)|glycoprotein metabolic process (GO:0009100)|glycosphingolipid metabolic process (GO:0006687)|glycosylceramide metabolic process (GO:0006677)|oligosaccharide biosynthetic process (GO:0009312)|protein glycosylation (GO:0006486)|sialylation (GO:0097503)	cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	alpha-N-acetylgalactosaminide alpha-2,6-sialyltransferase activity (GO:0001665)|sialyltransferase activity (GO:0008373)			endometrium(3)|large_intestine(3)|lung(4)|prostate(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	14						CCTTGTTGCCGAGAATGGGGA	0.587																																					p.L96L		Atlas-SNP	.											.	ST6GALNAC6	36	.	0			c.C288T						PASS	.	G		2,4404	4.2+/-10.8	0,2,2201	88.0	84.0	85.0		288	-9.8	0.1	9	dbSNP_120	85	2,8598	2.2+/-6.3	0,2,4298	no	coding-synonymous	ST6GALNAC6	NM_013443.3		0,4,6499	AA,AG,GG		0.0233,0.0454,0.0308		96/334	130656800	4,13002	2203	4300	6503	SO:0001819	synonymous_variant	30815	exon4			GTTGCCGAGAATG	BC006564	CCDS6882.1, CCDS69668.1, CCDS69669.1, CCDS75908.1	9q34.13	2013-03-01		2005-02-07	ENSG00000160408	ENSG00000160408		"""Sialyltransferases"""	23364	protein-coding gene	gene with protein product		610135	"""sialytransferase 7 ((alpha-N-acetylneuraminyl 2,3-betagalactosyl-1,3)-N-acetyl galactosaminide alpha-2,6-sialytransferase) F"""	SIAT7F		12668675	Standard	XM_005251952		Approved	ST6GALNACVI	uc004bso.1	Q969X2	OTTHUMG00000020718	ENST00000373146.1:c.288C>T	9.37:g.130656800G>A		34.0	0.0	0		40.0	18.0	0.45	NM_013443	B3KQ01|Q5T9C4|Q5T9C5|Q9H8A2|Q9ULB8	Silent	SNP	ENST00000373146.1	37	CCDS6882.1	.	.	.	.	.	.	.	.	.	.	G	11.08	1.533692	0.27387	4.54E-4	2.33E-4	ENSG00000160408	ENST00000542456	T	0.42900	0.96	4.88	-9.76	0.00503	.	.	.	.	.	T	0.21881	0.0527	.	.	.	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.19160	-1.0314	7	.	.	.	-18.7556	10.2126	0.43150	0.5137:0.3211:0.1652:0.0	rs11552227	32	B4DU80	.	L	32	ENSP00000438109:S32L	.	S	-	2	0	ST6GALNAC6	129696621	0.000000	0.05858	0.082000	0.20525	0.589000	0.36550	-2.451000	0.01006	-3.649000	0.00126	-1.224000	0.01588	TCG	G|0.999;A|0.001	0.001	strong		0.587	ST6GALNAC6-007	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000054278.1	NM_013443	
LTBP1	4052	hgsc.bcm.edu	37	2	33567971	33567971	+	Missense_Mutation	SNP	C	C	T	rs61751742	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr2:33567971C>T	ENST00000404816.2	+	25	4150	c.3797C>T	c.(3796-3798)tCc>tTc	p.S1266F	LTBP1_ENST00000402934.1_Missense_Mutation_p.S887F|LTBP1_ENST00000404525.1_Missense_Mutation_p.S887F|LTBP1_ENST00000390003.4_Missense_Mutation_p.S941F|LTBP1_ENST00000418533.2_Intron|LTBP1_ENST00000354476.3_Missense_Mutation_p.S1267F|LTBP1_ENST00000407925.1_Missense_Mutation_p.S940F|LTBP1_ENST00000272273.5_Intron			Q14766	LTBP1_HUMAN	latent transforming growth factor beta binding protein 1	1266	EGF-like 13; calcium-binding. {ECO:0000255|PROSITE-ProRule:PRU00076}.				extracellular matrix organization (GO:0030198)|sequestering of TGFbeta in extracellular matrix (GO:0035583)|transmembrane receptor protein serine/threonine kinase signaling pathway (GO:0007178)	extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|proteinaceous extracellular matrix (GO:0005578)	calcium ion binding (GO:0005509)|transforming growth factor beta binding (GO:0050431)|transforming growth factor beta-activated receptor activity (GO:0005024)			breast(2)|central_nervous_system(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(8)|large_intestine(13)|lung(60)|ovary(4)|pancreas(1)|prostate(2)|skin(3)|upper_aerodigestive_tract(4)|urinary_tract(3)	108	all_hematologic(175;0.115)	Medulloblastoma(90;0.215)				ACAGCTGGCTCCTTCCGCTGC	0.453													C|||	20	0.00399361	0.0	0.0072	5008	,	,		17041	0.0		0.0129	False		,,,				2504	0.002				p.S1266F		Atlas-SNP	.											LTBP1_ENST00000407925,NS,carcinoma,-1,2	LTBP1	317	2	0			c.C3797T						PASS	.	C	PHE/SER,,PHE/SER,,PHE/SER	15,4391	22.3+/-47.3	0,15,2188	124.0	105.0	111.0		2819,,2660,,3797	5.9	1.0	2	dbSNP_129	111	79,8521	46.7+/-105.8	0,79,4221	yes	missense,intron,missense,intron,missense	LTBP1	NM_000627.3,NM_001166264.1,NM_001166265.1,NM_001166266.1,NM_206943.2	155,,155,,155	0,94,6409	TT,TC,CC		0.9186,0.3404,0.7227	probably-damaging,,probably-damaging,,probably-damaging	940/1396,,887/1343,,1266/1722	33567971	94,12912	2203	4300	6503	SO:0001583	missense	4052	exon25			CTGGCTCCTTCCG		CCDS33177.1, CCDS33178.1, CCDS33177.2, CCDS33178.2, CCDS54344.1, CCDS54345.1	2p22-p21	2008-05-23			ENSG00000049323	ENSG00000049323		"""Latent transforming growth factor, beta binding proteins"""	6714	protein-coding gene	gene with protein product	"""TGF-beta1-BP-1"""	150390				2350783, 11104663	Standard	NM_206943		Approved		uc021vft.1	Q14766	OTTHUMG00000152118	ENST00000404816.2:c.3797C>T	2.37:g.33567971C>T	ENSP00000386043:p.Ser1266Phe	105.0	0.0	0		102.0	45.0	0.441176	NM_206943	A1L3V1|P22064|Q53SD8|Q53SF3|Q53SG1|Q59HF7|Q8TD95	Missense_Mutation	SNP	ENST00000404816.2	37	CCDS33177.2	13|13	0.005952380952380952|0.005952380952380952	0|0	0.0|0.0	2|2	0.0055248618784530384|0.0055248618784530384	0|0	0.0|0.0	11|11	0.014511873350923483|0.014511873350923483	C|C	29.1|29.1	4.974955|4.974955	0.92919|0.92919	0.003404|0.003404	0.009186|0.009186	ENSG00000049323|ENSG00000049323	ENST00000415140|ENST00000404816;ENST00000354476;ENST00000390003;ENST00000402934;ENST00000404525;ENST00000407925	.|D;D;D;D;D;D	.|0.95412	.|-3.7;-3.7;-3.7;-3.7;-3.7;-3.7	5.91|5.91	5.91|5.91	0.95273|0.95273	.|.	.|.	.|.	.|.	.|.	D|D	0.97961|0.97961	0.9329|0.9329	H|H	0.94264|0.94264	3.515|3.515	0.80722|0.80722	D|D	1|1	.|D;D;D;D	.|0.89917	.|0.994;1.0;1.0;1.0	.|P;D;D;D	.|0.91635	.|0.88;0.999;0.999;0.999	D|D	0.96283|0.96283	0.9208|0.9208	5|9	.|0.87932	.|D	.|0	.|.	20.3045|20.3045	0.98621|0.98621	0.0:1.0:0.0:0.0|0.0:1.0:0.0:0.0	rs61751742|rs61751742	.|887;940;941;1267	.|Q14766-3;Q14766-2;Q14766-5;Q14766-4	.|.;.;.;.	S|F	228|1266;1267;941;887;887;940	.|ENSP00000386043:S1266F;ENSP00000346467:S1267F;ENSP00000374653:S941F;ENSP00000384373:S887F;ENSP00000385359:S887F;ENSP00000384091:S940F	.|ENSP00000346467:S1267F	P|S	+|+	1|2	0|0	LTBP1|LTBP1	33421475|33421475	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.998000|0.998000	0.95712|0.95712	7.485000|7.485000	0.81204|0.81204	2.807000|2.807000	0.96579|0.96579	0.557000|0.557000	0.71058|0.71058	CCT|TCC	C|0.991;T|0.009	0.009	strong		0.453	LTBP1-014	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000326227.2	NM_206943	
GATA2	2624	hgsc.bcm.edu	37	3	128204960	128204960	+	Missense_Mutation	SNP	G	G	C	rs34799090	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr3:128204960G>C	ENST00000341105.2	-	3	812	c.481C>G	c.(481-483)Cct>Gct	p.P161A	GATA2_ENST00000487848.1_Missense_Mutation_p.P161A|GATA2_ENST00000430265.2_Missense_Mutation_p.P161A	NM_032638.4	NP_116027.2	P23769	GATA2_HUMAN	GATA binding protein 2	161					blood coagulation (GO:0007596)|cell differentiation in hindbrain (GO:0021533)|cell fate determination (GO:0001709)|cell maturation (GO:0048469)|central nervous system neuron development (GO:0021954)|commitment of neuronal cell to specific neuron type in forebrain (GO:0021902)|definitive hemopoiesis (GO:0060216)|embryonic placenta development (GO:0001892)|eosinophil fate commitment (GO:0035854)|GABAergic neuron differentiation (GO:0097154)|homeostasis of number of cells within a tissue (GO:0048873)|inner ear morphogenesis (GO:0042472)|negative regulation of fat cell differentiation (GO:0045599)|negative regulation of fat cell proliferation (GO:0070345)|negative regulation of macrophage differentiation (GO:0045650)|negative regulation of neural precursor cell proliferation (GO:2000178)|negative regulation of Notch signaling pathway (GO:0045746)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|phagocytosis (GO:0006909)|pituitary gland development (GO:0021983)|positive regulation of angiogenesis (GO:0045766)|positive regulation of erythrocyte differentiation (GO:0045648)|positive regulation of megakaryocyte differentiation (GO:0045654)|positive regulation of phagocytosis (GO:0050766)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of forebrain neuron differentiation (GO:2000977)|regulation of histone acetylation (GO:0035065)|semicircular canal development (GO:0060872)|somatic stem cell maintenance (GO:0035019)|transcription, DNA-templated (GO:0006351)|urogenital system development (GO:0001655)|ventral spinal cord interneuron differentiation (GO:0021514)	nucleoplasm (GO:0005654)|nucleus (GO:0005634)|protein complex (GO:0043234)	C2H2 zinc finger domain binding (GO:0070742)|chromatin binding (GO:0003682)|enhancer sequence-specific DNA binding (GO:0001158)|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 (GO:0000980)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription factor binding (GO:0008134)|zinc ion binding (GO:0008270)			central_nervous_system(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(58)|kidney(2)|large_intestine(3)|lung(9)|prostate(3)|skin(1)|urinary_tract(1)	79				GBM - Glioblastoma multiforme(114;0.173)		GCTGCTGTAGGGGTGAGGGAG	0.687			Mis		AML(CML blast transformation)								G|||	8	0.00159744	0.0008	0.0043	5008	,	,		13302	0.0		0.003	False		,,,				2504	0.001				p.P161A		Atlas-SNP	.		Dom	yes		3	3q21.3	2624	GATA binding protein 2		L	.	GATA2	122	.	0			c.C481G						PASS	.	G	ALA/PRO,ALA/PRO,ALA/PRO	14,4392	21.2+/-45.6	0,14,2189	38.0	36.0	36.0		481,481,481	4.5	1.0	3	dbSNP_126	36	108,8492	52.3+/-112.8	0,108,4192	yes	missense,missense,missense	GATA2	NM_001145661.1,NM_001145662.1,NM_032638.4	27,27,27	0,122,6381	CC,CG,GG		1.2558,0.3177,0.938	probably-damaging,probably-damaging,probably-damaging	161/481,161/467,161/481	128204960	122,12884	2203	4300	6503	SO:0001583	missense	2624	exon3			CTGTAGGGGTGAG	AF169253	CCDS3049.1, CCDS46903.1	3q21	2014-09-17	2001-11-28		ENSG00000179348	ENSG00000179348		"""GATA zinc finger domain containing"""	4171	protein-coding gene	gene with protein product		137295	"""GATA-binding protein 2"""			1714909	Standard	NM_032638		Approved	NFE1B	uc003eko.2	P23769	OTTHUMG00000159689	ENST00000341105.2:c.481C>G	3.37:g.128204960G>C	ENSP00000345681:p.Pro161Ala	105.0	0.0	0		129.0	76.0	0.589147	NM_001145662	D3DNB3|Q53YE0|Q96BH0|Q96BH8|Q9BUJ6	Missense_Mutation	SNP	ENST00000341105.2	37	CCDS3049.1	3	0.0013736263736263737	0	0.0	2	0.0055248618784530384	0	0.0	1	0.0013192612137203166	G	12.68	2.010340	0.35511	0.003177	0.012558	ENSG00000179348	ENST00000341105;ENST00000430265;ENST00000487848	D;D;D	0.97114	-4.25;-4.23;-4.25	4.46	4.46	0.54185	.	0.568431	0.17408	N	0.175271	D	0.93864	0.8037	N	0.08118	0	0.48452	D	0.999652	D;B	0.76494	0.999;0.03	D;B	0.83275	0.996;0.014	D	0.91294	0.5061	10	0.08599	T	0.76	-26.4928	16.6918	0.85323	0.0:0.0:1.0:0.0	rs34799090	161;161	P23769-2;P23769	.;GATA2_HUMAN	A	161	ENSP00000345681:P161A;ENSP00000400259:P161A;ENSP00000417074:P161A	ENSP00000345681:P161A	P	-	1	0	GATA2	129687650	1.000000	0.71417	0.988000	0.46212	0.945000	0.59286	5.112000	0.64634	2.022000	0.59522	0.484000	0.47621	CCT	G|0.992;C|0.008	0.008	strong		0.687	GATA2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000356925.1	NM_032638	
MYO16	23026	hgsc.bcm.edu	37	13	109793246	109793246	+	Silent	SNP	G	G	C	rs80260507	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr13:109793246G>C	ENST00000357550.2	+	31	4661	c.4620G>C	c.(4618-4620)ccG>ccC	p.P1540P	MYO16_ENST00000356711.2_Silent_p.P1540P	NM_001198950.1	NP_001185879.1			myosin XVI											NS(3)|breast(4)|central_nervous_system(2)|endometrium(10)|kidney(8)|large_intestine(27)|lung(51)|ovary(9)|prostate(2)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)	121	all_lung(23;0.000332)|all_neural(89;0.00294)|Medulloblastoma(90;0.00596)|Lung NSC(43;0.00751)|Lung SC(71;0.104)		BRCA - Breast invasive adenocarcinoma(86;0.19)|all cancers(43;0.201)			CGCTGTCCCCGCAGTACTCCA	0.711													G|||	231	0.0461262	0.0272	0.0648	5008	,	,		5556	0.0		0.1083	False		,,,				2504	0.0419				p.P1562P		Atlas-SNP	.											MYO16,NS,carcinoma,0,2	MYO16	285	2	0			c.G4686C						PASS	.	G	,	129,4247		2,125,2061	16.0	20.0	18.0		4686,4620	-7.8	0.0	13	dbSNP_131	18	799,7773		42,715,3529	no	coding-synonymous,coding-synonymous	MYO16	NM_001198950.1,NM_015011.1	,	44,840,5590	CC,CG,GG		9.321,2.9479,7.1671	,	1562/1881,1540/1859	109793246	928,12020	2188	4286	6474	SO:0001819	synonymous_variant	23026	exon32			GTCCCCGCAGTAC		CCDS32008.1, CCDS73598.1	13q33.3	2014-06-12			ENSG00000041515	ENSG00000041515		"""Myosins / Myosin superfamily : Class XVI"", ""Ankyrin repeat domain containing"""	29822	protein-coding gene	gene with protein product	"""neuronal tyrosine-phosphorylated phosphoinositide-3-kinase adaptor 3"", ""protein phosphatase 1, regulatory subunit 107"""	615479				11588169, 17029291, 21946561	Standard	NM_001198950		Approved	MYR8, KIAA0865, Myo16b, NYAP3, PPP1R107	uc001vqt.1	Q9Y6X6	OTTHUMG00000017333	ENST00000357550.2:c.4620G>C	13.37:g.109793246G>C		33.0	0.0	0		31.0	14.0	0.451613	NM_001198950		Silent	SNP	ENST00000357550.2	37	CCDS32008.1																																																																																			G|0.933;C|0.067	0.067	strong		0.711	MYO16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045746.1	NM_015011	
MPEG1	219972	hgsc.bcm.edu	37	11	58978434	58978434	+	Silent	SNP	C	C	A	rs180770562	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr11:58978434C>A	ENST00000361050.3	-	1	1990	c.1905G>T	c.(1903-1905)ccG>ccT	p.P635P		NM_001039396.1	NP_001034485.1	Q2M385	MPEG1_HUMAN	macrophage expressed 1	635						integral component of membrane (GO:0016021)				NS(1)|cervix(1)|endometrium(2)|kidney(1)|large_intestine(5)|lung(21)|ovary(1)|prostate(3)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	39		all_epithelial(135;0.125)				GCAGCTCTATCGGTTCTCCCA	0.567													C|||	10	0.00199681	0.0023	0.0014	5008	,	,		17979	0.0		0.005	False		,,,				2504	0.001				p.P635P		Atlas-SNP	.											.	MPEG1	72	.	0			c.G1905T						PASS	.	C		7,3897		0,7,1945	95.0	104.0	101.0		1905	-11.4	0.0	11	dbSNP_134	101	66,8194		0,66,4064	no	coding-synonymous	MPEG1	NM_001039396.1		0,73,6009	AA,AC,CC		0.799,0.1793,0.6001		635/717	58978434	73,12091	1952	4130	6082	SO:0001819	synonymous_variant	219972	exon1			CTCTATCGGTTCT	AK097211	CCDS41650.1	11q12.1	2013-07-31				ENSG00000197629			29619	protein-coding gene	gene with protein product	"""macrophage expressed gene 1"""	610390				7888681, 23257510	Standard	NM_001039396		Approved	MPG1	uc001nnu.4	Q2M385		ENST00000361050.3:c.1905G>T	11.37:g.58978434C>A		113.0	0.0	0		133.0	59.0	0.443609	NM_001039396	Q2M1T6|Q8TEF8	Silent	SNP	ENST00000361050.3	37	CCDS41650.1																																																																																			C|0.996;A|0.004	0.004	strong		0.567	MPEG1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000370027.1	NM_001039396	
LRP1	4035	hgsc.bcm.edu	37	12	57594552	57594552	+	Silent	SNP	C	C	T	rs139916336	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr12:57594552C>T	ENST00000243077.3	+	64	10645	c.10179C>T	c.(10177-10179)tgC>tgT	p.C3393C		NM_002332.2	NP_002323.2	Q07954	LRP1_HUMAN	low density lipoprotein receptor-related protein 1	3393	LDL-receptor class A 22. {ECO:0000255|PROSITE-ProRule:PRU00124}.				aging (GO:0007568)|aorta morphogenesis (GO:0035909)|apoptotic cell clearance (GO:0043277)|beta-amyloid clearance (GO:0097242)|cell proliferation (GO:0008283)|cholesterol metabolic process (GO:0008203)|lipoprotein metabolic process (GO:0042157)|lipoprotein transport (GO:0042953)|negative regulation of neuron apoptotic process (GO:0043524)|negative regulation of platelet-derived growth factor receptor-beta signaling pathway (GO:2000587)|negative regulation of smooth muscle cell migration (GO:0014912)|negative regulation of Wnt signaling pathway (GO:0030178)|phototransduction, visible light (GO:0007603)|positive regulation of cholesterol efflux (GO:0010875)|positive regulation of lipid transport (GO:0032370)|positive regulation of protein transport (GO:0051222)|protein kinase C-activating G-protein coupled receptor signaling pathway (GO:0007205)|receptor-mediated endocytosis (GO:0006898)|regulation of actin cytoskeleton organization (GO:0032956)|regulation of cholesterol transport (GO:0032374)|regulation of phospholipase A2 activity (GO:0032429)|retinoid metabolic process (GO:0001523)	clathrin-coated vesicle (GO:0030136)|coated pit (GO:0005905)|dendrite (GO:0030425)|endocytic vesicle membrane (GO:0030666)|endosome (GO:0005768)|focal adhesion (GO:0005925)|integral component of plasma membrane (GO:0005887)|lysosomal membrane (GO:0005765)|neuronal cell body (GO:0043025)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	apolipoprotein binding (GO:0034185)|calcium ion binding (GO:0005509)|lipoprotein particle receptor binding (GO:0070325)|lipoprotein transporter activity (GO:0042954)|poly(A) RNA binding (GO:0044822)|protein complex binding (GO:0032403)|receptor activity (GO:0004872)			NS(1)|breast(9)|central_nervous_system(3)|cervix(3)|endometrium(33)|haematopoietic_and_lymphoid_tissue(4)|kidney(10)|large_intestine(26)|lung(58)|ovary(10)|pancreas(2)|prostate(11)|skin(7)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(5)	184				BRCA - Breast invasive adenocarcinoma(357;0.0103)	Antihemophilic Factor(DB00025)|Coagulation Factor IX(DB00100)|Tenecteplase(DB00031)	CCTTCATCTGCGATGGCGACA	0.617													C|||	14	0.00279553	0.0	0.0072	5008	,	,		12339	0.0		0.008	False		,,,				2504	0.001				p.C3393C		Atlas-SNP	.											.	LRP1	428	.	0			c.C10179T						PASS	.	C		10,4396	16.8+/-37.8	0,10,2193	91.0	78.0	83.0		10179	0.9	1.0	12	dbSNP_134	83	73,8527	43.6+/-101.6	0,73,4227	no	coding-synonymous	LRP1	NM_002332.2		0,83,6420	TT,TC,CC		0.8488,0.227,0.6382		3393/4545	57594552	83,12923	2203	4300	6503	SO:0001819	synonymous_variant	4035	exon64			CATCTGCGATGGC	X13916	CCDS8932.1	12q13.3	2013-05-28	2010-01-26		ENSG00000123384	ENSG00000123384		"""CD molecules"", ""Low density lipoprotein receptors"""	6692	protein-coding gene	gene with protein product		107770	"""alpha-2-macroglobulin receptor"""	APR, A2MR		2548950	Standard	NM_002332		Approved	LRP, CD91, LRP1A, APOER	uc001snd.3	Q07954	OTTHUMG00000044412	ENST00000243077.3:c.10179C>T	12.37:g.57594552C>T		165.0	0.0	0		183.0	90.0	0.491803	NM_002332	Q2PP12|Q86SW0|Q8IVG8	Silent	SNP	ENST00000243077.3	37	CCDS8932.1																																																																																			C|0.995;T|0.005	0.005	strong		0.617	LRP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000412772.2	NM_002332	
PLOD1	5351	hgsc.bcm.edu	37	1	12012748	12012748	+	Missense_Mutation	SNP	G	G	C	rs188165334		TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr1:12012748G>C	ENST00000196061.4	+	5	562	c.535G>C	c.(535-537)Gat>Cat	p.D179H	PLOD1_ENST00000376369.3_Missense_Mutation_p.D226H|PLOD1_ENST00000485046.1_3'UTR	NM_000302.3	NP_000293.2	Q02809	PLOD1_HUMAN	procollagen-lysine, 2-oxoglutarate 5-dioxygenase 1	179					cellular protein modification process (GO:0006464)|epidermis development (GO:0008544)|extracellular matrix organization (GO:0030198)|hydroxylysine biosynthetic process (GO:0046947)|oxidation-reduction process (GO:0055114)|response to hypoxia (GO:0001666)	endoplasmic reticulum membrane (GO:0005789)|extracellular vesicular exosome (GO:0070062)	iron ion binding (GO:0005506)|L-ascorbic acid binding (GO:0031418)|procollagen-lysine 5-dioxygenase activity (GO:0008475)|protein homodimerization activity (GO:0042803)			breast(1)|cervix(1)|endometrium(1)|kidney(1)|large_intestine(5)|lung(15)|ovary(3)|prostate(1)|upper_aerodigestive_tract(1)	29	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)|Ovarian(437;0.00965)|Hepatocellular(190;0.0202)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0228)|Colorectal(212;6.06e-06)|COAD - Colon adenocarcinoma(227;0.000273)|BRCA - Breast invasive adenocarcinoma(304;0.000311)|Kidney(185;0.000809)|KIRC - Kidney renal clear cell carcinoma(229;0.00267)|STAD - Stomach adenocarcinoma(313;0.00743)|READ - Rectum adenocarcinoma(331;0.0649)	Succinic acid(DB00139)|Vitamin C(DB00126)	CAGCGACAGCGATCAGCTGTT	0.622																																					p.D179H		Atlas-SNP	.											PLOD1_ENST00000429000,colon,carcinoma,0,2	PLOD1	75	2	0			c.G535C						PASS	.						97.0	89.0	92.0					1																	12012748		2203	4300	6503	SO:0001583	missense	5351	exon5			GACAGCGATCAGC	BC016657	CCDS142.1	1p36.22	2011-08-25	2011-08-24	2004-12-14	ENSG00000083444	ENSG00000083444	1.14.11.4		9081	protein-coding gene	gene with protein product	"""lysyl hydroxlase 1"""	153454	"""procollagen-lysine 1, 2-oxoglutarate 5-dioxygenase (lysine hydroxylase, Ehlers-Danlos syndrome type VI)"""	LLH, PLOD		1577494	Standard	NM_000302		Approved	LH1	uc001atm.3	Q02809	OTTHUMG00000002393	ENST00000196061.4:c.535G>C	1.37:g.12012748G>C	ENSP00000196061:p.Asp179His	105.0	0.0	0		96.0	42.0	0.4375	NM_000302	B4DR87|Q96AV9|Q9H132	Missense_Mutation	SNP	ENST00000196061.4	37	CCDS142.1	.	.	.	.	.	.	.	.	.	.	G	25.4	4.629555	0.87660	.	.	ENSG00000083444	ENST00000358133;ENST00000376369;ENST00000429000;ENST00000196061	T;T;T	0.40756	1.02;1.02;1.02	4.61	4.61	0.57282	.	0.000000	0.85682	D	0.000000	T	0.71005	0.3289	M	0.90425	3.115	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;1.0	T	0.78807	-0.2059	10	0.87932	D	0	.	16.5981	0.84802	0.0:0.0:1.0:0.0	.	226;179	B4DR87;Q02809	.;PLOD1_HUMAN	H	179;226;179;179	ENSP00000365548:D226H;ENSP00000405372:D179H;ENSP00000196061:D179H	ENSP00000196061:D179H	D	+	1	0	PLOD1	11935335	1.000000	0.71417	0.945000	0.38365	0.821000	0.46438	9.585000	0.98223	2.380000	0.81148	0.555000	0.69702	GAT	G|1.000;T|0.000	.	alt		0.622	PLOD1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000006865.1	NM_000302	
LRIT3	345193	hgsc.bcm.edu	37	4	110791526	110791526	+	Missense_Mutation	SNP	A	A	G	rs35997283	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr4:110791526A>G	ENST00000594814.1	+	4	1621	c.1621A>G	c.(1621-1623)Ata>Gta	p.I541V	LRIT3_ENST00000379920.3_Missense_Mutation_p.I496V|LRIT3_ENST00000327908.3_Missense_Mutation_p.I358V|LRIT3_ENST00000409621.2_Missense_Mutation_p.I358V	NM_198506.3	NP_940908.3	Q3SXY7	LRIT3_HUMAN	leucine-rich repeat, immunoglobulin-like and transmembrane domains 3	541	Fibronectin type-III. {ECO:0000255|PROSITE-ProRule:PRU00316}.				regulation of fibroblast growth factor receptor signaling pathway (GO:0040036)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)				cervix(1)|kidney(1)|large_intestine(3)|lung(8)|prostate(2)|skin(1)	16				OV - Ovarian serous cystadenocarcinoma(123;0.0011)		CCAAGTAACCATAGATGGCTT	0.488													A|||	8	0.00159744	0.0015	0.0029	5008	,	,		20846	0.0		0.002	False		,,,				2504	0.002				p.I541V		Atlas-SNP	.											.	LRIT3	107	.	0			c.A1621G						PASS	.	A	VAL/ILE	3,4403	6.2+/-15.9	0,3,2200	104.0	99.0	101.0		1486	2.6	1.0	4	dbSNP_126	101	59,8541	36.4+/-91.3	0,59,4241	yes	missense	LRIT3	NM_198506.2	29	0,62,6441	GG,GA,AA		0.686,0.0681,0.4767	benign	496/635	110791526	62,12944	2203	4300	6503	SO:0001583	missense	345193	exon4			GTAACCATAGATG	AK126648	CCDS3688.2, CCDS3688.3	4q25	2014-01-28	2007-06-19		ENSG00000183423	ENSG00000183423		"""Immunoglobulin superfamily / I-set domain containing"""	24783	protein-coding gene	gene with protein product	"""fibronectin type III, immunoglobulin and leucine rich repeat domains 4"""	615004					Standard	NM_198506		Approved	FLJ44691, FIGLER4, CSNB1F	uc031sgv.1	Q3SXY7	OTTHUMG00000132043	ENST00000594814.1:c.1621A>G	4.37:g.110791526A>G	ENSP00000469759:p.Ile541Val	122.0	0.0	0		142.0	71.0	0.5	NM_198506	C9J1C2|Q6ZTG1	Missense_Mutation	SNP	ENST00000594814.1	37	CCDS3688.3	2	9.157509157509158E-4	1	0.0020325203252032522	0	0.0	0	0.0	1	0.0013192612137203166	A	13.22	2.171157	0.38315	6.81E-4	0.00686	ENSG00000183423	ENST00000327908;ENST00000379920;ENST00000409621	T;T;T	0.27557	1.66;1.66;1.66	5.16	2.63	0.31362	Fibronectin, type III (2);Immunoglobulin-like fold (1);	0.106920	0.64402	D	0.000004	T	0.31136	0.0787	M	0.76838	2.35	0.40389	D	0.979528	P;P	0.46277	0.802;0.875	B;P	0.45037	0.206;0.467	T	0.36286	-0.9754	10	0.72032	D	0.01	.	11.922	0.52797	0.7234:0.2765:0.0:0.0	rs35997283	496;358	Q3SXY7;Q3SXY7-2	LRIT3_HUMAN;.	V	358;496;358	ENSP00000328222:I358V;ENSP00000369252:I496V;ENSP00000386734:I358V	ENSP00000328222:I358V	I	+	1	0	LRIT3	111010975	1.000000	0.71417	0.982000	0.44146	0.969000	0.65631	1.641000	0.37197	0.266000	0.21894	-0.313000	0.08912	ATA	A|0.996;G|0.004	0.004	strong		0.488	LRIT3-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000335270.2	NM_198506	
FIBCD1	84929	hgsc.bcm.edu	37	9	133779563	133779563	+	Missense_Mutation	SNP	C	C	T	rs138892175		TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr9:133779563C>T	ENST00000372338.4	-	7	1516	c.1274G>A	c.(1273-1275)cGc>cAc	p.R425H	FIBCD1_ENST00000372337.2_Missense_Mutation_p.R267H|FIBCD1_ENST00000448616.1_Missense_Mutation_p.R425H|FIBCD1_ENST00000253018.4_Intron	NM_032843.4	NP_116232.3	Q8N539	FBCD1_HUMAN	fibrinogen C domain containing 1	425	Fibrinogen C-terminal. {ECO:0000255|PROSITE-ProRule:PRU00739}.					integral component of membrane (GO:0016021)|membrane (GO:0016020)	chitin binding (GO:0008061)|metal ion binding (GO:0046872)			kidney(1)|large_intestine(3)|lung(2)|prostate(5)|urinary_tract(1)	12	all_hematologic(7;0.0028)			OV - Ovarian serous cystadenocarcinoma(145;3.52e-05)|Epithelial(140;0.00019)		GTGCGCACCGCGCAGGTACTG	0.627																																					p.R425H		Atlas-SNP	.											FIBCD1,NS,carcinoma,+1,2	FIBCD1	34	2	0			c.G1274A						PASS	.	C	HIS/ARG,HIS/ARG	0,4406		0,0,2203	133.0	112.0	119.0		1274,1274	3.8	0.9	9	dbSNP_134	119	1,8599	1.2+/-3.3	0,1,4299	no	missense,missense	FIBCD1	NM_001145106.1,NM_032843.4	29,29	0,1,6502	TT,TC,CC		0.0116,0.0,0.0077	possibly-damaging,possibly-damaging	425/462,425/462	133779563	1,13005	2203	4300	6503	SO:0001583	missense	84929	exon8			GCACCGCGCAGGT	AK027716	CCDS6937.1	9q34.2	2013-02-06			ENSG00000130720	ENSG00000130720		"""Fibrinogen C domain containing"""	25922	protein-coding gene	gene with protein product		613357				12975309	Standard	NM_001145106		Approved	FLJ14810	uc004bzz.3	Q8N539	OTTHUMG00000020814	ENST00000372338.4:c.1274G>A	9.37:g.133779563C>T	ENSP00000361413:p.Arg425His	96.0	0.0	0		117.0	61.0	0.521368	NM_001145106	A3KFK0|Q6UXK6|Q96SJ7	Missense_Mutation	SNP	ENST00000372338.4	37	CCDS6937.1	.	.	.	.	.	.	.	.	.	.	C	17.08	3.298660	0.60195	0.0	1.16E-4	ENSG00000130720	ENST00000448616;ENST00000372338;ENST00000372337	T;T;T	0.76060	-0.99;-0.99;-0.99	4.66	3.75	0.43078	Fibrinogen, alpha/beta/gamma chain, C-terminal globular (4);Fibrinogen, alpha/beta/gamma chain, C-terminal globular, subdomain 2 (1);	0.108817	0.56097	D	0.000024	T	0.58566	0.2131	L	0.46614	1.455	0.48288	D	0.999625	P	0.40619	0.724	B	0.25291	0.059	T	0.64309	-0.6438	10	0.54805	T	0.06	.	8.3984	0.32570	0.0:0.8277:0.0:0.1723	.	425	Q8N539	FBCD1_HUMAN	H	425;425;267	ENSP00000414501:R425H;ENSP00000361413:R425H;ENSP00000361412:R267H	ENSP00000361412:R267H	R	-	2	0	FIBCD1	132769384	0.842000	0.29525	0.881000	0.34555	0.103000	0.19146	1.528000	0.35985	2.138000	0.66242	0.455000	0.32223	CGC	C|1.000;T|0.000	0.000	weak		0.627	FIBCD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054687.2	NM_032843	
DCSTAMP	81501	hgsc.bcm.edu	37	8	105361803	105361803	+	Silent	SNP	C	C	T	rs117086639	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr8:105361803C>T	ENST00000297581.2	+	2	1072	c.1023C>T	c.(1021-1023)caC>caT	p.H341H	DCSTAMP_ENST00000517991.1_Intron|DPYS_ENST00000521601.1_Intron	NM_030788.3	NP_110415.1	Q9H295	DCSTP_HUMAN	dendrocyte expressed seven transmembrane protein	341					cellular response to interleukin-4 (GO:0071353)|cellular response to macrophage colony-stimulating factor stimulus (GO:0036006)|cellular response to tumor necrosis factor (GO:0071356)|membrane fusion (GO:0061025)|myeloid dendritic cell differentiation (GO:0043011)|negative regulation of cell growth (GO:0030308)|osteoclast differentiation (GO:0030316)|osteoclast fusion (GO:0072675)|positive regulation of bone resorption (GO:0045780)|positive regulation of macrophage fusion (GO:0034241)|positive regulation of monocyte differentiation (GO:0045657)	cell surface (GO:0009986)|endoplasmic reticulum membrane (GO:0005789)|endosome membrane (GO:0010008)|integral component of endoplasmic reticulum membrane (GO:0030176)|integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)											TGAAACTGCACGGAGAGGTAG	0.502													C|||	94	0.01877	0.0182	0.0086	5008	,	,		19755	0.0288		0.0169	False		,,,				2504	0.0184				p.H341H		Atlas-SNP	.											.	.	.	.	0			c.C1023T						PASS	.	C		39,4367	43.1+/-76.7	0,39,2164	99.0	100.0	100.0		1023	-2.0	0.6	8	dbSNP_132	100	69,8531	39.8+/-96.3	1,67,4232	no	coding-synonymous	TM7SF4	NM_030788.2		1,106,6396	TT,TC,CC		0.8023,0.8852,0.8304		341/471	105361803	108,12898	2203	4300	6503	SO:0001819	synonymous_variant	81501	exon2			ACTGCACGGAGAG	AF305068	CCDS6301.1, CCDS59111.1	8q22.3	2012-08-10	2012-03-27	2012-03-27	ENSG00000164935	ENSG00000164935			18549	protein-coding gene	gene with protein product	"""Dendritic cells (DC)-specific transmembrane protein"", ""IL-Four INDuced"""	605933	"""transmembrane 7 superfamily member 4"""	TM7SF4		11169400, 11345591	Standard	NM_030788		Approved	DC-STAMP, FIND	uc003ylx.2	Q9H295	OTTHUMG00000164890	ENST00000297581.2:c.1023C>T	8.37:g.105361803C>T		84.0	0.0	0		80.0	45.0	0.5625	NM_030788	B7ZVW2|E7ESG0|Q2M2D5	Silent	SNP	ENST00000297581.2	37	CCDS6301.1																																																																																			C|0.989;T|0.011	0.011	strong		0.502	DCSTAMP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000380810.1	NM_030788	
CSF1R	1436	hgsc.bcm.edu	37	5	149460553	149460553	+	Silent	SNP	A	A	G	rs216123	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr5:149460553A>G	ENST00000286301.3	-	3	375	c.84T>C	c.(82-84)ccT>ccC	p.P28P	CSF1R_ENST00000543093.1_Silent_p.P28P	NM_005211.3	NP_005202.2	P07333	CSF1R_HUMAN	colony stimulating factor 1 receptor	28	Ig-like C2-type 1.				cell proliferation (GO:0008283)|cell-cell junction maintenance (GO:0045217)|cellular response to cytokine stimulus (GO:0071345)|cellular response to macrophage colony-stimulating factor stimulus (GO:0036006)|cytokine-mediated signaling pathway (GO:0019221)|hemopoiesis (GO:0030097)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|macrophage differentiation (GO:0030225)|mammary gland duct morphogenesis (GO:0060603)|monocyte differentiation (GO:0030224)|multicellular organismal development (GO:0007275)|osteoclast differentiation (GO:0030316)|peptidyl-tyrosine phosphorylation (GO:0018108)|phosphatidylinositol metabolic process (GO:0046488)|phosphatidylinositol-mediated signaling (GO:0048015)|positive regulation of cell migration (GO:0030335)|positive regulation of cell motility (GO:2000147)|positive regulation of cell proliferation (GO:0008284)|positive regulation of chemokine secretion (GO:0090197)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of protein serine/threonine kinase activity (GO:0071902)|positive regulation of protein tyrosine kinase activity (GO:0061098)|positive regulation of tyrosine phosphorylation of Stat3 protein (GO:0042517)|protein autophosphorylation (GO:0046777)|regulation of actin cytoskeleton reorganization (GO:2000249)|regulation of bone resorption (GO:0045124)|regulation of cell shape (GO:0008360)|ruffle organization (GO:0031529)|signal transduction (GO:0007165)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)	cell surface (GO:0009986)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	ATP binding (GO:0005524)|cytokine binding (GO:0019955)|macrophage colony-stimulating factor receptor activity (GO:0005011)|protein homodimerization activity (GO:0042803)			NS(2)|breast(2)|central_nervous_system(3)|endometrium(3)|haematopoietic_and_lymphoid_tissue(38)|kidney(2)|large_intestine(6)|liver(3)|lung(23)|ovary(2)|pancreas(1)|prostate(3)|upper_aerodigestive_tract(2)|urinary_tract(3)	93			KIRC - Kidney renal clear cell carcinoma(527;0.000962)|Kidney(363;0.00147)		Imatinib(DB00619)|Sunitinib(DB01268)	CGACCAGCTCAGGGACACTGG	0.607													A|||	1679	0.335264	0.2587	0.353	5008	,	,		21664	0.0893		0.5527	False		,,,				2504	0.456				p.P28P		Atlas-SNP	.											.	CSF1R	250	.	0			c.T84C						PASS	.	A		1287,3119	437.2+/-344.9	183,921,1099	86.0	61.0	69.0		84	-8.2	0.9	5	dbSNP_79	69	4874,3726	618.5+/-396.8	1407,2060,833	no	coding-synonymous	CSF1R	NM_005211.3		1590,2981,1932	GG,GA,AA		43.3256,29.2102,47.3704		28/973	149460553	6161,6845	2203	4300	6503	SO:0001819	synonymous_variant	1436	exon3			CAGCTCAGGGACA	U63963	CCDS4302.1	5q32	2013-01-11	2008-08-01		ENSG00000182578	ENSG00000182578		"""CD molecules"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	2433	protein-coding gene	gene with protein product		164770	"""McDonough feline sarcoma viral (v-fms) oncogene homolog"""	FMS		1611909	Standard	NM_005211		Approved	C-FMS, CSFR, CD115	uc003lrm.3	P07333	OTTHUMG00000130050	ENST00000286301.3:c.84T>C	5.37:g.149460553A>G		168.0	0.0	0		159.0	158.0	0.993711	NM_005211	B5A955|D3DQG2|Q6LDW5|Q6LDY4|Q86VW7	Silent	SNP	ENST00000286301.3	37	CCDS4302.1																																																																																			A|0.588;G|0.411	0.411	strong		0.607	CSF1R-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252329.2	NM_005211	
KCTD17	79734	hgsc.bcm.edu	37	22	37458571	37458571	+	Silent	SNP	C	C	T	rs142739650	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr22:37458571C>T	ENST00000403888.3	+	9	904	c.903C>T	c.(901-903)taC>taT	p.Y301Y	KCTD17_ENST00000402077.3_Silent_p.Y277Y	NM_001282684.1	NP_001269613.1	Q8N5Z5	KCD17_HUMAN	potassium channel tetramerization domain containing 17	301	Pro-rich.				protein homooligomerization (GO:0051260)		identical protein binding (GO:0042802)			NS(1)|breast(1)|endometrium(1)|lung(1)|prostate(1)	5						CTAGCTGTTACAAGCCAGAGG	0.612																																					p.Y277Y		Atlas-SNP	.											.	KCTD17	17	.	0			c.C831T						PASS	.	C		0,4406		0,0,2203	48.0	48.0	48.0		831	3.8	1.0	22	dbSNP_134	48	7,8593	5.0+/-18.6	0,7,4293	no	coding-synonymous	KCTD17	NM_024681.2		0,7,6496	TT,TC,CC		0.0814,0.0,0.0538		277/298	37458571	7,12999	2203	4300	6503	SO:0001819	synonymous_variant	79734	exon8			CTGTTACAAGCCA	BC025403	CCDS13940.2, CCDS74854.1, CCDS74855.1	22q12.3	2013-06-20	2013-06-20		ENSG00000100379	ENSG00000100379			25705	protein-coding gene	gene with protein product			"""potassium channel tetramerisation domain containing 17"""			12477932	Standard	XM_005261741		Approved	FLJ12242	uc011amv.2	Q8N5Z5	OTTHUMG00000150532	ENST00000403888.3:c.903C>T	22.37:g.37458571C>T		71.0	0.0	0		80.0	44.0	0.55	NM_024681	B0QYA9|B0QYB0|O95517	Silent	SNP	ENST00000403888.3	37																																																																																				C|0.999;T|0.001	0.001	strong		0.612	KCTD17-002	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000318781.1	NM_024681	
SYNGAP1	8831	hgsc.bcm.edu	37	6	33419593	33419593	+	Silent	SNP	G	G	A	rs372190836		TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr6:33419593G>A	ENST00000418600.2	+	19	4043	c.3942G>A	c.(3940-3942)ccG>ccA	p.P1314P	SYNGAP1_ENST00000428982.2_Silent_p.P1255P|ZBTB9_ENST00000395064.2_5'Flank|SYNGAP1_ENST00000496374.1_3'UTR	NM_006772.2	NP_006763.2	Q96PV0	SYGP1_HUMAN	synaptic Ras GTPase activating protein 1	1314					dendrite development (GO:0016358)|negative regulation of axonogenesis (GO:0050771)|negative regulation of neuron apoptotic process (GO:0043524)|negative regulation of Ras protein signal transduction (GO:0046580)|pattern specification process (GO:0007389)|positive regulation of Ras GTPase activity (GO:0032320)|Ras protein signal transduction (GO:0007265)|receptor clustering (GO:0043113)|regulation of long-term neuronal synaptic plasticity (GO:0048169)|regulation of MAPK cascade (GO:0043408)|regulation of synapse structure and activity (GO:0050803)|regulation of synaptic plasticity (GO:0048167)|visual learning (GO:0008542)	cytoplasm (GO:0005737)|dendritic shaft (GO:0043198)|intrinsic component of the cytoplasmic side of the plasma membrane (GO:0031235)	Rab GTPase activator activity (GO:0005097)|Ras GTPase activator activity (GO:0005099)			breast(2)|central_nervous_system(1)|cervix(1)|endometrium(3)|kidney(2)|large_intestine(9)|lung(15)|ovary(7)|pancreas(1)|stomach(1)|urinary_tract(1)	43						TGGCCCCACCGTGGAATGGCC	0.642																																					p.P1314P		Atlas-SNP	.											SYNGAP1,caecum,carcinoma,0,1	SYNGAP1	202	1	0			c.G3942A						scavenged	.	A		0,4406		0,0,2203	16.0	15.0	15.0		3942	-0.8	1.0	6		15	1,8597		0,1,4298	no	coding-synonymous	SYNGAP1	NM_006772.2		0,1,6501	AA,AG,GG		0.0116,0.0,0.0077		1314/1344	33419593	1,13003	2203	4299	6502	SO:0001819	synonymous_variant	8831	exon19			CCCACCGTGGAAT	AB067525	CCDS34434.2	6p21.3	2010-06-25	2010-06-25		ENSG00000197283	ENSG00000197283			11497	protein-coding gene	gene with protein product		603384	"""synaptic Ras GTPase activating protein 1 homolog (rat)"""			9581761, 18323856	Standard	NM_006772		Approved	SYNGAP, RASA5, KIAA1938	uc011dri.2	Q96PV0	OTTHUMG00000031096	ENST00000418600.2:c.3942G>A	6.37:g.33419593G>A		54.0	1.0	0.0185185		83.0	46.0	0.554217	NM_006772	A2AB17|A2BEL6|A2BEL7|A8MQC4|Q8TCS2|Q9UGE2	Silent	SNP	ENST00000418600.2	37	CCDS34434.2																																																																																			.	.	weak		0.642	SYNGAP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076151.4	XM_166407	
TNFAIP2	7127	hgsc.bcm.edu	37	14	103601637	103601637	+	Silent	SNP	C	C	T	rs2234147	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr14:103601637C>T	ENST00000560869.1	+	12	2544	c.1905C>T	c.(1903-1905)gaC>gaT	p.D635D	TNFAIP2_ENST00000451723.2_Silent_p.D304D|TNFAIP2_ENST00000333007.1_Silent_p.D635D|TNFAIP2_ENST00000538222.1_Silent_p.D118D			Q03169	TNAP2_HUMAN	tumor necrosis factor, alpha-induced protein 2	635					angiogenesis (GO:0001525)|cell differentiation (GO:0030154)|exocytosis (GO:0006887)	exocyst (GO:0000145)|extracellular space (GO:0005615)				NS(1)|breast(1)|central_nervous_system(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(1)|lung(4)|prostate(1)|upper_aerodigestive_tract(1)	11		Melanoma(154;0.155)	Epithelial(46;0.191)			GCATCTTGGACGTCAGCATGG	0.577													c|||	59	0.0117812	0.0015	0.0159	5008	,	,		19498	0.0		0.0119	False		,,,				2504	0.0348				p.D635D		Atlas-SNP	.											.	TNFAIP2	53	.	0			c.C1905T						PASS	.			19,4387	26.2+/-53.5	0,19,2184	167.0	172.0	170.0		1905	0.2	0.5	14	dbSNP_98	170	87,8513	49.8+/-109.6	0,87,4213	no	coding-synonymous	TNFAIP2	NM_006291.2		0,106,6397	TT,TC,CC		1.0116,0.4312,0.815		635/655	103601637	106,12900	2203	4300	6503	SO:0001819	synonymous_variant	7127	exon11			CTTGGACGTCAGC		CCDS9979.1	14q32	2011-01-31				ENSG00000185215			11895	protein-coding gene	gene with protein product	"""exocyst complex component 3-like 3"""	603300				1374453	Standard	NM_006291		Approved	B94, EXOC3L3	uc001ymm.1	Q03169		ENST00000560869.1:c.1905C>T	14.37:g.103601637C>T		93.0	0.0	0		70.0	34.0	0.485714	NM_006291	Q86VI0	Silent	SNP	ENST00000560869.1	37	CCDS9979.1																																																																																			C|0.993;T|0.007	0.007	strong		0.577	TNFAIP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000415674.1	NM_006291	
DYM	54808	hgsc.bcm.edu	37	18	46623854	46623854	+	Missense_Mutation	SNP	T	T	C	rs146000214		TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr18:46623854T>C	ENST00000269445.6	-	16	2235	c.1778A>G	c.(1777-1779)cAa>cGa	p.Q593R	DYM_ENST00000442713.2_Missense_Mutation_p.Q403R	NM_017653.3	NP_060123.3	Q7RTS9	DYM_HUMAN	dymeclin	593					bone development (GO:0060348)|Golgi organization (GO:0007030)	cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)	enzyme binding (GO:0019899)			NS(1)|cervix(1)|endometrium(3)|kidney(2)|large_intestine(3)|lung(6)|skin(1)|upper_aerodigestive_tract(1)	18						AGCTCCAGCTTGCAGCAACCT	0.433													T|||	1	0.000199681	0.0	0.0014	5008	,	,		22199	0.0		0.0	False		,,,				2504	0.0				p.Q593R		Atlas-SNP	.											.	DYM	52	.	0			c.A1778G						PASS	.	T	ARG/GLN	0,4406		0,0,2203	86.0	78.0	81.0		1778	5.6	0.4	18	dbSNP_134	81	9,8591	7.1+/-27.0	0,9,4291	yes	missense	DYM	NM_017653.3	43	0,9,6494	CC,CT,TT		0.1047,0.0,0.0692	benign	593/670	46623854	9,12997	2203	4300	6503	SO:0001583	missense	54808	exon16			CCAGCTTGCAGCA	AK000078	CCDS11937.1	18q21.1	2008-03-12			ENSG00000141627	ENSG00000141627			21317	protein-coding gene	gene with protein product		607461					Standard	NM_017653		Approved	FLJ20071, DMC, SMC	uc002ldi.1	Q7RTS9	OTTHUMG00000132659	ENST00000269445.6:c.1778A>G	18.37:g.46623854T>C	ENSP00000269445:p.Gln593Arg	72.0	0.0	0		92.0	38.0	0.413043	NM_017653	A8K5I8|B2RCF9|B4DKI7|Q3ZTS8|Q6P2P5|Q8N2M0|Q9BVE9|Q9NPU7	Missense_Mutation	SNP	ENST00000269445.6	37	CCDS11937.1	1	4.578754578754579E-4	0	0.0	1	0.0027624309392265192	0	0.0	0	0.0	T	14.50	2.554677	0.45487	0.0	0.001047	ENSG00000141627	ENST00000442713;ENST00000269445	D;D	0.82619	-1.63;-1.63	5.61	5.61	0.85477	.	0.053248	0.85682	D	0.000000	D	0.87478	0.6187	L	0.49640	1.575	0.80722	D	1	P;D	0.59357	0.908;0.985	P;D	0.74023	0.888;0.982	D	0.84012	0.0349	10	0.15952	T	0.53	-13.7508	15.7757	0.78214	0.0:0.0:0.0:1.0	.	403;593	Q7RTS9-2;Q7RTS9	.;DYM_HUMAN	R	403;593	ENSP00000395942:Q403R;ENSP00000269445:Q593R	ENSP00000269445:Q593R	Q	-	2	0	DYM	44877852	1.000000	0.71417	0.351000	0.25721	0.899000	0.52679	7.142000	0.77339	2.254000	0.74563	0.533000	0.62120	CAA	T|0.999;C|0.001	0.001	strong		0.433	DYM-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255912.3	NM_017653	
SMIM11	54065	hgsc.bcm.edu	37	21	35757787	35757787	+	Silent	SNP	C	C	T	rs61747964	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr21:35757787C>T	ENST00000399295.2	+	3	394	c.24C>T	c.(22-24)caC>caT	p.H8H	SMIM11_ENST00000481710.1_3'UTR|SMIM11_ENST00000399292.3_Silent_p.H8H|SMIM11_ENST00000399299.1_Intron			P58511	SIM11_HUMAN	small integral membrane protein 11	8						integral component of membrane (GO:0016021)											TTCTTGAGCACGTGCCCCTGC	0.403													C|||	121	0.0241613	0.0408	0.0245	5008	,	,		20251	0.002		0.0129	False		,,,				2504	0.0358				p.H8H		Atlas-SNP	.											.	.	.	.	0			c.C24T						PASS	.	C		200,4206	126.1+/-163.2	2,196,2005	106.0	89.0	95.0		24	0.4	0.8	21	dbSNP_129	95	269,8331	103.8+/-164.8	4,261,4035	no	coding-synonymous	FAM165B	NM_058182.4		6,457,6040	TT,TC,CC		3.1279,4.5393,3.606		8/59	35757787	469,12537	2203	4300	6503	SO:0001819	synonymous_variant	54065	exon3			TGAGCACGTGCCC	BC015596	CCDS33550.1	21q22.12	2012-12-03	2012-12-03	2012-12-03	ENSG00000205670	ENSG00000205670			1293	protein-coding gene	gene with protein product			"""chromosome 21 open reading frame 51"", ""family with sequence similarity 165, member B"""	C21orf51, FAM165B			Standard	NM_058182		Approved		uc002ytu.4	P58511	OTTHUMG00000086193	ENST00000399295.2:c.24C>T	21.37:g.35757787C>T		241.0	0.0	0		263.0	135.0	0.513308	NM_058182		Silent	SNP	ENST00000399295.2	37	CCDS33550.1																																																																																			C|0.971;T|0.029	0.029	strong		0.403	SMIM11-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000194078.1	NM_058182	
ALG6	29929	hgsc.bcm.edu	37	1	63881583	63881583	+	Missense_Mutation	SNP	A	A	G			TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr1:63881583A>G	ENST00000371108.4	+	11	1247	c.942A>G	c.(940-942)atA>atG	p.I314M	ALG6_ENST00000263440.4_Missense_Mutation_p.I316M	NM_013339.3	NP_037471.2	Q9Y672	ALG6_HUMAN	ALG6, alpha-1,3-glucosyltransferase	314					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						CTGCATGCATAAAATTAATAC	0.294																																					p.I314M		Atlas-SNP	.											.	ALG6	33	.	0			c.A942G						PASS	.						63.0	67.0	66.0					1																	63881583		2202	4297	6499	SO:0001583	missense	29929	exon11			ATGCATAAAATTA	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.942A>G	1.37:g.63881583A>G	ENSP00000360149:p.Ile314Met	285.0	0.0	0		294.0	138.0	0.469388	NM_013339	B3KMU2|Q5SXR9|Q9H3I0	Missense_Mutation	SNP	ENST00000371108.4	37	CCDS30735.1	.	.	.	.	.	.	.	.	.	.	A	11.01	1.513855	0.27123	.	.	ENSG00000088035	ENST00000371108;ENST00000263440	D;D	0.85339	-1.97;-1.97	5.06	2.55	0.30701	.	0.276621	0.39615	N	0.001314	T	0.78065	0.4225	M	0.86502	2.82	0.41346	D	0.987339	B	0.13145	0.007	B	0.21360	0.034	T	0.76713	-0.2858	10	0.45353	T	0.12	-4.5375	8.1541	0.31158	0.566:0.3205:0.0:0.1136	.	316	A2A2G4	.	M	314;316	ENSP00000360149:I314M;ENSP00000263440:I316M	ENSP00000263440:I316M	I	+	3	3	ALG6	63654171	0.999000	0.42202	0.266000	0.24541	0.836000	0.47400	0.610000	0.24253	0.870000	0.35726	0.533000	0.62120	ATA	.	.	none		0.294	ALG6-001	KNOWN	non_canonical_conserved|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000025330.2	NM_013339	
CDC25C	995	hgsc.bcm.edu	37	5	137654980	137654980	+	Silent	SNP	G	G	A	rs111911741	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr5:137654980G>A	ENST00000323760.6	-	7	821	c.543C>T	c.(541-543)aaC>aaT	p.N181N	CDC25C_ENST00000415130.2_Silent_p.N108N|CDC25C_ENST00000513970.1_Silent_p.N181N|CDC25C_ENST00000348983.3_Silent_p.N108N|CDC25C_ENST00000357274.3_Silent_p.N138N|CDC25C_ENST00000514555.1_Silent_p.N151N|CDC25C_ENST00000356505.3_Silent_p.N151N	NM_001790.3	NP_001781.2	P30307	MPIP3_HUMAN	cell division cycle 25C	181					cell proliferation (GO:0008283)|DNA replication (GO:0006260)|G2/M transition of mitotic cell cycle (GO:0000086)|mitotic cell cycle (GO:0000278)|mitotic nuclear division (GO:0007067)|peptidyl-tyrosine dephosphorylation (GO:0035335)|regulation of cell cycle (GO:0051726)|regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0000079)|regulation of mitosis (GO:0007088)|spermatogenesis (GO:0007283)|viral process (GO:0016032)	cytosol (GO:0005829)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)	protein kinase binding (GO:0019901)|protein tyrosine phosphatase activity (GO:0004725)|WW domain binding (GO:0050699)			endometrium(2)|kidney(3)|large_intestine(5)|lung(5)|skin(1)	16			KIRC - Kidney renal clear cell carcinoma(527;0.004)|Kidney(363;0.00592)			CTTCTCCTAGGTTTGGATTTT	0.378													G|||	2	0.000399361	0.0	0.0029	5008	,	,		16400	0.0		0.0	False		,,,				2504	0.0				p.N181N		Atlas-SNP	.											.	CDC25C	37	.	0			c.C543T						PASS	.	G	,	3,4403	4.2+/-10.8	0,3,2200	136.0	133.0	134.0		543,324	-4.2	0.0	5	dbSNP_132	134	26,8574	19.2+/-60.6	0,26,4274	no	coding-synonymous,coding-synonymous	CDC25C	NM_001790.3,NM_022809.2	,	0,29,6474	AA,AG,GG		0.3023,0.0681,0.223	,	181/474,108/401	137654980	29,12977	2203	4300	6503	SO:0001819	synonymous_variant	995	exon7			TCCTAGGTTTGGA	M34065	CCDS4202.1, CCDS4203.1	5q31	2013-01-17	2013-01-17		ENSG00000158402	ENSG00000158402		"""Protein tyrosine phosphatases / Class III Cys-based PTPs"", ""Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"""	1727	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 60"""	157680	"""cell division cycle 25C"", ""cell division cycle 25 homolog C (S. cerevisiae)"", ""cell division cycle 25 homolog C (S. pombe)"""	CDC25		1703321	Standard	XM_005272145		Approved	PPP1R60	uc003lcp.1	P30307	OTTHUMG00000129203	ENST00000323760.6:c.543C>T	5.37:g.137654980G>A		131.0	0.0	0		155.0	67.0	0.432258	NM_001790	D3DQB8|Q96PL3|Q9H168|Q9H2E8|Q9H2E9|Q9H2F1	Silent	SNP	ENST00000323760.6	37	CCDS4202.1																																																																																			G|0.999;A|0.001	0.001	strong		0.378	CDC25C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251280.1		
CHML	1122	hgsc.bcm.edu	37	1	241797791	241797791	+	Silent	SNP	A	A	G	rs372360469		TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr1:241797791A>G	ENST00000366553.1	-	1	1441	c.1278T>C	c.(1276-1278)ggT>ggC	p.G426G	OPN3_ENST00000331838.5_Intron|OPN3_ENST00000469376.1_Intron|OPN3_ENST00000366554.2_Intron	NM_001821.3	NP_001812.2	P26374	RAE2_HUMAN	choroideremia-like (Rab escort protein 2)	426					intracellular protein transport (GO:0006886)|protein geranylgeranylation (GO:0018344)	Rab-protein geranylgeranyltransferase complex (GO:0005968)	GTPase activator activity (GO:0005096)|Rab geranylgeranyltransferase activity (GO:0004663)|Rab GTPase binding (GO:0017137)			breast(2)|endometrium(1)|kidney(2)|large_intestine(6)|lung(7)|ovary(4)|skin(3)|stomach(1)	26	Ovarian(103;0.103)|all_lung(81;0.23)	all_cancers(173;0.0231)	OV - Ovarian serous cystadenocarcinoma(106;0.0125)			TTATTCTTTGACCAAAGTGAT	0.363																																					p.G426G		Atlas-SNP	.											.	CHML	82	.	0			c.T1278C						PASS	.	A	,	0,4406		0,0,2203	75.0	79.0	78.0		1278,	-0.2	1.0	1		78	1,8595	1.2+/-3.3	0,1,4297	no	coding-synonymous,intron	CHML,OPN3	NM_001821.3,NM_014322.2	,	0,1,6500	GG,GA,AA		0.0116,0.0,0.0077	,	426/657,	241797791	1,13001	2203	4298	6501	SO:0001819	synonymous_variant	1122	exon1			TCTTTGACCAAAG	X64728	CCDS31073.1	1q43	2013-09-19			ENSG00000203668	ENSG00000203668			1941	protein-coding gene	gene with protein product		118825				7981670	Standard	NM_001821		Approved	REP-2	uc001hzd.3	P26374	OTTHUMG00000039690	ENST00000366553.1:c.1278T>C	1.37:g.241797791A>G		55.0	0.0	0		52.0	23.0	0.442308	NM_001821	B2RAB9|Q17RE0|Q9H1Y4	Silent	SNP	ENST00000366553.1	37	CCDS31073.1																																																																																			.	.	none		0.363	CHML-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000095712.1	NM_001821	
TBL3	10607	hgsc.bcm.edu	37	16	2028220	2028220	+	Splice_Site	SNP	A	A	G			TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr16:2028220A>G	ENST00000568546.1	+	20	2261	c.2133A>G	c.(2131-2133)aaA>aaG	p.K711K		NM_006453.2	NP_006444.2	Q12788	TBL3_HUMAN	transducin (beta)-like 3	711					G-protein coupled receptor signaling pathway coupled to cGMP nucleotide second messenger (GO:0007199)|intracellular signal transduction (GO:0035556)|rRNA processing (GO:0006364)	nucleolus (GO:0005730)|nucleus (GO:0005634)|small-subunit processome (GO:0032040)	poly(A) RNA binding (GO:0044822)|receptor signaling protein activity (GO:0005057)			breast(1)|endometrium(2)|kidney(4)|lung(7)|ovary(1)|prostate(2)|skin(1)	18						GCGACCAGAAAGGTTGGCGGC	0.662																																					p.K711K	Melanoma(118;616 1651 35077 38081 48633)	Atlas-SNP	.											.	TBL3	54	.	0			c.A2133G						PASS	.						43.0	48.0	47.0					16																	2028220		2197	4296	6493	SO:0001630	splice_region_variant	10607	exon20			CCAGAAAGGTTGG	U02609	CCDS10453.1	16p13.3	2013-01-10			ENSG00000183751	ENSG00000183751		"""WD repeat domain containing"""	11587	protein-coding gene	gene with protein product		605915				8307582	Standard	NM_006453		Approved	SAZD, UTP13	uc002cnu.1	Q12788	OTTHUMG00000128710	ENST00000568546.1:c.2134+1A>G	16.37:g.2028220A>G		90.0	0.0	0		108.0	50.0	0.462963	NM_006453	Q59GD6|Q8IVB7|Q96A78	Silent	SNP	ENST00000568546.1	37	CCDS10453.1																																																																																			.	.	none		0.662	TBL3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250615.3	NM_006453	Silent
ATP5SL	55101	hgsc.bcm.edu	37	19	41944270	41944270	+	Missense_Mutation	SNP	T	T	C	rs2231939	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr19:41944270T>C	ENST00000221943.9	-	2	73	c.68A>G	c.(67-69)cAt>cGt	p.H23R	ATP5SL_ENST00000597457.1_Missense_Mutation_p.H23R|ATP5SL_ENST00000590641.2_Missense_Mutation_p.H29R|ATP5SL_ENST00000589970.1_Missense_Mutation_p.H23R|ATP5SL_ENST00000301183.11_Missense_Mutation_p.H29R|ATP5SL_ENST00000417807.3_Missense_Mutation_p.H29R|ATP5SL_ENST00000438807.3_Missense_Mutation_p.H23R|ATP5SL_ENST00000592922.2_Missense_Mutation_p.H23R|ATP5SL_ENST00000595425.1_Missense_Mutation_p.H23R	NM_018035.2	NP_060505.2	Q9NW81	AT5SL_HUMAN	ATP5S-like	23			H -> R (in dbSNP:rs2231939). {ECO:0000269|PubMed:14702039}.			mitochondrion (GO:0005739)				breast(2)|cervix(1)|endometrium(2)|kidney(1)|large_intestine(2)|lung(2)|stomach(1)	11						ACCCAGGCGATGGATGCCCCT	0.602													T|||	10	0.00199681	0.0	0.0058	5008	,	,		18463	0.0		0.004	False		,,,				2504	0.002				p.H29R		Atlas-SNP	.											.	ATP5SL	20	.	0			c.A86G						PASS	.	T	ARG/HIS,ARG/HIS,ARG/HIS,ARG/HIS,ARG/HIS,ARG/HIS	6,4400	11.4+/-27.6	0,6,2197	80.0	73.0	76.0		86,86,68,68,68,68	-1.9	0.0	19	dbSNP_98	76	95,8505	52.7+/-113.3	0,95,4205	yes	missense,missense,missense,missense,missense,missense	ATP5SL	NM_001167867.1,NM_001167868.1,NM_001167869.1,NM_001167870.1,NM_001167871.1,NM_018035.2	29,29,29,29,29,29	0,101,6402	CC,CT,TT		1.1047,0.1362,0.7766	benign,benign,benign,benign,benign,benign	29/264,29/192,23/186,23/159,23/231,23/258	41944270	101,12905	2203	4300	6503	SO:0001583	missense	55101	exon2			AGGCGATGGATGC	AK001103	CCDS33032.1, CCDS54269.1, CCDS54270.1, CCDS54271.1, CCDS59389.1, CCDS59390.1	19q13.2	2007-12-13				ENSG00000105341			25496	protein-coding gene	gene with protein product						12477932	Standard	NM_001167867		Approved	FLJ10241	uc002oqv.3	Q9NW81		ENST00000221943.9:c.68A>G	19.37:g.41944270T>C	ENSP00000221943:p.His23Arg	96.0	0.0	0		109.0	51.0	0.46789	NM_001167867	B4DDC0|B4DMZ4|B4DP55|B4DXE8|F5H4W7|K7EMF6|Q96D43	Missense_Mutation	SNP	ENST00000221943.9	37	CCDS33032.1	4	0.0018315018315018315	0	0.0	1	0.0027624309392265192	0	0.0	3	0.00395778364116095	T	4.961	0.178467	0.09443	0.001362	0.011047	ENSG00000105341	ENST00000221943;ENST00000438807;ENST00000417807;ENST00000301183;ENST00000507129	T;T;T;T	0.21191	3.29;2.07;3.26;2.02	3.28	-1.89	0.07689	.	0.628545	0.14348	N	0.325281	T	0.04998	0.0134	N	0.04705	-0.18	0.09310	N	1	B;B;B;B;B;B	0.09022	0.001;0.001;0.002;0.001;0.001;0.001	B;B;B;B;B;B	0.08055	0.002;0.001;0.001;0.003;0.003;0.003	T	0.40384	-0.9566	10	0.10377	T	0.69	-11.0354	8.2202	0.31537	0.0:0.6733:0.0:0.3267	rs2231939;rs2231939	29;29;23;23;23;29	B4DFT4;B4DDC0;Q9NW81-2;E9PDC6;Q9NW81;F5H4W7	.;.;.;.;AT5SL_HUMAN;.	R	23;23;29;29;99	ENSP00000221943:H23R;ENSP00000397413:H23R;ENSP00000403910:H29R;ENSP00000301183:H29R	ENSP00000221943:H23R	H	-	2	0	ATP5SL	46636110	0.101000	0.21875	0.002000	0.10522	0.018000	0.09664	0.329000	0.19698	-0.358000	0.08162	-0.250000	0.11733	CAT	T|0.996;C|0.004	0.004	strong		0.602	ATP5SL-007	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000460602.1	NM_018035	
PTGIR	5739	hgsc.bcm.edu	37	19	47126807	47126807	+	Missense_Mutation	SNP	G	G	T	rs138619017	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr19:47126807G>T	ENST00000291294.2	-	2	809	c.676C>A	c.(676-678)Cca>Aca	p.P226T	PTGIR_ENST00000597185.1_Intron|PTGIR_ENST00000598865.1_Missense_Mutation_p.P14T|PTGIR_ENST00000596260.1_Missense_Mutation_p.P226T|PTGIR_ENST00000594275.1_5'UTR	NM_000960.3	NP_000951.1	P43119	PI2R_HUMAN	prostaglandin I2 (prostacyclin) receptor (IP)	226					adenylate cyclase-activating G-protein coupled receptor signaling pathway (GO:0007189)|blood coagulation (GO:0007596)|cell-cell signaling (GO:0007267)|G-protein coupled receptor signaling pathway, coupled to cyclic nucleotide second messenger (GO:0007187)|negative regulation of platelet-derived growth factor receptor signaling pathway (GO:0010642)|negative regulation of smooth muscle cell proliferation (GO:0048662)|positive regulation of cAMP biosynthetic process (GO:0030819)|positive regulation of cAMP-mediated signaling (GO:0043950)|positive regulation of GTPase activity (GO:0043547)|response to lipopolysaccharide (GO:0032496)	cytosol (GO:0005829)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|guanyl-nucleotide exchange factor activity (GO:0005085)			endometrium(1)|kidney(1)|large_intestine(1)|lung(5)|ovary(1)|prostate(1)|skin(2)|urinary_tract(1)	13		Ovarian(192;0.0129)|all_neural(266;0.0459)|Breast(70;0.212)		OV - Ovarian serous cystadenocarcinoma(262;0.000327)|all cancers(93;0.000641)|Epithelial(262;0.0174)|GBM - Glioblastoma multiforme(486;0.0331)	Dinoprost Tromethamine(DB01160)|Epoprostenol(DB01240)|Iloprost(DB01088)|Treprostinil(DB00374)	CGCGGCCGTGGACCCAGAGAG	0.672													G|||	6	0.00119808	0.0	0.0029	5008	,	,		16491	0.0		0.003	False		,,,				2504	0.001				p.P226T		Atlas-SNP	.											.	PTGIR	31	.	0			c.C676A						PASS	.	G	THR/PRO	0,4362		0,0,2181	14.0	15.0	15.0		676	4.8	0.0	19	dbSNP_134	15	30,8496		0,30,4233	yes	missense	PTGIR	NM_000960.3	38	0,30,6414	TT,TG,GG		0.3519,0.0,0.2328	benign	226/387	47126807	30,12858	2181	4263	6444	SO:0001583	missense	5739	exon2			GCCGTGGACCCAG		CCDS12686.1	19q13.3	2012-08-08				ENSG00000160013		"""GPCR / Class A : Prostanoid receptors"""	9602	protein-coding gene	gene with protein product		600022				7759114	Standard	NM_000960		Approved	IP	uc002pex.3	P43119		ENST00000291294.2:c.676C>A	19.37:g.47126807G>T	ENSP00000291294:p.Pro226Thr	51.0	0.0	0		65.0	27.0	0.415385	NM_000960		Missense_Mutation	SNP	ENST00000291294.2	37	CCDS12686.1	3	0.0013736263736263737	0	0.0	1	0.0027624309392265192	0	0.0	2	0.002638522427440633	G	0.270	-0.993357	0.02145	0.0	0.003519	ENSG00000160013	ENST00000291294	T	0.71341	-0.56	4.75	4.75	0.60458	GPCR, rhodopsin-like superfamily (1);	0.212063	0.37669	N	0.001994	T	0.57755	0.2075	L	0.34521	1.04	0.23156	N	0.998204	B	0.06786	0.001	B	0.11329	0.006	T	0.31971	-0.9924	10	0.09590	T	0.72	-14.1054	15.2825	0.73797	0.0:0.0:1.0:0.0	.	226	P43119	PI2R_HUMAN	T	226	ENSP00000291294:P226T	ENSP00000291294:P226T	P	-	1	0	PTGIR	51818647	0.995000	0.38212	0.012000	0.15200	0.002000	0.02628	3.196000	0.51020	2.454000	0.82982	0.563000	0.77884	CCA	G|0.999;T|0.001	0.001	strong		0.672	PTGIR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466581.1		
ANKRD26	22852	hgsc.bcm.edu	37	10	27322306	27322306	+	Splice_Site	SNP	C	C	T	rs146819984	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr10:27322306C>T	ENST00000376087.4	-	25	3820	c.3655G>A	c.(3655-3657)Gtt>Att	p.V1219I	ANKRD26_ENST00000376070.3_Splice_Site_p.V776I|ANKRD26_ENST00000436985.2_Splice_Site_p.V1235I	NM_001256053.1|NM_014915.2	NP_001242982.1|NP_055730.2	Q9UPS8	ANR26_HUMAN	ankyrin repeat domain 26	1218			V -> L (in dbSNP:rs12572862).		glucose homeostasis (GO:0042593)|negative regulation of ERK1 and ERK2 cascade (GO:0070373)|negative regulation of fat cell differentiation (GO:0045599)|negative regulation of insulin receptor signaling pathway (GO:0046627)|negative regulation of multicellular organism growth (GO:0040015)|negative regulation of organ growth (GO:0046621)|regulation of fatty acid metabolic process (GO:0019217)|regulation of feeding behavior (GO:0060259)	actin filament (GO:0005884)|centrosome (GO:0005813)				breast(4)|cervix(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(14)|lung(30)|ovary(1)|pancreas(1)|prostate(3)|skin(2)|urinary_tract(2)	70						CTCACAACAACCTGATAAGAC	0.279													C|||	42	0.00838658	0.0045	0.0058	5008	,	,		14044	0.0		0.0129	False		,,,				2504	0.0194				p.V1219I		Atlas-SNP	.											.	ANKRD26	179	.	0			c.G3655A						PASS	.	C	ILE/VAL	8,3660		0,8,1826	136.0	120.0	125.0		3655	4.5	0.5	10	dbSNP_134	125	90,8082		1,88,3997	no	missense-near-splice	ANKRD26	NM_014915.2	29	1,96,5823	TT,TC,CC		1.1013,0.2181,0.8277	benign	1219/1711	27322306	98,11742	1834	4086	5920	SO:0001630	splice_region_variant	22852	exon25			CAACAACCTGATA	AB028997	CCDS41499.1	10p12.1	2014-09-17			ENSG00000107890	ENSG00000107890		"""Ankyrin repeat domain containing"""	29186	protein-coding gene	gene with protein product		610855	"""thrombocytopenia 2 (autosomal dominant)"""	THC2		10470851, 21211618	Standard	NM_014915		Approved	KIAA1074	uc009xku.1	Q9UPS8	OTTHUMG00000017851	ENST00000376087.4:c.3655-1G>A	10.37:g.27322306C>T		65.0	0.0	0		88.0	53.0	0.602273	NM_014915	A6NH29|Q2TAZ3|Q6ZR14|Q9H1Q1|Q9NSK9|Q9NTD5|Q9NW69	Missense_Mutation	SNP	ENST00000376087.4	37	CCDS41499.1	17	0.007783882783882784	2	0.0040650406504065045	4	0.011049723756906077	0	0.0	11	0.014511873350923483	C	11.08	1.534978	0.27475	0.002181	0.011013	ENSG00000107890	ENST00000376070;ENST00000376087;ENST00000436985	T;T;T	0.34667	3.83;1.35;1.36	5.41	4.51	0.55191	.	0.433404	0.18085	N	0.152181	T	0.26919	0.0659	M	0.62209	1.925	0.28550	N	0.911682	B;B;B	0.11235	0.003;0.001;0.004	B;B;B	0.10450	0.005;0.002;0.004	T	0.23154	-1.0196	10	0.48119	T	0.1	.	8.3454	0.32270	0.0:0.8224:0.0:0.1776	.	1219;1218;1235	Q9UPS8-3;Q9UPS8;A1L497	.;ANR26_HUMAN;.	I	776;1219;1235	ENSP00000365238:V776I;ENSP00000365255:V1219I;ENSP00000405112:V1235I	ENSP00000365238:V776I	V	-	1	0	ANKRD26	27362312	0.551000	0.26497	0.507000	0.27676	0.934000	0.57294	1.015000	0.29963	1.320000	0.45209	0.586000	0.80456	GTT	C|0.991;T|0.009	0.009	strong		0.279	ANKRD26-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047296.1		Missense_Mutation
ABCC12	94160	hgsc.bcm.edu	37	16	48151202	48151202	+	Silent	SNP	C	C	T			TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr16:48151202C>T	ENST00000311303.3	-	12	2100	c.1755G>A	c.(1753-1755)ctG>ctA	p.L585L	ABCC12_ENST00000416054.1_Intron|ABCC12_ENST00000448542.1_Silent_p.L585L	NM_033226.2	NP_150229.2	Q96J65	MRP9_HUMAN	ATP-binding cassette, sub-family C (CFTR/MRP), member 12	585	ABC transporter 1. {ECO:0000255|PROSITE- ProRule:PRU00434}.					integral component of membrane (GO:0016021)	ATP binding (GO:0005524)|ATPase activity, coupled to transmembrane movement of substances (GO:0042626)			NS(1)|breast(5)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(15)|liver(1)|lung(43)|ovary(2)|prostate(3)|skin(7)|urinary_tract(1)	90		all_cancers(37;0.0474)|all_lung(18;0.047)				GGAGGTTGCTCAGGTCCTTCT	0.582																																					p.L585L		Atlas-SNP	.											.	ABCC12	190	.	0			c.G1755A						PASS	.						82.0	75.0	77.0					16																	48151202		2201	4300	6501	SO:0001819	synonymous_variant	94160	exon12			GTTGCTCAGGTCC	AY040220	CCDS10730.1	16q12.1	2012-03-14			ENSG00000140798	ENSG00000140798		"""ATP binding cassette transporters / subfamily C"""	14640	protein-coding gene	gene with protein product		607041				11435397, 11483364	Standard	NM_033226		Approved	MRP9	uc002efc.1	Q96J65	OTTHUMG00000133143	ENST00000311303.3:c.1755G>A	16.37:g.48151202C>T		84.0	0.0	0		123.0	59.0	0.479675	NM_033226	Q49AL2|Q8TAF0|Q8TEY2	Silent	SNP	ENST00000311303.3	37	CCDS10730.1																																																																																			.	.	none		0.582	ABCC12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256837.1	NM_033226	
DBNDD1	79007	hgsc.bcm.edu	37	16	90076445	90076445	+	Intron	SNP	G	G	A			TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr16:90076445G>A	ENST00000002501.6	-	2	163				DBNDD1_ENST00000304733.3_Missense_Mutation_p.T4I|DBNDD1_ENST00000568838.1_Intron|DBNDD1_ENST00000392973.3_5'UTR	NM_001042610.1	NP_001036075.1	Q9H9R9	DBND1_HUMAN	dysbindin (dystrobrevin binding protein 1) domain containing 1							cytoplasm (GO:0005737)				kidney(1)|large_intestine(1)|lung(1)	3		all_cancers(9;4.44e-13)|Lung NSC(15;1.56e-06)|all_lung(18;2.18e-06)|all_neural(9;0.00118)|all_hematologic(23;0.0194)		BRCA - Breast invasive adenocarcinoma(80;0.0275)		ATTCTTCCAGGTTTCTCCCAT	0.473																																					p.T4I		Atlas-SNP	.											.	DBNDD1	9	.	0			c.C11T						PASS	.						91.0	86.0	87.0					16																	90076445		1848	4097	5945	SO:0001627	intron_variant	79007	exon1			TTCCAGGTTTCTC	AK090696	CCDS10991.2, CCDS42223.1, CCDS73931.1	16q24.3	2008-02-05			ENSG00000003249	ENSG00000003249			28455	protein-coding gene	gene with protein product						12477932	Standard	NM_001288708		Approved	MGC3101, FLJ12582	uc002fqe.1	Q9H9R9	OTTHUMG00000138984	ENST00000002501.6:c.32-607C>T	16.37:g.90076445G>A		152.0	0.0	0		156.0	71.0	0.455128	NM_024043	B4DQS3|Q69YT2|Q9BW25	Missense_Mutation	SNP	ENST00000002501.6	37	CCDS42223.1	.	.	.	.	.	.	.	.	.	.	G	11.39	1.624552	0.28889	.	.	ENSG00000003249	ENST00000304733	T	0.47177	0.85	1.92	0.867	0.19085	.	.	.	.	.	T	0.26557	0.0649	.	.	.	0.09310	N	1	B	0.30889	0.299	B	0.21546	0.035	T	0.12682	-1.0538	7	.	.	.	.	6.0374	0.19716	0.0:0.3279:0.6721:0.0	.	4	Q9H9R9-2	.	I	4	ENSP00000306407:T4I	.	T	-	2	0	DBNDD1	88603946	0.300000	0.24435	0.004000	0.12327	0.007000	0.05969	0.637000	0.24659	0.326000	0.23384	0.591000	0.81541	ACC	.	.	none		0.473	DBNDD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000272872.1	NM_024043	
BAIAP2L2	80115	hgsc.bcm.edu	37	22	38483174	38483174	+	Missense_Mutation	SNP	A	A	T	rs374089121|rs200930717|rs78489217	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr22:38483174A>T	ENST00000381669.3	-	11	1360	c.1216T>A	c.(1216-1218)Tcc>Acc	p.S406T	CTA-228A9.3_ENST00000609162.1_lincRNA	NM_025045.4	NP_079321.3	Q6UXY1	BI2L2_HUMAN	BAI1-associated protein 2-like 2	406					filopodium assembly (GO:0046847)|membrane organization (GO:0061024)|regulation of actin cytoskeleton organization (GO:0032956)|signal transduction (GO:0007165)	cell-cell contact zone (GO:0044291)|cytoplasmic vesicle (GO:0031410)|plasma membrane (GO:0005886)|vesicle membrane (GO:0012506)	phospholipid binding (GO:0005543)	p.M405_S406insTSM(1)		large_intestine(2)|lung(1)|ovary(2)|pancreas(1)|prostate(1)|stomach(1)	8	Melanoma(58;0.045)					gtcatgggggacatggaggtc	0.657													A|||	84	0.0167732	0.0076	0.0159	5008	,	,		13137	0.001		0.0278	False		,,,				2504	0.0348				p.S406T		Atlas-SNP	.											.	BAIAP2L2	39	.	1	Insertion - In frame(1)	ovary(1)	c.T1216A						PASS	.						32.0	38.0	36.0					22																	38483174		1925	4121	6046	SO:0001583	missense	80115	exon11			TGGGGGACATGGA	BC015619	CCDS43018.1	22q13.1	2005-02-09			ENSG00000128298	ENSG00000128298			26203	protein-coding gene	gene with protein product							Standard	NM_025045		Approved	FLJ22582	uc003auw.3	Q6UXY1	OTTHUMG00000151197	ENST00000381669.3:c.1216T>A	22.37:g.38483174A>T	ENSP00000371085:p.Ser406Thr	76.0	0.0	0		79.0	58.0	0.734177	NM_025045	B0QYE2|Q96BG7	Missense_Mutation	SNP	ENST00000381669.3	37	CCDS43018.1	254	0.1163003663003663	58	0.11788617886178862	58	0.16022099447513813	32	0.055944055944055944	106	0.13984168865435356	A	0.010	-1.753658	0.00663	.	.	ENSG00000128298	ENST00000381669;ENST00000402500;ENST00000428572	T;T	0.21543	2.0;2.0	0.235	-0.47	0.12131	.	2.310980	0.01612	N	0.022579	T	0.00039	0.0001	N	0.08118	0	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.27434	-1.0074	9	0.18276	T	0.48	.	.	.	.	.	406	Q6UXY1	BI2L2_HUMAN	T	406;406;97	ENSP00000371085:S406T;ENSP00000410074:S97T	ENSP00000371085:S406T	S	-	1	0	BAIAP2L2	36813120	0.121000	0.22262	0.001000	0.08648	0.001000	0.01503	0.410000	0.21098	-2.434000	0.00554	-2.582000	0.00168	TCC	A|0.886;T|0.114	0.114	strong		0.657	BAIAP2L2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000321727.1	NM_025045	
HYOU1	10525	hgsc.bcm.edu	37	11	118925935	118925935	+	Silent	SNP	G	G	A	rs511134	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr11:118925935G>A	ENST00000404233.3	-	5	505	c.381C>T	c.(379-381)ttC>ttT	p.F127F	HYOU1_ENST00000525859.1_Silent_p.F127F|HYOU1_ENST00000543287.1_Silent_p.F40F|HYOU1_ENST00000529972.1_Silent_p.F127F	NM_001130991.1|NM_006389.3	NP_001124463.1|NP_006380.1	Q9Y4L1	HYOU1_HUMAN	hypoxia up-regulated 1	127					activation of signaling protein activity involved in unfolded protein response (GO:0006987)|cellular protein metabolic process (GO:0044267)|endoplasmic reticulum unfolded protein response (GO:0030968)|response to ischemia (GO:0002931)|response to stress (GO:0006950)	endocytic vesicle lumen (GO:0071682)|endoplasmic reticulum (GO:0005783)|endoplasmic reticulum lumen (GO:0005788)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|membrane (GO:0016020)	ATP binding (GO:0005524)			NS(1)|breast(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(9)|lung(10)|prostate(1)|skin(2)	33	all_hematologic(175;0.0839)	Medulloblastoma(222;0.0425)|Breast(348;0.052)|all_neural(223;0.112)|all_hematologic(192;0.207)		BRCA - Breast invasive adenocarcinoma(274;7.78e-05)		TCTGTGGGTCGAAAGTCAGCT	0.582													G|||	232	0.0463259	0.1104	0.0216	5008	,	,		20549	0.0089		0.0089	False		,,,				2504	0.0542				p.F127F		Atlas-SNP	.											.	HYOU1	88	.	0			c.C381T						PASS	.	G	,	367,4033	188.8+/-215.1	20,327,1853	118.0	113.0	114.0		381,381	-1.2	0.6	11	dbSNP_83	114	104,8486	56.8+/-118.0	2,100,4193	no	coding-synonymous,coding-synonymous	HYOU1	NM_001130991.1,NM_006389.3	,	22,427,6046	AA,AG,GG		1.2107,8.3409,3.6259	,	127/1000,127/1000	118925935	471,12519	2200	4295	6495	SO:0001819	synonymous_variant	10525	exon5			TGGGTCGAAAGTC	U65785	CCDS8408.1	11q23.1-q23.3	2011-09-02			ENSG00000149428	ENSG00000149428		"""Heat shock proteins / HSP70"""	16931	protein-coding gene	gene with protein product	"""glucose-regulated protein 170"""	601746				9020069, 10037731	Standard	XM_005271390		Approved	ORP150, HSP12A, Grp170	uc001pux.3	Q9Y4L1	OTTHUMG00000166354	ENST00000404233.3:c.381C>T	11.37:g.118925935G>A		126.0	0.0	0		121.0	63.0	0.520661	NM_006389	A8C1Z0|B7Z909|Q2I204|Q53H25	Silent	SNP	ENST00000404233.3	37	CCDS8408.1																																																																																			G|0.962;A|0.038	0.038	strong		0.582	HYOU1-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000389353.1	NM_006389	
KDR	3791	hgsc.bcm.edu	37	4	55972946	55972946	+	Missense_Mutation	SNP	A	A	G	rs34231037	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr4:55972946A>G	ENST00000263923.4	-	11	1739	c.1444T>C	c.(1444-1446)Tgt>Cgt	p.C482R		NM_002253.2	NP_002244.1	P35968	VGFR2_HUMAN	kinase insert domain receptor (a type III receptor tyrosine kinase)	482	Ig-like C2-type 5.		C -> R (in HCI susceptibility; expression of FLT1 in hemangioma endothelial cells is markedly reduced and KDR activity is increased compared to controls; low FLT1 expression in hemangioma cells is caused by reduced activity of a pathway involving ITGB1, ANTXR1, KDR and NFATC2IP; the mutation predicts to result in loss-of-function and disruption of the normal association of these molecules; dbSNP:rs34231037). {ECO:0000269|PubMed:17344846, ECO:0000269|PubMed:18931684}.		angiogenesis (GO:0001525)|branching morphogenesis of an epithelial tube (GO:0048754)|calcium ion homeostasis (GO:0055074)|calcium-mediated signaling using intracellular calcium source (GO:0035584)|cell fate commitment (GO:0045165)|cell maturation (GO:0048469)|cell migration involved in sprouting angiogenesis (GO:0002042)|cellular response to vascular endothelial growth factor stimulus (GO:0035924)|embryonic hemopoiesis (GO:0035162)|endothelial cell differentiation (GO:0045446)|endothelium development (GO:0003158)|extracellular matrix organization (GO:0030198)|lung alveolus development (GO:0048286)|lymph vessel development (GO:0001945)|negative regulation of apoptotic process (GO:0043066)|negative regulation of endothelial cell apoptotic process (GO:2000352)|ovarian follicle development (GO:0001541)|peptidyl-tyrosine autophosphorylation (GO:0038083)|peptidyl-tyrosine phosphorylation (GO:0018108)|positive regulation of angiogenesis (GO:0045766)|positive regulation of cell migration (GO:0030335)|positive regulation of cell proliferation (GO:0008284)|positive regulation of endothelial cell migration (GO:0010595)|positive regulation of endothelial cell proliferation (GO:0001938)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of focal adhesion assembly (GO:0051894)|positive regulation of MAPK cascade (GO:0043410)|positive regulation of mesenchymal cell proliferation (GO:0002053)|positive regulation of nitric-oxide synthase biosynthetic process (GO:0051770)|positive regulation of phosphatidylinositol 3-kinase signaling (GO:0014068)|positive regulation of positive chemotaxis (GO:0050927)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of vasculogenesis (GO:2001214)|protein autophosphorylation (GO:0046777)|regulation of cell shape (GO:0008360)|signal transduction by phosphorylation (GO:0023014)|surfactant homeostasis (GO:0043129)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)|vascular endothelial growth factor receptor signaling pathway (GO:0048010)|vascular endothelial growth factor signaling pathway (GO:0038084)|vasculogenesis (GO:0001570)|viral process (GO:0016032)	cell junction (GO:0030054)|cytoplasmic vesicle (GO:0031410)|early endosome (GO:0005769)|endosome (GO:0005768)|external side of plasma membrane (GO:0009897)|extracellular region (GO:0005576)|Golgi apparatus (GO:0005794)|integral component of plasma membrane (GO:0005887)|membrane raft (GO:0045121)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|sorting endosome (GO:0097443)	ATP binding (GO:0005524)|growth factor binding (GO:0019838)|Hsp90 protein binding (GO:0051879)|integrin binding (GO:0005178)|protein tyrosine kinase activity (GO:0004713)|receptor signaling protein tyrosine kinase activity (GO:0004716)|transmembrane receptor protein tyrosine kinase activity (GO:0004714)|vascular endothelial growth factor binding (GO:0038085)|vascular endothelial growth factor-activated receptor activity (GO:0005021)			NS(1)|breast(3)|central_nervous_system(4)|endometrium(2)|haematopoietic_and_lymphoid_tissue(6)|kidney(8)|large_intestine(16)|lung(71)|ovary(2)|prostate(2)|skin(10)|soft_tissue(4)|stomach(3)|upper_aerodigestive_tract(1)|urinary_tract(2)	135	all_cancers(7;0.0255)|all_lung(4;0.00175)|Lung NSC(11;0.00384)|all_epithelial(27;0.034)|Glioma(25;0.08)|all_neural(26;0.101)		Epithelial(7;0.189)		Axitinib(DB06626)|Cabozantinib(DB08875)|Pazopanib(DB06589)|Ponatinib(DB08901)|Regorafenib(DB08896)|Sorafenib(DB00398)|Sunitinib(DB01268)	CATTCTTCACAAGGGTATGGG	0.333			Mis		"""NSCLC, angiosarcoma"""					TSP Lung(20;0.16)			A|||	45	0.00898562	0.0015	0.0144	5008	,	,		18156	0.0		0.0308	False		,,,				2504	0.002				p.C482R		Atlas-SNP	.		Dom	yes		4	4q11-q12	3791	vascular endothelial growth factor receptor 2		E	KDR,middle_lobe,carcinoma,+2,1	KDR	307	1	0			c.T1444C						PASS	.	A	ARG/CYS	23,4383	31.7+/-61.6	0,23,2180	81.0	85.0	83.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	1444	5.7	0.9	4	dbSNP_126	83	242,8358	97.2+/-158.9	4,234,4062	yes	missense	KDR	NM_002253.2	180	4,257,6242	GG,GA,AA		2.814,0.522,2.0375	probably-damaging	482/1357	55972946	265,12741	2203	4300	6503	SO:0001583	missense	3791	exon11			CTTCACAAGGGTA	AF035121	CCDS3497.1	4q11-q12	2013-01-29			ENSG00000128052	ENSG00000128052	2.7.10.1	"""CD molecules"", ""Immunoglobulin superfamily / V-set domain containing"", ""Immunoglobulin superfamily / I-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	6307	protein-coding gene	gene with protein product		191306				1417831	Standard	NM_002253		Approved	FLK1, VEGFR, VEGFR2, CD309	uc003has.3	P35968	OTTHUMG00000128734	ENST00000263923.4:c.1444T>C	4.37:g.55972946A>G	ENSP00000263923:p.Cys482Arg	210.0	0.0	0		224.0	100.0	0.446429	NM_002253	A2RRS0|B5A925|C5IFA0|O60723|Q14178	Missense_Mutation	SNP	ENST00000263923.4	37	CCDS3497.1	30	0.013736263736263736	0	0.0	6	0.016574585635359115	0	0.0	24	0.0316622691292876	A	13.84	2.356951	0.41801	0.00522	0.02814	ENSG00000128052	ENST00000263923	T	0.76839	-1.05	5.67	5.67	0.87782	Immunoglobulin subtype (1);Immunoglobulin-like (1);	0.000000	0.85682	D	0.000000	T	0.75436	0.3849	M	0.81497	2.545	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.91635	0.999;0.999	T	0.82382	-0.0485	10	0.40728	T	0.16	.	15.905	0.79419	1.0:0.0:0.0:0.0	rs34231037	482;482	P35968-2;P35968	.;VGFR2_HUMAN	R	482	ENSP00000263923:C482R	ENSP00000263923:C482R	C	-	1	0	KDR	55667703	1.000000	0.71417	0.927000	0.36925	0.088000	0.18126	6.349000	0.73013	2.150000	0.67090	0.533000	0.62120	TGT	A|0.980;G|0.020	0.020	strong		0.333	KDR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250645.1		
CHD6	84181	hgsc.bcm.edu	37	20	40049450	40049450	+	Missense_Mutation	SNP	T	T	A	rs140143834	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr20:40049450T>A	ENST00000373233.3	-	31	6002	c.5825A>T	c.(5824-5826)cAc>cTc	p.H1942L		NM_032221.3	NP_115597.3	Q8TD26	CHD6_HUMAN	chromodomain helicase DNA binding protein 6	1942					ATP catabolic process (GO:0006200)|chromatin modification (GO:0016568)|positive regulation of transcription from RNA polymerase II promoter in response to oxidative stress (GO:0036091)|transcription, DNA-templated (GO:0006351)	nucleoplasm (GO:0005654)	ATP binding (GO:0005524)|ATP-dependent helicase activity (GO:0008026)|chromatin binding (GO:0003682)|DNA binding (GO:0003677)|DNA-dependent ATPase activity (GO:0008094)|transcription cofactor binding (GO:0001221)			breast(8)|central_nervous_system(2)|cervix(2)|endometrium(5)|kidney(4)|large_intestine(24)|lung(53)|ovary(8)|prostate(5)|skin(8)|stomach(1)|urinary_tract(9)	129		Myeloproliferative disorder(115;0.00425)				CCTCTCCATGTGTTTGCAGTG	0.478													T|||	13	0.00259585	0.0008	0.0029	5008	,	,		19525	0.0		0.007	False		,,,				2504	0.0031				p.H1942L		Atlas-SNP	.											.	CHD6	312	.	0			c.A5825T						PASS	.	T	LEU/HIS	3,4403	6.2+/-15.9	0,3,2200	138.0	131.0	134.0		5825	3.6	1.0	20	dbSNP_134	134	59,8541	37.8+/-93.5	0,59,4241	yes	missense	CHD6	NM_032221.3	99	0,62,6441	AA,AT,TT		0.686,0.0681,0.4767	benign	1942/2716	40049450	62,12944	2203	4300	6503	SO:0001583	missense	84181	exon31			TCCATGTGTTTGC	AF525085	CCDS13317.1	20q12	2003-03-07			ENSG00000124177	ENSG00000124177			19057	protein-coding gene	gene with protein product						11889561	Standard	NM_032221		Approved	KIAA1335, FLJ22369, dJ620E11.1, CHD5, RIGB	uc002xka.1	Q8TD26	OTTHUMG00000032487	ENST00000373233.3:c.5825A>T	20.37:g.40049450T>A	ENSP00000362330:p.His1942Leu	244.0	0.0	0		263.0	136.0	0.51711	NM_032221	Q5JYQ0|Q5TGZ9|Q5TH00|Q5TH01|Q8IZR2|Q8WTY0|Q9H4H6|Q9H6D4|Q9NTT7|Q9P2L1	Missense_Mutation	SNP	ENST00000373233.3	37	CCDS13317.1	8	0.003663003663003663	1	0.0020325203252032522	1	0.0027624309392265192	0	0.0	6	0.0079155672823219	T	12.05	1.822032	0.32237	6.81E-4	0.00686	ENSG00000124177	ENST00000373233	D	0.85339	-1.97	5.86	3.56	0.40772	.	0.195101	0.36101	N	0.002783	T	0.72293	0.3442	L	0.51422	1.61	0.80722	D	1	B	0.06786	0.001	B	0.06405	0.002	T	0.67952	-0.5537	10	0.26408	T	0.33	-16.7152	8.1319	0.31033	0.1166:0.0:0.1688:0.7146	.	1942	Q8TD26	CHD6_HUMAN	L	1942	ENSP00000362330:H1942L	ENSP00000362330:H1942L	H	-	2	0	CHD6	39482864	0.810000	0.29049	0.998000	0.56505	0.808000	0.45660	1.583000	0.36579	1.005000	0.39183	0.533000	0.62120	CAC	T|0.995;A|0.005	0.005	strong		0.478	CHD6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079270.1		
APBA3	9546	hgsc.bcm.edu	37	19	3752601	3752601	+	Missense_Mutation	SNP	G	G	A	rs147130540	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr19:3752601G>A	ENST00000316757.3	-	8	1500	c.1300C>T	c.(1300-1302)Cgc>Tgc	p.R434C	AC005954.3_ENST00000591962.1_RNA|AC005954.4_ENST00000586503.1_RNA	NM_004886.3	NP_004877.1	O96018	APBA3_HUMAN	amyloid beta (A4) precursor protein-binding, family A, member 3	434	PDZ 1. {ECO:0000255|PROSITE- ProRule:PRU00143}.				in utero embryonic development (GO:0001701)|negative regulation of catalytic activity (GO:0043086)|protein transport (GO:0015031)|regulation of gene expression (GO:0010468)|synaptic transmission (GO:0007268)	perinuclear region of cytoplasm (GO:0048471)	beta-amyloid binding (GO:0001540)|enzyme binding (GO:0019899)|enzyme inhibitor activity (GO:0004857)			endometrium(1)|large_intestine(1)|skin(1)	3		Hepatocellular(1079;0.137)		UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|BRCA - Breast invasive adenocarcinoma(158;0.00467)|STAD - Stomach adenocarcinoma(1328;0.18)		GCCCCCGAGCGCTCAGCAGGC	0.751													G|||	57	0.0113818	0.0083	0.0288	5008	,	,		13216	0.0		0.0199	False		,,,				2504	0.0061				p.R434C		Atlas-SNP	.											.	APBA3	28	.	0			c.C1300T						PASS	.	G	CYS/ARG	29,4221		0,29,2096	6.0	9.0	8.0		1300	4.2	0.9	19	dbSNP_134	8	160,8140		1,158,3991	yes	missense	APBA3	NM_004886.3	180	1,187,6087	AA,AG,GG		1.9277,0.6824,1.506	probably-damaging	434/576	3752601	189,12361	2125	4150	6275	SO:0001583	missense	9546	exon8			CCGAGCGCTCAGC	AB021638	CCDS12110.1	19p13.3	2008-07-18	2008-07-18			ENSG00000011132			580	protein-coding gene	gene with protein product	"""X11-like 2"""	604262				10049767	Standard	NM_004886		Approved	X11L2, mint3	uc002lyp.1	O96018		ENST00000316757.3:c.1300C>T	19.37:g.3752601G>A	ENSP00000315136:p.Arg434Cys	3.0	0.0	0		12.0	9.0	0.75	NM_004886	O60483|Q9UPZ2	Missense_Mutation	SNP	ENST00000316757.3	37	CCDS12110.1	28	0.01282051282051282	6	0.012195121951219513	8	0.022099447513812154	0	0.0	14	0.018469656992084433	G	14.60	2.583092	0.46006	0.006824	0.019277	ENSG00000011132	ENST00000316757	T	0.29655	1.56	4.21	4.21	0.49690	PDZ/DHR/GLGF (4);	0.000000	0.64402	D	0.000001	T	0.49660	0.1570	H	0.95574	3.69	0.80722	D	1	D	0.89917	1.0	D	0.85130	0.997	T	0.72030	-0.4413	10	0.87932	D	0	.	12.3996	0.55405	0.0:0.0:0.8316:0.1684	.	434	O96018	APBA3_HUMAN	C	434	ENSP00000315136:R434C	ENSP00000315136:R434C	R	-	1	0	APBA3	3703601	1.000000	0.71417	0.911000	0.35937	0.297000	0.27493	1.807000	0.38902	1.894000	0.54839	0.462000	0.41574	CGC	G|0.987;A|0.013	0.013	strong		0.751	APBA3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000453634.2		
COL22A1	169044	hgsc.bcm.edu	37	8	139712355	139712355	+	Splice_Site	SNP	G	G	A	rs77613350	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr8:139712355G>A	ENST00000303045.6	-	32	3038	c.2592C>T	c.(2590-2592)ccC>ccT	p.P864P	COL22A1_ENST00000435777.1_Splice_Site_p.P864P|COL22A1_ENST00000341807.4_5'UTR	NM_152888.1	NP_690848.1	Q8NFW1	COMA1_HUMAN	collagen, type XXII, alpha 1	864	Gly-rich.|Pro-rich.				extracellular matrix organization (GO:0030198)	collagen trimer (GO:0005581)|endoplasmic reticulum lumen (GO:0005788)|extracellular region (GO:0005576)|proteinaceous extracellular matrix (GO:0005578)				breast(1)|endometrium(10)|haematopoietic_and_lymphoid_tissue(2)|kidney(14)|large_intestine(29)|lung(107)|ovary(13)|pancreas(1)|prostate(3)|skin(12)|upper_aerodigestive_tract(15)|urinary_tract(4)	211	all_epithelial(106;1.55e-12)|Lung NSC(106;1.67e-05)|all_lung(105;3.39e-05)|Ovarian(258;0.00672)|Acute lymphoblastic leukemia(118;0.155)		BRCA - Breast invasive adenocarcinoma(115;0.0517)			TACTACTTACGGGCATCCGTG	0.552										HNSCC(7;0.00092)			G|||	168	0.0335463	0.0787	0.0187	5008	,	,		17017	0.0278		0.0189	False		,,,				2504	0.0041				p.P864P		Atlas-SNP	.											.	COL22A1	390	.	0			c.C2592T						PASS	.	G		268,4138	151.4+/-185.3	5,258,1940	80.0	69.0	73.0		2592	-8.3	0.0	8	dbSNP_131	73	138,8462	68.0+/-130.5	1,136,4163	yes	coding-synonymous-near-splice	COL22A1	NM_152888.1		6,394,6103	AA,AG,GG		1.6047,6.0826,3.1216		864/1627	139712355	406,12600	2203	4300	6503	SO:0001630	splice_region_variant	169044	exon32			ACTTACGGGCATC	AF406780	CCDS6376.1	8q24.3	2013-01-16			ENSG00000169436	ENSG00000169436		"""Collagens"""	22989	protein-coding gene	gene with protein product		610026					Standard	NM_152888		Approved		uc003yvd.3	Q8NFW1	OTTHUMG00000150035	ENST00000303045.6:c.2592+1C>T	8.37:g.139712355G>A		52.0	0.0	0		56.0	26.0	0.464286	NM_152888	B7ZMH0|C9K0G4|Q8IVT9	Silent	SNP	ENST00000303045.6	37	CCDS6376.1																																																																																			G|0.967;A|0.033	0.033	strong		0.552	COL22A1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000315905.2	XM_291257	Silent
PCSK4	54760	hgsc.bcm.edu	37	19	1487059	1487059	+	Silent	SNP	G	G	T			TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr19:1487059G>T	ENST00000300954.5	-	8	922	c.861C>A	c.(859-861)cgC>cgA	p.R287R	PCSK4_ENST00000587784.1_5'Flank|CTB-25B13.6_ENST00000585643.1_RNA	NM_017573.3	NP_060043.2			proprotein convertase subtilisin/kexin type 4											cervix(2)|endometrium(2)|kidney(1)|lung(6)|ovary(2)|skin(1)|upper_aerodigestive_tract(1)	15		Acute lymphoblastic leukemia(61;3.02e-13)|all_hematologic(61;4.32e-09)|Hepatocellular(1079;0.137)		UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|OV - Ovarian serous cystadenocarcinoma(105;1.09e-113)|Epithelial(107;3.79e-112)|all cancers(105;1.67e-104)|BRCA - Breast invasive adenocarcinoma(158;0.00136)|STAD - Stomach adenocarcinoma(1328;0.18)		CCAGCCCGCCGCGGCCCTGGG	0.697																																					p.R287R		Atlas-SNP	.											.	PCSK4	44	.	0			c.C861A						PASS	.						28.0	29.0	29.0					19																	1487059		2199	4296	6495	SO:0001819	synonymous_variant	54760	exon8			CCCGCCGCGGCCC	AK057235	CCDS12069.2	19p13.3	2008-02-05			ENSG00000115257	ENSG00000115257			8746	protein-coding gene	gene with protein product		600487				7782070	Standard	XM_005259586		Approved	PC4, SPC5, DKFZp434B217, MGC34749	uc002ltb.1	Q6UW60	OTTHUMG00000128541	ENST00000300954.5:c.861C>A	19.37:g.1487059G>T		17.0	0.0	0		21.0	15.0	0.714286	NM_017573		Silent	SNP	ENST00000300954.5	37	CCDS12069.2																																																																																			.	.	none		0.697	PCSK4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000449703.1	NM_017573	
OR51I2	390064	hgsc.bcm.edu	37	11	5475505	5475505	+	Missense_Mutation	SNP	C	C	T	rs75620804	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr11:5475505C>T	ENST00000341449.2	+	1	868	c.787C>T	c.(787-789)Cgc>Tgc	p.R263C	HBE1_ENST00000380237.1_Intron|AC104389.28_ENST00000415970.1_RNA|HBG2_ENST00000380252.1_Intron|HBG2_ENST00000380259.2_Intron	NM_001004754.2	NP_001004754.1	Q9H344	O51I2_HUMAN	olfactory receptor, family 51, subfamily I, member 2	263			R -> H (in dbSNP:rs11037502).		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)			endometrium(3)|kidney(1)|large_intestine(7)|lung(8)|ovary(2)|prostate(1)|skin(6)|upper_aerodigestive_tract(1)	29		Medulloblastoma(188;0.0075)|all_neural(188;0.0572)|Breast(177;0.0675)		Epithelial(150;1.09e-10)|BRCA - Breast invasive adenocarcinoma(625;0.135)		CACAGTGCACCGCTTTGGGAA	0.483													C|||	38	0.00758786	0.0	0.0101	5008	,	,		22942	0.001		0.0239	False		,,,				2504	0.0061				p.R263C		Atlas-SNP	.											.	OR51I2	76	.	0			c.C787T						PASS	.	C	CYS/ARG	18,4384	25.3+/-52.1	0,18,2183	221.0	187.0	198.0		787	4.7	1.0	11	dbSNP_131	198	242,8352	96.6+/-158.3	2,238,4057	yes	missense	OR51I2	NM_001004754.2	180	2,256,6240	TT,TC,CC		2.8159,0.4089,2.0006	probably-damaging	263/313	5475505	260,12736	2201	4297	6498	SO:0001583	missense	390064	exon1			GTGCACCGCTTTG	BK004381	CCDS31383.1	11p15.4	2012-08-09			ENSG00000187918	ENSG00000187918		"""GPCR / Class A : Olfactory receptors"""	15201	protein-coding gene	gene with protein product							Standard	NM_001004754		Approved		uc010qzf.2	Q9H344	OTTHUMG00000066902	ENST00000341449.2:c.787C>T	11.37:g.5475505C>T	ENSP00000341987:p.Arg263Cys	207.0	0.0	0		229.0	113.0	0.49345	NM_001004754	Q6IF81	Missense_Mutation	SNP	ENST00000341449.2	37	CCDS31383.1	30	0.013736263736263736	0	0.0	7	0.019337016574585635	1	0.0017482517482517483	22	0.029023746701846966	C	11.07	1.529354	0.27387	0.004089	0.028159	ENSG00000187918	ENST00000341449	T	0.37411	1.2	5.58	4.68	0.58851	GPCR, rhodopsin-like superfamily (1);	0.096182	0.46758	N	0.000280	T	0.38054	0.1026	M	0.91354	3.2	0.40176	D	0.977235	D	0.89917	1.0	D	0.87578	0.998	T	0.61520	-0.7046	10	0.72032	D	0.01	.	5.4856	0.16747	0.1603:0.6806:0.0:0.1591	.	263	Q9H344	O51I2_HUMAN	C	263	ENSP00000341987:R263C	ENSP00000341987:R263C	R	+	1	0	OR51I2	5432081	0.002000	0.14202	0.985000	0.45067	0.048000	0.14542	0.094000	0.15107	1.610000	0.50200	-0.126000	0.14955	CGC	C|0.983;T|0.017	0.017	strong		0.483	OR51I2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000143385.1	NM_001004754	
PIK3C2G	5288	hgsc.bcm.edu	37	12	18719972	18719972	+	Missense_Mutation	SNP	T	T	G	rs12099555	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr12:18719972T>G	ENST00000266497.5	+	27	3907	c.3869T>G	c.(3868-3870)gTa>gGa	p.V1290G	PIK3C2G_ENST00000433979.1_Missense_Mutation_p.V1290G|PIK3C2G_ENST00000538779.1_Missense_Mutation_p.V1331G			O75747	P3C2G_HUMAN	phosphatidylinositol-4-phosphate 3-kinase, catalytic subunit type 2 gamma	1290	PX. {ECO:0000255|PROSITE- ProRule:PRU00147}.		V -> G (in dbSNP:rs12099555).		chemotaxis (GO:0006935)|phosphatidylinositol biosynthetic process (GO:0006661)|phosphatidylinositol-3-phosphate biosynthetic process (GO:0036092)|phosphatidylinositol-mediated signaling (GO:0048015)|phospholipid metabolic process (GO:0006644)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)|phosphatidylinositol 3-kinase complex (GO:0005942)|plasma membrane (GO:0005886)	1-phosphatidylinositol-3-kinase activity (GO:0016303)|1-phosphatidylinositol-4-phosphate 3-kinase activity (GO:0035005)|ATP binding (GO:0005524)|phosphatidylinositol binding (GO:0035091)|phosphatidylinositol phosphate kinase activity (GO:0016307)			breast(5)|central_nervous_system(6)|endometrium(2)|kidney(4)|large_intestine(8)|lung(31)|ovary(2)|prostate(1)|skin(2)|stomach(4)|upper_aerodigestive_tract(1)	66		Hepatocellular(102;0.194)				ATATTAAATGTATCACATGAA	0.289													G|||	438	0.0874601	0.2943	0.036	5008	,	,		16621	0.0		0.0229	False		,,,				2504	0.001				p.V1290G		Atlas-SNP	.											.	PIK3C2G	315	.	0			c.T3869G						PASS	.	G	GLY/VAL	924,2712		118,688,1012	76.0	74.0	75.0		3869	4.2	0.7	12	dbSNP_120	75	143,7987		4,135,3926	yes	missense	PIK3C2G	NM_004570.4	109	122,823,4938	GG,GT,TT		1.7589,25.4125,9.0685	benign	1290/1446	18719972	1067,10699	1818	4065	5883	SO:0001583	missense	5288	exon28			TAAATGTATCACA	AJ000008	CCDS44839.1, CCDS73452.1	12p12	2012-07-13	2012-07-13		ENSG00000139144	ENSG00000139144	2.7.1.154		8973	protein-coding gene	gene with protein product		609001	"""phosphoinositide-3-kinase, class 2, gamma polypeptide"""			9878262	Standard	XM_005253393		Approved		uc001rdt.3	O75747	OTTHUMG00000168841	ENST00000266497.5:c.3869T>G	12.37:g.18719972T>G	ENSP00000266497:p.Val1290Gly	124.0	0.0	0		117.0	55.0	0.470085	NM_004570	A1L3U0	Missense_Mutation	SNP	ENST00000266497.5	37	CCDS44839.1	164	0.07509157509157509	135	0.27439024390243905	12	0.03314917127071823	0	0.0	17	0.022427440633245383	G	0.026	-1.369431	0.01225	0.254125	0.017589	ENSG00000139144	ENST00000433979;ENST00000266497;ENST00000538779	T;T;T	0.39056	1.1;1.1;1.1	4.18	4.18	0.49190	Phox homologous domain (5);	0.274240	0.29424	N	0.012196	T	0.00012	0.0000	N	0.01048	-1.04	0.32557	P	0.531612	B;B;B	0.02656	0.0;0.0;0.0	B;B;B	0.01281	0.0;0.0;0.0	T	0.25257	-1.0137	9	0.10111	T	0.7	-12.3348	11.8575	0.52446	0.0:0.0:0.8243:0.1756	rs12099555;rs60425948;rs12099555	1330;1331;1290	B7ZLY6;F5H369;O75747	.;.;P3C2G_HUMAN	G	1290;1290;1331	ENSP00000404845:V1290G;ENSP00000266497:V1290G;ENSP00000445381:V1331G	ENSP00000266497:V1290G	V	+	2	0	PIK3C2G	18611239	1.000000	0.71417	0.661000	0.29709	0.096000	0.18686	2.898000	0.48672	1.370000	0.46153	-0.121000	0.15023	GTA	T|0.912;G|0.088	0.088	strong		0.289	PIK3C2G-002	KNOWN	NAGNAG_splice_site|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000401316.1	NM_004570	
CORT	1325	hgsc.bcm.edu	37	1	10511534	10511534	+	Missense_Mutation	SNP	G	G	T	rs201163116		TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr1:10511534G>T	ENST00000377049.3	+	2	705	c.200G>T	c.(199-201)gGa>gTa	p.G67V	APITD1-CORT_ENST00000470413.2_3'UTR|APITD1_ENST00000602787.1_Missense_Mutation_p.G126V|APITD1_ENST00000602296.1_3'UTR|APITD1-CORT_ENST00000465026.1_3'UTR|APITD1-CORT_ENST00000400900.2_Missense_Mutation_p.G126V|CORT_ENST00000320498.4_Missense_Mutation_p.G117V	NM_001302.4	NP_001293.3	O00230	CORT_HUMAN	cortistatin	67					adenylate cyclase-inhibiting G-protein coupled receptor signaling pathway (GO:0007193)|synaptic transmission (GO:0007268)	extracellular space (GO:0005615)	G-protein coupled receptor binding (GO:0001664)|neuropeptide hormone activity (GO:0005184)			breast(1)|endometrium(1)|stomach(1)	3	Ovarian(185;0.203)	all_lung(284;1.31e-05)|Lung NSC(185;2.19e-05)|Renal(390;0.000147)|Breast(348;0.00093)|Colorectal(325;0.00205)|Hepatocellular(190;0.00913)|Ovarian(437;0.0228)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0228)|Colorectal(212;3.12e-07)|COAD - Colon adenocarcinoma(227;7.07e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000293)|Kidney(185;0.000722)|KIRC - Kidney renal clear cell carcinoma(229;0.00258)|STAD - Stomach adenocarcinoma(132;0.0165)|READ - Rectum adenocarcinoma(331;0.0487)		CCCCTCATAGGAGAGGAAGCC	0.627																																					p.G126V		Atlas-SNP	.											.	.	.	.	0			c.G377T						PASS	.						26.0	32.0	30.0					1																	10511534		2200	4298	6498	SO:0001583	missense	100526739	exon5			TCATAGGAGAGGA	AF013252	CCDS117.1, CCDS117.2	1p36.22	2013-02-25			ENSG00000241563	ENSG00000241563		"""Endogenous ligands"""	2257	protein-coding gene	gene with protein product	"""prepro-cortistatin"""	602784				9205124	Standard	NM_001302		Approved	MGC32686		O00230	OTTHUMG00000001906	ENST00000377049.3:c.200G>T	1.37:g.10511534G>T	ENSP00000366248:p.Gly67Val	175.0	0.0	0		191.0	82.0	0.429319	NM_198544	Q5T6G0|Q6UX11	Missense_Mutation	SNP	ENST00000377049.3	37	CCDS117.2	.	.	.	.	.	.	.	.	.	.	G	16.62	3.173907	0.57692	.	.	ENSG00000175279;ENSG00000251503;ENSG00000241563;ENSG00000241563	ENST00000556104;ENST00000400900;ENST00000377049;ENST00000320498	.	.	.	5.39	2.33	0.28932	.	0.777718	0.12758	N	0.441634	T	0.24586	0.0596	L	0.50333	1.59	0.09310	N	0.999994	P;B	0.37781	0.608;0.019	B;B	0.31290	0.127;0.015	T	0.13098	-1.0522	9	0.23302	T	0.38	-15.679	4.4404	0.11572	0.0813:0.2856:0.4862:0.1469	.	67;126	O00230;Q8N2Z9-2	CORT_HUMAN;.	V	126;126;67;117	.	ENSP00000383692:G126V	G	+	2	0	APITD1-CORT;APITD1;CORT	10434121	0.005000	0.15991	0.006000	0.13384	0.188000	0.23474	0.349000	0.20055	0.196000	0.20367	0.591000	0.81541	GGA	G|0.999;T|0.001	0.001	weak		0.627	CORT-001	KNOWN	upstream_ATG|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000005410.3	NM_001302	
ZNF222	7673	hgsc.bcm.edu	37	19	44536397	44536397	+	Silent	SNP	T	T	C	rs151037918	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr19:44536397T>C	ENST00000187879.8	+	4	732	c.570T>C	c.(568-570)acT>acC	p.T190T	ZNF223_ENST00000591793.1_Intron|ZNF222_ENST00000391960.3_Silent_p.T230T	NM_013360.2	NP_037492.2	Q9UK12	ZN222_HUMAN	zinc finger protein 222	190					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)|large_intestine(7)|lung(6)|ovary(3)|prostate(1)|skin(1)|urinary_tract(1)	20		Prostate(69;0.0435)				GTCTGCAAACTCATCAAAGAG	0.428													T|||	12	0.00239617	0.0008	0.0029	5008	,	,		21542	0.0		0.008	False		,,,				2504	0.001				p.T230T		Atlas-SNP	.											.	ZNF222	90	.	0			c.T690C						PASS	.	T	,	9,4397	15.5+/-35.6	0,9,2194	135.0	138.0	137.0		690,570	0.3	0.0	19	dbSNP_134	137	59,8541	36.9+/-92.0	0,59,4241	no	coding-synonymous,coding-synonymous	ZNF222	NM_001129996.1,NM_013360.2	,	0,68,6435	CC,CT,TT		0.686,0.2043,0.5228	,	230/492,190/452	44536397	68,12938	2203	4300	6503	SO:0001819	synonymous_variant	7673	exon4			GCAAACTCATCAA	AF187988	CCDS33045.1, CCDS46098.1	19q13.2	2013-01-08				ENSG00000159885		"""Zinc fingers, C2H2-type"", ""-"""	13015	protein-coding gene	gene with protein product							Standard	NM_013360		Approved		uc002oye.3	Q9UK12		ENST00000187879.8:c.570T>C	19.37:g.44536397T>C		143.0	0.0	0		124.0	62.0	0.5	NM_001129996	G5E9B9|Q8N6G7|Q9P1U5	Silent	SNP	ENST00000187879.8	37	CCDS33045.1																																																																																			T|0.996;C|0.004	0.004	strong		0.428	ZNF222-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000460465.2		
KIAA1755	85449	hgsc.bcm.edu	37	20	36869741	36869741	+	Silent	SNP	G	G	A			TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr20:36869741G>A	ENST00000279024.4	-	3	1063	c.792C>T	c.(790-792)gaC>gaT	p.D264D		NM_001029864.1	NP_001025035.1	Q5JYT7	K1755_HUMAN	KIAA1755	264										breast(2)|endometrium(3)|kidney(1)|large_intestine(5)|lung(31)|ovary(5)|pancreas(2)|skin(4)|stomach(1)	54		Myeloproliferative disorder(115;0.00874)				TGACCACCTCGTCCATCCTGA	0.572																																					p.D264D		Atlas-SNP	.											KIAA1755,NS,malignant_melanoma,-2,2	KIAA1755	145	2	0			c.C792T						scavenged	.						138.0	122.0	127.0					20																	36869741		2203	4300	6503	SO:0001819	synonymous_variant	85449	exon3			CACCTCGTCCATC	AB051542	CCDS33467.1	20q11.23	2007-12-07			ENSG00000149633	ENSG00000149633			29372	protein-coding gene	gene with protein product						11214970	Standard	NM_001029864		Approved	RP5-1054A22.3	uc002xhy.1	Q5JYT7	OTTHUMG00000032436	ENST00000279024.4:c.792C>T	20.37:g.36869741G>A		162.0	1.0	0.00617284		185.0	89.0	0.481081	NM_001029864	Q9C0A8	Silent	SNP	ENST00000279024.4	37	CCDS33467.1																																																																																			.	.	none		0.572	KIAA1755-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000079144.3	NM_001029864	
PCDHGA7	56108	hgsc.bcm.edu	37	5	140763339	140763339	+	Missense_Mutation	SNP	G	G	A	rs187406135	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr5:140763339G>A	ENST00000518325.1	+	1	873	c.873G>A	c.(871-873)atG>atA	p.M291I	PCDHGA6_ENST00000517434.1_Intron|PCDHGB1_ENST00000523390.1_Intron|PCDHGB3_ENST00000576222.1_Intron|PCDHGA4_ENST00000571252.1_Intron|PCDHGA3_ENST00000253812.6_Intron|PCDHGA1_ENST00000517417.1_Intron|PCDHGB2_ENST00000522605.1_Intron|PCDHGA5_ENST00000518069.1_Intron|PCDHGA2_ENST00000394576.2_Intron	NM_018920.2	NP_061743.1	Q9Y5G6	PCDG7_HUMAN	protocadherin gamma subfamily A, 7	291	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(1)|endometrium(8)|kidney(4)|large_intestine(10)|lung(19)|ovary(1)|skin(1)|stomach(3)|urinary_tract(1)	49			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			TTCCAAAGATGTTTCATCTGA	0.413													.|||	2	0.000399361	0.0	0.0029	5008	,	,		22196	0.0		0.0	False		,,,				2504	0.0				p.M291I		Atlas-SNP	.											.	PCDHGA7	130	.	0			c.G873A						PASS	.						56.0	56.0	56.0					5																	140763339		1866	4110	5976	SO:0001583	missense	56108	exon1			AAAGATGTTTCAT	AF152514	CCDS54927.1, CCDS75336.1	5q31	2010-01-26				ENSG00000253537		"""Cadherins / Protocadherins : Clustered"""	8705	other	protocadherin		606294				10380929	Standard	NM_018920		Approved	PCDH-GAMMA-A7		Q9Y5G6		ENST00000518325.1:c.873G>A	5.37:g.140763339G>A	ENSP00000430024:p.Met291Ile	104.0	0.0	0		103.0	41.0	0.398058	NM_032087	B2RN87|Q9Y5D0	Missense_Mutation	SNP	ENST00000518325.1	37	CCDS54927.1	1	4.578754578754579E-4	0	0.0	1	0.0027624309392265192	0	0.0	0	0.0	.	0.004	-2.295701	0.00245	.	.	ENSG00000253537	ENST00000518325	T	0.51574	0.7	5.15	-3.98	0.04082	Cadherin (4);Cadherin-like (1);	.	.	.	.	T	0.12646	0.0307	N	0.01048	-1.04	0.09310	N	0.999997	B;B	0.02656	0.0;0.0	B;B	0.06405	0.002;0.001	T	0.25363	-1.0134	9	0.13108	T	0.6	.	2.6961	0.05135	0.189:0.2096:0.4053:0.1961	.	291;291	Q9Y5G6;Q9Y5G6-2	PCDG7_HUMAN;.	I	291	ENSP00000430024:M291I	ENSP00000430024:M291I	M	+	3	0	PCDHGA7	140743523	0.000000	0.05858	0.081000	0.20488	0.030000	0.12068	-1.451000	0.02387	-0.495000	0.06659	-0.302000	0.09304	ATG	G|1.000;A|0.000	0.000	strong		0.413	PCDHGA7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000374744.1	NM_018920	
DHX33	56919	hgsc.bcm.edu	37	17	5347788	5347788	+	Missense_Mutation	SNP	G	G	A	rs75426953	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr17:5347788G>A	ENST00000225296.3	-	12	2061	c.1861C>T	c.(1861-1863)Cgc>Tgc	p.R621C	DHX33_ENST00000433302.3_Missense_Mutation_p.R397C	NM_001199699.1|NM_020162.3	NP_001186628.1|NP_064547.2	Q9H6R0	DHX33_HUMAN	DEAH (Asp-Glu-Ala-His) box polypeptide 33	621					positive regulation of transcription from RNA polymerase I promoter (GO:0045943)	nucleolus (GO:0005730)|nucleoplasm (GO:0005654)	ATP binding (GO:0005524)|ATP-dependent helicase activity (GO:0008026)|poly(A) RNA binding (GO:0044822)|rDNA binding (GO:0000182)			breast(1)|cervix(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(2)|lung(2)|ovary(1)|pancreas(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	17						AGGCAGCGGCGGACACTCTCC	0.607													G|||	35	0.00698882	0.0008	0.0086	5008	,	,		19061	0.001		0.0239	False		,,,				2504	0.0031				p.R621C		Atlas-SNP	.											DHX33,NS,carcinoma,0,1	DHX33	41	1	0			c.C1861T						PASS	.	G	CYS/ARG,CYS/ARG	24,4382	30.8+/-60.4	1,22,2180	74.0	69.0	70.0		1342,1861	4.6	1.0	17	dbSNP_131	70	203,8397	88.4+/-150.7	2,199,4099	yes	missense,missense	DHX33	NM_001199699.1,NM_020162.3	180,180	3,221,6279	AA,AG,GG		2.3605,0.5447,1.7453	probably-damaging,probably-damaging	448/535,621/708	5347788	227,12779	2203	4300	6503	SO:0001583	missense	56919	exon12			AGCGGCGGACACT	AL359945	CCDS11072.1	17p13	2003-06-13	2003-06-13	2003-06-13	ENSG00000005100	ENSG00000005100		"""DEAH-boxes"""	16718	protein-coding gene	gene with protein product		614405	"""DEAD/H (Asp-Glu-Ala-Asp/His) box polypeptide 33"""	DDX33			Standard	NM_020162		Approved	FLJ21972, DKFZp762F2011	uc002gca.3	Q9H6R0	OTTHUMG00000102041	ENST00000225296.3:c.1861C>T	17.37:g.5347788G>A	ENSP00000225296:p.Arg621Cys	97.0	0.0	0		125.0	65.0	0.52	NM_020162	B4DHF9|Q4G149|Q5CZ73|Q9H5M9	Missense_Mutation	SNP	ENST00000225296.3	37	CCDS11072.1	24	0.01098901098901099	1	0.0020325203252032522	5	0.013812154696132596	1	0.0017482517482517483	17	0.022427440633245383	G	25.8	4.678553	0.88542	0.005447	0.023605	ENSG00000005100	ENST00000225296;ENST00000433302	T;T	0.02890	4.12;4.12	4.59	4.59	0.56863	Domain of unknown function DUF1605 (1);	0.000000	0.85682	D	0.000000	T	0.08846	0.0219	M	0.85373	2.75	0.80722	D	1	D;P	0.89917	1.0;0.626	D;B	0.81914	0.995;0.287	T	0.00235	-1.1892	10	0.66056	D	0.02	.	16.9197	0.86161	0.0:0.0:1.0:0.0	.	397;621	Q05BE5;Q9H6R0	.;DHX33_HUMAN	C	621;397	ENSP00000225296:R621C;ENSP00000413779:R397C	ENSP00000225296:R621C	R	-	1	0	DHX33	5288512	1.000000	0.71417	1.000000	0.80357	0.931000	0.56810	9.073000	0.93992	2.548000	0.85928	0.561000	0.74099	CGC	A|0.014;C|0.000;G|0.986	0.014	strong		0.607	DHX33-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000219826.2	NM_020162	
PSKH2	85481	hgsc.bcm.edu	37	8	87060927	87060927	+	Missense_Mutation	SNP	G	G	A			TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr8:87060927G>A	ENST00000276616.2	-	3	996	c.922C>T	c.(922-924)Cgc>Tgc	p.R308C		NM_033126.1	NP_149117.1	Q96QS6	KPSH2_HUMAN	protein serine kinase H2	308	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.						ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)			NS(1)|breast(1)|kidney(11)|large_intestine(2)|lung(26)|ovary(1)|prostate(1)|stomach(3)|urinary_tract(1)	47			STAD - Stomach adenocarcinoma(118;0.129)			GCTGACATGCGATGACCAGCC	0.478																																					p.R308C		Atlas-SNP	.											PSKH2,caecum,carcinoma,+1,2	PSKH2	79	2	0			c.C922T						PASS	.						75.0	82.0	80.0					8																	87060927		2203	4300	6503	SO:0001583	missense	85481	exon3			ACATGCGATGACC	AY037806	CCDS6240.1	8q21.13	2004-06-03				ENSG00000147613			18997	protein-coding gene	gene with protein product							Standard	NM_033126		Approved		uc011lfy.2	Q96QS6		ENST00000276616.2:c.922C>T	8.37:g.87060927G>A	ENSP00000276616:p.Arg308Cys	131.0	0.0	0		127.0	61.0	0.480315	NM_033126	A0AV22	Missense_Mutation	SNP	ENST00000276616.2	37	CCDS6240.1	.	.	.	.	.	.	.	.	.	.	G	21.6	4.178342	0.78564	.	.	ENSG00000147613	ENST00000276616	T	0.80738	-1.41	4.94	4.05	0.47172	Serine/threonine-protein kinase-like domain (1);Serine/threonine-protein kinase, catalytic  domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	.	.	.	.	D	0.92938	0.7753	H	0.98646	4.29	0.46260	D	0.998955	D	0.89917	1.0	D	0.97110	1.0	D	0.93418	0.6774	9	0.87932	D	0	.	10.2011	0.43084	0.1009:0.0:0.8991:0.0	.	308	Q96QS6	KPSH2_HUMAN	C	308	ENSP00000276616:R308C	ENSP00000276616:R308C	R	-	1	0	PSKH2	87130043	1.000000	0.71417	0.998000	0.56505	0.986000	0.74619	3.946000	0.56644	1.034000	0.39945	0.555000	0.69702	CGC	.	.	none		0.478	PSKH2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000374628.1	NM_033126	
CTAGE5	4253	hgsc.bcm.edu	37	14	39818076	39818076	+	Missense_Mutation	SNP	A	A	G	rs61742363	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr14:39818076A>G	ENST00000280083.3	+	23	2457	c.2143A>G	c.(2143-2145)Aga>Gga	p.R715G	RP11-407N17.3_ENST00000553728.1_Missense_Mutation_p.R1250G|CTAGE5_ENST00000556148.1_Missense_Mutation_p.R640G|CTAGE5_ENST00000396165.4_Missense_Mutation_p.R686G|CTAGE5_ENST00000396158.2_Missense_Mutation_p.R720G|CTAGE5_ENST00000553352.1_Missense_Mutation_p.R686G|CTAGE5_ENST00000348007.3_Missense_Mutation_p.R672G|RP11-407N17.3_ENST00000603904.1_Missense_Mutation_p.R686G|CTAGE5_ENST00000341502.5_Missense_Mutation_p.R715G|CTAGE5_ENST00000341749.3_Missense_Mutation_p.R703G|CTAGE5_ENST00000557038.1_Missense_Mutation_p.R635G|CTAGE5_ENST00000553383.1_3'UTR			O15320	CTGE5_HUMAN	CTAGE family, member 5	715	Pro-rich.				positive regulation of catalytic activity (GO:0043085)	membrane (GO:0016020)	enzyme activator activity (GO:0008047)		CTAGE5/SIP1(2)	breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(5)|lung(11)|prostate(1)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(2)	28	Hepatocellular(127;0.213)		LUAD - Lung adenocarcinoma(48;0.000565)|Lung(238;0.000711)	GBM - Glioblastoma multiforme(112;0.0475)		ATTCTTGAGAAGAGGACCTCC	0.532													A|||	27	0.00539137	0.0	0.0173	5008	,	,		14299	0.0		0.0149	False		,,,				2504	0.0				p.R720G		Atlas-SNP	.											.	CTAGE5	75	.	0			c.A2158G						PASS	.	A	GLY/ARG,GLY/ARG,GLY/ARG,GLY/ARG	16,4390	22.3+/-47.3	0,16,2187	125.0	130.0	129.0		2143,2107,2014,2056	3.1	1.0	14	dbSNP_129	129	156,8444	73.5+/-136.2	0,156,4144	yes	missense,missense,missense,missense	CTAGE5	NM_005930.3,NM_203354.2,NM_203355.2,NM_203356.2	125,125,125,125	0,172,6331	GG,GA,AA		1.814,0.3631,1.3225	probably-damaging,probably-damaging,probably-damaging,probably-damaging	715/805,703/793,672/762,686/776	39818076	172,12834	2203	4300	6503	SO:0001583	missense	4253	exon23			TTGAGAAGAGGAC	U94780	CCDS9673.1, CCDS9674.1, CCDS9675.1, CCDS9676.1, CCDS58316.1, CCDS58317.1	14q21.1	2009-09-11	2004-08-24	2004-08-26	ENSG00000150527	ENSG00000150527			7057	protein-coding gene	gene with protein product		602132	"""meningioma expressed antigen 6 (coiled-coil proline-rich)"""	MGEA, MGEA6		9356211, 11149944	Standard	NM_203355		Approved	MEA6, cTAGE-5A, cTAGE-5B, cTAGE-5C, cTAGE-5D, MGEA11	uc001wvi.4	O15320	OTTHUMG00000140258	ENST00000280083.3:c.2143A>G	14.37:g.39818076A>G	ENSP00000280083:p.Arg715Gly	197.0	0.0	0		169.0	98.0	0.579882	NM_001247989	B3KRA6|B4DQS6|D3DSA6|G3XAC5|O00169|Q6MZN2|Q6P2R8|Q86TF6|Q8IX92|Q8IX93	Missense_Mutation	SNP	ENST00000280083.3	37	CCDS9674.1	22	0.010073260073260074	0	0.0	8	0.022099447513812154	0	0.0	14	0.018469656992084433	A	14.78	2.638501	0.47153	0.003631	0.01814	ENSG00000258941;ENSG00000150527;ENSG00000150527;ENSG00000150527;ENSG00000150527;ENSG00000150527;ENSG00000150527;ENSG00000150527;ENSG00000150527;ENSG00000150527	ENST00000553728;ENST00000341749;ENST00000557038;ENST00000396165;ENST00000341502;ENST00000396158;ENST00000280083;ENST00000556148;ENST00000348007;ENST00000553352	T;T;T;T;T;T;T;T;T;T	0.16324	2.35;2.4;2.37;2.36;2.91;2.63;2.64;2.36;3.17;2.36	5.64	3.12	0.35913	.	0.000000	0.37623	N	0.002009	T	0.12178	0.0296	M	0.83312	2.635	0.29744	N	0.83689	B;B;B;B;B	0.28713	0.22;0.181;0.22;0.181;0.22	B;B;B;B;B	0.29267	0.1;0.074;0.1;0.074;0.1	T	0.06588	-1.0818	9	.	.	.	.	11.6343	0.51194	0.6083:0.3917:0.0:0.0	rs61742363	720;672;715;643;703	O15320-5;O15320-2;O15320;O15320-7;G3XAC5	.;.;CTGE5_HUMAN;.;.	G	1250;703;635;686;715;720;715;640;672;686	ENSP00000452252:R1250G;ENSP00000343897:R703G;ENSP00000450869:R635G;ENSP00000379468:R686G;ENSP00000339286:R715G;ENSP00000379462:R720G;ENSP00000280083:R715G;ENSP00000452562:R640G;ENSP00000343912:R672G;ENSP00000450449:R686G	.	R	+	1	2	CTAGE5;RP11-407N17.3	38887827	1.000000	0.71417	0.992000	0.48379	0.895000	0.52256	0.816000	0.27267	0.940000	0.37473	0.533000	0.62120	AGA	A|0.988;G|0.012	0.012	strong		0.532	CTAGE5-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000276771.2	NM_005930	
TMEM99	147184	hgsc.bcm.edu	37	17	38991100	38991100	+	Missense_Mutation	SNP	A	A	G	rs199620244		TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr17:38991100A>G	ENST00000301665.3	+	3	636	c.332A>G	c.(331-333)aAc>aGc	p.N111S		NM_001195386.1|NM_001195387.1|NM_145274.3	NP_001182315.1|NP_001182316.1|NP_660317.2	Q8N816	TMM99_HUMAN	transmembrane protein 99	111						integral component of membrane (GO:0016021)				cervix(1)|large_intestine(1)|lung(5)|skin(2)|urinary_tract(1)	10		Breast(137;0.000301)				CTCTTCAACAACTGGACTGGA	0.502																																					p.N111S		Atlas-SNP	.											.	TMEM99	21	.	0			c.A332G						PASS	.	A	SER/ASN,SER/ASN,SER/ASN	0,3846		0,0,1923	141.0	139.0	140.0		332,332,332	-0.5	0.0	17		140	3,8281		0,3,4139	yes	missense,missense,missense	TMEM99	NM_001195386.1,NM_001195387.1,NM_145274.3	46,46,46	0,3,6062	GG,GA,AA		0.0362,0.0,0.0247	benign,benign,benign	111/259,111/259,111/259	38991100	3,12127	1923	4142	6065	SO:0001583	missense	147184	exon3			TCAACAACTGGAC	AK097454	CCDS42319.1	17q21.2	2008-11-06			ENSG00000167920	ENSG00000167920			28305	protein-coding gene	gene with protein product						12477932	Standard	NM_001195386		Approved	MGC21518	uc021txc.1	Q8N816	OTTHUMG00000133579	ENST00000301665.3:c.332A>G	17.37:g.38991100A>G	ENSP00000301665:p.Asn111Ser	140.0	0.0	0		170.0	76.0	0.447059	NM_001195386	B4DQ34|Q96BP9	Missense_Mutation	SNP	ENST00000301665.3	37	CCDS42319.1	.	.	.	.	.	.	.	.	.	.	A	2.048	-0.418367	0.04766	0.0	3.62E-4	ENSG00000167920	ENST00000436612;ENST00000301665	T;T	0.27402	1.67;1.67	0.235	-0.47	0.12131	.	.	.	.	.	T	0.13329	0.0323	N	0.08118	0	0.09310	N	1	B	0.19073	0.033	B	0.15870	0.014	T	0.21280	-1.0250	8	0.87932	D	0	.	.	.	.	.	111	Q8N816	TMM99_HUMAN	S	111	ENSP00000390036:N111S;ENSP00000301665:N111S	ENSP00000301665:N111S	N	+	2	0	TMEM99	36244626	0.001000	0.12720	0.002000	0.10522	0.002000	0.02628	-1.620000	0.02046	-0.738000	0.04817	-0.736000	0.03550	AAC	.	.	weak		0.502	TMEM99-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257681.1	NM_145274	
ATP8A1	10396	hgsc.bcm.edu	37	4	42576646	42576646	+	Missense_Mutation	SNP	C	C	T	rs61755862	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr4:42576646C>T	ENST00000381668.5	-	14	1516	c.1285G>A	c.(1285-1287)Gtt>Att	p.V429I	ATP8A1_ENST00000264449.10_Missense_Mutation_p.V429I	NM_006095.2	NP_006086.1	Q9Y2Q0	AT8A1_HUMAN	ATPase, aminophospholipid transporter (APLT), class I, type 8A, member 1	429					cation transmembrane transport (GO:0098655)|ion transmembrane transport (GO:0034220)|phospholipid translocation (GO:0045332)|transmembrane transport (GO:0055085)	cytoplasmic vesicle (GO:0031410)|endoplasmic reticulum (GO:0005783)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|cation-transporting ATPase activity (GO:0019829)|magnesium ion binding (GO:0000287)|phospholipid-translocating ATPase activity (GO:0004012)			NS(1)|central_nervous_system(3)|cervix(1)|endometrium(3)|kidney(2)|large_intestine(13)|lung(18)|pancreas(1)|skin(5)|upper_aerodigestive_tract(1)|urinary_tract(3)	51					Phosphatidylserine(DB00144)	CCATAAGCAACTCCCGCTATG	0.343													C|||	126	0.0251597	0.0923	0.0058	5008	,	,		17551	0.0		0.0	False		,,,				2504	0.0				p.V429I		Atlas-SNP	.											ATP8A1_ENST00000264449,NS,carcinoma,+1,2	ATP8A1	206	2	0			c.G1285A						PASS	.	C	ILE/VAL,ILE/VAL	297,4109	159.6+/-192.1	13,271,1919	55.0	56.0	56.0		1285,1285	3.4	1.0	4	dbSNP_129	56	2,8596	1.2+/-3.3	0,2,4297	yes	missense,missense	ATP8A1	NM_001105529.1,NM_006095.2	29,29	13,273,6216	TT,TC,CC		0.0233,6.7408,2.2993	benign,benign	429/1150,429/1165	42576646	299,12705	2203	4299	6502	SO:0001583	missense	10396	exon14			AAGCAACTCCCGC	AF067820	CCDS3466.1, CCDS47049.1	4p13	2010-04-20	2007-09-19		ENSG00000124406	ENSG00000124406		"""ATPases / P-type"""	13531	protein-coding gene	gene with protein product		609542	"""ATPase, aminophospholipid transporter (APLT), Class I, type 8A, member 1"""			10198212, 9548971	Standard	NM_006095		Approved	ATPIA	uc003gwr.2	Q9Y2Q0	OTTHUMG00000099403	ENST00000381668.5:c.1285G>A	4.37:g.42576646C>T	ENSP00000371084:p.Val429Ile	198.0	0.0	0		218.0	110.0	0.504587	NM_001105529	Q32M35|Q32M36|Q4W5J7|Q4W5P2	Missense_Mutation	SNP	ENST00000381668.5	37	CCDS3466.1	40	0.018315018315018316	38	0.07723577235772358	2	0.0055248618784530384	0	0.0	0	0.0	C	4.770	0.143139	0.09083	0.067408	2.33E-4	ENSG00000124406	ENST00000381668;ENST00000264449	T;T	0.74947	-0.89;-0.89	5.27	3.4	0.38934	ATPase, cation-transporting, domain N (1);HAD-like domain (1);ATPase, P-type, cytoplasmic domain N (1);	0.068109	0.64402	D	0.000017	T	0.04137	0.0115	N	0.11845	0.185	0.80722	D	1	B;B;B	0.02656	0.0;0.0;0.0	B;B;B	0.08055	0.001;0.003;0.001	T	0.03325	-1.1048	10	0.09338	T	0.73	.	6.9831	0.24713	0.0:0.6446:0.0:0.3554	.	429;429;429	B4DII6;Q32M35;Q9Y2Q0	.;.;AT8A1_HUMAN	I	429	ENSP00000371084:V429I;ENSP00000264449:V429I	ENSP00000264449:V429I	V	-	1	0	ATP8A1	42271403	0.999000	0.42202	1.000000	0.80357	0.986000	0.74619	0.657000	0.24963	1.459000	0.47892	0.591000	0.81541	GTT	C|0.975;T|0.025	0.025	strong		0.343	ATP8A1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000216861.2	NM_006095	
PMM2	5373	hgsc.bcm.edu	37	16	8906914	8906914	+	Missense_Mutation	SNP	A	A	C	rs34258285	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr16:8906914A>C	ENST00000268261.4	+	7	656	c.590A>C	c.(589-591)gAa>gCa	p.E197A	PMM2_ENST00000537352.1_Missense_Mutation_p.E72A|PMM2_ENST00000569958.1_Missense_Mutation_p.E106A|PMM2_ENST00000566983.1_Missense_Mutation_p.E170A|PMM2_ENST00000539622.1_Missense_Mutation_p.E114A	NM_000303.2	NP_000294.1	O15305	PMM2_HUMAN	phosphomannomutase 2	197			E -> A (in CDG1A; dbSNP:rs34258285). {ECO:0000269|PubMed:11058895, ECO:0000269|PubMed:15844218}.		cellular protein metabolic process (GO:0044267)|dolichol-linked oligosaccharide biosynthetic process (GO:0006488)|GDP-mannose biosynthetic process (GO:0009298)|mannose biosynthetic process (GO:0019307)|post-translational protein modification (GO:0043687)|protein glycosylation (GO:0006486)|protein N-linked glycosylation via asparagine (GO:0018279)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|neuronal cell body (GO:0043025)	phosphomannomutase activity (GO:0004615)			breast(3)|cervix(1)|endometrium(2)|large_intestine(1)|ovary(1)|skin(1)	9						CGACATGTGGAAAATGACGGT	0.463													A|||	45	0.00898562	0.0015	0.0216	5008	,	,		21288	0.0		0.0249	False		,,,				2504	0.0031				p.E197A	Esophageal Squamous(154;1308 1842 2827 29799 42829)	Atlas-SNP	.											.	PMM2	25	.	0			c.A590C	GRCh37	CM002843	PMM2	M	rs34258285	PASS	.	A	ALA/GLU	21,4373	28.1+/-56.4	0,21,2176	148.0	131.0	137.0		590	4.9	0.9	16	dbSNP_126	137	219,8381	92.1+/-154.2	6,207,4087	yes	missense	PMM2	NM_000303.2	107	6,228,6263	CC,CA,AA		2.5465,0.4779,1.847	benign	197/247	8906914	240,12754	2197	4300	6497	SO:0001583	missense	5373	exon7			ATGTGGAAAATGA	BC008310	CCDS10536.1	16p13	2012-09-06			ENSG00000140650	ENSG00000140650	5.3.1.8		9115	protein-coding gene	gene with protein product	"""phosphomannose isomerase 1"""	601785		CDG1		9140401	Standard	NM_000303		Approved	CDGS, CDG1a, PMI, PMI1	uc002czf.4	O15305	OTTHUMG00000129697	ENST00000268261.4:c.590A>C	16.37:g.8906914A>C	ENSP00000268261:p.Glu197Ala	122.0	0.0	0		131.0	56.0	0.427481	NM_000303	A8K672|B7Z6R0|D3DUF3	Missense_Mutation	SNP	ENST00000268261.4	37	CCDS10536.1	28	0.01282051282051282	0	0.0	10	0.027624309392265192	0	0.0	18	0.023746701846965697	A	9.835	1.189414	0.21954	0.004779	0.025465	ENSG00000140650	ENST00000268261;ENST00000539622;ENST00000537352	D;D;D	0.98474	-4.95;-4.95;-4.95	4.89	4.89	0.63831	HAD-like domain (2);	0.049443	0.85682	D	0.000000	D	0.90113	0.6911	L	0.52364	1.645	0.58432	D	0.999991	B;B;B	0.16603	0.018;0.0;0.002	B;B;B	0.19148	0.021;0.008;0.024	D	0.89308	0.3631	10	0.18710	T	0.47	.	10.2623	0.43434	0.8343:0.1657:0.0:0.0	rs34258285	50;114;197	B7Z922;F5H0W0;O15305	.;.;PMM2_HUMAN	A	197;114;72	ENSP00000268261:E197A;ENSP00000445879:E114A;ENSP00000438359:E72A	ENSP00000268261:E197A	E	+	2	0	PMM2	8814415	0.971000	0.33674	0.909000	0.35828	0.101000	0.19017	2.489000	0.45285	1.839000	0.53478	0.533000	0.62120	GAA	A|0.984;C|0.016	0.016	strong		0.463	PMM2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251904.1	NM_000303	
MAP4K3	8491	hgsc.bcm.edu	37	2	39494378	39494378	+	Missense_Mutation	SNP	C	C	T			TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr2:39494378C>T	ENST00000263881.3	-	27	2308	c.1984G>A	c.(1984-1986)Gta>Ata	p.V662I	MAP4K3_ENST00000536018.1_Missense_Mutation_p.V215I|MAP4K3_ENST00000341681.5_Missense_Mutation_p.V641I|MAP4K3_ENST00000437545.1_Missense_Mutation_p.V578I	NM_003618.3	NP_003609.2	Q8IVH8	M4K3_HUMAN	mitogen-activated protein kinase kinase kinase kinase 3	662	CNH. {ECO:0000255|PROSITE- ProRule:PRU00795}.				intracellular signal transduction (GO:0035556)|JNK cascade (GO:0007254)|protein phosphorylation (GO:0006468)|response to tumor necrosis factor (GO:0034612)|response to UV (GO:0009411)		ATP binding (GO:0005524)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)|small GTPase regulator activity (GO:0005083)			NS(1)|endometrium(4)|kidney(2)|large_intestine(8)|lung(17)|ovary(4)|pancreas(1)|prostate(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	44		all_hematologic(82;0.211)				TTTGCTGATACAGAAAATTTC	0.348																																					p.V662I		Atlas-SNP	.											MAP4K3,right_lower_lobe,carcinoma,0,1	MAP4K3	109	1	0			c.G1984A						scavenged	.						109.0	110.0	110.0					2																	39494378		2203	4300	6503	SO:0001583	missense	8491	exon27			CTGATACAGAAAA	AF000145	CCDS1803.1, CCDS58707.1	2p22.3	2011-06-09			ENSG00000011566	ENSG00000011566		"""Mitogen-activated protein kinase cascade / Kinase kinase kinase kinases"""	6865	protein-coding gene	gene with protein product		604921		RAB8IPL1		9275185	Standard	NM_003618		Approved	GLK, MAPKKKK3	uc002rro.4	Q8IVH8	OTTHUMG00000102127	ENST00000263881.3:c.1984G>A	2.37:g.39494378C>T	ENSP00000263881:p.Val662Ile	53.0	0.0	0		71.0	3.0	0.0422535	NM_003618	Q6IQ39|Q8IVH7|Q9UDM5|Q9Y6R5	Missense_Mutation	SNP	ENST00000263881.3	37	CCDS1803.1	.	.	.	.	.	.	.	.	.	.	C	17.37	3.371764	0.61624	.	.	ENSG00000011566	ENST00000263881;ENST00000437545;ENST00000341681;ENST00000536018	T;T;T;T	0.04862	3.54;3.54;3.54;3.54	5.42	5.42	0.78866	Citron-like (3);	0.000000	0.85682	D	0.000000	T	0.10680	0.0261	L	0.33485	1.01	0.58432	D	0.999997	P;P	0.39903	0.694;0.624	P;P	0.46718	0.452;0.525	T	0.32214	-0.9915	10	0.21540	T	0.41	.	19.6002	0.95559	0.0:1.0:0.0:0.0	.	641;662	Q8IVH8-3;Q8IVH8	.;M4K3_HUMAN	I	662;578;641;215	ENSP00000263881:V662I;ENSP00000416958:V578I;ENSP00000345434:V641I;ENSP00000440580:V215I	ENSP00000263881:V662I	V	-	1	0	MAP4K3	39347882	0.999000	0.42202	1.000000	0.80357	0.983000	0.72400	3.286000	0.51724	2.691000	0.91804	0.655000	0.94253	GTA	.	.	none		0.348	MAP4K3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000219966.2	NM_003618	
F5	2153	hgsc.bcm.edu	37	1	169526019	169526019	+	Missense_Mutation	SNP	C	C	T			TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr1:169526019C>T	ENST00000367797.3	-	6	1018	c.817G>A	c.(817-819)Ggc>Agc	p.G273S	F5_ENST00000367796.3_Missense_Mutation_p.G273S|F5_ENST00000546081.1_Missense_Mutation_p.G136S	NM_000130.4	NP_000121	P12259	FA5_HUMAN	coagulation factor V (proaccelerin, labile factor)	273	F5/8 type A 1.|Plastocyanin-like 2.				blood circulation (GO:0008015)|blood coagulation (GO:0007596)|cell adhesion (GO:0007155)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|membrane (GO:0016020)|plasma membrane (GO:0005886)|platelet alpha granule lumen (GO:0031093)|vesicle (GO:0031982)	copper ion binding (GO:0005507)			NS(1)|breast(4)|central_nervous_system(4)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(10)|large_intestine(24)|lung(55)|ovary(3)|prostate(4)|skin(5)|stomach(1)|upper_aerodigestive_tract(7)|urinary_tract(1)	128	all_hematologic(923;0.208)				ART-123(DB05777)|Drotrecogin alfa(DB00055)	AGGACCTGGCCGTTGAAATGA	0.507																																					p.G273S		Atlas-SNP	.											F5,colon,carcinoma,0,1	F5	301	1	0			c.G817A						PASS	.						139.0	112.0	121.0					1																	169526019		2203	4300	6503	SO:0001583	missense	2153	exon6			CCTGGCCGTTGAA	M14335	CCDS1281.1	1q23	2012-10-02			ENSG00000198734	ENSG00000198734			3542	protein-coding gene	gene with protein product		612309					Standard	NM_000130		Approved		uc001ggg.1	P12259	OTTHUMG00000034595	ENST00000367797.3:c.817G>A	1.37:g.169526019C>T	ENSP00000356771:p.Gly273Ser	196.0	0.0	0		208.0	95.0	0.456731	NM_000130	A8K6E8|Q14285|Q2EHR5|Q5R346|Q5R347|Q6UPU6|Q8WWQ6	Missense_Mutation	SNP	ENST00000367797.3	37	CCDS1281.1	.	.	.	.	.	.	.	.	.	.	C	36	5.703228	0.96812	.	.	ENSG00000198734	ENST00000367797;ENST00000367796;ENST00000546081	D;D;D	0.99894	-7.58;-7.58;-7.58	6.07	6.07	0.98685	Cupredoxin (2);	0.090272	0.85682	D	0.000000	D	0.99921	0.9963	M	0.90369	3.11	0.44018	D	0.996733	D	0.89917	1.0	D	0.91635	0.999	D	0.96555	0.9411	9	0.87932	D	0	-22.8868	20.6439	0.99570	0.0:1.0:0.0:0.0	.	273	P12259	FA5_HUMAN	S	273;273;136	ENSP00000356771:G273S;ENSP00000356770:G273S;ENSP00000439664:G136S	ENSP00000356770:G273S	G	-	1	0	F5	167792643	1.000000	0.71417	0.983000	0.44433	0.973000	0.67179	7.456000	0.80751	2.890000	0.99128	0.650000	0.86243	GGC	.	.	none		0.507	F5-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000083712.1	NM_000130	
ZSWIM4	65249	hgsc.bcm.edu	37	19	13919757	13919757	+	Missense_Mutation	SNP	T	T	C			TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr19:13919757T>C	ENST00000254323.2	+	4	1009	c.820T>C	c.(820-822)Tac>Cac	p.Y274H	ZSWIM4_ENST00000440752.2_5'UTR	NM_023072.2	NP_075560.2	Q9H7M6	ZSWM4_HUMAN	zinc finger, SWIM-type containing 4	274							zinc ion binding (GO:0008270)			central_nervous_system(3)|cervix(1)|endometrium(3)|kidney(1)|large_intestine(2)|lung(11)|ovary(2)|prostate(1)|skin(1)|upper_aerodigestive_tract(2)	27			OV - Ovarian serous cystadenocarcinoma(19;2.94e-23)|Epithelial(5;4.58e-19)			CAATGGCGGCTACTACGGGGC	0.701																																					p.Y274H		Atlas-SNP	.											.	ZSWIM4	69	.	0			c.T820C						PASS	.						18.0	18.0	18.0					19																	13919757		2184	4276	6460	SO:0001583	missense	65249	exon4			GGCGGCTACTACG	AK022283	CCDS32924.1	19p13.13	2012-02-23			ENSG00000132003	ENSG00000132003		"""Zinc fingers, SWIM-type"""	25704	protein-coding gene	gene with protein product							Standard	NM_023072		Approved	FLJ12221	uc002mxh.1	Q9H7M6		ENST00000254323.2:c.820T>C	19.37:g.13919757T>C	ENSP00000254323:p.Tyr274His	96.0	0.0	0		77.0	4.0	0.0519481	NM_023072		Missense_Mutation	SNP	ENST00000254323.2	37	CCDS32924.1	.	.	.	.	.	.	.	.	.	.	T	14.41	2.527572	0.44969	.	.	ENSG00000132003	ENST00000254323	T	0.41400	1.0	4.07	3.03	0.35002	.	0.129202	0.33895	N	0.004453	T	0.38108	0.1028	M	0.68593	2.085	0.80722	D	1	B	0.02656	0.0	B	0.10450	0.005	T	0.20438	-1.0275	10	0.51188	T	0.08	-0.0495	6.9161	0.24361	0.0:0.1211:0.0:0.8789	.	274	Q9H7M6	ZSWM4_HUMAN	H	274	ENSP00000254323:Y274H	ENSP00000254323:Y274H	Y	+	1	0	ZSWIM4	13780757	1.000000	0.71417	1.000000	0.80357	0.342000	0.28953	4.760000	0.62235	0.456000	0.26937	0.155000	0.16302	TAC	.	.	none		0.701	ZSWIM4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000457457.1	XM_031342	
SPZ1	84654	hgsc.bcm.edu	37	5	79617039	79617039	+	Silent	SNP	A	A	G	rs374023153		TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr5:79617039A>G	ENST00000296739.4	+	1	1250	c.1005A>G	c.(1003-1005)gtA>gtG	p.V335V		NM_032567.3	NP_115956.3	Q9BXG8	SPZ1_HUMAN	spermatogenic leucine zipper 1	335					transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	DNA binding (GO:0003677)|sequence-specific DNA binding transcription factor activity (GO:0003700)			endometrium(2)|kidney(5)|large_intestine(4)|lung(12)|ovary(1)|skin(2)	26		Lung NSC(167;0.0393)|all_lung(232;0.0428)|Ovarian(174;0.113)		OV - Ovarian serous cystadenocarcinoma(54;3.43e-47)|Epithelial(54;2.25e-41)|all cancers(79;4.19e-36)		AGCAGAGAGTAGAGATTCTCA	0.423													A|||	1	0.000199681	0.0	0.0014	5008	,	,		19001	0.0		0.0	False		,,,				2504	0.0				p.V335V		Atlas-SNP	.											.	SPZ1	60	.	0			c.A1005G						PASS	.	A		0,3766		0,0,1883	112.0	106.0	108.0		1005	-6.3	0.0	5		108	3,8245		0,3,4121	no	coding-synonymous	SPZ1	NM_032567.3		0,3,6004	GG,GA,AA		0.0364,0.0,0.025		335/431	79617039	3,12011	1883	4124	6007	SO:0001819	synonymous_variant	84654	exon1			GAGAGTAGAGATT		CCDS43336.1	5q14.1	2014-06-13				ENSG00000164299			30721	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 148"""					11165476, 12778315, 15226296, 15829580, 15899793	Standard	NM_032567		Approved	NYD-TSP1, FLJ25709, PPP1R148	uc003kgn.3	Q9BXG8		ENST00000296739.4:c.1005A>G	5.37:g.79617039A>G		136.0	0.0	0		145.0	70.0	0.482759	NM_032567	B2RA21|Q8N4P1|Q8N7E9	Silent	SNP	ENST00000296739.4	37	CCDS43336.1																																																																																			.	.	weak		0.423	SPZ1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000369322.1	NM_032567	
FGG	2266	hgsc.bcm.edu	37	4	155533035	155533035	+	Missense_Mutation	SNP	G	G	C	rs148685782	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr4:155533035G>C	ENST00000336098.3	-	4	361	c.323C>G	c.(322-324)gCt>gGt	p.A108G	FGG_ENST00000405164.1_Missense_Mutation_p.A108G|FGG_ENST00000407946.1_Missense_Mutation_p.A108G|FGG_ENST00000404648.3_Missense_Mutation_p.A108G	NM_021870.2	NP_068656.2	P02679	FIBG_HUMAN	fibrinogen gamma chain	108					blood coagulation (GO:0007596)|cell-matrix adhesion (GO:0007160)|cellular protein complex assembly (GO:0043623)|extracellular matrix organization (GO:0030198)|negative regulation of endothelial cell apoptotic process (GO:2000352)|negative regulation of extrinsic apoptotic signaling pathway via death domain receptors (GO:1902042)|platelet activation (GO:0030168)|platelet aggregation (GO:0070527)|platelet degranulation (GO:0002576)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of exocytosis (GO:0045921)|positive regulation of heterotypic cell-cell adhesion (GO:0034116)|positive regulation of peptide hormone secretion (GO:0090277)|positive regulation of protein secretion (GO:0050714)|positive regulation of substrate adhesion-dependent cell spreading (GO:1900026)|positive regulation of vasoconstriction (GO:0045907)|protein polymerization (GO:0051258)|response to calcium ion (GO:0051592)|signal transduction (GO:0007165)	blood microparticle (GO:0072562)|cell cortex (GO:0005938)|cell surface (GO:0009986)|external side of plasma membrane (GO:0009897)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|fibrinogen complex (GO:0005577)|plasma membrane (GO:0005886)|platelet alpha granule (GO:0031091)|platelet alpha granule lumen (GO:0031093)	cell adhesion molecule binding (GO:0050839)|metal ion binding (GO:0046872)|receptor binding (GO:0005102)|structural molecule activity (GO:0005198)			breast(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(7)|lung(9)|prostate(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	27	all_hematologic(180;0.215)	Renal(120;0.0458)			Sucralfate(DB00364)	CTTCAAAGTAGCAGCGTCTAT	0.294													G|||	8	0.00159744	0.0	0.0	5008	,	,		16621	0.0		0.006	False		,,,				2504	0.002				p.A108G		Atlas-SNP	.											.	FGG	71	.	0			c.C323G	GRCh37	CM000383	FGG	M	rs148685782	PASS	.	G	GLY/ALA,GLY/ALA	4,4398	8.1+/-20.4	0,4,2197	74.0	75.0	75.0		323,323	5.1	0.7	4	dbSNP_134	75	30,8564	21.0+/-64.5	0,30,4267	yes	missense,missense	FGG	NM_000509.4,NM_021870.2	60,60	0,34,6464	CC,CG,GG		0.3491,0.0909,0.2616	benign,benign	108/438,108/454	155533035	34,12962	2201	4297	6498	SO:0001583	missense	2266	exon4			AAAGTAGCAGCGT		CCDS3788.1, CCDS47153.1	4q28	2014-09-17			ENSG00000171557	ENSG00000171557		"""Fibrinogen C domain containing"", ""Endogenous ligands"""	3694	protein-coding gene	gene with protein product		134850	"""fibrinogen, gamma polypeptide"""				Standard	NM_000509		Approved		uc003ioj.3	P02679	OTTHUMG00000150329	ENST00000336098.3:c.323C>G	4.37:g.155533035G>C	ENSP00000336829:p.Ala108Gly	89.0	0.0	0		72.0	27.0	0.375	NM_000509	A8K057|P04469|P04470|Q53Y18|Q96A14|Q96KJ3|Q9UC62|Q9UC63|Q9UCF3	Missense_Mutation	SNP	ENST00000336098.3	37	CCDS3788.1	6	0.0027472527472527475	0	0.0	0	0.0	0	0.0	6	0.0079155672823219	G	11.32	1.605287	0.28623	9.09E-4	0.003491	ENSG00000171557	ENST00000404648;ENST00000405164;ENST00000336098;ENST00000407946;ENST00000443553;ENST00000393846	D;D;D;D;D;D	0.82893	-1.66;-1.66;-1.66;-1.66;-1.66;-1.66	6.02	5.07	0.68467	Fibrinogen, alpha/beta/gamma chain, coiled coil domain (2);	0.481885	0.23983	N	0.042648	T	0.69513	0.3119	M	0.69463	2.115	0.25585	N	0.986755	B;B;B;B	0.06786	0.001;0.001;0.001;0.001	B;B;B;B	0.08055	0.002;0.003;0.003;0.001	T	0.56378	-0.7989	10	0.25751	T	0.34	.	2.5551	0.04758	0.2099:0.0:0.5124:0.2777	.	108;108;108;108	C9JC84;P02679;C9JEU5;P02679-2	.;FIBG_HUMAN;.;.	G	108;108;108;108;5;5	ENSP00000384860:A108G;ENSP00000384101:A108G;ENSP00000336829:A108G;ENSP00000384552:A108G;ENSP00000407562:A5G;ENSP00000377429:A5G	ENSP00000336829:A108G	A	-	2	0	FGG	155752485	0.594000	0.26849	0.681000	0.30009	0.005000	0.04900	2.105000	0.41825	2.857000	0.98124	0.650000	0.86243	GCT	G|0.998;C|0.002	0.002	strong		0.294	FGG-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000317581.1	NM_021870	
SETMAR	6419	hgsc.bcm.edu	37	3	4358476	4358476	+	Missense_Mutation	SNP	C	C	T	rs115195721	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr3:4358476C>T	ENST00000358065.4	+	3	1668	c.1601C>T	c.(1600-1602)aCt>aTt	p.T534I	SUMF1_ENST00000534863.1_Intron|SETMAR_ENST00000425863.1_Missense_Mutation_p.T395I	NM_006515.3	NP_006506.3	Q53H47	SETMR_HUMAN	SET domain and mariner transposase fusion gene	534	Mariner transposase Hsmar1.				DNA catabolic process, endonucleolytic (GO:0000737)|DNA double-strand break processing (GO:0000729)|DNA integration (GO:0015074)|negative regulation of cell cycle arrest (GO:0071157)|negative regulation of chromosome organization (GO:2001251)|positive regulation of double-strand break repair via nonhomologous end joining (GO:2001034)|transposition, DNA-mediated (GO:0006313)	chromosome (GO:0005694)|nucleus (GO:0005634)	endonuclease activity (GO:0004519)|histone-lysine N-methyltransferase activity (GO:0018024)|protein homodimerization activity (GO:0042803)|structure-specific DNA binding (GO:0043566)|transposase activity (GO:0004803)|zinc ion binding (GO:0008270)			endometrium(3)|kidney(2)|large_intestine(2)|lung(1)|ovary(1)	9		Melanoma(143;0.0657)		Epithelial(13;0.0025)|OV - Ovarian serous cystadenocarcinoma(96;0.011)|all cancers(10;0.0114)		gtcatggtcactatttggtgg	0.463								Chromatin Structure					C|||	43	0.00858626	0.0008	0.0144	5008	,	,		19453	0.0		0.0258	False		,,,				2504	0.0061				p.T534I		Atlas-SNP	.											SETMAR,NS,carcinoma,0,1	SETMAR	30	1	0			c.C1601T						PASS	.	C	ILE/THR	13,3159		0,13,1573	9.0	6.0	7.0		1601	0.2	0.8	3	dbSNP_132	7	122,5474		0,122,2676	no	missense	SETMAR	NM_006515.3	89	0,135,4249	TT,TC,CC		2.1801,0.4098,1.5397	possibly-damaging	534/685	4358476	135,8633	1586	2798	4384	SO:0001583	missense	6419	exon3			TGGTCACTATTTG	U80776	CCDS2563.2, CCDS58814.1, CCDS63528.1	3p26.2	2013-01-31			ENSG00000170364	ENSG00000170364			10762	protein-coding gene	gene with protein product		609834				9461395	Standard	NM_006515		Approved	metnase	uc011asp.2	Q53H47	OTTHUMG00000090265	ENST00000358065.4:c.1601C>T	3.37:g.4358476C>T	ENSP00000373354:p.Thr534Ile	37.0	0.0	0		31.0	8.0	0.258065	NM_006515	B4DY74|E7EN68|Q13579|Q1G668|Q96F41	Missense_Mutation	SNP	ENST00000358065.4	37	CCDS2563.2	20	0.009157509157509158	0	0.0	8	0.022099447513812154	0	0.0	12	0.0158311345646438	C	11.57	1.678774	0.29783	0.004098	0.021801	ENSG00000170364	ENST00000358065;ENST00000425863	D;T	0.94931	-3.56;0.57	0.235	0.235	0.15431	.	.	.	.	.	D	0.90820	0.7117	M	0.65975	2.015	0.20926	N	0.999826	P;P;P;D	0.52996	0.908;0.898;0.91;0.957	P;P;P;P	0.56648	0.796;0.775;0.803;0.803	D	0.84476	0.0602	8	0.56958	D	0.05	.	.	.	.	.	278;395;521;279	B4DND2;E7EN68;Q53H47;Q96H41	.;.;SETMR_HUMAN;.	I	534;395	ENSP00000373354:T534I;ENSP00000403145:T395I	ENSP00000373354:T534I	T	+	2	0	SETMAR	4333476	0.851000	0.29673	0.754000	0.31244	0.760000	0.43138	0.305000	0.19254	0.308000	0.22923	0.313000	0.20887	ACT	C|0.991;T|0.009	0.009	strong		0.463	SETMAR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206587.4	NM_006515	
VWF	7450	hgsc.bcm.edu	37	12	6172138	6172138	+	Silent	SNP	G	G	A	rs377198574		TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr12:6172138G>A	ENST00000261405.5	-	13	1769	c.1515C>T	c.(1513-1515)cgC>cgT	p.R505R		NM_000552.3	NP_000543	P04275	VWF_HUMAN	von Willebrand factor	505	VWFD 2. {ECO:0000255|PROSITE- ProRule:PRU00580}.				blood coagulation (GO:0007596)|blood coagulation, intrinsic pathway (GO:0007597)|cell adhesion (GO:0007155)|cell-substrate adhesion (GO:0031589)|extracellular matrix organization (GO:0030198)|hemostasis (GO:0007599)|liver development (GO:0001889)|placenta development (GO:0001890)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|protein homooligomerization (GO:0051260)|response to wounding (GO:0009611)	endoplasmic reticulum (GO:0005783)|external side of plasma membrane (GO:0009897)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|platelet alpha granule (GO:0031091)|platelet alpha granule lumen (GO:0031093)|proteinaceous extracellular matrix (GO:0005578)|Weibel-Palade body (GO:0033093)	chaperone binding (GO:0051087)|collagen binding (GO:0005518)|glycoprotein binding (GO:0001948)|identical protein binding (GO:0042802)|immunoglobulin binding (GO:0019865)|integrin binding (GO:0005178)|protease binding (GO:0002020)|protein homodimerization activity (GO:0042803)|protein N-terminus binding (GO:0047485)			NS(1)|breast(6)|central_nervous_system(5)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(8)|large_intestine(25)|lung(41)|ovary(7)|pancreas(2)|prostate(6)|skin(15)|stomach(1)|upper_aerodigestive_tract(5)	129					Antihemophilic Factor(DB00025)	GCAGCCTCCCGCGGCCATCCC	0.632											OREG0021618	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.R505R		Atlas-SNP	.											.	VWF	338	.	0			c.C1515T						PASS	.	G		0,4406		0,0,2203	49.0	40.0	43.0		1515	-10.4	0.2	12		43	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous	VWF	NM_000552.3		0,1,6502	AA,AG,GG		0.0116,0.0,0.0077		505/2814	6172138	1,13005	2203	4300	6503	SO:0001819	synonymous_variant	7450	exon13			CCTCCCGCGGCCA		CCDS8539.1	12p13.3	2014-09-17			ENSG00000110799	ENSG00000110799		"""Endogenous ligands"""	12726	protein-coding gene	gene with protein product		613160		F8VWF		2251280	Standard	NM_000552		Approved		uc001qnn.1	P04275	OTTHUMG00000168265	ENST00000261405.5:c.1515C>T	12.37:g.6172138G>A		48.0	0.0	0	632	31.0	18.0	0.580645	NM_000552	Q8TCE8|Q99806	Silent	SNP	ENST00000261405.5	37	CCDS8539.1																																																																																			.	.	weak		0.632	VWF-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000399020.1	NM_000552	
FAM150B	285016	hgsc.bcm.edu	37	2	287646	287646	+	Silent	SNP	G	G	T			TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr2:287646G>T	ENST00000403610.4	-	2	530	c.190C>A	c.(190-192)Cgg>Agg	p.R64R	FAM150B_ENST00000401503.1_5'Flank|FAM150B_ENST00000405290.1_5'Flank|AC079779.4_ENST00000427831.1_RNA|FAM150B_ENST00000344414.5_5'Flank	NM_001002919.2	NP_001002919.2	Q6UX46	F150B_HUMAN	family with sequence similarity 150, member B	64						extracellular region (GO:0005576)				breast(1)|kidney(2)	3	all_hematologic(175;0.0429)|Acute lymphoblastic leukemia(172;0.0627)	all_cancers(51;0.00175)|Lung NSC(108;0.216)|all_epithelial(98;0.236)		all cancers(51;0.00091)|Epithelial(75;0.00656)|OV - Ovarian serous cystadenocarcinoma(76;0.00954)|GBM - Glioblastoma multiforme(21;0.128)		GCGCAGTCCCGCCCGAGGAGC	0.776																																					p.R64R		Atlas-SNP	.											.	FAM150B	12	.	0			c.C190A						PASS	.						1.0	1.0	1.0					2																	287646		772	1574	2346	SO:0001819	synonymous_variant	285016	exon2			AGTCCCGCCCGAG		CCDS46218.1	2p25.3	2008-05-02			ENSG00000189292	ENSG00000189292			27683	protein-coding gene	gene with protein product							Standard	NM_001002919		Approved		uc002qwi.4	Q6UX46	OTTHUMG00000151366	ENST00000403610.4:c.190C>A	2.37:g.287646G>T		4.0	0.0	0		4.0	4.0	1	NM_001002919	B5MC76	Silent	SNP	ENST00000403610.4	37	CCDS46218.1																																																																																			.	.	none		0.776	FAM150B-001	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000322394.2	NM_001002919	
MYO1E	4643	hgsc.bcm.edu	37	15	59517011	59517011	+	Silent	SNP	G	G	A	rs373337685		TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr15:59517011G>A	ENST00000288235.4	-	8	1053	c.654C>T	c.(652-654)ggC>ggT	p.G218G	MYO1E_ENST00000558814.1_5'UTR	NM_004998.3	NP_004989.2	Q12965	MYO1E_HUMAN	myosin IE	218	Myosin motor.				actin filament-based movement (GO:0030048)|ATP catabolic process (GO:0006200)|endocytosis (GO:0006897)|glomerular basement membrane development (GO:0032836)|glomerular filtration (GO:0003094)|glomerular visceral epithelial cell development (GO:0072015)|in utero embryonic development (GO:0001701)|platelet-derived growth factor receptor signaling pathway (GO:0048008)|post-embryonic hemopoiesis (GO:0035166)|vasculogenesis (GO:0001570)	actin cytoskeleton (GO:0015629)|adherens junction (GO:0005912)|cell-cell junction (GO:0005911)|cytoplasm (GO:0005737)|cytoplasmic vesicle (GO:0031410)|cytoskeleton (GO:0005856)|extracellular vesicular exosome (GO:0070062)|myosin complex (GO:0016459)	actin filament binding (GO:0051015)|ATP binding (GO:0005524)|ATPase activity, coupled (GO:0042623)|calmodulin binding (GO:0005516)|microfilament motor activity (GO:0000146)|motor activity (GO:0003774)|phosphatidylinositol binding (GO:0035091)			breast(1)|central_nervous_system(3)|endometrium(5)|kidney(4)|large_intestine(6)|lung(10)|pancreas(2)|prostate(1)|urinary_tract(1)	33				all cancers(107;0.207)		CTGCAGAGGCGCCCTCGATGA	0.537																																					p.G218G		Atlas-SNP	.											.	MYO1E	99	.	0			c.C654T						PASS	.	G		0,4380		0,0,2190	93.0	73.0	80.0		654	-5.0	1.0	15		80	3,8577	3.0+/-9.4	0,3,4287	no	coding-synonymous	MYO1E	NM_004998.2		0,3,6477	AA,AG,GG		0.035,0.0,0.0231		218/1109	59517011	3,12957	2190	4290	6480	SO:0001819	synonymous_variant	4643	exon8			AGAGGCGCCCTCG	U14391	CCDS32254.1	15q21-q22	2011-09-27				ENSG00000157483		"""Myosins / Myosin superfamily : Class I"""	7599	protein-coding gene	gene with protein product	"""myosin-IC"""	601479				8884266	Standard	NM_004998		Approved	MYO1C, HuncM-IC, MGC104638	uc002aga.4	Q12965		ENST00000288235.4:c.654C>T	15.37:g.59517011G>A		90.0	0.0	0		82.0	38.0	0.463415	NM_004998	Q14778	Silent	SNP	ENST00000288235.4	37	CCDS32254.1																																																																																			.	.	weak		0.537	MYO1E-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000416024.1	NM_004998	
EGFR	1956	hgsc.bcm.edu	37	7	55238087	55238087	+	Intron	SNP	C	C	T	rs10258429	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr7:55238087C>T	ENST00000275493.2	+	16	2057				EGFR_ENST00000455089.1_Intron|EGFR_ENST00000344576.2_Silent_p.H656H|EGFR_ENST00000442591.1_Intron|EGFR_ENST00000454757.2_Intron	NM_005228.3	NP_005219.2	P00533	EGFR_HUMAN	epidermal growth factor receptor						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)	GCGTGTCCCACCAGAGCGGGA	0.512		8	"""A, O, Mis"""		"""glioma, NSCLC"""	NSCLC			Lung Cancer, Familial Clustering of	TCGA GBM(3;<1E-08)|TSP Lung(4;<1E-08)			C|||	563	0.11242	0.2398	0.049	5008	,	,		20745	0.0496		0.0736	False		,,,				2504	0.09				p.H656H		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.C1968T						PASS	.	C	,	922,3484	352.1+/-311.5	101,720,1382	108.0	89.0	95.0		,1968	2.4	0.0	7	dbSNP_119	95	606,7994	158.6+/-212.1	23,560,3717	no	intron,coding-synonymous	EGFR	NM_005228.3,NM_201284.1	,	124,1280,5099	TT,TC,CC		7.0465,20.926,11.7484	,	,656/706	55238087	1528,11478	2203	4300	6503	SO:0001627	intron_variant	1956	exon16	Familial Cancer Database	incl. Hereditary Lung cancer, Hereditary Non-Small Cell Lung cancer	GTCCCACCAGAGC		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.1881-781C>T	7.37:g.55238087C>T		160.0	0.0	0		189.0	93.0	0.492063	NM_201284	O00688|O00732|P06268|Q14225|Q68GS5|Q92795|Q9BZS2|Q9GZX1|Q9H2C9|Q9H3C9|Q9UMD7|Q9UMD8|Q9UMG5	Silent	SNP	ENST00000275493.2	37	CCDS5514.1																																																																																			C|0.889;T|0.111	0.111	strong		0.512	EGFR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251456.2	NM_005228	
IQSEC2	23096	hgsc.bcm.edu	37	X	53263764	53263764	+	Silent	SNP	C	C	T	rs184087864		TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chrX:53263764C>T	ENST00000375368.5	-	14	4274	c.4074G>A	c.(4072-4074)ctG>ctA	p.L1358L	IQSEC2_ENST00000396435.3_Silent_p.L1368L|IQSEC2_ENST00000375365.2_3'UTR			Q5JU85	IQEC2_HUMAN	IQ motif and Sec7 domain 2	1358	Pro-rich.				actin cytoskeleton organization (GO:0030036)|positive regulation of GTPase activity (GO:0043547)|regulation of ARF protein signal transduction (GO:0032012)	cell junction (GO:0030054)|cytoplasm (GO:0005737)|nucleus (GO:0005634)	ARF guanyl-nucleotide exchange factor activity (GO:0005086)			breast(2)|central_nervous_system(1)|cervix(1)|endometrium(5)|kidney(1)|large_intestine(4)|lung(10)|ovary(4)|skin(1)	29						TGTACAGGGGCAGTGGGGATG	0.672													c|||	294	0.0778808	0.2133	0.0173	3775	,	,		4478	0.0		0.0	False		,,,				2504	0.0				p.L1368L		Atlas-SNP	.											.	IQSEC2	195	.	0			c.G4104A						PASS	.						10.0	11.0	10.0					X																	53263764		689	1580	2269	SO:0001819	synonymous_variant	23096	exon15			CAGGGGCAGTGGG	AB011094	CCDS35298.1, CCDS48130.1	Xp11.23	2014-01-31			ENSG00000124313	ENSG00000124313			29059	protein-coding gene	gene with protein product		300522	"""mental retardation, X-linked 1 (non-dysmorphic)"""	MRX1		9628581, 20473311	Standard	NM_001243197		Approved	KIAA0522	uc004dsd.3	Q5JU85	OTTHUMG00000021608	ENST00000375368.5:c.4074G>A	X.37:g.53263764C>T		80.0	0.0	0		103.0	96.0	0.932039	NM_001111125	B3KT97|C7SDG1|O60275|Q5JUX1	Silent	SNP	ENST00000375368.5	37																																																																																				C|0.937;T|0.063	0.063	strong		0.672	IQSEC2-201	KNOWN	basic	protein_coding	protein_coding		XM_291345	
SLC22A23	63027	hgsc.bcm.edu	37	6	3284097	3284097	+	Silent	SNP	C	C	T	rs142838841	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr6:3284097C>T	ENST00000406686.3	-	9	1691	c.1692G>A	c.(1690-1692)ccG>ccA	p.P564P	SLC22A23_ENST00000380302.4_Silent_p.P283P|SLC22A23_ENST00000436008.2_Silent_p.P572P|PSMG4_ENST00000451246.2_Intron|SLC22A23_ENST00000490273.1_Silent_p.P283P	NM_015482.1	NP_056297.1	A1A5C7	S22AN_HUMAN	solute carrier family 22, member 23	564					ion transport (GO:0006811)	integral component of membrane (GO:0016021)	transmembrane transporter activity (GO:0022857)			endometrium(3)|kidney(1)|large_intestine(2)|lung(6)|ovary(1)|prostate(1)	14	Ovarian(93;0.0493)	all_hematologic(90;0.0905)				TTATCACCGTCGGGGTGATCT	0.587													c|||	4	0.000798722	0.0	0.0	5008	,	,		19259	0.0		0.004	False		,,,				2504	0.0				p.P564P		Atlas-SNP	.											.	SLC22A23	89	.	0			c.G1692A						PASS	.	T	,	4,4402	8.1+/-20.4	0,4,2199	74.0	67.0	69.0		1692,849	0.3	0.9	6	dbSNP_134	69	39,8561	26.3+/-74.7	0,39,4261	no	coding-synonymous,coding-synonymous	SLC22A23	NM_015482.1,NM_021945.5	,	0,43,6460	TT,TC,CC		0.4535,0.0908,0.3306	,	564/687,283/406	3284097	43,12963	2203	4300	6503	SO:0001819	synonymous_variant	63027	exon9			CACCGTCGGGGTG	AJ420525	CCDS34331.1, CCDS47363.1, CCDS75389.1	6p25.2	2013-05-22	2008-01-11	2008-01-11	ENSG00000137266	ENSG00000137266		"""Solute carriers"""	21106	protein-coding gene	gene with protein product		611697	"""chromosome 6 open reading frame 85"""	C6orf85		17714910	Standard	NM_015482		Approved	FLJ22174	uc003mvm.3	A1A5C7	OTTHUMG00000014144	ENST00000406686.3:c.1692G>A	6.37:g.3284097C>T		57.0	0.0	0		44.0	19.0	0.431818	NM_015482	A1A5C8|Q5T8B8|Q6ZMH3|Q8IW73	Silent	SNP	ENST00000406686.3	37	CCDS47363.1																																																																																			C|0.997;T|0.003	0.003	strong		0.587	SLC22A23-006	KNOWN	not_organism_supported|basic|CCDS	protein_coding	protein_coding	OTTHUMT00000353059.1	NM_021945	
POF1B	79983	hgsc.bcm.edu	37	X	84563194	84563194	+	Missense_Mutation	SNP	C	C	T	rs75398746	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chrX:84563194C>T	ENST00000262753.4	-	10	1131	c.986G>A	c.(985-987)cGa>cAa	p.R329Q	POF1B_ENST00000373145.3_Missense_Mutation_p.R329Q	NM_024921.3	NP_079197.3	Q8WVV4	POF1B_HUMAN	premature ovarian failure, 1B	329			R -> Q (in POF2B; disrupts binding to nonmuscle actin filaments; abolishes tight junction localization; altered ciliogenesis and cystogenesis; dbSNP:rs75398746). {ECO:0000269|PubMed:15459172, ECO:0000269|PubMed:16773570}.			tight junction (GO:0005923)				central_nervous_system(4)|endometrium(5)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(3)|liver(2)|lung(17)|ovary(1)|prostate(1)	35						CAGCACTAGTCGGAGTGACTT	0.343													C|||	11	0.00291391	0.0045	0.0058	3775	,	,		11719	0.0		0.001	False		,,,				2504	0.0				p.R329Q		Atlas-SNP	.											.	POF1B	77	.	0			c.G986A	GRCh37	CM066591	POF1B	M	rs75398746	PASS	.	C	GLN/ARG	26,3809		0,23,3,1609,568	93.0	80.0	84.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	986	5.0	0.7	X	dbSNP_131	84	17,6711		0,12,5,2416,1867	yes	missense	POF1B	NM_024921.3	43	0,35,8,4025,2435	TT,TC,T,CC,C		0.2527,0.678,0.4071	probably-damaging	329/590	84563194	43,10520	2203	4300	6503	SO:0001583	missense	79983	exon10			ACTAGTCGGAGTG	BC017500	CCDS14452.1	Xq21.2	2008-02-05			ENSG00000124429	ENSG00000124429			13711	protein-coding gene	gene with protein product		300603				11299520	Standard	NM_024921		Approved	POF, FLJ22792	uc004eer.2	Q8WVV4	OTTHUMG00000021934	ENST00000262753.4:c.986G>A	X.37:g.84563194C>T	ENSP00000262753:p.Arg329Gln	158.0	0.0	0		139.0	139.0	1	NM_024921	A8K2U5|Q5H9E9|Q5H9F0|Q8NG12|Q9H5Y2|Q9H738|Q9H744	Missense_Mutation	SNP	ENST00000262753.4	37	CCDS14452.1	6	0.003616636528028933	1	0.0020408163265306124	3	0.008333333333333333	0	0.0	0	0.0	C	16.37	3.102992	0.56183	0.00678	0.002527	ENSG00000124429	ENST00000262753;ENST00000373145	T;T	0.16073	2.37;2.37	5.86	5.0	0.66597	.	0.101855	0.64402	N	0.000003	T	0.12347	0.0300	L	0.58101	1.795	0.29902	A	0.175686	B;B	0.32968	0.392;0.392	B;B	0.19946	0.027;0.027	T	0.16424	-1.0403	9	0.72032	D	0.01	-4.9537	12.8282	0.57731	0.0:0.9187:0.0:0.0813	.	329;329	Q8WVV4-1;Q8WVV4	.;POF1B_HUMAN	Q	329	ENSP00000262753:R329Q;ENSP00000362238:R329Q	ENSP00000262753:R329Q	R	-	2	0	POF1B	84449850	0.934000	0.31675	0.671000	0.29857	0.941000	0.58515	2.969000	0.49232	1.236000	0.43740	0.600000	0.82982	CGA	C|0.996;T|0.004	0.004	strong		0.343	POF1B-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000057391.2	NM_024921	
PAK4	10298	hgsc.bcm.edu	37	19	39663757	39663757	+	Missense_Mutation	SNP	G	G	A	rs56099436	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr19:39663757G>A	ENST00000593690.1	+	5	831	c.404G>A	c.(403-405)cGa>cAa	p.R135Q	PAK4_ENST00000321944.4_Intron|PAK4_ENST00000599386.1_Intron|PAK4_ENST00000358301.3_Missense_Mutation_p.R135Q|PAK4_ENST00000599470.1_Intron|PAK4_ENST00000435673.2_Missense_Mutation_p.R135Q|PAK4_ENST00000360442.3_Missense_Mutation_p.R135Q	NM_001014831.2	NP_001014831.1	O96013	PAK4_HUMAN	p21 protein (Cdc42/Rac)-activated kinase 4	135	Linker.		R -> Q (in dbSNP:rs56099436). {ECO:0000269|PubMed:17344846}.		apoptotic process (GO:0006915)|cell cycle (GO:0007049)|cell growth (GO:0016049)|cell migration (GO:0016477)|cell proliferation (GO:0008283)|cellular component movement (GO:0006928)|cytoskeleton organization (GO:0007010)|signal transduction (GO:0007165)	focal adhesion (GO:0005925)|Golgi apparatus (GO:0005794)	ATP binding (GO:0005524)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)			central_nervous_system(1)|kidney(2)|large_intestine(1)|lung(7)|ovary(1)|prostate(1)	13	all_cancers(60;1.03e-07)|all_epithelial(25;9.66e-08)|all_lung(34;1.58e-07)|Lung NSC(34;1.88e-07)|Ovarian(47;0.0454)		Epithelial(26;4.82e-25)|all cancers(26;2.94e-22)|Lung(45;0.000797)|LUSC - Lung squamous cell carcinoma(53;0.00113)			GCAGGCAGCCGAGGCCGGTTC	0.736													g|||	34	0.00678914	0.0008	0.0115	5008	,	,		10680	0.0		0.0189	False		,,,				2504	0.0061				p.R135Q		Atlas-SNP	.											.	PAK4	40	.	0			c.G404A						PASS	.		GLN/ARG,GLN/ARG,,,GLN/ARG	13,3671		0,13,1829	3.0	4.0	4.0		404,404,,,404	1.7	0.0	19	dbSNP_129	4	147,7075		0,147,3464	no	missense,missense,intron,intron,missense	PAK4	NM_001014831.2,NM_001014832.1,NM_001014834.2,NM_001014835.1,NM_005884.3	43,43,,,43	0,160,5293	AA,AG,GG		2.0354,0.3529,1.4671	possibly-damaging,possibly-damaging,,,possibly-damaging	135/592,135/592,,,135/592	39663757	160,10746	1842	3611	5453	SO:0001583	missense	10298	exon3			GCAGCCGAGGCCG	AJ011855	CCDS12528.1, CCDS33019.1	19p11-q11	2008-06-17	2008-06-17						16059	protein-coding gene	gene with protein product		605451	"""p21(CDKN1A)-activated kinase 4"""			9822598, 10461188	Standard	NM_001014831		Approved		uc002okn.1	O96013		ENST00000593690.1:c.404G>A	19.37:g.39663757G>A	ENSP00000469413:p.Arg135Gln	10.0	0.0	0		10.0	8.0	0.8	NM_001014832	B4DGG6|Q8N4E1|Q8NCH5|Q8NDE3|Q9BU33|Q9ULS8	Missense_Mutation	SNP	ENST00000593690.1	37	CCDS12528.1	25	0.011446886446886446	2	0.0040650406504065045	8	0.022099447513812154	0	0.0	15	0.01978891820580475	G	0.017	-1.510561	0.00984	0.003529	0.020354	ENSG00000130669	ENST00000358301;ENST00000435673;ENST00000360442	T;T;T	0.71103	-0.54;-0.54;-0.54	3.9	1.73	0.24493	.	1.445110	0.04338	N	0.353591	T	0.32734	0.0839	N	0.08118	0	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.21075	-1.0256	10	0.12430	T	0.62	.	7.4578	0.27276	0.3592:0.0:0.6408:0.0	rs56099436	135	O96013	PAK4_HUMAN	Q	135	ENSP00000351049:R135Q;ENSP00000392753:R135Q;ENSP00000353625:R135Q	ENSP00000351049:R135Q	R	+	2	0	PAK4	44355597	0.000000	0.05858	0.026000	0.17262	0.011000	0.07611	0.293000	0.19029	-0.014000	0.14175	-1.157000	0.01802	CGA	G|0.989;A|0.011	0.011	strong		0.736	PAK4-004	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000463823.1		
ZNF202	7753	hgsc.bcm.edu	37	11	123599897	123599897	+	Silent	SNP	G	G	A	rs11825443	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr11:123599897G>A	ENST00000529691.1	-	4	858	c.639C>T	c.(637-639)gaC>gaT	p.D213D	ZNF202_ENST00000336139.4_Silent_p.D213D|ZNF202_ENST00000530393.1_Silent_p.D213D			O95125	ZN202_HUMAN	zinc finger protein 202	213					lipid metabolic process (GO:0006629)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|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)			endometrium(4)|kidney(1)|large_intestine(5)|lung(17)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)	30		Breast(109;0.00204)|Lung NSC(97;0.0177)|all_lung(97;0.0179)|Medulloblastoma(222;0.0425)|all_neural(223;0.112)		BRCA - Breast invasive adenocarcinoma(274;5.1e-06)|OV - Ovarian serous cystadenocarcinoma(99;0.03)		CTGCAGGAAGGTCTGGGTCCT	0.502													G|||	130	0.0259585	0.0953	0.0058	5008	,	,		19804	0.0		0.0	False		,,,				2504	0.0				p.D213D		Atlas-SNP	.											.	ZNF202	72	.	0			c.C639T						PASS	.	G		351,4053	181.5+/-209.5	12,327,1863	72.0	65.0	67.0		639	0.8	0.9	11	dbSNP_120	67	0,8598		0,0,4299	no	coding-synonymous	ZNF202	NM_003455.2		12,327,6162	AA,AG,GG		0.0,7.97,2.6996		213/649	123599897	351,12651	2202	4299	6501	SO:0001819	synonymous_variant	7753	exon6			AGGAAGGTCTGGG	AF027219	CCDS8443.1	11q23.3	2013-01-09				ENSG00000166261		"""Zinc fingers, C2H2-type"", ""-"", ""-"", ""-"""	12994	protein-coding gene	gene with protein product		603430				9790754	Standard	XM_005271659		Approved	ZKSCAN10, ZSCAN42	uc001pzd.1	O95125		ENST00000529691.1:c.639C>T	11.37:g.123599897G>A		40.0	0.0	0		58.0	21.0	0.362069	NM_003455	B0LPH9|Q4JG21|Q9H1B9|Q9NSM4	Silent	SNP	ENST00000529691.1	37	CCDS8443.1																																																																																			G|0.965;A|0.035	0.035	strong		0.502	ZNF202-003	PUTATIVE	alternative_5_UTR|basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000387419.1	NM_003455	
LINGO1	84894	hgsc.bcm.edu	37	15	77907658	77907658	+	Silent	SNP	C	C	T			TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr15:77907658C>T	ENST00000355300.6	-	2	765	c.591G>A	c.(589-591)acG>acA	p.T197T	LINGO1_ENST00000561030.1_Silent_p.T191T	NM_032808.5	NP_116197.4	Q96FE5	LIGO1_HUMAN	leucine rich repeat and Ig domain containing 1	197					central nervous system neuron development (GO:0021954)|negative regulation of axonogenesis (GO:0050771)|negative regulation of oligodendrocyte differentiation (GO:0048715)|neuron projection development (GO:0031175)|neurotrophin TRK receptor signaling pathway (GO:0048011)|protein kinase B signaling (GO:0043491)|regulation of axonogenesis (GO:0050770)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				breast(1)|central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(7)|lung(16)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)	31						ATTTCTCCAGCGTCAGCTGCT	0.602																																					p.T197T		Atlas-SNP	.											.	LINGO1	76	.	0			c.G591A						PASS	.						111.0	119.0	117.0					15																	77907658		2175	4274	6449	SO:0001819	synonymous_variant	84894	exon2			CTCCAGCGTCAGC	AK027500	CCDS45313.1, CCDS73766.1	15q24	2013-01-11	2007-02-01	2007-02-01		ENSG00000169783		"""Immunoglobulin superfamily / I-set domain containing"""	21205	protein-coding gene	gene with protein product		609791	"""leucine rich repeat neuronal 6A"""	LRRN6A		14686891	Standard	XM_006720723		Approved	FLJ14594, LERN1	uc002bct.1	Q96FE5		ENST00000355300.6:c.591G>A	15.37:g.77907658C>T		104.0	0.0	0		124.0	62.0	0.5	NM_032808	D3DW80|Q6NUK3|Q6UXM3|Q6VVG0|Q6VVG1|Q6VVG2|Q8N3K5|Q96K52	Silent	SNP	ENST00000355300.6	37	CCDS45313.1																																																																																			.	.	none		0.602	LINGO1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000419546.1	NM_032808	
POSTN	10631	hgsc.bcm.edu	37	13	38156538	38156538	+	Missense_Mutation	SNP	C	C	T	rs117103342	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr13:38156538C>T	ENST00000379747.4	-	10	1474	c.1357G>A	c.(1357-1359)Gga>Aga	p.G453R	POSTN_ENST00000379749.4_Missense_Mutation_p.G453R|POSTN_ENST00000541179.1_Missense_Mutation_p.G453R|POSTN_ENST00000541481.1_Missense_Mutation_p.G453R|POSTN_ENST00000379743.4_Missense_Mutation_p.G453R|POSTN_ENST00000379742.4_Missense_Mutation_p.G453R	NM_006475.2	NP_006466.2	Q15063	POSTN_HUMAN	periostin, osteoblast specific factor	453	FAS1 3. {ECO:0000255|PROSITE- ProRule:PRU00082, ECO:0000305}.				cell adhesion (GO:0007155)|extracellular matrix organization (GO:0030198)|regulation of Notch signaling pathway (GO:0008593)|skeletal system development (GO:0001501)|tissue development (GO:0009888)	proteinaceous extracellular matrix (GO:0005578)|trans-Golgi network (GO:0005802)	heparin binding (GO:0008201)			cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(3)|kidney(4)|large_intestine(16)|lung(22)|ovary(2)|pancreas(1)|prostate(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)	59		Lung NSC(96;2.09e-05)|Prostate(109;0.0513)|Breast(139;0.0538)|Lung SC(185;0.0743)		all cancers(112;2.48e-08)|Epithelial(112;2.78e-06)|OV - Ovarian serous cystadenocarcinoma(117;0.000853)|BRCA - Breast invasive adenocarcinoma(63;0.013)|GBM - Glioblastoma multiforme(144;0.0154)		TGTTTGCCTCCGATGGTTTCC	0.373													C|||	17	0.00339457	0.0	0.0101	5008	,	,		17409	0.0		0.0089	False		,,,				2504	0.001				p.G453R		Atlas-SNP	.											.	POSTN	161	.	0			c.G1357A						PASS	.	C	ARG/GLY,ARG/GLY,ARG/GLY,ARG/GLY	4,4402	9.9+/-24.2	0,4,2199	155.0	149.0	151.0		1357,1357,1357,1357	6.1	1.0	13	dbSNP_132	151	77,8523	45.8+/-104.6	1,75,4224	yes	missense,missense,missense,missense	POSTN	NM_001135934.1,NM_001135935.1,NM_001135936.1,NM_006475.2	125,125,125,125	1,79,6423	TT,TC,CC		0.8953,0.0908,0.6228	probably-damaging,probably-damaging,probably-damaging,probably-damaging	453/780,453/782,453/752,453/837	38156538	81,12925	2203	4300	6503	SO:0001583	missense	10631	exon10			TGCCTCCGATGGT	D13665	CCDS9364.1, CCDS45034.1, CCDS53864.1, CCDS66530.1, CCDS66531.1	13q13.3	2008-02-05			ENSG00000133110	ENSG00000133110			16953	protein-coding gene	gene with protein product		608777				8363580, 12235007	Standard	NM_006475		Approved	OSF-2, PN, periostin	uc001uwo.4	Q15063	OTTHUMG00000016751	ENST00000379747.4:c.1357G>A	13.37:g.38156538C>T	ENSP00000369071:p.Gly453Arg	92.0	0.0	0		117.0	56.0	0.478632	NM_006475	B1ALD8|C0IMJ1|C0IMJ2|C0IMJ4|D2KRH7|F5H628|Q15064|Q29XZ0|Q3KPJ5|Q5VSY5|Q8IZF9	Missense_Mutation	SNP	ENST00000379747.4	37	CCDS9364.1	11	0.005036630036630037	0	0.0	5	0.013812154696132596	0	0.0	6	0.0079155672823219	C	23.8	4.459234	0.84317	9.08E-4	0.008953	ENSG00000133110	ENST00000541179;ENST00000379749;ENST00000379747;ENST00000379743;ENST00000379742;ENST00000541481	T;T;T;T;T;T	0.72615	-0.67;-0.67;-0.67;-0.67;-0.67;-0.67	6.07	6.07	0.98685	FAS1 domain (5);	0.154285	0.56097	D	0.000022	T	0.79215	0.4408	M	0.61703	1.905	0.47476	D	0.999438	D;D;D;D;D;D;D	0.89917	1.0;1.0;1.0;1.0;1.0;0.999;1.0	D;D;D;D;D;D;D	0.97110	1.0;1.0;0.995;1.0;0.999;0.951;0.995	T	0.78788	-0.2067	10	0.42905	T	0.14	-22.8572	20.6593	0.99626	0.0:1.0:0.0:0.0	.	453;453;453;453;453;453;453	C0IMJ4;F5H628;B1ALD8;Q15063-3;Q15063-4;Q15063-2;Q15063	.;.;.;.;.;.;POSTN_HUMAN	R	453	ENSP00000437959:G453R;ENSP00000369073:G453R;ENSP00000369071:G453R;ENSP00000369067:G453R;ENSP00000369066:G453R;ENSP00000437953:G453R	ENSP00000369066:G453R	G	-	1	0	POSTN	37054538	1.000000	0.71417	1.000000	0.80357	0.823000	0.46562	5.590000	0.67530	2.885000	0.99019	0.655000	0.94253	GGA	C|0.994;T|0.006	0.006	strong		0.373	POSTN-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000044566.2	NM_006475	
ZNF780B	163131	hgsc.bcm.edu	37	19	40540812	40540812	+	Missense_Mutation	SNP	G	G	A	rs115484124	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr19:40540812G>A	ENST00000434248.1	-	5	2019	c.1954C>T	c.(1954-1956)Cgt>Tgt	p.R652C	ZNF780B_ENST00000221355.6_Missense_Mutation_p.R504C	NM_001005851.2	NP_001005851.1	Q9Y6R6	Z780B_HUMAN	zinc finger protein 780B	652					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			endometrium(3)|kidney(2)|large_intestine(3)|lung(12)|ovary(1)|pancreas(1)|upper_aerodigestive_tract(1)	23	all_cancers(60;9.55e-06)|all_lung(34;1.17e-07)|Lung NSC(34;1.41e-07)|Ovarian(47;0.0925)					TTTGAGACACGATTAAAGGAC	0.403													g|||	156	0.0311502	0.0666	0.0101	5008	,	,		22218	0.0069		0.0089	False		,,,				2504	0.046				p.R652C		Atlas-SNP	.											ZNF780B_ENST00000434248,NS,carcinoma,+1,2	ZNF780B	143	2	0			c.C1954T						PASS	.	G	CYS/ARG	266,4134	138.8+/-174.5	5,256,1939	169.0	182.0	178.0		1954	-1.2	0.0	19	dbSNP_132	178	57,8543	35.9+/-90.5	1,55,4244	no	missense	ZNF780B	NM_001005851.2	180	6,311,6183	AA,AG,GG		0.6628,6.0455,2.4846	benign	652/834	40540812	323,12677	2200	4300	6500	SO:0001583	missense	163131	exon5			AGACACGATTAAA	AK127063	CCDS46077.1	19q13.2	2013-01-08	2006-08-15	2006-08-15	ENSG00000128000	ENSG00000128000		"""Zinc fingers, C2H2-type"", ""-"""	33109	protein-coding gene	gene with protein product			"""zinc finger protein 779"""	ZNF779			Standard	NM_001005851		Approved		uc002omu.3	Q9Y6R6	OTTHUMG00000155118	ENST00000434248.1:c.1954C>T	19.37:g.40540812G>A	ENSP00000391641:p.Arg652Cys	113.0	0.0	0		118.0	54.0	0.457627	NM_001005851	B9EH00	Missense_Mutation	SNP	ENST00000434248.1	37	CCDS46077.1	52	0.023809523809523808	34	0.06910569105691057	6	0.016574585635359115	5	0.008741258741258742	7	0.009234828496042216	g	8.444	0.851485	0.17034	0.060455	0.006628	ENSG00000128000	ENST00000434248;ENST00000221355	T;T	0.16073	2.37;2.37	2.56	-1.21	0.09524	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.00695	0.0023	N	0.25957	0.775	0.09310	N	1	B	0.14012	0.009	B	0.06405	0.002	T	0.33214	-0.9877	9	0.33141	T	0.24	.	6.8154	0.23826	0.3924:0.0:0.6076:0.0	.	652	Q9Y6R6	Z780B_HUMAN	C	652;504	ENSP00000391641:R652C;ENSP00000221355:R504C	ENSP00000221355:R504C	R	-	1	0	ZNF780B	45232652	0.000000	0.05858	0.001000	0.08648	0.172000	0.22775	-1.463000	0.02361	-0.088000	0.12506	-0.448000	0.05591	CGT	G|0.979;A|0.021	0.021	strong		0.403	ZNF780B-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000338466.1	NM_001005851	
ZNF287	57336	hgsc.bcm.edu	37	17	16469879	16469879	+	Missense_Mutation	SNP	T	T	C	rs149325980		TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr17:16469879T>C	ENST00000395824.1	-	3	1078	c.461A>G	c.(460-462)cAt>cGt	p.H154R	ZNF287_ENST00000395825.3_Missense_Mutation_p.H154R|ZNF287_ENST00000461555.1_5'Flank			Q9HBT7	ZN287_HUMAN	zinc finger protein 287	147					positive regulation of transcription, DNA-templated (GO:0045893)|regulation of cytokine biosynthetic process (GO:0042035)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(1)|endometrium(3)|kidney(2)|large_intestine(7)|lung(5)|prostate(1)|urinary_tract(1)	20				UCEC - Uterine corpus endometrioid carcinoma (92;0.083)		CTGGAAAGCATGTTTTCCTCT	0.438																																					p.H154R		Atlas-SNP	.											.	ZNF287	60	.	0			c.A461G						PASS	.						170.0	167.0	168.0					17																	16469879		2203	4300	6503	SO:0001583	missense	57336	exon3			AAAGCATGTTTTC	AF217227	CCDS11179.2	17p11.2	2013-01-09			ENSG00000141040	ENSG00000141040		"""Zinc fingers, C2H2-type"", ""-"", ""-"", ""-"""	13502	protein-coding gene	gene with protein product							Standard	NM_020653		Approved	ZKSCAN13, ZSCAN45	uc002gqi.2	Q9HBT7	OTTHUMG00000058993	ENST00000395824.1:c.461A>G	17.37:g.16469879T>C	ENSP00000379168:p.His154Arg	131.0	0.0	0		154.0	85.0	0.551948	NM_020653	Q6IAG1	Missense_Mutation	SNP	ENST00000395824.1	37	CCDS11179.2	.	.	.	.	.	.	.	.	.	.	T	5.385	0.256302	0.10185	.	.	ENSG00000141040	ENST00000395825;ENST00000395824	T;T	0.04809	3.55;3.55	4.18	-2.2	0.06994	Transcription regulator SCAN (1);	1.448190	0.04304	N	0.347863	T	0.02533	0.0077	N	0.08118	0	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.45556	-0.9253	10	0.15952	T	0.53	.	5.8246	0.18546	0.0:0.189:0.5011:0.3099	.	147	Q9HBT7	ZN287_HUMAN	R	154	ENSP00000379169:H154R;ENSP00000379168:H154R	ENSP00000379168:H154R	H	-	2	0	ZNF287	16410604	0.001000	0.12720	0.026000	0.17262	0.849000	0.48306	-0.217000	0.09253	-0.462000	0.06984	-0.290000	0.09829	CAT	T|1.000;A|0.000	.	alt		0.438	ZNF287-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000130504.1		
PCTP	58488	hgsc.bcm.edu	37	17	53844742	53844742	+	Missense_Mutation	SNP	G	G	A	rs112454522	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr17:53844742G>A	ENST00000268896.5	+	2	313	c.188G>A	c.(187-189)tGc>tAc	p.C63Y	PCTP_ENST00000576183.1_Missense_Mutation_p.C63Y|PCTP_ENST00000325214.6_5'UTR|PCTP_ENST00000573500.1_Missense_Mutation_p.C63Y	NM_021213.3	NP_067036.2	Q9UKL6	PPCT_HUMAN	phosphatidylcholine transfer protein	63	START. {ECO:0000255|PROSITE- ProRule:PRU00197}.				cholesterol metabolic process (GO:0008203)|lipid transport (GO:0006869)|phospholipid transport (GO:0015914)	cytosol (GO:0005829)	phosphatidylcholine binding (GO:0031210)|phosphatidylcholine transporter activity (GO:0008525)			endometrium(1)|kidney(1)|large_intestine(2)|lung(5)|skin(1)	10			BRCA - Breast invasive adenocarcinoma(1;0.00207)			CTGGAGGACTGCTCACCAACT	0.383													G|||	11	0.00219649	0.0	0.0029	5008	,	,		18999	0.0		0.0089	False		,,,				2504	0.0				p.C63Y		Atlas-SNP	.											.	PCTP	17	.	0			c.G188A						PASS	.	G	,TYR/CYS	7,4399	12.9+/-30.5	0,7,2196	138.0	125.0	129.0		,188	5.6	0.1	17	dbSNP_132	129	84,8516	48.5+/-108.0	1,82,4217	yes	utr-5,missense	PCTP	NM_001102402.2,NM_021213.3	,194	1,89,6413	AA,AG,GG		0.9767,0.1589,0.6997	,probably-damaging	,63/215	53844742	91,12915	2203	4300	6503	SO:0001583	missense	58488	exon2			AGGACTGCTCACC	AK024667	CCDS11588.1, CCDS45741.1	17q21-q24	2011-09-13				ENSG00000141179		"""StAR-related lipid transfer (START) domain containing"""	8752	protein-coding gene	gene with protein product	"""StAR-related lipid transfer (START) domain containing 2"""	606055					Standard	NM_021213		Approved	STARD2	uc002iul.4	Q9UKL6		ENST00000268896.5:c.188G>A	17.37:g.53844742G>A	ENSP00000268896:p.Cys63Tyr	112.0	0.0	0		97.0	51.0	0.525773	NM_021213	Q9BSC9|Q9UIT3|Q9UKW7	Missense_Mutation	SNP	ENST00000268896.5	37	CCDS11588.1	9	0.004120879120879121	0	0.0	2	0.0055248618784530384	0	0.0	7	0.009234828496042216	G	25.3	4.628072	0.87560	0.001589	0.009767	ENSG00000141179	ENST00000268896;ENST00000325214	T	0.42131	0.98	5.64	5.64	0.86602	Lipid-binding START (3);START-like domain (1);	0.111691	0.64402	D	0.000007	T	0.56202	0.1969	M	0.77820	2.39	0.80722	D	1	D;D	0.67145	0.996;0.996	D;D	0.66497	0.944;0.944	T	0.63712	-0.6575	10	0.56958	D	0.05	-12.5478	15.2077	0.73192	0.0:0.0:1.0:0.0	.	63;63	Q549N3;Q9UKL6	.;PPCT_HUMAN	Y	63;42	ENSP00000268896:C63Y	ENSP00000268896:C63Y	C	+	2	0	PCTP	51199741	1.000000	0.71417	0.093000	0.20910	0.500000	0.33767	6.637000	0.74304	2.642000	0.89623	0.650000	0.86243	TGC	G|0.993;A|0.007	0.007	strong		0.383	PCTP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000439271.2	NM_021213	
HAGH	3029	hgsc.bcm.edu	37	16	1869940	1869940	+	Silent	SNP	G	G	A	rs146440574	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr16:1869940G>A	ENST00000397356.3	-	4	796	c.390C>T	c.(388-390)atC>atT	p.I130I	HAGH_ENST00000566709.1_Silent_p.I82I|HAGH_ENST00000455446.2_Silent_p.I130I|HAGH_ENST00000397353.2_Silent_p.I82I	NM_005326.4	NP_005317.2	Q16775	GLO2_HUMAN	hydroxyacylglutathione hydrolase	130					glutathione biosynthetic process (GO:0006750)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)	hydroxyacylglutathione hydrolase activity (GO:0004416)|zinc ion binding (GO:0008270)			kidney(2)|lung(1)|ovary(1)|skin(1)	5		Hepatocellular(780;0.00335)			Glutathione(DB00143)	TCAGGGCCCCGATACGGTCGT	0.612													G|||	6	0.00119808	0.003	0.0014	5008	,	,		15540	0.0		0.0	False		,,,				2504	0.001				p.I130I	Pancreas(55;1048 1176 25227 40124 41333)	Atlas-SNP	.											.	HAGH	20	.	0			c.C390T						PASS	.	G	,	19,4379	25.3+/-52.1	0,19,2180	126.0	99.0	108.0		246,390	-10.0	0.6	16	dbSNP_134	108	3,8597	3.0+/-9.4	0,3,4297	no	coding-synonymous,coding-synonymous	HAGH	NM_001040427.1,NM_005326.4	,	0,22,6477	AA,AG,GG		0.0349,0.432,0.1693	,	82/261,130/309	1869940	22,12976	2199	4300	6499	SO:0001819	synonymous_variant	3029	exon4			GGCCCCGATACGG	X90999	CCDS32366.1, CCDS10447.2, CCDS66900.1	16p13.3	2012-10-02	2003-11-04		ENSG00000063854	ENSG00000063854	3.1.2.6		4805	protein-coding gene	gene with protein product		138760	"""hydroxyacyl glutathione hydrolase"""			3025077, 7327557	Standard	NM_001286249		Approved	GLO2, GLXII, HAGH1	uc002cna.3	Q16775	OTTHUMG00000128662	ENST00000397356.3:c.390C>T	16.37:g.1869940G>A		89.0	0.0	0		94.0	50.0	0.531915	NM_005326	A8K290|B4DP33|B4DRA7|E7EN93	Silent	SNP	ENST00000397356.3	37	CCDS10447.2																																																																																			G|0.999;A|0.001	0.001	strong		0.612	HAGH-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000250548.2	NM_005326	
DEK	7913	hgsc.bcm.edu	37	6	18258286	18258286	+	Silent	SNP	C	C	T	rs144486575	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr6:18258286C>T	ENST00000397239.3	-	4	702	c.255G>A	c.(253-255)ggG>ggA	p.G85G	DEK_ENST00000244776.7_Silent_p.G51G	NM_003472.3	NP_003463.1	P35659	DEK_HUMAN	DEK proto-oncogene	85					chromatin modification (GO:0016568)|regulation of double-strand break repair (GO:2000779)|regulation of double-strand break repair via nonhomologous end joining (GO:2001032)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|signal transduction (GO:0007165)|transcription from RNA polymerase II promoter (GO:0006366)|viral genome replication (GO:0019079)	nucleus (GO:0005634)	DNA binding (GO:0003677)|histone binding (GO:0042393)|poly(A) RNA binding (GO:0044822)			endometrium(1)|kidney(1)|large_intestine(2)|lung(1)|prostate(1)|upper_aerodigestive_tract(1)	7	Ovarian(93;0.00769)|Breast(50;0.0495)	all_hematologic(90;0.053)	OV - Ovarian serous cystadenocarcinoma(7;0.00291)|all cancers(50;0.031)|Epithelial(50;0.0332)			AAAGTTTCTGCCCCTTTCCTG	0.308			T	NUP214	AML																																p.G85G		Atlas-SNP	.		Dom	yes		6	6p23	7913	DEK oncogene (DNA binding)		L	.	DEK	31	.	0			c.G255A						PASS	.	C	,	2,4402	4.2+/-10.8	0,2,2200	59.0	58.0	58.0		153,255	-7.4	0.6	6	dbSNP_134	58	4,8594	3.0+/-9.4	0,4,4295	no	coding-synonymous,coding-synonymous	DEK	NM_001134709.1,NM_003472.3	,	0,6,6495	TT,TC,CC		0.0465,0.0454,0.0461	,	51/342,85/376	18258286	6,12996	2202	4299	6501	SO:0001819	synonymous_variant	7913	exon4			TTTCTGCCCCTTT	X64229	CCDS34344.1, CCDS47382.1	6p23	2014-06-25	2014-06-25		ENSG00000124795	ENSG00000124795			2768	protein-coding gene	gene with protein product		125264	"""DEK oncogene (DNA binding)"", ""DEK oncogene"""			1549122	Standard	NM_003472		Approved	D6S231E	uc003ncr.1	P35659	OTTHUMG00000014319	ENST00000397239.3:c.255G>A	6.37:g.18258286C>T		35.0	0.0	0		42.0	20.0	0.47619	NM_003472	B2R6K6|B4DN37|Q5TGV4|Q5TGV5	Silent	SNP	ENST00000397239.3	37	CCDS34344.1																																																																																			C|0.999;T|0.001	0.001	strong		0.308	DEK-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000039962.4		
NDUFAF7	55471	hgsc.bcm.edu	37	2	37459326	37459326	+	Missense_Mutation	SNP	C	C	T	rs146409773		TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr2:37459326C>T	ENST00000002125.4	+	2	173	c.133C>T	c.(133-135)Cgg>Tgg	p.R45W	NDUFAF7_ENST00000483999.1_Intron|CEBPZ_ENST00000234170.5_5'Flank|NDUFAF7_ENST00000336237.6_Missense_Mutation_p.R45W	NM_144736.4	NP_653337.1	Q7L592	NDUF7_HUMAN	NADH dehydrogenase (ubiquinone) complex I, assembly factor 7	45					methylation (GO:0032259)|mitochondrial respiratory chain complex I assembly (GO:0032981)	extracellular space (GO:0005615)|mitochondrion (GO:0005739)	enzyme binding (GO:0019899)|methyltransferase activity (GO:0008168)										GCCGATGCTGCGGCATCTTAT	0.483																																					p.R45W		Atlas-SNP	.											.	.	.	.	0			c.C133T						PASS	.	C	TRP/ARG,TRP/ARG	1,4405	2.1+/-5.4	0,1,2202	110.0	103.0	105.0		133,133	3.7	1.0	2	dbSNP_134	105	1,8599	1.2+/-3.3	0,1,4299	no	missense,missense	C2orf56	NM_001083946.1,NM_144736.4	101,101	0,2,6501	TT,TC,CC		0.0116,0.0227,0.0154	probably-damaging,probably-damaging	45/344,45/442	37459326	2,13004	2203	4300	6503	SO:0001583	missense	55471	exon2			ATGCTGCGGCATC		CCDS1788.1, CCDS42673.1	2p22.2	2012-10-12	2012-10-12	2012-10-12	ENSG00000003509	ENSG00000003509		"""Mitochondrial respiratory chain complex assembly factors"""	28816	protein-coding gene	gene with protein product	"""mitochondrial dysfunction protein A homolog"""	615898	"""chromosome 2 open reading frame 56"""	C2orf56			Standard	NM_144736		Approved	PRO1853, MidA	uc002rqa.4	Q7L592	OTTHUMG00000128468	ENST00000002125.4:c.133C>T	2.37:g.37459326C>T	ENSP00000002125:p.Arg45Trp	115.0	0.0	0		133.0	65.0	0.488722	NM_001083946	Q7Z399|Q9P1G3	Missense_Mutation	SNP	ENST00000002125.4	37	CCDS1788.1	.	.	.	.	.	.	.	.	.	.	C	19.76	3.887012	0.72410	2.27E-4	1.16E-4	ENSG00000003509	ENST00000002125;ENST00000336237;ENST00000416653;ENST00000439218;ENST00000432075	T;T	0.76448	-1.02;-1.02	5.51	3.7	0.42460	.	0.339095	0.29631	N	0.011611	D	0.88392	0.6424	M	0.86864	2.845	0.21499	N	0.999661	D;D;D;D	0.89917	0.999;1.0;1.0;0.999	D;D;D;D	0.68765	0.929;0.913;0.96;0.929	T	0.82281	-0.0535	10	0.87932	D	0	-12.9679	13.9833	0.64317	0.5203:0.4797:0.0:0.0	.	45;45;45;45	E7EUC2;B4DQY3;Q7L592-2;Q7L592	.;.;.;MIDA_HUMAN	W	45;45;3;3;3	ENSP00000002125:R45W;ENSP00000337431:R45W	ENSP00000002125:R45W	R	+	1	2	C2orf56	37312830	1.000000	0.71417	1.000000	0.80357	0.966000	0.64601	1.134000	0.31442	0.677000	0.31305	-0.270000	0.10280	CGG	C|1.000;T|0.000	0.000	weak		0.483	NDUFAF7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250267.1	NM_144736	
MGEA5	10724	hgsc.bcm.edu	37	10	103577629	103577629	+	Missense_Mutation	SNP	C	C	T	rs35402016	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr10:103577629C>T	ENST00000361464.3	-	1	546	c.151G>A	c.(151-153)Gcc>Acc	p.A51T	MGEA5_ENST00000419011.2_Missense_Mutation_p.A51T|MGEA5_ENST00000439817.1_Missense_Mutation_p.A51T|MGEA5_ENST00000357797.5_Missense_Mutation_p.A51T|KCNIP2-AS1_ENST00000412353.1_RNA|MGEA5_ENST00000370094.3_Missense_Mutation_p.A51T	NM_012215.3	NP_036347.1	O60502	OGA_HUMAN	meningioma expressed antigen 5 (hyaluronidase)	51					aging (GO:0007568)|dATP metabolic process (GO:0046060)|glycoprotein catabolic process (GO:0006516)|N-acetylglucosamine metabolic process (GO:0006044)|necrotic cell death (GO:0070265)|negative regulation of cardiac muscle adaptation (GO:0010616)|negative regulation of protein glycosylation (GO:0060051)|positive regulation of calcium ion transport into cytosol (GO:0010524)|positive regulation of cell killing (GO:0031343)|positive regulation of DNA metabolic process (GO:0051054)|positive regulation of glucose import (GO:0046326)|positive regulation of growth hormone secretion (GO:0060124)|positive regulation of insulin secretion (GO:0032024)|positive regulation of mitochondrial depolarization (GO:0051901)|positive regulation of protein complex disassembly (GO:0043243)|positive regulation of proteolysis (GO:0045862)|protein targeting to membrane (GO:0006612)|response to steroid hormone (GO:0048545)	cytoplasm (GO:0005737)|membrane (GO:0016020)|nucleus (GO:0005634)	histone acetyltransferase activity (GO:0004402)|hyalurononglucosaminidase activity (GO:0004415)			central_nervous_system(1)|endometrium(2)|kidney(2)|large_intestine(3)|lung(11)|ovary(2)|skin(1)|urinary_tract(1)	23		Colorectal(252;0.207)		Epithelial(162;4.67e-09)|all cancers(201;2.54e-07)		GCAGCCCCGGCCACCGCCGCT	0.721													C|||	10	0.00199681	0.0	0.0014	5008	,	,		11090	0.0		0.006	False		,,,				2504	0.0031				p.A51T		Atlas-SNP	.											.	MGEA5	53	.	0			c.G151A						PASS	.	C	THR/ALA,THR/ALA	2,3740		0,2,1869	6.0	7.0	6.0		151,151	1.8	0.2	10	dbSNP_126	6	38,7546		0,38,3754	no	missense,missense	MGEA5	NM_001142434.1,NM_012215.3	58,58	0,40,5623	TT,TC,CC		0.5011,0.0534,0.3532	benign,benign	51/864,51/917	103577629	40,11286	1871	3792	5663	SO:0001583	missense	10724	exon1			CCCCGGCCACCGC	AF036144	CCDS7520.1, CCDS44471.1	10q24.1-q24.3	2008-08-01			ENSG00000198408	ENSG00000198408			7056	protein-coding gene	gene with protein product	"""nuclear cytoplasmic O-GlcNAcase and acetyltransferase"""	604039				9811929, 16356930	Standard	NM_012215		Approved	MEA5, NCOAT, OGA	uc001ktv.2	O60502	OTTHUMG00000018939	ENST00000361464.3:c.151G>A	10.37:g.103577629C>T	ENSP00000354850:p.Ala51Thr	13.0	0.0	0		21.0	11.0	0.52381	NM_001142434	B7WPB9|D3DR79|E9PGF9|O75166|Q86WV0|Q8IV98|Q9BVA5|Q9HAR0	Missense_Mutation	SNP	ENST00000361464.3	37	CCDS7520.1	7	0.003205128205128205	0	0.0	1	0.0027624309392265192	0	0.0	6	0.0079155672823219	C	10.90	1.481501	0.26598	5.34E-4	0.005011	ENSG00000198408	ENST00000439817;ENST00000361464;ENST00000357797;ENST00000370094;ENST00000419011	T;T;T;T;T	0.47869	1.49;1.5;1.5;1.49;0.83	4.71	1.76	0.24704	.	0.766530	0.11933	N	0.515498	T	0.18173	0.0436	N	0.14661	0.345	0.21020	N	0.999804	B;B;B;B	0.06786	0.0;0.0;0.001;0.0	B;B;B;B	0.06405	0.0;0.001;0.002;0.0	T	0.22417	-1.0217	10	0.13853	T	0.58	-0.0165	5.4435	0.16521	0.0:0.5247:0.1481:0.3272	rs35402016	51;51;51;51	E9PGF9;O60502-2;O60502-3;O60502	.;.;.;NCOAT_HUMAN	T	51	ENSP00000409973:A51T;ENSP00000354850:A51T;ENSP00000350445:A51T;ENSP00000359112:A51T;ENSP00000407081:A51T	ENSP00000350445:A51T	A	-	1	0	MGEA5	103567619	0.070000	0.21116	0.189000	0.23252	0.328000	0.28507	-0.171000	0.09883	0.141000	0.18875	0.561000	0.74099	GCC	C|0.996;T|0.004	0.004	strong		0.721	MGEA5-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049987.1	NM_012215	
SLC9A3R2	9351	hgsc.bcm.edu	37	16	2079665	2079665	+	Missense_Mutation	SNP	G	G	A	rs55864883		TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr16:2079665G>A	ENST00000424542.2	+	2	434	c.296G>A	c.(295-297)cGg>cAg	p.R99Q	SLC9A3R2_ENST00000563587.1_5'UTR|SLC9A3R2_ENST00000432365.2_Missense_Mutation_p.R99Q	NM_001130012.2|NM_004785.5	NP_001123484.1|NP_004776.3	Q15599	NHRF2_HUMAN	solute carrier family 9, subfamily A (NHE3, cation proton antiporter 3), member 3 regulator 2	99					negative regulation of phosphatidylinositol 3-kinase signaling (GO:0014067)|protein complex assembly (GO:0006461)	apical plasma membrane (GO:0016324)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	beta-catenin binding (GO:0008013)|phosphatase binding (GO:0019902)|protein C-terminus binding (GO:0008022)|receptor binding (GO:0005102)			central_nervous_system(1)|endometrium(1)	2						CTCCGCCGGCGGCAGCTGACC	0.682																																					p.R99Q	Ovarian(69;105 1552 17724 23473)	Atlas-SNP	.											.	SLC9A3R2	24	.	0			c.G296A						PASS	.	G	GLN/ARG,GLN/ARG	1,4107		0,1,2053	27.0	38.0	34.0		296,296	3.7	1.0	16	dbSNP_129	34	8,8288		0,8,4140	no	missense,missense	SLC9A3R2	NM_001130012.1,NM_004785.4	43,43	0,9,6193	AA,AG,GG		0.0964,0.0243,0.0726	possibly-damaging,possibly-damaging	99/338,99/327	2079665	9,12395	2054	4148	6202	SO:0001583	missense	9351	exon2			GCCGGCGGCAGCT	AF004900	CCDS45382.1, CCDS45383.1, CCDS58407.1	16p13.3	2014-09-04	2012-03-22		ENSG00000065054	ENSG00000065054			11076	protein-coding gene	gene with protein product		606553	"""solute carrier family 9 (sodium/hydrogen exchanger), isoform 3 regulatory factor 2"", ""solute carrier family 9 (sodium/hydrogen exchanger), isoform 3 regulator 2"", ""solute carrier family 9 (sodium/hydrogen exchanger), member 3 regulator 2"""			9054412, 9671706	Standard	NM_001130012		Approved	SIP-1, TKA-1, NHERF-2, E3KARP	uc002coi.3	Q15599	OTTHUMG00000176956	ENST00000424542.2:c.296G>A	16.37:g.2079665G>A	ENSP00000408005:p.Arg99Gln	107.0	0.0	0		101.0	48.0	0.475248	NM_004785	D3DU84|D3DU85|H3BSV6|O00272|O00556|Q3KQY7	Missense_Mutation	SNP	ENST00000424542.2	37	CCDS45382.1	.	.	.	.	.	.	.	.	.	.	G	15.33	2.801819	0.50315	2.43E-4	9.64E-4	ENSG00000065054	ENST00000424542;ENST00000432365	T;T	0.20463	2.09;2.07	4.8	3.74	0.42951	PDZ/DHR/GLGF (1);	0.398384	0.22670	N	0.057068	T	0.12646	0.0307	N	0.22421	0.69	0.80722	D	1	B;P	0.49862	0.146;0.929	B;B	0.41619	0.012;0.361	T	0.07065	-1.0792	10	0.11794	T	0.64	-7.4822	11.2924	0.49258	0.0:0.0:0.7611:0.2389	rs55864883;rs62617116	99;99	D3DU85;Q15599	.;NHRF2_HUMAN	Q	99	ENSP00000408005:R99Q;ENSP00000402857:R99Q	ENSP00000408005:R99Q	R	+	2	0	SLC9A3R2	2019666	1.000000	0.71417	1.000000	0.80357	0.985000	0.73830	1.942000	0.40243	2.215000	0.71742	0.561000	0.74099	CGG	.	.	weak		0.682	SLC9A3R2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000434448.1		
CNOT4	4850	hgsc.bcm.edu	37	7	135123060	135123060	+	Missense_Mutation	SNP	G	G	C	rs17480616	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr7:135123060G>C	ENST00000315544.5	-	2	299	c.20C>G	c.(19-21)gCg>gGg	p.A7G	CNOT4_ENST00000423368.2_Missense_Mutation_p.A7G|CNOT4_ENST00000451834.1_Missense_Mutation_p.A7G|CNOT4_ENST00000541284.1_Missense_Mutation_p.A7G|CNOT4_ENST00000356162.4_Missense_Mutation_p.A7G|CNOT4_ENST00000361528.4_Missense_Mutation_p.A7G|CNOT4_ENST00000428680.2_Missense_Mutation_p.A7G|CNOT4_ENST00000414802.1_Missense_Mutation_p.A7G	NM_001190848.1	NP_001177777.1	O95628	CNOT4_HUMAN	CCR4-NOT transcription complex, subunit 4	7			A -> G (in dbSNP:rs17480616). {ECO:0000269|Ref.3}.		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						GTCTTCCTTCGCATCAGGACT	0.433													G|||	37	0.00738818	0.0023	0.0173	5008	,	,		17128	0.0		0.0209	False		,,,				2504	0.001				p.A7G	Ovarian(51;766 1130 5502 35047 50875)	Atlas-SNP	.											.	CNOT4	146	.	0			c.C20G						PASS	.	G	GLY/ALA,GLY/ALA,GLY/ALA,GLY/ALA,GLY/ALA,GLY/ALA	17,3759		0,17,1871	67.0	63.0	65.0		20,20,20,20,20,20	1.5	1.0	7	dbSNP_123	65	228,7992		4,220,3886	yes	missense,missense,missense,missense,missense,missense	CNOT4	NM_001008225.2,NM_001190847.1,NM_001190848.1,NM_001190849.1,NM_001190850.1,NM_013316.3	60,60,60,60,60,60	4,237,5757	CC,CG,GG		2.7737,0.4502,2.0423	benign,benign,benign,benign,benign,benign	7/573,7/643,7/576,7/711,7/714,7/640	135123060	245,11751	1888	4110	5998	SO:0001583	missense	4850	exon2			TCCTTCGCATCAG	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.20C>G	7.37:g.135123060G>C	ENSP00000326731:p.Ala7Gly	133.0	0.0	0		105.0	49.0	0.466667	NM_001190850	B7Z6I4|E7ET38|F8VQP3|O95339|O95627|Q8IYM7|Q8NCL0|Q9NPQ1|Q9NZN6	Missense_Mutation	SNP	ENST00000315544.5	37	CCDS55166.1	27	0.012362637362637362	2	0.0040650406504065045	11	0.03038674033149171	0	0.0	14	0.018469656992084433	G	12.53	1.964625	0.34659	0.004502	0.027737	ENSG00000080802	ENST00000541284;ENST00000451834;ENST00000423368;ENST00000262563;ENST00000361528;ENST00000414802;ENST00000356162;ENST00000428680;ENST00000315544	D;D;D;D;D;D;D;D	0.86164	-2.08;-2.08;-2.08;-2.08;-2.08;-2.08;-2.08;-2.08	5.87	1.55	0.23275	Zinc finger, RING/FYVE/PHD-type (1);	0.373548	0.33938	N	0.004417	T	0.50103	0.1596	N	0.14661	0.345	0.21290	N	0.999735	B;B;B;P;B;B	0.34997	0.211;0.315;0.405;0.479;0.019;0.019	B;B;B;B;B;B	0.31946	0.071;0.138;0.102;0.119;0.022;0.022	T	0.54063	-0.8349	10	0.32370	T	0.25	0.5143	9.3711	0.38254	0.4834:0.0:0.5166:0.0	rs17480616;rs52814664;rs17480616	7;7;7;7;7;7	E7ET38;F8VQP3;O95628;O95628-2;O95628-4;O95628-8	.;.;CNOT4_HUMAN;.;.;.	G	7	ENSP00000445508:A7G;ENSP00000388491:A7G;ENSP00000406777:A7G;ENSP00000354673:A7G;ENSP00000416532:A7G;ENSP00000348485:A7G;ENSP00000399108:A7G;ENSP00000326731:A7G	ENSP00000262563:A7G	A	-	2	0	CNOT4	134773600	0.999000	0.42202	0.976000	0.42696	0.929000	0.56500	1.442000	0.35046	-0.007000	0.14345	0.655000	0.94253	GCG	G|0.983;C|0.017	0.017	strong		0.433	CNOT4-201	KNOWN	basic|CCDS	protein_coding	protein_coding		NM_013316	
CIT	11113	hgsc.bcm.edu	37	12	120260706	120260706	+	Silent	SNP	G	G	A	rs145804827		TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr12:120260706G>A	ENST00000261833.7	-	9	1081	c.1029C>T	c.(1027-1029)tgC>tgT	p.C343C	CIT_ENST00000392521.2_Silent_p.C343C	NM_007174.2	NP_009105.1	O14578	CTRO_HUMAN	citron rho-interacting serine/threonine kinase	343	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				cytokinesis (GO:0000910)|dendrite development (GO:0016358)|G2/M transition of mitotic cell cycle (GO:0000086)|generation of neurons (GO:0048699)|Golgi organization (GO:0007030)|intracellular signal transduction (GO:0035556)|metaphase/anaphase transition of mitotic cell cycle (GO:0007091)|mitotic nuclear division (GO:0007067)|mitotic sister chromatid segregation (GO:0000070)|negative regulation of dendrite morphogenesis (GO:0050774)|regulation of actin polymerization or depolymerization (GO:0008064)|spermatogenesis (GO:0007283)	actin cytoskeleton (GO:0015629)|Golgi cisterna (GO:0031985)|membrane (GO:0016020)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)|ruffle (GO:0001726)|vacuole (GO:0005773)	ATP binding (GO:0005524)|metal ion binding (GO:0046872)|PDZ domain binding (GO:0030165)|protein serine/threonine kinase activity (GO:0004674)|small GTPase regulator activity (GO:0005083)			breast(6)|endometrium(9)|kidney(4)|large_intestine(15)|liver(1)|lung(29)|ovary(7)|prostate(4)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(6)	86	all_neural(191;0.0804)|Medulloblastoma(191;0.0922)	Myeloproliferative disorder(1001;0.0255)		BRCA - Breast invasive adenocarcinoma(302;0.211)		CTTTCTGGCCGCACAACAAGC	0.388													A|||	1	0.000199681	0.0	0.0	5008	,	,		17060	0.0		0.001	False		,,,				2504	0.0				p.C343C		Atlas-SNP	.											.	CIT	535	.	0			c.C1029T						PASS	.	A	,	1,4405	826.1+/-416.6	0,1,2202	100.0	94.0	96.0		1029,1029	4.6	1.0	12	dbSNP_134	96	8,8592	818.9+/-406.8	0,8,4292	no	coding-synonymous,coding-synonymous	CIT	NM_001206999.1,NM_007174.2	,	0,9,6494	AA,AG,GG		0.093,0.0227,0.0692	,	343/2070,343/2028	120260706	9,12997	2203	4300	6503	SO:0001819	synonymous_variant	11113	exon9			CTGGCCGCACAAC	AB023166	CCDS9192.1, CCDS55891.1	12q24.23	2014-04-23	2014-04-23		ENSG00000122966	ENSG00000122966			1985	protein-coding gene	gene with protein product	"""serine/threonine kinase 21"""	605629	"""citron (rho-interacting, serine/threonine kinase 21)"""			9792683	Standard	NM_001206999		Approved	KIAA0949, STK21, CRIK	uc001txj.2	O14578	OTTHUMG00000134325	ENST00000261833.7:c.1029C>T	12.37:g.120260706G>A		146.0	0.0	0		139.0	64.0	0.460432	NM_001206999	Q2M5E1|Q6XUH8|Q86UQ9|Q9UPZ7	Silent	SNP	ENST00000261833.7	37	CCDS9192.1																																																																																			G|0.999;A|0.001	0.001	strong		0.388	CIT-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000259410.4	NM_007174	
UGT3A2	167127	hgsc.bcm.edu	37	5	36037933	36037933	+	Missense_Mutation	SNP	C	C	T			TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr5:36037933C>T	ENST00000282507.3	-	6	1362	c.1261G>A	c.(1261-1263)Gct>Act	p.A421T	UGT3A2_ENST00000513300.1_Missense_Mutation_p.A387T|UGT3A2_ENST00000545528.1_Missense_Mutation_p.A119T|UGT3A2_ENST00000504954.1_5'Flank	NM_174914.3	NP_777574.2	Q3SY77	UD3A2_HUMAN	UDP glycosyltransferase 3 family, polypeptide A2	421					cellular response to genistein (GO:0071412)	integral component of membrane (GO:0016021)	glucuronosyltransferase activity (GO:0015020)|UDP-glycosyltransferase activity (GO:0008194)			NS(1)|autonomic_ganglia(1)|breast(1)|cervix(1)|endometrium(2)|kidney(1)|large_intestine(9)|lung(20)|ovary(2)|pancreas(1)|prostate(1)|skin(3)	43	all_lung(31;0.000179)		Lung(74;0.111)|Epithelial(62;0.113)|COAD - Colon adenocarcinoma(61;0.14)|Colorectal(62;0.202)			ATCTTAAGAGCCAATGTCTCT	0.438																																					p.A421T		Atlas-SNP	.											.	UGT3A2	117	.	0			c.G1261A						PASS	.						174.0	160.0	165.0					5																	36037933		2203	4300	6503	SO:0001583	missense	167127	exon6			TAAGAGCCAATGT		CCDS3914.1, CCDS54842.1	5p13.2	2014-05-20			ENSG00000168671	ENSG00000168671		"""UDP glucuronosyltransferases"""	27266	protein-coding gene	gene with protein product						12975309	Standard	NM_174914		Approved		uc003jjz.2	Q3SY77	OTTHUMG00000131108	ENST00000282507.3:c.1261G>A	5.37:g.36037933C>T	ENSP00000282507:p.Ala421Thr	96.0	0.0	0		128.0	57.0	0.445312	NM_174914	B4DUQ7|E9PFK7|Q6UXC4|Q8NBP2	Missense_Mutation	SNP	ENST00000282507.3	37	CCDS3914.1	.	.	.	.	.	.	.	.	.	.	C	8.741	0.918940	0.17982	.	.	ENSG00000168671	ENST00000282507;ENST00000513300;ENST00000545528	T;T;T	0.63580	-0.05;-0.05;3.2	3.18	0.239	0.15484	.	0.283721	0.27802	U	0.017798	T	0.48677	0.1513	L	0.42581	1.335	0.09310	N	1	B;B	0.26400	0.009;0.148	B;B	0.31191	0.024;0.125	T	0.36939	-0.9727	10	0.37606	T	0.19	.	6.4334	0.21809	0.3166:0.5888:0.0:0.0946	.	387;421	E9PFK7;Q3SY77	.;UD3A2_HUMAN	T	421;387;119	ENSP00000282507:A421T;ENSP00000427404:A387T;ENSP00000445367:A119T	ENSP00000282507:A421T	A	-	1	0	UGT3A2	36073690	0.000000	0.05858	0.014000	0.15608	0.623000	0.37688	-0.069000	0.11542	0.018000	0.15052	0.563000	0.77884	GCT	.	.	none		0.438	UGT3A2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253771.2	NM_174914	
FAM175B	23172	hgsc.bcm.edu	37	10	126515249	126515249	+	Missense_Mutation	SNP	G	G	A	rs140695652	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr10:126515249G>A	ENST00000298492.5	+	5	398	c.353G>A	c.(352-354)cGc>cAc	p.R118H		NM_032182.3	NP_115558.3	Q15018	F175B_HUMAN	family with sequence similarity 175, member B	118					cellular response to freezing (GO:0071497)	BRISC complex (GO:0070552)|cytoplasm (GO:0005737)	polyubiquitin binding (GO:0031593)			NS(1)	1						CAGCTCACCCGCATCCTCGGC	0.498													G|||	2	0.000399361	0.0	0.0014	5008	,	,		20576	0.0		0.001	False		,,,				2504	0.0				p.R118H		Atlas-SNP	.											.	FAM175B	39	.	0			c.G353A						PASS	.	G	HIS/ARG	1,4405	2.1+/-5.4	0,1,2202	195.0	173.0	180.0		353	3.8	1.0	10	dbSNP_134	180	5,8595	4.3+/-15.6	0,5,4295	yes	missense	FAM175B	NM_032182.3	29	0,6,6497	AA,AG,GG		0.0581,0.0227,0.0461	benign	118/416	126515249	6,13000	2203	4300	6503	SO:0001583	missense	23172	exon5			TCACCCGCATCCT	D63877	CCDS31308.2	10q26.2	2013-01-24	2008-07-02	2008-07-02	ENSG00000165660	ENSG00000165660			28975	protein-coding gene	gene with protein product	"""Abraxas brother"""	611144	"""KIAA0157"""	KIAA0157		8590280	Standard	NM_032182		Approved	Em:AC068896.4, ABRO1	uc001lib.4	Q15018	OTTHUMG00000019218	ENST00000298492.5:c.353G>A	10.37:g.126515249G>A	ENSP00000298492:p.Arg118His	138.0	0.0	0		132.0	60.0	0.454545	NM_032182	B4DKR2|Q96H11	Missense_Mutation	SNP	ENST00000298492.5	37	CCDS31308.2	0	0.0	0	0.0	0	0.0	0	0.0	0	0.0	G	14.64	2.596729	0.46318	2.27E-4	5.81E-4	ENSG00000165660	ENST00000298492	T	0.43294	0.95	5.82	3.76	0.43208	.	0.413144	0.28459	N	0.015269	T	0.21267	0.0512	N	0.11560	0.145	0.35051	D	0.760609	B	0.12630	0.006	B	0.08055	0.003	T	0.13629	-1.0502	10	0.40728	T	0.16	-9.0446	6.6535	0.22975	0.3087:0.0:0.6913:0.0	.	118	Q15018	F175B_HUMAN	H	118	ENSP00000298492:R118H	ENSP00000298492:R118H	R	+	2	0	FAM175B	126505239	1.000000	0.71417	0.999000	0.59377	0.982000	0.71751	4.660000	0.61511	1.470000	0.48102	0.557000	0.71058	CGC	G|1.000;A|0.000	0.000	strong		0.498	FAM175B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050891.2	NM_032182	
CEP41	95681	hgsc.bcm.edu	37	7	130038814	130038814	+	Missense_Mutation	SNP	T	T	C			TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr7:130038814T>C	ENST00000223208.5	-	11	1310	c.1040A>G	c.(1039-1041)aAt>aGt	p.N347S	CEP41_ENST00000541543.1_Missense_Mutation_p.N259S|CEP41_ENST00000343969.5_Missense_Mutation_p.N275S	NM_001257158.1|NM_018718.2	NP_001244087.1|NP_061188.1	Q9BYV8	CEP41_HUMAN	centrosomal protein 41kDa	347					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)											ACCTGGCAGATTCTGAGCGCT	0.582																																					p.N347S		Atlas-SNP	.											.	.	.	.	0			c.A1040G						PASS	.						104.0	120.0	115.0					7																	130038814		2203	4300	6503	SO:0001583	missense	95681	exon11			GGCAGATTCTGAG	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.1040A>G	7.37:g.130038814T>C	ENSP00000223208:p.Asn347Ser	49.0	0.0	0		89.0	49.0	0.550562	NM_018718	A4D1M0|B4DQ35|F5H0V6|Q7Z496|Q86TM1|Q8NFU8|Q9H6A3|Q9NPV3	Missense_Mutation	SNP	ENST00000223208.5	37	CCDS5821.1	.	.	.	.	.	.	.	.	.	.	T	0.124	-1.121417	0.01785	.	.	ENSG00000106477	ENST00000223208;ENST00000541543;ENST00000343969	D;D;D	0.88586	-2.27;-2.08;-2.4	4.97	-6.65	0.01795	.	0.854162	0.10676	N	0.646990	T	0.67306	0.2879	N	0.04203	-0.255	0.09310	N	1	B;B;B	0.09022	0.001;0.002;0.0	B;B;B	0.06405	0.0;0.002;0.0	T	0.61647	-0.7020	10	0.08599	T	0.76	-0.4038	8.3272	0.32165	0.0:0.5135:0.2736:0.2129	.	259;275;347	F5H0V6;Q9BYV8-2;Q9BYV8	.;.;CEP41_HUMAN	S	347;259;275	ENSP00000223208:N347S;ENSP00000445888:N259S;ENSP00000342738:N275S	ENSP00000223208:N347S	N	-	2	0	TSGA14	129826050	0.807000	0.29009	0.020000	0.16555	0.048000	0.14542	-0.534000	0.06150	-0.868000	0.04058	-0.250000	0.11733	AAT	.	.	none		0.582	CEP41-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000349702.2	NM_018718	
ZNF326	284695	hgsc.bcm.edu	37	1	90482944	90482944	+	Missense_Mutation	SNP	A	A	G	rs200399673		TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr1:90482944A>G	ENST00000340281.4	+	8	1138	c.995A>G	c.(994-996)gAa>gGa	p.E332G	ZNF326_ENST00000370447.3_Missense_Mutation_p.E243G|ZNF326_ENST00000455342.2_Missense_Mutation_p.E126G	NM_182976.2	NP_892021.1	Q5BKZ1	ZN326_HUMAN	zinc finger protein 326	332					mRNA processing (GO:0006397)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of DNA-templated transcription, elongation (GO:0032784)|RNA splicing (GO:0008380)|transcription, DNA-templated (GO:0006351)	DBIRD complex (GO:0044609)|nuclear matrix (GO:0016363)	DNA binding (GO:0003677)|poly(A) RNA binding (GO:0044822)|RNA polymerase II core binding (GO:0000993)|zinc ion binding (GO:0008270)			central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(12)|lung(7)|ovary(1)	25		all_lung(203;0.0116)|Lung NSC(277;0.0417)		all cancers(265;0.00728)|Epithelial(280;0.0265)		CTGCATCTGGAAAGTTCTTCA	0.284																																					p.E332G		Atlas-SNP	.											.	ZNF326	60	.	0			c.A995G						PASS	.	A	GLY/GLU	0,4402		0,0,2201	61.0	62.0	62.0		995	5.5	1.0	1		62	2,8584		0,2,4291	yes	missense	ZNF326	NM_182976.2	98	0,2,6492	GG,GA,AA		0.0233,0.0,0.0154	benign	332/583	90482944	2,12986	2201	4293	6494	SO:0001583	missense	284695	exon8			ATCTGGAAAGTTC	BC013102	CCDS727.1, CCDS728.1	1p22	2012-04-19			ENSG00000162664	ENSG00000162664		"""Zinc fingers, C2H2-type"""	14104	protein-coding gene	gene with protein product	"""ZNF-protein interacting with nuclear mRNPs and DBC1"""	614601				22446626	Standard	NM_182976		Approved	Zfp326, ZAN75, FLJ20403, ZIRD	uc001dnq.2	Q5BKZ1	OTTHUMG00000010675	ENST00000340281.4:c.995A>G	1.37:g.90482944A>G	ENSP00000340796:p.Glu332Gly	141.0	0.0	0		121.0	48.0	0.396694	NM_182976	A8MYX1|B4DLN0|B4E179|Q5VW93|Q5VW94|Q5VW96|Q5VW97|Q6NSA2|Q7Z638|Q7Z6C2	Missense_Mutation	SNP	ENST00000340281.4	37	CCDS727.1	.	.	.	.	.	.	.	.	.	.	A	13.17	2.156916	0.38119	0.0	2.33E-4	ENSG00000162664	ENST00000394590;ENST00000340281;ENST00000370447;ENST00000455342	T;T;T	0.46063	0.88;0.88;0.88	5.48	5.48	0.80851	Zinc finger, C2H2-like (1);	0.187115	0.46758	D	0.000280	T	0.17152	0.0412	L	0.29908	0.895	0.33497	D	0.589491	P;B	0.39094	0.659;0.449	B;B	0.36567	0.228;0.191	T	0.11108	-1.0601	10	0.41790	T	0.15	-16.081	11.5747	0.50854	0.8508:0.1492:0.0:0.0	.	332;332	A8MYX1;Q5BKZ1	.;ZN326_HUMAN	G	332;332;243;126	ENSP00000340796:E332G;ENSP00000359476:E243G;ENSP00000403470:E126G	ENSP00000340796:E332G	E	+	2	0	ZNF326	90255532	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	3.363000	0.52321	2.082000	0.62665	0.529000	0.55759	GAA	A|0.999;G|0.001	0.001	weak		0.284	ZNF326-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000029428.2	NM_181781	
GNB5	10681	hgsc.bcm.edu	37	15	52433397	52433397	+	Silent	SNP	C	C	T	rs17612637	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr15:52433397C>T	ENST00000261837.7	-	7	632	c.567G>A	c.(565-567)aaG>aaA	p.K189K	GNB5_ENST00000358784.7_Silent_p.K147K|CTD-2184D3.7_ENST00000557898.1_RNA|GNB5_ENST00000559348.1_5'Flank|GNB5_ENST00000396335.4_Intron|CTD-2184D3.7_ENST00000560613.1_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		116.0	0.0	0		121.0	60.0	0.495868	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		
MT-ND4	4538	hgsc.bcm.edu	37	M	11920	11920	+	Silent	SNP	C	C	T			TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chrM:11920C>T	ENST00000361381.2	+	1	1161	c.1161C>T	c.(1159-1161)tcC>tcT	p.S387S	MT-CYB_ENST00000361789.2_5'Flank|MT-ND5_ENST00000361567.2_5'Flank|MT-TR_ENST00000387439.1_RNA|MT-TL2_ENST00000387456.1_RNA|MT-TS2_ENST00000387449.1_RNA|MT-TE_ENST00000387459.1_RNA|MT-TG_ENST00000387429.1_RNA|MT-TH_ENST00000387441.1_RNA			P03905	NU4M_HUMAN	mitochondrially encoded NADH dehydrogenase 4	387					cellular metabolic process (GO:0044237)|mitochondrial electron transport, NADH to ubiquinone (GO:0006120)|respiratory electron transport chain (GO:0022904)|small molecule metabolic process (GO:0044281)	integral component of membrane (GO:0016021)|mitochondrial inner membrane (GO:0005743)|mitochondrial respiratory chain complex I (GO:0005747)	NADH dehydrogenase (ubiquinone) activity (GO:0008137)			breast(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(3)|kidney(4)|prostate(1)	13						ACCACGTTCTCCTGATCAAAT	0.458																																					p.S387S		Atlas-SNP	.											.	.	.	.	0			c.C1161T						PASS	.																																			SO:0001819	synonymous_variant	0	exon1			GTTCTCCTGATCA			mitochondria	2014-02-03	2005-02-15	2005-02-16	ENSG00000198886	ENSG00000198886	1.6.5.3	"""Mitochondrial respiratory chain complex / Complex I"""	7459	protein-coding gene	gene with protein product	"""complex I ND4 subunit"", ""NADH-ubiquinone oxidoreductase chain 4"""	516003	"""NADH dehydrogenase 4"", ""Leber optic neuropathy"""	MTND4, LHON		8103501	Standard			Approved	ND4, NAD4		P03905		ENST00000361381.2:c.1161C>T	M.37:g.11920C>T		9.0	0.0	0		8.0	8.0	1	ENST00000361381	Q6RL39|Q6RQN9|Q8HNR8	Silent	SNP	ENST00000361381.2	37																																																																																				.	.	none		0.458	MT-ND4-201	KNOWN	basic|appris_principal	protein_coding	protein_coding		YP_003024035	
RNF157	114804	hgsc.bcm.edu	37	17	74208466	74208466	+	Silent	SNP	A	A	G	rs61760884	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr17:74208466A>G	ENST00000269391.6	-	2	318	c.186T>C	c.(184-186)ttT>ttC	p.F62F	RNF157_ENST00000319945.6_Silent_p.F62F|RNF157_ENST00000592271.1_Silent_p.F62F	NM_052916.2	NP_443148.1	Q96PX1	RN157_HUMAN	ring finger protein 157	62							zinc ion binding (GO:0008270)			breast(1)|central_nervous_system(1)|cervix(1)|large_intestine(3)|lung(12)|ovary(2)|prostate(1)|skin(1)|stomach(2)|urinary_tract(1)	25			LUSC - Lung squamous cell carcinoma(166;0.187)			TGTTCCCCAGAAAGTTCAGAT	0.413													A|||	11	0.00219649	0.0	0.0014	5008	,	,		19125	0.0		0.0099	False		,,,				2504	0.0				p.F62F	GBM(186;507 2120 27388 27773 52994)	Atlas-SNP	.											.	RNF157	66	.	0			c.T186C						PASS	.	A		5,4401	9.9+/-24.2	0,5,2198	123.0	116.0	119.0		186	-2.6	1.0	17	dbSNP_129	119	51,8549	33.3+/-86.6	0,51,4249	no	coding-synonymous	RNF157	NM_052916.2		0,56,6447	GG,GA,AA		0.593,0.1135,0.4306		62/680	74208466	56,12950	2203	4300	6503	SO:0001819	synonymous_variant	114804	exon2			CCCCAGAAAGTTC	AK091467	CCDS32740.1	17q25.3	2004-02-27			ENSG00000141576	ENSG00000141576		"""RING-type (C3HC4) zinc fingers"""	29402	protein-coding gene	gene with protein product						11572484	Standard	NM_052916		Approved	KIAA1917	uc002jqz.3	Q96PX1	OTTHUMG00000132627	ENST00000269391.6:c.186T>C	17.37:g.74208466A>G		140.0	0.0	0		192.0	83.0	0.432292	NM_052916	Q8NB72|Q96N56	Silent	SNP	ENST00000269391.6	37	CCDS32740.1																																																																																			A|0.996;G|0.004	0.004	strong		0.413	RNF157-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255874.2	XM_290732	
AFF2	2334	hgsc.bcm.edu	37	X	148035200	148035200	+	Silent	SNP	G	G	A	rs12011040	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chrX:148035200G>A	ENST00000370460.2	+	10	1967	c.1488G>A	c.(1486-1488)tcG>tcA	p.S496S	AFF2_ENST00000286437.5_Silent_p.S137S|AFF2_ENST00000370457.5_Silent_p.S463S|AFF2_ENST00000342251.3_Silent_p.S463S	NM_001169123.1|NM_002025.3	NP_001162594.1|NP_002016.2	P51816	AFF2_HUMAN	AF4/FMR2 family, member 2	496					brain development (GO:0007420)|learning or memory (GO:0007611)|mRNA processing (GO:0006397)|regulation of RNA splicing (GO:0043484)|RNA splicing (GO:0008380)	nuclear speck (GO:0016607)	G-quadruplex RNA binding (GO:0002151)			breast(5)|central_nervous_system(2)|endometrium(7)|haematopoietic_and_lymphoid_tissue(2)|kidney(4)|large_intestine(29)|liver(2)|lung(39)|ovary(4)|pancreas(5)|prostate(1)|skin(7)|upper_aerodigestive_tract(1)|urinary_tract(1)	109	Acute lymphoblastic leukemia(192;6.56e-05)					GCTCTGAGTCGGATTCAGACA	0.587													A|||	536	0.141987	0.3381	0.0476	3775	,	,		11768	0.003		0.0388	False		,,,				2504	0.0143				p.S496S		Atlas-SNP	.											.	AFF2	679	.	0			c.G1488A						PASS	.	A	,,,,,	1531,2304		268,774,221,590,350	126.0	118.0	121.0		1389,1458,1383,1371,411,1488	-10.0	0.0	X	dbSNP_120	121	287,6441		3,196,85,2229,1787	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	AFF2	NM_001169122.1,NM_001169123.1,NM_001169124.1,NM_001169125.1,NM_001170628.1,NM_002025.3	,,,,,	271,970,306,2819,2137	AA,AG,A,GG,G		4.2658,39.9218,17.211	,,,,,	463/1277,486/1302,461/1277,457/1273,137/953,496/1312	148035200	1818,8745	2203	4300	6503	SO:0001819	synonymous_variant	2334	exon10			TGAGTCGGATTCA	U48436	CCDS14684.1, CCDS55521.1, CCDS76040.1	Xq28	2008-02-05	2005-06-27	2005-06-27	ENSG00000155966	ENSG00000155966			3776	protein-coding gene	gene with protein product		300806	"""fragile X mental retardation 2"""	FMR2			Standard	NM_002025		Approved	FRAXE	uc004fcp.3	P51816	OTTHUMG00000022613	ENST00000370460.2:c.1488G>A	X.37:g.148035200G>A		183.0	0.0	0		171.0	170.0	0.994152	NM_002025	A2RTY4|B4DXD5|B7WNQ1|B7ZLD6|B7ZLD9|O43786|O60215|P78407|Q13521|Q14323|Q7Z2F7|Q7Z400|Q9UNA5	Silent	SNP	ENST00000370460.2	37	CCDS14684.1																																																																																			0|0.003;A|0.180	0.180	strong		0.587	AFF2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000058673.2	NM_002025	
GPR98	84059	hgsc.bcm.edu	37	5	90151620	90151620	+	Missense_Mutation	SNP	C	C	A	rs201254386		TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr5:90151620C>A	ENST00000405460.2	+	82	17753	c.17657C>A	c.(17656-17658)gCc>gAc	p.A5886D	GPR98_ENST00000425867.2_Missense_Mutation_p.A1547D	NM_032119.3	NP_115495.3	Q8WXG9	GPR98_HUMAN	G protein-coupled receptor 98	5886	GPS. {ECO:0000255|PROSITE- ProRule:PRU00098}.				detection of mechanical stimulus involved in sensory perception of sound (GO:0050910)|G-protein coupled receptor signaling pathway (GO:0007186)|inner ear receptor stereocilium organization (GO:0060122)|maintenance of organ identity (GO:0048496)|nervous system development (GO:0007399)|neurological system process (GO:0050877)|neuropeptide signaling pathway (GO:0007218)|photoreceptor cell maintenance (GO:0045494)|sensory perception of light stimulus (GO:0050953)|sensory perception of sound (GO:0007605)|single organismal cell-cell adhesion (GO:0016337)|visual perception (GO:0007601)	cell surface (GO:0009986)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)|stereocilia ankle link complex (GO:0002142)	calcium ion binding (GO:0005509)|G-protein coupled receptor activity (GO:0004930)			NS(4)|breast(7)|central_nervous_system(6)|cervix(1)|endometrium(13)|haematopoietic_and_lymphoid_tissue(3)|kidney(18)|large_intestine(46)|liver(2)|lung(80)|ovary(12)|pancreas(5)|prostate(1)|skin(50)|stomach(7)|upper_aerodigestive_tract(8)|urinary_tract(6)	269		all_cancers(142;1.05e-09)|all_epithelial(76;1.81e-12)|all_lung(232;5.41e-06)|Lung NSC(167;1.72e-05)|Ovarian(174;0.00948)|Colorectal(57;0.133)|Breast(839;0.192)		OV - Ovarian serous cystadenocarcinoma(54;7.01e-30)|Epithelial(54;6.79e-25)|all cancers(79;1.88e-20)		GTGGAATGTGCCTGTTCACAC	0.413																																					p.A5886D		Atlas-SNP	.											.	GPR98	605	.	0			c.C17657A						PASS	.	C	ASP/ALA	0,3922		0,0,1961	292.0	273.0	279.0		17657	5.5	1.0	5		279	2,8298		0,2,4148	yes	missense	GPR98	NM_032119.3	126	0,2,6109	AA,AC,CC		0.0241,0.0,0.0164	benign	5886/6307	90151620	2,12220	1961	4150	6111	SO:0001583	missense	84059	exon82			AATGTGCCTGTTC	AB014586	CCDS47246.1	5q13	2014-08-08	2006-05-26	2006-05-26	ENSG00000164199	ENSG00000164199		"""-"", ""GPCR / Class B : Orphans"""	17416	protein-coding gene	gene with protein product		602851	"""monogenic, audiogenic seizure susceptibility 1 homolog (mouse)"""	USH2C, MASS1		10976914, 14740321	Standard	NM_032119		Approved	DKFZp761P0710, KIAA0686, FEB4, VLGR1b	uc003kju.3	Q8WXG9	OTTHUMG00000162668	ENST00000405460.2:c.17657C>A	5.37:g.90151620C>A	ENSP00000384582:p.Ala5886Asp	257.0	0.0	0		226.0	96.0	0.424779	NM_032119	O75171|Q8TF58|Q9H0X5|Q9UL61	Missense_Mutation	SNP	ENST00000405460.2	37	CCDS47246.1	.	.	.	.	.	.	.	.	.	.	C	29.8	5.039679	0.93630	0.0	2.41E-4	ENSG00000164199	ENST00000405460;ENST00000296619;ENST00000425867	T;T	0.69306	-0.39;-0.39	5.5	5.5	0.81552	GPS domain (3);	0.000000	0.85682	D	0.000000	T	0.81955	0.4932	M	0.76574	2.34	0.80722	D	1	D;D;D	0.71674	0.975;0.998;0.968	P;D;P	0.71656	0.776;0.974;0.667	T	0.81193	-0.1044	9	.	.	.	.	19.7578	0.96301	0.0:1.0:0.0:0.0	.	1547;5886;1547	E7EML1;Q8WXG9;Q8WXG9-2	.;GPR98_HUMAN;.	D	5886;5886;1547	ENSP00000384582:A5886D;ENSP00000392618:A1547D	.	A	+	2	0	GPR98	90187376	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	7.083000	0.76859	2.746000	0.94184	0.591000	0.81541	GCC	.	.	weak		0.413	GPR98-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000369993.2	NM_032119	
IFNA8	3445	hgsc.bcm.edu	37	9	21409439	21409439	+	Silent	SNP	C	C	T			TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr9:21409439C>T	ENST00000380205.1	+	1	294	c.264C>T	c.(262-264)ttC>ttT	p.F88F		NM_002170.3	NP_002161.2	P32881	IFNA8_HUMAN	interferon, alpha 8	88					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)			endometrium(1)|kidney(1)|large_intestine(1)|lung(5)|ovary(1)	9				Lung(24;7.66e-27)|LUSC - Lung squamous cell carcinoma(38;1.4e-13)|OV - Ovarian serous cystadenocarcinoma(39;0.0174)		AGCAGACCTTCAACCTCTTCA	0.473																																					p.F88F		Atlas-SNP	.											.	IFNA8	19	.	0			c.C264T						PASS	.						102.0	95.0	98.0					9																	21409439		2203	4300	6503	SO:0001819	synonymous_variant	3445	exon1			GACCTTCAACCTC		CCDS6507.1	9p22	2010-08-24			ENSG00000120242	ENSG00000120242		"""Interferons"""	5429	protein-coding gene	gene with protein product	"""interferon alpha-B''"", ""interferon alpha type 201"""	147568				1385305	Standard	NM_002170		Approved	IFN-alphaB	uc003zpc.1	P32881	OTTHUMG00000019677	ENST00000380205.1:c.264C>T	9.37:g.21409439C>T		192.0	0.0	0		205.0	81.0	0.395122	NM_002170	P01565|P09236|Q5VWV7|Q5VYQ3	Silent	SNP	ENST00000380205.1	37	CCDS6507.1																																																																																			.	.	none		0.473	IFNA8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051906.1	NM_002170	
KRTAP4-6	81871	hgsc.bcm.edu	37	17	39296675	39296675	+	Missense_Mutation	SNP	C	C	T	rs147498528	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr17:39296675C>T	ENST00000345847.4	-	1	64	c.65G>A	c.(64-66)cGc>cAc	p.R22H		NM_030976.1	NP_112238.1	Q9BYQ5	KRA46_HUMAN	keratin associated protein 4-6	22	30 X 5 AA repeats of C-C-[IRQVEL]-[SPTR]- [STVQRCP].					keratin filament (GO:0045095)				endometrium(3)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|lung(1)|prostate(1)|urinary_tract(1)	9						GCAGCTGGGGCGGCAGCAGGT	0.632													C|||	10	0.00199681	0.0076	0.0	5008	,	,		17854	0.0		0.0	False		,,,				2504	0.0				p.R22H		Atlas-SNP	.											KRTAP4-6,NS,carcinoma,+1,2	KRTAP4-6	46	2	0			c.G65A						PASS	.																																			SO:0001583	missense	81871	exon1			CTGGGGCGGCAGC	AJ406938	CCDS54125.1	17q21.2	2013-06-25			ENSG00000198090	ENSG00000198090		"""Keratin associated proteins"""	18909	protein-coding gene	gene with protein product			"""keratin associated protein 4-15"""	KRTAP4-15			Standard	NM_030976		Approved	KAP4.6, KAP4.15	uc010cxk.2	Q9BYQ5	OTTHUMG00000133634	ENST00000345847.4:c.65G>A	17.37:g.39296675C>T	ENSP00000328270:p.Arg22His	118.0	0.0	0		86.0	37.0	0.430233	NM_030976	Q9BYR1	Missense_Mutation	SNP	ENST00000345847.4	37	CCDS54125.1	6	0.0027472527472527475	6	0.012195121951219513	0	0.0	0	0.0	0	0.0	.	7.766	0.706433	0.15239	.	.	ENSG00000198090	ENST00000345847	T	0.01430	4.9	4.15	-5.03	0.02973	.	3.358020	0.01113	U	0.005612	T	0.02119	0.0066	M	0.71296	2.17	0.09310	N	1	.	.	.	.	.	.	T	0.33828	-0.9853	8	0.41790	T	0.15	.	6.0155	0.19601	0.1242:0.3795:0.0:0.4963	.	.	.	.	H	22	ENSP00000328270:R22H	ENSP00000328270:R22H	R	-	2	0	KRTAP4-6	36550201	0.000000	0.05858	0.000000	0.03702	0.046000	0.14306	-1.428000	0.02439	-1.147000	0.02851	-0.265000	0.10407	CGC	C|0.997;T|0.003	0.003	strong		0.632	KRTAP4-6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257779.1		
USP25	29761	hgsc.bcm.edu	37	21	17172112	17172112	+	Silent	SNP	C	C	T	rs145029756	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr21:17172112C>T	ENST00000285679.6	+	6	961	c.592C>T	c.(592-594)Ctg>Ttg	p.L198L	USP25_ENST00000547201.1_3'UTR|USP25_ENST00000285681.2_Silent_p.L198L|USP25_ENST00000351097.5_Silent_p.L198L|USP25_ENST00000400183.2_Silent_p.L198L	NM_013396.3	NP_037528.3	Q9UHP3	UBP25_HUMAN	ubiquitin specific peptidase 25	198	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)		AAGATTAGTTCTGAATTACAA	0.289													C|||	2	0.000399361	0.0	0.0	5008	,	,		16107	0.0		0.002	False		,,,				2504	0.0				p.L198L		Atlas-SNP	.											.	USP25	156	.	0			c.C592T						PASS	.	C		3,4403	6.2+/-15.9	0,3,2200	90.0	89.0	89.0		592	2.2	1.0	21	dbSNP_134	89	28,8558	17.9+/-57.8	0,28,4265	no	coding-synonymous	USP25	NM_013396.3		0,31,6465	TT,TC,CC		0.3261,0.0681,0.2386		198/1056	17172112	31,12961	2203	4293	6496	SO:0001819	synonymous_variant	29761	exon6			TTAGTTCTGAATT	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.592C>T	21.37:g.17172112C>T		201.0	0.0	0		178.0	87.0	0.488764	NM_013396	C0LSZ0|Q6DHZ9|Q9H9W1	Silent	SNP	ENST00000285679.6	37	CCDS33515.1																																																																																			C|0.998;T|0.002	0.002	strong		0.289	USP25-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000157964.1		
UPK3B	80761	hgsc.bcm.edu	37	7	76140315	76140315	+	Missense_Mutation	SNP	G	G	A	rs144609046	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr7:76140315G>A	ENST00000257632.5	+	1	474	c.346G>A	c.(346-348)Gat>Aat	p.D116N	UPK3B_ENST00000334348.3_Missense_Mutation_p.D61N|UPK3B_ENST00000448265.3_Missense_Mutation_p.D116N|UPK3B_ENST00000394849.1_Missense_Mutation_p.D61N|UPK3B_ENST00000443097.2_Missense_Mutation_p.D61N|UPK3B_ENST00000419923.2_Missense_Mutation_p.D116N			Q9BT76	UPK3B_HUMAN	uroplakin 3B	116					negative regulation of gene expression (GO:0010629)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				breast(1)|central_nervous_system(2)|kidney(1)|large_intestine(1)|lung(1)|skin(2)	8		Myeloproliferative disorder(862;0.204)				CTGTGTCTTCGATGGGCTTGC	0.632													.|||	3	0.000599042	0.0	0.0	5008	,	,		18847	0.0		0.001	False		,,,				2504	0.002				p.D116N		Atlas-SNP	.											.	UPK3B	15	.	0			c.G346A						PASS	.	G	ASN/ASP,ASN/ASP	0,4310		0,0,2155	9.0	8.0	9.0		346,181	3.0	0.2	7	dbSNP_134	9	10,8410		0,10,4200	no	missense,missense	UPK3B	NM_030570.2,NM_182684.1	23,23	0,10,6355	AA,AG,GG		0.1188,0.0,0.0786	possibly-damaging,possibly-damaging	116/321,61/277	76140315	10,12720	2155	4210	6365	SO:0001583	missense	80761	exon1			GTCTTCGATGGGC	BC004304	CCDS5588.1, CCDS5589.1, CCDS64693.1	7q11.2	2003-07-29			ENSG00000243566	ENSG00000243566			21444	protein-coding gene	gene with protein product	"""uroplakin IIIb"""	611887				12446744	Standard	XM_005250612		Approved	MGC10902, p35, UPIIIb, FLJ32198	uc003ufq.3	Q9BT76	OTTHUMG00000149929	ENST00000257632.5:c.346G>A	7.37:g.76140315G>A	ENSP00000257632:p.Asp116Asn	649.0	1.0	0.00154083		535.0	226.0	0.42243	NM_030570	A6NHH5|A8K231|A8MZA8|B3KPU5|Q75MM5|Q86W06	Missense_Mutation	SNP	ENST00000257632.5	37	CCDS5588.1	.	.	.	.	.	.	.	.	.	.	.	12.85	2.061280	0.36373	0.0	0.001188	ENSG00000243566	ENST00000334348;ENST00000419923;ENST00000448265;ENST00000443097;ENST00000257632;ENST00000394849	T;T;T;T;T;T	0.58358	0.34;1.28;1.28;0.34;1.28;1.29	4.93	2.99	0.34606	.	0.412335	0.23849	N	0.043977	T	0.48554	0.1506	N	0.17474	0.49	0.09310	N	1	D;D;D	0.76494	0.999;0.999;0.991	D;P;P	0.63381	0.914;0.9;0.539	T	0.22941	-1.0202	10	0.46703	T	0.11	-8.2617	7.7594	0.28944	0.0919:0.0:0.7447:0.1633	.	61;116;61	Q9BT76-2;Q9BT76;A6NHH5	.;UPK3B_HUMAN;.	N	61;116;116;61;116;61	ENSP00000334938:D61N;ENSP00000441602:D116N;ENSP00000441284:D116N;ENSP00000444585:D61N;ENSP00000257632:D116N;ENSP00000378319:D61N	ENSP00000257632:D116N	D	+	1	0	UPK3B	75978251	0.037000	0.19845	0.162000	0.22713	0.010000	0.07245	0.841000	0.27613	2.281000	0.76405	0.400000	0.26472	GAT	G|0.999;A|0.001	0.001	strong		0.632	UPK3B-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000313978.2	NM_030570	
OR51B5	282763	hgsc.bcm.edu	37	11	5364522	5364522	+	Missense_Mutation	SNP	G	G	T	rs57273781	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr11:5364522G>T	ENST00000300773.2	-	1	287	c.233C>A	c.(232-234)aCg>aAg	p.T78K	HBE1_ENST00000380237.1_Intron|AC104389.28_ENST00000415970.1_RNA|HBG2_ENST00000380252.1_Intron|HBG2_ENST00000380259.2_Intron	NM_001005567.2	NP_001005567.2	Q9H339	O51B5_HUMAN	olfactory receptor, family 51, subfamily B, member 5	78			T -> K (in dbSNP:rs57273781).		detection of chemical stimulus involved in sensory perception of smell (GO:0050911)|sensory perception of smell (GO:0007608)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			NS(1)|central_nervous_system(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(4)|lung(13)|prostate(1)|skin(5)|upper_aerodigestive_tract(2)	28		Medulloblastoma(188;0.0075)|all_neural(188;0.0572)|Breast(177;0.0675)		Epithelial(150;3.05e-09)|BRCA - Breast invasive adenocarcinoma(625;0.135)		TCCCAGCACCGTGGGCATTGT	0.542													G|||	487	0.0972444	0.3048	0.0476	5008	,	,		18344	0.0		0.0457	False		,,,				2504	0.0051				p.T78K		Atlas-SNP	.											OR51B5,NS,malignant_melanoma,+1,2	OR51B5	60	2	0			c.C233A						PASS	.	G	LYS/THR	1219,3183	416.7+/-337.7	164,891,1146	44.0	46.0	45.0		233	3.9	0.3	11	dbSNP_129	45	445,8149	132.5+/-190.1	13,419,3865	yes	missense	OR51B5	NM_001005567.2	78	177,1310,5011	TT,TG,GG		5.178,27.692,12.8039	probably-damaging	78/313	5364522	1664,11332	2201	4297	6498	SO:0001583	missense	282763	exon5			AGCACCGTGGGCA	BK004430	CCDS31378.1	11p15.4	2012-08-09			ENSG00000242180	ENSG00000242180		"""GPCR / Class A : Olfactory receptors"""	19599	protein-coding gene	gene with protein product							Standard	NM_001005567		Approved		uc001maq.2	Q9H339	OTTHUMG00000066676	ENST00000300773.2:c.233C>A	11.37:g.5364522G>T	ENSP00000300773:p.Thr78Lys	54.0	0.0	0		68.0	29.0	0.426471	NM_001005567	B2RN59	Missense_Mutation	SNP	ENST00000300773.2	37	CCDS31378.1	188	0.08608058608058608	135	0.27439024390243905	20	0.055248618784530384	0	0.0	33	0.04353562005277045	G	17.13	3.311894	0.60414	0.27692	0.05178	ENSG00000242180	ENST00000300773	T	0.01538	4.79	4.76	3.86	0.44501	GPCR, rhodopsin-like superfamily (1);	0.000000	0.42420	D	0.000713	T	0.00012	0.0000	L	0.27944	0.81	0.58432	P	1.0000000000287557E-6	D	0.67145	0.996	P	0.57846	0.828	T	0.61720	-0.7005	9	0.52906	T	0.07	.	11.866	0.52493	0.0855:0.0:0.9145:0.0	rs57273781;rs61738468	78	Q9H339	O51B5_HUMAN	K	78	ENSP00000300773:T78K	ENSP00000300773:T78K	T	-	2	0	OR51B5	5321098	0.000000	0.05858	0.313000	0.25210	0.802000	0.45316	0.385000	0.20685	1.255000	0.44051	0.650000	0.86243	ACG	G|0.889;T|0.111	0.111	strong		0.542	OR51B5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000142975.1	NM_001005567	
MYH13	8735	hgsc.bcm.edu	37	17	10261086	10261086	+	Missense_Mutation	SNP	G	G	A			TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr17:10261086G>A	ENST00000418404.3	-	7	867	c.704C>T	c.(703-705)gCc>gTc	p.A235V	MYH13_ENST00000252172.4_Missense_Mutation_p.A235V			Q9UKX3	MYH13_HUMAN	myosin, heavy chain 13, skeletal muscle	235	Myosin motor.				cellular response to starvation (GO:0009267)|metabolic process (GO:0008152)|muscle contraction (GO:0006936)	extracellular vesicular exosome (GO:0070062)|muscle myosin complex (GO:0005859)|myofibril (GO:0030016)|myosin filament (GO:0032982)	ATP binding (GO:0005524)|microfilament motor activity (GO:0000146)			breast(3)|cervix(2)|endometrium(11)|kidney(7)|large_intestine(21)|lung(48)|ovary(7)|skin(2)|upper_aerodigestive_tract(5)|urinary_tract(2)	108						CACAGTCTTGGCATTTCCAAA	0.453																																					p.A235V		Atlas-SNP	.											.	MYH13	533	.	0			c.C704T						PASS	.						99.0	107.0	105.0					17																	10261086		2180	4296	6476	SO:0001583	missense	8735	exon8			GTCTTGGCATTTC	AF075248	CCDS45613.1	17p13	2011-09-27	2006-09-29			ENSG00000006788		"""Myosins / Myosin superfamily : Class II"""	7571	protein-coding gene	gene with protein product	"""extraocular muscle myosin heavy chain"", ""extraocular myosin heavy chain"""	603487	"""myosin, heavy polypeptide 13, skeletal muscle"""			9806854	Standard	NM_003802		Approved	MyHC-eo	uc002gmk.1	Q9UKX3		ENST00000418404.3:c.704C>T	17.37:g.10261086G>A	ENSP00000404570:p.Ala235Val	137.0	0.0	0		143.0	62.0	0.433566	NM_003802	O95252|Q9P0U8	Missense_Mutation	SNP	ENST00000418404.3	37	CCDS45613.1	.	.	.	.	.	.	.	.	.	.	G	29.4	5.001634	0.93227	.	.	ENSG00000006788	ENST00000252172	D	0.83914	-1.78	3.94	3.94	0.45596	Myosin head, motor domain (3);	.	.	.	.	D	0.94810	0.8324	H	0.99249	4.485	0.53005	D	0.999965	D	0.67145	0.996	D	0.69142	0.962	D	0.97360	0.9969	9	0.87932	D	0	.	16.5222	0.84320	0.0:0.0:1.0:0.0	.	235	Q9UKX3	MYH13_HUMAN	V	235	ENSP00000252172:A235V	ENSP00000252172:A235V	A	-	2	0	MYH13	10201811	1.000000	0.71417	1.000000	0.80357	0.944000	0.59088	9.450000	0.97607	2.200000	0.70718	0.467000	0.42956	GCC	.	.	none		0.453	MYH13-003	KNOWN	alternative_3_UTR|alternative_5_UTR|NMD_exception|not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000442255.1	NM_003802	
DDX60	55601	hgsc.bcm.edu	37	4	169146815	169146815	+	Missense_Mutation	SNP	C	C	T	rs146255632	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr4:169146815C>T	ENST00000393743.3	-	34	4837	c.4546G>A	c.(4546-4548)Gat>Aat	p.D1516N		NM_017631.5	NP_060101.3	Q8IY21	DDX60_HUMAN	DEAD (Asp-Glu-Ala-Asp) box polypeptide 60	1516					defense response to virus (GO:0051607)|innate immune response (GO:0045087)|positive regulation of MDA-5 signaling pathway (GO:1900245)|positive regulation of RIG-I signaling pathway (GO:1900246)|response to virus (GO:0009615)	cytoplasm (GO:0005737)|intermediate filament cytoskeleton (GO:0045111)	ATP binding (GO:0005524)|double-stranded DNA binding (GO:0003690)|double-stranded RNA binding (GO:0003725)|helicase activity (GO:0004386)|single-stranded RNA binding (GO:0003727)			breast(1)|central_nervous_system(3)|endometrium(6)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(15)|liver(1)|lung(21)|ovary(1)|pancreas(2)|prostate(1)|skin(4)|urinary_tract(4)	63		Prostate(90;0.00876)|Renal(120;0.0183)|all_neural(102;0.0837)|Melanoma(52;0.132)		GBM - Glioblastoma multiforme(119;0.0485)		TCAGGGAGATCATCAAGGAAC	0.353																																					p.D1516N		Atlas-SNP	.											.	DDX60	304	.	0			c.G4546A						PASS	.	C	ASN/ASP	0,4406		0,0,2203	79.0	81.0	80.0		4546	5.0	0.5	4	dbSNP_134	80	14,8584	10.5+/-38.8	0,14,4285	yes	missense	DDX60	NM_017631.5	23	0,14,6488	TT,TC,CC		0.1628,0.0,0.1077	probably-damaging	1516/1713	169146815	14,12990	2203	4299	6502	SO:0001583	missense	55601	exon34			GGAGATCATCAAG	AK001649	CCDS34097.1	4q32.3	2010-02-17			ENSG00000137628	ENSG00000137628			25942	protein-coding gene	gene with protein product		613974				12477932	Standard	NM_017631		Approved	FLJ20035	uc003irp.3	Q8IY21	OTTHUMG00000161350	ENST00000393743.3:c.4546G>A	4.37:g.169146815C>T	ENSP00000377344:p.Asp1516Asn	74.0	0.0	0		59.0	24.0	0.40678	NM_017631	Q6PK35|Q9NVE3	Missense_Mutation	SNP	ENST00000393743.3	37	CCDS34097.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	15.89|15.89	2.966660|2.966660	0.53507|0.53507	0.0|0.0	0.001628|0.001628	ENSG00000137628|ENSG00000137628	ENST00000393743|ENST00000511317	T|.	0.18810|.	2.19|.	5.82|5.82	4.97|4.97	0.65823|0.65823	.|.	0.190110|.	0.37012|.	N|.	0.002284|.	T|T	0.64136|0.64136	0.2571|0.2571	M|M	0.80982|0.80982	2.52|2.52	0.26026|0.26026	N|N	0.981803|0.981803	D|.	0.56287|.	0.975|.	P|.	0.50754|.	0.649|.	T|T	0.58847|0.58847	-0.7564|-0.7564	10|5	0.35671|.	T|.	0.21|.	.|.	14.3138|14.3138	0.66434|0.66434	0.0:0.9259:0.0:0.0741|0.0:0.9259:0.0:0.0741	.|.	1516|.	Q8IY21|.	DDX60_HUMAN|.	N|I	1516|8	ENSP00000377344:D1516N|.	ENSP00000377344:D1516N|.	D|M	-|-	1|3	0|0	DDX60|DDX60	169383390|169383390	0.995000|0.995000	0.38212|0.38212	0.540000|0.540000	0.28089|0.28089	0.111000|0.111000	0.19643|0.19643	2.338000|2.338000	0.43957|0.43957	2.755000|2.755000	0.94549|0.94549	0.563000|0.563000	0.77884|0.77884	GAT|ATG	C|0.999;T|0.001	0.001	strong		0.353	DDX60-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000364622.1	NM_017631	
NUP107	57122	hgsc.bcm.edu	37	12	69090684	69090684	+	Silent	SNP	A	A	G	rs35054844	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr12:69090684A>G	ENST00000229179.4	+	6	866	c.534A>G	c.(532-534)gaA>gaG	p.E178E	NUP107_ENST00000378905.2_Silent_p.E27E|NUP107_ENST00000539906.1_Silent_p.E149E	NM_020401.2	NP_065134.1	P57740	NU107_HUMAN	nucleoporin 107kDa	178					carbohydrate metabolic process (GO:0005975)|cytokine-mediated signaling pathway (GO:0019221)|glucose transport (GO:0015758)|hexose transport (GO:0008645)|mitotic cell cycle (GO:0000278)|mitotic nuclear envelope disassembly (GO:0007077)|mRNA export from nucleus (GO:0006406)|nuclear pore complex assembly (GO:0051292)|protein transport (GO:0015031)|regulation of glucose transport (GO:0010827)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)|viral process (GO:0016032)	centrosome (GO:0005813)|cytosol (GO:0005829)|kinetochore (GO:0000776)|membrane (GO:0016020)|nuclear envelope (GO:0005635)|nuclear membrane (GO:0031965)|nuclear periphery (GO:0034399)|nuclear pore (GO:0005643)|nuclear pore outer ring (GO:0031080)|nucleus (GO:0005634)	nucleocytoplasmic transporter activity (GO:0005487)|structural constituent of nuclear pore (GO:0017056)		NUP107/LGR5(2)	breast(3)|endometrium(4)|kidney(4)|large_intestine(12)|lung(11)|prostate(1)|skin(2)|urinary_tract(2)	39	Breast(13;6.25e-06)		Lung(24;0.000131)|LUAD - Lung adenocarcinoma(15;0.00107)|STAD - Stomach adenocarcinoma(21;0.00694)			AAGAGTATGAAAACATCTGTG	0.353													A|||	154	0.0307508	0.0507	0.0403	5008	,	,		19586	0.001		0.0229	False		,,,				2504	0.0358				p.E178E		Atlas-SNP	.											NUP107,NS,carcinoma,+2,1	NUP107	88	1	0			c.A534G						PASS	.	A		178,4228	116.3+/-154.2	3,172,2028	115.0	106.0	109.0		534	1.9	1.0	12	dbSNP_126	109	194,8406	85.3+/-147.7	3,188,4109	no	coding-synonymous	NUP107	NM_020401.2		6,360,6137	GG,GA,AA		2.2558,4.0399,2.8602		178/926	69090684	372,12634	2203	4300	6503	SO:0001819	synonymous_variant	57122	exon6			GTATGAAAACATC	AK055629	CCDS8985.1	12q14	2004-03-19			ENSG00000111581	ENSG00000111581			29914	protein-coding gene	gene with protein product		607617				12552102, 12705868	Standard	XM_005269037		Approved	NUP84	uc001suf.3	P57740	OTTHUMG00000169265	ENST00000229179.4:c.534A>G	12.37:g.69090684A>G		65.0	0.0	0		82.0	45.0	0.548781	NM_020401	B4DZ67|Q6PJE1	Silent	SNP	ENST00000229179.4	37	CCDS8985.1																																																																																			A|0.975;G|0.025	0.025	strong		0.353	NUP107-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000403195.1	NM_020401	
SMIM24	284422	hgsc.bcm.edu	37	19	3474941	3474941	+	Missense_Mutation	SNP	T	T	G			TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr19:3474941T>G	ENST00000215531.4	-	4	371	c.293A>C	c.(292-294)aAg>aCg	p.K98T	C19orf77_ENST00000591708.1_Missense_Mutation_p.K28T|C19orf77_ENST00000587847.1_Missense_Mutation_p.K28T	NM_001136503.1	NP_001129975.1	O75264	SIM24_HUMAN		98						extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)											ctttttctccttcttcctctt	0.463																																					p.K98T		Atlas-SNP	.											.	C19orf77	6	.	0			c.A293C						PASS	.						137.0	120.0	125.0					19																	3474941		692	1591	2283	SO:0001583	missense	284422	exon4			TTCTCCTTCTTCC																												ENST00000215531.4:c.293A>C	19.37:g.3474941T>G	ENSP00000215531:p.Lys98Thr	143.0	0.0	0		144.0	77.0	0.534722	NM_001136503	B9EJF4|Q9P059	Missense_Mutation	SNP	ENST00000215531.4	37	CCDS45915.1	.	.	.	.	.	.	.	.	.	.	T	1.844	-0.466592	0.04476	.	.	ENSG00000095932	ENST00000215531	.	.	.	1.97	0.911	0.19343	.	.	.	.	.	T	0.26195	0.0639	N	0.14661	0.345	0.09310	N	1	P	0.39665	0.682	P	0.48030	0.564	T	0.15636	-1.0430	8	0.48119	T	0.1	.	3.8581	0.08984	0.0:0.197:0.0:0.803	.	98	O75264	CS077_HUMAN	T	98	.	ENSP00000215531:K98T	K	-	2	0	C19orf77	3425941	0.002000	0.14202	0.001000	0.08648	0.227000	0.25037	0.318000	0.19504	0.214000	0.20742	0.402000	0.26972	AAG	.	.	none		0.463	C19orf77-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000452929.1		
ACOX2	8309	hgsc.bcm.edu	37	3	58494661	58494661	+	Missense_Mutation	SNP	G	G	A			TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr3:58494661G>A	ENST00000302819.5	-	14	2233	c.1942C>T	c.(1942-1944)Cgc>Tgc	p.R648C	ACOX2_ENST00000459701.2_Missense_Mutation_p.R634C|ACOX2_ENST00000481527.1_5'UTR	NM_003500.3	NP_003491.1	Q99424	ACOX2_HUMAN	acyl-CoA oxidase 2, branched chain	648					bile acid biosynthetic process (GO:0006699)|bile acid metabolic process (GO:0008206)|cellular lipid metabolic process (GO:0044255)|fatty acid beta-oxidation using acyl-CoA oxidase (GO:0033540)|small molecule metabolic process (GO:0044281)	peroxisomal matrix (GO:0005782)|peroxisome (GO:0005777)	3alpha,7alpha,12alpha-trihydroxy-5beta-cholestanoyl-CoA 24-hydroxylase activity (GO:0033791)|acyl-CoA dehydrogenase activity (GO:0003995)|acyl-CoA oxidase activity (GO:0003997)|flavin adenine dinucleotide binding (GO:0050660)|pristanoyl-CoA oxidase activity (GO:0016402)|receptor binding (GO:0005102)			breast(3)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(3)|lung(8)|prostate(1)|skin(3)|urinary_tract(1)	25				BRCA - Breast invasive adenocarcinoma(55;0.000194)|Kidney(10;0.00255)|KIRC - Kidney renal clear cell carcinoma(10;0.00268)|OV - Ovarian serous cystadenocarcinoma(275;0.156)		TGGAACAGGCGTTCGTAGACG	0.433																																					p.R648C		Atlas-SNP	.											.	ACOX2	53	.	0			c.C1942T						PASS	.						130.0	114.0	119.0					3																	58494661		2203	4300	6503	SO:0001583	missense	8309	exon14			ACAGGCGTTCGTA	X95190	CCDS33775.1	3p14.3	2012-07-13	2010-04-30		ENSG00000168306	ENSG00000168306	1.17.99.3		120	protein-coding gene	gene with protein product	"""trihydroxycoprostanoyl-CoA oxidase"", ""3-alpha,7-alpha,12-alpha-trihydroxy-5-beta-cholestanoyl-CoA 24-hydroxylase"""	601641	"""acyl-Coenzyme A oxidase 2, branched chain"""			8943006, 9070889	Standard	NM_003500		Approved	BRCACOX, BRCOX, THCCox	uc003dkl.3	Q99424	OTTHUMG00000159154	ENST00000302819.5:c.1942C>T	3.37:g.58494661G>A	ENSP00000307697:p.Arg648Cys	91.0	0.0	0		103.0	49.0	0.475728	NM_003500	A6NF16|B2R8U5	Missense_Mutation	SNP	ENST00000302819.5	37	CCDS33775.1	.	.	.	.	.	.	.	.	.	.	G	19.75	3.885004	0.72410	.	.	ENSG00000168306	ENST00000459701;ENST00000302819	T;T	0.47528	0.84;0.84	5.43	4.52	0.55395	Acyl-CoA oxidase, C-terminal (1);Acyl-CoA dehydrogenase/oxidase C-terminal (1);	0.198277	0.34959	N	0.003549	T	0.71022	0.3291	M	0.87682	2.9	0.48571	D	0.999672	D	0.89917	1.0	D	0.79784	0.993	T	0.76408	-0.2970	10	0.87932	D	0	-16.8637	13.3882	0.60807	0.0:0.0:0.7178:0.2822	.	648	Q99424	ACOX2_HUMAN	C	634;648	ENSP00000418562:R634C;ENSP00000307697:R648C	ENSP00000307697:R648C	R	-	1	0	ACOX2	58469701	1.000000	0.71417	1.000000	0.80357	0.984000	0.73092	2.978000	0.49305	2.583000	0.87209	0.579000	0.79373	CGC	.	.	none		0.433	ACOX2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000353541.1		
ASB2	51676	hgsc.bcm.edu	37	14	94417531	94417531	+	Missense_Mutation	SNP	T	T	C	rs11555542	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr14:94417531T>C	ENST00000315988.4	-	4	1038	c.550A>G	c.(550-552)Aac>Gac	p.N184D	ASB2_ENST00000556337.1_Intron|ASB2_ENST00000555019.1_Missense_Mutation_p.N232D|MIR4506_ENST00000584693.1_RNA	NM_016150.4	NP_057234.2	Q96Q27	ASB2_HUMAN	ankyrin repeat and SOCS box containing 2	184					intracellular signal transduction (GO:0035556)|myoblast differentiation (GO:0045445)|protein polyubiquitination (GO:0000209)|protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:0042787)|signal transduction (GO:0007165)|skeletal muscle cell differentiation (GO:0035914)	Cul5-RING ubiquitin ligase complex (GO:0031466)	ubiquitin-protein transferase activity (GO:0004842)			breast(1)|endometrium(2)|kidney(1)|large_intestine(6)|lung(8)|ovary(2)|pancreas(1)|prostate(3)|skin(1)|soft_tissue(1)|urinary_tract(1)	27		all_cancers(154;0.13)		COAD - Colon adenocarcinoma(157;0.217)|Epithelial(152;0.232)		CAGCGGTGGTTGGTGTCTGCA	0.632													T|||	104	0.0207668	0.0023	0.0605	5008	,	,		19972	0.001		0.0567	False		,,,				2504	0.001				p.N232D		Atlas-SNP	.											.	ASB2	71	.	0			c.A694G						PASS	.	T	ASP/ASN,ASP/ASN	50,4356	50.9+/-86.3	0,50,2153	76.0	63.0	67.0		694,550	5.6	1.0	14	dbSNP_120	67	469,8131	139.0+/-195.8	10,449,3841	yes	missense,missense	ASB2	NM_001202429.1,NM_016150.4	23,23	10,499,5994	CC,CT,TT		5.4535,1.1348,3.9905	possibly-damaging,possibly-damaging	232/636,184/588	94417531	519,12487	2203	4300	6503	SO:0001583	missense	51676	exon6			GGTGGTTGGTGTC	AF159164	CCDS9915.1, CCDS55940.1	14q31-q32	2013-01-10	2011-01-25					"""Ankyrin repeat domain containing"""	16012	protein-coding gene	gene with protein product		605759	"""ankyrin repeat and SOCS box-containing 2"""				Standard	NM_016150		Approved	ASB-2	uc001ycd.3	Q96Q27		ENST00000315988.4:c.550A>G	14.37:g.94417531T>C	ENSP00000320675:p.Asn184Asp	47.0	0.0	0		69.0	32.0	0.463768	NM_001202429	B2RDP9|B4E166|Q9NSU5|Q9Y567	Missense_Mutation	SNP	ENST00000315988.4	37	CCDS9915.1	67	0.030677655677655676	2	0.0040650406504065045	25	0.06906077348066299	1	0.0017482517482517483	39	0.051451187335092345	T	27.5	4.840814	0.91197	0.011348	0.054535	ENSG00000100628	ENST00000555019;ENST00000434324;ENST00000315988;ENST00000543546;ENST00000555507;ENST00000556062	T;T;T;T	0.73789	-0.5;-0.5;-0.5;-0.78	5.62	5.62	0.85841	Ankyrin repeat-containing domain (4);	0.000000	0.85682	D	0.000000	T	0.25044	0.0608	N	0.25201	0.72	0.54753	D	0.999986	P;D;P	0.76494	0.922;0.999;0.922	P;D;P	0.83275	0.841;0.996;0.677	T	0.60742	-0.7203	10	0.30078	T	0.28	-2.7607	15.8384	0.78818	0.0:0.0:0.0:1.0	rs11555542;rs11555542	200;232;184	B3KPZ6;B4E166;Q96Q27	.;.;ASB2_HUMAN	D	232;200;184;130;130;78	ENSP00000451575:N232D;ENSP00000320675:N184D;ENSP00000450940:N130D;ENSP00000451694:N78D	ENSP00000320675:N184D	N	-	1	0	ASB2	93487284	1.000000	0.71417	1.000000	0.80357	0.985000	0.73830	6.258000	0.72487	2.137000	0.66172	0.459000	0.35465	AAC	T|0.964;C|0.036	0.036	strong		0.632	ASB2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000412845.1		
KIRREL3	84623	hgsc.bcm.edu	37	11	126294661	126294661	+	Silent	SNP	G	G	A	rs34844660	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr11:126294661G>A	ENST00000525144.2	-	17	2400	c.2151C>T	c.(2149-2151)agC>agT	p.S717S	KIRREL3_ENST00000529097.2_Silent_p.S705S|KIRREL3_ENST00000416561.2_Silent_p.S184S	NM_032531.3	NP_115920.1	Q8IZU9	KIRR3_HUMAN	kin of IRRE like 3 (Drosophila)	717	Ser-rich.				hemopoiesis (GO:0030097)	extracellular region (GO:0005576)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				central_nervous_system(1)|endometrium(5)|large_intestine(11)|lung(8)|ovary(3)|prostate(1)	29	all_hematologic(175;0.145)	Lung NSC(97;0.0484)|all_lung(97;0.0522)|Medulloblastoma(222;0.0523)|Breast(109;0.0949)|all_neural(223;0.224)		BRCA - Breast invasive adenocarcinoma(274;6.03e-06)|OV - Ovarian serous cystadenocarcinoma(99;0.12)		AGCTGCTGTCGCTGAGGGAGC	0.627													G|||	69	0.013778	0.0514	0.0014	5008	,	,		19048	0.0		0.0	False		,,,				2504	0.0				p.S717S		Atlas-SNP	.											.	KIRREL3	183	.	0			c.C2151T						PASS	.	G		148,4198		0,148,2025	74.0	82.0	79.0		2151	4.0	1.0	11	dbSNP_126	79	0,8562		0,0,4281	no	coding-synonymous	KIRREL3	NM_032531.3		0,148,6306	AA,AG,GG		0.0,3.4054,1.1466		717/779	126294661	148,12760	2173	4281	6454	SO:0001819	synonymous_variant	84623	exon17			GCTGTCGCTGAGG	AB058770	CCDS53723.1, CCDS55796.1, CCDS73413.1	11q24	2013-01-29			ENSG00000149571	ENSG00000149571		"""Immunoglobulin superfamily / I-set domain containing"", ""Immunoglobulin superfamily / C2-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	23204	protein-coding gene	gene with protein product		607761				12424224, 11347906	Standard	NM_032531		Approved	NEPH2, KIAA1867, KIRRE	uc001qea.3	Q8IZU9	OTTHUMG00000165831	ENST00000525144.2:c.2151C>T	11.37:g.126294661G>A		112.0	0.0	0		111.0	51.0	0.459459	NM_032531	Q3MIJ7|Q6UWJ9|Q6UWL5|Q96JG0	Silent	SNP	ENST00000525144.2	37	CCDS53723.1																																																																																			G|0.992;A|0.008	0.008	strong		0.627	KIRREL3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000386479.2	NM_032531	
FHAD1	114827	hgsc.bcm.edu	37	1	15708557	15708557	+	Silent	SNP	G	G	A	rs35816204	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr1:15708557G>A	ENST00000375998.4	+	29	3990	c.3990G>A	c.(3988-3990)tcG>tcA	p.S1330S	FHAD1_ENST00000417793.1_Silent_p.S1294S|FHAD1_ENST00000375999.3_Silent_p.S1330S|FHAD1_ENST00000314740.8_Silent_p.S583S|FHAD1_ENST00000358897.4_Silent_p.S1330S|FHAD1_ENST00000471347.1_3'UTR			B1AJZ9	FHAD1_HUMAN	forkhead-associated (FHA) phosphopeptide binding domain 1	1330										skin(1)|stomach(1)	2						TGTACCAGTCGCAGGTGGCAA	0.542													G|||	64	0.0127796	0.0015	0.0173	5008	,	,		21738	0.0		0.0437	False		,,,				2504	0.0061				p.S1330S		Atlas-SNP	.											.	FHAD1	78	.	0			c.G3990A						PASS	.	G		7,1377		0,7,685	70.0	72.0	71.0		3990	-6.5	0.7	1	dbSNP_126	71	102,3080		1,100,1490	no	coding-synonymous	FHAD1	NM_052929.1		1,107,2175	AA,AG,GG		3.2055,0.5058,2.3872		1330/1413	15708557	109,4457	692	1591	2283	SO:0001819	synonymous_variant	114827	exon30			CCAGTCGCAGGTG	AK093300		1p36.21	2012-04-19			ENSG00000142621	ENSG00000142621			29408	protein-coding gene	gene with protein product						11572484	Standard	NM_052929		Approved	KIAA1937	uc001awb.2	B1AJZ9	OTTHUMG00000002088	ENST00000375998.4:c.3990G>A	1.37:g.15708557G>A		305.0	1.0	0.00327869		318.0	147.0	0.462264	NM_052929	Q0P6F5|Q8N8D3|Q8N9T6|Q8NA05	Silent	SNP	ENST00000375998.4	37		49	0.022435897435897436	6	0.012195121951219513	10	0.027624309392265192	0	0.0	33	0.04353562005277045	G	4.900	0.167197	0.09339	0.005058	0.032055	ENSG00000142621	ENST00000444385	.	.	.	5.95	-6.47	0.01902	.	.	.	.	.	T	0.18383	0.0441	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.46034	-0.9220	4	.	.	.	-10.4491	8.2849	0.31922	0.2893:0.2408:0.4699:0.0	rs35816204	.	.	.	H	649	.	.	R	+	2	0	FHAD1	15581144	0.000000	0.05858	0.746000	0.31095	0.416000	0.31233	-2.185000	0.01252	-1.616000	0.01572	-1.224000	0.01588	CGC	G|0.975;A|0.025	0.025	strong		0.542	FHAD1-026	PUTATIVE	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000393400.2	NM_052929	
DNAH7	56171	hgsc.bcm.edu	37	2	196922836	196922836	+	Missense_Mutation	SNP	T	T	A	rs72917299	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr2:196922836T>A	ENST00000312428.6	-	2	120	c.20A>T	c.(19-21)aAa>aTa	p.K7I	DNAH7_ENST00000410072.1_Missense_Mutation_p.K7I	NM_018897.2	NP_061720.2	Q8WXX0	DYH7_HUMAN	dynein, axonemal, heavy chain 7	7	Stem. {ECO:0000250}.				cilium movement (GO:0003341)|cilium or flagellum-dependent cell motility (GO:0001539)|metabolic process (GO:0008152)	axonemal dynein complex (GO:0005858)|cilium (GO:0005929)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|calcium ion binding (GO:0005509)|microtubule motor activity (GO:0003777)			NS(4)|breast(2)|endometrium(12)|haematopoietic_and_lymphoid_tissue(1)|kidney(15)|large_intestine(28)|liver(3)|lung(100)|ovary(4)|prostate(5)|skin(26)|upper_aerodigestive_tract(2)|urinary_tract(3)	205						GCTGGCCGATTTATCCTGTAT	0.313													T|||	16	0.00319489	0.0008	0.0029	5008	,	,		16097	0.0		0.0129	False		,,,				2504	0.0				p.K7I		Atlas-SNP	.											.	DNAH7	512	.	0			c.A20T						PASS	.	T	ILE/LYS	10,3592		0,10,1791	181.0	174.0	176.0		20	4.3	0.9	2	dbSNP_130	176	108,8028		1,106,3961	yes	missense	DNAH7	NM_018897.2	102	1,116,5752	AA,AT,TT		1.3274,0.2776,1.0053	possibly-damaging	7/4025	196922836	118,11620	1801	4068	5869	SO:0001583	missense	56171	exon2			GCCGATTTATCCT	AF327442	CCDS42794.1	2q33.1	2013-01-10	2006-09-04		ENSG00000118997	ENSG00000118997		"""Axonemal dyneins"", ""EF-hand domain containing"""	18661	protein-coding gene	gene with protein product		610061	"""dynein, axonemal, heavy polypeptide 7"""			9373155, 11877439	Standard	NM_018897		Approved	KIAA0944	uc002utj.4	Q8WXX0	OTTHUMG00000154438	ENST00000312428.6:c.20A>T	2.37:g.196922836T>A	ENSP00000311273:p.Lys7Ile	131.0	0.0	0		98.0	46.0	0.469388	NM_018897	B8ZZX8|O00433|O95492|Q4G152|Q53QX7|Q53S64|Q53T02|Q68CY5|Q8N1Z2|Q9UMS3|Q9Y2F3	Missense_Mutation	SNP	ENST00000312428.6	37	CCDS42794.1	13	0.005952380952380952	0	0.0	2	0.0055248618784530384	1	0.0017482517482517483	10	0.013192612137203167	T	13.85	2.361068	0.41801	0.002776	0.013274	ENSG00000118997	ENST00000312428;ENST00000410072;ENST00000312446	T;T	0.23754	1.89;2.52	4.29	4.29	0.51040	.	.	.	.	.	T	0.26919	0.0659	N	0.22421	0.69	0.31255	N	0.693556	D	0.65815	0.995	D	0.75484	0.986	T	0.19712	-1.0297	9	0.87932	D	0	.	10.1288	0.42665	0.0:0.0:0.0:1.0	.	7	Q8WXX0	DYH7_HUMAN	I	7	ENSP00000311273:K7I;ENSP00000386260:K7I	ENSP00000311273:K7I	K	-	2	0	DNAH7	196631081	0.996000	0.38824	0.876000	0.34364	0.572000	0.35998	3.399000	0.52586	2.155000	0.67459	0.460000	0.39030	AAA	T|0.991;A|0.009	0.009	strong		0.313	DNAH7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000335202.3	NM_018897	
PDZD7	79955	hgsc.bcm.edu	37	10	102783354	102783354	+	Silent	SNP	C	C	G			TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr10:102783354C>G	ENST00000370215.3	-	4	606	c.381G>C	c.(379-381)ctG>ctC	p.L127L	PDZD7_ENST00000470414.1_Silent_p.L127L	NM_024895.4	NP_079171.1	Q9H5P4	PDZD7_HUMAN	PDZ domain containing 7	127	PDZ 1. {ECO:0000255|PROSITE- ProRule:PRU00143}.					cilium (GO:0005929)|extracellular space (GO:0005615)|nucleus (GO:0005634)				breast(1)|central_nervous_system(1)|endometrium(2)|large_intestine(5)|lung(7)|ovary(2)|prostate(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	22				Epithelial(162;6.98e-09)|all cancers(201;3.55e-07)		CCCCCACGCACAGGCCAGCCC	0.652																																					p.L127L		Atlas-SNP	.											.	PDZD7	101	.	0			c.G381C						PASS	.						63.0	54.0	57.0					10																	102783354		2203	4300	6503	SO:0001819	synonymous_variant	79955	exon4			CACGCACAGGCCA	AK026862	CCDS31269.1, CCDS73182.1	10q24.32	2006-01-24		2006-01-24	ENSG00000186862	ENSG00000186862			26257	protein-coding gene	gene with protein product		612971		PDZK7		12477932	Standard	NM_024895		Approved	FLJ23209, bA108L7.8	uc021pxc.1	Q9H5P4	OTTHUMG00000018916	ENST00000370215.3:c.381G>C	10.37:g.102783354C>G		48.0	0.0	0		60.0	33.0	0.55	NM_001195263	D5FJ77|Q8N321	Silent	SNP	ENST00000370215.3	37	CCDS31269.1																																																																																			.	.	none		0.652	PDZD7-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049883.1	NM_024895	
PDAP1	11333	hgsc.bcm.edu	37	7	98997955	98997955	+	Silent	SNP	G	G	A	rs148987199		TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr7:98997955G>A	ENST00000350498.3	-	4	586	c.306C>T	c.(304-306)gaC>gaT	p.D102D	PDAP1_ENST00000496335.1_5'Flank	NM_014891.6	NP_055706.1	Q13442	HAP28_HUMAN	PDGFA associated protein 1	102					cell proliferation (GO:0008283)|signal transduction (GO:0007165)		poly(A) RNA binding (GO:0044822)			breast(1)|endometrium(1)|kidney(1)|large_intestine(2)|ovary(2)|prostate(1)|skin(1)	9	all_cancers(62;3.49e-09)|all_epithelial(64;2.57e-10)|Lung NSC(181;0.0053)|all_lung(186;0.00895)|Esophageal squamous(72;0.0166)		STAD - Stomach adenocarcinoma(171;0.215)			CCTTTGGCCCGTCCAGATCCA	0.552													G|||	1	0.000199681	0.0	0.0	5008	,	,		20454	0.0		0.001	False		,,,				2504	0.0				p.D102D		Atlas-SNP	.											.	PDAP1	17	.	0			c.C306T						PASS	.	G		0,4406		0,0,2203	168.0	123.0	138.0		306	-10.5	0.8	7	dbSNP_134	138	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous	PDAP1	NM_014891.6		0,1,6502	AA,AG,GG		0.0116,0.0,0.0077		102/182	98997955	1,13005	2203	4300	6503	SO:0001819	synonymous_variant	11333	exon4			TGGCCCGTCCAGA	U41745	CCDS5662.1	7q	2008-07-18			ENSG00000106244	ENSG00000106244			14634	protein-coding gene	gene with protein product	"""PDGF associated protein"""	607075				8780057	Standard	NM_014891		Approved	PAP1, PAP, HASPP28	uc003uqe.3	Q13442	OTTHUMG00000154629	ENST00000350498.3:c.306C>T	7.37:g.98997955G>A		394.0	1.0	0.00253807		369.0	175.0	0.474255	NM_014891	D6W5S5|Q92906	Silent	SNP	ENST00000350498.3	37	CCDS5662.1																																																																																			G|1.000;A|0.000	0.000	strong		0.552	PDAP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000336388.2	NM_014891	
DSG3	1830	hgsc.bcm.edu	37	18	29055635	29055635	+	Silent	SNP	C	C	T	rs117661169	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr18:29055635C>T	ENST00000257189.4	+	16	2495	c.2412C>T	c.(2410-2412)gaC>gaT	p.D804D		NM_001944.2	NP_001935.2	P32926	DSG3_HUMAN	desmoglein 3	804					apoptotic process (GO:0006915)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|homophilic cell adhesion (GO:0007156)	cell junction (GO:0030054)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			breast(1)|central_nervous_system(2)|cervix(3)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(10)|lung(28)|ovary(4)|prostate(1)|skin(8)|upper_aerodigestive_tract(1)	62			OV - Ovarian serous cystadenocarcinoma(10;0.00504)			CGGAGGAAGACGATGGCCAGG	0.418													C|||	92	0.0183706	0.0015	0.0202	5008	,	,		19856	0.0		0.0298	False		,,,				2504	0.047				p.D804D		Atlas-SNP	.											.	DSG3	172	.	0			c.C2412T						PASS	.	C		24,4382	32.6+/-62.9	0,24,2179	120.0	115.0	117.0		2412	-10.6	0.0	18	dbSNP_132	117	288,8312	107.8+/-168.5	2,284,4014	no	coding-synonymous	DSG3	NM_001944.2		2,308,6193	TT,TC,CC		3.3488,0.5447,2.3989		804/1000	29055635	312,12694	2203	4300	6503	SO:0001819	synonymous_variant	1830	exon16			GGAAGACGATGGC	M76482	CCDS11898.1	18q12.1	2010-06-24	2010-06-24		ENSG00000134757	ENSG00000134757		"""Cadherins / Major cadherins"""	3050	protein-coding gene	gene with protein product	"""pemphigus vulgaris antigen"""	169615	"""desmoglein 3 (pemphigus vulgaris antigen)"""			1601426	Standard	NM_001944		Approved	CDHF6	uc002kws.3	P32926	OTTHUMG00000131985	ENST00000257189.4:c.2412C>T	18.37:g.29055635C>T		68.0	0.0	0		78.0	37.0	0.474359	NM_001944	A8K2V2	Silent	SNP	ENST00000257189.4	37	CCDS11898.1																																																																																			C|0.976;T|0.024	0.024	strong		0.418	DSG3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254949.1	NM_001944	
GJD4	219770	hgsc.bcm.edu	37	10	35896700	35896700	+	Missense_Mutation	SNP	C	C	T	rs76906304	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr10:35896700C>T	ENST00000321660.1	+	2	417	c.259C>T	c.(259-261)Ctc>Ttc	p.L87F	RP11-425A6.5_ENST00000609313.1_RNA	NM_153368.2	NP_699199.2	Q96KN9	CXD4_HUMAN	gap junction protein, delta 4, 40.1kDa	87					cell communication (GO:0007154)|regulation of satellite cell activation involved in skeletal muscle regeneration (GO:0014717)	connexon complex (GO:0005922)|integral component of membrane (GO:0016021)				central_nervous_system(1)|endometrium(1)|large_intestine(6)|lung(5)|pancreas(1)|skin(1)|upper_aerodigestive_tract(1)	16						GTGCGTCCTCCTCCCCTCCGC	0.706													C|||	33	0.00658946	0.0	0.013	5008	,	,		11126	0.0		0.0119	False		,,,				2504	0.0123				p.L87F		Atlas-SNP	.											GJD4,NS,carcinoma,0,1	GJD4	38	1	0			c.C259T						PASS	.	C	PHE/LEU	16,4390	21.2+/-45.6	0,16,2187	148.0	122.0	131.0		259	4.3	0.1	10	dbSNP_131	131	148,8452	70.7+/-133.2	1,146,4153	yes	missense	GJD4	NM_153368.2	22	1,162,6340	TT,TC,CC		1.7209,0.3631,1.261	probably-damaging	87/371	35896700	164,12842	2203	4300	6503	SO:0001583	missense	219770	exon2			GTCCTCCTCCCCT	AJ414564	CCDS7191.1	10p11.22	2007-11-27			ENSG00000177291	ENSG00000177291		"""Ion channels / Gap junction proteins (connexins)"""	23296	protein-coding gene	gene with protein product	"""connexin 40.1"""	611922				12477932	Standard	NM_153368		Approved	CX40.1, FLJ90023	uc001iyy.1	Q96KN9	OTTHUMG00000017957	ENST00000321660.1:c.259C>T	10.37:g.35896700C>T	ENSP00000315070:p.Leu87Phe	58.0	0.0	0		64.0	30.0	0.46875	NM_153368	Q8N2R7	Missense_Mutation	SNP	ENST00000321660.1	37	CCDS7191.1	12	0.005494505494505495	0	0.0	5	0.013812154696132596	0	0.0	7	0.009234828496042216	C	15.31	2.795160	0.50208	0.003631	0.017209	ENSG00000177291	ENST00000321660	D	0.99129	-5.46	6.11	4.27	0.50696	Connexin, N-terminal (1);	0.215706	0.41938	N	0.000797	D	0.97228	0.9094	L	0.56769	1.78	0.51233	D	0.999916	D	0.52996	0.957	P	0.55087	0.768	D	0.93664	0.6984	10	0.62326	D	0.03	.	13.6296	0.62188	0.0:0.8795:0.0:0.1205	.	87	Q96KN9	CXD4_HUMAN	F	87	ENSP00000315070:L87F	ENSP00000315070:L87F	L	+	1	0	GJD4	35936706	0.680000	0.27605	0.144000	0.22314	0.036000	0.12997	1.246000	0.32803	0.916000	0.36871	0.655000	0.94253	CTC	C|0.989;T|0.011	0.011	strong		0.706	GJD4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047576.1	NM_153368	
RRN3	54700	hgsc.bcm.edu	37	16	15166809	15166809	+	Silent	SNP	A	A	G	rs72774849	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr16:15166809A>G	ENST00000198767.6	-	12	1209	c.1126T>C	c.(1126-1128)Ttg>Ctg	p.L376L	RRN3_ENST00000429751.2_Silent_p.L346L|RRN3_ENST00000563559.1_Silent_p.L376L|RRN3_ENST00000540462.1_Silent_p.L194L|RRN3_ENST00000327307.7_Silent_p.L343L|PDXDC1_ENST00000535621.2_Intron	NM_018427.3	NP_060897.3	Q9NYV6	RRN3_HUMAN	RRN3 RNA polymerase I transcription factor homolog (S. cerevisiae)	376					cell proliferation (GO:0008283)|cytoplasm organization (GO:0007028)|gene expression (GO:0010467)|homeostasis of number of cells (GO:0048872)|in utero embryonic development (GO:0001701)|negative regulation of intrinsic apoptotic signaling pathway by p53 class mediator (GO:1902254)|nucleolus organization (GO:0007000)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of DNA-templated transcription, initiation (GO:2000142)|ribosome biogenesis (GO:0042254)|transcription from RNA polymerase I promoter (GO:0006360)|transcription initiation from RNA polymerase I promoter (GO:0006361)	nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)				NS(2)|central_nervous_system(3)|endometrium(1)|kidney(1)|large_intestine(2)|lung(7)|ovary(2)|prostate(2)	20						TTACTCACCAATTTGAAACTA	0.383													.|||	22	0.00439297	0.0008	0.0043	5008	,	,		17623	0.0		0.0159	False		,,,				2504	0.002				p.L376L		Atlas-SNP	.											.	RRN3	36	.	0			c.T1126C						PASS	.	A		8,4386		0,8,2189	107.0	93.0	98.0		1126	-0.7	0.9	16	dbSNP_130	98	154,8446		1,152,4147	no	coding-synonymous	RRN3	NM_018427.3		1,160,6336	GG,GA,AA		1.7907,0.1821,1.2467		376/652	15166809	162,12832	2197	4300	6497	SO:0001819	synonymous_variant	54700	exon12			TCACCAATTTGAA	AF227156	CCDS10559.1, CCDS73833.1	16p13.11	2009-10-26	2006-04-04		ENSG00000085721	ENSG00000085721			30346	protein-coding gene	gene with protein product		605121	"""RRN3 RNA polymerase I transcription factor homolog (yeast)"""			10758157, 11250903	Standard	XM_005255375		Approved	DKFZp566E104	uc002dde.3	Q9NYV6	OTTHUMG00000129847	ENST00000198767.6:c.1126T>C	16.37:g.15166809A>G		102.0	0.0	0		105.0	51.0	0.485714	NM_018427	A2RTY9|B4E0J7|B4E3T2|Q3MHU9|Q6IPL4|Q9H4F0	Silent	SNP	ENST00000198767.6	37	CCDS10559.1																																																																																			A|0.987;G|0.013	0.013	strong		0.383	RRN3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252087.2	NM_018427	
BRAF	673	hgsc.bcm.edu	37	7	140449150	140449150	+	Silent	SNP	T	T	C	rs9648696	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr7:140449150T>C	ENST00000288602.6	-	16	1989	c.1929A>G	c.(1927-1929)ggA>ggG	p.G643G		NM_004333.4	NP_004324.2	P15056	BRAF_HUMAN	B-Raf proto-oncogene, serine/threonine kinase	643	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				activation of MAPKK activity (GO:0000186)|CD4-positive, alpha-beta T cell differentiation (GO:0043367)|cellular response to calcium ion (GO:0071277)|cellular response to drug (GO:0035690)|fibroblast growth factor receptor signaling pathway (GO:0008543)|long-term synaptic potentiation (GO:0060291)|myeloid progenitor cell differentiation (GO:0002318)|negative regulation of apoptotic process (GO:0043066)|negative regulation of endothelial cell apoptotic process (GO:2000352)|negative regulation of fibroblast migration (GO:0010764)|negative regulation of neuron apoptotic process (GO:0043524)|negative regulation of synaptic vesicle exocytosis (GO:2000301)|neurotrophin TRK receptor signaling pathway (GO:0048011)|organ morphogenesis (GO:0009887)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of gene expression (GO:0010628)|positive regulation of peptidyl-serine phosphorylation (GO:0033138)|positive regulation of stress fiber assembly (GO:0051496)|positive regulation of substrate adhesion-dependent cell spreading (GO:1900026)|positive T cell selection (GO:0043368)|protein heterooligomerization (GO:0051291)|protein phosphorylation (GO:0006468)|regulation of cell proliferation (GO:0042127)|response to cAMP (GO:0051591)|response to epidermal growth factor (GO:0070849)|response to peptide hormone (GO:0043434)|small GTPase mediated signal transduction (GO:0007264)|somatic stem cell maintenance (GO:0035019)|synaptic transmission (GO:0007268)|visual learning (GO:0008542)	cell body (GO:0044297)|cytosol (GO:0005829)|mitochondrion (GO:0005739)|neuron projection (GO:0043005)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|identical protein binding (GO:0042802)|MAP kinase kinase kinase activity (GO:0004709)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)		SLC45A3/BRAF(2)|AGTRAP/BRAF(2)|FAM131B_ENST00000443739/BRAF(7)|AKAP9_ENST00000356239/BRAF(10)|KIAA1549/BRAF(703)|FCHSD1/BRAF(2)	NS(588)|adrenal_gland(3)|autonomic_ganglia(3)|biliary_tract(29)|bone(7)|breast(21)|central_nervous_system(99)|cervix(6)|endometrium(33)|eye(72)|gastrointestinal_tract_(site_indeterminate)(2)|genital_tract(4)|haematopoietic_and_lymphoid_tissue(436)|kidney(3)|large_intestine(6953)|liver(17)|lung(192)|oesophagus(4)|ovary(275)|pancreas(15)|pituitary(1)|prostate(25)|salivary_gland(1)|skin(6285)|small_intestine(12)|soft_tissue(40)|stomach(11)|testis(7)|thyroid(12220)|upper_aerodigestive_tract(13)|urinary_tract(3)	27380	Melanoma(164;0.00956)				Dabrafenib(DB08912)|Regorafenib(DB08896)|Sorafenib(DB00398)|Vemurafenib(DB08881)	ACAGAACAATTCCAAATGCAT	0.348		61	"""Mis, T, O"""	"""AKAP9, KIAA1549"""	"""melanoma, colorectal, papillary thyroid, borderline ov, Non small-cell lung cancer (NSCLC), cholangiocarcinoma, pilocytic astrocytoma"""		Cardio-facio-cutaneous syndrome		Cardiofaciocutaneous syndrome				C|||	1758	0.351038	0.7451	0.1585	5008	,	,		17576	0.1825		0.1531	False		,,,				2504	0.3323				p.G643G	Colon(40;35 892 2973 5743 27438)	Atlas-SNP	.		Dom	yes		7	7q34	673	v-raf murine sarcoma viral oncogene homolog B1	yes	E	.	BRAF	36346	.	0			c.A1929G						PASS	.	C		2904,1502	476.8+/-357.7	963,978,262	105.0	108.0	107.0		1929	2.1	1.0	7	dbSNP_119	107	1258,7342	758.6+/-407.5	114,1030,3156	no	coding-synonymous	BRAF	NM_004333.4		1077,2008,3418	CC,CT,TT		14.6279,34.0899,32.0006		643/767	140449150	4162,8844	2203	4300	6503	SO:0001819	synonymous_variant	673	exon16	Familial Cancer Database	CFC, CFCS	AACAATTCCAAAT	M95712	CCDS5863.1	7q34	2014-09-17	2014-06-26		ENSG00000157764	ENSG00000157764			1097	protein-coding gene	gene with protein product		164757	"""v-raf murine sarcoma viral oncogene homolog B"""			2284096, 1565476	Standard	NM_004333		Approved	BRAF1	uc003vwc.4	P15056	OTTHUMG00000157457	ENST00000288602.6:c.1929A>G	7.37:g.140449150T>C		167.0	0.0	0		138.0	65.0	0.471014	NM_004333	A4D1T4|B6HY61|B6HY62|B6HY63|B6HY64|B6HY65|B6HY66|Q13878|Q3MIN6|Q9UDP8|Q9Y6T3	Silent	SNP	ENST00000288602.6	37	CCDS5863.1	611	0.27976190476190477	355	0.7215447154471545	58	0.16022099447513813	91	0.1590909090909091	107	0.14116094986807387	C	9.723	1.160251	0.21454	0.659101	0.146279	ENSG00000157764	ENST00000496384	.	.	.	5.02	2.11	0.27256	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.09310	P	1.0	.	.	.	.	.	.	T	0.33317	-0.9873	3	.	.	.	.	5.8585	0.18732	0.0:0.5864:0.1264:0.2872	rs9648696;rs10238189;rs60896634	.	.	.	G	251	.	.	E	-	2	0	BRAF	140095619	1.000000	0.71417	0.998000	0.56505	0.947000	0.59692	1.503000	0.35715	-0.010000	0.14271	-0.355000	0.07637	GAA	T|0.696;C|0.304	0.304	strong		0.348	BRAF-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000348886.1	NM_004333	
MTTP	4547	hgsc.bcm.edu	37	4	100532602	100532602	+	Missense_Mutation	SNP	G	G	A	rs113337987	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr4:100532602G>A	ENST00000265517.5	+	14	2184	c.1981G>A	c.(1981-1983)Ggt>Agt	p.G661S	RP11-766F14.1_ENST00000508578.1_RNA|MTTP_ENST00000457717.1_Missense_Mutation_p.G661S|MTTP_ENST00000511045.1_Missense_Mutation_p.G688S			P55157	MTP_HUMAN	microsomal triglyceride transfer protein	661					cholesterol homeostasis (GO:0042632)|lipid metabolic process (GO:0006629)|lipoprotein metabolic process (GO:0042157)|lipoprotein transport (GO:0042953)|protein lipidation (GO:0006497)|response to calcium ion (GO:0051592)|small molecule metabolic process (GO:0044281)|triglyceride metabolic process (GO:0006641)	basolateral plasma membrane (GO:0016323)|brush border membrane (GO:0031526)|endoplasmic reticulum lumen (GO:0005788)|Golgi apparatus (GO:0005794)|membrane-bounded vesicle (GO:0031988)|microvillus membrane (GO:0031528)|receptor complex (GO:0043235)|rough endoplasmic reticulum (GO:0005791)	lipid binding (GO:0008289)|lipid transporter activity (GO:0005319)			breast(3)|central_nervous_system(2)|cervix(1)|endometrium(4)|kidney(3)|large_intestine(14)|lung(19)|ovary(4)|prostate(5)|skin(1)|urinary_tract(1)	57				OV - Ovarian serous cystadenocarcinoma(123;6.04e-09)	Hesperetin(DB01094)|Lomitapide(DB08827)	TGGTCTTCACGGTAGCCAGGT	0.413													G|||	49	0.00978435	0.0	0.036	5008	,	,		19260	0.001		0.0209	False		,,,				2504	0.002				p.G661S		Atlas-SNP	.											MTTP,caecum,carcinoma,0,1	MTTP	127	1	0			c.G1981A						PASS	.	G	SER/GLY	26,4380	31.7+/-61.6	0,26,2177	144.0	132.0	136.0		1981	3.7	0.0	4	dbSNP_132	136	305,8295	110.0+/-170.5	11,283,4006	yes	missense	MTTP	NM_000253.2	56	11,309,6183	AA,AG,GG		3.5465,0.5901,2.545	benign	661/895	100532602	331,12675	2203	4300	6503	SO:0001583	missense	4547	exon15			CTTCACGGTAGCC		CCDS3651.1, CCDS75169.1	4q24	2008-02-05	2005-11-04	2005-11-04	ENSG00000138823	ENSG00000138823			7467	protein-coding gene	gene with protein product		157147	"""microsomal triglyceride transfer protein (large polypeptide, 88kD)"", ""microsomal triglyceride transfer protein (large polypeptide, 88kDa)"""	MTP		8111381	Standard	XM_005263025		Approved	ABL	uc003hvc.4	P55157	OTTHUMG00000131023	ENST00000265517.5:c.1981G>A	4.37:g.100532602G>A	ENSP00000265517:p.Gly661Ser	116.0	0.0	0		104.0	64.0	0.615385	NM_000253	A8K428|Q08AM4|Q6P5T3	Missense_Mutation	SNP	ENST00000265517.5	37	CCDS3651.1	38	0.0173992673992674	0	0.0	22	0.06077348066298342	0	0.0	16	0.021108179419525065	G	7.432	0.639007	0.14386	0.005901	0.035465	ENSG00000138823	ENST00000511045;ENST00000457717;ENST00000265517	T;T;T	0.60299	0.2;0.21;0.21	5.62	3.68	0.42216	.	0.320705	0.36703	N	0.002460	T	0.07503	0.0189	L	0.34521	1.04	0.34748	D	0.731457	B;B	0.17852	0.024;0.008	B;B	0.09377	0.003;0.004	T	0.21895	-1.0232	10	0.36615	T	0.2	-11.0583	11.7253	0.51706	0.1287:0.0:0.8713:0.0	.	688;661	E9PBP6;P55157	.;MTP_HUMAN	S	688;661;661	ENSP00000427679:G688S;ENSP00000400821:G661S;ENSP00000265517:G661S	ENSP00000265517:G661S	G	+	1	0	MTTP	100751625	1.000000	0.71417	0.004000	0.12327	0.011000	0.07611	4.409000	0.59768	0.533000	0.28675	0.655000	0.94253	GGT	G|0.970;A|0.030	0.030	strong		0.413	MTTP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253662.3		
ALK	238	hgsc.bcm.edu	37	2	29497967	29497967	+	Missense_Mutation	SNP	G	G	A	rs35228363	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr2:29497967G>A	ENST00000389048.3	-	11	2945	c.2039C>T	c.(2038-2040)aCa>aTa	p.T680I	ALK_ENST00000431873.1_Intron	NM_004304.4	NP_004295.2	Q9UM73	ALK_HUMAN	anaplastic lymphoma receptor tyrosine kinase	680			T -> I (in dbSNP:rs35228363). {ECO:0000269|PubMed:17344846}.		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)	ACCCTTACCTGTAGGGTCAAA	0.463			"""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				G|||	50	0.00998403	0.0	0.0288	5008	,	,		19632	0.001		0.0268	False		,,,				2504	0.002				p.T680I		Atlas-SNP	.	yes	Dom	yes	Familial neuroblastoma	2	2p23	238	anaplastic lymphoma kinase (Ki-1)		"""L, E, M"""	.	ALK	533	.	0			c.C2039T						PASS	.	G	ILE/THR	23,4383	29.0+/-57.7	0,23,2180	91.0	92.0	91.0		2039	5.2	1.0	2	dbSNP_126	91	250,8350	99.0+/-160.6	4,242,4054	yes	missense	ALK	NM_004304.4	89	4,265,6234	AA,AG,GG		2.907,0.522,2.099	benign	680/1621	29497967	273,12733	2203	4300	6503	SO:0001583	missense	238	exon11	Familial Cancer Database	Familial Neuroblastoma;CCHS, Ondine Curse, incl. Ondine-Hirschsprung Disease	TTACCTGTAGGGT	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.2039C>T	2.37:g.29497967G>A	ENSP00000373700:p.Thr680Ile	207.0	0.0	0		224.0	113.0	0.504464	NM_004304	Q4ZFX9|Q53QQ6|Q53RZ4|Q59FI3|Q9Y4K6	Missense_Mutation	SNP	ENST00000389048.3	37	CCDS33172.1	21	0.009615384615384616	0	0.0	9	0.024861878453038673	0	0.0	12	0.0158311345646438	G	14.36	2.511497	0.44660	0.00522	0.02907	ENSG00000171094	ENST00000389048	T	0.78246	-1.16	5.21	5.21	0.72293	.	0.304589	0.23175	U	0.051094	T	0.49677	0.1571	L	0.53249	1.67	0.80722	D	1	B	0.22983	0.078	B	0.15484	0.013	T	0.60905	-0.7170	9	.	.	.	.	14.2919	0.66284	0.0:0.0:1.0:0.0	rs35228363;rs61730441	680	Q9UM73	ALK_HUMAN	I	680	ENSP00000373700:T680I	.	T	-	2	0	ALK	29351471	1.000000	0.71417	1.000000	0.80357	0.443000	0.32047	4.489000	0.60309	2.433000	0.82419	0.561000	0.74099	ACA	G|0.984;A|0.016	0.016	strong		0.463	ALK-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000324994.1	NM_004304	
PCNT	5116	hgsc.bcm.edu	37	21	47856916	47856916	+	Silent	SNP	C	C	T			TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr21:47856916C>T	ENST00000359568.5	+	40	9128	c.9021C>T	c.(9019-9021)tcC>tcT	p.S3007S	PCNT_ENST00000480896.1_3'UTR	NM_006031.5	NP_006022.3	O95613	PCNT_HUMAN	pericentrin	3007	Interaction with NEK2.				brain morphogenesis (GO:0048854)|cerebellar cortex morphogenesis (GO:0021696)|cilium assembly (GO:0042384)|G2/M transition of mitotic cell cycle (GO:0000086)|in utero embryonic development (GO:0001701)|limb morphogenesis (GO:0035108)|microtubule cytoskeleton organization (GO:0000226)|mitotic cell cycle (GO:0000278)|multicellular organism growth (GO:0035264)|negative regulation of apoptotic process (GO:0043066)|neural precursor cell proliferation (GO:0061351)|neuron migration (GO:0001764)|olfactory bulb development (GO:0021772)|positive regulation of intracellular protein transport (GO:0090316)|spindle organization (GO:0007051)	centriolar satellite (GO:0034451)|centriole (GO:0005814)|centrosome (GO:0005813)|ciliary basal body (GO:0036064)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|intercellular bridge (GO:0045171)|membrane (GO:0016020)|microtubule (GO:0005874)|motile cilium (GO:0031514)|pericentriolar material (GO:0000242)				NS(1)|breast(5)|central_nervous_system(2)|cervix(1)|endometrium(11)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(15)|liver(2)|lung(41)|ovary(5)|pancreas(3)|prostate(3)|skin(5)|upper_aerodigestive_tract(2)|urinary_tract(2)	104	Breast(49;0.112)					GGACGTCATCCAATGAGAAAG	0.498																																					p.S3007S		Atlas-SNP	.											.	PCNT	283	.	0			c.C9021T						PASS	.						111.0	94.0	100.0					21																	47856916		2203	4300	6503	SO:0001819	synonymous_variant	5116	exon40			GTCATCCAATGAG	AB007862	CCDS33592.1	21q22.3	2014-02-20	2008-01-30	2005-11-03	ENSG00000160299	ENSG00000160299			16068	protein-coding gene	gene with protein product	"""kendrin"", ""Seckel syndrome 4"""	605925	"""pericentrin 2 (kendrin)"""	PCNT2		8812505, 9455477	Standard	NM_006031		Approved	KEN, KIAA0402, PCN, PCNTB, SCKL4	uc002zji.4	O95613	OTTHUMG00000090665	ENST00000359568.5:c.9021C>T	21.37:g.47856916C>T		53.0	0.0	0		77.0	4.0	0.0519481	NM_006031	O43152|Q7Z7C9	Silent	SNP	ENST00000359568.5	37	CCDS33592.1																																																																																			.	.	none		0.498	PCNT-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207336.1	NM_006031	
PRRC2B	84726	hgsc.bcm.edu	37	9	134340174	134340174	+	Missense_Mutation	SNP	C	C	T			TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr9:134340174C>T	ENST00000357304.4	+	11	1484	c.1429C>T	c.(1429-1431)Cgg>Tgg	p.R477W	PRRC2B_ENST00000458550.1_Missense_Mutation_p.R477W|PRRC2B_ENST00000405995.1_Missense_Mutation_p.R477W|PRRC2B_ENST00000372249.1_5'UTR	NM_013318.3	NP_037450.2	Q5JSZ5	PRC2B_HUMAN	proline-rich coiled-coil 2B	477							poly(A) RNA binding (GO:0044822)			cervix(2)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(7)|lung(20)|ovary(2)	44						CAGCATGTTCCGGCAACAGTC	0.582																																					p.R477W		Atlas-SNP	.											.	PRRC2B	266	.	0			c.C1429T						PASS	.						30.0	32.0	32.0					9																	134340174		2030	4175	6205	SO:0001583	missense	84726	exon11			ATGTTCCGGCAAC	AB011087	CCDS48044.1	9q34.13	2010-12-09	2010-12-09	2010-12-09	ENSG00000130723	ENSG00000130723			28121	protein-coding gene	gene with protein product			"""KIAA0515"", ""HLA-B associated transcript 2-like"", ""HLA-B associated transcript 2-like 1"""	KIAA0515, BAT2L, BAT2L1		9628581	Standard	NM_013318		Approved	MGC10526, LQFBS-1	uc004can.4	Q5JSZ5	OTTHUMG00000020827	ENST00000357304.4:c.1429C>T	9.37:g.134340174C>T	ENSP00000349856:p.Arg477Trp	115.0	0.0	0		125.0	55.0	0.44	NM_013318	O60270|Q5JSZ7|Q66VZ2|Q68CR0|Q96EI9|Q9H683	Missense_Mutation	SNP	ENST00000357304.4	37	CCDS48044.1	.	.	.	.	.	.	.	.	.	.	C	19.33	3.806464	0.70682	.	.	ENSG00000130723	ENST00000405995;ENST00000357304;ENST00000458550;ENST00000422467	T;T;T;T	0.26373	4.12;4.46;4.12;1.74	5.61	3.64	0.41730	.	0.000000	0.39210	U	0.001428	T	0.45478	0.1344	L	0.60455	1.87	0.80722	D	1	D	0.89917	1.0	D	0.79784	0.993	T	0.45991	-0.9223	10	0.66056	D	0.02	-3.5568	13.2394	0.59987	0.3749:0.6251:0.0:0.0	.	477	Q5JSZ5	PRC2B_HUMAN	W	477;477;477;17	ENSP00000384606:R477W;ENSP00000349856:R477W;ENSP00000398853:R477W;ENSP00000391063:R17W	ENSP00000349856:R477W	R	+	1	2	PRRC2B	133329995	1.000000	0.71417	1.000000	0.80357	0.938000	0.57974	1.986000	0.40677	1.355000	0.45865	0.655000	0.94253	CGG	.	.	none		0.582	PRRC2B-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding			
MYO1D	4642	hgsc.bcm.edu	37	17	31048141	31048141	+	Missense_Mutation	SNP	G	G	A	rs375202047		TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr17:31048141G>A	ENST00000318217.5	-	15	2117	c.1813C>T	c.(1813-1815)Cgc>Tgc	p.R605C	MYO1D_ENST00000579584.1_Missense_Mutation_p.R605C|MYO1D_ENST00000394649.4_Missense_Mutation_p.R517C	NM_015194.1	NP_056009.1	O94832	MYO1D_HUMAN	myosin ID	605	Myosin motor.				early endosome to recycling endosome transport (GO:0061502)|negative regulation of phosphatase activity (GO:0010923)	axolemma (GO:0030673)|endosome (GO:0005768)|extracellular vesicular exosome (GO:0070062)|myosin complex (GO:0016459)|smooth endoplasmic reticulum (GO:0005790)	actin-dependent ATPase activity (GO:0030898)|ATP binding (GO:0005524)|microfilament motor activity (GO:0000146)			breast(1)|central_nervous_system(1)|endometrium(6)|kidney(2)|large_intestine(8)|lung(14)|ovary(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	39			BRCA - Breast invasive adenocarcinoma(9;0.0362)			TGCCGGCAGCGTTCATCATCA	0.428																																					p.R605C		Atlas-SNP	.											.	MYO1D	93	.	0			c.C1813T						PASS	.	G	CYS/ARG	0,4406		0,0,2203	164.0	172.0	169.0		1813	4.3	1.0	17		169	1,8599	1.2+/-3.3	0,1,4299	no	missense	MYO1D	NM_015194.1	180	0,1,6502	AA,AG,GG		0.0116,0.0,0.0077	probably-damaging	605/1007	31048141	1,13005	2203	4300	6503	SO:0001583	missense	4642	exon15			GGCAGCGTTCATC	AB018270	CCDS32615.1	17q11-q12	2014-06-12				ENSG00000176658		"""Myosins / Myosin superfamily : Class I"""	7598	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 108"""	606539				8884266	Standard	NM_015194		Approved	KIAA0727, myr4, PPP1R108	uc002hho.1	O94832		ENST00000318217.5:c.1813C>T	17.37:g.31048141G>A	ENSP00000324527:p.Arg605Cys	140.0	0.0	0		162.0	84.0	0.518519	NM_015194	A6H8V3|Q8NHP9	Missense_Mutation	SNP	ENST00000318217.5	37	CCDS32615.1	.	.	.	.	.	.	.	.	.	.	G	25.3	4.620942	0.87460	0.0	1.16E-4	ENSG00000176658	ENST00000318217	D	0.87179	-2.22	5.33	4.32	0.51571	Myosin head, motor domain (2);	0.000000	0.33834	U	0.004520	D	0.93294	0.7863	M	0.87900	2.915	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.87578	0.998;0.993	D	0.93324	0.6695	10	0.72032	D	0.01	.	11.2797	0.49186	0.0:0.0:0.7002:0.2998	.	516;605	Q7Z3N6;O94832	.;MYO1D_HUMAN	C	605	ENSP00000324527:R605C	ENSP00000324527:R605C	R	-	1	0	MYO1D	28072254	1.000000	0.71417	0.996000	0.52242	0.991000	0.79684	6.347000	0.73004	2.781000	0.95711	0.650000	0.86243	CGC	.	.	weak		0.428	MYO1D-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000447457.1		
SLC27A5	10998	hgsc.bcm.edu	37	19	59009949	59009949	+	Missense_Mutation	SNP	G	G	C	rs145618122	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr19:59009949G>C	ENST00000263093.2	-	10	2115	c.2006C>G	c.(2005-2007)gCc>gGc	p.A669G	SLC27A5_ENST00000601355.1_Missense_Mutation_p.A585G|SLC27A5_ENST00000599700.1_5'UTR|SLC27A5_ENST00000594786.1_Missense_Mutation_p.A74G	NM_012254.2	NP_036386.1	Q9Y2P5	S27A5_HUMAN	solute carrier family 27 (fatty acid transporter), member 5	669					bile acid and bile salt transport (GO:0015721)|bile acid biosynthetic process (GO:0006699)|bile acid metabolic process (GO:0008206)|ketone body biosynthetic process (GO:0046951)|plasma membrane long-chain fatty acid transport (GO:0015911)|small molecule metabolic process (GO:0044281)|triglyceride mobilization (GO:0006642)|very long-chain fatty acid metabolic process (GO:0000038)	basal plasma membrane (GO:0009925)|endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|integral component of endoplasmic reticulum membrane (GO:0030176)|protein complex (GO:0043234)	ATP binding (GO:0005524)|cholate-CoA ligase activity (GO:0047747)|fatty acid transporter activity (GO:0015245)|very long-chain fatty acid-CoA ligase activity (GO:0031957)			central_nervous_system(1)|endometrium(2)|kidney(2)|large_intestine(4)|lung(7)|ovary(1)|skin(1)|urinary_tract(1)	19		all_cancers(17;4.4e-22)|all_epithelial(17;2.15e-16)|Lung NSC(17;1.24e-06)|all_lung(17;5.41e-06)|Colorectal(82;3.46e-05)|Renal(17;0.00179)|all_neural(62;0.00607)|Ovarian(87;0.0443)|Breast(46;0.0928)|Medulloblastoma(540;0.184)		UCEC - Uterine corpus endometrioid carcinoma (67;0.168)|GBM - Glioblastoma multiforme(193;0.0168)|Lung(386;0.181)		GAAGGACTGGGCCCGGTTGTC	0.582													G|||	22	0.00439297	0.0015	0.0043	5008	,	,		18662	0.0		0.008	False		,,,				2504	0.0092				p.A669G		Atlas-SNP	.											.	SLC27A5	58	.	0			c.C2006G						PASS	.	G	GLY/ALA	2,4404	4.2+/-10.8	0,2,2201	124.0	106.0	112.0		2006	2.5	0.0	19	dbSNP_134	112	78,8522	42.2+/-99.7	0,78,4222	yes	missense	SLC27A5	NM_012254.2	60	0,80,6423	CC,CG,GG		0.907,0.0454,0.6151	benign	669/691	59009949	80,12926	2203	4300	6503	SO:0001583	missense	10998	exon10			GACTGGGCCCGGT	AF064255	CCDS12983.1	19q13.43	2013-07-15			ENSG00000083807	ENSG00000083807		"""Acyl-CoA synthetase family"", ""Solute carriers"""	10999	protein-coding gene	gene with protein product	"""fatty-acid-Coenzyme A ligase, very long-chain 3"""	603314				10479480, 10749848	Standard	NM_012254		Approved	FATP5, VLACSR, VLCS-H2, VLCSH2, FACVL3, FLJ22987, ACSVL6, ACSB	uc002qtc.2	Q9Y2P5	OTTHUMG00000183543	ENST00000263093.2:c.2006C>G	19.37:g.59009949G>C	ENSP00000263093:p.Ala669Gly	83.0	0.0	0		52.0	25.0	0.480769	NM_012254	B3KVP6|B4DPQ1	Missense_Mutation	SNP	ENST00000263093.2	37	CCDS12983.1	11	0.005036630036630037	1	0.0020325203252032522	2	0.0055248618784530384	0	0.0	8	0.010554089709762533	G	7.891	0.732413	0.15507	4.54E-4	0.00907	ENSG00000083807	ENST00000263093	T	0.53423	0.62	4.85	2.51	0.30379	.	0.370857	0.28130	N	0.016500	T	0.22742	0.0549	N	0.25245	0.725	0.09310	N	1	B	0.11235	0.004	B	0.16289	0.015	T	0.12426	-1.0548	10	0.27082	T	0.32	-8.9846	9.675	0.40034	0.0:0.0:0.6228:0.3772	.	669	Q9Y2P5	S27A5_HUMAN	G	669	ENSP00000263093:A669G	ENSP00000263093:A669G	A	-	2	0	SLC27A5	63701761	0.000000	0.05858	0.005000	0.12908	0.392000	0.30506	0.058000	0.14301	1.137000	0.42214	0.655000	0.94253	GCC	G|0.992;C|0.008	0.008	strong		0.582	SLC27A5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000467060.1	NM_012254	
TBXAS1	6916	hgsc.bcm.edu	37	7	139717523	139717523	+	Missense_Mutation	SNP	G	G	T	rs561266357|rs149988492	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr7:139717523G>T	ENST00000336425.5	+	16	1806	c.1417G>T	c.(1417-1419)Ggg>Tgg	p.G473W	TBXAS1_ENST00000263552.6_Missense_Mutation_p.G474W|TBXAS1_ENST00000436047.2_Missense_Mutation_p.G474W|TBXAS1_ENST00000458722.1_Missense_Mutation_p.G519W|TBXAS1_ENST00000416849.2_Missense_Mutation_p.G520W|TBXAS1_ENST00000414508.2_Intron|TBXAS1_ENST00000425687.1_Missense_Mutation_p.G406W|TBXAS1_ENST00000448866.1_Missense_Mutation_p.G473W|TBXAS1_ENST00000411653.1_Intron			P24557	THAS_HUMAN	thromboxane A synthase 1 (platelet)	473					arachidonic acid metabolic process (GO:0019369)|cellular chloride ion homeostasis (GO:0030644)|cyclooxygenase pathway (GO:0019371)|icosanoid metabolic process (GO:0006690)|positive regulation of vasoconstriction (GO:0045907)|small molecule metabolic process (GO:0044281)|xenobiotic metabolic process (GO:0006805)	endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)	heme binding (GO:0020037)|iron ion binding (GO:0005506)|monooxygenase activity (GO:0004497)|oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen (GO:0016705)|thromboxane-A synthase activity (GO:0004796)			breast(3)|endometrium(1)|kidney(1)|large_intestine(5)|lung(11)|ovary(2)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	28	Melanoma(164;0.0142)				Ridogrel(DB01207)|Sulfasalazine(DB00795)	CCTGCCCTTCGGGGCCGGCCC	0.682																																					p.G520W		Atlas-SNP	.											.	TBXAS1	121	.	0			c.G1558T						PASS	.	G	TRP/GLY,TRP/GLY,TRP/GLY,TRP/GLY,	1,4405	2.1+/-5.4	0,1,2202	41.0	46.0	44.0		1420,1420,1558,1216,	4.7	0.3	7	dbSNP_134	44	0,8598		0,0,4299	no	missense,missense,missense,missense,intron	TBXAS1	NM_001061.4,NM_001130966.2,NM_001166253.1,NM_001166254.1,NM_030984.3	184,184,184,184,	0,1,6501	TT,TG,GG		0.0,0.0227,0.0077	probably-damaging,probably-damaging,probably-damaging,probably-damaging,	474/535,474/535,520/581,406/467,	139717523	1,13003	2203	4299	6502	SO:0001583	missense	6916	exon13			CCCTTCGGGGCCG	L36085	CCDS5855.1, CCDS5856.1, CCDS55174.1, CCDS55175.1	7q34-q35	2014-09-17	2008-07-31		ENSG00000059377	ENSG00000059377	5.3.99.5	"""Cytochrome P450s"""	11609	protein-coding gene	gene with protein product	"""cytochrome P450, family 5, subfamily A, polypeptide 1"""	274180	"""thromboxane A synthase 1 (platelet, cytochrome P450, subfamily V)"""			1714723, 8964509	Standard	NM_001061		Approved	CYP5, CYP5A1, THAS, TXS, TXAS, TS	uc011kqv.2	P24557	OTTHUMG00000157302	ENST00000336425.5:c.1417G>T	7.37:g.139717523G>T	ENSP00000338087:p.Gly473Trp	246.0	0.0	0		324.0	182.0	0.561728	NM_001166253	B4DJG6|E7EMU9|E7EP08|E7ESB5|O14987|Q16843|Q16844|Q8IUN1|Q96CN2|Q9GZW4|Q9HD77|Q9HD78|Q9HD79|Q9HD80|Q9HD81|Q9HD82|Q9HD83|Q9HD84	Missense_Mutation	SNP	ENST00000336425.5	37		.	.	.	.	.	.	.	.	.	.	G	22.0	4.228603	0.79576	2.27E-4	0.0	ENSG00000059377	ENST00000425687;ENST00000263552;ENST00000336425;ENST00000416849;ENST00000436047;ENST00000448866;ENST00000458722	T;T;T;T;T;T;T	0.80304	-1.36;-1.36;-1.36;-1.36;-1.36;-1.36;-1.36	4.69	4.69	0.59074	Cytochrome P450, conserved site (1);	0.000000	0.85682	D	0.000000	D	0.93242	0.7847	H	0.97291	3.975	0.80722	D	1	D;D;D;D;D	0.89917	1.0;1.0;1.0;1.0;1.0	D;D;D;D;D	0.97110	1.0;1.0;1.0;1.0;1.0	D	0.95589	0.8653	10	0.87932	D	0	.	15.4076	0.74890	0.0:0.0:1.0:0.0	.	454;520;406;474;473	B4DVP1;E7EP08;E7ESB5;Q53F23;P24557	.;.;.;.;THAS_HUMAN	W	406;474;473;520;474;473;519	ENSP00000388736:G406W;ENSP00000263552:G474W;ENSP00000338087:G473W;ENSP00000389414:G520W;ENSP00000392361:G474W;ENSP00000402536:G473W;ENSP00000411274:G519W	ENSP00000263552:G474W	G	+	1	0	TBXAS1	139363992	1.000000	0.71417	0.334000	0.25495	0.882000	0.50991	6.773000	0.75006	2.162000	0.67917	0.561000	0.74099	GGG	G|1.000;T|0.000	0.000	strong		0.682	TBXAS1-001	KNOWN	basic|appris_candidate	protein_coding	protein_coding	OTTHUMT00000348373.1		
RPH3AL	9501	hgsc.bcm.edu	37	17	96910	96910	+	Missense_Mutation	SNP	C	C	T	rs376959240		TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr17:96910C>T	ENST00000331302.7	-	7	912	c.605G>A	c.(604-606)cGa>cAa	p.R202Q	RPH3AL_ENST00000536489.2_Missense_Mutation_p.R173Q|RPH3AL_ENST00000576001.1_5'UTR|RPH3AL_ENST00000323434.8_Missense_Mutation_p.R173Q	NM_001190411.1|NM_006987.3	NP_001177340.1|NP_008918.1	Q9UNE2	RPH3L_HUMAN	rabphilin 3A-like (without C2 domains)	202					exocytosis (GO:0006887)|glucose homeostasis (GO:0042593)|intracellular protein transport (GO:0006886)|negative regulation of G-protein coupled receptor protein signaling pathway (GO:0045744)|positive regulation of protein secretion (GO:0050714)|regulation of calcium ion-dependent exocytosis (GO:0017158)|response to drug (GO:0042493)	cytoplasm (GO:0005737)|secretory granule membrane (GO:0030667)	cytoskeletal protein binding (GO:0008092)|metal ion binding (GO:0046872)			NS(2)|breast(1)|kidney(1)|large_intestine(1)|skin(1)	6				UCEC - Uterine corpus endometrioid carcinoma (25;0.023)|all cancers(1;4.96e-06)|Epithelial(1;2.86e-05)|BRCA - Breast invasive adenocarcinoma(1;0.00453)|OV - Ovarian serous cystadenocarcinoma(1;0.0716)|LUAD - Lung adenocarcinoma(1115;0.102)|COAD - Colon adenocarcinoma(4;0.107)		ACCTCTTCCTCGGGCCCACGT	0.632													c|||	1	0.000199681	0.0	0.0	5008	,	,		17004	0.001		0.0	False		,,,				2504	0.0				p.R202Q		Atlas-SNP	.											.	RPH3AL	18	.	0			c.G605A						PASS	.		GLN/ARG,GLN/ARG,GLN/ARG,GLN/ARG	1,4405	2.1+/-5.4	0,1,2202	98.0	91.0	93.0		605,518,518,605	5.1	1.0	17		93	0,8600		0,0,4300	no	missense,missense,missense,missense	RPH3AL	NM_001190411.1,NM_001190412.1,NM_001190413.1,NM_006987.3	43,43,43,43	0,1,6502	TT,TC,CC		0.0,0.0227,0.0077	possibly-damaging,possibly-damaging,possibly-damaging,possibly-damaging	202/316,173/287,173/287,202/316	96910	1,13005	2203	4300	6503	SO:0001583	missense	9501	exon7			CTTCCTCGGGCCC		CCDS10994.1, CCDS54059.1	17p13.3	2014-07-02			ENSG00000181031	ENSG00000181031		"""Synaptotagmins"""	10296	protein-coding gene	gene with protein product		604881				10395805	Standard	NM_006987		Approved	Noc2	uc021tmx.1	Q9UNE2	OTTHUMG00000090273	ENST00000331302.7:c.605G>A	17.37:g.96910C>T	ENSP00000328977:p.Arg202Gln	98.0	0.0	0		85.0	39.0	0.458824	NM_006987	D3DTG7|Q9BSB3	Missense_Mutation	SNP	ENST00000331302.7	37	CCDS10994.1	.	.	.	.	.	.	.	.	.	.	c	18.68	3.676535	0.67928	2.27E-4	0.0	ENSG00000181031	ENST00000323434;ENST00000331302;ENST00000536489	.	.	.	5.06	5.06	0.68205	.	0.114746	0.35235	N	0.003345	T	0.62011	0.2393	M	0.77103	2.36	0.22710	N	0.998827	D;D;D	0.76494	0.981;0.999;0.999	P;D;P	0.64237	0.551;0.923;0.849	T	0.55786	-0.8086	9	0.21540	T	0.41	-5.7361	9.6113	0.39665	0.0:0.9048:0.0:0.0952	.	173;173;202	A8K7D5;Q9UNE2-2;Q9UNE2	.;.;RPH3L_HUMAN	Q	202;173;173	.	ENSP00000319210:R202Q	R	-	2	0	RPH3AL	96910	1.000000	0.71417	1.000000	0.80357	0.315000	0.28087	2.084000	0.41625	2.378000	0.81104	0.544000	0.68410	CGA	.	.	weak		0.632	RPH3AL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206597.2	NM_006987	
CSF1R	1436	hgsc.bcm.edu	37	5	149457678	149457678	+	Silent	SNP	G	G	A	rs2228422	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr5:149457678G>A	ENST00000286301.3	-	5	1017	c.726C>T	c.(724-726)acC>acT	p.T242T	CSF1R_ENST00000543093.1_Silent_p.T242T	NM_005211.3	NP_005202.2	P07333	CSF1R_HUMAN	colony stimulating factor 1 receptor	242	Ig-like C2-type 3.				cell proliferation (GO:0008283)|cell-cell junction maintenance (GO:0045217)|cellular response to cytokine stimulus (GO:0071345)|cellular response to macrophage colony-stimulating factor stimulus (GO:0036006)|cytokine-mediated signaling pathway (GO:0019221)|hemopoiesis (GO:0030097)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|macrophage differentiation (GO:0030225)|mammary gland duct morphogenesis (GO:0060603)|monocyte differentiation (GO:0030224)|multicellular organismal development (GO:0007275)|osteoclast differentiation (GO:0030316)|peptidyl-tyrosine phosphorylation (GO:0018108)|phosphatidylinositol metabolic process (GO:0046488)|phosphatidylinositol-mediated signaling (GO:0048015)|positive regulation of cell migration (GO:0030335)|positive regulation of cell motility (GO:2000147)|positive regulation of cell proliferation (GO:0008284)|positive regulation of chemokine secretion (GO:0090197)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of protein serine/threonine kinase activity (GO:0071902)|positive regulation of protein tyrosine kinase activity (GO:0061098)|positive regulation of tyrosine phosphorylation of Stat3 protein (GO:0042517)|protein autophosphorylation (GO:0046777)|regulation of actin cytoskeleton reorganization (GO:2000249)|regulation of bone resorption (GO:0045124)|regulation of cell shape (GO:0008360)|ruffle organization (GO:0031529)|signal transduction (GO:0007165)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)	cell surface (GO:0009986)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	ATP binding (GO:0005524)|cytokine binding (GO:0019955)|macrophage colony-stimulating factor receptor activity (GO:0005011)|protein homodimerization activity (GO:0042803)	p.T242T(1)		NS(2)|breast(2)|central_nervous_system(3)|endometrium(3)|haematopoietic_and_lymphoid_tissue(38)|kidney(2)|large_intestine(6)|liver(3)|lung(23)|ovary(2)|pancreas(1)|prostate(3)|upper_aerodigestive_tract(2)|urinary_tract(3)	93			KIRC - Kidney renal clear cell carcinoma(527;0.000962)|Kidney(363;0.00147)		Imatinib(DB00619)|Sunitinib(DB01268)	GACTGACCTTGGTGTTGTTGT	0.572													G|||	1940	0.38738	0.2799	0.366	5008	,	,		20014	0.2113		0.5457	False		,,,				2504	0.5665				p.T242T		Atlas-SNP	.											CSF1R_ENST00000286301,NS,carcinoma,0,1	CSF1R	250	1	1	Substitution - coding silent(1)	stomach(1)	c.C726T						scavenged	.	G		1388,3018	457.5+/-351.6	220,948,1035	224.0	186.0	199.0		726	-0.9	1.0	5	dbSNP_98	199	4864,3736	618.2+/-396.8	1391,2082,827	no	coding-synonymous	CSF1R	NM_005211.3		1611,3030,1862	AA,AG,GG		43.4419,31.5025,48.0701		242/973	149457678	6252,6754	2203	4300	6503	SO:0001819	synonymous_variant	1436	exon5			GACCTTGGTGTTG	U63963	CCDS4302.1	5q32	2013-01-11	2008-08-01		ENSG00000182578	ENSG00000182578		"""CD molecules"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	2433	protein-coding gene	gene with protein product		164770	"""McDonough feline sarcoma viral (v-fms) oncogene homolog"""	FMS		1611909	Standard	NM_005211		Approved	C-FMS, CSFR, CD115	uc003lrm.3	P07333	OTTHUMG00000130050	ENST00000286301.3:c.726C>T	5.37:g.149457678G>A		188.0	1.0	0.00531915		195.0	80.0	0.410256	NM_005211	B5A955|D3DQG2|Q6LDW5|Q6LDY4|Q86VW7	Silent	SNP	ENST00000286301.3	37	CCDS4302.1																																																																																			G|0.561;A|0.439	0.439	strong		0.572	CSF1R-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252329.2	NM_005211	
KRTAP1-1	81851	hgsc.bcm.edu	37	17	39197173	39197173	+	Silent	SNP	A	A	G	rs144980478	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr17:39197173A>G	ENST00000306271.4	-	1	540	c.477T>C	c.(475-477)tgT>tgC	p.C159C		NM_030967.2	NP_112229.1	Q07627	KRA11_HUMAN	keratin associated protein 1-1	159						keratin filament (GO:0045095)				NS(2)|endometrium(2)|kidney(5)|lung(4)|prostate(1)	14		Breast(137;0.000496)	STAD - Stomach adenocarcinoma(17;0.000371)			AGGACTGTCCACAGTAGGATG	0.617													a|||	10	0.00199681	0.0	0.0029	5008	,	,		17718	0.0		0.008	False		,,,				2504	0.0				p.C159C		Atlas-SNP	.											.	KRTAP1-1	23	.	0			c.T477C						PASS	.	A		5,4099		0,5,2047	31.0	35.0	34.0		477	4.1	1.0	17	dbSNP_134	34	34,8330		0,34,4148	no	coding-synonymous	KRTAP1-1	NM_030967.2		0,39,6195	GG,GA,AA		0.4065,0.1218,0.3128		159/178	39197173	39,12429	2052	4182	6234	SO:0001819	synonymous_variant	81851	exon1			CTGTCCACAGTAG	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.477T>C	17.37:g.39197173A>G		177.0	0.0	0		180.0	96.0	0.533333	NM_030967	A6NC32|Q96S60|Q96S67	Silent	SNP	ENST00000306271.4	37	CCDS42324.1																																																																																			A|0.996;G|0.004	0.004	strong		0.617	KRTAP1-1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257696.1	NM_030967	
DENND1A	57706	hgsc.bcm.edu	37	9	126144441	126144441	+	Missense_Mutation	SNP	G	G	A	rs200503663		TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr9:126144441G>A	ENST00000373624.2	-	22	2501	c.2300C>T	c.(2299-2301)cCg>cTg	p.P767L	DENND1A_ENST00000473039.1_5'UTR|DENND1A_ENST00000542603.1_Missense_Mutation_p.P552L|DENND1A_ENST00000394219.3_Missense_Mutation_p.P778L	NM_020946.1	NP_065997.1	Q8TEH3	DEN1A_HUMAN	DENN/MADD domain containing 1A	767	Pro-rich.				endocytosis (GO:0006897)|positive regulation of Rab GTPase activity (GO:0032851)|protein transport (GO:0015031)|regulation of Rab protein signal transduction (GO:0032483)|synaptic vesicle endocytosis (GO:0048488)	cell junction (GO:0030054)|clathrin-coated vesicle (GO:0030136)|clathrin-coated vesicle membrane (GO:0030665)|dendrite (GO:0030425)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)|synapse (GO:0045202)	Rab guanyl-nucleotide exchange factor activity (GO:0017112)			breast(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(12)|liver(2)|lung(18)|ovary(2)|prostate(1)|skin(1)|stomach(1)	43						AGGGCTGAGCGGCTGGAGCAG	0.701																																					p.P767L		Atlas-SNP	.											DENND1A,colon,carcinoma,-1,1	DENND1A	112	1	0			c.C2300T						PASS	.	G	LEU/PRO	0,4364		0,0,2182	11.0	16.0	15.0		2300	4.8	0.9	9		15	1,8551		0,1,4275	yes	missense	DENND1A	NM_020946.1	98	0,1,6457	AA,AG,GG		0.0117,0.0,0.0077	probably-damaging	767/1010	126144441	1,12915	2182	4276	6458	SO:0001583	missense	57706	exon22			CTGAGCGGCTGGA	AB046828	CCDS35133.1, CCDS35134.1	9q34.11	2012-10-03	2005-08-17	2005-08-17	ENSG00000119522	ENSG00000119522		"""DENN/MADD domain containing"""	29324	protein-coding gene	gene with protein product		613633	"""KIAA1608"""	KIAA1608		10997877	Standard	XM_005252109		Approved	FLJ21129, FAM31A	uc004bnz.1	Q8TEH3	OTTHUMG00000020643	ENST00000373624.2:c.2300C>T	9.37:g.126144441G>A	ENSP00000362727:p.Pro767Leu	34.0	0.0	0		28.0	15.0	0.535714	NM_020946	A8MZA3|B1AM80|B7Z3C8|B7Z669|D3PFD3|Q05C88|Q5VWF0|Q6PJZ5|Q8IVD6|Q9H796	Missense_Mutation	SNP	ENST00000373624.2	37	CCDS35133.1	.	.	.	.	.	.	.	.	.	.	G	16.96	3.267066	0.59540	0.0	1.17E-4	ENSG00000119522	ENST00000373624;ENST00000542603;ENST00000394219	T;T;T	0.28895	2.99;1.59;2.9	4.83	4.83	0.62350	.	0.133128	0.51477	D	0.000095	T	0.47358	0.1441	M	0.63843	1.955	0.80722	D	1	D;D;D;D	0.67145	0.996;0.996;0.993;0.979	P;P;P;P	0.56398	0.742;0.797;0.557;0.481	T	0.49466	-0.8937	10	0.56958	D	0.05	-7.2386	16.1301	0.81422	0.0:0.0:1.0:0.0	.	778;768;767;630	Q8TEH3-6;Q8TEH3-7;Q8TEH3;Q9HCG4	.;.;DEN1A_HUMAN;.	L	767;552;778	ENSP00000362727:P767L;ENSP00000437457:P552L;ENSP00000377766:P778L	ENSP00000362727:P767L	P	-	2	0	DENND1A	125184262	1.000000	0.71417	0.906000	0.35671	0.485000	0.33311	6.349000	0.73013	2.224000	0.72417	0.557000	0.71058	CCG	.	.	weak		0.701	DENND1A-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000053997.1	NM_024820	
MUC4	4585	hgsc.bcm.edu	37	3	195506014	195506014	+	Missense_Mutation	SNP	G	G	A	rs200152370		TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr3:195506014G>A	ENST00000463781.3	-	2	12896	c.12437C>T	c.(12436-12438)cCt>cTt	p.P4146L	MUC4_ENST00000346145.4_Intron|MUC4_ENST00000349607.4_Intron|MUC4_ENST00000475231.1_Missense_Mutation_p.P4146L	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)		GATGGTGACAGGAAGAGGCGT	0.587																																					p.P4146L		Atlas-SNP	.											.	MUC4	1505	.	0			c.C12437T						PASS	.						35.0	20.0	25.0					3																	195506014		647	1559	2206	SO:0001583	missense	4585	exon2			GTGACAGGAAGAG	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.12437C>T	3.37:g.195506014G>A	ENSP00000417498:p.Pro4146Leu	154.0	0.0	0		135.0	19.0	0.140741	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	4.464	0.086057	0.08583	.	.	ENSG00000145113	ENST00000463781;ENST00000475231	T;T	0.39056	1.42;1.1	.	.	.	.	.	.	.	.	T	0.39279	0.1072	N	0.19112	0.55	0.09310	N	1	D	0.64830	0.994	P	0.62885	0.908	T	0.23940	-1.0174	7	.	.	.	.	5.8679	0.18786	8.0E-4:0.0:0.9992:0.0	.	4018	E7ESK3	.	L	4146	ENSP00000417498:P4146L;ENSP00000420243:P4146L	.	P	-	2	0	MUC4	196990793	0.001000	0.12720	0.016000	0.15963	0.017000	0.09413	0.709000	0.25734	0.088000	0.17205	0.089000	0.15464	CCT	.	.	weak		0.587	MUC4-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000324081.6	NM_018406	
MTRR	4552	hgsc.bcm.edu	37	5	7892933	7892933	+	Silent	SNP	A	A	G	rs35890938	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr5:7892933A>G	ENST00000264668.2	+	11	1575	c.1545A>G	c.(1543-1545)gtA>gtG	p.V515V	MTRR_ENST00000440940.2_Silent_p.V488V	NM_002454.2|NM_024010.2	NP_002445.2|NP_076915.2	Q9UBK8	MTRR_HUMAN	5-methyltetrahydrofolate-homocysteine methyltransferase reductase	515	FAD-binding FR-type. {ECO:0000255|PROSITE-ProRule:PRU00716}.				cellular nitrogen compound metabolic process (GO:0034641)|cobalamin metabolic process (GO:0009235)|DNA methylation (GO:0006306)|folic acid metabolic process (GO:0046655)|methionine biosynthetic process (GO:0009086)|methionine metabolic process (GO:0006555)|methylation (GO:0032259)|oxidation-reduction process (GO:0055114)|small molecule metabolic process (GO:0044281)|sulfur amino acid metabolic process (GO:0000096)|vitamin metabolic process (GO:0006766)|water-soluble vitamin metabolic process (GO:0006767)|xenobiotic metabolic process (GO:0006805)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|intermediate filament cytoskeleton (GO:0045111)|nucleus (GO:0005634)	[methionine synthase] reductase activity (GO:0030586)|flavin adenine dinucleotide binding (GO:0050660)|FMN binding (GO:0010181)|iron ion binding (GO:0005506)|NADP binding (GO:0050661)|oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, NAD(P)H as one donor, and incorporation of one atom of oxygen (GO:0016709)|oxidoreductase activity, oxidizing metal ions, NAD or NADP as acceptor (GO:0016723)			NS(1)|breast(3)|endometrium(2)|kidney(1)|large_intestine(4)|liver(1)|lung(14)|ovary(1)|prostate(3)|stomach(1)	31					Cyanocobalamin(DB00115)|Hydroxocobalamin(DB00200)|L-Methionine(DB00134)	GGAAGGGAGTATGTACAGGCT	0.473													G|||	40	0.00798722	0.0015	0.0245	5008	,	,		18051	0.0		0.0189	False		,,,				2504	0.002				p.V515V		Atlas-SNP	.											.	MTRR	74	.	0			c.A1545G						PASS	.	G	,	46,4360	822.1+/-416.4	0,46,2157	150.0	129.0	136.0		1464,1545	0.7	0.5	5	dbSNP_126	136	207,8393	810.1+/-407.1	2,203,4095	no	coding-synonymous,coding-synonymous	MTRR	NM_002454.2,NM_024010.2	,	2,249,6252	GG,GA,AA		2.407,1.044,1.9453	,	488/699,515/726	7892933	253,12753	2203	4300	6503	SO:0001819	synonymous_variant	4552	exon11			GGGAGTATGTACA	AF025794	CCDS3874.1, CCDS47190.1	5p15.31	2011-05-12			ENSG00000124275	ENSG00000124275	1.16.1.8		7473	protein-coding gene	gene with protein product		602568				9501215	Standard	NM_024010		Approved	cblE	uc003jed.3	Q9UBK8	OTTHUMG00000090477	ENST00000264668.2:c.1545A>G	5.37:g.7892933A>G		131.0	0.0	0		158.0	72.0	0.455696	NM_024010	O60471|Q32MA9|Q7Z4M8	Silent	SNP	ENST00000264668.2	37	CCDS3874.1																																																																																			A|0.981;G|0.019	0.019	strong		0.473	MTRR-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000206931.1		
DSPP	1834	hgsc.bcm.edu	37	4	88537294	88537294	+	Silent	SNP	T	T	C	rs111216206		TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr4:88537294T>C	ENST00000282478.7	+	4	3513	c.3480T>C	c.(3478-3480)agT>agC	p.S1160S	RP11-742B18.1_ENST00000506480.1_RNA|DSPP_ENST00000399271.1_Silent_p.S1160S			Q9NZW4	DSPP_HUMAN	dentin sialophosphoprotein	1160	Asp/Ser-rich.				biomineral tissue development (GO:0031214)|cellular response to cell-matrix adhesion (GO:0071460)|extracellular matrix organization (GO:0030198)|multicellular organismal development (GO:0007275)|ossification (GO:0001503)|skeletal system development (GO:0001501)	cytoplasm (GO:0005737)|extracellular region (GO:0005576)|proteinaceous extracellular matrix (GO:0005578)	calcium ion binding (GO:0005509)|collagen binding (GO:0005518)|extracellular matrix structural constituent (GO:0005201)			breast(2)|central_nervous_system(1)|endometrium(9)|kidney(4)|large_intestine(8)|lung(13)|ovary(1)|skin(3)|stomach(3)|upper_aerodigestive_tract(2)|urinary_tract(1)	47		Hepatocellular(203;0.114)|all_hematologic(202;0.236)		OV - Ovarian serous cystadenocarcinoma(123;0.000508)		gcgacagcagtgacagcagcg	0.567																																					p.S1160S		Atlas-SNP	.											.	DSPP	174	.	0			c.T3480C						PASS	.						43.0	58.0	53.0					4																	88537294		1580	2849	4429	SO:0001819	synonymous_variant	1834	exon5			CAGCAGTGACAGC	AF163151	CCDS43248.1	4q21.3	2008-02-05			ENSG00000152591	ENSG00000152591			3054	protein-coding gene	gene with protein product		125485		DFNA39, DGI1		8995371, 9533027	Standard	NM_014208		Approved	DMP3	uc003hqu.3	Q9NZW4	OTTHUMG00000161061	ENST00000282478.7:c.3480T>C	4.37:g.88537294T>C		216.0	0.0	0		177.0	17.0	0.0960452	NM_014208	A8MUI0|O95815	Silent	SNP	ENST00000282478.7	37	CCDS43248.1																																																																																			.	.	weak		0.567	DSPP-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000363616.3	NM_014208	
MST1L	11223	hgsc.bcm.edu	37	1	17084078	17084078	+	RNA	SNP	G	G	A			TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr1:17084078G>A	ENST00000455405.2	-	0	634							Q2TV78	MST1L_HUMAN	macrophage stimulating 1-like							extracellular region (GO:0005576)	serine-type endopeptidase activity (GO:0004252)										ACATGTCCTCGGTGCTTGATG	0.602																																					p.R615X		Atlas-SNP	.											Q13209_HUMAN,NS,haematopoietic_neoplasm,0,1	.	.	1	0			c.C1843T						scavenged	.																																					11223	exon14			GTCCTCGGTGCTT	U28055, AF083416		1p36.33	2013-03-27	2012-11-09	2012-11-09	ENSG00000186715	ENSG00000186715			7390	other	unknown			"""macrophage stimulating, pseudogene 7"", ""macrophage stimulating, pseudogene 9"", ""macrophage stimulating 1 (hepatocyte growth factor-like) pseudogene 9"""	MSTP7, MSTP9, MST1P9		10728827	Standard	NM_001271733		Approved	D1F15S1A, MSPL7, MSPL-7	uc010ock.3	Q2TV78	OTTHUMG00000002578		1.37:g.17084078G>A		1222.0	1.0	0.000818331		1404.0	117.0	0.0833333	NM_001271733	B7WPB1|Q13209	Nonsense_Mutation	SNP	ENST00000455405.2	37		.	.	.	.	.	.	.	.	.	.	.	18.45	3.625708	0.66901	.	.	ENSG00000186715	ENST00000334998;ENST00000442552	.	.	.	.	.	.	.	0.000000	0.34777	N	0.003682	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	4.089	0.09960	0.0:1.0E-4:0.3481:0.6518	.	.	.	.	X	615;641	.	ENSP00000439273:R615X	R	-	1	2	MST1P9	16956665	0.991000	0.36638	0.124000	0.21820	0.000000	0.00434	1.469000	0.35343	-0.879000	0.04002	0.000000	0.15137	CGA	.	.	none		0.602	MST1L-002	KNOWN	basic	processed_transcript	pseudogene	OTTHUMT00000400328.1	NM_001271733	
SCUBE1	80274	hgsc.bcm.edu	37	22	43618695	43618695	+	Missense_Mutation	SNP	C	C	A	rs148458324	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr22:43618695C>A	ENST00000360835.4	-	12	1507	c.1381G>T	c.(1381-1383)Gcg>Tcg	p.A461S		NM_173050.3	NP_766638.2	Q8IWY4	SCUB1_HUMAN	signal peptide, CUB domain, EGF-like 1	461					adult heart development (GO:0007512)|blood coagulation (GO:0007596)|endothelial cell differentiation (GO:0045446)|inflammatory response (GO:0006954)|post-embryonic development (GO:0009791)|protein homooligomerization (GO:0051260)	cell surface (GO:0009986)|external side of plasma membrane (GO:0009897)|extracellular space (GO:0005615)|extrinsic component of plasma membrane (GO:0019897)	calcium ion binding (GO:0005509)|identical protein binding (GO:0042802)|protein heterodimerization activity (GO:0046982)			autonomic_ganglia(1)|breast(1)|central_nervous_system(2)|endometrium(2)|kidney(4)|large_intestine(4)|lung(11)|ovary(2)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	31		all_neural(38;0.0414)|Ovarian(80;0.07)				TTCTGCAGCGCCTTGCCCTGC	0.657													C|||	13	0.00259585	0.0	0.0072	5008	,	,		18680	0.0		0.008	False		,,,				2504	0.0				p.A461S		Atlas-SNP	.											.	SCUBE1	105	.	0			c.G1381T						PASS	.	C	SER/ALA	6,4392	9.9+/-24.2	0,6,2193	52.0	40.0	44.0		1381	-1.2	0.0	22	dbSNP_134	44	96,8502	51.9+/-112.3	2,92,4205	yes	missense	SCUBE1	NM_173050.3	99	2,98,6398	AA,AC,CC		1.1165,0.1364,0.7849	benign	461/989	43618695	102,12894	2199	4299	6498	SO:0001583	missense	80274	exon12			GCAGCGCCTTGCC		CCDS14048.1	22q13	2008-07-01			ENSG00000159307	ENSG00000159307			13441	protein-coding gene	gene with protein product		611746				11087664	Standard	NM_173050		Approved		uc003bdt.2	Q8IWY4	OTTHUMG00000150679	ENST00000360835.4:c.1381G>T	22.37:g.43618695C>A	ENSP00000354080:p.Ala461Ser	71.0	0.0	0		82.0	49.0	0.597561	NM_173050	Q5R336	Missense_Mutation	SNP	ENST00000360835.4	37	CCDS14048.1	10	0.004578754578754579	0	0.0	3	0.008287292817679558	0	0.0	7	0.009234828496042216	C	0.029	-1.348806	0.01266	0.001364	0.011165	ENSG00000159307	ENST00000360835	D	0.84873	-1.91	5.16	-1.2	0.09554	.	0.847688	0.11048	N	0.605376	T	0.49949	0.1587	N	0.02391	-0.57	0.54753	D	0.999981	B	0.02656	0.0	B	0.04013	0.001	T	0.48692	-0.9013	10	0.07030	T	0.85	.	6.1713	0.20418	0.2337:0.4632:0.0:0.3031	.	461	Q8IWY4	SCUB1_HUMAN	S	461	ENSP00000354080:A461S	ENSP00000354080:A461S	A	-	1	0	SCUBE1	41948639	0.001000	0.12720	0.034000	0.17996	0.045000	0.14185	-0.867000	0.04241	-0.138000	0.11434	-0.302000	0.09304	GCG	C|0.994;A|0.006	0.006	strong		0.657	SCUBE1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000319582.3	NM_173050	
FICD	11153	hgsc.bcm.edu	37	12	108912621	108912621	+	Missense_Mutation	SNP	C	C	A	rs146316463		TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr12:108912621C>A	ENST00000552695.1	+	3	981	c.746C>A	c.(745-747)aCc>aAc	p.T249N	FICD_ENST00000361549.2_3'UTR	NM_007076.2	NP_009007.2	Q9BVA6	FICD_HUMAN	FIC domain containing	249					negative regulation of Rho GTPase activity (GO:0034259)|protein adenylylation (GO:0018117)	integral component of membrane (GO:0016021)	ATP binding (GO:0005524)|protein adenylyltransferase activity (GO:0070733)			NS(3)|endometrium(3)|kidney(1)|large_intestine(4)|lung(1)|prostate(1)|upper_aerodigestive_tract(2)	15						ATCCTGGAGACCCGCTACGCC	0.582													C|||	1	0.000199681	0.0	0.0	5008	,	,		22220	0.0		0.001	False		,,,				2504	0.0				p.T249N		Atlas-SNP	.											.	FICD	35	.	0			c.C746A						PASS	.	C	ASN/THR	0,4406		0,0,2203	108.0	81.0	90.0		746	6.1	1.0	12	dbSNP_134	90	3,8597	3.7+/-12.6	0,3,4297	yes	missense	FICD	NM_007076.2	65	0,3,6500	AA,AC,CC		0.0349,0.0,0.0231	possibly-damaging	249/459	108912621	3,13003	2203	4300	6503	SO:0001583	missense	11153	exon3			TGGAGACCCGCTA	AF049611	CCDS9116.1	12q24.1	2007-12-05				ENSG00000198855			18416	protein-coding gene	gene with protein product	"""huntingtin interacting protein 13"", ""fic S-phase protein cell division homolog (E. coli)"""					9700202	Standard	NM_007076		Approved	HYPE, HIP13	uc001tmx.1	Q9BVA6		ENST00000552695.1:c.746C>A	12.37:g.108912621C>A	ENSP00000446479:p.Thr249Asn	106.0	0.0	0		134.0	76.0	0.567164	NM_007076	O75406	Missense_Mutation	SNP	ENST00000552695.1	37	CCDS9116.1	1	4.578754578754579E-4	0	0.0	0	0.0	0	0.0	1	0.0013192612137203166	C	23.8	4.461591	0.84317	0.0	3.49E-4	ENSG00000198855	ENST00000552695	.	.	.	6.07	6.07	0.98685	Filamentation induced by cAMP/death on curing-related (1);	0.000000	0.85682	D	0.000000	T	0.58221	0.2107	L	0.31926	0.97	0.80722	D	1	D	0.56035	0.974	P	0.51701	0.677	T	0.46610	-0.9179	9	0.11485	T	0.65	-9.4005	20.6439	0.99570	0.0:1.0:0.0:0.0	.	249	Q9BVA6	FICD_HUMAN	N	249	.	ENSP00000446479:T249N	T	+	2	0	FICD	107436751	1.000000	0.71417	1.000000	0.80357	0.989000	0.77384	7.818000	0.86416	2.884000	0.98904	0.655000	0.94253	ACC	C|0.999;A|0.001	0.001	strong		0.582	FICD-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000404842.1	NM_007076	
UBXN11	91544	hgsc.bcm.edu	37	1	26608866	26608866	+	Missense_Mutation	SNP	C	C	G	rs188535926		TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr1:26608866C>G	ENST00000374222.1	-	16	1951	c.1487G>C	c.(1486-1488)gGt>gCt	p.G496A	UBXN11_ENST00000374217.2_Missense_Mutation_p.G463A|UBXN11_ENST00000357089.4_Missense_Mutation_p.G463A|UBXN11_ENST00000374221.3_Missense_Mutation_p.G496A|UBXN11_ENST00000314675.7_Missense_Mutation_p.G376A|UBXN11_ENST00000374223.1_Missense_Mutation_p.G253A			Q5T124	UBX11_HUMAN	UBX domain protein 11	496	3 X 8 AA tandem repeats of P-G-P-G-P-G-P- S.|Pro-rich.		Missing.			cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)		p.G490_P515delGPGPSPGPGPGPSPGPGPGPSPCPGP(1)		endometrium(3)|kidney(2)|large_intestine(4)|lung(6)|ovary(2)|prostate(3)|upper_aerodigestive_tract(3)	23						gggaccgggaccgggactggg	0.721																																					p.G496A		Atlas-SNP	.											UBXN11,colon,carcinoma,-1,2	UBXN11	54	2	1	Deletion - In frame(1)	ovary(1)	c.G1487C						PASS	.						25.0	29.0	28.0					1																	26608866		1767	4017	5784	SO:0001583	missense	91544	exon16			CCGGGACCGGGAC	AF521017	CCDS41286.1, CCDS41287.1, CCDS41288.1	1p36.11	2008-07-25	2008-07-25	2008-07-25	ENSG00000158062	ENSG00000158062		"""UBX domain containing"""	30600	protein-coding gene	gene with protein product	"""socius"""	609151	"""UBX domain containing 5"""	UBXD5		11940653	Standard	NM_183008		Approved	SOC, SOCI	uc001blw.3	Q5T124	OTTHUMG00000003382	ENST00000374222.1:c.1487G>C	1.37:g.26608866C>G	ENSP00000363339:p.Gly496Ala	25.0	0.0	0		35.0	8.0	0.228571	NM_183008	D3DPK6|Q5T117|Q5T120|Q5T125|Q5T126|Q5T129|Q5T131|Q5T133|Q63HM6|Q71RB3|Q8IY27|Q8N1L6|Q8N9M4|Q8NA18|Q8NFE3|Q8NFE4|Q8NFE6	Missense_Mutation	SNP	ENST00000374222.1	37	CCDS41288.1	20	0.009157509157509158	6	0.012195121951219513	1	0.0027624309392265192	5	0.008741258741258742	8	0.010554089709762533	C	2.556	-0.303022	0.05495	.	.	ENSG00000158062	ENST00000314675;ENST00000374223;ENST00000357089;ENST00000374221;ENST00000374222;ENST00000374217	T;T;T;T;T;T	0.21932	1.98;2.16;2.48;2.34;2.34;2.48	.	.	.	.	.	.	.	.	T	0.06325	0.0163	N	0.08118	0	0.58432	P	2.9999999999752447E-6	P;P;P;P	0.49961	0.93;0.93;0.93;0.886	B;B;B;B	0.40444	0.329;0.329;0.329;0.176	T	0.15292	-1.0442	7	0.45353	T	0.12	.	5.6498	0.17610	0.0:0.6576:0.3424:0.0	.	463;458;376;496	Q5T124-2;Q5T124-4;Q5T124-3;Q5T124	.;.;.;UBX11_HUMAN	A	376;253;463;496;496;463	ENSP00000324721:G376A;ENSP00000363340:G253A;ENSP00000349601:G463A;ENSP00000363338:G496A;ENSP00000363339:G496A;ENSP00000363334:G463A	ENSP00000324721:G376A	G	-	2	0	UBXN11	26481453	0.000000	0.05858	0.127000	0.21898	0.134000	0.20937	-0.138000	0.10374	0.392000	0.25172	0.391000	0.25812	GGT	C|0.991;G|0.009	0.009	strong		0.721	UBXN11-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000009500.1	NM_145345	
BZRAP1	9256	hgsc.bcm.edu	37	17	56386732	56386732	+	Missense_Mutation	SNP	C	C	T	rs61741210	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr17:56386732C>T	ENST00000343736.4	-	22	4064	c.3901G>A	c.(3901-3903)Gac>Aac	p.D1301N	BZRAP1_ENST00000355701.3_Missense_Mutation_p.D1301N|BZRAP1_ENST00000268893.6_Missense_Mutation_p.D1241N			O95153	RIMB1_HUMAN	benzodiazepine receptor (peripheral) associated protein 1	1301						cytoplasm (GO:0005737)|mitochondrion (GO:0005739)	benzodiazepine receptor binding (GO:0030156)			cervix(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(11)|liver(2)|lung(16)|ovary(1)|prostate(1)|skin(6)|upper_aerodigestive_tract(2)|urinary_tract(1)	54	Medulloblastoma(34;0.127)|all_neural(34;0.237)					CAAAAGGGGTCGGGCTGGGAC	0.577													C|||	78	0.0155751	0.0008	0.013	5008	,	,		18724	0.0		0.0328	False		,,,				2504	0.0358				p.D1301N		Atlas-SNP	.											.	BZRAP1	287	.	0			c.G3901A						PASS	.	C	ASN/ASP,ASN/ASP	25,4379	30.8+/-60.4	0,25,2177	39.0	39.0	39.0		3901,3721	5.6	0.9	17	dbSNP_129	39	223,8377	86.9+/-149.2	3,217,4080	yes	missense,missense	BZRAP1	NM_004758.2,NM_024418.1	23,23	3,242,6257	TT,TC,CC		2.593,0.5677,1.9071	benign,benign	1301/1858,1241/1798	56386732	248,12756	2202	4300	6502	SO:0001583	missense	9256	exon22			AGGGGTCGGGCTG	AB014512	CCDS11605.1, CCDS45742.1	17q22-q23	2014-01-09	2014-01-09						16831	protein-coding gene	gene with protein product		610764				9734811, 9915832	Standard	NM_004758		Approved	PRAX-1, KIAA0612, RIM-BP1, RIMBP1	uc002ivx.5	O95153		ENST00000343736.4:c.3901G>A	17.37:g.56386732C>T	ENSP00000345824:p.Asp1301Asn	36.0	0.0	0		40.0	17.0	0.425	NM_004758	O75111|Q8N5W3	Missense_Mutation	SNP	ENST00000343736.4	37	CCDS11605.1	32	0.014652014652014652	0	0.0	4	0.011049723756906077	0	0.0	28	0.036939313984168866	C	14.65	2.599495	0.46318	0.005677	0.02593	ENSG00000005379	ENST00000355701;ENST00000343736;ENST00000268893	D;D;D	0.87491	-2.26;-2.26;-2.26	5.59	5.59	0.84812	.	0.222124	0.39146	N	0.001447	T	0.60495	0.2273	L	0.59436	1.845	0.26084	N	0.981058	P;B;B	0.51240	0.943;0.014;0.004	B;B;B	0.40825	0.341;0.012;0.001	T	0.70193	-0.4939	10	0.15952	T	0.53	.	16.3282	0.82996	0.0:1.0:0.0:0.0	rs61741210	1301;1241;1301	B7ZVZ7;O95153-2;O95153	.;.;RIMB1_HUMAN	N	1301;1301;1241	ENSP00000347929:D1301N;ENSP00000345824:D1301N;ENSP00000268893:D1241N	ENSP00000268893:D1241N	D	-	1	0	BZRAP1	53741731	0.081000	0.21417	0.906000	0.35671	0.818000	0.46254	2.225000	0.42954	2.643000	0.89663	0.655000	0.94253	GAC	C|0.982;T|0.018	0.018	strong		0.577	BZRAP1-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000443980.1	NM_004758	
CDKN2B	1030	hgsc.bcm.edu	37	9	22006147	22006147	+	Missense_Mutation	SNP	C	C	T	rs148421170	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr9:22006147C>T	ENST00000276925.6	-	2	665	c.256G>A	c.(256-258)Gat>Aat	p.D86N	CDKN2B-AS1_ENST00000428597.1_RNA|CDKN2B-AS1_ENST00000582301.1_RNA|CDKN2B-AS1_ENST00000580576.1_RNA|CDKN2B_ENST00000380142.4_3'UTR|CDKN2B-AS1_ENST00000584816.1_RNA|CDKN2B-AS1_ENST00000583719.1_RNA|CDKN2B-AS1_ENST00000468603.2_RNA|CDKN2B-AS1_ENST00000584351.1_RNA|CDKN2B-AS1_ENST00000584020.1_RNA|CDKN2B-AS1_ENST00000455933.2_RNA|CDKN2B-AS1_ENST00000580467.1_RNA|CDKN2B-AS1_ENST00000584637.1_RNA|CDKN2B-AS1_ENST00000585267.1_RNA|CDKN2B-AS1_ENST00000577551.1_RNA|CDKN2B-AS1_ENST00000582072.1_RNA|RP11-145E5.5_ENST00000404796.2_Intron|CDKN2B-AS1_ENST00000581051.1_RNA	NM_004936.3|NM_078487.2	NP_004927.2|NP_511042.1	P42772	CDN2B_HUMAN	cyclin-dependent kinase inhibitor 2B (p15, inhibits CDK4)	86					aging (GO:0007568)|cell cycle arrest (GO:0007050)|cellular response to extracellular stimulus (GO:0031668)|cellular response to nutrient (GO:0031670)|G2/M transition of mitotic cell cycle (GO:0000086)|gene expression (GO:0010467)|liver development (GO:0001889)|megakaryocyte differentiation (GO:0030219)|mitotic cell cycle (GO:0000278)|mitotic cell cycle checkpoint (GO:0007093)|negative regulation of cell proliferation (GO:0008285)|negative regulation of epithelial cell proliferation (GO:0050680)|negative regulation of G1/S transition of mitotic cell cycle (GO:2000134)|negative regulation of phosphorylation (GO:0042326)|negative regulation of protein serine/threonine kinase activity (GO:0071901)|positive regulation of epithelial cell differentiation (GO:0030858)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transforming growth factor beta receptor signaling pathway (GO:0030511)|regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0000079)|response to cytokine (GO:0034097)|response to organic cyclic compound (GO:0014070)|spleen development (GO:0048536)|transcription initiation from RNA polymerase II promoter (GO:0006367)|transcription, DNA-templated (GO:0006351)|transforming growth factor beta receptor signaling pathway (GO:0007179)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleus (GO:0005634)	cyclin-dependent protein serine/threonine kinase inhibitor activity (GO:0004861)|protein kinase binding (GO:0019901)	p.0(1)|p.0?(1)		lung(2)	2		all_cancers(5;0)|Acute lymphoblastic leukemia(3;0)|all_hematologic(3;0)|all_epithelial(2;1.31e-280)|Lung NSC(2;2.28e-131)|all_lung(2;2.11e-123)|Glioma(2;5.66e-57)|all_neural(2;3.05e-50)|Renal(3;1.07e-46)|Esophageal squamous(3;3.83e-46)|Melanoma(2;8.01e-33)|Breast(3;1.14e-11)|Ovarian(3;0.000128)|Hepatocellular(5;0.00369)|Colorectal(97;0.172)		all cancers(2;0)|GBM - Glioblastoma multiforme(3;0)|Lung(2;3.29e-71)|Epithelial(2;9.08e-60)|LUSC - Lung squamous cell carcinoma(2;5.8e-46)|LUAD - Lung adenocarcinoma(2;1.43e-25)|BRCA - Breast invasive adenocarcinoma(2;5.37e-09)|STAD - Stomach adenocarcinoma(4;4.63e-07)|Kidney(2;6.92e-07)|KIRC - Kidney renal clear cell carcinoma(2;8.63e-07)|OV - Ovarian serous cystadenocarcinoma(39;0.014)|COAD - Colon adenocarcinoma(8;0.143)		CGGGCAGCATCATGCACCGGT	0.716													C|||	2	0.000399361	0.0	0.0	5008	,	,		14208	0.0		0.002	False		,,,				2504	0.0				p.D86N		Atlas-SNP	.											.	CDKN2B	12	.	2	Whole gene deletion(2)	lung(2)	c.G256A						PASS	.	C	ASN/ASP,	1,4381		0,1,2190	19.0	23.0	22.0		256,	4.8	1.0	9	dbSNP_134	22	26,8552		0,26,4263	no	missense,utr-3	CDKN2B	NM_004936.3,NM_078487.2	23,	0,27,6453	TT,TC,CC		0.3031,0.0228,0.2083	probably-damaging,	86/139,	22006147	27,12933	2191	4289	6480	SO:0001583	missense	1030	exon2			CAGCATCATGCAC	AB060808	CCDS6512.1, CCDS6513.1	9p21	2008-07-21			ENSG00000147883	ENSG00000147883			1788	protein-coding gene	gene with protein product		600431				8078588	Standard	NM_004936		Approved	P15, MTS2, INK4B, TP15, CDK4I, p15INK4b	uc003zpo.3	P42772	OTTHUMG00000019691	ENST00000276925.6:c.256G>A	9.37:g.22006147C>T	ENSP00000276925:p.Asp86Asn	52.0	0.0	0		46.0	27.0	0.586957	NM_004936	O15125|Q6FI09	Missense_Mutation	SNP	ENST00000276925.6	37	CCDS6512.1	.	.	.	.	.	.	.	.	.	.	C	33	5.278680	0.95459	2.28E-4	0.003031	ENSG00000147883	ENST00000276925	D	0.93906	-3.31	4.78	4.78	0.61160	Ankyrin repeat-containing domain (4);	0.000000	0.85682	D	0.000000	D	0.93893	0.8046	L	0.28400	0.85	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	D	0.93080	0.6490	10	0.35671	T	0.21	-31.5885	15.3443	0.74324	0.0:1.0:0.0:0.0	.	86	P42772	CDN2B_HUMAN	N	86	ENSP00000276925:D86N	ENSP00000276925:D86N	D	-	1	0	CDKN2B	21996147	1.000000	0.71417	1.000000	0.80357	0.804000	0.45430	4.857000	0.62939	2.472000	0.83506	0.655000	0.94253	GAT	C|0.998;T|0.002	0.002	strong		0.716	CDKN2B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051932.2	NM_004936	
E2F4	1874	hgsc.bcm.edu	37	16	67234197	67234197	+	IGR	SNP	T	T	C			TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr16:67234197T>C	ENST00000379378.3	+	0	2096				ELMO3_ENST00000393997.2_Missense_Mutation_p.F169L|MIR328_ENST00000385213.1_RNA|ELMO3_ENST00000571638.1_3'UTR|ELMO3_ENST00000360833.1_Missense_Mutation_p.F152L|ELMO3_ENST00000477898.1_Missense_Mutation_p.F3L	NM_001950.3	NP_001941.2	Q16254	E2F4_HUMAN	E2F transcription factor 4, p107/p130-binding						blood circulation (GO:0008015)|cell volume homeostasis (GO:0006884)|cilium assembly (GO:0042384)|epithelial cell development (GO:0002064)|gene expression (GO:0010467)|mitotic cell cycle (GO:0000278)|organ morphogenesis (GO:0009887)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of cell proliferation (GO:0042127)|regulation of cell size (GO:0008361)|regulation of transcription involved in G1/S transition of mitotic cell cycle (GO:0000083)|transcription initiation from RNA polymerase II promoter (GO:0006367)|transcription, DNA-templated (GO:0006351)|transforming growth factor beta receptor signaling pathway (GO:0007179)	cytoplasm (GO:0005737)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	DNA binding (GO:0003677)|protein domain specific binding (GO:0019904)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription factor binding (GO:0008134)			breast(4)|central_nervous_system(2)|endometrium(2)|kidney(1)|large_intestine(2)	11		Ovarian(137;0.0563)		OV - Ovarian serous cystadenocarcinoma(108;0.000697)|Epithelial(162;0.00303)|all cancers(182;0.0325)		GGACATGATCTTTGCCAGGGA	0.602																																					p.F169L		Atlas-SNP	.											.	ELMO3	41	.	0			c.T505C						PASS	.						49.0	52.0	51.0					16																	67234197		2067	4182	6249	SO:0001628	intergenic_variant	79767	exon5			ATGATCTTTGCCA	BC021050	CCDS32464.1	16q22.1	2014-05-06			ENSG00000205250	ENSG00000205250			3118	protein-coding gene	gene with protein product		600659				7958924, 7892279	Standard	NM_001950		Approved	E2F-4	uc002erz.3	Q16254	OTTHUMG00000172975		16.37:g.67234197T>C		119.0	0.0	0		121.0	5.0	0.0413223	NM_024712	A6NGR8|B5BU56|Q12991|Q15328	Missense_Mutation	SNP	ENST00000379378.3	37	CCDS32464.1	.	.	.	.	.	.	.	.	.	.	T	27.0	4.795457	0.90453	.	.	ENSG00000102890	ENST00000360833;ENST00000393997	T;T	0.43688	0.94;0.94	5.2	5.2	0.72013	Armadillo-like helical (1);Armadillo-type fold (1);	0.000000	0.85682	D	0.000000	T	0.66056	0.2751	M	0.80616	2.505	0.80722	D	1	D;D;D	0.76494	0.999;0.999;0.999	D;D;D	0.85130	0.997;0.995;0.99	T	0.71523	-0.4567	10	0.87932	D	0	-9.902	13.9039	0.63821	0.0:0.0:0.0:1.0	.	116;152;169	Q96BJ8;F8W9E7;Q96BJ8-3	ELMO3_HUMAN;.;.	L	152;169	ENSP00000354077:F152L;ENSP00000377566:F169L	ENSP00000354077:F152L	F	+	1	0	ELMO3	65791698	1.000000	0.71417	1.000000	0.80357	0.546000	0.35178	7.179000	0.77665	1.971000	0.57363	0.379000	0.24179	TTT	.	.	none		0.602	E2F4-001	KNOWN	non_canonical_conserved|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000421565.1	NM_001950	
PHF2	5253	hgsc.bcm.edu	37	9	96407953	96407953	+	Silent	SNP	G	G	A	rs35505758	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr9:96407953G>A	ENST00000359246.4	+	4	709	c.342G>A	c.(340-342)acG>acA	p.T114T	PHF2_ENST00000375376.4_Intron	NM_005392.3	NP_005383.3	O75151	PHF2_HUMAN	PHD finger protein 2	114					liver development (GO:0001889)|negative regulation of chromatin silencing at rDNA (GO:0061188)|protein demethylation (GO:0006482)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleolus (GO:0005730)|nucleus (GO:0005634)	dioxygenase activity (GO:0051213)|histone demethylase activity (H3-K9 specific) (GO:0032454)|iron ion binding (GO:0005506)|methylated histone binding (GO:0035064)|zinc ion binding (GO:0008270)			breast(1)|central_nervous_system(2)|endometrium(6)|large_intestine(9)|lung(14)|ovary(2)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	40		Myeloproliferative disorder(762;0.0255)		OV - Ovarian serous cystadenocarcinoma(323;9.11e-28)		GTCAGCTCACGCTGGGCTACA	0.642													G|||	88	0.0175719	0.0227	0.0058	5008	,	,		19930	0.0139		0.0268	False		,,,				2504	0.0133				p.T114T		Atlas-SNP	.											.	PHF2	113	.	0			c.G342A						PASS	.	G		95,4311	78.8+/-117.2	1,93,2109	87.0	80.0	82.0		342	-9.2	0.0	9	dbSNP_126	82	166,8434	77.5+/-140.1	3,160,4137	no	coding-synonymous	PHF2	NM_005392.3		4,253,6246	AA,AG,GG		1.9302,2.1562,2.0068		114/1097	96407953	261,12745	2203	4300	6503	SO:0001819	synonymous_variant	5253	exon4			GCTCACGCTGGGC	AF043725	CCDS35069.1	9q22	2013-01-28			ENSG00000197724	ENSG00000197724		"""Chromatin-modifying enzymes / K-demethylases"", ""Zinc fingers, PHD-type"""	8920	protein-coding gene	gene with protein product	"""jumonji C domain-containing histone demethylase 1E"", ""centromere protein 35"""	604351				10051327, 20129925	Standard	NM_005392		Approved	KIAA0662, JHDM1E, CENP-35	uc004aub.3	O75151	OTTHUMG00000020253	ENST00000359246.4:c.342G>A	9.37:g.96407953G>A		42.0	0.0	0		69.0	34.0	0.492754	NM_005392	Q4VXG0|Q8N3K2|Q9Y6N4	Silent	SNP	ENST00000359246.4	37	CCDS35069.1																																																																																			G|0.980;A|0.020	0.020	strong		0.642	PHF2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053162.1	NM_005392	
OR51B5	282763	hgsc.bcm.edu	37	11	5364476	5364476	+	Silent	SNP	C	C	T	rs61738485	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr11:5364476C>T	ENST00000300773.2	-	1	333	c.279G>A	c.(277-279)gcG>gcA	p.A93A	HBE1_ENST00000380237.1_Intron|AC104389.28_ENST00000415970.1_RNA|HBG2_ENST00000380252.1_Intron|HBG2_ENST00000380259.2_Intron	NM_001005567.2	NP_001005567.2	Q9H339	O51B5_HUMAN	olfactory receptor, family 51, subfamily B, member 5	93					detection of chemical stimulus involved in sensory perception of smell (GO:0050911)|sensory perception of smell (GO:0007608)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			NS(1)|central_nervous_system(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(4)|lung(13)|prostate(1)|skin(5)|upper_aerodigestive_tract(2)	28		Medulloblastoma(188;0.0075)|all_neural(188;0.0572)|Breast(177;0.0675)		Epithelial(150;3.05e-09)|BRCA - Breast invasive adenocarcinoma(625;0.135)		AAAAGCAGGCCGCACTTCCAA	0.562													T|||	491	0.0980431	0.3071	0.049	5008	,	,		18817	0.0		0.0457	False		,,,				2504	0.0051				p.A93A		Atlas-SNP	.											OR51B5,NS,carcinoma,-1,1	OR51B5	60	1	0			c.G279A						PASS	.	T		1240,3162	701.9+/-406.8	168,904,1129	43.0	42.0	42.0		279	-8.9	0.0	11	dbSNP_129	42	455,8139	796.1+/-407.5	13,429,3855	no	coding-synonymous	OR51B5	NM_001005567.2		181,1333,4984	TT,TC,CC		5.2944,28.169,13.0425		93/313	5364476	1695,11301	2201	4297	6498	SO:0001819	synonymous_variant	282763	exon5			GCAGGCCGCACTT	BK004430	CCDS31378.1	11p15.4	2012-08-09			ENSG00000242180	ENSG00000242180		"""GPCR / Class A : Olfactory receptors"""	19599	protein-coding gene	gene with protein product							Standard	NM_001005567		Approved		uc001maq.2	Q9H339	OTTHUMG00000066676	ENST00000300773.2:c.279G>A	11.37:g.5364476C>T		35.0	0.0	0		51.0	25.0	0.490196	NM_001005567	B2RN59	Silent	SNP	ENST00000300773.2	37	CCDS31378.1																																																																																			C|0.885;T|0.115	0.115	strong		0.562	OR51B5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000142975.1	NM_001005567	
PRR27	401137	hgsc.bcm.edu	37	4	71024466	71024466	+	Missense_Mutation	SNP	C	C	T	rs201012961		TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr4:71024466C>T	ENST00000344526.5	+	3	686	c.497C>T	c.(496-498)gCt>gTt	p.A166V	C4orf40_ENST00000502294.1_Missense_Mutation_p.A166V|C4orf40_ENST00000502441.2_3'UTR	NM_214711.3	NP_999876.2	Q6MZM9	PRR27_HUMAN		166	Ala/Pro-rich.					extracellular vesicular exosome (GO:0070062)		p.A166V(1)		breast(2)|central_nervous_system(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(1)|lung(3)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	12						CCTGTTGGAGCTGAGCCTGCT	0.632																																					p.A166V		Atlas-SNP	.											.	C4orf40	19	.	1	Substitution - Missense(1)	lung(1)	c.C497T						PASS	.						30.0	30.0	30.0					4																	71024466		2203	4298	6501	SO:0001583	missense	401137	exon3			TTGGAGCTGAGCC																												ENST00000344526.5:c.497C>T	4.37:g.71024466C>T	ENSP00000343172:p.Ala166Val	139.0	0.0	0		113.0	26.0	0.230089	NM_214711	A8MXP0|Q6MZR6	Missense_Mutation	SNP	ENST00000344526.5	37	CCDS3535.1	.	.	.	.	.	.	.	.	.	.	C	10.07	1.250256	0.22880	.	.	ENSG00000187533	ENST00000502294;ENST00000344526	T;T	0.33654	1.4;1.4	4.45	-4.02	0.04034	.	.	.	.	.	T	0.14874	0.0359	N	0.14661	0.345	0.09310	N	1	B	0.28713	0.22	B	0.22880	0.042	T	0.14952	-1.0454	9	0.45353	T	0.12	-4.1741	1.4635	0.02401	0.1179:0.3066:0.2443:0.3312	.	166	Q6MZM9	CD040_HUMAN	V	166	ENSP00000426249:A166V;ENSP00000343172:A166V	ENSP00000343172:A166V	A	+	2	0	C4orf40	71059055	0.000000	0.05858	0.000000	0.03702	0.035000	0.12851	-1.976000	0.01497	-0.789000	0.04498	0.609000	0.83330	GCT	C|0.999;T|0.001	0.001	weak		0.632	C4orf40-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251558.1		
DNAH5	1767	hgsc.bcm.edu	37	5	13867949	13867949	+	Silent	SNP	T	T	C	rs146191243	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr5:13867949T>C	ENST00000265104.4	-	25	4091	c.3987A>G	c.(3985-3987)aaA>aaG	p.K1329K	CTB-51A17.1_ENST00000503244.1_RNA	NM_001369.2	NP_001360.1	Q8TE73	DYH5_HUMAN	dynein, axonemal, heavy chain 5	1329	Stem. {ECO:0000250}.				cilium movement (GO:0003341)|lateral ventricle development (GO:0021670)|left/right axis specification (GO:0070986)	axonemal dynein complex (GO:0005858)|axoneme (GO:0005930)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)			NS(6)|breast(14)|central_nervous_system(4)|cervix(2)|endometrium(23)|haematopoietic_and_lymphoid_tissue(8)|kidney(11)|large_intestine(85)|liver(1)|lung(129)|ovary(16)|pancreas(2)|prostate(5)|skin(48)|stomach(5)|upper_aerodigestive_tract(11)|urinary_tract(8)	378	Lung NSC(4;0.00476)					TAATAAGCTCTTTCTTGAAAC	0.453									Kartagener syndrome				T|||	16	0.00319489	0.0	0.0058	5008	,	,		17132	0.0		0.008	False		,,,				2504	0.0041				p.K1329K		Atlas-SNP	.											.	DNAH5	868	.	0			c.A3987G						PASS	.	T		12,4394	19.1+/-41.9	1,10,2192	131.0	124.0	126.0		3987	-0.1	1.0	5	dbSNP_134	126	158,8442	74.5+/-137.1	0,158,4142	no	coding-synonymous	DNAH5	NM_001369.2		1,168,6334	CC,CT,TT		1.8372,0.2724,1.3071		1329/4625	13867949	170,12836	2203	4300	6503	SO:0001819	synonymous_variant	1767	exon25	Familial Cancer Database	Ciliary Dyskinesia, Primary (CILD1 - CILD13), Immotile Cilia Syndrome	AAGCTCTTTCTTG	AJ132090	CCDS3882.1	5p15.2	2008-07-18	2006-09-04		ENSG00000039139	ENSG00000039139		"""Axonemal dyneins"""	2950	protein-coding gene	gene with protein product	"""dynein heavy chain 5"""	603335	"""dynein, axonemal, heavy polypeptide 5"""			9256245, 11788826	Standard	NM_001369		Approved	Dnahc5, HL1, PCD, CILD3, KTGNR	uc003jfd.2	Q8TE73	OTTHUMG00000090533	ENST00000265104.4:c.3987A>G	5.37:g.13867949T>C		158.0	0.0	0		174.0	96.0	0.551724	NM_001369	Q92860|Q96L74|Q9H5S7|Q9HCG9	Silent	SNP	ENST00000265104.4	37	CCDS3882.1																																																																																			T|0.990;C|0.010	0.010	strong		0.453	DNAH5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207057.2	NM_001369	
LRBA	987	hgsc.bcm.edu	37	4	151388906	151388906	+	Silent	SNP	T	T	C			TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr4:151388906T>C	ENST00000357115.3	-	45	6975	c.6732A>G	c.(6730-6732)ccA>ccG	p.P2244P	LRBA_ENST00000535741.1_Silent_p.P2233P|LRBA_ENST00000503716.1_5'UTR|LRBA_ENST00000507224.1_Silent_p.P2233P|LRBA_ENST00000510413.1_Silent_p.P2233P	NM_006726.4	NP_006717.2	P50851	LRBA_HUMAN	LPS-responsive vesicle trafficking, beach and anchor containing	2244	BEACH. {ECO:0000255|PROSITE- ProRule:PRU00026}.					cytoplasmic membrane-bounded vesicle (GO:0016023)|endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|lysosome (GO:0005764)|membrane (GO:0016020)|plasma membrane (GO:0005886)				breast(6)|cervix(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(9)|large_intestine(20)|lung(32)|ovary(4)|prostate(6)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	91	all_hematologic(180;0.151)					AAGGAAACACTGGATACTGAT	0.323																																					p.P2244P		Atlas-SNP	.											.	LRBA	253	.	0			c.A6732G						PASS	.						117.0	110.0	113.0					4																	151388906		2203	4297	6500	SO:0001819	synonymous_variant	987	exon45			AAACACTGGATAC	AF216648	CCDS3773.1, CCDS58928.1	4q13	2013-01-10		2001-10-05	ENSG00000198589	ENSG00000198589		"""WD repeat domain containing"""	1742	protein-coding gene	gene with protein product		606453		CDC4L		1505956, 11254716	Standard	NM_006726		Approved	BGL, LAB300, LBA	uc010ipj.3	P50851	OTTHUMG00000161443	ENST00000357115.3:c.6732A>G	4.37:g.151388906T>C		226.0	0.0	0		241.0	101.0	0.419087	NM_006726	Q4W5J4|Q4W5L6|Q8NFQ0|Q9H2U3|Q9H2U4	Silent	SNP	ENST00000357115.3	37	CCDS3773.1	.	.	.	.	.	.	.	.	.	.	T	10.20	1.283943	0.23392	.	.	ENSG00000198589	ENST00000509835	.	.	.	4.98	-2.12	0.07165	.	.	.	.	.	T	0.51143	0.1657	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.47129	-0.9141	4	.	.	.	.	7.1251	0.25467	0.4743:0.0795:0.0:0.4462	.	.	.	.	R	886	.	.	Q	-	2	0	LRBA	151608356	0.547000	0.26465	0.999000	0.59377	0.998000	0.95712	-0.270000	0.08584	-0.014000	0.14175	0.477000	0.44152	CAG	.	.	none		0.323	LRBA-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000364939.1		
EGLN1	54583	hgsc.bcm.edu	37	1	231557164	231557164	+	Missense_Mutation	SNP	C	C	G	rs61750991	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr1:231557164C>G	ENST00000366641.3	-	1	3626	c.471G>C	c.(469-471)caG>caC	p.Q157H	EGLN1_ENST00000476717.1_5'Flank	NM_022051.2	NP_071334.1			egl-9 family hypoxia-inducible factor 1											breast(1)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(1)|lung(4)|prostate(1)|urinary_tract(1)	16		Prostate(94;0.194)|Acute lymphoblastic leukemia(190;0.244)				TCGCCTTCTCCTGGAACAGCG	0.766													C|||	33	0.00658946	0.0	0.0029	5008	,	,		9987	0.001		0.0268	False		,,,				2504	0.0031				p.Q157H		Atlas-SNP	.											.	EGLN1	38	.	0			c.G471C						PASS	.	C	HIS/GLN	17,3709		0,17,1846	6.0	6.0	6.0		471	-2.4	0.0	1	dbSNP_129	6	157,7197		2,153,3522	yes	missense	EGLN1	NM_022051.2	24	2,170,5368	GG,GC,CC		2.1349,0.4563,1.5704	possibly-damaging	157/427	231557164	174,10906	1863	3677	5540	SO:0001583	missense	54583	exon1			CTTCTCCTGGAAC	AJ310543	CCDS1595.1	1q42.1	2013-08-21	2013-08-21	2001-08-24	ENSG00000135766	ENSG00000135766		"""Zinc fingers, MYND-type"""	1232	protein-coding gene	gene with protein product	"""HIF prolyl hydroxylase 2"""	606425	"""EGL nine (C.elegans) homolog 1"", ""egl nine homolog 1 (C. elegans)"""	C1orf12		11056053	Standard	NM_022051		Approved	SM-20, PHD2, ZMYND6, HIFPH2	uc001huv.2	Q9GZT9	OTTHUMG00000038027	ENST00000366641.3:c.471G>C	1.37:g.231557164C>G	ENSP00000355601:p.Gln157His	17.0	0.0	0		13.0	11.0	0.846154	NM_022051		Missense_Mutation	SNP	ENST00000366641.3	37	CCDS1595.1	27	0.012362637362637362	4	0.008130081300813009	2	0.0055248618784530384	0	0.0	21	0.027704485488126648	C	14.92	2.680157	0.47886	0.004563	0.021349	ENSG00000135766	ENST00000366641	D	0.86164	-2.08	4.06	-2.39	0.06602	.	.	.	.	.	T	0.49201	0.1543	N	0.14661	0.345	0.09310	N	1	B	0.30664	0.289	B	0.28916	0.096	T	0.53788	-0.8389	9	0.38643	T	0.18	0.2922	5.8621	0.18754	0.1263:0.41:0.3885:0.0752	rs61750991	157	Q9GZT9	EGLN1_HUMAN	H	157	ENSP00000355601:Q157H	ENSP00000355601:Q157H	Q	-	3	2	EGLN1	229623787	0.007000	0.16637	0.000000	0.03702	0.015000	0.08874	0.147000	0.16202	-0.278000	0.09180	0.557000	0.71058	CAG	C|0.988;G|0.012	0.012	strong		0.766	EGLN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000092879.1	NM_022051	
CACNA1H	8912	hgsc.bcm.edu	37	16	1272655	1272655	+	IGR	SNP	C	C	T	rs117769620	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr16:1272655C>T	ENST00000348261.5	+	0	8084				TPSG1_ENST00000234798.4_Missense_Mutation_p.G170R	NM_021098.2	NP_066921.2	O95180	CAC1H_HUMAN	calcium channel, voltage-dependent, T type, alpha 1H subunit						aldosterone biosynthetic process (GO:0032342)|axon guidance (GO:0007411)|calcium ion import (GO:0070509)|cellular response to hormone stimulus (GO:0032870)|cellular response to potassium ion (GO:0035865)|cortisol biosynthetic process (GO:0034651)|membrane depolarization during action potential (GO:0086010)|muscle contraction (GO:0006936)|muscle organ development (GO:0007517)|myoblast fusion (GO:0007520)|positive regulation of acrosome reaction (GO:2000344)|regulation of heart contraction (GO:0008016)|regulation of membrane potential (GO:0042391)|transport (GO:0006810)	caveola (GO:0005901)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|sarcolemma (GO:0042383)|voltage-gated calcium channel complex (GO:0005891)	low voltage-gated calcium channel activity (GO:0008332)|metal ion binding (GO:0046872)|scaffold protein binding (GO:0097110)			breast(4)|endometrium(5)|kidney(2)|lung(23)	34		Hepatocellular(780;0.00369)			Amiodarone(DB01118)|Bepridil(DB01244)|Cinnarizine(DB00568)|Felodipine(DB01023)|Flunarizine(DB04841)|Isradipine(DB00270)|Nifedipine(DB01115)|Nitrendipine(DB01054)|Spironolactone(DB00421)|Zonisamide(DB00909)	TCCTCACCTCCCTCCCGCGTA	0.667													c|||	13	0.00259585	0.0	0.0014	5008	,	,		15592	0.0		0.0109	False		,,,				2504	0.001				p.G170R		Atlas-SNP	.											.	TPSG1	19	.	0			c.G508A						PASS	.		ARG/GLY	3,4389	6.2+/-15.9	0,3,2193	70.0	87.0	81.0		508	2.5	0.8	16	dbSNP_132	81	56,8540	32.8+/-85.7	0,56,4242	yes	missense	TPSG1	NM_012467.3	125	0,59,6435	TT,TC,CC		0.6515,0.0683,0.4543	possibly-damaging	170/322	1272655	59,12929	2196	4298	6494	SO:0001628	intergenic_variant	25823	exon4			CACCTCCCTCCCG	AL031703	CCDS45375.1, CCDS45376.1	16p13.3	2012-03-07	2007-02-16					"""Calcium channel subunits"", ""Voltage-gated ion channels / Calcium channels"""	1395	protein-coding gene	gene with protein product		607904				9670923, 16382099	Standard	NM_021098		Approved	Cav3.2	uc002cks.3	O95180			16.37:g.1272655C>T		130.0	0.0	0		110.0	53.0	0.481818	NM_012467	B5ME00|F8WFD1|O95802|Q8WWI6|Q96QI6|Q96RZ9|Q9NYY4|Q9NYY5	Missense_Mutation	SNP	ENST00000348261.5	37	CCDS45375.1	11	0.005036630036630037	0	0.0	1	0.0027624309392265192	0	0.0	10	0.013192612137203167	c	13.73	2.323926	0.41096	6.83E-4	0.006515	ENSG00000116176	ENST00000234798	D	0.93763	-3.28	3.47	2.48	0.30137	Peptidase cysteine/serine, trypsin-like (1);Peptidase S1/S6, chymotrypsin/Hap (3);	.	.	.	.	D	0.90123	0.6914	L	0.58101	1.795	0.39248	D	0.963972	D	0.52996	0.957	P	0.52031	0.688	D	0.87282	0.2293	9	0.25751	T	0.34	.	9.1608	0.37021	0.0:0.8827:0.0:0.1173	.	170	Q9NRR2	TRYG1_HUMAN	R	170	ENSP00000234798:G170R	ENSP00000234798:G170R	G	-	1	0	TPSG1	1212656	0.119000	0.22226	0.814000	0.32528	0.083000	0.17756	0.758000	0.26447	0.518000	0.28383	0.556000	0.70494	GGA	C|0.995;T|0.005	0.005	strong		0.667	CACNA1H-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000421601.1	NM_001005407	
SPTA1	6708	hgsc.bcm.edu	37	1	158592847	158592847	+	Missense_Mutation	SNP	G	G	A	rs78394850	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr1:158592847G>A	ENST00000368147.4	-	43	6226	c.6046C>T	c.(6046-6048)Cgc>Tgc	p.R2016C		NM_003126.2	NP_003117.2	P02549	SPTA1_HUMAN	spectrin, alpha, erythrocytic 1	2016					actin filament capping (GO:0051693)|actin filament organization (GO:0007015)|axon guidance (GO:0007411)|hemopoiesis (GO:0030097)|lymphocyte homeostasis (GO:0002260)|plasma membrane organization (GO:0007009)|porphyrin-containing compound biosynthetic process (GO:0006779)|positive regulation of protein binding (GO:0032092)|positive regulation of T cell proliferation (GO:0042102)|regulation of cell shape (GO:0008360)	actin cytoskeleton (GO:0015629)|cuticular plate (GO:0032437)|cytosol (GO:0005829)|intrinsic component of the cytoplasmic side of the plasma membrane (GO:0031235)|spectrin (GO:0008091)|spectrin-associated cytoskeleton (GO:0014731)	actin filament binding (GO:0051015)|calcium ion binding (GO:0005509)|structural constituent of cytoskeleton (GO:0005200)			NS(3)|breast(7)|cervix(1)|endometrium(22)|kidney(9)|large_intestine(29)|liver(2)|lung(183)|ovary(5)|prostate(18)|skin(11)|soft_tissue(1)|stomach(1)|upper_aerodigestive_tract(9)|urinary_tract(6)	307	all_hematologic(112;0.0378)					TGTTCCCAGCGCTTCAGCAGA	0.478													G|||	272	0.0543131	0.1407	0.0317	5008	,	,		16998	0.0		0.0239	False		,,,				2504	0.0409				p.R2016C		Atlas-SNP	.											SPTA1,colon,carcinoma,+1,3	SPTA1	720	3	0			c.C6046T						PASS	.	G	CYS/ARG	541,3327		26,489,1419	237.0	236.0	236.0		6046	4.8	0.6	1	dbSNP_132	236	131,8137		2,127,4005	yes	missense	SPTA1	NM_003126.2	180	28,616,5424	AA,AG,GG		1.5844,13.9866,5.5372	probably-damaging	2016/2420	158592847	672,11464	1934	4134	6068	SO:0001583	missense	6708	exon43			CCCAGCGCTTCAG	M61877	CCDS41423.1	1q21	2014-06-23	2014-06-23		ENSG00000163554	ENSG00000163554		"""EF-hand domain containing"""	11272	protein-coding gene	gene with protein product	"""elliptocytosis 2"""	182860	"""spectrin, alpha, erythrocytic 1 (elliptocytosis 2)"""				Standard	NM_003126		Approved	EL2	uc001fst.1	P02549	OTTHUMG00000019636	ENST00000368147.4:c.6046C>T	1.37:g.158592847G>A	ENSP00000357129:p.Arg2016Cys	206.0	0.0	0		204.0	86.0	0.421569	NM_003126	Q15514|Q5VYL1|Q5VYL2|Q6LDY5	Missense_Mutation	SNP	ENST00000368147.4	37	CCDS41423.1	103	0.04716117216117216	75	0.1524390243902439	11	0.03038674033149171	0	0.0	17	0.022427440633245383	G	17.61	3.432615	0.62844	0.139866	0.015844	ENSG00000163554	ENST00000368148;ENST00000368147	T;T	0.41758	0.99;0.99	4.78	4.78	0.61160	.	.	.	.	.	T	0.60728	0.2291	M	0.79693	2.465	0.58432	D	0.999993	D	0.89917	1.0	D	0.83275	0.996	T	0.64918	-0.6294	9	0.56958	D	0.05	.	16.5446	0.84426	0.0:0.0:1.0:0.0	.	2016	P02549	SPTA1_HUMAN	C	2016;2013	ENSP00000357130:R2016C;ENSP00000357129:R2013C	ENSP00000357129:R2013C	R	-	1	0	SPTA1	156859471	1.000000	0.71417	0.631000	0.29282	0.015000	0.08874	8.964000	0.93389	2.481000	0.83766	0.655000	0.94253	CGC	G|0.959;A|0.041	0.041	strong		0.478	SPTA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051851.3	NM_003126	
LILRB4	11006	hgsc.bcm.edu	37	19	55177358	55177358	+	Missense_Mutation	SNP	C	C	T	rs200475774		TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr19:55177358C>T	ENST00000391736.1	+	9	1165	c.850C>T	c.(850-852)Cgt>Tgt	p.R284C	LILRB4_ENST00000270452.2_Missense_Mutation_p.R284C|LILRB4_ENST00000391733.3_Missense_Mutation_p.R284C|LILRB4_ENST00000430952.2_Missense_Mutation_p.R284C|LILRB4_ENST00000391734.3_Missense_Mutation_p.R284C	NM_001278426.2|NM_001278428.2|NM_001278429.2|NM_001278430.2	NP_001265355.1|NP_001265357.1|NP_001265358.1|NP_001265359.1	Q8NHJ6	LIRB4_HUMAN	leukocyte immunoglobulin-like receptor, subfamily B (with TM and ITIM domains), member 4	284					immune system process (GO:0002376)|negative regulation of osteoclast differentiation (GO:0045671)|signal transduction (GO:0007165)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	antigen binding (GO:0003823)|receptor activity (GO:0004872)			breast(1)|cervix(1)|endometrium(2)|kidney(2)|large_intestine(4)|lung(20)|ovary(3)|skin(1)|stomach(2)|upper_aerodigestive_tract(3)	39				GBM - Glioblastoma multiforme(193;0.035)		ccAACACTGGCGTCAGGGAAA	0.592																																					p.R284C		Atlas-SNP	.											LILRB4,NS,carcinoma,0,2	LILRB4	86	2	0			c.C850T						PASS	.	C	CYS/ARG,CYS/ARG	0,4406		0,0,2203	138.0	92.0	108.0		850,850	-0.5	0.0	19		108	4,8596	3.7+/-12.6	0,4,4296	yes	missense,missense	LILRB4	NM_001081438.1,NM_006847.3	180,180	0,4,6499	TT,TC,CC		0.0465,0.0,0.0308	probably-damaging,probably-damaging	284/448,284/449	55177358	4,13002	2203	4300	6503	SO:0001583	missense	11006	exon7			CACTGGCGTCAGG	U82979	CCDS12902.1, CCDS42618.1	19q13.4	2013-01-11				ENSG00000186818		"""Leukocyte immunoglobulin-like receptors"", ""CD molecules"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	6608	protein-coding gene	gene with protein product		604821				9151699, 9079806	Standard	XM_005277050		Approved	LIR-5, ILT3, HM18, LIR5, CD85k	uc002qgp.3	Q8NHJ6		ENST00000391736.1:c.850C>T	19.37:g.55177358C>T	ENSP00000375616:p.Arg284Cys	146.0	0.0	0		127.0	60.0	0.472441	NM_006847	A8MVL8|O15468|O75021|Q6FGQ9|Q8N1C7|Q8NHL5	Missense_Mutation	SNP	ENST00000391736.1	37	CCDS12902.1	.	.	.	.	.	.	.	.	.	.	C	6.615	0.481950	0.12581	0.0	4.65E-4	ENSG00000186818	ENST00000391736;ENST00000270452;ENST00000430952;ENST00000391734;ENST00000391733;ENST00000434286	T;T;T;T;T;T	0.00490	7.1;7.1;7.1;7.03;7.12;7.03	1.86	-0.498	0.12019	.	.	.	.	.	T	0.00356	0.0011	L	0.43701	1.375	0.09310	N	1	D;D;P;P;B	0.62365	0.991;0.978;0.954;0.875;0.017	B;B;B;P;B	0.44561	0.446;0.265;0.335;0.453;0.002	T	0.50734	-0.8793	9	0.49607	T	0.09	.	2.8633	0.05593	0.0:0.4992:0.3032:0.1976	.	284;283;284;284;284	A8MUE1;C9JST2;Q8NHJ6-3;Q8NHJ6-2;Q8NHJ6	.;.;.;.;LIRB4_HUMAN	C	284;284;284;284;284;283	ENSP00000375616:R284C;ENSP00000270452:R284C;ENSP00000408995:R284C;ENSP00000375614:R284C;ENSP00000375613:R284C;ENSP00000401962:R283C	ENSP00000270452:R284C	R	+	1	0	LILRB4	59869170	0.000000	0.05858	0.000000	0.03702	0.008000	0.06430	-1.104000	0.03326	-0.054000	0.13266	0.407000	0.27541	CGT	C|0.999;T|0.001	0.001	weak		0.592	LILRB4-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000141127.3		
HNF1A	6927	hgsc.bcm.edu	37	12	121416622	121416622	+	Silent	SNP	C	C	G	rs1169289	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr12:121416622C>G	ENST00000257555.6	+	1	277	c.51C>G	c.(49-51)ctC>ctG	p.L17L	HNF1A_ENST00000544413.1_Silent_p.L17L|HNF1A-AS1_ENST00000537361.1_RNA|HNF1A_ENST00000402929.1_Silent_p.L17L|HNF1A_ENST00000400024.2_Silent_p.L17L|HNF1A-AS1_ENST00000535301.1_RNA|HNF1A_ENST00000543427.1_Intron|HNF1A_ENST00000538626.1_Silent_p.L17L|HNF1A-AS1_ENST00000433033.2_RNA|HNF1A_ENST00000541395.1_Silent_p.L17L			P20823	HNF1A_HUMAN	HNF1 homeobox A	17	Dimerization.				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)	p.?(1)		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)					CGGCCCTGCTCGAGTCAGGGC	0.687									Hepatic Adenoma, Familial Clustering of				C|||	2146	0.428514	0.3169	0.438	5008	,	,		11818	0.3819		0.4692	False		,,,				2504	0.5787				p.L17L		Atlas-SNP	.											HNF1A,NS,carcinoma,0,1	HNF1A	302	1	1	Unknown(1)	endometrium(1)	c.C51G						PASS	.	C		1508,2894		278,952,971	24.0	29.0	27.0		51	-3.7	0.9	12	dbSNP_87	27	3915,4673		915,2085,1294	no	coding-synonymous	HNF1A	NM_000545.5		1193,3037,2265	GG,GC,CC		45.5869,34.2572,41.7475		17/632	121416622	5423,7567	2201	4294	6495	SO:0001819	synonymous_variant	6927	exon1	Familial Cancer Database	incl. Maturity-Onset Diabetes of the Young type 3, MODY3	CCTGCTCGAGTCA	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.51C>G	12.37:g.121416622C>G		169.0	0.0	0		144.0	63.0	0.4375	NM_000545	A5Z2R8|E0YMJ5|E0YMK0|E0YMK1|E2I9R4|E2I9R5|F5H5U3|Q2M3H2|Q99861	Silent	SNP	ENST00000257555.6	37	CCDS9209.1																																																																																			G|0.405;C|0.595	0.405	strong		0.687	HNF1A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000320957.5	NM_000545	
ZKSCAN4	387032	hgsc.bcm.edu	37	6	28219695	28219695	+	Missense_Mutation	SNP	G	G	A	rs62638680	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr6:28219695G>A	ENST00000377294.2	-	1	307	c.64C>T	c.(64-66)Ctc>Ttc	p.L22F	ZKSCAN4_ENST00000423974.2_Intron	NM_019110.3	NP_061983.2	Q969J2	ZKSC4_HUMAN	zinc finger with KRAB and SCAN domains 4	22					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(2)|large_intestine(2)|lung(10)|ovary(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	18						ACGGTCAGGAGCCCCGTCTGG	0.637													G|||	179	0.0357428	0.1082	0.0187	5008	,	,		15084	0.006		0.0139	False		,,,				2504	0.0031				p.L22F		Atlas-SNP	.											.	ZKSCAN4	42	.	0			c.C64T						PASS	.	G	PHE/LEU	433,3917		24,385,1766	63.0	69.0	67.0		64	-0.6	0.1	6	dbSNP_129	67	51,8447		0,51,4198	yes	missense	ZKSCAN4	NM_019110.3	22	24,436,5964	AA,AG,GG		0.6001,9.954,3.7671	benign	22/546	28219695	484,12364	2175	4249	6424	SO:0001583	missense	387032	exon1			TCAGGAGCCCCGT	AK056698	CCDS4647.1	6p21	2013-01-09	2007-02-20	2007-02-20	ENSG00000187626	ENSG00000187626		"""Zinc fingers, C2H2-type"", ""-"", ""-"", ""-"""	13854	protein-coding gene	gene with protein product		611643	"""zinc finger protein 307"", ""zinc finger protein 427"""	ZNF307, ZNF427		12477932	Standard	NM_019110		Approved	p373c6.1, P1P373C6, FLJ32136, ZSCAN36	uc003nks.1	Q969J2	OTTHUMG00000014511	ENST00000377294.2:c.64C>T	6.37:g.28219695G>A	ENSP00000366509:p.Leu22Phe	65.0	0.0	0		97.0	39.0	0.402062	NM_019110	B2RE32|Q5U7L4	Missense_Mutation	SNP	ENST00000377294.2	37	CCDS4647.1	77	0.035256410256410256	52	0.10569105691056911	9	0.024861878453038673	5	0.008741258741258742	11	0.014511873350923483	G	16.83	3.231677	0.58777	0.09954	0.006001	ENSG00000187626	ENST00000377294	T	0.08896	3.04	4.21	-0.602	0.11634	.	.	.	.	.	T	0.02047	0.0064	L	0.27053	0.805	0.09310	N	0.999995	P	0.46706	0.883	P	0.44732	0.459	T	0.39901	-0.9591	9	0.46703	T	0.11	.	3.0342	0.06116	0.0972:0.1668:0.458:0.278	.	22	Q969J2	ZKSC4_HUMAN	F	22	ENSP00000366509:L22F	ENSP00000366509:L22F	L	-	1	0	ZKSCAN4	28327674	0.000000	0.05858	0.050000	0.19076	0.678000	0.39670	-0.612000	0.05616	0.044000	0.15775	0.563000	0.77884	CTC	G|0.968;A|0.032	0.032	strong		0.637	ZKSCAN4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040179.1	NM_019110	
ZNF780A	284323	hgsc.bcm.edu	37	19	40580426	40580426	+	Silent	SNP	A	A	G	rs399405	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr19:40580426A>G	ENST00000595687.2	-	6	2132	c.1923T>C	c.(1921-1923)tcT>tcC	p.S641S	ZNF780A_ENST00000594395.1_Silent_p.S642S|ZNF780A_ENST00000450241.2_Silent_p.S607S|ZNF780A_ENST00000455521.1_Silent_p.S642S|ZNF780A_ENST00000414720.2_Intron|AC005614.5_ENST00000595508.1_RNA|ZNF780A_ENST00000340963.5_Silent_p.S641S	NM_001010880.2	NP_001010880.2	O75290	Z780A_HUMAN	zinc finger protein 780A	641					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(1)|large_intestine(7)|lung(16)|upper_aerodigestive_tract(3)|urinary_tract(1)	31	all_cancers(60;9.55e-06)|all_lung(34;1.17e-07)|Lung NSC(34;1.41e-07)|Ovarian(47;0.0925)					CTTACATTCAAGATGCCTTCT	0.418													a|||	547	0.109225	0.3449	0.0403	5008	,	,		22537	0.0069		0.0109	False		,,,				2504	0.046				p.S642S		Atlas-SNP	.											.	ZNF780A	156	.	0			c.T1926C						PASS	.	A	,,,	1370,3036	454.7+/-350.8	220,930,1053	153.0	148.0	150.0		1923,1926,1923,	-2.3	0.0	19	dbSNP_80	150	68,8532	41.7+/-99.0	1,66,4233	no	coding-synonymous,coding-synonymous,coding-synonymous,intron	ZNF780A	NM_001010880.2,NM_001142577.1,NM_001142578.1,NM_001142579.1	,,,	221,996,5286	GG,GA,AA		0.7907,31.094,11.0564	,,,	641/642,642/643,641/642,	40580426	1438,11568	2203	4300	6503	SO:0001819	synonymous_variant	284323	exon6			CATTCAAGATGCC	AK091274	CCDS33026.2, CCDS46078.1, CCDS46079.1	19q13.2	2014-02-12	2006-08-15		ENSG00000197782	ENSG00000197782		"""Zinc fingers, C2H2-type"", ""-"""	27603	protein-coding gene	gene with protein product							Standard	NM_001142577		Approved	ZNF780	uc010xvh.2	O75290	OTTHUMG00000155119	ENST00000595687.2:c.1923T>C	19.37:g.40580426A>G		190.0	0.0	0		199.0	90.0	0.452261	NM_001142577	E9PB48|Q6ZN87	Silent	SNP	ENST00000595687.2	37	CCDS33026.2																																																																																			A|0.899;G|0.101	0.101	strong		0.418	ZNF780A-009	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000470066.1	NM_001010880	
SYNE2	23224	hgsc.bcm.edu	37	14	64580061	64580061	+	Silent	SNP	C	C	T	rs114604397	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr14:64580061C>T	ENST00000344113.4	+	66	12824	c.12612C>T	c.(12610-12612)ggC>ggT	p.G4204G	SYNE2_ENST00000358025.3_Silent_p.G4204G|SYNE2_ENST00000555002.1_Silent_p.G838G|SYNE2_ENST00000357395.3_Silent_p.G589G|SYNE2_ENST00000394768.2_Silent_p.G589G|ESR2_ENST00000542956.1_Intron|SYNE2_ENST00000554584.1_Silent_p.G4219G	NM_015180.4	NP_055995.4	Q8WXH0	SYNE2_HUMAN	spectrin repeat containing, nuclear envelope 2	4204					centrosome localization (GO:0051642)|cytoskeletal anchoring at nuclear membrane (GO:0090286)|establishment or maintenance of cell polarity (GO:0007163)|fibroblast migration (GO:0010761)|nuclear envelope organization (GO:0006998)|nuclear migration (GO:0007097)|nuclear migration along microfilament (GO:0031022)|positive regulation of cell migration (GO:0030335)|protein localization to nucleus (GO:0034504)	aggresome (GO:0016235)|cytoplasm (GO:0005737)|filopodium membrane (GO:0031527)|focal adhesion (GO:0005925)|integral component of membrane (GO:0016021)|intermediate filament cytoskeleton (GO:0045111)|lamellipodium membrane (GO:0031258)|mitochondrion (GO:0005739)|nuclear envelope (GO:0005635)|nuclear lumen (GO:0031981)|nuclear membrane (GO:0031965)|nucleus (GO:0005634)|sarcoplasmic reticulum (GO:0016529)|SUN-KASH complex (GO:0034993)|Z disc (GO:0030018)	actin binding (GO:0003779)			NS(5)|breast(17)|central_nervous_system(3)|cervix(8)|endometrium(17)|haematopoietic_and_lymphoid_tissue(2)|kidney(21)|large_intestine(34)|lung(75)|ovary(10)|pancreas(2)|prostate(8)|skin(8)|stomach(1)|upper_aerodigestive_tract(9)|urinary_tract(4)	224				all cancers(60;0.00153)|OV - Ovarian serous cystadenocarcinoma(108;0.00444)|BRCA - Breast invasive adenocarcinoma(234;0.0681)		TCTCTTAGGGCACCACACCTC	0.522													C|||	30	0.00599042	0.0219	0.0014	5008	,	,		18493	0.0		0.0	False		,,,				2504	0.0				p.G4204G		Atlas-SNP	.											.	SYNE2	577	.	0			c.C12612T						PASS	.	C	,	75,4331	67.0+/-104.6	1,73,2129	54.0	55.0	55.0		12612,12612	2.3	1.0	14	dbSNP_132	55	0,8600		0,0,4300	no	coding-synonymous,coding-synonymous	SYNE2	NM_015180.4,NM_182914.2	,	1,73,6429	TT,TC,CC		0.0,1.7022,0.5767	,	4204/6886,4204/6908	64580061	75,12931	2203	4300	6503	SO:0001819	synonymous_variant	23224	exon66			TTAGGGCACCACA	AB023228	CCDS9761.2, CCDS41963.1, CCDS45124.1, CCDS45125.1	14q22.1-q22.3	2014-09-17			ENSG00000054654	ENSG00000054654			17084	protein-coding gene	gene with protein product	"""nuclear envelope spectrin repeat-2"", ""nucleus and actin connecting element"""	608442				10231032, 10878022	Standard	NM_182910		Approved	SYNE-2, DKFZP434H2235, Nesprin-2, NUANCE, NUA, KIAA1011, Nesp2	uc001xgl.3	Q8WXH0	OTTHUMG00000140349	ENST00000344113.4:c.12612C>T	14.37:g.64580061C>T		58.0	0.0	0		54.0	20.0	0.37037	NM_182914	Q540G1|Q8N1S3|Q8NF49|Q8TER7|Q8WWW3|Q8WWW4|Q8WWW5|Q8WXH1|Q9NU50|Q9UFQ4|Q9Y2L4|Q9Y4R1	Silent	SNP	ENST00000344113.4	37	CCDS41963.1																																																																																			C|0.993;T|0.007	0.007	strong		0.522	SYNE2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276994.2	NM_182914	
SRPK1	6732	hgsc.bcm.edu	37	6	35803103	35803103	+	Missense_Mutation	SNP	C	C	T	rs35124200	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr6:35803103C>T	ENST00000373825.2	-	16	2231	c.1946G>A	c.(1945-1947)cGg>cAg	p.R649Q	SRPK1_ENST00000373822.1_Missense_Mutation_p.R541Q|SRPK1_ENST00000423325.2_Missense_Mutation_p.R633Q					SRSF protein kinase 1											endometrium(2)|large_intestine(10)|lung(6)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)	21						CCAAGGGTGCCGGAGACACTC	0.562													C|||	15	0.00299521	0.0008	0.0043	5008	,	,		17497	0.002		0.006	False		,,,				2504	0.0031				p.R649Q	NSCLC(31;67 978 16289 24856 26454)	Atlas-SNP	.											.	SRPK1	61	.	0			c.G1946A						PASS	.	C	GLN/ARG	11,4087		0,11,2038	48.0	56.0	54.0		1946	4.8	1.0	6	dbSNP_126	54	98,8296		1,96,4100	yes	missense	SRPK1	NM_003137.4	43	1,107,6138	TT,TC,CC		1.1675,0.2684,0.8726	benign	649/656	35803103	109,12383	2049	4197	6246	SO:0001583	missense	6732	exon16			GGGTGCCGGAGAC	U09564	CCDS47415.1	6p21.31	2010-06-23	2010-06-23		ENSG00000096063	ENSG00000096063			11305	protein-coding gene	gene with protein product	"""SR protein kinase 1"", ""serine/arginine-rich splicing factor kinase 1"""	601939	"""SFRS protein kinase 1"""			8208298, 10198174	Standard	NM_003137		Approved	SFRSK1	uc003olj.3	Q96SB4	OTTHUMG00000014583	ENST00000373825.2:c.1946G>A	6.37:g.35803103C>T	ENSP00000362931:p.Arg649Gln	110.0	0.0	0		120.0	65.0	0.541667	NM_003137		Missense_Mutation	SNP	ENST00000373825.2	37	CCDS47415.1	8	0.003663003663003663	1	0.0020325203252032522	1	0.0027624309392265192	2	0.0034965034965034965	4	0.005277044854881266	C	10.84	1.464011	0.26335	0.002684	0.011675	ENSG00000096063	ENST00000373825;ENST00000361690;ENST00000423325;ENST00000373822	T;T;T;T	0.63913	-0.07;-0.07;-0.07;-0.07	5.64	4.77	0.60923	Serine/threonine-protein kinase-like domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	.	.	.	.	T	0.10252	0.0251	N	0.01146	-0.985	0.50039	D	0.999849	P;B	0.45240	0.854;0.093	B;B	0.32393	0.145;0.007	T	0.22800	-1.0206	9	0.08179	T	0.78	-5.1123	10.6703	0.45755	0.0:0.8541:0.0:0.1459	rs35124200	633;649	B4DS61;Q96SB4	.;SRPK1_HUMAN	Q	649;665;633;541	ENSP00000362931:R649Q;ENSP00000354674:R665Q;ENSP00000391069:R633Q;ENSP00000362928:R541Q	ENSP00000354674:R665Q	R	-	2	0	SRPK1	35911081	1.000000	0.71417	1.000000	0.80357	0.826000	0.46750	2.142000	0.42177	1.381000	0.46364	0.655000	0.94253	CGG	C|0.996;T|0.004	0.004	strong		0.562	SRPK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040319.3	NM_003137	
ERMP1	79956	hgsc.bcm.edu	37	9	5805741	5805741	+	Silent	SNP	C	C	T	rs35643913	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr9:5805741C>T	ENST00000339450.5	-	9	1682	c.1593G>A	c.(1591-1593)tcG>tcA	p.S531S	ERMP1_ENST00000214893.5_5'UTR|ERMP1_ENST00000381506.3_Silent_p.S307S|ERMP1_ENST00000543230.1_Silent_p.S109S	NM_024896.2	NP_079172.2	Q7Z2K6	ERMP1_HUMAN	endoplasmic reticulum metallopeptidase 1	531						endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|membrane (GO:0016020)	metal ion binding (GO:0046872)|metallopeptidase activity (GO:0008237)			endometrium(2)|kidney(1)|large_intestine(9)|lung(4)|ovary(1)|prostate(2)|skin(1)	20		Acute lymphoblastic leukemia(23;0.158)		GBM - Glioblastoma multiforme(50;0.00115)|Lung(218;0.111)		GGACAAACAGCGAAATGTCAA	0.423													C|||	35	0.00698882	0.0	0.0029	5008	,	,		18923	0.0		0.006	False		,,,				2504	0.0276				p.S531S		Atlas-SNP	.											.	ERMP1	63	.	0			c.G1593A						PASS	.	C		5,4401	9.9+/-24.2	0,5,2198	90.0	81.0	84.0		1593	-1.9	0.5	9	dbSNP_126	84	67,8533	40.3+/-97.0	0,67,4233	no	coding-synonymous	ERMP1	NM_024896.2		0,72,6431	TT,TC,CC		0.7791,0.1135,0.5536		531/905	5805741	72,12934	2203	4300	6503	SO:0001819	synonymous_variant	79956	exon9			AAACAGCGAAATG	AB058718	CCDS34983.1	9p24	2008-02-05	2007-07-05	2007-07-05	ENSG00000099219	ENSG00000099219			23703	protein-coding gene	gene with protein product	"""Felix-ina"""	611156	"""KIAA1815"""	KIAA1815		11347906	Standard	XM_005251587		Approved	FLJ23309, FXNA	uc003zjm.1	Q7Z2K6	OTTHUMG00000019508	ENST00000339450.5:c.1593G>A	9.37:g.5805741C>T		74.0	0.0	0		106.0	45.0	0.424528	NM_024896	B2RNA4|B3KSB1|Q8N5T5|Q9H5M1	Silent	SNP	ENST00000339450.5	37	CCDS34983.1																																																																																			C|0.995;T|0.005	0.005	strong		0.423	ERMP1-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000354877.1	NM_024896	
GTF2H4	2968	hgsc.bcm.edu	37	6	30881103	30881103	+	Silent	SNP	C	C	A	rs1132408	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr6:30881103C>A	ENST00000259895.4	+	13	1378	c.1155C>A	c.(1153-1155)ccC>ccA	p.P385P	GTF2H4_ENST00000376316.2_Silent_p.P385P|VARS2_ENST00000416670.2_5'Flank|VARS2_ENST00000542001.1_5'Flank|VARS2_ENST00000541562.1_5'Flank|VARS2_ENST00000321897.5_5'Flank	NM_001517.4	NP_001508.1	Q92759	TF2H4_HUMAN	general transcription factor IIH, polypeptide 4, 52kDa	385					7-methylguanosine mRNA capping (GO:0006370)|ATP catabolic process (GO:0006200)|DNA repair (GO:0006281)|gene expression (GO:0010467)|nucleotide-excision repair (GO:0006289)|nucleotide-excision repair, DNA damage removal (GO:0000718)|positive regulation of viral transcription (GO:0050434)|protein phosphorylation (GO:0006468)|termination of RNA polymerase I transcription (GO:0006363)|transcription elongation from RNA polymerase I promoter (GO:0006362)|transcription elongation from RNA polymerase II promoter (GO:0006368)|transcription from RNA polymerase I promoter (GO:0006360)|transcription from RNA polymerase II promoter (GO:0006366)|transcription initiation from RNA polymerase I promoter (GO:0006361)|transcription initiation from RNA polymerase II promoter (GO:0006367)|transcription-coupled nucleotide-excision repair (GO:0006283)|viral process (GO:0016032)	core TFIIH complex (GO:0000439)|holo TFIIH complex (GO:0005675)|nucleoplasm (GO:0005654)	ATP-dependent DNA helicase activity (GO:0004003)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(1)|endometrium(3)|lung(3)|ovary(2)|skin(1)|upper_aerodigestive_tract(1)	11						TGCTGCCCCCCACCATCACCG	0.577								Nucleotide excision repair (NER)					C|||	69	0.013778	0.0166	0.0072	5008	,	,		16179	0.0149		0.0179	False		,,,				2504	0.0092				p.P385P		Atlas-SNP	.											.	GTF2H4	38	.	0			c.C1155A						PASS	.	C		92,2930		0,92,1419	77.0	87.0	83.0		1155	4.7	1.0	6	dbSNP_86	83	85,5331		0,85,2623	no	coding-synonymous	GTF2H4	NM_001517.4		0,177,4042	AA,AC,CC		1.5694,3.0443,2.0977		385/463	30881103	177,8261	1511	2708	4219	SO:0001819	synonymous_variant	2968	exon13			GCCCCCCACCATC	Y07595	CCDS34386.1	6p21.3	2012-11-05	2002-08-29		ENSG00000213780	ENSG00000213780		"""General transcription factors"", ""General transcription factor IIH complex subunits"""	4658	protein-coding gene	gene with protein product		601760	"""general transcription factor IIH, polypeptide 4 (52kD subunit)"""			9118947	Standard	NM_001517		Approved	TFB2, TFIIH, P52	uc003nsa.1	Q92759	OTTHUMG00000031043	ENST00000259895.4:c.1155C>A	6.37:g.30881103C>A		200.0	1.0	0.005		220.0	218.0	0.990909	NM_001517	B4DTJ5|Q76KU4	Silent	SNP	ENST00000259895.4	37	CCDS34386.1																																																																																			C|0.980;A|0.020	0.020	strong		0.577	GTF2H4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076044.3	NM_001517	
IL1R1	3554	hgsc.bcm.edu	37	2	102791086	102791086	+	Missense_Mutation	SNP	C	C	T	rs28362304	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr2:102791086C>T	ENST00000410023.1	+	10	1349	c.1031C>T	c.(1030-1032)aCg>aTg	p.T344M	IL1R1_ENST00000409589.1_Intron|IL1R1_ENST00000409288.1_Missense_Mutation_p.T344M|IL1R1_ENST00000409929.1_Missense_Mutation_p.T344M|IL1R1_ENST00000233946.3_Missense_Mutation_p.T344M|AC007271.3_ENST00000428188.1_RNA|IL1R1_ENST00000424272.1_Missense_Mutation_p.T344M|IL1R1_ENST00000409329.1_Missense_Mutation_p.T344M			P14778	IL1R1_HUMAN	interleukin 1 receptor, type I	344			T -> M (in dbSNP:rs28362304).		cell surface receptor signaling pathway (GO:0007166)|immune response (GO:0006955)|interleukin-1-mediated signaling pathway (GO:0070498)|regulation of inflammatory response (GO:0050727)|response to interleukin-1 (GO:0070555)	cell surface (GO:0009986)|extracellular region (GO:0005576)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)	interleukin-1 receptor activity (GO:0004908)|interleukin-1, Type I, activating receptor activity (GO:0004909)|platelet-derived growth factor receptor binding (GO:0005161)|signal transducer activity (GO:0004871)|transmembrane signaling receptor activity (GO:0004888)			breast(2)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(4)|lung(4)|prostate(2)|skin(3)	19					Anakinra(DB00026)	ATATGTGTCACGTTGACAGTC	0.313													C|||	228	0.0455272	0.0083	0.0072	5008	,	,		17379	0.0714		0.006	False		,,,				2504	0.137				p.T344M		Atlas-SNP	.											.	IL1R1	52	.	0			c.C1031T						PASS	.	C	MET/THR	49,4355	50.2+/-85.5	0,49,2153	185.0	167.0	173.0		1031	-3.8	0.0	2	dbSNP_125	173	43,8551	28.5+/-78.6	0,43,4254	yes	missense	IL1R1	NM_000877.2	81	0,92,6407	TT,TC,CC		0.5003,1.1126,0.7078	benign	344/570	102791086	92,12906	2202	4297	6499	SO:0001583	missense	3554	exon9			GTGTCACGTTGAC	M27492	CCDS2055.1, CCDS74547.1	2q12	2013-01-29			ENSG00000115594	ENSG00000115594		"""Interleukins and interleukin receptors"", ""CD molecules"", ""Immunoglobulin superfamily / I-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	5993	protein-coding gene	gene with protein product		147810		IL1R, IL1RA		1833184, 10191101	Standard	XM_005263929		Approved	D2S1473, CD121A	uc002tbr.3	P14778	OTTHUMG00000130783	ENST00000410023.1:c.1031C>T	2.37:g.102791086C>T	ENSP00000386380:p.Thr344Met	112.0	0.0	0		92.0	34.0	0.369565	NM_000877	Q587I7	Missense_Mutation	SNP	ENST00000410023.1	37	CCDS2055.1	50	0.022893772893772892	2	0.0040650406504065045	3	0.008287292817679558	40	0.06993006993006994	5	0.006596306068601583	C	9.085	1.000223	0.19121	0.011126	0.005003	ENSG00000115594	ENST00000409929;ENST00000424272;ENST00000409329;ENST00000428279;ENST00000409288;ENST00000410023;ENST00000233946	T;T;T;T;T;T;T	0.05447	4.36;3.75;3.75;3.44;3.75;4.38;4.38	5.57	-3.75	0.04372	.	1.033190	0.07574	N	0.919117	T	0.00328	0.0010	N	0.04880	-0.145	0.09310	N	1	B;B;B	0.13145	0.003;0.002;0.007	B;B;B	0.09377	0.001;0.002;0.004	T	0.42882	-0.9425	10	0.37606	T	0.19	.	14.2823	0.66221	0.0:0.7461:0.0:0.2539	rs28362304;rs28362304	344;344;344	B8ZZW4;P14778;B8ZZ73	.;IL1R1_HUMAN;.	M	344;344;344;200;344;344;344	ENSP00000386776:T344M;ENSP00000415366:T344M;ENSP00000387131:T344M;ENSP00000410461:T200M;ENSP00000386478:T344M;ENSP00000386380:T344M;ENSP00000233946:T344M	ENSP00000233946:T344M	T	+	2	0	IL1R1	102157518	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	0.517000	0.22832	-0.397000	0.07691	-0.982000	0.02568	ACG	C|0.985;T|0.015	0.015	strong		0.313	IL1R1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253299.1		
RPTOR	57521	hgsc.bcm.edu	37	17	78936339	78936339	+	Silent	SNP	G	G	A	rs17848671	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr17:78936339G>A	ENST00000306801.3	+	32	4133	c.3771G>A	c.(3769-3771)acG>acA	p.T1257T	CTD-2561B21.3_ENST00000571591.1_RNA|RPTOR_ENST00000544334.2_Silent_p.T1099T|RPTOR_ENST00000575542.1_3'UTR	NM_020761.2	NP_065812.1	Q8N122	RPTOR_HUMAN	regulatory associated protein of MTOR, complex 1	1257					cell cycle arrest (GO:0007050)|cell growth (GO:0016049)|cellular response to amino acid stimulus (GO:0071230)|cellular response to nutrient levels (GO:0031669)|insulin receptor signaling pathway (GO:0008286)|positive regulation of endothelial cell proliferation (GO:0001938)|positive regulation of protein serine/threonine kinase activity (GO:0071902)|positive regulation of TOR signaling (GO:0032008)|positive regulation of transcription from RNA polymerase III promoter (GO:0045945)|regulation of cell size (GO:0008361)|TOR signaling (GO:0031929)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|lysosomal membrane (GO:0005765)|lysosome (GO:0005764)|TORC1 complex (GO:0031931)	14-3-3 protein binding (GO:0071889)|protein complex binding (GO:0032403)|protein kinase binding (GO:0019901)|RNA polymerase III type 1 promoter DNA binding (GO:0001030)|RNA polymerase III type 2 promoter DNA binding (GO:0001031)|RNA polymerase III type 3 promoter DNA binding (GO:0001032)|TFIIIC-class transcription factor binding (GO:0001156)			breast(1)|endometrium(4)|kidney(1)|large_intestine(12)|lung(17)|ovary(3)|prostate(1)|skin(1)|stomach(1)|urinary_tract(3)	44						AGGGGCTGACGGCCCTGGACA	0.632													G|||	3	0.000599042	0.0	0.0029	5008	,	,		17401	0.001		0.0	False		,,,				2504	0.0				p.T1257T		Atlas-SNP	.											.	RPTOR	122	.	0			c.G3771A						PASS	.						95.0	83.0	87.0					17																	78936339		2203	4300	6503	SO:0001819	synonymous_variant	57521	exon32			GCTGACGGCCCTG		CCDS11773.1, CCDS54175.1	17q25.3	2013-01-10				ENSG00000141564		"""WD repeat domain containing"""	30287	protein-coding gene	gene with protein product	"""regulatory associated protein of mTOR"""	607130				10718198, 12150926	Standard	NM_001163034		Approved	KOG1, Mip1, KIAA1303, raptor	uc002jyt.1	Q8N122		ENST00000306801.3:c.3771G>A	17.37:g.78936339G>A		105.0	0.0	0		136.0	62.0	0.455882	NM_020761	B2RN36|C6KEF2|F5H7J5|Q8N4V9|Q8TB32|Q9P2P3	Silent	SNP	ENST00000306801.3	37	CCDS11773.1																																																																																			G|0.999;A|0.001	0.001	strong		0.632	RPTOR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000438125.1	NM_020761	
CDHR4	389118	hgsc.bcm.edu	37	3	49831032	49831032	+	Missense_Mutation	SNP	A	A	G	rs115485248	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr3:49831032A>G	ENST00000412678.2	-	12	1615	c.1607T>C	c.(1606-1608)aTt>aCt	p.I536T	CDHR4_ENST00000462108.1_5'Flank	NM_001007540.2	NP_001007541.2	A6H8M9	CDHR4_HUMAN	cadherin-related family member 4	536	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)|breast(1)|endometrium(3)|large_intestine(3)|lung(3)	11						CTCGATGGTAATGGTACAGGA	0.488													A|||	3	0.000599042	0.0	0.0	5008	,	,		22546	0.0		0.003	False		,,,				2504	0.0				p.I536T		Atlas-SNP	.											.	CDHR4	37	.	0			c.T1607C						PASS	.	A	THR/ILE	0,1384		0,0,692	186.0	175.0	178.0		1607	5.7	1.0	3	dbSNP_132	178	9,3173		0,9,1582	yes	missense	CDHR4	NM_001007540.2	89	0,9,2274	GG,GA,AA		0.2828,0.0,0.1971	probably-damaging	536/789	49831032	9,4557	692	1591	2283	SO:0001583	missense	389118	exon12			ATGGTAATGGTAC		CCDS46829.1	3p21.31	2011-07-01	2010-01-25	2010-01-25	ENSG00000187492	ENSG00000187492		"""Cadherins / Cadherin-related"""	34527	protein-coding gene	gene with protein product			"""cadherin-like 29"""	CDH29			Standard	NM_001007540		Approved	VLLR9392	uc010hkz.3	A6H8M9	OTTHUMG00000158198	ENST00000412678.2:c.1607T>C	3.37:g.49831032A>G	ENSP00000391409:p.Ile536Thr	127.0	0.0	0		100.0	44.0	0.44	NM_001007540	Q6UXT0	Missense_Mutation	SNP	ENST00000412678.2	37	CCDS46829.1	2	9.157509157509158E-4	0	0.0	0	0.0	0	0.0	2	0.002638522427440633	A	17.57	3.423523	0.62733	0.0	0.002828	ENSG00000187492	ENST00000412678	T	0.43688	0.94	5.67	5.67	0.87782	Cadherin (5);Cadherin-like (1);	.	.	.	.	T	0.66396	0.2785	M	0.84511	2.7	0.80722	D	1	D	0.76494	0.999	D	0.70487	0.969	T	0.72253	-0.4347	9	0.87932	D	0	.	12.3323	0.55046	1.0:0.0:0.0:0.0	.	536	A6H8M9	CDHR4_HUMAN	T	536	ENSP00000391409:I536T	ENSP00000391409:I536T	I	-	2	0	CDHR4	49806036	0.899000	0.30636	0.997000	0.53966	0.981000	0.71138	4.401000	0.59716	2.170000	0.68504	0.529000	0.55759	ATT	A|0.999;G|0.001	0.001	strong		0.488	CDHR4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000350387.1	NM_001007540	
NRK	203447	hgsc.bcm.edu	37	X	105193709	105193709	+	Missense_Mutation	SNP	A	A	G			TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chrX:105193709A>G	ENST00000243300.9	+	27	4799	c.4496A>G	c.(4495-4497)gAc>gGc	p.D1499G	NRK_ENST00000540278.1_Missense_Mutation_p.D80G|NRK_ENST00000428173.2_Missense_Mutation_p.D1500G	NM_198465.2	NP_940867.2	Q7Z2Y5	NRK_HUMAN	Nik related kinase	1499	CNH. {ECO:0000255|PROSITE- ProRule:PRU00795}.				activation of JNKK activity (GO:0007256)|negative regulation of cell proliferation (GO:0008285)|parturition (GO:0007567)|regulation of spongiotrophoblast cell proliferation (GO:0060721)		ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)|small GTPase regulator activity (GO:0005083)			breast(8)|central_nervous_system(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(14)|lung(36)|ovary(3)|prostate(1)|skin(2)	76						ATGTGGAAAGACATACCATCT	0.383										HNSCC(51;0.14)																											p.D1499G		Atlas-SNP	.											.	NRK	321	.	0			c.A4496G						PASS	.						70.0	59.0	62.0					X																	105193709		1868	4085	5953	SO:0001583	missense	203447	exon27			GGAAAGACATACC	BX538345	CCDS65305.1	Xq22.3	2008-02-05			ENSG00000123572	ENSG00000123572			25391	protein-coding gene	gene with protein product		300791					Standard	NM_198465		Approved	DKFZp686A17109	uc004emd.3	Q7Z2Y5	OTTHUMG00000022143	ENST00000243300.9:c.4496A>G	X.37:g.105193709A>G	ENSP00000434830:p.Asp1499Gly	100.0	1.0	0.01		110.0	110.0	1	NM_198465	Q32ND6|Q5H9K2|Q6ZMP2	Missense_Mutation	SNP	ENST00000243300.9	37		.	.	.	.	.	.	.	.	.	.	A	18.18	3.567047	0.65651	.	.	ENSG00000123572	ENST00000243300;ENST00000428173;ENST00000540278	T;T;T	0.03982	3.74;3.74;3.74	5.96	5.96	0.96718	Citron-like (2);	0.000000	0.47093	D	0.000252	T	0.10895	0.0266	L	0.36672	1.1	0.39530	D	0.968642	P;P	0.49447	0.674;0.924	P;P	0.55785	0.457;0.784	T	0.02505	-1.1149	10	0.87932	D	0	.	12.9799	0.58557	1.0:0.0:0.0:0.0	.	80;1499	B7Z1I7;Q7Z2Y5	.;NRK_HUMAN	G	1499;1500;80	ENSP00000434830:D1499G;ENSP00000438378:D1500G;ENSP00000438148:D80G	ENSP00000434830:D1499G	D	+	2	0	NRK	105080365	1.000000	0.71417	0.998000	0.56505	0.958000	0.62258	6.778000	0.75043	2.002000	0.58637	0.486000	0.48141	GAC	.	.	none		0.383	NRK-001	KNOWN	non_canonical_conserved|basic|appris_candidate	protein_coding	protein_coding	OTTHUMT00000106480.6	NM_198465	
FCRLA	84824	hgsc.bcm.edu	37	1	161680617	161680617	+	Silent	SNP	G	G	A			TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr1:161680617G>A	ENST00000236938.6	+	2	440	c.198G>A	c.(196-198)gaG>gaA	p.E66E	FCRLA_ENST00000367953.3_Silent_p.E55E|FCRLA_ENST00000470841.1_3'UTR|FCRLA_ENST00000540926.1_Silent_p.E55E|FCRLA_ENST00000349527.4_Silent_p.E49E|FCRLA_ENST00000350710.3_Intron|FCRLA_ENST00000546024.1_Silent_p.E66E|FCRLA_ENST00000309691.6_Silent_p.E49E|FCRLA_ENST00000540521.1_Intron|FCRLA_ENST00000367957.2_Intron|FCRLA_ENST00000367949.2_Silent_p.E66E|FCRLA_ENST00000294796.4_Intron|FCRLA_ENST00000367950.1_Silent_p.E26E|FCRLA_ENST00000367959.2_Silent_p.E72E	NM_032738.3	NP_116127.3	Q7L513	FCRLA_HUMAN	Fc receptor-like A	49					cell differentiation (GO:0030154)	cytoplasm (GO:0005737)|extracellular region (GO:0005576)				breast(1)|kidney(12)|large_intestine(4)|lung(13)|prostate(1)|skin(2)|stomach(1)	34	all_cancers(52;2.55e-15)|all_hematologic(112;0.0359)		BRCA - Breast invasive adenocarcinoma(70;0.00301)			GCCACACGGAGGATGACTTGA	0.557																																					p.E72E		Atlas-SNP	.											.	FCRLA	101	.	0			c.G216A						PASS	.						108.0	81.0	90.0					1																	161680617		2203	4300	6503	SO:0001819	synonymous_variant	84824	exon3			CACGGAGGATGAC	AF531423	CCDS30926.1, CCDS53415.1, CCDS53416.1, CCDS53417.1, CCDS53418.1, CCDS53419.1, CCDS53420.1	1q23.3	2014-01-28	2006-09-26	2006-09-26	ENSG00000132185	ENSG00000132185		"""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	18504	protein-coding gene	gene with protein product		606891	"""Fc receptor-like and mucin-like 1"""	FCRLM1		11754007	Standard	NM_001184866		Approved	MGC4595, FCRLc2, FCRLb, FCRLc1, FCRLd, FCRLe, FCRL, FCRLa, FREB, FCRLX	uc001gbe.3	Q7L513	OTTHUMG00000034537	ENST00000236938.6:c.198G>A	1.37:g.161680617G>A		90.0	0.0	0		77.0	33.0	0.428571	NM_001184866	A0N0M1|A6NC03|A6NL20|F5H720|F8W743|G3V1J2|Q5VXA1|Q5VXA2|Q5VXA3|Q5VXA4|Q5VXB0|Q5VXB1|Q8NEW4|Q8WXH3|Q96PC6|Q96PJ0|Q96PJ1|Q96PJ2|Q96PJ4|Q9BR57	Silent	SNP	ENST00000236938.6	37	CCDS30926.1																																																																																			.	.	none		0.557	FCRLA-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000083574.1	NM_032738	
PTCD3	55037	hgsc.bcm.edu	37	2	86352925	86352925	+	Silent	SNP	A	A	G	rs139474497	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr2:86352925A>G	ENST00000254630.7	+	12	939	c.873A>G	c.(871-873)gtA>gtG	p.V291V	PTCD3_ENST00000409277.3_3'UTR	NM_017952.5	NP_060422.4	Q96EY7	PTCD3_HUMAN	pentatricopeptide repeat domain 3	291					mitochondrial translation (GO:0032543)|regulation of translation (GO:0006417)	mitochondrion (GO:0005739)	poly(A) RNA binding (GO:0044822)|ribosomal small subunit binding (GO:0043024)|rRNA binding (GO:0019843)			NS(1)|breast(2)|endometrium(3)|kidney(4)|large_intestine(4)|lung(6)|ovary(1)|prostate(1)	22						CAGCTGATGTATACACATTTA	0.338													A|||	28	0.00559105	0.0	0.0086	5008	,	,		20926	0.0		0.0219	False		,,,				2504	0.0				p.V291V		Atlas-SNP	.											.	PTCD3	51	.	0			c.A873G						PASS	.	A		6,4400	11.4+/-27.6	0,6,2197	44.0	49.0	47.0		873	-11.5	0.0	2	dbSNP_134	47	127,8473	64.6+/-126.8	1,125,4174	no	coding-synonymous	PTCD3	NM_017952.5		1,131,6371	GG,GA,AA		1.4767,0.1362,1.0226		291/690	86352925	133,12873	2203	4300	6503	SO:0001819	synonymous_variant	55037	exon12			TGATGTATACACA		CCDS33235.1	2p11.2	2014-02-12	2012-02-24		ENSG00000132300	ENSG00000132300			24717	protein-coding gene	gene with protein product		614918				8889548	Standard	NM_017952		Approved	FLJ20758, DKFZp666K071	uc002sqw.2	Q96EY7	OTTHUMG00000153168	ENST00000254630.7:c.873A>G	2.37:g.86352925A>G		93.0	0.0	0		101.0	55.0	0.544554	NM_017952	A6NHD2|D6W5M1|Q597H0|Q658Y9|Q9BUZ8|Q9NWL0	Silent	SNP	ENST00000254630.7	37	CCDS33235.1																																																																																			A|0.991;G|0.009	0.009	strong		0.338	PTCD3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000329854.1	NM_017952	
BOK	666	hgsc.bcm.edu	37	2	242501765	242501765	+	Missense_Mutation	SNP	G	G	A			TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr2:242501765G>A	ENST00000318407.3	+	3	525	c.223G>A	c.(223-225)Gat>Aat	p.D75N		NM_032515.4	NP_115904.1	Q9UMX3	BOK_HUMAN	BCL2-related ovarian killer	75					activation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0006919)|apoptotic process (GO:0006915)|brain development (GO:0007420)|cell proliferation (GO:0008283)|extrinsic apoptotic signaling pathway in absence of ligand (GO:0097192)|intrinsic apoptotic signaling pathway by p53 class mediator (GO:0072332)|intrinsic apoptotic signaling pathway in response to DNA damage (GO:0008630)|male gonad development (GO:0008584)|neuron apoptotic process (GO:0051402)|oligodendrocyte differentiation (GO:0048709)|positive regulation of apoptotic process (GO:0043065)|positive regulation of execution phase of apoptosis (GO:1900119)	cytoplasm (GO:0005737)|mitochondrial membrane (GO:0031966)|mitochondrial outer membrane (GO:0005741)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)			large_intestine(1)|lung(3)|ovary(1)	5		all_cancers(19;1.09e-40)|all_epithelial(40;2.03e-18)|Breast(86;1.53e-05)|all_lung(227;0.00338)|Renal(207;0.00502)|Ovarian(221;0.00716)|Lung NSC(271;0.012)|Esophageal squamous(248;0.129)|Melanoma(123;0.144)|all_hematologic(139;0.158)|all_neural(83;0.243)|Hepatocellular(293;0.244)		Epithelial(32;2.04e-33)|all cancers(36;7.87e-31)|OV - Ovarian serous cystadenocarcinoma(60;3.52e-15)|Kidney(56;3.04e-09)|KIRC - Kidney renal clear cell carcinoma(57;3.23e-08)|BRCA - Breast invasive adenocarcinoma(100;1.64e-06)|Lung(119;0.000152)|LUSC - Lung squamous cell carcinoma(224;0.00154)|Colorectal(34;0.0129)|COAD - Colon adenocarcinoma(134;0.0835)		CCACACAGGCGATGAGCTGGA	0.647																																					p.D75N		Atlas-SNP	.											.	BOK	16	.	0			c.G223A						PASS	.						84.0	66.0	72.0					2																	242501765		2203	4300	6503	SO:0001583	missense	666	exon3			ACAGGCGATGAGC	AF174487	CCDS2550.1	2q37.3	2008-05-22			ENSG00000176720	ENSG00000176720			1087	protein-coding gene	gene with protein product		605404				9356461, 11034351, 15102863	Standard	NM_032515		Approved	BCL2L9, BOKL, MGC4631	uc002wbq.3	Q9UMX3	OTTHUMG00000133411	ENST00000318407.3:c.223G>A	2.37:g.242501765G>A	ENSP00000314132:p.Asp75Asn	56.0	0.0	0		52.0	26.0	0.5	NM_032515		Missense_Mutation	SNP	ENST00000318407.3	37	CCDS2550.1	.	.	.	.	.	.	.	.	.	.	G	31	5.087479	0.94100	.	.	ENSG00000176720	ENST00000318407	T	0.55588	0.51	4.97	4.97	0.65823	Apoptosis regulator, Bcl2-like (1);Apoptosis regulator, Bcl-2, BH (2);	0.116231	0.56097	D	0.000026	T	0.74222	0.3688	M	0.80183	2.485	0.80722	D	1	D	0.89917	1.0	D	0.71414	0.973	T	0.78360	-0.2234	10	0.62326	D	0.03	-17.3648	18.2203	0.89899	0.0:0.0:1.0:0.0	.	75	Q9UMX3	BOK_HUMAN	N	75	ENSP00000314132:D75N	ENSP00000314132:D75N	D	+	1	0	BOK	242150438	1.000000	0.71417	0.978000	0.43139	0.758000	0.43043	9.034000	0.93747	2.283000	0.76528	0.655000	0.94253	GAT	.	.	none		0.647	BOK-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257268.2	NM_032515	
LLGL2	3993	hgsc.bcm.edu	37	17	73569211	73569211	+	Silent	SNP	C	C	T	rs376055189		TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr17:73569211C>T	ENST00000392550.3	+	20	2694	c.2577C>T	c.(2575-2577)taC>taT	p.Y859Y	LLGL2_ENST00000167462.5_Silent_p.Y859Y|LLGL2_ENST00000577200.1_Silent_p.Y859Y	NM_001031803.1	NP_001026973.1	Q6P1M3	L2GL2_HUMAN	lethal giant larvae homolog 2 (Drosophila)	859					cell cycle (GO:0007049)|cell division (GO:0051301)|exocytosis (GO:0006887)|regulation of establishment or maintenance of cell polarity (GO:0032878)	cytoplasm (GO:0005737)	PDZ domain binding (GO:0030165)			NS(1)|breast(3)|cervix(2)|endometrium(2)|kidney(1)|large_intestine(2)|lung(9)|ovary(2)|pancreas(1)|prostate(1)|skin(5)|upper_aerodigestive_tract(1)|urinary_tract(1)	31	all_cancers(13;3.15e-09)|all_epithelial(9;5.78e-10)|Breast(9;5.8e-10)|all_lung(278;0.246)		all cancers(21;1.8e-07)|Epithelial(20;1.38e-06)|Lung(188;0.0696)|LUSC - Lung squamous cell carcinoma(166;0.112)			CCGAGGACTACGGGGAGCACC	0.662																																					p.Y859Y		Atlas-SNP	.											.	LLGL2	155	.	0			c.C2577T						PASS	.	C	,	1,4405		0,1,2202	59.0	50.0	53.0		2577,2577	-6.2	0.8	17		53	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous,coding-synonymous	LLGL2	NM_001031803.1,NM_004524.2	,	0,2,6501	TT,TC,CC		0.0116,0.0227,0.0154	,	859/1021,859/1016	73569211	2,13004	2203	4300	6503	SO:0001819	synonymous_variant	3993	exon20			GGACTACGGGGAG	X87342	CCDS11725.1, CCDS32733.1, CCDS45776.1	17q25.1	2013-01-10	2001-11-28			ENSG00000073350		"""WD repeat domain containing"""	6629	protein-coding gene	gene with protein product			"""lethal giant larvae (Drosophila) homolog 2"""				Standard	XR_243659		Approved	HGL	uc002joh.3	Q6P1M3		ENST00000392550.3:c.2577C>T	17.37:g.73569211C>T		188.0	0.0	0		179.0	81.0	0.452514	NM_004524	Q14521|Q9BR62	Silent	SNP	ENST00000392550.3	37	CCDS32733.1																																																																																			.	.	weak		0.662	LLGL2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000447633.1	NM_004524	
BCL10	8915	hgsc.bcm.edu	37	1	85733328	85733328	+	Silent	SNP	A	A	G			TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr1:85733328A>G	ENST00000370580.1	-	3	1421	c.684T>C	c.(682-684)cgT>cgC	p.R228R		NM_003921.4	NP_003912.1	O95999	BCL10_HUMAN	B-cell CLL/lymphoma 10	228					adaptive immune response (GO:0002250)|B cell apoptotic process (GO:0001783)|cell death (GO:0008219)|cellular defense response (GO:0006968)|cellular response to mechanical stimulus (GO:0071260)|Fc-epsilon receptor signaling pathway (GO:0038095)|immunoglobulin mediated immune response (GO:0016064)|innate immune response (GO:0045087)|interleukin-6 biosynthetic process (GO:0042226)|lymphotoxin A biosynthetic process (GO:0042109)|negative regulation of mature B cell apoptotic process (GO:0002906)|neural tube closure (GO:0001843)|positive regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043280)|positive regulation of extrinsic apoptotic signaling pathway (GO:2001238)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of interleukin-8 biosynthetic process (GO:0045416)|positive regulation of mast cell cytokine production (GO:0032765)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of phosphorylation (GO:0042327)|positive regulation of protein ubiquitination (GO:0031398)|positive regulation of T cell activation (GO:0050870)|positive regulation of transcription, DNA-templated (GO:0045893)|protein homooligomerization (GO:0051260)|protein oligomerization (GO:0051259)|regulation of T cell receptor signaling pathway (GO:0050856)|response to food (GO:0032094)|response to fungus (GO:0009620)|response to molecule of bacterial origin (GO:0002237)|T cell apoptotic process (GO:0070231)|T cell receptor signaling pathway (GO:0050852)|toll-like receptor signaling pathway (GO:0002224)	CBM complex (GO:0032449)|cytoplasm (GO:0005737)|cytoplasmic microtubule (GO:0005881)|cytosol (GO:0005829)|immunological synapse (GO:0001772)|lysosome (GO:0005764)|membrane raft (GO:0045121)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|protein complex (GO:0043234)	enzyme binding (GO:0019899)|kinase binding (GO:0019900)|NF-kappaB binding (GO:0051059)|protease binding (GO:0002020)|protein C-terminus binding (GO:0008022)|protein kinase B binding (GO:0043422)|protein kinase binding (GO:0019901)|protein self-association (GO:0043621)|transcription coactivator activity (GO:0003713)|transcription factor binding (GO:0008134)|ubiquitin binding (GO:0043130)|ubiquitin protein ligase binding (GO:0031625)			haematopoietic_and_lymphoid_tissue(7)|kidney(1)|large_intestine(4)|lung(4)|ovary(1)|stomach(1)|urinary_tract(1)	19				all cancers(265;0.0114)|Epithelial(280;0.0311)		GTGAAACAGTACGTGATCTTA	0.363			T	IGH@	MALT																																p.R228R	NSCLC(34;993 1034 12176 32621 50182)	Atlas-SNP	.		Dom	yes		1	1p22	8915	B-cell CLL/lymphoma 10		L	.	BCL10	39	.	0			c.T684C						PASS	.						62.0	65.0	64.0					1																	85733328		2203	4300	6503	SO:0001819	synonymous_variant	8915	exon3			AACAGTACGTGAT	AJ006288	CCDS704.1	1p22	2008-07-18			ENSG00000142867	ENSG00000142867			989	protein-coding gene	gene with protein product	"""CARD-like apoptotic protein"", ""CARD-containing apoptotic signaling protein"", ""CARD containing molecule enhancing NF-kB"", ""caspase-recruiting domain-containing protein"", ""CARD-containing proapoptotic protein"""	603517				9989495	Standard	NM_003921		Approved	CARMEN, CIPER, mE10, c-E10, CLAP	uc021opd.1	O95999	OTTHUMG00000009965	ENST00000370580.1:c.684T>C	1.37:g.85733328A>G		63.0	0.0	0		67.0	4.0	0.0597015	NM_003921	Q5VUF1	Silent	SNP	ENST00000370580.1	37	CCDS704.1																																																																																			.	.	none		0.363	BCL10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000027612.1	NM_003921	
MAP3K11	4296	hgsc.bcm.edu	37	11	65373249	65373249	+	Missense_Mutation	SNP	G	G	T	rs145297254	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr11:65373249G>T	ENST00000530153.1	-	8	1564	c.1043C>A	c.(1042-1044)aCa>aAa	p.T348K	MAP3K11_ENST00000532507.1_Missense_Mutation_p.T21K|MAP3K11_ENST00000534432.1_5'UTR|MAP3K11_ENST00000309100.3_Missense_Mutation_p.T605K					mitogen-activated protein kinase kinase kinase 11											breast(3)|central_nervous_system(1)|kidney(1)|large_intestine(4)|lung(14)|skin(1)	24						TGCTGGGGGTGTGGAAGGAGA	0.602																																					p.T605K		Atlas-SNP	.											.	MAP3K11	67	.	0			c.C1814A						PASS	.	G	LYS/THR	0,4402		0,0,2201	58.0	51.0	54.0		1814	4.1	1.0	11	dbSNP_134	54	6,8588	5.0+/-18.6	0,6,4291	yes	missense	MAP3K11	NM_002419.3	78	0,6,6492	TT,TG,GG		0.0698,0.0,0.0462	probably-damaging	605/848	65373249	6,12990	2201	4297	6498	SO:0001583	missense	4296	exon8			GGGGGTGTGGAAG		CCDS8107.1	11q13.1-q13.3	2011-06-09			ENSG00000173327	ENSG00000173327	2.7.10.1	"""Mitogen-activated protein kinase cascade / Kinase kinase kinases"""	6850	protein-coding gene	gene with protein product		600050		MLK3, PTK1		9267807, 8183572	Standard	NM_002419		Approved	SPRK, MEKK11	uc001oew.3	Q16584	OTTHUMG00000166529	ENST00000530153.1:c.1043C>A	11.37:g.65373249G>T	ENSP00000433886:p.Thr348Lys	81.0	0.0	0		75.0	41.0	0.546667	NM_002419		Missense_Mutation	SNP	ENST00000530153.1	37		.	.	.	.	.	.	.	.	.	.	G	20.3	3.969099	0.74131	0.0	6.98E-4	ENSG00000173327	ENST00000309100;ENST00000532507;ENST00000530153	T;T	0.73681	-0.67;-0.77	5.04	4.12	0.48240	.	0.292498	0.28312	N	0.015805	T	0.65228	0.2671	L	0.29908	0.895	0.35129	D	0.767737	P;D	0.54207	0.911;0.965	P;P	0.48704	0.587;0.456	T	0.67616	-0.5625	10	0.19147	T	0.46	.	9.1853	0.37168	0.0976:0.0:0.9024:0.0	.	112;605	B3KQY4;Q16584	.;M3K11_HUMAN	K	605;21;348	ENSP00000309597:T605K;ENSP00000433886:T348K	ENSP00000309597:T605K	T	-	2	0	MAP3K11	65129825	0.998000	0.40836	1.000000	0.80357	0.997000	0.91878	1.629000	0.37071	1.354000	0.45846	0.655000	0.94253	ACA	G|0.999;T|0.001	0.001	strong		0.602	MAP3K11-004	PUTATIVE	basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000390233.2		
EXOC2	55770	hgsc.bcm.edu	37	6	592566	592566	+	Silent	SNP	C	C	T	rs62385137		TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr6:592566C>T	ENST00000230449.4	-	11	1230	c.1095G>A	c.(1093-1095)gcG>gcA	p.A365A	EXOC2_ENST00000448181.3_Intron	NM_018303.5	NP_060773.3	Q96KP1	EXOC2_HUMAN	exocyst complex component 2	365					cellular protein metabolic process (GO:0044267)|exocytosis (GO:0006887)|Golgi to plasma membrane transport (GO:0006893)|membrane organization (GO:0061024)|protein transport (GO:0015031)	exocyst (GO:0000145)|intracellular membrane-bounded organelle (GO:0043231)|membrane (GO:0016020)|plasma membrane (GO:0005886)				breast(4)|endometrium(6)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(9)|liver(1)|lung(16)|ovary(4)|pancreas(1)|prostate(2)	46	Ovarian(93;0.0733)	Breast(5;0.0014)|all_lung(73;0.0697)|all_hematologic(90;0.0897)		OV - Ovarian serous cystadenocarcinoma(45;0.0507)|BRCA - Breast invasive adenocarcinoma(62;0.14)		GGTCACCAGACGCATGAAGGT	0.448																																					p.A365A		Atlas-SNP	.											EXOC2,colon,carcinoma,-1,1	EXOC2	81	1	0			c.G1095A						PASS	.	G		0,4406		0,0,2203	110.0	94.0	99.0		1095	-11.2	0.0	6	dbSNP_129	99	2,8598		0,2,4298	no	coding-synonymous	EXOC2	NM_018303.4		0,2,6501	TT,TC,CC		0.0233,0.0,0.0154		365/925	592566	2,13004	2203	4300	6503	SO:0001819	synonymous_variant	55770	exon11			ACCAGACGCATGA	AJ420556	CCDS34327.1	6p25.3	2013-01-22	2005-11-01	2005-11-01	ENSG00000112685	ENSG00000112685			24968	protein-coding gene	gene with protein product		615329	"""SEC5-like 1 (S. cerevisiae)"""	SEC5L1		12575951, 12459492	Standard	NM_018303		Approved	FLJ11026, Sec5p	uc003mtd.4	Q96KP1	OTTHUMG00000137437	ENST00000230449.4:c.1095G>A	6.37:g.592566C>T		72.0	0.0	0		95.0	47.0	0.494737	NM_018303	B2RBE6|Q5JPC8|Q96AN6|Q9NUZ8|Q9UJM7	Silent	SNP	ENST00000230449.4	37	CCDS34327.1																																																																																			C|1.000;T|0.000	0.000	weak		0.448	EXOC2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000039627.1	NM_018303	
CASP2	835	hgsc.bcm.edu	37	7	142988726	142988726	+	Silent	SNP	G	G	A	rs4647288	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr7:142988726G>A	ENST00000310447.5	+	2	409	c.168G>A	c.(166-168)ttG>ttA	p.L56L	CASP2_ENST00000392925.2_Silent_p.L56L|CASP2_ENST00000493642.1_3'UTR|RN7SL535P_ENST00000479087.2_RNA	NM_032982.3|NM_032983.3	NP_116764.2|NP_116765.2	P42575	CASP2_HUMAN	caspase 2, apoptosis-related cysteine peptidase	56	CARD. {ECO:0000255|PROSITE- ProRule:PRU00046}.				aging (GO:0007568)|apoptotic process (GO:0006915)|apoptotic signaling pathway (GO:0097190)|brain development (GO:0007420)|cellular response to mechanical stimulus (GO:0071260)|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest (GO:0006977)|ectopic germ cell programmed cell death (GO:0035234)|execution phase of apoptosis (GO:0097194)|extrinsic apoptotic signaling pathway in absence of ligand (GO:0097192)|intrinsic apoptotic signaling pathway in response to DNA damage (GO:0008630)|luteolysis (GO:0001554)|neural retina development (GO:0003407)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of apoptotic process (GO:0043065)|positive regulation of apoptotic signaling pathway (GO:2001235)|positive regulation of neuron apoptotic process (GO:0043525)|protein processing (GO:0016485)|regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043281)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|membrane (GO:0016020)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	cysteine-type endopeptidase activity (GO:0004197)|cysteine-type endopeptidase activity involved in apoptotic process (GO:0097153)|enzyme binding (GO:0019899)|protein domain specific binding (GO:0019904)			endometrium(2)|kidney(2)|large_intestine(5)|lung(11)|ovary(1)	21	Melanoma(164;0.059)					TGAGCGAATTGTTAGAACATC	0.448													G|||	58	0.0115815	0.0008	0.0202	5008	,	,		17867	0.0		0.0328	False		,,,				2504	0.0102				p.L56L		Atlas-SNP	.											.	CASP2	55	.	0			c.G168A						PASS	.	G	,,	35,4371	40.8+/-73.8	0,35,2168	189.0	191.0	190.0		75,168,168	2.8	1.0	7	dbSNP_111	190	272,8328	103.8+/-164.8	4,264,4032	no	coding-synonymous,coding-synonymous,coding-synonymous	CASP2	NM_001224.4,NM_032982.3,NM_032983.3	,,	4,299,6200	AA,AG,GG		3.1628,0.7944,2.3604	,,	25/313,56/453,56/109	142988726	307,12699	2203	4300	6503	SO:0001819	synonymous_variant	835	exon2			CGAATTGTTAGAA	AK096245, BC002427, BM998653, BX537669, CB988674, U13021	CCDS5879.1, CCDS47733.1	7q34-q35	2014-01-20	2008-08-01		ENSG00000106144	ENSG00000106144		"""Caspases"", ""Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"""	1503	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 57"""	600639	"""neural precursor cell expressed, developmentally down-regulated 2"""	NEDD2		7789948, 8780721	Standard	NM_032982		Approved	ICH1, PPP1R57, MGC2181	uc003wco.3	P42575	OTTHUMG00000023641	ENST00000310447.5:c.168G>A	7.37:g.142988726G>A		96.0	0.0	0		114.0	47.0	0.412281	NM_032982	A8K5F9|D3DXD6|E9PDN0|P42576|Q59F21|Q7KZL6|Q86UJ3|Q9BUP7|Q9BZK9|Q9BZL0	Silent	SNP	ENST00000310447.5	37	CCDS5879.1																																																																																			G|0.981;A|0.019	0.019	strong		0.448	CASP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000059962.3	NM_032982	
LNPEP	4012	hgsc.bcm.edu	37	5	96315320	96315320	+	Missense_Mutation	SNP	C	C	G	rs61752351	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr5:96315320C>G	ENST00000231368.5	+	2	1190	c.498C>G	c.(496-498)atC>atG	p.I166M	LNPEP_ENST00000395770.3_Missense_Mutation_p.I152M	NM_005575.2	NP_005566.2	Q9UIQ6	LCAP_HUMAN	leucyl/cystinyl aminopeptidase	166					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-independent (GO:0002480)|antigen processing and presentation of peptide antigen via MHC class I (GO:0002474)|cell-cell signaling (GO:0007267)|female pregnancy (GO:0007565)|membrane organization (GO:0061024)|protein catabolic process (GO:0030163)|protein polyubiquitination (GO:0000209)|proteolysis (GO:0006508)	cytoplasmic vesicle membrane (GO:0030659)|cytosol (GO:0005829)|early endosome lumen (GO:0031905)|extracellular region (GO:0005576)|integral component of plasma membrane (GO:0005887)|intracellular (GO:0005622)|lysosomal membrane (GO:0005765)|membrane (GO:0016020)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)	aminopeptidase activity (GO:0004177)|metallopeptidase activity (GO:0008237)|zinc ion binding (GO:0008270)			breast(2)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(9)|lung(10)|ovary(3)|skin(1)|urinary_tract(1)	34		all_cancers(142;7e-07)|all_epithelial(76;9.52e-10)|all_lung(232;0.00101)|Lung NSC(167;0.00137)|Ovarian(225;0.024)|Colorectal(57;0.0269)|Breast(839;0.244)		COAD - Colon adenocarcinoma(37;0.072)		GGGCACAGATCAGGCTTCCCA	0.458													C|||	33	0.00658946	0.0008	0.0115	5008	,	,		21134	0.0		0.0209	False		,,,				2504	0.0031				p.I166M		Atlas-SNP	.											.	LNPEP	80	.	0			c.C498G						PASS	.	C	MET/ILE,MET/ILE	19,4387	26.2+/-53.5	0,19,2184	94.0	92.0	93.0		498,456	-1.4	0.2	5	dbSNP_129	93	168,8432	78.9+/-141.6	2,164,4134	yes	missense,missense	LNPEP	NM_005575.2,NM_175920.3	10,10	2,183,6318	GG,GC,CC		1.9535,0.4312,1.4378	benign,benign	166/1026,152/1012	96315320	187,12819	2203	4300	6503	SO:0001583	missense	4012	exon2			ACAGATCAGGCTT	D50810	CCDS4087.1, CCDS43346.1	5q15	2011-07-25			ENSG00000113441	ENSG00000113441	3.4.11.3		6656	protein-coding gene	gene with protein product	"""cystinyl aminopeptidase"", ""placental leucine aminopeptidase"""	151300				8550619	Standard	NM_175920		Approved	CAP, PLAP, P-LAP	uc003kmw.1	Q9UIQ6	OTTHUMG00000128719	ENST00000231368.5:c.498C>G	5.37:g.96315320C>G	ENSP00000231368:p.Ile166Met	118.0	0.0	0		114.0	58.0	0.508772	NM_005575	O00769|Q15145|Q59H76|Q9TNQ2|Q9TNQ3|Q9UIQ7	Missense_Mutation	SNP	ENST00000231368.5	37	CCDS4087.1	23	0.010531135531135532	0	0.0	5	0.013812154696132596	0	0.0	18	0.023746701846965697	C	0.007	-1.961172	0.00465	0.004312	0.019535	ENSG00000113441	ENST00000231368;ENST00000395770	T;T	0.04275	3.66;3.66	5.78	-1.36	0.09085	.	1.298990	0.04688	N	0.413675	T	0.01222	0.0040	N	0.08118	0	0.09310	N	0.999999	B	0.06786	0.001	B	0.17098	0.017	T	0.45833	-0.9234	10	0.25751	T	0.34	.	3.8746	0.09051	0.1147:0.1325:0.4957:0.2571	rs61752351	166	Q9UIQ6	LCAP_HUMAN	M	166;152	ENSP00000231368:I166M;ENSP00000379117:I152M	ENSP00000231368:I166M	I	+	3	3	LNPEP	96341076	0.048000	0.20356	0.200000	0.23457	0.089000	0.18198	-0.030000	0.12308	0.047000	0.15862	-0.226000	0.12346	ATC	C|0.986;G|0.014	0.014	strong		0.458	LNPEP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250624.1	NM_005575	
NCOR1	9611	hgsc.bcm.edu	37	17	16005030	16005030	+	Missense_Mutation	SNP	T	T	C	rs150909544		TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr17:16005030T>C	ENST00000268712.3	-	20	2481	c.2224A>G	c.(2224-2226)Act>Gct	p.T742A	NCOR1_ENST00000583226.1_5'Flank|RNU6-314P_ENST00000516574.1_RNA|NCOR1_ENST00000395848.1_Missense_Mutation_p.T649A|NCOR1_ENST00000395851.1_Missense_Mutation_p.T758A	NM_006311.3	NP_006302.2	O75376	NCOR1_HUMAN	nuclear receptor corepressor 1	742					CD4-positive, CD25-positive, alpha-beta regulatory T cell differentiation (GO:0002361)|cellular lipid metabolic process (GO:0044255)|cholesterol homeostasis (GO:0042632)|chromatin modification (GO:0016568)|circadian regulation of gene expression (GO:0032922)|definitive erythrocyte differentiation (GO:0060318)|gene expression (GO:0010467)|negative regulation of JNK cascade (GO:0046329)|negative regulation of phosphatidylinositol 3-kinase signaling (GO:0014067)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|Notch signaling pathway (GO:0007219)|positive regulation of histone deacetylation (GO:0031065)|regulation of fatty acid transport (GO:2000191)|regulation of glycolytic process by negative regulation of transcription from RNA polymerase II promoter (GO:0072362)|regulation of lipid transport by negative regulation of transcription from RNA polymerase II promoter (GO:0072368)|regulation of multicellular organism growth (GO:0040014)|small molecule metabolic process (GO:0044281)|spindle assembly (GO:0051225)|thalamus development (GO:0021794)|transcription from RNA polymerase II promoter (GO:0006366)|transcription initiation from RNA polymerase II promoter (GO:0006367)|transcription, DNA-templated (GO:0006351)|transforming growth factor beta receptor signaling pathway (GO:0007179)	cytoplasm (GO:0005737)|membrane (GO:0016020)|nuclear chromatin (GO:0000790)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|spindle microtubule (GO:0005876)|transcription factor complex (GO:0005667)|transcriptional repressor complex (GO:0017053)	chromatin binding (GO:0003682)|histone deacetylase binding (GO:0042826)|histone deacetylase regulator activity (GO:0035033)|nuclear hormone receptor binding (GO:0035257)|RNA polymerase II activating transcription factor binding (GO:0001102)|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)			NS(2)|breast(13)|central_nervous_system(2)|cervix(3)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(9)|large_intestine(17)|lung(26)|ovary(1)|prostate(7)|skin(2)|upper_aerodigestive_tract(6)|urinary_tract(10)	107				UCEC - Uterine corpus endometrioid carcinoma (92;0.101)		CCTCGAGAAGTAGCATTTTCA	0.483													T|||	1	0.000199681	0.0008	0.0	5008	,	,		21166	0.0		0.0	False		,,,				2504	0.0				p.T758A		Atlas-SNP	.											.	NCOR1	240	.	0			c.A2272G						PASS	.	T	ALA/THR,ALA/THR,ALA/THR	1,4405	2.1+/-5.4	0,1,2202	93.0	88.0	90.0		1945,2272,2224	-10.8	0.0	17	dbSNP_134	90	0,8600		0,0,4300	no	missense,missense,missense	NCOR1	NM_001190438.1,NM_001190440.1,NM_006311.3	58,58,58	0,1,6502	CC,CT,TT		0.0,0.0227,0.0077	benign,benign,benign	649/915,758/2338,742/2441	16005030	1,13005	2203	4300	6503	SO:0001583	missense	9611	exon19			GAGAAGTAGCATT	AF044209	CCDS11175.1, CCDS54094.1, CCDS54095.1	17p11.2	2014-06-12	2010-06-10		ENSG00000141027	ENSG00000141027			7672	protein-coding gene	gene with protein product	"""thyroid hormone- and retinoic acid receptor-associated corepressor 1"", ""protein phosphatase 1, regulatory subunit 109"""	600849	"""nuclear receptor co-repressor 1"""			7566114, 9724795	Standard	NM_006311		Approved	N-CoR, hCIT529I10, TRAC1, hN-CoR, KIAA1047, MGC104216, PPP1R109	uc002gpo.3	O75376	OTTHUMG00000059309	ENST00000268712.3:c.2224A>G	17.37:g.16005030T>C	ENSP00000268712:p.Thr742Ala	93.0	0.0	0		96.0	41.0	0.427083	NM_001190440	B3DLF8|E9PGV6|Q86YY0|Q9UPV5|Q9UQ18	Missense_Mutation	SNP	ENST00000268712.3	37	CCDS11175.1	.	.	.	.	.	.	.	.	.	.	T	7.122	0.578209	0.13686	2.27E-4	0.0	ENSG00000141027	ENST00000268712;ENST00000395851;ENST00000395849;ENST00000395848	T;T;T	0.27402	3.47;1.67;1.67	5.77	-10.8	0.00216	.	0.521213	0.24063	N	0.041899	T	0.08313	0.0207	N	0.08118	0	0.80722	D	1	B;B;B	0.02656	0.0;0.0;0.0	B;B;B	0.04013	0.001;0.0;0.0	T	0.25187	-1.0139	10	0.27082	T	0.32	0.119	4.1227	0.10112	0.1739:0.4619:0.1847:0.1796	.	649;742;758	E9PGV6;O75376;O75376-2	.;NCOR1_HUMAN;.	A	742;758;649;649	ENSP00000268712:T742A;ENSP00000379192:T758A;ENSP00000379189:T649A	ENSP00000268712:T742A	T	-	1	0	NCOR1	15945755	0.008000	0.16893	0.027000	0.17364	0.990000	0.78478	-0.887000	0.04152	-1.821000	0.01213	-0.290000	0.09829	ACT	T|1.000;C|0.000	0.000	weak		0.483	NCOR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000131751.5	NM_006311	
ZIM2	23619	hgsc.bcm.edu	37	19	57286688	57286688	+	Missense_Mutation	SNP	G	G	A			TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr19:57286688G>A	ENST00000391708.3	-	12	1494	c.952C>T	c.(952-954)Ccc>Tcc	p.P318S	ZIM2_ENST00000599935.1_Missense_Mutation_p.P318S|ZIM2_ENST00000221722.5_Missense_Mutation_p.P318S|ZIM2_ENST00000593711.1_Missense_Mutation_p.P318S|ZIM2_ENST00000601070.1_Missense_Mutation_p.P318S|AC006115.3_ENST00000595954.1_RNA|AC006115.3_ENST00000594400.1_RNA|AC006115.3_ENST00000597946.1_RNA	NM_001146326.1|NM_001146327.1	NP_001139798.1|NP_001139799.1	Q9NZV7	ZIM2_HUMAN	zinc finger, imprinted 2	318					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)			NS(1)|breast(1)|endometrium(1)|kidney(1)|large_intestine(10)|lung(20)|ovary(3)|prostate(2)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	44		Colorectal(82;0.000256)|all_neural(62;0.103)|Ovarian(87;0.243)		GBM - Glioblastoma multiforme(193;0.0314)		GCTGACTGGGGACTCGTACAT	0.448																																					p.P318S		Atlas-SNP	.											ZIM2,NS,malignant_melanoma,+1,1	ZIM2	511	1	0			c.C952T						PASS	.						136.0	126.0	130.0					19																	57286688		2203	4300	6503	SO:0001583	missense	23619	exon11			ACTGGGGACTCGT	AF166122	CCDS33123.1	19q13.4	2012-10-31				ENSG00000269699		"""Zinc fingers, C2H2-type"""	12875	protein-coding gene	gene with protein product							Standard	NM_015363		Approved	ZNF656		Q9NZV7		ENST00000391708.3:c.952C>T	19.37:g.57286688G>A	ENSP00000375589:p.Pro318Ser	268.0	0.0	0		310.0	149.0	0.480645	NM_015363	Q2M3K1	Missense_Mutation	SNP	ENST00000391708.3	37	CCDS33123.1	.	.	.	.	.	.	.	.	.	.	G	5.759	0.324523	0.10900	.	.	ENSG00000198300	ENST00000391708;ENST00000221722	T;T	0.05081	3.5;3.5	3.89	-0.711	0.11230	.	.	.	.	.	T	0.02970	0.0088	N	0.08118	0	.	.	.	B	0.23058	0.079	B	0.18263	0.021	T	0.39354	-0.9618	8	0.87932	D	0	.	3.4921	0.07641	0.3462:0.1968:0.4569:0.0	.	318	Q9NZV7	ZIM2_HUMAN	S	318	ENSP00000375589:P318S;ENSP00000221722:P318S	ENSP00000221722:P318S	P	-	1	0	ZIM2	61978500	.	.	0.000000	0.03702	0.211000	0.24417	.	.	-0.024000	0.13941	0.655000	0.94253	CCC	.	.	none		0.448	ZIM2-202	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000416094.2		
SCTR	6344	hgsc.bcm.edu	37	2	120194680	120194680	+	IGR	SNP	C	C	G	rs72833259	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr2:120194680C>G	ENST00000019103.5	-	0	1865				TMEM37_ENST00000465296.1_3'UTR|TMEM37_ENST00000409826.1_Silent_p.A91A|TMEM37_ENST00000306406.4_Silent_p.A79A	NM_002980.2	NP_002971.2	P47872	SCTR_HUMAN	secretin receptor						digestion (GO:0007586)|excretion (GO:0007588)|G-protein coupled receptor signaling pathway (GO:0007186)	cytoplasmic microtubule (GO:0005881)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	secretin receptor activity (GO:0015055)			central_nervous_system(2)|endometrium(1)|kidney(1)|large_intestine(3)|lung(7)|ovary(1)|prostate(1)|skin(3)	19					Secretin(DB00021)	TGGGCCAGGCCCATGTGCCCG	0.667													C|||	71	0.0141773	0.003	0.0144	5008	,	,		14497	0.001		0.0209	False		,,,				2504	0.0358				p.A79A		Atlas-SNP	.											.	TMEM37	40	.	0			c.C237G						PASS	.	C		21,4383	28.1+/-56.4	0,21,2181	50.0	53.0	52.0		237	1.8	0.0	2	dbSNP_130	52	234,8366	95.2+/-157.0	2,230,4068	no	coding-synonymous	TMEM37	NM_183240.2		2,251,6249	GG,GC,CC		2.7209,0.4768,1.9609		79/191	120194680	255,12749	2202	4300	6502	SO:0001628	intergenic_variant	140738	exon2			CCAGGCCCATGTG		CCDS2127.1	2q14.1	2012-08-10			ENSG00000080293	ENSG00000080293		"""GPCR / Class B : Glucagon receptors"""	10608	protein-coding gene	gene with protein product		182098				1646711	Standard	NM_002980		Approved		uc002tma.3	P47872	OTTHUMG00000131407		2.37:g.120194680C>G		35.0	0.0	0		42.0	27.0	0.642857	NM_183240	Q12961|Q13213|Q53T00	Silent	SNP	ENST00000019103.5	37	CCDS2127.1																																																																																			C|0.983;G|0.017	0.017	strong		0.667	SCTR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254198.2		
SEZ6L	23544	hgsc.bcm.edu	37	22	26693026	26693026	+	Missense_Mutation	SNP	C	C	A	rs146559583	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr22:26693026C>A	ENST00000248933.6	+	4	1237	c.1142C>A	c.(1141-1143)aCc>aAc	p.T381N	SEZ6L_ENST00000404234.3_Missense_Mutation_p.T381N|SEZ6L_ENST00000360929.3_Missense_Mutation_p.T381N|SEZ6L_ENST00000403121.1_Missense_Mutation_p.T154N|SEZ6L_ENST00000402979.1_Missense_Mutation_p.T154N|SEZ6L_ENST00000343706.4_Missense_Mutation_p.T381N|SEZ6L_ENST00000529632.2_Missense_Mutation_p.T381N			Q9BYH1	SE6L1_HUMAN	seizure related 6 homolog (mouse)-like	381	CUB 1. {ECO:0000255|PROSITE- ProRule:PRU00059}.				adult locomotory behavior (GO:0008344)|cerebellar Purkinje cell layer development (GO:0021680)|regulation of protein kinase C signaling (GO:0090036)|synapse maturation (GO:0060074)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|neuronal cell body (GO:0043025)				breast(1)|central_nervous_system(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(18)|lung(35)|ovary(4)|pancreas(1)|prostate(3)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)	80						GGCCTTGGGACCTTCCAGCTT	0.542																																					p.T381N		Atlas-SNP	.											.	SEZ6L	174	.	0			c.C1142A						PASS	.	C	ASN/THR,ASN/THR,ASN/THR,ASN/THR,ASN/THR,ASN/THR	0,4406		0,0,2203	41.0	37.0	38.0		1142,1142,1142,1142,1142,1142	1.7	0.9	22	dbSNP_134	38	6,8594	4.3+/-15.6	0,6,4294	yes	missense,missense,missense,missense,missense,missense	SEZ6L	NM_001184773.1,NM_001184774.1,NM_001184775.1,NM_001184776.1,NM_001184777.1,NM_021115.4	65,65,65,65,65,65	0,6,6497	AA,AC,CC		0.0698,0.0,0.0461	probably-damaging,probably-damaging,probably-damaging,probably-damaging,probably-damaging,probably-damaging	381/1024,381/1014,381/1012,381/950,381/949,381/1025	26693026	6,13000	2203	4300	6503	SO:0001583	missense	23544	exon4			TTGGGACCTTCCA	AL050253	CCDS13833.1, CCDS54508.1, CCDS54510.1, CCDS54511.1, CCDS74837.1	22q12.1	2008-05-14	2001-11-28		ENSG00000100095	ENSG00000100095			10763	protein-coding gene	gene with protein product		607021	"""seizure related gene 6 (mouse)-like"""				Standard	NM_021115		Approved		uc003acb.3	Q9BYH1	OTTHUMG00000150870	ENST00000248933.6:c.1142C>A	22.37:g.26693026C>A	ENSP00000248933:p.Thr381Asn	109.0	0.0	0		107.0	48.0	0.448598	NM_001184777	A0AUW7|B0QYG4|B0QYG5|B7ZLJ6|G8JLP3|O95917|Q5THY5|Q6IBZ4|Q6UXD4|Q9NUI3|Q9NUI4|Q9NUI5|Q9Y2E1|Q9Y3J6	Missense_Mutation	SNP	ENST00000248933.6	37	CCDS13833.1	.	.	.	.	.	.	.	.	.	.	C	12.94	2.088478	0.36855	0.0	6.98E-4	ENSG00000100095	ENST00000404234;ENST00000529632;ENST00000360929;ENST00000248933;ENST00000343706;ENST00000403121;ENST00000402979	T;T;T;T;T;T;T	0.18016	2.24;2.24;2.24;2.24;2.24;2.24;2.24	5.13	1.7	0.24286	CUB (5);	0.214517	0.31071	N	0.008302	T	0.16128	0.0388	L	0.55481	1.735	0.80722	D	1	B;B;B;B;B;B;B	0.23990	0.033;0.075;0.016;0.061;0.095;0.034;0.044	B;B;B;B;B;B;B	0.24848	0.03;0.056;0.016;0.033;0.038;0.022;0.056	T	0.05468	-1.0883	10	0.34782	T	0.22	.	10.0647	0.42297	0.2781:0.5879:0.134:0.0	.	381;381;154;381;381;381;381	B7ZLJ8;B7ZLJ6;B0QYH4;Q9BYH1-5;Q9BYH1-4;B0QYG3;Q9BYH1	.;.;.;.;.;.;SE6L1_HUMAN	N	381;381;381;381;381;154;154	ENSP00000384772:T381N;ENSP00000437037:T381N;ENSP00000354185:T381N;ENSP00000248933:T381N;ENSP00000342661:T381N;ENSP00000384838:T154N;ENSP00000384733:T154N	ENSP00000248933:T381N	T	+	2	0	SEZ6L	25023026	0.954000	0.32549	0.916000	0.36221	0.995000	0.86356	1.759000	0.38420	0.139000	0.18822	0.561000	0.74099	ACC	C|1.000;A|0.000	0.000	strong		0.542	SEZ6L-005	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000320359.3		
ZNF638	27332	hgsc.bcm.edu	37	2	71650236	71650236	+	Missense_Mutation	SNP	T	T	C	rs79157966	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr2:71650236T>C	ENST00000409544.1	+	22	4222	c.3592T>C	c.(3592-3594)Tgt>Cgt	p.C1198R	ZNF638_ENST00000355812.3_Intron|ZNF638_ENST00000264447.4_Missense_Mutation_p.C1198R|ZNF638_ENST00000409407.1_Missense_Mutation_p.C138R	NM_001252612.1	NP_001239541.1	Q14966	ZN638_HUMAN	zinc finger protein 638	1198	Glu-rich.				regulation of transcription, DNA-templated (GO:0006355)|RNA splicing (GO:0008380)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|intracellular membrane-bounded organelle (GO:0043231)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	double-stranded DNA binding (GO:0003690)|nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)|zinc ion binding (GO:0008270)			breast(4)|central_nervous_system(1)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(16)|lung(28)|ovary(2)|pancreas(2)|prostate(1)|skin(2)|urinary_tract(1)	63						TGCCGAGGAGTGTGCTTTAAA	0.408													T|||	9	0.00179712	0.0	0.0014	5008	,	,		19971	0.0		0.008	False		,,,				2504	0.0				p.C1198R		Atlas-SNP	.											.	ZNF638	179	.	0			c.T3592C						PASS	.	T	ARG/CYS,ARG/CYS	4,4402	8.1+/-20.4	0,4,2199	96.0	96.0	96.0		3592,3592	4.4	1.0	2	dbSNP_131	96	74,8526	44.5+/-102.8	0,74,4226	yes	missense,missense	ZNF638	NM_001014972.1,NM_014497.3	180,180	0,78,6425	CC,CT,TT		0.8605,0.0908,0.5997	benign,benign	1198/1979,1198/1979	71650236	78,12928	2203	4300	6503	SO:0001583	missense	27332	exon22			GAGGAGTGTGCTT	D83032	CCDS1917.1	2p13.1	2013-02-12	2004-07-29	2004-07-30	ENSG00000075292	ENSG00000075292		"""RNA binding motif (RRM) containing"""	17894	protein-coding gene	gene with protein product		614349	"""zinc finger, matrin-like"""	ZFML		8647861	Standard	NM_014497		Approved	NP220, MGC26130, Zfp638	uc002shy.3	Q14966	OTTHUMG00000129735	ENST00000409544.1:c.3592T>C	2.37:g.71650236T>C	ENSP00000386433:p.Cys1198Arg	99.0	0.0	0		101.0	59.0	0.584158	NM_014497	B5MDV1|B7ZLD1|Q53R34|Q5XJ05|Q68DP3|Q6P2H2|Q7Z3T7|Q8NF92|Q8TCA1|Q9H2G1|Q9NP37	Missense_Mutation	SNP	ENST00000409544.1	37	CCDS1917.1	7	0.003205128205128205	0	0.0	1	0.0027624309392265192	0	0.0	6	0.0079155672823219	T	9.920	1.211800	0.22289	9.08E-4	0.008605	ENSG00000075292	ENST00000394137;ENST00000264447;ENST00000409544;ENST00000409407;ENST00000462695	T;T;T	0.30182	1.54;1.54;1.82	5.55	4.36	0.52297	.	0.556954	0.16511	N	0.211226	T	0.12305	0.0299	N	0.24115	0.695	0.80722	D	1	B;B;B	0.29432	0.244;0.144;0.089	B;B;B	0.21151	0.032;0.033;0.032	T	0.05209	-1.0899	10	0.15499	T	0.54	-1.0544	8.8782	0.35358	0.1665:0.0:0.0:0.8335	.	1198;1198;1198	A8K583;Q14966-3;Q14966	.;.;ZN638_HUMAN	R	777;1198;1198;138;138	ENSP00000264447:C1198R;ENSP00000386433:C1198R;ENSP00000386813:C138R	ENSP00000264447:C1198R	C	+	1	0	ZNF638	71503744	0.997000	0.39634	0.998000	0.56505	0.476000	0.33039	1.649000	0.37281	0.991000	0.38814	0.533000	0.62120	TGT	T|0.994;C|0.006	0.006	strong		0.408	ZNF638-002	NOVEL	alternative_5_UTR|basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000327431.1	NM_014497	
ERN1	2081	hgsc.bcm.edu	37	17	62132160	62132160	+	Silent	SNP	C	C	T	rs55653398	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr17:62132160C>T	ENST00000433197.3	-	14	1796	c.1701G>A	c.(1699-1701)ggG>ggA	p.G567G		NM_001433.3	NP_001424.3			endoplasmic reticulum to nucleus signaling 1											central_nervous_system(4)|kidney(1)|lung(2)|ovary(1)|stomach(1)	9						AGGAAATTTTCCCAACTATCA	0.488													C|||	59	0.0117812	0.0015	0.0072	5008	,	,		21939	0.0		0.0169	False		,,,				2504	0.0358				p.G567G		Atlas-SNP	.											.	ERN1	102	.	0			c.G1701A						PASS	.	C		15,4003		0,15,1994	52.0	53.0	53.0		1701	1.1	0.9	17	dbSNP_129	53	191,8155		4,183,3986	no	coding-synonymous	ERN1	NM_001433.3		4,198,5980	TT,TC,CC		2.2885,0.3733,1.6661		567/978	62132160	206,12158	2009	4173	6182	SO:0001819	synonymous_variant	2081	exon14			AATTTTCCCAACT	AF059198	CCDS45762.1	17q23	2011-08-12	2007-08-14			ENSG00000178607			3449	protein-coding gene	gene with protein product	"""inositol-requiring enzyme 1"""	604033	"""ER to nucleus signalling 1"""			9637683	Standard	NM_001433		Approved	IRE1, IRE1P	uc002jdz.2	O75460		ENST00000433197.3:c.1701G>A	17.37:g.62132160C>T		57.0	0.0	0		41.0	21.0	0.512195	NM_001433		Silent	SNP	ENST00000433197.3	37	CCDS45762.1																																																																																			C|0.988;T|0.012	0.012	strong		0.488	ERN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000443734.2	NM_001433	
MTMR6	9107	hgsc.bcm.edu	37	13	25831928	25831928	+	Silent	SNP	C	C	T	rs186466011	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr13:25831928C>T	ENST00000381801.5	-	8	1676	c.915G>A	c.(913-915)tcG>tcA	p.S305S	MTMR6_ENST00000482345.1_5'Flank|MTMR6_ENST00000540661.1_Silent_p.S305S	NM_004685.3	NP_004676.3	Q9Y217	MTMR6_HUMAN	myotubularin related protein 6	305	Myotubularin phosphatase. {ECO:0000255|PROSITE-ProRule:PRU00669}.				peptidyl-tyrosine dephosphorylation (GO:0035335)|phosphatidylinositol biosynthetic process (GO:0006661)|phospholipid metabolic process (GO:0006644)|potassium ion transmembrane transport (GO:0071805)|protein dephosphorylation (GO:0006470)|small molecule metabolic process (GO:0044281)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleus (GO:0005634)	calcium-activated potassium channel activity (GO:0015269)|protein serine/threonine phosphatase activity (GO:0004722)|protein tyrosine phosphatase activity (GO:0004725)			breast(2)|endometrium(3)|kidney(3)|large_intestine(5)|lung(12)|ovary(2)|prostate(1)|skin(5)|stomach(3)	36		Lung SC(185;0.0225)|Breast(139;0.0351)		all cancers(112;0.00927)|Epithelial(112;0.0474)|OV - Ovarian serous cystadenocarcinoma(117;0.164)		GAAGCCATCCCGAGCTCTCCA	0.383													C|||	2	0.000399361	0.0	0.0014	5008	,	,		16484	0.0		0.001	False		,,,				2504	0.0				p.S305S		Atlas-SNP	.											.	MTMR6	75	.	0			c.G915A						PASS	.	C		0,4406		0,0,2203	70.0	75.0	74.0		915	-5.6	0.3	13		74	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous	MTMR6	NM_004685.3		0,1,6502	TT,TC,CC		0.0116,0.0,0.0077		305/622	25831928	1,13005	2203	4300	6503	SO:0001819	synonymous_variant	9107	exon8			CCATCCCGAGCTC	AF072928	CCDS9313.1	13q12	2011-06-09			ENSG00000139505	ENSG00000139505		"""Protein tyrosine phosphatases / Class I Cys-based PTPs : Myotubularins"""	7453	protein-coding gene	gene with protein product		603561				9736772	Standard	NM_004685		Approved		uc001uqf.4	Q9Y217	OTTHUMG00000016606	ENST00000381801.5:c.915G>A	13.37:g.25831928C>T		56.0	0.0	0		42.0	23.0	0.547619	NM_004685	B2RBB5|B3KSB4|Q5JRG6|Q86TB7|Q86YH4|Q96P80	Silent	SNP	ENST00000381801.5	37	CCDS9313.1																																																																																			C|1.000;T|0.000	0.000	strong		0.383	MTMR6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044225.1	NM_004685	
FANCM	57697	hgsc.bcm.edu	37	14	45665434	45665434	+	Silent	SNP	A	A	G			TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr14:45665434A>G	ENST00000267430.5	+	21	5485	c.5400A>G	c.(5398-5400)ccA>ccG	p.P1800P	FANCM_ENST00000542564.2_Silent_p.P1774P	NM_020937.2	NP_065988.1	Q8IYD8	FANCM_HUMAN	Fanconi anemia, complementation group M	1800	Interaction with FAAP24 and EME1.				DNA repair (GO:0006281)|replication fork processing (GO:0031297)|resolution of meiotic recombination intermediates (GO:0000712)	FANCM-MHF complex (GO:0071821)|Fanconi anaemia nuclear complex (GO:0043240)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	ATP binding (GO:0005524)|chromatin binding (GO:0003682)|DNA binding (GO:0003677)|helicase activity (GO:0004386)|nuclease activity (GO:0004518)			breast(4)|central_nervous_system(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(18)|liver(2)|lung(31)|ovary(4)|prostate(2)|skin(1)|upper_aerodigestive_tract(6)|urinary_tract(1)	85						AGTCAAGACCACATTTAGCTG	0.433								Involved in tolerance or repair of DNA crosslinks	Fanconi Anemia																												p.P1800P		Atlas-SNP	.											.	FANCM	225	.	0			c.A5400G						PASS	.						137.0	134.0	135.0					14																	45665434		2203	4300	6503	SO:0001819	synonymous_variant	57697	exon21	Familial Cancer Database	Pancytopenia Dysmelia, FA (several complementation groups)	AAGACCACATTTA	AK001672	CCDS32070.1	14q21.3	2014-09-17	2005-09-01	2005-09-01		ENSG00000187790		"""Fanconi anemia, complementation groups"""	23168	protein-coding gene	gene with protein product		609644	"""KIAA1596"""	KIAA1596		10997877, 16116422	Standard	NM_020937		Approved	FAAP250	uc001wwd.4	Q8IYD8		ENST00000267430.5:c.5400A>G	14.37:g.45665434A>G		131.0	0.0	0		140.0	74.0	0.528571	NM_020937	B2RTQ9|Q3YFH9|Q8N9X6|Q9HCH6	Silent	SNP	ENST00000267430.5	37	CCDS32070.1	.	.	.	.	.	.	.	.	.	.	A	6.666	0.491392	0.12702	.	.	ENSG00000187790	ENST00000554809	.	.	.	5.39	1.43	0.22495	.	.	.	.	.	T	0.26195	0.0639	.	.	.	0.09310	N	1	.	.	.	.	.	.	T	0.24119	-1.0169	4	.	.	.	.	5.1811	0.15160	0.6463:0.0:0.0786:0.2751	.	.	.	.	A	768	.	.	T	+	1	0	FANCM	44735184	0.000000	0.05858	0.040000	0.18447	0.278000	0.26855	0.476000	0.22180	-0.008000	0.14320	0.460000	0.39030	ACA	.	.	none		0.433	FANCM-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000410474.1	XM_048128	
KLHL26	55295	hgsc.bcm.edu	37	19	18779113	18779113	+	Silent	SNP	C	C	T	rs17852385	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr19:18779113C>T	ENST00000300976.4	+	3	996	c.906C>T	c.(904-906)acC>acT	p.T302T	KLHL26_ENST00000599006.1_Intron	NM_018316.1	NP_060786.1	Q53HC5	KLH26_HUMAN	kelch-like family member 26	302										breast(1)|central_nervous_system(1)|kidney(1)|lung(10)|ovary(2)|prostate(1)|upper_aerodigestive_tract(1)	17						CTCCGCGCACCGCCGTGCGCT	0.657													C|||	81	0.0161741	0.003	0.0288	5008	,	,		16478	0.0		0.0477	False		,,,				2504	0.0092				p.T302T		Atlas-SNP	.											.	KLHL26	43	.	0			c.C906T						PASS	.	C		39,4351		0,39,2156	42.0	44.0	43.0		906	-10.1	0.0	19	dbSNP_123	43	461,8099		12,437,3831	no	coding-synonymous	KLHL26	NM_018316.1		12,476,5987	TT,TC,CC		5.3855,0.8884,3.861		302/616	18779113	500,12450	2195	4280	6475	SO:0001819	synonymous_variant	55295	exon3			GCGCACCGCCGTG		CCDS12384.1	19p13.11	2013-10-15	2013-02-22		ENSG00000167487	ENSG00000167487		"""Kelch-like"", ""BTB/POZ domain containing"""	25623	protein-coding gene	gene with protein product			"""kelch-like 26 (Drosophila)"""				Standard	XM_006722785		Approved		uc002njz.1	Q53HC5	OTTHUMG00000183114	ENST00000300976.4:c.906C>T	19.37:g.18779113C>T		30.0	0.0	0		37.0	25.0	0.675676	NM_018316	Q8TAP0|Q9NUX3	Silent	SNP	ENST00000300976.4	37	CCDS12384.1																																																																																			C|0.969;T|0.031	0.031	strong		0.657	KLHL26-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000465145.1	NM_018316	
LGMN	5641	hgsc.bcm.edu	37	14	93172903	93172903	+	Silent	SNP	C	C	T	rs143184687	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr14:93172903C>T	ENST00000393218.2	-	13	1453	c.1116G>A	c.(1114-1116)ccG>ccA	p.P372P	LGMN_ENST00000555699.1_Intron|LGMN_ENST00000557434.1_Intron|LGMN_ENST00000334869.4_Silent_p.P372P	NM_001008530.2	NP_001008530.1	Q99538	LGMN_HUMAN	legumain	372					antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|innate immune response (GO:0045087)|negative regulation of ERBB signaling pathway (GO:1901185)|negative regulation of multicellular organism growth (GO:0040015)|negative regulation of neuron apoptotic process (GO:0043524)|proteolysis (GO:0006508)|proteolysis involved in cellular protein catabolic process (GO:0051603)|receptor catabolic process (GO:0032801)|renal system process (GO:0003014)|response to acidic pH (GO:0010447)|small molecule metabolic process (GO:0044281)|steroid metabolic process (GO:0008202)|toll-like receptor signaling pathway (GO:0002224)|vitamin D metabolic process (GO:0042359)	apical part of cell (GO:0045177)|extracellular vesicular exosome (GO:0070062)|late endosome (GO:0005770)|lysosomal lumen (GO:0043202)|lysosome (GO:0005764)	cysteine-type endopeptidase activity (GO:0004197)|peptidase activity (GO:0008233)			endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(5)|lung(5)|skin(2)	18		all_cancers(154;0.0706)		COAD - Colon adenocarcinoma(157;0.224)		GCCCCGTGAGCGGGGCTCTCT	0.647													C|||	31	0.0061901	0.0008	0.0072	5008	,	,		17490	0.0		0.0229	False		,,,				2504	0.002				p.P372P		Atlas-SNP	.											.	LGMN	28	.	0			c.G1116A						PASS	.	C	,	18,4388	23.3+/-48.9	0,18,2185	45.0	46.0	46.0		1116,1116	-1.2	0.0	14	dbSNP_134	46	216,8384	92.1+/-154.2	0,216,4084	no	coding-synonymous,coding-synonymous	LGMN	NM_001008530.2,NM_005606.6	,	0,234,6269	TT,TC,CC		2.5116,0.4085,1.7992	,	372/434,372/434	93172903	234,12772	2203	4300	6503	SO:0001819	synonymous_variant	5641	exon12			CGTGAGCGGGGCT	D55696	CCDS9904.1	14q32.12	2011-04-08		2002-01-18	ENSG00000100600	ENSG00000100600			9472	protein-coding gene	gene with protein product		602620	"""protease, cysteine, 1 (legumain)"""	PRSC1		8893817, 9065484	Standard	NM_001008530		Approved	LGMN1	uc001yaw.3	Q99538		ENST00000393218.2:c.1116G>A	14.37:g.93172903C>T		85.0	0.0	0		129.0	74.0	0.573643	NM_005606	O00123|Q86TV2|Q86TV3|Q9BTY1	Silent	SNP	ENST00000393218.2	37	CCDS9904.1																																																																																			C|0.984;T|0.016	0.016	strong		0.647	LGMN-005	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000412288.1	NM_005606	
C19orf57	79173	hgsc.bcm.edu	37	19	14000196	14000196	+	Missense_Mutation	SNP	G	G	T	rs61732721	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr19:14000196G>T	ENST00000586783.1	-	5	1472	c.1473C>A	c.(1471-1473)gaC>gaA	p.D491E	C19orf57_ENST00000591586.1_Intron|C19orf57_ENST00000346736.2_Missense_Mutation_p.D491E|C19orf57_ENST00000454313.1_Missense_Mutation_p.D491E			Q0VDD7	CS057_HUMAN	chromosome 19 open reading frame 57	491				D -> E (in Ref. 2; AAI19720). {ECO:0000305}.	multicellular organismal development (GO:0007275)					breast(2)|kidney(1)|lung(3)|ovary(4)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)	14			OV - Ovarian serous cystadenocarcinoma(19;2e-21)			CCTGGAGAGGGTCGTCTGCTA	0.617													G|||	11	0.00219649	0.0	0.0029	5008	,	,		17053	0.0		0.008	False		,,,				2504	0.001				p.D491E		Atlas-SNP	.											.	C19orf57	34	.	0			c.C1473A						PASS	.	G	GLU/ASP	7,4399	12.9+/-30.5	0,7,2196	66.0	72.0	70.0		1473	1.3	0.0	19	dbSNP_129	70	85,8515	48.1+/-107.5	0,85,4215	yes	missense	C19orf57	NM_024323.3	45	0,92,6411	TT,TG,GG		0.9884,0.1589,0.7074	benign	491/638	14000196	92,12914	2203	4300	6503	SO:0001583	missense	79173	exon6			GAGAGGGTCGTCT	BC012945	CCDS12299.1	19p13.12	2012-10-26			ENSG00000132016	ENSG00000132016			28153	protein-coding gene	gene with protein product						8228263	Standard	NM_024323		Approved	MGC11271	uc002mxl.1	Q0VDD7	OTTHUMG00000181851	ENST00000586783.1:c.1473C>A	19.37:g.14000196G>T	ENSP00000465822:p.Asp491Glu	88.0	0.0	0		86.0	39.0	0.453488	NM_024323	Q13411|Q8N825|Q96D63|Q9BU49	Missense_Mutation	SNP	ENST00000586783.1	37		8	0.003663003663003663	0	0.0	1	0.0027624309392265192	0	0.0	7	0.009234828496042216	G	12.21	1.868899	0.32977	0.001589	0.009884	ENSG00000132016	ENST00000454313;ENST00000346736	T;T	0.52057	0.68;0.68	4.73	1.32	0.21799	.	1.305730	0.05407	N	0.541685	T	0.25382	0.0617	N	0.19112	0.55	0.09310	N	1	B;B	0.15473	0.013;0.013	B;B	0.21917	0.025;0.037	T	0.26121	-1.0112	10	0.41790	T	0.15	-2.8432	5.2907	0.15725	0.3744:0.0:0.6256:0.0	.	491;491	Q0VDD7-2;Q0VDD7	.;CS057_HUMAN	E	491	ENSP00000404382:D491E;ENSP00000254336:D491E	ENSP00000254336:D491E	D	-	3	2	C19orf57	13861196	0.007000	0.16637	0.003000	0.11579	0.014000	0.08584	0.845000	0.27668	0.599000	0.29845	0.637000	0.83480	GAC	G|0.996;T|0.004	0.004	strong		0.617	C19orf57-003	NOVEL	basic	protein_coding	protein_coding	OTTHUMT00000457947.1	NM_024323	
ITLN2	142683	hgsc.bcm.edu	37	1	160922421	160922421	+	Missense_Mutation	SNP	T	T	G	rs145457015	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr1:160922421T>G	ENST00000368029.3	-	3	239	c.182A>C	c.(181-183)cAt>cCt	p.H61P	ITLN2_ENST00000494442.1_5'Flank|RP11-544M22.1_ENST00000356006.3_RNA	NM_080878.2	NP_543154.1	Q8WWU7	ITLN2_HUMAN	intelectin 2	61	Fibrinogen C-terminal. {ECO:0000255|PROSITE-ProRule:PRU00739}.					extracellular region (GO:0005576)	carbohydrate binding (GO:0030246)			endometrium(4)|large_intestine(4)|lung(5)|ovary(1)|pancreas(1)|skin(2)|stomach(1)|urinary_tract(1)	19	all_cancers(52;2.99e-17)|all_hematologic(112;0.093)		BRCA - Breast invasive adenocarcinoma(70;0.00275)			ACCTGCACTATGGCAGCGTTC	0.483													T|||	44	0.00878594	0.0	0.0029	5008	,	,		21066	0.0		0.0	False		,,,				2504	0.0429				p.H61P		Atlas-SNP	.											.	ITLN2	35	.	0			c.A182C						PASS	.	T	PRO/HIS	5,4401	9.9+/-24.2	0,5,2198	101.0	95.0	97.0		182	-7.9	0.0	1	dbSNP_134	97	17,8583	11.9+/-42.8	0,17,4283	yes	missense	ITLN2	NM_080878.2	77	0,22,6481	GG,GT,TT		0.1977,0.1135,0.1692	benign	61/326	160922421	22,12984	2203	4300	6503	SO:0001583	missense	142683	exon3			GCACTATGGCAGC	AY065973	CCDS1212.1	1q22-q23.5	2013-02-06			ENSG00000158764	ENSG00000158764		"""Fibrinogen C domain containing"""	20599	protein-coding gene	gene with protein product		609874				11181563	Standard	NM_080878		Approved	HL-2	uc001fxd.3	Q8WWU7	OTTHUMG00000028605	ENST00000368029.3:c.182A>C	1.37:g.160922421T>G	ENSP00000357008:p.His61Pro	67.0	0.0	0		67.0	30.0	0.447761	NM_080878	Q17RR2|Q5VYI0	Missense_Mutation	SNP	ENST00000368029.3	37	CCDS1212.1	1	4.578754578754579E-4	0	0.0	1	0.0027624309392265192	0	0.0	0	0.0	T	3.839	-0.034106	0.07543	0.001135	0.001977	ENSG00000158764	ENST00000368029	D	0.91631	-2.88	3.95	-7.9	0.01169	Fibrinogen, alpha/beta/gamma chain, C-terminal globular (4);Fibrinogen, alpha/beta/gamma chain, C-terminal globular, subdomain 1 (1);	1.289890	0.06467	N	0.730523	T	0.52549	0.1741	N	0.02181	-0.65	0.09310	N	1	B;B	0.02656	0.0;0.0	B;B	0.09377	0.004;0.004	T	0.57189	-0.7854	10	0.13470	T	0.59	0.3882	10.3753	0.44079	0.0:0.1869:0.1496:0.6635	.	60;61	A6NI51;Q8WWU7	.;ITLN2_HUMAN	P	61	ENSP00000357008:H61P	ENSP00000357008:H61P	H	-	2	0	ITLN2	159189045	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-6.326000	0.00070	-2.805000	0.00350	-0.396000	0.06452	CAT	T|0.999;G|0.001	0.001	strong		0.483	ITLN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000071465.1	NM_080878	
CLNK	116449	hgsc.bcm.edu	37	4	10586571	10586571	+	Missense_Mutation	SNP	G	G	A	rs61759824	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr4:10586571G>A	ENST00000226951.6	-	4	331	c.92C>T	c.(91-93)cCt>cTt	p.P31L	CLNK_ENST00000442825.2_5'UTR|CLNK_ENST00000507719.1_5'UTR	NM_052964.2	NP_443196.2	Q7Z7G1	CLNK_HUMAN	cytokine-dependent hematopoietic cell linker	31					immune response (GO:0006955)|intracellular signal transduction (GO:0035556)|positive regulation of signal transduction (GO:0009967)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)	intracellular (GO:0005622)	SH3/SH2 adaptor activity (GO:0005070)			NS(1)|endometrium(1)|large_intestine(5)|lung(9)|ovary(1)	17						ATTGATGCGAGGCCATGACCT	0.507													G|||	130	0.0259585	0.0091	0.0389	5008	,	,		16233	0.0		0.0567	False		,,,				2504	0.0348				p.P31L	GBM(87;402 1286 6949 13902 35851)	Atlas-SNP	.											.	CLNK	85	.	0			c.C92T						PASS	.	G	LEU/PRO	48,4018		1,46,1986	98.0	106.0	103.0		92	3.9	0.8	4	dbSNP_129	103	515,7829		15,485,3672	yes	missense	CLNK	NM_052964.2	98	16,531,5658	AA,AG,GG		6.1721,1.1805,4.5367	probably-damaging	31/429	10586571	563,11847	2033	4172	6205	SO:0001583	missense	116449	exon4			ATGCGAGGCCATG	AB032369	CCDS47024.1	4p16.1	2013-02-14			ENSG00000109684	ENSG00000109684		"""SH2 domain containing"""	17438	protein-coding gene	gene with protein product	"""mast cell immunoreceptor signal transducer"""	611434				10562326, 10744659	Standard	NM_052964		Approved	MIST	uc003gmo.4	Q7Z7G1	OTTHUMG00000160062	ENST00000226951.6:c.92C>T	4.37:g.10586571G>A	ENSP00000226951:p.Pro31Leu	50.0	0.0	0		45.0	20.0	0.444444	NM_052964	Q05C27|Q9P2U9	Missense_Mutation	SNP	ENST00000226951.6	37	CCDS47024.1	65	0.02976190476190476	7	0.014227642276422764	12	0.03314917127071823	0	0.0	46	0.06068601583113457	G	10.66	1.412027	0.25465	0.011805	0.061721	ENSG00000109684	ENST00000226951;ENST00000429087	T	0.26660	1.72	4.79	3.94	0.45596	.	0.000000	0.44902	D	0.000411	T	0.03477	0.0100	L	0.29908	0.895	0.80722	D	1	D	0.60160	0.987	P	0.55011	0.766	T	0.00389	-1.1770	10	0.87932	D	0	-2.6544	10.4696	0.44629	0.0:0.0:0.8061:0.1939	rs61759824	31	Q7Z7G1	CLNK_HUMAN	L	31	ENSP00000226951:P31L	ENSP00000226951:P31L	P	-	2	0	CLNK	10195669	0.974000	0.33945	0.843000	0.33291	0.044000	0.14063	1.881000	0.39638	1.357000	0.45904	0.563000	0.77884	CCT	G|0.967;A|0.033	0.033	strong		0.507	CLNK-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000359047.1	NM_052964	
PUS7	54517	hgsc.bcm.edu	37	7	105148683	105148683	+	Missense_Mutation	SNP	A	A	G	rs139058270	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr7:105148683A>G	ENST00000356362.2	-	2	491	c.277T>C	c.(277-279)Tgc>Cgc	p.C93R	PUS7_ENST00000469408.1_Missense_Mutation_p.C93R	NM_019042.3	NP_061915.2	Q96PZ0	PUS7_HUMAN	pseudouridylate synthase 7 (putative)	93					pseudouridine synthesis (GO:0001522)|tRNA processing (GO:0008033)		enzyme binding (GO:0019899)|poly(A) RNA binding (GO:0044822)|pseudouridine synthase activity (GO:0009982)			breast(1)|endometrium(2)|kidney(1)|large_intestine(9)|lung(8)|pancreas(1)|skin(1)	23						TCCTCCTCGCACTCCTCTGAA	0.493													A|||	8	0.00159744	0.0008	0.0014	5008	,	,		17461	0.0		0.006	False		,,,				2504	0.0				p.C93R	Colon(138;2387 3051 17860)	Atlas-SNP	.											.	PUS7	59	.	0			c.T277C						PASS	.	A	ARG/CYS	6,4400	11.4+/-27.6	0,6,2197	212.0	178.0	190.0		277	4.7	0.1	7	dbSNP_134	190	61,8539	38.3+/-94.2	0,61,4239	yes	missense	PUS7	NM_019042.3	180	0,67,6436	GG,GA,AA		0.7093,0.1362,0.5151	benign	93/662	105148683	67,12939	2203	4300	6503	SO:0001583	missense	54517	exon2			CCTCGCACTCCTC	AK128629	CCDS34725.1	7q22.3	2014-02-14	2014-02-14		ENSG00000091127	ENSG00000091127			26033	protein-coding gene	gene with protein product			"""pseudouridylate synthase 7 homolog (S. cerevisiae)"""			11572484	Standard	NM_019042		Approved	FLJ20485	uc003vcx.3	Q96PZ0	OTTHUMG00000157399	ENST00000356362.2:c.277T>C	7.37:g.105148683A>G	ENSP00000348722:p.Cys93Arg	246.0	0.0	0		244.0	112.0	0.459016	NM_019042	Q75MG4|Q9NX19	Missense_Mutation	SNP	ENST00000356362.2	37	CCDS34725.1	6	0.0027472527472527475	1	0.0020325203252032522	0	0.0	0	0.0	5	0.006596306068601583	A	1.729	-0.494708	0.04322	0.001362	0.007093	ENSG00000091127	ENST00000356362;ENST00000544995;ENST00000469408	T;T	0.39592	1.07;1.07	5.58	4.69	0.59074	.	0.706924	0.14641	N	0.307220	T	0.15089	0.0364	N	0.08118	0	0.29644	N	0.844509	B;B	0.12630	0.006;0.006	B;B	0.09377	0.004;0.004	T	0.16424	-1.0403	10	0.16420	T	0.52	-6.8005	8.3068	0.32047	0.1631:0.759:0.0:0.0779	.	93;93	B3KY42;Q96PZ0	.;PUS7_HUMAN	R	93	ENSP00000348722:C93R;ENSP00000417402:C93R	ENSP00000348722:C93R	C	-	1	0	PUS7	104935919	0.000000	0.05858	0.097000	0.21041	0.261000	0.26267	0.758000	0.26447	1.326000	0.45319	-0.648000	0.03929	TGC	A|0.995;G|0.005	0.005	strong		0.493	PUS7-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000348681.1	NM_019042	
BOK	666	hgsc.bcm.edu	37	2	242501828	242501828	+	Silent	SNP	C	C	T	rs145137590	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr2:242501828C>T	ENST00000318407.3	+	3	588	c.286C>T	c.(286-288)Ctg>Ttg	p.L96L		NM_032515.4	NP_115904.1	Q9UMX3	BOK_HUMAN	BCL2-related ovarian killer	96					activation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0006919)|apoptotic process (GO:0006915)|brain development (GO:0007420)|cell proliferation (GO:0008283)|extrinsic apoptotic signaling pathway in absence of ligand (GO:0097192)|intrinsic apoptotic signaling pathway by p53 class mediator (GO:0072332)|intrinsic apoptotic signaling pathway in response to DNA damage (GO:0008630)|male gonad development (GO:0008584)|neuron apoptotic process (GO:0051402)|oligodendrocyte differentiation (GO:0048709)|positive regulation of apoptotic process (GO:0043065)|positive regulation of execution phase of apoptosis (GO:1900119)	cytoplasm (GO:0005737)|mitochondrial membrane (GO:0031966)|mitochondrial outer membrane (GO:0005741)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)	p.L96L(1)		large_intestine(1)|lung(3)|ovary(1)	5		all_cancers(19;1.09e-40)|all_epithelial(40;2.03e-18)|Breast(86;1.53e-05)|all_lung(227;0.00338)|Renal(207;0.00502)|Ovarian(221;0.00716)|Lung NSC(271;0.012)|Esophageal squamous(248;0.129)|Melanoma(123;0.144)|all_hematologic(139;0.158)|all_neural(83;0.243)|Hepatocellular(293;0.244)		Epithelial(32;2.04e-33)|all cancers(36;7.87e-31)|OV - Ovarian serous cystadenocarcinoma(60;3.52e-15)|Kidney(56;3.04e-09)|KIRC - Kidney renal clear cell carcinoma(57;3.23e-08)|BRCA - Breast invasive adenocarcinoma(100;1.64e-06)|Lung(119;0.000152)|LUSC - Lung squamous cell carcinoma(224;0.00154)|Colorectal(34;0.0129)|COAD - Colon adenocarcinoma(134;0.0835)		GCACATCTCCCTGCAGTCTGA	0.637													C|||	11	0.00219649	0.0008	0.0029	5008	,	,		19434	0.0		0.008	False		,,,				2504	0.0				p.L96L		Atlas-SNP	.											BOK,NS,carcinoma,0,1	BOK	16	1	1	Substitution - coding silent(1)	lung(1)	c.C286T						PASS	.	C		12,4390	16.8+/-37.8	0,12,2189	116.0	85.0	95.0		286	5.0	1.0	2	dbSNP_134	95	75,8525	43.1+/-100.9	2,71,4227	no	coding-synonymous	BOK	NM_032515.4		2,83,6416	TT,TC,CC		0.8721,0.2726,0.6691		96/213	242501828	87,12915	2201	4300	6501	SO:0001819	synonymous_variant	666	exon3			ATCTCCCTGCAGT	AF174487	CCDS2550.1	2q37.3	2008-05-22			ENSG00000176720	ENSG00000176720			1087	protein-coding gene	gene with protein product		605404				9356461, 11034351, 15102863	Standard	NM_032515		Approved	BCL2L9, BOKL, MGC4631	uc002wbq.3	Q9UMX3	OTTHUMG00000133411	ENST00000318407.3:c.286C>T	2.37:g.242501828C>T		88.0	0.0	0		88.0	48.0	0.545455	NM_032515		Silent	SNP	ENST00000318407.3	37	CCDS2550.1																																																																																			C|0.995;T|0.005	0.005	strong		0.637	BOK-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257268.2	NM_032515	
COG3	83548	hgsc.bcm.edu	37	13	46099171	46099171	+	Missense_Mutation	SNP	C	C	T	rs144497765		TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr13:46099171C>T	ENST00000349995.5	+	20	2327	c.2215C>T	c.(2215-2217)Cct>Tct	p.P739S		NM_031431.3	NP_113619	Q96JB2	COG3_HUMAN	component of oligomeric golgi complex 3	739					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)		CTCACAGCAGCCTTGGGCACA	0.388													C|||	1	0.000199681	0.0	0.0	5008	,	,		18679	0.0		0.001	False		,,,				2504	0.0				p.P739S	Ovarian(150;1048 1859 18083 21577 42700)	Atlas-SNP	.											.	COG3	52	.	0			c.C2215T						PASS	.	C	SER/PRO	2,4404	4.2+/-10.8	0,2,2201	93.0	87.0	89.0		2215	5.2	1.0	13	dbSNP_134	89	9,8591	7.1+/-27.0	0,9,4291	yes	missense	COG3	NM_031431.3	74	0,11,6492	TT,TC,CC		0.1047,0.0454,0.0846	benign	739/829	46099171	11,12995	2203	4300	6503	SO:0001583	missense	83548	exon20			CAGCAGCCTTGGG	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.2215C>T	13.37:g.46099171C>T	ENSP00000258654:p.Pro739Ser	114.0	0.0	0		128.0	66.0	0.515625	NM_031431	B2RAW5|Q5VT70|Q8IXX4|Q9BZ92	Missense_Mutation	SNP	ENST00000349995.5	37	CCDS9398.1	1	4.578754578754579E-4	0	0.0	0	0.0	0	0.0	1	0.0013192612137203166	C	15.16	2.750401	0.49257	4.54E-4	0.001047	ENSG00000136152	ENST00000349995	T	0.54071	0.59	5.18	5.18	0.71444	.	0.000000	0.85682	D	0.000000	T	0.62720	0.2451	M	0.64997	1.995	0.80722	D	1	B;D	0.60575	0.264;0.988	B;P	0.54815	0.074;0.761	T	0.58352	-0.7651	10	0.20046	T	0.44	-11.7744	17.7148	0.88333	0.0:1.0:0.0:0.0	.	576;739	B4E2F3;Q96JB2	.;COG3_HUMAN	S	739	ENSP00000258654:P739S	ENSP00000258654:P739S	P	+	1	0	COG3	44997172	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.666000	0.83877	2.426000	0.82243	0.655000	0.94253	CCT	C|0.999;T|0.001	0.001	strong		0.388	COG3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044777.2		
CPVL	54504	hgsc.bcm.edu	37	7	29111950	29111950	+	Silent	SNP	A	A	G	rs62442642	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr7:29111950A>G	ENST00000409850.1	-	12	1345	c.699T>C	c.(697-699)atT>atC	p.I233I	CPVL_ENST00000265394.5_Silent_p.I233I|CPVL_ENST00000396276.3_Silent_p.I233I			Q9H3G5	CPVL_HUMAN	carboxypeptidase, vitellogenic-like	233						extracellular vesicular exosome (GO:0070062)	serine-type carboxypeptidase activity (GO:0004185)			NS(1)|breast(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(4)|lung(13)|ovary(2)|prostate(1)|skin(1)	28						CTCCAATAGCAATTCCGTTCA	0.438													A|||	15	0.00299521	0.0015	0.0058	5008	,	,		20173	0.001		0.007	False		,,,				2504	0.001				p.I233I		Atlas-SNP	.											.	CPVL	60	.	0			c.T699C						PASS	.	A	,	9,4397	15.5+/-35.6	0,9,2194	154.0	129.0	138.0		699,699	-3.6	0.9	7	dbSNP_129	138	58,8542	36.4+/-91.3	0,58,4242	no	coding-synonymous,coding-synonymous	CPVL	NM_019029.2,NM_031311.3	,	0,67,6436	GG,GA,AA		0.6744,0.2043,0.5151	,	233/477,233/477	29111950	67,12939	2203	4300	6503	SO:0001819	synonymous_variant	54504	exon8			AATAGCAATTCCG	AF106704	CCDS5419.1	7p15.1	2012-02-10			ENSG00000106066	ENSG00000106066			14399	protein-coding gene	gene with protein product	"""carboxypeptidase WUG"", ""vitellogenic carboxypeptidase-like protein"", ""CP-Mac carboxypeptidase"""	609780				11401439	Standard	XM_005249786		Approved		uc003szw.3	Q9H3G5	OTTHUMG00000023669	ENST00000409850.1:c.699T>C	7.37:g.29111950A>G		124.0	0.0	0		120.0	59.0	0.491667	NM_019029	A4D1A4|Q6UX20|Q8NBL7|Q96AR7|Q9HB41	Silent	SNP	ENST00000409850.1	37	CCDS5419.1																																																																																			A|0.995;G|0.005	0.005	strong		0.438	CPVL-009	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000328305.1	NM_019029	
TEKT4	150483	hgsc.bcm.edu	37	2	95537330	95537330	+	Silent	SNP	G	G	A	rs140196891	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr2:95537330G>A	ENST00000295201.4	+	1	143	c.6G>A	c.(4-6)gcG>gcA	p.A2A	AC097374.2_ENST00000568768.1_RNA|TEKT4_ENST00000427593.2_Silent_p.A2A	NM_144705.2	NP_653306.1	Q8WW24	TEKT4_HUMAN	tektin 4	2					cell projection organization (GO:0030030)	cytoplasm (GO:0005737)|microtubule (GO:0005874)|motile cilium (GO:0031514)|nucleus (GO:0005634)				NS(1)|breast(1)|endometrium(2)|kidney(2)|large_intestine(3)|lung(15)|ovary(1)|skin(2)|upper_aerodigestive_tract(1)	28						GCACCATGGCGCAGACAGTGC	0.697													.|||	17	0.00339457	0.0015	0.0043	5008	,	,		17151	0.0		0.007	False		,,,				2504	0.0051				p.A2A		Atlas-SNP	.											.	TEKT4	72	.	0			c.G6A						PASS	.	G		5,4261		0,5,2128	9.0	10.0	10.0		6	0.6	0.3	2	dbSNP_134	10	48,8290		0,48,4121	no	coding-synonymous	TEKT4	NM_144705.2		0,53,6249	AA,AG,GG		0.5757,0.1172,0.4205		2/436	95537330	53,12551	2133	4169	6302	SO:0001819	synonymous_variant	150483	exon1			CATGGCGCAGACA	AK097438	CCDS2005.1	2q11.2	2008-02-05			ENSG00000163060	ENSG00000163060			31012	protein-coding gene	gene with protein product							Standard	XM_005263876		Approved	MGC27019	uc002stw.1	Q8WW24	OTTHUMG00000130396	ENST00000295201.4:c.6G>A	2.37:g.95537330G>A		47.0	0.0	0		55.0	28.0	0.509091	NM_144705		Silent	SNP	ENST00000295201.4	37	CCDS2005.1																																																																																			G|0.995;A|0.005	0.005	strong		0.697	TEKT4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252777.1	NM_144705	
DUSP19	142679	hgsc.bcm.edu	37	2	183951888	183951888	+	Missense_Mutation	SNP	T	T	C			TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr2:183951888T>C	ENST00000354221.4	+	3	569	c.394T>C	c.(394-396)Tgt>Cgt	p.C132R	AC064871.3_ENST00000444562.1_RNA|DUSP19_ENST00000469344.1_3'UTR|DUSP19_ENST00000342619.6_Intron	NM_080876.3	NP_543152.1	Q8WTR2	DUS19_HUMAN	dual specificity phosphatase 19	132					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						TTTTCCAGAATGTTTTGAATT	0.343																																					p.C132R		Atlas-SNP	.											.	DUSP19	41	.	0			c.T394C						PASS	.						93.0	92.0	92.0					2																	183951888		2202	4299	6501	SO:0001583	missense	142679	exon3			CCAGAATGTTTTG	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.394T>C	2.37:g.183951888T>C	ENSP00000346160:p.Cys132Arg	70.0	0.0	0		63.0	34.0	0.539683	NM_080876	B2RA79|Q547H4|Q8WYN4	Missense_Mutation	SNP	ENST00000354221.4	37	CCDS2289.1	.	.	.	.	.	.	.	.	.	.	t	19.13	3.768014	0.69878	.	.	ENSG00000162999	ENST00000354221	T	0.60424	0.19	5.37	4.18	0.49190	Dual specificity phosphatase, catalytic domain (1);Dual specificity phosphatase, subgroup, catalytic domain (2);	0.082767	0.85682	D	0.000000	T	0.81432	0.4821	H	0.95079	3.62	0.80722	D	1	D	0.76494	0.999	D	0.77557	0.99	D	0.85083	0.0947	10	0.72032	D	0.01	.	11.6994	0.51562	0.1327:0.0:0.0:0.8673	.	132	Q8WTR2	DUS19_HUMAN	R	132	ENSP00000346160:C132R	ENSP00000346160:C132R	C	+	1	0	DUSP19	183660133	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	7.113000	0.77095	0.934000	0.37316	0.520000	0.50463	TGT	.	.	none		0.343	DUSP19-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255866.1		
RNF133	168433	hgsc.bcm.edu	37	7	122338664	122338664	+	Silent	SNP	T	T	C	rs373664210		TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr7:122338664T>C	ENST00000340112.2	-	1	546	c.309A>G	c.(307-309)gcA>gcG	p.A103A	CADPS2_ENST00000334010.7_Intron|CADPS2_ENST00000313070.7_Intron|CADPS2_ENST00000412584.2_Intron|CADPS2_ENST00000449022.2_Intron	NM_139175.1	NP_631914.1	Q8WVZ7	RN133_HUMAN	ring finger protein 133	103	PA.				protein autoubiquitination (GO:0051865)	endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)	ligase activity (GO:0016874)|zinc ion binding (GO:0008270)			NS(1)|biliary_tract(1)|breast(1)|central_nervous_system(1)|large_intestine(3)|lung(11)|ovary(1)|skin(1)|urinary_tract(1)	21						GTTCAATAAGTGCAAGCCAGG	0.458																																					p.A103A	Colon(198;1778 2057 7449 19869 45985)	Atlas-SNP	.											.	RNF133	41	.	0			c.A309G						PASS	.	T	,,,	0,4406		0,0,2203	155.0	165.0	162.0		,,,309	-5.2	0.7	7		162	2,8596	2.2+/-6.3	0,2,4297	no	intron,intron,intron,coding-synonymous	CADPS2,RNF133	NM_001009571.3,NM_001167940.1,NM_017954.10,NM_139175.1	,,,	0,2,6500	CC,CT,TT		0.0233,0.0,0.0154	,,,	,,,103/377	122338664	2,13002	2203	4299	6502	SO:0001819	synonymous_variant	168433	exon1			AATAAGTGCAAGC	AF447589	CCDS5784.1	7q31.33	2013-01-09			ENSG00000188050	ENSG00000188050		"""RING-type (C3HC4) zinc fingers"""	21154	protein-coding gene	gene with protein product							Standard	NM_139175		Approved		uc003vkj.1	Q8WVZ7	OTTHUMG00000157092	ENST00000340112.2:c.309A>G	7.37:g.122338664T>C		167.0	0.0	0		153.0	69.0	0.45098	NM_139175	A4D0W2|Q8N7G7	Silent	SNP	ENST00000340112.2	37	CCDS5784.1																																																																																			.	.	weak		0.458	RNF133-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347413.1	NM_139175	
TJP2	9414	hgsc.bcm.edu	37	9	71864319	71864319	+	Missense_Mutation	SNP	G	G	A	rs150494393		TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr9:71864319G>A	ENST00000377245.4	+	20	3117	c.2909G>A	c.(2908-2910)cGa>cAa	p.R970Q	TJP2_ENST00000535702.1_Intron|TJP2_ENST00000453658.2_Intron|TJP2_ENST00000348208.4_Intron|TJP2_ENST00000539225.1_Missense_Mutation_p.R1001Q	NM_004817.3	NP_004808.2	Q9UDY2	ZO2_HUMAN	tight junction protein 2	970					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						CCAGAGCCACGAGCTCAGATG	0.542																																					p.R1001Q		Atlas-SNP	.											TJP2,caecum,carcinoma,0,1	TJP2	120	1	0			c.G3002A						PASS	.	G	,,GLN/ARG,,GLN/ARG,	0,4406		0,0,2203	40.0	33.0	35.0		,,3002,,2909,	3.0	1.0	9	dbSNP_134	35	2,8598	2.2+/-6.3	0,2,4298	no	intron,intron,missense,utr-3,missense,intron	TJP2	NM_001170414.1,NM_001170415.1,NM_001170416.1,NM_001170630.1,NM_004817.3,NM_201629.3	,,43,,43,	0,2,6501	AA,AG,GG		0.0233,0.0,0.0154	,,probably-damaging,,probably-damaging,	,,1001/1222,,970/1191,	71864319	2,13004	2203	4300	6503	SO:0001583	missense	9414	exon20			AGCCACGAGCTCA	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.2909G>A	9.37:g.71864319G>A	ENSP00000366453:p.Arg970Gln	78.0	0.0	0		103.0	70.0	0.679612	NM_001170416	A2A3H9|B7Z2R8|B7Z7T6|F5H301|F5H886|Q15883|Q5VXL0|Q5VXL1|Q8N756|Q8NI14|Q99839|Q9UDY0|Q9UDY1	Missense_Mutation	SNP	ENST00000377245.4	37	CCDS6627.1	.	.	.	.	.	.	.	.	.	.	G	17.44	3.390626	0.62066	0.0	2.33E-4	ENSG00000119139	ENST00000377245;ENST00000539225	T;T	0.09350	2.99;3.03	5.82	2.96	0.34315	.	0.136502	0.47093	N	0.000255	T	0.17152	0.0412	L	0.53249	1.67	0.80722	D	1	D;D	0.67145	0.996;0.985	P;P	0.55871	0.786;0.638	T	0.07424	-1.0773	10	0.16896	T	0.51	.	9.3062	0.37876	0.1309:0.1201:0.749:0.0	.	1001;970	F5H301;Q9UDY2	.;ZO2_HUMAN	Q	970;1001	ENSP00000366453:R970Q;ENSP00000438262:R1001Q	ENSP00000366453:R970Q	R	+	2	0	TJP2	71054139	1.000000	0.71417	0.968000	0.41197	0.993000	0.82548	1.825000	0.39081	0.363000	0.24346	0.563000	0.77884	CGA	G|1.000;A|0.000	0.000	weak		0.542	TJP2-003	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000052572.2	NM_201629	
MAMDC4	158056	hgsc.bcm.edu	37	9	139748690	139748690	+	Missense_Mutation	SNP	A	A	G	rs151266186	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr9:139748690A>G	ENST00000317446.2	+	7	748	c.698A>G	c.(697-699)cAc>cGc	p.H233R	MAMDC4_ENST00000485732.1_3'UTR|MAMDC4_ENST00000445819.1_Missense_Mutation_p.H233R	NM_206920.2	NP_996803.2			MAM domain containing 4											breast(4)|central_nervous_system(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(1)|lung(4)|pancreas(1)|prostate(2)|upper_aerodigestive_tract(2)	19	all_cancers(76;0.0763)|all_epithelial(76;0.198)	Myeloproliferative disorder(178;0.0511)		OV - Ovarian serous cystadenocarcinoma(145;1.52e-05)|Epithelial(140;0.000171)		CCCCCGGGACACCACCACTGC	0.657													A|||	2	0.000399361	0.0	0.0	5008	,	,		13727	0.0		0.002	False		,,,				2504	0.0				p.H233R		Atlas-SNP	.											.	MAMDC4	117	.	0			c.A698G						PASS	.	A	ARG/HIS	1,4379		0,1,2189	24.0	26.0	25.0		698	4.3	0.0	9	dbSNP_134	25	14,8574		0,14,4280	yes	missense	MAMDC4	NM_206920.2	29	0,15,6469	GG,GA,AA		0.163,0.0228,0.1157	probably-damaging	233/1138	139748690	15,12953	2190	4294	6484	SO:0001583	missense	158056	exon7			CGGGACACCACCA	AL834531	CCDS7010.1	9q34.3	2013-10-21			ENSG00000177943	ENSG00000177943			24083	protein-coding gene	gene with protein product	"""apical early endosomal glycoprotein precursor"", ""endotubin"""					7829488	Standard	NM_206920		Approved	AEGP, DKFZp434M1411	uc004cjs.3	Q6UXC1	OTTHUMG00000020951	ENST00000317446.2:c.698A>G	9.37:g.139748690A>G	ENSP00000319388:p.His233Arg	109.0	0.0	0		95.0	34.0	0.357895	NM_206920		Missense_Mutation	SNP	ENST00000317446.2	37	CCDS7010.1	2	9.157509157509158E-4	0	0.0	0	0.0	0	0.0	2	0.002638522427440633	.	8.328	0.825771	0.16749	2.28E-4	0.00163	ENSG00000177943	ENST00000317446;ENST00000445819	D;D	0.95272	-3.66;-3.66	4.34	4.34	0.51931	.	0.426385	0.21311	N	0.076630	D	0.91236	0.7238	L	0.48935	1.535	0.09310	N	1	B	0.28636	0.218	B	0.31101	0.124	T	0.82218	-0.0566	10	0.25106	T	0.35	-8.7896	12.4851	0.55868	1.0:0.0:0.0:0.0	.	233	Q6UXC1-2	.	R	233	ENSP00000319388:H233R;ENSP00000411339:H233R	ENSP00000319388:H233R	H	+	2	0	MAMDC4	138868511	0.004000	0.15560	0.013000	0.15412	0.461000	0.32589	1.047000	0.30367	1.818000	0.53035	0.459000	0.35465	CAC	A|0.999;G|0.001	0.001	strong		0.657	MAMDC4-005	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000254642.3	NM_206920	
RNF165	494470	hgsc.bcm.edu	37	18	44015315	44015315	+	Silent	SNP	A	A	G	rs139779598	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr18:44015315A>G	ENST00000269439.7	+	3	492	c.441A>G	c.(439-441)caA>caG	p.Q147Q	RNF165_ENST00000543885.1_Intron	NM_152470.2	NP_689683.2	Q6ZSG1	RN165_HUMAN	ring finger protein 165	147							zinc ion binding (GO:0008270)			NS(1)|large_intestine(4)|lung(6)	11				READ - Rectum adenocarcinoma(1;0.0873)		ACTTCGGCCAACTGCAGACAC	0.642													A|||	30	0.00599042	0.0008	0.0159	5008	,	,		17217	0.0		0.0159	False		,,,				2504	0.002				p.Q147Q		Atlas-SNP	.											.	RNF165	34	.	0			c.A441G						PASS	.	A		9,4397	15.5+/-35.6	0,9,2194	63.0	54.0	57.0		441	5.7	1.0	18	dbSNP_134	57	93,8507	52.3+/-112.8	0,93,4207	no	coding-synonymous	RNF165	NM_152470.2		0,102,6401	GG,GA,AA		1.0814,0.2043,0.7843		147/347	44015315	102,12904	2203	4300	6503	SO:0001819	synonymous_variant	494470	exon3			CGGCCAACTGCAG	BC012190	CCDS32823.1, CCDS58621.1	18q21.1	2014-01-03			ENSG00000141622	ENSG00000141622		"""RING-type (C3HC4) zinc fingers"""	31696	protein-coding gene	gene with protein product							Standard	NR_046357		Approved	ARKL2, RNF111L2	uc002lcb.1	Q6ZSG1		ENST00000269439.7:c.441A>G	18.37:g.44015315A>G		58.0	0.0	0		69.0	34.0	0.492754	NM_152470	B3KVD1	Silent	SNP	ENST00000269439.7	37	CCDS32823.1																																																																																			A|0.992;G|0.008	0.008	strong		0.642	RNF165-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000445358.1	NM_152470	
TULP3	7289	hgsc.bcm.edu	37	12	3047365	3047365	+	Missense_Mutation	SNP	G	G	C	rs34246393	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr12:3047365G>C	ENST00000448120.2	+	10	1160	c.1109G>C	c.(1108-1110)aGt>aCt	p.S370T	TULP3_ENST00000397132.2_Missense_Mutation_p.S370T	NM_003324.4	NP_003315.2	O75386	TULP3_HUMAN	tubby like protein 3	370					anterior/posterior pattern specification (GO:0009952)|bone development (GO:0060348)|brain development (GO:0007420)|bronchus morphogenesis (GO:0060434)|central nervous system neuron differentiation (GO:0021953)|embryonic camera-type eye development (GO:0031076)|embryonic digit morphogenesis (GO:0042733)|embryonic neurocranium morphogenesis (GO:0048702)|G-protein coupled receptor signaling pathway (GO:0007186)|ganglion development (GO:0061548)|negative regulation of smoothened signaling pathway (GO:0045879)|negative regulation of smoothened signaling pathway involved in dorsal/ventral neural tube patterning (GO:1901621)|negative regulation of smoothened signaling pathway involved in ventral spinal cord patterning (GO:0021914)|neural tube closure (GO:0001843)|regulation of G-protein coupled receptor protein signaling pathway (GO:0008277)|regulation of transcription, DNA-templated (GO:0006355)|smoothened signaling pathway involved in dorsal/ventral neural tube patterning (GO:0060831)	axoneme (GO:0005930)|ciliary base (GO:0097546)|cilium (GO:0005929)|extracellular region (GO:0005576)|nucleolus (GO:0005730)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|primary cilium (GO:0072372)	enzyme binding (GO:0019899)|phosphatidylinositol binding (GO:0035091)|phosphatidylinositol-4,5-bisphosphate binding (GO:0005546)|protein complex binding (GO:0032403)			endometrium(1)|large_intestine(4)|lung(13)|prostate(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	22			OV - Ovarian serous cystadenocarcinoma(31;0.000818)			GTCTGGAACAGTGACACTCAG	0.507													g|||	2	0.000399361	0.0008	0.0	5008	,	,		19047	0.0		0.001	False		,,,				2504	0.0				p.S370T		Atlas-SNP	.											.	TULP3	45	.	0			c.G1109C						PASS	.		THR/SER,THR/SER	4,4402	8.1+/-20.4	0,4,2199	127.0	118.0	121.0		1109,1109	2.8	0.2	12	dbSNP_126	121	24,8576	17.3+/-56.4	0,24,4276	yes	missense,missense	TULP3	NM_001160408.1,NM_003324.4	58,58	0,28,6475	CC,CG,GG		0.2791,0.0908,0.2153	benign,benign	370/502,370/443	3047365	28,12978	2203	4300	6503	SO:0001583	missense	7289	exon10			GGAACAGTGACAC	AF045583	CCDS8519.1, CCDS53737.1	12p13	2014-02-21			ENSG00000078246	ENSG00000078246		"""Intraflagellar transport homologs"""	12425	protein-coding gene	gene with protein product		604730				9828123	Standard	NM_003324		Approved	TUBL3	uc001qlj.2	O75386	OTTHUMG00000168152	ENST00000448120.2:c.1109G>C	12.37:g.3047365G>C	ENSP00000410051:p.Ser370Thr	121.0	0.0	0		118.0	62.0	0.525424	NM_003324	B3KNB7|B7Z6A2|D3DUQ4|F8WBZ9|Q8N5B0	Missense_Mutation	SNP	ENST00000448120.2	37	CCDS8519.1	2|2	9.157509157509158E-4|9.157509157509158E-4	0|0	0.0|0.0	1|1	0.0027624309392265192|0.0027624309392265192	0|0	0.0|0.0	1|1	0.0013192612137203166|0.0013192612137203166	g|g	13.39|13.39	2.224334|2.224334	0.39300|0.39300	9.08E-4|9.08E-4	0.002791|0.002791	ENSG00000078246|ENSG00000078246	ENST00000541678;ENST00000538704|ENST00000228245;ENST00000544943;ENST00000542730;ENST00000448120;ENST00000397132	.|D;D;D	.|0.85088	.|-1.94;-1.94;-1.94	5.2|5.2	2.83|2.83	0.33086|0.33086	.|Tubby, C-terminal (4);	.|0.196879	.|0.52532	.|D	.|0.000064	T|T	0.72843|0.72843	0.3511|0.3511	N|N	0.19112|0.19112	0.55|0.55	0.22918|0.22918	N|N	0.998569|0.998569	.|B;B;P	.|0.44946	.|0.126;0.249;0.846	.|B;B;B	.|0.41135	.|0.247;0.348;0.333	T|T	0.65911|0.65911	-0.6053|-0.6053	5|10	.|0.87932	.|D	.|0	-2.0951|-2.0951	6.7817|6.7817	0.23650|0.23650	0.766:0.1528:0.0812:0.0|0.766:0.1528:0.0812:0.0	rs34246393|rs34246393	.|194;370;370	.|B7Z1E7;O75386;F8WBZ9	.|.;TULP3_HUMAN;.	H|T	46;35|370;97;194;370;370	.|ENSP00000442631:S97T;ENSP00000410051:S370T;ENSP00000380321:S370T	.|ENSP00000228245:S370T	Q|S	+|+	3|2	2|0	TULP3|TULP3	2917626|2917626	1.000000|1.000000	0.71417|0.71417	0.175000|0.175000	0.22980|0.22980	0.619000|0.619000	0.37552|0.37552	7.521000|7.521000	0.81832|0.81832	0.302000|0.302000	0.22762|0.22762	-1.075000|-1.075000	0.02238|0.02238	CAG|AGT	G|0.998;C|0.002	0.002	strong		0.507	TULP3-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000398468.1	NM_003324	
ATG9A	79065	hgsc.bcm.edu	37	2	220088468	220088468	+	Silent	SNP	A	A	G			TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr2:220088468A>G	ENST00000409618.1	-	10	1877	c.1438T>C	c.(1438-1440)Ttg>Ctg	p.L480L	ATG9A_ENST00000396761.2_Silent_p.L480L|ATG9A_ENST00000361242.4_Silent_p.L480L|ATG9A_ENST00000409422.1_Silent_p.L419L|AC068946.1_ENST00000408417.1_RNA			Q7Z3C6	ATG9A_HUMAN	autophagy related 9A	480					autophagic vacuole assembly (GO:0000045)|late nucleophagy (GO:0044805)|mitochondrion degradation (GO:0000422)|piecemeal microautophagy of nucleus (GO:0034727)|protein localization to pre-autophagosomal structure (GO:0034497)|protein transport (GO:0015031)	autophagic vacuole (GO:0005776)|cytoplasmic vesicle (GO:0031410)|endoplasmic reticulum (GO:0005783)|endosome (GO:0005768)|integral component of membrane (GO:0016021)|late endosome (GO:0005770)|membrane (GO:0016020)|pre-autophagosomal structure (GO:0000407)|recycling endosome (GO:0055037)|trans-Golgi network (GO:0005802)				endometrium(2)|large_intestine(5)|lung(3)|prostate(1)|skin(1)|stomach(1)	13		Renal(207;0.0474)		Epithelial(149;1.37e-06)|all cancers(144;0.000222)|LUSC - Lung squamous cell carcinoma(224;0.008)|Lung(261;0.00942)		GGGCTCAGCAACTCTTCCAAA	0.577																																					p.L480L		Atlas-SNP	.											.	ATG9A	50	.	0			c.T1438C						PASS	.						57.0	66.0	63.0					2																	220088468		2035	4206	6241	SO:0001819	synonymous_variant	79065	exon10			TCAGCAACTCTTC	AK021732	CCDS42820.1	2q35	2014-02-12	2012-06-06	2005-09-11	ENSG00000198925	ENSG00000198925			22408	protein-coding gene	gene with protein product		612204	"""APG9 autophagy 9-like 1 (S. cerevisiae)"", ""ATG9 autophagy related 9 homolog A (S. cerevisiae)"""	APG9L1			Standard	NM_024085		Approved	FLJ22169	uc002vkf.1	Q7Z3C6	OTTHUMG00000154557	ENST00000409618.1:c.1438T>C	2.37:g.220088468A>G		61.0	0.0	0		91.0	44.0	0.483516	NM_001077198	Q3ZAQ6|Q6P0N7|Q7Z317|Q7Z320|Q8NDK6|Q8WU65|Q9BVL5|Q9H6L1|Q9HAG7	Silent	SNP	ENST00000409618.1	37	CCDS42820.1																																																																																			.	.	none		0.577	ATG9A-004	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000335930.1	NM_024085	
THNSL1	79896	hgsc.bcm.edu	37	10	25313254	25313254	+	Missense_Mutation	SNP	C	C	A	rs41279892	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr10:25313254C>A	ENST00000524413.1	+	3	1449	c.1102C>A	c.(1102-1104)Cca>Aca	p.P368T	THNSL1_ENST00000376356.4_Missense_Mutation_p.P368T			Q8IYQ7	THNS1_HUMAN	threonine synthase-like 1 (S. cerevisiae)	368						cytoplasm (GO:0005737)|mitochondrion (GO:0005739)|nucleus (GO:0005634)				NS(1)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(7)|lung(5)|pancreas(1)|prostate(3)|skin(1)|stomach(1)|upper_aerodigestive_tract(3)	28					L-Threonine(DB00156)	CTGTATCCCACCAAGTTGCAA	0.383													C|||	51	0.0101837	0.0023	0.0187	5008	,	,		19468	0.0		0.0258	False		,,,				2504	0.0092				p.P368T		Atlas-SNP	.											.	THNSL1	70	.	0			c.C1102A						PASS	.	C	THR/PRO	19,4387	25.3+/-52.1	0,19,2184	93.0	91.0	92.0		1102	3.9	0.3	10	dbSNP_127	92	198,8402	86.9+/-149.2	0,198,4102	yes	missense	THNSL1	NM_024838.4	38	0,217,6286	AA,AC,CC		2.3023,0.4312,1.6685	benign	368/744	25313254	217,12789	2203	4300	6503	SO:0001583	missense	79896	exon3			ATCCCACCAAGTT	AK025655	CCDS7147.1	10p12.31	2008-02-05	2007-06-20		ENSG00000185875	ENSG00000185875			26160	protein-coding gene	gene with protein product		611260	"""threonine synthase-like 1 (bacterial)"""			12477932	Standard	NM_024838		Approved	FLJ22002	uc001isi.4	Q8IYQ7	OTTHUMG00000017828	ENST00000524413.1:c.1102C>A	10.37:g.25313254C>A	ENSP00000434887:p.Pro368Thr	84.0	0.0	0		96.0	42.0	0.4375	NM_024838	B3KWL1|D3DRV3|Q5VV21	Missense_Mutation	SNP	ENST00000524413.1	37	CCDS7147.1	29	0.013278388278388278	1	0.0020325203252032522	10	0.027624309392265192	0	0.0	18	0.023746701846965697	C	2.420	-0.333296	0.05278	0.004312	0.023023	ENSG00000185875	ENST00000524413;ENST00000376356	T;T	0.10860	2.83;2.83	5.71	3.88	0.44766	Threonine synthase (1);Pyridoxal phosphate-dependent enzyme, beta subunit (2);	0.324845	0.30269	N	0.010010	T	0.02304	0.0071	N	0.25789	0.76	0.09310	N	1	B	0.19445	0.036	B	0.21546	0.035	T	0.29366	-1.0014	10	0.72032	D	0.01	-24.6105	6.0648	0.19858	0.2421:0.6037:0.0:0.1541	rs41279892	368	Q8IYQ7	THNS1_HUMAN	T	368	ENSP00000434887:P368T;ENSP00000365534:P368T	ENSP00000365534:P368T	P	+	1	0	THNSL1	25353260	0.056000	0.20664	0.287000	0.24848	0.804000	0.45430	3.083000	0.50136	0.783000	0.33636	-0.143000	0.13931	CCA	C|0.984;A|0.016	0.016	strong		0.383	THNSL1-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000394913.1	NM_024838	
ERP27	121506	hgsc.bcm.edu	37	12	15068620	15068620	+	Splice_Site	SNP	T	T	A			TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr12:15068620T>A	ENST00000266397.2	-	6	1150	c.577A>T	c.(577-579)Att>Ttt	p.I193F	ERP27_ENST00000544881.1_5'UTR|ERP27_ENST00000540097.1_Splice_Site_p.I92F	NM_152321.2	NP_689534.1	Q96DN0	ERP27_HUMAN	endoplasmic reticulum protein 27	193						endoplasmic reticulum (GO:0005783)				breast(2)|cervix(2)|endometrium(2)|kidney(3)|large_intestine(4)|lung(3)|prostate(2)|skin(1)	19						ATAAAGAGAATCTGCAGTTGG	0.388																																					p.I193F		Atlas-SNP	.											.	ERP27	37	.	0			c.A577T						PASS	.						52.0	52.0	52.0					12																	15068620		2203	4300	6503	SO:0001630	splice_region_variant	121506	exon6			AGAGAATCTGCAG	AK056677	CCDS8670.1, CCDS73450.1	12p12.3	2011-10-19	2009-02-23	2007-03-26	ENSG00000139055	ENSG00000139055		"""Protein disulfide isomerases"""	26495	protein-coding gene	gene with protein product	"""protein disulfide isomerase family A, member 8"""	610642	"""chromosome 12 open reading frame 46"", ""endoplasmic reticulum protein 27 kDa"""	C12orf46		12975309, 16940051	Standard	XM_005253303		Approved	FLJ32115, ERp27, PDIA8	uc001rco.3	Q96DN0	OTTHUMG00000168741	ENST00000266397.2:c.577-1A>T	12.37:g.15068620T>A		110.0	0.0	0		95.0	45.0	0.473684	NM_152321		Missense_Mutation	SNP	ENST00000266397.2	37	CCDS8670.1	.	.	.	.	.	.	.	.	.	.	T	11.57	1.679429	0.29783	.	.	ENSG00000139055	ENST00000266397;ENST00000540097	T;T	0.33654	1.4;1.4	4.79	1.17	0.20885	Thioredoxin-like fold (1);	0.393229	0.28109	N	0.016563	T	0.26268	0.0641	L	0.46741	1.465	0.42936	D	0.99433	B	0.22983	0.078	B	0.18871	0.023	T	0.05402	-1.0887	10	0.41790	T	0.15	-22.2204	6.2103	0.20626	0.0:0.3251:0.0:0.6749	.	193	Q96DN0	ERP27_HUMAN	F	193;92	ENSP00000266397:I193F;ENSP00000440573:I92F	ENSP00000266397:I193F	I	-	1	0	ERP27	14959887	0.999000	0.42202	0.998000	0.56505	0.833000	0.47200	0.155000	0.16362	0.200000	0.20447	-0.290000	0.09829	ATT	.	.	none		0.388	ERP27-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000400868.1	NM_152321	Missense_Mutation
SCTR	6344	hgsc.bcm.edu	37	2	120194674	120194674	+	IGR	SNP	C	C	T	rs72833258	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr2:120194674C>T	ENST00000019103.5	-	0	1865				TMEM37_ENST00000465296.1_3'UTR|TMEM37_ENST00000409826.1_Silent_p.G89G|TMEM37_ENST00000306406.4_Silent_p.G77G	NM_002980.2	NP_002971.2	P47872	SCTR_HUMAN	secretin receptor						digestion (GO:0007586)|excretion (GO:0007588)|G-protein coupled receptor signaling pathway (GO:0007186)	cytoplasmic microtubule (GO:0005881)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	secretin receptor activity (GO:0015055)			central_nervous_system(2)|endometrium(1)|kidney(1)|large_intestine(3)|lung(7)|ovary(1)|prostate(1)|skin(3)	19					Secretin(DB00021)	GAGACCTGGGCCAGGCCCATG	0.657													C|||	72	0.014377	0.003	0.0144	5008	,	,		14624	0.001		0.0209	False		,,,				2504	0.0368				p.G77G		Atlas-SNP	.											.	TMEM37	40	.	0			c.C231T						PASS	.	C		21,4383	28.1+/-56.4	0,21,2181	50.0	53.0	52.0		231	-4.2	0.1	2	dbSNP_130	52	232,8366	94.2+/-156.2	2,228,4069	no	coding-synonymous	TMEM37	NM_183240.2		2,249,6250	TT,TC,CC		2.6983,0.4768,1.9459		77/191	120194674	253,12749	2202	4299	6501	SO:0001628	intergenic_variant	140738	exon2			CCTGGGCCAGGCC		CCDS2127.1	2q14.1	2012-08-10			ENSG00000080293	ENSG00000080293		"""GPCR / Class B : Glucagon receptors"""	10608	protein-coding gene	gene with protein product		182098				1646711	Standard	NM_002980		Approved		uc002tma.3	P47872	OTTHUMG00000131407		2.37:g.120194674C>T		37.0	0.0	0		44.0	28.0	0.636364	NM_183240	Q12961|Q13213|Q53T00	Silent	SNP	ENST00000019103.5	37	CCDS2127.1																																																																																			C|0.983;T|0.017	0.017	strong		0.657	SCTR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254198.2		
PALB2	79728	hgsc.bcm.edu	37	16	23635348	23635348	+	Missense_Mutation	SNP	A	A	C	rs45478192	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr16:23635348A>C	ENST00000261584.4	-	8	2968	c.2816T>G	c.(2815-2817)tTg>tGg	p.L939W	CTD-2196E14.3_ENST00000561764.1_RNA	NM_024675.3	NP_078951.2	Q86YC2	PALB2_HUMAN	partner and localizer of BRCA2	939	Interaction with RAD51, BRCA2 and POLH.|Required for interaction with POLH and POLH DNA synthesis stimulation.		L -> W (may be associated with breast cancer susceptibility; reduces interaction with BRCA2, RAD51 and XRCC3; decreases double-stranded DNA break- initiated homologous recombination; increases sensitivity to IR; dbSNP:rs45478192). {ECO:0000269|PubMed:21618343}.		DNA repair (GO:0006281)|double-strand break repair via homologous recombination (GO:0000724)|inner cell mass cell proliferation (GO:0001833)|mesoderm development (GO:0007498)|negative regulation of apoptotic process (GO:0043066)|organ morphogenesis (GO:0009887)|post-anal tail morphogenesis (GO:0036342)|somitogenesis (GO:0001756)	nucleoplasm (GO:0005654)|nucleus (GO:0005634)	DNA binding (GO:0003677)			breast(5)|central_nervous_system(1)|endometrium(3)|kidney(2)|large_intestine(11)|lung(21)|ovary(3)|pancreas(1)|prostate(3)|skin(1)|stomach(1)|urinary_tract(3)	55				GBM - Glioblastoma multiforme(48;0.0167)		TCTGATTTCCAAATTTCCCAA	0.378			"""F, N, Mis"""			"""Wilms tumor, medulloblastoma, AML ,breast"""		Involved in tolerance or repair of DNA crosslinks					A|||	4	0.000798722	0.0008	0.0014	5008	,	,		17096	0.0		0.002	False		,,,				2504	0.0				p.L939W		Atlas-SNP	.	yes	Rec		"""Fanconi anaemia N, breast cancer susceptibility """	16	16p12.1	79728	partner and localizer of BRCA2		"""L, O, E"""	.	PALB2	108	.	0			c.T2816G						PASS	.	A	TRP/LEU	0,4394		0,0,2197	101.0	94.0	96.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	2816	5.8	1.0	16	dbSNP_127	96	20,8580	15.3+/-51.7	0,20,4280	yes	missense	PALB2	NM_024675.3	61	0,20,6477	CC,CA,AA		0.2326,0.0,0.1539	probably-damaging	939/1187	23635348	20,12974	2197	4300	6497	SO:0001583	missense	79728	exon8			ATTTCCAAATTTC		CCDS32406.1	16p12.1	2014-09-17				ENSG00000083093		"""Fanconi anemia, complementation groups"""	26144	protein-coding gene	gene with protein product	"""Fanconi anemia, complementation group N"""	610355				16793542, 17200672	Standard	NM_024675		Approved	FLJ21816, FANCN	uc002dlx.1	Q86YC2		ENST00000261584.4:c.2816T>G	16.37:g.23635348A>C	ENSP00000261584:p.Leu939Trp	110.0	0.0	0		119.0	43.0	0.361345	NM_024675	A6NIE1|Q8N7Y6|Q8ND31|Q9H6W1	Missense_Mutation	SNP	ENST00000261584.4	37	CCDS32406.1	2	9.157509157509158E-4	0	0.0	1	0.0027624309392265192	0	0.0	1	0.0013192612137203166	A	20.9	4.060595	0.76074	0.0	0.002326	ENSG00000083093	ENST00000261584	T	0.28666	1.6	5.81	5.81	0.92471	WD40 repeat-like-containing domain (1);	0.000000	0.64402	D	0.000005	T	0.56171	0.1967	M	0.77103	2.36	0.45914	D	0.998756	D	0.89917	1.0	D	0.97110	1.0	T	0.60994	-0.7152	10	0.87932	D	0	-7.0825	12.557	0.56258	1.0:0.0:0.0:0.0	rs45478192;rs61755167	939	Q86YC2	PALB2_HUMAN	W	939	ENSP00000261584:L939W	ENSP00000261584:L939W	L	-	2	0	PALB2	23542849	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	5.166000	0.64965	2.230000	0.72887	0.528000	0.53228	TTG	A|0.999;C|0.001	0.001	strong		0.378	PALB2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000435287.2	NM_024675	
CATSPER2	117155	hgsc.bcm.edu	37	15	43928340	43928340	+	Missense_Mutation	SNP	C	C	G	rs146701338	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr15:43928340C>G	ENST00000321596.5	-	8	1119	c.920G>C	c.(919-921)tGg>tCg	p.W307S	CATSPER2_ENST00000396879.1_Missense_Mutation_p.W307S|CATSPER2_ENST00000354127.4_Missense_Mutation_p.W307S|STRC_ENST00000541030.1_Intron|CATSPER2_ENST00000381761.1_Missense_Mutation_p.W313S|RNU6-610P_ENST00000384264.1_RNA|CATSPER2_ENST00000355438.2_Missense_Mutation_p.W307S			Q96P56	CTSR2_HUMAN	cation channel, sperm associated 2	307					calcium ion import (GO:0070509)|cell differentiation (GO:0030154)|membrane depolarization during action potential (GO:0086010)|multicellular organism reproduction (GO:0032504)|multicellular organismal development (GO:0007275)|single fertilization (GO:0007338)|sperm motility (GO:0030317)|sperm-egg recognition (GO:0035036)|spermatogenesis (GO:0007283)	CatSper complex (GO:0036128)|motile cilium (GO:0031514)|plasma membrane (GO:0005886)	calcium activated cation channel activity (GO:0005227)|voltage-gated calcium channel activity (GO:0005245)			breast(3)|central_nervous_system(1)|cervix(1)|endometrium(1)|large_intestine(3)|lung(8)|ovary(1)|prostate(1)|skin(1)|urinary_tract(2)	22		all_cancers(109;3.26e-15)|all_epithelial(112;1.48e-12)|Lung NSC(122;2.76e-08)|all_lung(180;3.1e-07)|Melanoma(134;0.027)|Colorectal(260;0.215)		GBM - Glioblastoma multiforme(94;3.56e-07)		AGGCACCTTCCAGACGTCCTG	0.443													.|||	6	0.00119808	0.0	0.0	5008	,	,		20134	0.0		0.004	False		,,,				2504	0.002				p.W307S		Atlas-SNP	.											.	CATSPER2	49	.	0			c.G920C						PASS	.	C	SER/TRP,SER/TRP	4,4390		0,4,2193	27.0	27.0	27.0		920,920	4.8	1.0	15	dbSNP_134	27	33,8511		0,33,4239	no	missense,missense	CATSPER2	NM_054020.2,NM_172095.1	177,177	0,37,6432	GG,GC,CC		0.3862,0.091,0.286	probably-damaging,probably-damaging	307/529,307/531	43928340	37,12901	2197	4272	6469	SO:0001583	missense	117155	exon8			ACCTTCCAGACGT	AF411817	CCDS10099.1, CCDS32216.1, CCDS73714.1	15q15.3	2011-07-05			ENSG00000166762	ENSG00000166762		"""Voltage-gated ion channels / Cation channels, sperm associated"""	18810	protein-coding gene	gene with protein product		607249				11675491, 16382101	Standard	NM_172095		Approved		uc001zsh.3	Q96P56	OTTHUMG00000059902	ENST00000321596.5:c.920G>C	15.37:g.43928340C>G	ENSP00000321463:p.Trp307Ser	394.0	0.0	0		459.0	192.0	0.418301	NM_054020	Q8NHT9|Q96P54|Q96P55	Missense_Mutation	SNP	ENST00000321596.5	37	CCDS10099.1	4	0.0018315018315018315	0	0.0	0	0.0	0	0.0	4	0.005277044854881266	C	8.365	0.834073	0.16820	9.1E-4	0.003862	ENSG00000166762	ENST00000396879;ENST00000299989;ENST00000381761;ENST00000321596;ENST00000354127;ENST00000355438	D;D;D;D;D	0.97161	-4.27;-4.27;-4.27;-4.27;-4.27	4.81	4.81	0.61882	Ion transport (1);	0.472448	0.20479	N	0.091522	D	0.96386	0.8821	L	0.54323	1.7	0.53688	D	0.999972	D;D	0.71674	0.997;0.998	D;D	0.71184	0.953;0.972	D	0.94092	0.7354	10	0.26408	T	0.33	.	13.2328	0.59953	0.0:1.0:0.0:0.0	.	313;307	F8W9H2;Q96P56	.;CTSR2_HUMAN	S	307;307;313;307;307;307	ENSP00000380088:W307S;ENSP00000371180:W313S;ENSP00000321463:W307S;ENSP00000339137:W307S;ENSP00000347613:W307S	ENSP00000299989:W307S	W	-	2	0	CATSPER2	41715632	1.000000	0.71417	1.000000	0.80357	0.096000	0.18686	4.485000	0.60279	2.488000	0.83962	0.655000	0.94253	TGG	C|0.997;G|0.003	0.003	strong		0.443	CATSPER2-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000133151.2	NM_054020	
IGFN1	91156	hgsc.bcm.edu	37	1	201193964	201193964	+	Missense_Mutation	SNP	G	G	C			TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr1:201193964G>C	ENST00000335211.4	+	21	10578	c.10448G>C	c.(10447-10449)gGg>gCg	p.G3483A	IGFN1_ENST00000295591.8_Intron|RP11-567E21.3_ENST00000453155.1_RNA	NM_001164586.1	NP_001158058.1	Q86VF2	IGFN1_HUMAN	immunoglobulin-like and fibronectin type III domain containing 1	1026						nucleus (GO:0005634)|Z disc (GO:0030018)				autonomic_ganglia(2)|cervix(1)|endometrium(3)|kidney(1)|large_intestine(6)|lung(21)|ovary(2)|pancreas(1)|prostate(1)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(1)	45						ACCCTGCAGGGGAAGGAGGTT	0.602																																					p.G3483A		Atlas-SNP	.											IGFN1_ENST00000335211,NS,carcinoma,+1,2	IGFN1	220	2	0			c.G10448C						PASS	.						68.0	54.0	59.0					1																	201193964		2203	4300	6503	SO:0001583	missense	91156	exon21			TGCAGGGGAAGGA	AY245430	CCDS53455.1	1q32.1	2013-02-11			ENSG00000163395	ENSG00000163395		"""Immunoglobulin superfamily / I-set domain containing"", ""Fibronectin type III domain containing"""	24607	protein-coding gene	gene with protein product							Standard	NM_001164586		Approved	DKFZp434B1231, EEF1A2BP1	uc001gwc.3	Q86VF2	OTTHUMG00000035728	ENST00000335211.4:c.10448G>C	1.37:g.201193964G>C	ENSP00000334714:p.Gly3483Ala	145.0	0.0	0		123.0	58.0	0.471545	NM_001164586	F8WAI1|Q9NT72	Missense_Mutation	SNP	ENST00000335211.4	37	CCDS53455.1	.	.	.	.	.	.	.	.	.	.	G	17.30	3.355022	0.61293	.	.	ENSG00000163395	ENST00000335211	T	0.81247	-1.47	4.11	3.16	0.36331	.	0.071084	0.56097	N	0.000031	D	0.89619	0.6767	M	0.86343	2.81	0.80722	D	1	D	0.76494	0.999	D	0.79784	0.993	D	0.90409	0.4408	10	0.87932	D	0	.	11.9403	0.52896	0.0:0.1757:0.8242:0.0	.	3483	F8WAI1	.	A	3483	ENSP00000334714:G3483A	ENSP00000334714:G3483A	G	+	2	0	IGFN1	199460587	1.000000	0.71417	0.112000	0.21494	0.893000	0.52053	5.952000	0.70282	0.878000	0.35920	0.491000	0.48974	GGG	.	.	none		0.602	IGFN1-202	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_178275	
PLCXD1	55344	hgsc.bcm.edu	37	X	200939	200939	+	Missense_Mutation	SNP	C	C	T			TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chrX:200939C>T	ENST00000381657.2	+	2	599	c.85C>T	c.(85-87)Ccc>Tcc	p.P29S	PLCXD1_ENST00000399012.1_Missense_Mutation_p.P29S|PLCXD1_ENST00000484611.2_3'UTR|PLCXD1_ENST00000381663.3_Missense_Mutation_p.P29S	NM_018390.3	NP_060860.1	Q9NUJ7	PLCX1_HUMAN	phosphatidylinositol-specific phospholipase C, X domain containing 1	29					lipid metabolic process (GO:0006629)		phosphoric diester hydrolase activity (GO:0008081)			endometrium(3)|large_intestine(1)|lung(7)	11		all_cancers(21;4.28e-07)|all_epithelial(21;2.07e-08)|all_lung(23;2.81e-05)|Lung NSC(23;0.000693)|Lung SC(21;0.122)				GGCACTGTGTCCCCGGCTCTG	0.652													c|||	7	0.00139776	0.0008	0.0058	5008	,	,		15888	0.0		0.002	False		,,,				2504	0.0				p.P29S		Atlas-SNP	.											.	PLCXD1	18	.	0			c.C85T						PASS	.		SER/PRO	7,4399		0,7,2196	131.0	118.0	123.0		85	2.0	0.4	X	dbSNP_134	123	74,8518		0,74,4222	no	missense	PLCXD1	NM_018390.3	74	0,81,6418	TT,TC,CC		0.8613,0.1589,0.6232	benign	29/324	200939	81,12917	2203	4296	6499	SO:0001583	missense	55344	exon2			CTGTGTCCCCGGC	AK002185	CCDS14103.1	Xp22.33 and Yp11.32	2010-07-28			ENSG00000182378	ENSG00000182378		"""Pseudoautosomal regions / PAR1"""	23148	protein-coding gene	gene with protein product							Standard	NM_018390		Approved	FLJ11323	uc004cpc.3	Q9NUJ7	OTTHUMG00000022693	ENST00000381657.2:c.85C>T	X.37:g.200939C>T	ENSP00000371073:p.Pro29Ser	376.0	1.0	0.00265957		343.0	169.0	0.492711	NM_018390	A2BH51|A2BH52	Missense_Mutation	SNP	ENST00000381657.2	37	CCDS14103.1	5	0.0022893772893772895	1	0.0020325203252032522	2	0.0055248618784530384	0	0.0	2	0.002638522427440633	.	0.110	-1.139616	0.01728	0.001589	0.008613	ENSG00000182378	ENST00000399012;ENST00000430923;ENST00000445062;ENST00000381657;ENST00000429181;ENST00000381663;ENST00000443019;ENST00000415337;ENST00000447472;ENST00000448477	.	.	.	1.98	1.98	0.26296	PLC-like phosphodiesterase, TIM beta/alpha-barrel domain (2);	0.820267	0.11258	U	0.582867	T	0.10208	0.0250	.	.	.	0.09310	N	1	B	0.09022	0.002	B	0.04013	0.001	T	0.27262	-1.0079	8	0.05721	T	0.95	.	7.6567	0.28379	0.0:1.0:0.0:0.0	.	29	Q9NUJ7	PLCX1_HUMAN	S	29	.	ENSP00000371073:P29S	P	+	1	0	PLCXD1	140939	0.000000	0.05858	0.388000	0.26195	0.309000	0.27889	-0.301000	0.08232	0.793000	0.33875	0.449000	0.29647	CCC	C|0.995;T|0.005	0.005	strong		0.652	PLCXD1-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000058879.2	NM_018390	
FZD10	11211	hgsc.bcm.edu	37	12	130648576	130648576	+	Silent	SNP	G	G	T			TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr12:130648576G>T	ENST00000229030.4	+	1	1573	c.1089G>T	c.(1087-1089)gcG>gcT	p.A363A	FZD10-AS1_ENST00000505807.2_RNA|FZD10_ENST00000539839.1_Missense_Mutation_p.G331C			Q9ULW2	FZD10_HUMAN	frizzled class receptor 10	363					brain development (GO:0007420)|canonical Wnt signaling pathway (GO:0060070)|cellular response to retinoic acid (GO:0071300)|gonad development (GO:0008406)|negative regulation of Rho GTPase activity (GO:0034259)|neuron differentiation (GO:0030182)|non-canonical Wnt signaling pathway via JNK cascade (GO:0038031)|positive regulation of JUN kinase activity (GO:0043507)|positive regulation of Rac GTPase activity (GO:0032855)|regulation of actin cytoskeleton organization (GO:0032956)|vasculature development (GO:0001944)	cell projection (GO:0042995)|cell surface (GO:0009986)|cytoplasm (GO:0005737)|integral component of plasma membrane (GO:0005887)|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)	p.A363A(1)		breast(1)|central_nervous_system(1)|endometrium(3)|kidney(4)|large_intestine(7)|lung(14)|pancreas(1)|prostate(3)|urinary_tract(1)	35	all_neural(191;0.101)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;1.3e-06)|Epithelial(86;1.66e-05)|all cancers(50;5.18e-05)		CCATCCCGGCGGTGAAGACCA	0.667																																					p.A363A		Atlas-SNP	.											FZD10,NS,carcinoma,0,1	FZD10	95	1	1	Substitution - coding silent(1)	prostate(1)	c.G1089T						PASS	.						55.0	52.0	53.0					12																	130648576		2203	4300	6503	SO:0001819	synonymous_variant	11211	exon1			CCCGGCGGTGAAG	AB027464	CCDS9267.1	12q24.33	2014-01-29	2014-01-29			ENSG00000111432		"""GPCR / Class F : Frizzled receptors"", ""CD molecules"""	4039	protein-coding gene	gene with protein product		606147	"""frizzled (Drosophila) homolog 10"", ""frizzled homolog 10 (Drosophila)"", ""frizzled 10, seven transmembrane spanning receptor"", ""frizzled family receptor 10"""			10448064	Standard	NM_007197		Approved	CD350	uc001uii.3	Q9ULW2		ENST00000229030.4:c.1089G>T	12.37:g.130648576G>T		78.0	0.0	0		103.0	55.0	0.533981	NM_007197		Silent	SNP	ENST00000229030.4	37	CCDS9267.1	.	.	.	.	.	.	.	.	.	.	G	9.518	1.107438	0.20714	.	.	ENSG00000111432	ENST00000539839	.	.	.	5.1	-2.97	0.05530	.	.	.	.	.	T	0.69214	0.3086	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.73575	-0.3939	5	0.87932	D	0	.	12.6005	0.56494	0.0:0.2627:0.5494:0.1879	.	.	.	.	C	331	.	ENSP00000438460:G331C	G	+	1	0	FZD10	129214529	0.004000	0.15560	0.985000	0.45067	0.997000	0.91878	-1.256000	0.02869	-0.391000	0.07763	0.561000	0.74099	GGT	.	.	none		0.667	FZD10-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding			
OR4A47	403253	hgsc.bcm.edu	37	11	48511050	48511050	+	Missense_Mutation	SNP	T	T	C	rs76991989	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr11:48511050T>C	ENST00000446524.1	+	1	782	c.706T>C	c.(706-708)Tca>Cca	p.S236P		NM_001005512.2	NP_001005512.2	Q6IF82	O4A47_HUMAN	olfactory receptor, family 4, subfamily A, member 47	236						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(2)|endometrium(1)|kidney(1)|large_intestine(2)|lung(18)|ovary(1)|skin(1)|urinary_tract(2)	29						AAAAGCCCTCTCAACCTGCAG	0.428													T|||	41	0.0081869	0.0015	0.0086	5008	,	,		18021	0.0		0.0268	False		,,,				2504	0.0061				p.S236P		Atlas-SNP	.											OR4A47,bladder,carcinoma,-1,1	OR4A47	72	1	0			c.T706C						PASS	.	T	PRO/SER	23,4379		0,23,2178	148.0	144.0	145.0		706	2.4	0.1	11	dbSNP_131	145	217,8379		3,211,4084	yes	missense	OR4A47	NM_001005512.2	74	3,234,6262	CC,CT,TT		2.5244,0.5225,1.8464	benign	236/310	48511050	240,12758	2201	4298	6499	SO:0001583	missense	403253	exon1			GCCCTCTCAACCT	BK004380	CCDS31490.1	11p11.2	2012-08-09			ENSG00000237388	ENSG00000237388		"""GPCR / Class A : Olfactory receptors"""	31266	protein-coding gene	gene with protein product							Standard	NM_001005512		Approved		uc010rhx.2	Q6IF82	OTTHUMG00000166581	ENST00000446524.1:c.706T>C	11.37:g.48511050T>C	ENSP00000412752:p.Ser236Pro	150.0	0.0	0		140.0	62.0	0.442857	NM_001005512		Missense_Mutation	SNP	ENST00000446524.1	37	CCDS31490.1	23	0.010531135531135532	1	0.0020325203252032522	5	0.013812154696132596	0	0.0	17	0.022427440633245383	N	11.71	1.719811	0.30503	0.005225	0.025244	ENSG00000237388	ENST00000446524	T	0.00309	8.16	4.59	2.36	0.29203	GPCR, rhodopsin-like superfamily (1);	0.553031	0.16377	N	0.217096	T	0.00300	0.0009	H	0.98407	4.225	0.09310	N	0.999997	D	0.53462	0.96	P	0.54965	0.765	T	0.40098	-0.9581	10	0.87932	D	0	.	5.4392	0.16498	0.0:0.2998:0.0:0.7002	.	236	Q6IF82	O4A47_HUMAN	P	236	ENSP00000412752:S236P	ENSP00000412752:S236P	S	+	1	0	OR4A47	48467626	0.000000	0.05858	0.139000	0.22197	0.222000	0.24845	0.081000	0.14823	0.225000	0.20959	0.172000	0.16884	TCA	T|0.981;C|0.019	0.019	strong		0.428	OR4A47-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000390559.1	NM_001005512	
GAS2L1	10634	hgsc.bcm.edu	37	22	29704627	29704627	+	Missense_Mutation	SNP	C	C	T	rs191844093	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr22:29704627C>T	ENST00000406549.3	+	2	682	c.532C>T	c.(532-534)Cct>Tct	p.P178S	GAS2L1_ENST00000403764.1_Missense_Mutation_p.P178S|GAS2L1_ENST00000407854.1_Missense_Mutation_p.P178S|GAS2L1_ENST00000407647.2_Missense_Mutation_p.P178S|GAS2L1_ENST00000471961.1_Missense_Mutation_p.P178S|GAS2L1_ENST00000360113.2_Missense_Mutation_p.P178S|GAS2L1_ENST00000341313.6_Missense_Mutation_p.P178S	NM_001278730.1	NP_001265659.1	Q99501	GA2L1_HUMAN	growth arrest-specific 2 like 1	178					cell cycle arrest (GO:0007050)|cellular response to starvation (GO:0009267)|cellular response to thyroid hormone stimulus (GO:0097067)|microtubule bundle formation (GO:0001578)|negative regulation of cell growth (GO:0030308)|negative regulation of erythrocyte differentiation (GO:0045647)|negative regulation of gene expression (GO:0010629)|negative regulation of microtubule depolymerization (GO:0007026)|regulation of cell cycle (GO:0051726)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)	cytoskeletal adaptor activity (GO:0008093)|microtubule binding (GO:0008017)|thyroid hormone receptor binding (GO:0046966)			endometrium(2)|lung(2)|prostate(1)	5						CCCCAACGCCCCTGCCGCTGG	0.726													C|||	10	0.00199681	0.0008	0.0072	5008	,	,		14057	0.0		0.004	False		,,,				2504	0.0				p.P178S		Atlas-SNP	.											.	GAS2L1	54	.	0			c.C532T						PASS	.	C	SER/PRO,SER/PRO,SER/PRO	1,4357		0,1,2178	10.0	14.0	13.0		532,532,532	3.8	0.1	22		13	45,8529		0,45,4242	yes	missense,missense,missense	GAS2L1	NM_006478.3,NM_152236.1,NM_152237.1	74,74,74	0,46,6420	TT,TC,CC		0.5248,0.0229,0.3557	probably-damaging,probably-damaging,probably-damaging	178/682,178/682,178/338	29704627	46,12886	2179	4287	6466	SO:0001583	missense	10634	exon2			AACGCCCCTGCCG	BC001782	CCDS63438.1, CCDS74840.1	22q12.2	2008-06-11			ENSG00000185340	ENSG00000185340			16955	protein-coding gene	gene with protein product		602128				8975699, 12584248, 1607387	Standard	NM_001278730		Approved	GAR22	uc003afc.1	Q99501	OTTHUMG00000151108	ENST00000406549.3:c.532C>T	22.37:g.29704627C>T	ENSP00000383995:p.Pro178Ser	15.0	0.0	0		34.0	20.0	0.588235	NM_152237	B5MCR7|Q53EN7|Q92640|Q9BUY9	Missense_Mutation	SNP	ENST00000406549.3	37		8	0.003663003663003663	1	0.0020325203252032522	4	0.011049723756906077	0	0.0	3	0.00395778364116095	C	11.65	1.700485	0.30142	2.29E-4	0.005248	ENSG00000185340	ENST00000407647;ENST00000333679;ENST00000406549;ENST00000360113;ENST00000341313;ENST00000403764;ENST00000471961;ENST00000407854	T;T;T;T;T;T;T	0.49139	0.79;0.87;0.91;0.92;0.79;0.79;0.79	4.85	3.81	0.43845	Calponin homology domain (1);	0.846890	0.10081	N	0.718392	T	0.24198	0.0586	L	0.29908	0.895	0.09310	N	0.999996	P;B;B;B	0.35527	0.507;0.113;0.03;0.03	B;B;B;B	0.28232	0.087;0.04;0.031;0.031	T	0.03259	-1.1055	10	0.08837	T	0.75	-16.2742	12.6928	0.56985	0.0:0.6044:0.3956:0.0	.	178;178;178;178	B5MCR7;E7EQM6;A0A5E8;Q99501	.;.;.;GA2L1_HUMAN	S	178	ENSP00000385554:P178S;ENSP00000383995:P178S;ENSP00000353229:P178S;ENSP00000344012:P178S;ENSP00000385358:P178S;ENSP00000450152:P178S;ENSP00000385023:P178S	ENSP00000332834:P178S	P	+	1	0	GAS2L1	28034627	0.007000	0.16637	0.093000	0.20910	0.064000	0.16182	1.674000	0.37544	1.014000	0.39417	0.491000	0.48974	CCT	C|0.996;T|0.004	0.004	strong		0.726	GAS2L1-002	PUTATIVE	basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000321365.1	NM_006478	
C10orf105	414152	hgsc.bcm.edu	37	10	73492027	73492027	+	Intron	SNP	G	G	A	rs111033453	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr10:73492027G>A	ENST00000398786.2	-	1	97				CDH23_ENST00000224721.6_Silent_p.V1338V	NM_001168390.1	NP_001161862.1	Q8TEF2	CJ105_HUMAN	chromosome 10 open reading frame 105							integral component of membrane (GO:0016021)											CTGAGATTGTGCGGGTCCAGG	0.562													G|||	5	0.000998403	0.0	0.0043	5008	,	,		21580	0.0		0.002	False		,,,				2504	0.0				p.V1333V		Atlas-SNP	.											.	CDH23	365	.	0			c.G3999A						PASS	.	G	,,	2,4110		0,2,2054	68.0	70.0	69.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	,3999,3999	4.8	1.0	10	dbSNP_132	69	24,8384		0,24,4180	no	intron,coding-synonymous,coding-synonymous	CDH23,C10orf105	NM_001168390.1,NM_001171930.1,NM_022124.5	,,	0,26,6234	AA,AG,GG		0.2854,0.0486,0.2077	,,	,1333/1382,1333/3355	73492027	26,12494	2056	4204	6260	SO:0001627	intron_variant	64072	exon31			GATTGTGCGGGTC	AK074172	CCDS44430.1	10q22.1	2012-06-01			ENSG00000214688	ENSG00000214688			20304	protein-coding gene	gene with protein product							Standard	NM_001164375		Approved	FLJ00245	uc001jsa.2	Q8TEF2	OTTHUMG00000018427	ENST00000398786.2:c.4+5457C>T	10.37:g.73492027G>A		117.0	0.0	0		110.0	51.0	0.463636	NM_022124		Silent	SNP	ENST00000398786.2	37	CCDS44430.1																																																																																			G|0.998;A|0.002	0.002	strong		0.562	C10orf105-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048551.2	NM_001164375	
ENTHD2	146705	hgsc.bcm.edu	37	17	79204447	79204447	+	Missense_Mutation	SNP	C	C	T	rs143572077		TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr17:79204447C>T	ENST00000300714.3	-	11	983	c.926G>A	c.(925-927)aGc>aAc	p.S309N	ENTHD2_ENST00000374769.2_Missense_Mutation_p.S225N|AC027601.1_ENST00000575922.1_RNA|AC027601.1_ENST00000569559.1_RNA	NM_144679.2	NP_653280.1	Q96N21	AP4AT_HUMAN	ENTH domain containing 2	309						cytoplasmic vesicle (GO:0031410)											GAGGTCGCTGCTCCCCAGGGA	0.692											OREG0024811	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.S309N		Atlas-SNP	.											.	.	.	.	0			c.G926A						PASS	.	C	ASN/SER	0,4406		0,0,2203	23.0	25.0	24.0		926	3.1	0.0	17	dbSNP_134	24	1,8597		0,1,4298	no	missense	C17orf56	NM_144679.2	46	0,1,6501	TT,TC,CC		0.0116,0.0,0.0077	possibly-damaging	309/526	79204447	1,13003	2203	4299	6502	SO:0001583	missense	146705	exon11			TCGCTGCTCCCCA	AK056090	CCDS11779.1	17q25.3	2012-07-18	2012-07-18	2012-07-18	ENSG00000167302	ENSG00000167302			26458	protein-coding gene	gene with protein product			"""chromosome 17 open reading frame 56"""	C17orf56			Standard	NM_144679		Approved	FLJ31528	uc002jzu.2	Q96N21	OTTHUMG00000177866	ENST00000300714.3:c.926G>A	17.37:g.79204447C>T	ENSP00000300714:p.Ser309Asn	102.0	0.0	0	1189	108.0	57.0	0.527778	NM_144679	Q6ZQU0|Q6ZSQ9	Missense_Mutation	SNP	ENST00000300714.3	37	CCDS11779.1	.	.	.	.	.	.	.	.	.	.	C	7.062	0.566626	0.13560	0.0	1.16E-4	ENSG00000167302	ENST00000300714;ENST00000374769	T;T	0.27720	1.65;1.65	5.17	3.13	0.36017	.	1.579650	0.03019	N	0.150445	T	0.24624	0.0597	L	0.29908	0.895	0.09310	N	1	P;P	0.41265	0.454;0.744	B;B	0.35813	0.105;0.211	T	0.24941	-1.0146	10	0.38643	T	0.18	-0.3904	8.4158	0.32670	0.0:0.7609:0.1556:0.0835	.	309;225	Q96N21;Q96N21-2	CQ056_HUMAN;.	N	309;225	ENSP00000300714:S309N;ENSP00000363901:S225N	ENSP00000300714:S309N	S	-	2	0	C17orf56	76819042	0.044000	0.20184	0.004000	0.12327	0.007000	0.05969	1.325000	0.33724	0.544000	0.28883	0.555000	0.69702	AGC	C|1.000;T|0.000	0.000	weak		0.692	ENTHD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000439315.1	NM_144679	
CSMD3	114788	hgsc.bcm.edu	37	8	113364697	113364697	+	Missense_Mutation	SNP	T	T	C	rs139786530	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr8:113364697T>C	ENST00000297405.5	-	39	6447	c.6203A>G	c.(6202-6204)tAt>tGt	p.Y2068C	CSMD3_ENST00000352409.3_Missense_Mutation_p.Y1998C|CSMD3_ENST00000343508.3_Missense_Mutation_p.Y2028C|CSMD3_ENST00000455883.2_Missense_Mutation_p.Y1964C	NM_198123.1	NP_937756.1	Q7Z407	CSMD3_HUMAN	CUB and Sushi multiple domains 3	2068	Sushi 11. {ECO:0000255|PROSITE- ProRule:PRU00302}.					integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)		p.Y2028C(1)|p.Y2068C(1)		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						TCCAACCATATATCTGTCTCC	0.343										HNSCC(6;0.00088)|TCGA Ovarian(7;0.080)			T|||	3	0.000599042	0.0	0.0014	5008	,	,		16755	0.0		0.002	False		,,,				2504	0.0				p.Y2068C		Atlas-SNP	.											CSMD3_ENST00000343508,NS,carcinoma,0,2	CSMD3	2325	2	2	Substitution - Missense(2)	lung(2)	c.A6203G						PASS	.	T	CYS/TYR,CYS/TYR,CYS/TYR	2,4404	4.2+/-10.8	0,2,2201	110.0	103.0	105.0		5891,6203,6083	5.0	1.0	8	dbSNP_134	105	16,8582	11.2+/-40.8	0,16,4283	yes	missense,missense,missense	CSMD3	NM_052900.2,NM_198123.1,NM_198124.1	194,194,194	0,18,6484	CC,CT,TT		0.1861,0.0454,0.1384	probably-damaging,probably-damaging,probably-damaging	1964/3539,2068/3708,2028/3668	113364697	18,12986	2203	4299	6502	SO:0001583	missense	114788	exon39			ACCATATATCTGT	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.6203A>G	8.37:g.113364697T>C	ENSP00000297405:p.Tyr2068Cys	135.0	0.0	0		141.0	48.0	0.340426	NM_198123	Q96PZ3	Missense_Mutation	SNP	ENST00000297405.5	37	CCDS6315.1	3	0.0013736263736263737	0	0.0	0	0.0	0	0.0	3	0.00395778364116095	T	18.72	3.684011	0.68157	4.54E-4	0.001861	ENSG00000164796	ENST00000343508;ENST00000297405;ENST00000339701;ENST00000455883;ENST00000352409	T;T;T;T;T	0.69926	-0.44;-0.44;-0.44;-0.44;-0.44	4.96	4.96	0.65561	Complement control module (2);Sushi/SCR/CCP (3);	0.084638	0.49305	D	0.000151	D	0.85652	0.5746	M	0.93808	3.46	0.50467	D	0.999878	D;D;D	0.76494	0.999;0.996;0.999	D;D;D	0.72625	0.959;0.926;0.978	D	0.89488	0.3755	10	0.72032	D	0.01	.	15.0773	0.72087	0.0:0.0:0.0:1.0	.	1964;2068;2028	Q7Z407-3;Q7Z407;Q7Z407-2	.;CSMD3_HUMAN;.	C	2028;2068;1338;1964;1998	ENSP00000345799:Y2028C;ENSP00000297405:Y2068C;ENSP00000341558:Y1338C;ENSP00000412263:Y1964C;ENSP00000343124:Y1998C	ENSP00000297405:Y2068C	Y	-	2	0	CSMD3	113433873	1.000000	0.71417	0.980000	0.43619	0.996000	0.88848	5.007000	0.63984	2.205000	0.71048	0.533000	0.62120	TAT	T|0.999;C|0.001	0.001	strong		0.343	CSMD3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347141.1	NM_052900	
TTN	7273	hgsc.bcm.edu	37	2	179606590	179606590	+	Silent	SNP	T	T	C	rs72648918	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr2:179606590T>C	ENST00000591111.1	-	46	10643	c.10419A>G	c.(10417-10419)caA>caG	p.Q3473Q	TTN-AS1_ENST00000578746.1_RNA|TTN_ENST00000342175.6_Silent_p.Q3619Q|TTN-AS1_ENST00000590773.1_RNA|TTN_ENST00000359218.5_Silent_p.Q3552Q|TTN_ENST00000460472.2_Silent_p.Q3427Q|TTN_ENST00000589042.1_Silent_p.Q3790Q|TTN-AS1_ENST00000585451.1_RNA|TTN_ENST00000342992.6_Intron|TTN-AS1_ENST00000582847.1_RNA			Q8WZ42	TITIN_HUMAN	titin	13796					adult heart development (GO:0007512)|blood coagulation (GO:0007596)|cardiac muscle contraction (GO:0060048)|cardiac muscle fiber development (GO:0048739)|cardiac muscle hypertrophy (GO:0003300)|cardiac muscle tissue morphogenesis (GO:0055008)|cardiac myofibril assembly (GO:0055003)|detection of muscle stretch (GO:0035995)|forward locomotion (GO:0043056)|in utero embryonic development (GO:0001701)|mitotic chromosome condensation (GO:0007076)|muscle contraction (GO:0006936)|muscle filament sliding (GO:0030049)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|regulation of catalytic activity (GO:0050790)|regulation of protein kinase activity (GO:0045859)|regulation of relaxation of cardiac muscle (GO:1901897)|response to calcium ion (GO:0051592)|sarcomere organization (GO:0045214)|sarcomerogenesis (GO:0048769)|skeletal muscle myosin thick filament assembly (GO:0030241)|skeletal muscle thin filament assembly (GO:0030240)|somitogenesis (GO:0001756)|striated muscle contraction (GO:0006941)	condensed nuclear chromosome (GO:0000794)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|I band (GO:0031674)|M band (GO:0031430)|nucleus (GO:0005634)|striated muscle thin filament (GO:0005865)|Z disc (GO:0030018)	actin filament binding (GO:0051015)|actinin binding (GO:0042805)|ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|calmodulin binding (GO:0005516)|enzyme binding (GO:0019899)|identical protein binding (GO:0042802)|muscle alpha-actinin binding (GO:0051371)|protease binding (GO:0002020)|protein kinase binding (GO:0019901)|protein self-association (GO:0043621)|protein serine/threonine kinase activity (GO:0004674)|structural constituent of muscle (GO:0008307)|structural molecule activity conferring elasticity (GO:0097493)|telethonin binding (GO:0031433)			NS(24)|autonomic_ganglia(1)|breast(64)|central_nervous_system(14)|cervix(14)|endometrium(96)|haematopoietic_and_lymphoid_tissue(16)|kidney(91)|large_intestine(303)|liver(1)|lung(595)|ovary(58)|pancreas(17)|prostate(38)|skin(60)|stomach(29)|upper_aerodigestive_tract(1)|urinary_tract(26)	1448			OV - Ovarian serous cystadenocarcinoma(117;0.023)|Epithelial(96;0.0454)|all cancers(119;0.134)			TTTTAGATAATTGAAGTTCGG	0.338													T|||	3	0.000599042	0.0	0.0014	5008	,	,		14760	0.0		0.002	False		,,,				2504	0.0				p.Q3790Q		Atlas-SNP	.											.	TTN	18412	.	0			c.A11370G						PASS	.	T	,,,	0,3592		0,0,1796	41.0	37.0	39.0		10281,,10656,10857	-1.6	0.0	2	dbSNP_130	39	8,8112		1,6,4053	no	coding-synonymous,intron,coding-synonymous,coding-synonymous	TTN	NM_003319.4,NM_133378.4,NM_133432.3,NM_133437.3	,,,	1,6,5849	CC,CT,TT		0.0985,0.0,0.0683	,,,	3427/26927,,3552/27052,3619/27119	179606590	8,11704	1796	4060	5856	SO:0001819	synonymous_variant	7273	exon48			AGATAATTGAAGT	X90568	CCDS54421.1, CCDS54422.1, CCDS54423.1, CCDS54424.1, CCDS33337.1, CCDS59435.1, CCDS74610.1	2q31	2014-09-17	2004-02-13		ENSG00000155657	ENSG00000155657		"""Immunoglobulin superfamily / I-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"", ""Fibronectin type III domain containing"""	12403	protein-coding gene	gene with protein product		188840	"""cardiomyopathy, dilated 1G (autosomal dominant)"""	CMD1G		2129545, 10051295	Standard	NM_003319		Approved	CMPD4, FLJ32040, TMD, CMH9, LGMD2J, MYLK5	uc031rqd.1	Q8WZ42	OTTHUMG00000154448	ENST00000591111.1:c.10419A>G	2.37:g.179606590T>C		50.0	0.0	0		63.0	31.0	0.492063	NM_001267550	A6NKB1|E7EQE6|E7ET18|K7ENY1|Q10465|Q10466|Q15598|Q2XUS3|Q32Q60|Q4U1Z6|Q4ZG20|Q6NSG0|Q6PDB1|Q6PJP0|Q7KYM2|Q7KYN4|Q7KYN5|Q7LDM3|Q7Z2X3|Q8TCG8|Q8WZ42|Q8WZ51|Q8WZ52|Q8WZ53|Q8WZB3|Q92761|Q92762|Q9UD97|Q9UP84|Q9Y6L9	Silent	SNP	ENST00000591111.1	37																																																																																				T|0.999;C|0.001	0.001	strong		0.338	TTN-019	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000460310.1	NM_133378	
GDPGP1	390637	hgsc.bcm.edu	37	15	90784632	90784632	+	Missense_Mutation	SNP	G	G	T	rs144466387	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr15:90784632G>T	ENST00000558017.1	+	4	912	c.492G>T	c.(490-492)tgG>tgT	p.W164C	GDPGP1_ENST00000329600.6_Missense_Mutation_p.W164C	NM_001013657.2	NP_001013679.2	Q6ZNW5	GDPP1_HUMAN	GDP-D-glucose phosphorylase 1	164					glucose metabolic process (GO:0006006)	cytoplasm (GO:0005737)	GDP-D-glucose phosphorylase activity (GO:0080048)|guanyl-nucleotide exchange factor activity (GO:0005085)|hydrolase activity (GO:0016787)|nucleotide binding (GO:0000166)|nucleotidyltransferase activity (GO:0016779)										CCCTGGAGTGGGGCCACGTGC	0.652													G|||	2	0.000399361	0.0	0.0014	5008	,	,		16490	0.0		0.001	False		,,,				2504	0.0				p.W164C		Atlas-SNP	.											.	.	.	.	0			c.G492T						PASS	.	G	CYS/TRP	0,4398		0,0,2199	49.0	53.0	52.0		492	3.9	1.0	15	dbSNP_134	52	13,8583	9.8+/-36.6	0,13,4285	yes	missense	C15orf58	NM_001013657.2	215	0,13,6484	TT,TG,GG		0.1512,0.0,0.1	probably-damaging	164/386	90784632	13,12981	2199	4298	6497	SO:0001583	missense	390637	exon4			GGAGTGGGGCCAC		CCDS32327.1	15q26.1	2012-05-04	2012-05-04	2012-05-04	ENSG00000183208	ENSG00000183208	2.7.7.78		34360	protein-coding gene	gene with protein product			"""chromosome 15 open reading frame 58"""	C15orf58		21507950	Standard	NM_001013657		Approved		uc002bpc.3	Q6ZNW5		ENST00000558017.1:c.492G>T	15.37:g.90784632G>T	ENSP00000452793:p.Trp164Cys	52.0	0.0	0		51.0	24.0	0.470588	NM_001013657		Missense_Mutation	SNP	ENST00000558017.1	37	CCDS32327.1	1	4.578754578754579E-4	0	0.0	1	0.0027624309392265192	0	0.0	0	0.0	G	15.09	2.729619	0.48833	0.0	0.001512	ENSG00000183208	ENST00000329600	T	0.22539	1.95	5.85	3.93	0.45458	.	0.291899	0.33591	N	0.004747	T	0.35248	0.0925	M	0.67953	2.075	0.58432	D	0.999999	D	0.64830	0.994	P	0.58391	0.838	T	0.04053	-1.0981	10	0.38643	T	0.18	-6.2663	9.1104	0.36723	0.0:0.2636:0.4647:0.2716	.	164	Q6ZNW5	VTC2_HUMAN	C	164	ENSP00000368405:W164C	ENSP00000368405:W164C	W	+	3	0	C15orf58	88585636	1.000000	0.71417	1.000000	0.80357	0.710000	0.40934	2.143000	0.42187	0.776000	0.33473	-0.165000	0.13383	TGG	G|0.999;T|0.001	0.001	strong		0.652	GDPGP1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000416973.1	NM_001013657	
ZNF57	126295	hgsc.bcm.edu	37	19	2917178	2917178	+	Missense_Mutation	SNP	G	G	A	rs61742111	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr19:2917178G>A	ENST00000306908.5	+	4	707	c.559G>A	c.(559-561)Gga>Aga	p.G187R	ZNF57_ENST00000523428.1_Missense_Mutation_p.G155R|AC006277.2_ENST00000520090.2_RNA	NM_173480.2	NP_775751.1	Q68EA5	ZNF57_HUMAN	zinc finger protein 57	187					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)|kidney(2)|large_intestine(5)|lung(2)|ovary(1)|pancreas(1)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	18				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)|GBM - Glioblastoma multiforme(1328;0.00161)|STAD - Stomach adenocarcinoma(1328;0.18)		ACACAGTCACGGAAGAACTGA	0.498													G|||	131	0.0261581	0.0257	0.0288	5008	,	,		21208	0.001		0.0169	False		,,,				2504	0.0603				p.G187R	NSCLC(150;910 1964 4303 10464 26498)	Atlas-SNP	.											.	ZNF57	57	.	0			c.G559A						PASS	.	G	ARG/GLY	95,4311	77.3+/-115.6	0,95,2108	109.0	81.0	90.0		559	-3.2	0.0	19	dbSNP_129	90	209,8391	88.9+/-151.2	4,201,4095	yes	missense	ZNF57	NM_173480.2	125	4,296,6203	AA,AG,GG		2.4302,2.1562,2.3374	benign	187/556	2917178	304,12702	2203	4300	6503	SO:0001583	missense	126295	exon4			AGTCACGGAAGAA	M88368	CCDS12098.1	19p13.3	2013-01-08			ENSG00000171970	ENSG00000171970		"""Zinc fingers, C2H2-type"", ""-"""	13125	protein-coding gene	gene with protein product			"""zinc finger protein 424"""	ZNF424		1505991	Standard	NM_173480		Approved		uc002lwr.3	Q68EA5	OTTHUMG00000164485	ENST00000306908.5:c.559G>A	19.37:g.2917178G>A	ENSP00000303696:p.Gly187Arg	108.0	0.0	0		107.0	46.0	0.429907	NM_173480	Q8N6R9	Missense_Mutation	SNP	ENST00000306908.5	37	CCDS12098.1	41	0.018772893772893772	17	0.034552845528455285	13	0.03591160220994475	1	0.0017482517482517483	10	0.013192612137203167	G	11.69	1.714569	0.30413	0.021562	0.024302	ENSG00000171970	ENST00000306908;ENST00000395204;ENST00000523428	T;T	0.14144	2.53;2.53	1.7	-3.23	0.05109	Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.00666	0.0022	N	0.00599	-1.345	0.09310	N	1	B	0.17667	0.023	B	0.08055	0.003	T	0.39292	-0.9621	9	0.44086	T	0.13	.	3.5597	0.07877	0.3623:0.3552:0.2825:0.0	rs61742111	187	Q68EA5	ZNF57_HUMAN	R	187;189;155	ENSP00000303696:G187R;ENSP00000430223:G155R	ENSP00000303696:G187R	G	+	1	0	ZNF57	2868178	0.006000	0.16342	0.000000	0.03702	0.004000	0.04260	-0.336000	0.07863	-0.406000	0.07588	0.407000	0.27541	GGA	G|0.973;A|0.027	0.027	strong		0.498	ZNF57-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000378969.1	NM_173480	
FOCAD	54914	hgsc.bcm.edu	37	9	20885216	20885216	+	Missense_Mutation	SNP	C	C	T	rs187654100		TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr9:20885216C>T	ENST00000380249.1	+	23	2976	c.2612C>T	c.(2611-2613)gCt>gTt	p.A871V	FOCAD_ENST00000338382.6_Missense_Mutation_p.A871V|FOCAD_ENST00000605086.1_Missense_Mutation_p.A307V	NM_017794.3	NP_060264.3	Q5VW36	FOCAD_HUMAN	focadhesin	871						focal adhesion (GO:0005925)|integral component of membrane (GO:0016021)											ACTTCACTTGCTCTTGTACAT	0.368													C|||	1	0.000199681	0.0	0.0014	5008	,	,		13975	0.0		0.0	False		,,,				2504	0.0				p.A871V		Atlas-SNP	.											.	.	.	.	0			c.C2612T						PASS	.						231.0	199.0	209.0					9																	20885216		2203	4300	6503	SO:0001583	missense	54914	exon23			CACTTGCTCTTGT	AB058700	CCDS34993.1	9p21	2012-03-23	2012-03-23	2012-03-23	ENSG00000188352	ENSG00000188352			23377	protein-coding gene	gene with protein product		614606	"""KIAA1797"""	KIAA1797		22427331	Standard	XM_006716794		Approved	FLJ20375	uc003zog.1	Q5VW36	OTTHUMG00000066930	ENST00000380249.1:c.2612C>T	9.37:g.20885216C>T	ENSP00000369599:p.Ala871Val	263.0	0.0	0		260.0	128.0	0.492308	NM_017794	D3DRJ9|Q6ZME1|Q8IZG0|Q96JM8|Q96MS9|Q9BVF3|Q9NX87	Missense_Mutation	SNP	ENST00000380249.1	37	CCDS34993.1	1	4.578754578754579E-4	0	0.0	1	0.0027624309392265192	0	0.0	0	0.0	C	14.10	2.435384	0.43224	.	.	ENSG00000188352	ENST00000380249;ENST00000338382	T;T	0.08370	3.1;3.1	5.3	5.3	0.74995	Armadillo-type fold (1);	0.224065	0.46145	D	0.000317	T	0.09686	0.0238	L	0.53249	1.67	0.53005	D	0.999965	P	0.43412	0.806	B	0.32393	0.145	T	0.21895	-1.0232	10	0.29301	T	0.29	-28.1342	19.3232	0.94250	0.0:1.0:0.0:0.0	.	871	Q5VW36	K1797_HUMAN	V	871	ENSP00000369599:A871V;ENSP00000344307:A871V	ENSP00000344307:A871V	A	+	2	0	KIAA1797	20875216	1.000000	0.71417	0.526000	0.27913	0.138000	0.21146	5.289000	0.65656	2.633000	0.89246	0.650000	0.86243	GCT	C|1.000;T|0.000	0.000	strong		0.368	FOCAD-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000143442.1	NM_017794	
SLCO3A1	28232	hgsc.bcm.edu	37	15	92647684	92647684	+	Missense_Mutation	SNP	A	A	C	rs72655652	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr15:92647684A>C	ENST00000318445.6	+	4	1135	c.921A>C	c.(919-921)agA>agC	p.R307S	SLCO3A1_ENST00000424469.2_Missense_Mutation_p.R307S|SLCO3A1_ENST00000555549.1_3'UTR	NM_013272.3	NP_037404.2	Q9UIG8	SO3A1_HUMAN	solute carrier organic anion transporter family, member 3A1	307					sodium-independent organic anion transport (GO:0043252)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	transporter activity (GO:0005215)			breast(1)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(7)|lung(6)|pancreas(1)|prostate(1)|skin(2)	25	Lung NSC(78;0.0158)|all_lung(78;0.0255)		BRCA - Breast invasive adenocarcinoma(143;0.0841)		Alprostadil(DB00770)|Aminohippurate(DB00345)|Benzylpenicillin(DB01053)|Conjugated Estrogens(DB00286)|Dinoprost Tromethamine(DB01160)|Dinoprostone(DB00917)|Iloprost(DB01088)|Methotrexate(DB00563)	TCTCCGAAAGAGAATACGAGA	0.592													A|||	35	0.00698882	0.0008	0.0058	5008	,	,		16771	0.0		0.0139	False		,,,				2504	0.0164				p.R307S		Atlas-SNP	.											.	SLCO3A1	84	.	0			c.A921C						PASS	.	A	SER/ARG,SER/ARG	7,4389	15.5+/-35.6	0,7,2191	81.0	71.0	74.0		921,921	5.3	1.0	15	dbSNP_130	74	123,8473	64.2+/-126.4	2,119,4177	yes	missense,missense	SLCO3A1	NM_001145044.1,NM_013272.3	110,110	2,126,6368	CC,CA,AA		1.4309,0.1592,1.0006	benign,benign	307/693,307/711	92647684	130,12862	2198	4298	6496	SO:0001583	missense	28232	exon4			CGAAAGAGAATAC	AB031050	CCDS10371.1, CCDS45354.1	15q26	2013-05-22	2003-11-25	2003-11-26	ENSG00000176463	ENSG00000176463		"""Solute carriers"""	10952	protein-coding gene	gene with protein product		612435	"""solute carrier family 21 (organic anion transporter), member 11"""	SLC21A11			Standard	NM_001145044		Approved	OATP-D, OATP3A1	uc002bqx.2	Q9UIG8	OTTHUMG00000149846	ENST00000318445.6:c.921A>C	15.37:g.92647684A>C	ENSP00000320634:p.Arg307Ser	157.0	0.0	0		191.0	96.0	0.502618	NM_013272	A8K4A7|B3KPY5|B3KUR7|C6G486|Q9BW73|Q9GZV2	Missense_Mutation	SNP	ENST00000318445.6	37	CCDS10371.1	14	0.00641025641025641	0	0.0	3	0.008287292817679558	0	0.0	11	0.014511873350923483	A	10.86	1.469546	0.26423	0.001592	0.014309	ENSG00000176463	ENST00000318445;ENST00000424469;ENST00000556649;ENST00000555549	T;T	0.38722	1.12;1.12	5.31	5.31	0.75309	Major facilitator superfamily domain, general substrate transporter (1);	0.648102	0.16571	N	0.208631	T	0.10680	0.0261	N	0.01640	-0.785	0.46203	D	0.998922	B;B;B	0.10296	0.001;0.003;0.0	B;B;B	0.11329	0.001;0.001;0.006	T	0.13737	-1.0498	10	0.09084	T	0.74	.	8.0237	0.30425	0.8765:0.0:0.1235:0.0	.	249;307;307	Q9UIG8-3;Q9UIG8-2;Q9UIG8	.;.;SO3A1_HUMAN	S	307;307;100;26	ENSP00000320634:R307S;ENSP00000387846:R307S	ENSP00000320634:R307S	R	+	3	2	SLCO3A1	90448688	1.000000	0.71417	0.988000	0.46212	0.864000	0.49448	2.032000	0.41127	1.987000	0.57996	0.533000	0.62120	AGA	A|0.990;C|0.010	0.010	strong		0.592	SLCO3A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000313529.1	NM_013272	
EFCAB5	374786	hgsc.bcm.edu	37	17	28381069	28381069	+	Silent	SNP	A	A	G			TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr17:28381069A>G	ENST00000394835.3	+	10	2289	c.2097A>G	c.(2095-2097)gaA>gaG	p.E699E	EFCAB5_ENST00000536908.2_Silent_p.E643E|EFCAB5_ENST00000320856.5_Silent_p.E699E|EFCAB5_ENST00000541045.1_Silent_p.E356E|EFCAB5_ENST00000378738.3_Silent_p.E699E|EFCAB5_ENST00000394832.2_Silent_p.E699E	NM_198529.3	NP_940931	A4FU69	EFCB5_HUMAN	EF-hand calcium binding domain 5	699							calcium ion binding (GO:0005509)			breast(7)|endometrium(2)|kidney(4)|large_intestine(11)|lung(14)|ovary(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	43						CTCTACAGGAAAAGAGGTCTT	0.378																																					p.E699E		Atlas-SNP	.											.	EFCAB5	122	.	0			c.A2097G						PASS	.						33.0	31.0	32.0					17																	28381069		1831	4083	5914	SO:0001819	synonymous_variant	374786	exon10			ACAGGAAAAGAGG	AL833911	CCDS11254.2, CCDS54103.1	17q11.2	2013-01-10			ENSG00000176927	ENSG00000176927		"""EF-hand domain containing"""	24801	protein-coding gene	gene with protein product							Standard	NM_198529		Approved	FLJ46247	uc002het.3	A4FU69	OTTHUMG00000132753	ENST00000394835.3:c.2097A>G	17.37:g.28381069A>G		180.0	0.0	0		222.0	112.0	0.504505	NM_198529	B2RPN0|B4DS75|B4DZR5|F5GYL2|Q0VD68|Q6ZRM6|Q8NDG9	Silent	SNP	ENST00000394835.3	37	CCDS11254.2																																																																																			.	.	none		0.378	EFCAB5-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256120.4	NM_198529	
SPZ1	84654	hgsc.bcm.edu	37	5	79616400	79616400	+	Missense_Mutation	SNP	G	G	A	rs200562315	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr5:79616400G>A	ENST00000296739.4	+	1	611	c.366G>A	c.(364-366)atG>atA	p.M122I		NM_032567.3	NP_115956.3	Q9BXG8	SPZ1_HUMAN	spermatogenic leucine zipper 1	122					transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	DNA binding (GO:0003677)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.M122I(1)		endometrium(2)|kidney(5)|large_intestine(4)|lung(12)|ovary(1)|skin(2)	26		Lung NSC(167;0.0393)|all_lung(232;0.0428)|Ovarian(174;0.113)		OV - Ovarian serous cystadenocarcinoma(54;3.43e-47)|Epithelial(54;2.25e-41)|all cancers(79;4.19e-36)		TCAATGAAATGTTATCAACAA	0.368																																					p.M122I		Atlas-SNP	.											SPZ1,trunk,malignant_melanoma,0,1	SPZ1	60	1	1	Substitution - Missense(1)	skin(1)	c.G366A						scavenged	.						49.0	44.0	45.0					5																	79616400		1799	4058	5857	SO:0001583	missense	84654	exon1			TGAAATGTTATCA		CCDS43336.1	5q14.1	2014-06-13				ENSG00000164299			30721	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 148"""					11165476, 12778315, 15226296, 15829580, 15899793	Standard	NM_032567		Approved	NYD-TSP1, FLJ25709, PPP1R148	uc003kgn.3	Q9BXG8		ENST00000296739.4:c.366G>A	5.37:g.79616400G>A	ENSP00000369611:p.Met122Ile	275.0	0.0	0		265.0	12.0	0.045283	NM_032567	B2RA21|Q8N4P1|Q8N7E9	Missense_Mutation	SNP	ENST00000296739.4	37	CCDS43336.1	.	.	.	.	.	.	.	.	.	.	G	8.567	0.879064	0.17395	.	.	ENSG00000164299	ENST00000511881;ENST00000296739	T;T	0.39787	1.06;1.62	2.92	-2.42	0.06542	.	.	.	.	.	T	0.17238	0.0414	N	0.05078	-0.115	0.09310	N	1	B	0.20988	0.05	B	0.10450	0.005	T	0.15178	-1.0446	9	0.33940	T	0.23	.	4.398	0.11372	0.5786:0.0:0.2498:0.1716	.	122	Q9BXG8	SPZ1_HUMAN	I	122	ENSP00000426530:M122I;ENSP00000369611:M122I	ENSP00000369611:M122I	M	+	3	0	SPZ1	79652156	0.000000	0.05858	0.000000	0.03702	0.514000	0.34195	-1.754000	0.01816	-0.613000	0.05694	0.313000	0.20887	ATG	G|0.998;A|0.002	0.002	strong		0.368	SPZ1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000369322.1	NM_032567	
PRDM16	63976	hgsc.bcm.edu	37	1	3319541	3319541	+	Missense_Mutation	SNP	G	G	A	rs141374404		TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr1:3319541G>A	ENST00000270722.5	+	6	912	c.863G>A	c.(862-864)cGg>cAg	p.R288Q	PRDM16_ENST00000378391.2_Missense_Mutation_p.R288Q|PRDM16_ENST00000511072.1_Missense_Mutation_p.R289Q|PRDM16_ENST00000442529.2_Missense_Mutation_p.R288Q|PRDM16_ENST00000512462.1_3'UTR|PRDM16_ENST00000441472.2_Missense_Mutation_p.R288Q|PRDM16_ENST00000378398.3_Missense_Mutation_p.R289Q|PRDM16_ENST00000514189.1_Missense_Mutation_p.R289Q			Q9HAZ2	PRD16_HUMAN	PR domain containing 16	288					brown fat cell differentiation (GO:0050873)|negative regulation of granulocyte differentiation (GO:0030853)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|negative regulation of transforming growth factor beta receptor signaling pathway (GO:0030512)|neurogenesis (GO:0022008)|palate development (GO:0060021)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of cellular respiration (GO:0043457)|somatic stem cell maintenance (GO:0035019)|tongue development (GO:0043586)|transcription, DNA-templated (GO:0006351)|white fat cell differentiation (GO:0050872)	nucleus (GO:0005634)|transcriptional repressor complex (GO:0017053)	metal ion binding (GO:0046872)|sequence-specific DNA binding (GO:0043565)|transcription coactivator activity (GO:0003713)			breast(4)|central_nervous_system(1)|endometrium(5)|kidney(4)|large_intestine(7)|lung(22)|ovary(2)|pancreas(1)|prostate(2)|skin(7)|upper_aerodigestive_tract(1)|urinary_tract(3)	59	all_cancers(77;0.00208)|all_epithelial(69;0.000732)|Ovarian(185;0.0634)|Lung NSC(156;0.109)|all_lung(157;0.111)	all_epithelial(116;2.03e-21)|all_lung(118;7.55e-09)|Lung NSC(185;1.28e-06)|Breast(487;0.000792)|Renal(390;0.00137)|Hepatocellular(190;0.00515)|Myeloproliferative disorder(586;0.0267)|Ovarian(437;0.0365)|Lung SC(97;0.114)|Medulloblastoma(700;0.134)		Epithelial(90;5.59e-35)|OV - Ovarian serous cystadenocarcinoma(86;1.99e-20)|GBM - Glioblastoma multiforme(42;3.72e-11)|Colorectal(212;0.000425)|BRCA - Breast invasive adenocarcinoma(365;0.000946)|COAD - Colon adenocarcinoma(227;0.000968)|Kidney(185;0.00155)|STAD - Stomach adenocarcinoma(132;0.00644)|KIRC - Kidney renal clear cell carcinoma(229;0.0175)|Lung(427;0.137)		GACTGCGAGCGGATGTTCCCC	0.657			T	EVI1	"""MDS, AML"""								G|||	1	0.000199681	0.0	0.0	5008	,	,		15244	0.0		0.001	False		,,,				2504	0.0				p.R288Q		Atlas-SNP	.		Dom	yes		1	1p36.23-p33	63976	PR domain containing 16		L	.	PRDM16	147	.	0			c.G863A						PASS	.						44.0	56.0	52.0					1																	3319541		2186	4274	6460	SO:0001583	missense	63976	exon6			GCGAGCGGATGTT	AF294278	CCDS41236.1, CCDS44048.1, CCDS41236.2, CCDS44048.2	1p36.23-p33	2013-01-08			ENSG00000142611	ENSG00000142611		"""Zinc fingers, C2H2-type"""	14000	protein-coding gene	gene with protein product	"""MDS1/EVI1-like"", ""PR-domain zinc finger protein 16"", ""transcription factor MEL1"""	605557				11050005	Standard	NM_199454		Approved	MEL1, PFM13, KIAA1675, MGC166915	uc001akf.3	Q9HAZ2	OTTHUMG00000000581	ENST00000270722.5:c.863G>A	1.37:g.3319541G>A	ENSP00000270722:p.Arg288Gln	225.0	0.0	0		266.0	115.0	0.432331	NM_022114	A6NHQ8|B1AJP7|B1AJP8|B1AJP9|B1WB48|Q8WYJ9|Q9C0I8	Missense_Mutation	SNP	ENST00000270722.5	37	CCDS41236.2	1	4.578754578754579E-4	0	0.0	0	0.0	0	0.0	1	0.0013192612137203166	G	6.953	0.545736	0.13312	.	.	ENSG00000142611	ENST00000511072;ENST00000378398;ENST00000441472;ENST00000442529;ENST00000378391;ENST00000514189;ENST00000270722;ENST00000512462;ENST00000408992;ENST00000509860	T;T;T;T;T;T;T;T;T	0.07567	3.18;3.18;3.18;3.18;3.18;3.18;3.18;3.18;3.18	4.32	3.39	0.38822	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	0.336202	0.19830	U	0.105113	T	0.09862	0.0242	L	0.29908	0.895	0.27992	N	0.935619	P;D;P;B	0.62365	0.85;0.991;0.636;0.39	B;P;B;B	0.49708	0.115;0.62;0.089;0.019	T	0.15607	-1.0431	10	0.21014	T	0.42	.	13.2179	0.59871	0.0:0.0:0.8395:0.1605	.	288;288;288;288	Q9HAZ2;Q9HAZ2-2;F8WEV3;D3YTA5	PRD16_HUMAN;.;.;.	Q	289;289;288;288;288;289;288;104;104;97	ENSP00000426975:R289Q;ENSP00000367651:R289Q;ENSP00000407968:R288Q;ENSP00000405253:R288Q;ENSP00000367643:R288Q;ENSP00000421400:R289Q;ENSP00000270722:R288Q;ENSP00000422504:R104Q;ENSP00000425796:R97Q	ENSP00000270722:R288Q	R	+	2	0	PRDM16	3309401	1.000000	0.71417	1.000000	0.80357	0.632000	0.37999	5.777000	0.68931	0.788000	0.33755	0.561000	0.74099	CGG	G|1.000;A|0.000	0.000	strong		0.657	PRDM16-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000001382.3	NM_022114	
DCSTAMP	81501	hgsc.bcm.edu	37	8	105360994	105360994	+	Missense_Mutation	SNP	C	C	A	rs61682032	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr8:105360994C>A	ENST00000297581.2	+	2	263	c.214C>A	c.(214-216)Ctg>Atg	p.L72M	DCSTAMP_ENST00000517991.1_Missense_Mutation_p.L72M|DPYS_ENST00000521601.1_Intron	NM_030788.3	NP_110415.1	Q9H295	DCSTP_HUMAN	dendrocyte expressed seven transmembrane protein	72					cellular response to interleukin-4 (GO:0071353)|cellular response to macrophage colony-stimulating factor stimulus (GO:0036006)|cellular response to tumor necrosis factor (GO:0071356)|membrane fusion (GO:0061025)|myeloid dendritic cell differentiation (GO:0043011)|negative regulation of cell growth (GO:0030308)|osteoclast differentiation (GO:0030316)|osteoclast fusion (GO:0072675)|positive regulation of bone resorption (GO:0045780)|positive regulation of macrophage fusion (GO:0034241)|positive regulation of monocyte differentiation (GO:0045657)	cell surface (GO:0009986)|endoplasmic reticulum membrane (GO:0005789)|endosome membrane (GO:0010008)|integral component of endoplasmic reticulum membrane (GO:0030176)|integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)											GTGTGTTCTGCTGTGTTGCTC	0.522													C|||	179	0.0357428	0.0794	0.0144	5008	,	,		18689	0.0288		0.0189	False		,,,				2504	0.0164				p.L72M		Atlas-SNP	.											.	.	.	.	0			c.C214A						PASS	.	C	MET/LEU	252,4154	145.7+/-180.5	5,242,1956	129.0	117.0	121.0		214	4.1	0.8	8	dbSNP_129	121	73,8527	43.1+/-100.9	1,71,4228	yes	missense	TM7SF4	NM_030788.2	15	6,313,6184	AA,AC,CC		0.8488,5.7195,2.4988	probably-damaging	72/471	105360994	325,12681	2203	4300	6503	SO:0001583	missense	81501	exon2			GTTCTGCTGTGTT	AF305068	CCDS6301.1, CCDS59111.1	8q22.3	2012-08-10	2012-03-27	2012-03-27	ENSG00000164935	ENSG00000164935			18549	protein-coding gene	gene with protein product	"""Dendritic cells (DC)-specific transmembrane protein"", ""IL-Four INDuced"""	605933	"""transmembrane 7 superfamily member 4"""	TM7SF4		11169400, 11345591	Standard	NM_030788		Approved	DC-STAMP, FIND	uc003ylx.2	Q9H295	OTTHUMG00000164890	ENST00000297581.2:c.214C>A	8.37:g.105360994C>A	ENSP00000297581:p.Leu72Met	157.0	0.0	0		172.0	81.0	0.47093	NM_001257317	B7ZVW2|E7ESG0|Q2M2D5	Missense_Mutation	SNP	ENST00000297581.2	37	CCDS6301.1	68	0.031135531135531136	32	0.06504065040650407	5	0.013812154696132596	19	0.033216783216783216	12	0.0158311345646438	C	14.48	2.548417	0.45383	0.057195	0.008488	ENSG00000164935	ENST00000297581;ENST00000517991	T	0.39229	1.09	5.84	4.05	0.47172	.	0.138356	0.49305	D	0.000154	T	0.08980	0.0222	M	0.64997	1.995	0.22779	N	0.998749	D	0.89917	1.0	D	0.79108	0.992	T	0.02437	-1.1159	9	.	.	.	-11.7717	8.7709	0.34731	0.0:0.7774:0.0:0.2226	rs61682032	72	Q9H295	TM7S4_HUMAN	M	72	ENSP00000297581:L72M	.	L	+	1	2	TM7SF4	105430170	.	.	0.761000	0.31378	0.580000	0.36256	.	.	1.496000	0.48567	0.655000	0.94253	CTG	C|0.973;A|0.027	0.027	strong		0.522	DCSTAMP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000380810.1	NM_030788	
FBF1	85302	hgsc.bcm.edu	37	17	73914040	73914040	+	Silent	SNP	C	C	T	rs376546796		TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr17:73914040C>T	ENST00000586717.1	-	21	2589	c.2316G>A	c.(2314-2316)ggG>ggA	p.G772G	FBF1_ENST00000319129.5_Silent_p.G771G|FBF1_ENST00000389570.4_Silent_p.G772G			Q8TES7	FBF1_HUMAN	Fas (TNFRSF6) binding factor 1	772					apical junction assembly (GO:0043297)|cilium assembly (GO:0042384)|establishment of epithelial cell polarity (GO:0090162)	cell junction (GO:0030054)|centriole (GO:0005814)|ciliary transition fiber (GO:0097539)|spindle pole (GO:0000922)				large_intestine(2)|ovary(1)|upper_aerodigestive_tract(1)	4						GCTGCCGGATCCCCAGCTCCC	0.677																																					p.G771G		Atlas-SNP	.											.	FBF1	48	.	0			c.G2313A						PASS	.	C		1,4061		0,1,2030	28.0	32.0	31.0		2313	-4.2	0.1	17		31	0,8382		0,0,4191	no	coding-synonymous	FBF1	NM_001080542.1		0,1,6221	TT,TC,CC		0.0,0.0246,0.0080		771/1134	73914040	1,12443	2031	4191	6222	SO:0001819	synonymous_variant	85302	exon21			CCGGATCCCCAGC	AK074045	CCDS45779.1	17q25.3	2011-04-21			ENSG00000188878	ENSG00000188878			24674	protein-coding gene	gene with protein product	"""albatross"""					11347906	Standard	NM_001080542		Approved	FLJ00103, FBF-1, KIAA1863, ALB	uc002jqc.3	Q8TES7		ENST00000586717.1:c.2316G>A	17.37:g.73914040C>T		56.0	0.0	0		53.0	33.0	0.622642	NM_001080542	B5MEM5|Q96IF6|Q96JG4|Q96MA8	Silent	SNP	ENST00000586717.1	37																																																																																				.	.	weak		0.677	FBF1-001	KNOWN	basic|appris_candidate	protein_coding	protein_coding	OTTHUMT00000448945.2	NM_001080542	
PRR27	401137	hgsc.bcm.edu	37	4	71024467	71024467	+	Silent	SNP	T	T	G	rs201990073		TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr4:71024467T>G	ENST00000344526.5	+	3	687	c.498T>G	c.(496-498)gcT>gcG	p.A166A	C4orf40_ENST00000502294.1_Silent_p.A166A|C4orf40_ENST00000502441.2_3'UTR	NM_214711.3	NP_999876.2	Q6MZM9	PRR27_HUMAN		166	Ala/Pro-rich.					extracellular vesicular exosome (GO:0070062)		p.A166V(1)		breast(2)|central_nervous_system(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(1)|lung(3)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	12						CTGTTGGAGCTGAGCCTGCTG	0.627																																					p.A166A		Atlas-SNP	.											.	C4orf40	19	.	1	Substitution - Missense(1)	lung(1)	c.T498G						PASS	.						30.0	31.0	30.0					4																	71024467		2203	4297	6500	SO:0001819	synonymous_variant	401137	exon3			TGGAGCTGAGCCT																												ENST00000344526.5:c.498T>G	4.37:g.71024467T>G		142.0	0.0	0		114.0	26.0	0.22807	NM_214711	A8MXP0|Q6MZR6	Silent	SNP	ENST00000344526.5	37	CCDS3535.1																																																																																			T|0.999;G|0.001	0.001	weak		0.627	C4orf40-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251558.1		
KIAA0195	9772	hgsc.bcm.edu	37	17	73492494	73492494	+	Missense_Mutation	SNP	C	C	G			TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr17:73492494C>G	ENST00000314256.7	+	24	3579	c.3185C>G	c.(3184-3186)cCc>cGc	p.P1062R	AC100787.1_ENST00000579379.1_RNA|KIAA0195_ENST00000375248.5_Missense_Mutation_p.P1072R|KIAA0195_ENST00000579208.1_Missense_Mutation_p.P713R	NM_014738.4	NP_055553.3	Q12767	K0195_HUMAN	KIAA0195	1062						integral component of membrane (GO:0016021)|nucleus (GO:0005634)				breast(2)|endometrium(5)|kidney(2)|large_intestine(7)|lung(17)|ovary(5)|skin(2)|stomach(1)|urinary_tract(1)	42	all_cancers(13;3.15e-09)|all_epithelial(9;5.94e-10)|Breast(9;1.85e-09)|all_lung(278;0.246)		all cancers(21;5.01e-07)|Epithelial(20;5e-06)|Lung(188;0.0809)|LUSC - Lung squamous cell carcinoma(166;0.154)			AACAGCCTGCCCTGTTCCCTG	0.617																																					p.P1062R		Atlas-SNP	.											.	KIAA0195	102	.	0			c.C3185G						PASS	.						57.0	54.0	55.0					17																	73492494		2203	4300	6503	SO:0001583	missense	9772	exon24			GCCTGCCCTGTTC		CCDS32732.1	17q25.1	2012-03-01			ENSG00000177728	ENSG00000177728			28983	protein-coding gene	gene with protein product						8724849	Standard	NM_014738		Approved	TMEM94	uc002jnz.4	Q12767		ENST00000314256.7:c.3185C>G	17.37:g.73492494C>G	ENSP00000313885:p.Pro1062Arg	170.0	0.0	0		199.0	100.0	0.502513	NM_014738	O75536|Q86XF1	Missense_Mutation	SNP	ENST00000314256.7	37	CCDS32732.1	.	.	.	.	.	.	.	.	.	.	C	14.72	2.620105	0.46736	.	.	ENSG00000177728	ENST00000314256;ENST00000375248	T;T	0.55760	0.5;0.5	5.54	5.54	0.83059	ATPase, P-type,  transmembrane domain (1);	0.253079	0.41500	D	0.000877	T	0.67674	0.2918	M	0.67397	2.05	0.53688	D	0.999973	B;P;P;B	0.39535	0.232;0.573;0.677;0.437	B;B;P;B	0.50970	0.077;0.219;0.655;0.109	T	0.68784	-0.5317	10	0.87932	D	0	-32.2942	19.8311	0.96636	0.0:1.0:0.0:0.0	.	1072;1072;1062;1062	B4DGC6;C9JL75;Q12767-2;Q12767	.;.;.;K0195_HUMAN	R	1062;1072	ENSP00000313885:P1062R;ENSP00000364397:P1072R	ENSP00000313885:P1062R	P	+	2	0	KIAA0195	71004089	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	4.656000	0.61483	2.768000	0.95171	0.561000	0.74099	CCC	.	.	none		0.617	KIAA0195-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000447303.1	NM_014738	
SYT8	90019	hgsc.bcm.edu	37	11	1857207	1857207	+	Missense_Mutation	SNP	G	G	A	rs139074200		TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr11:1857207G>A	ENST00000381968.3	+	4	520	c.392G>A	c.(391-393)aGc>aAc	p.S131N	SYT8_ENST00000436964.2_Missense_Mutation_p.S117N|SYT8_ENST00000341958.3_Missense_Mutation_p.S117N|SYT8_ENST00000483280.1_3'UTR|SYT8_ENST00000535046.1_Missense_Mutation_p.S269N	NM_138567.3	NP_612634	Q8NBV8	SYT8_HUMAN	synaptotagmin VIII	131	C2 1. {ECO:0000255|PROSITE- ProRule:PRU00041}.				acrosome reaction (GO:0007340)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|synaptic vesicle (GO:0008021)	transporter activity (GO:0005215)			breast(1)|large_intestine(1)|lung(2)|ovary(1)|skin(1)	6		all_epithelial(84;0.000138)|Breast(177;0.000962)|Ovarian(85;0.0014)|Medulloblastoma(188;0.0109)|all_neural(188;0.0299)|Lung NSC(207;0.229)		BRCA - Breast invasive adenocarcinoma(625;0.00136)|Lung(200;0.0681)|LUSC - Lung squamous cell carcinoma(625;0.082)		GACTTTGGAAGCCAGGAGGTG	0.652													G|||	1	0.000199681	0.0	0.0	5008	,	,		15882	0.0		0.001	False		,,,				2504	0.0				p.S131N		Atlas-SNP	.											.	SYT8	29	.	0			c.G392A						PASS	.						43.0	48.0	46.0					11																	1857207		2202	4299	6501	SO:0001583	missense	90019	exon4			TTGGAAGCCAGGA	AL137708	CCDS7726.2	11p15.5	2013-01-21			ENSG00000149043	ENSG00000149043		"""Synaptotagmins"""	19264	protein-coding gene	gene with protein product		607719				7791877	Standard	XM_005253216		Approved	DKFZp434K0322	uc001lue.1	Q8NBV8	OTTHUMG00000009026	ENST00000381968.3:c.392G>A	11.37:g.1857207G>A	ENSP00000371394:p.Ser131Asn	91.0	0.0	0		73.0	32.0	0.438356	NM_138567	A6NFJ4|Q9NSV9	Missense_Mutation	SNP	ENST00000381968.3	37	CCDS7726.2	1	4.578754578754579E-4	0	0.0	0	0.0	0	0.0	1	0.0013192612137203166	g	4.933	0.173312	0.09391	.	.	ENSG00000149043	ENST00000436964;ENST00000535046;ENST00000381968;ENST00000341958	T;T;T;T	0.19669	2.13;2.13;3.08;3.08	3.01	0.926	0.19430	C2 calcium/lipid-binding domain, CaLB (1);	.	.	.	.	T	0.12008	0.0292	L	0.28740	0.885	0.09310	N	0.999999	B;B;B	0.19583	0.037;0.031;0.031	B;B;B	0.15052	0.012;0.009;0.009	T	0.32587	-0.9901	9	0.26408	T	0.33	.	3.0174	0.06064	0.1045:0.3185:0.4148:0.1622	.	117;131;117	C9JSK3;Q8NBV8;A6NCR4	.;SYT8_HUMAN;.	N	117;269;131;117	ENSP00000414626:S117N;ENSP00000443325:S269N;ENSP00000371394:S131N;ENSP00000343691:S117N	ENSP00000343691:S117N	S	+	2	0	SYT8	1813783	0.003000	0.15002	0.654000	0.29608	0.166000	0.22503	0.440000	0.21592	0.108000	0.17862	0.305000	0.20034	AGC	G|1.000;A|0.000	0.000	strong		0.652	SYT8-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000025013.4		
IQCH	64799	hgsc.bcm.edu	37	15	67692566	67692566	+	Missense_Mutation	SNP	T	T	C	rs35933176	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr15:67692566T>C	ENST00000335894.4	+	14	2086	c.2020T>C	c.(2020-2022)Tac>Cac	p.Y674H	IQCH_ENST00000546225.1_Missense_Mutation_p.Y331H|IQCH_ENST00000358767.3_Missense_Mutation_p.Y410H|IQCH_ENST00000360277.4_Missense_Mutation_p.Y335H	NM_001031715.2	NP_001026885	Q86VS3	IQCH_HUMAN	IQ motif containing H	674										NS(1)|breast(1)|cervix(1)|endometrium(2)|large_intestine(9)|lung(9)|ovary(2)|pancreas(2)|skin(5)|upper_aerodigestive_tract(1)	33				Colorectal(3;0.0856)		TATTCCTTCCTACCTAAAGTG	0.428													T|||	5	0.000998403	0.0	0.0	5008	,	,		19892	0.0		0.005	False		,,,				2504	0.0				p.Y674H		Atlas-SNP	.											.	IQCH	81	.	0			c.T2020C						PASS	.	T	HIS/TYR	0,4402		0,0,2201	143.0	134.0	137.0		2020	2.5	1.0	15	dbSNP_126	137	41,8557	27.4+/-76.7	0,41,4258	yes	missense	IQCH	NM_001031715.2	83	0,41,6459	CC,CT,TT		0.4769,0.0,0.3154	benign	674/1028	67692566	41,12959	2201	4299	6500	SO:0001583	missense	64799	exon14			CCTTCCTACCTAA	AY014282	CCDS10223.1, CCDS32273.1, CCDS10223.2, CCDS61680.1, CCDS61681.1	15q23	2005-10-24			ENSG00000103599	ENSG00000103599			25721	protein-coding gene	gene with protein product		612523				12477932	Standard	NM_022784		Approved	FLJ12476	uc002aqo.2	Q86VS3	OTTHUMG00000133231	ENST00000335894.4:c.2020T>C	15.37:g.67692566T>C	ENSP00000336861:p.Tyr674His	197.0	0.0	0		224.0	107.0	0.477679	NM_001031715	A8K8W3|C9JPR6|D6RJ88|Q4G0S6|Q8NEH9|Q9BWX2|Q9H9Y1|Q9UF88	Missense_Mutation	SNP	ENST00000335894.4	37	CCDS32273.1	4	0.0018315018315018315	0	0.0	0	0.0	0	0.0	4	0.005277044854881266	T	2.755	-0.259212	0.05791	0.0	0.004769	ENSG00000103599	ENST00000358767;ENST00000546225;ENST00000335894;ENST00000360277	T;T;T;T	0.38722	1.12;1.13;1.15;1.12	5.43	2.45	0.29901	.	0.106121	0.64402	N	0.000006	T	0.06325	0.0163	N	0.00197	-1.87	0.27379	N	0.955461	B;B;B	0.06786	0.0;0.001;0.0	B;B;B	0.04013	0.001;0.001;0.001	T	0.33929	-0.9849	10	0.07644	T	0.81	-22.218	9.1639	0.37038	0.0:0.734:0.0:0.266	rs35933176	331;335;674	Q86VS3-2;Q86VS3-4;Q86VS3	.;.;IQCH_HUMAN	H	410;331;674;335	ENSP00000351617:Y410H;ENSP00000444118:Y331H;ENSP00000336861:Y674H;ENSP00000353419:Y335H	ENSP00000336861:Y674H	Y	+	1	0	IQCH	65479620	0.957000	0.32711	0.983000	0.44433	0.741000	0.42261	2.152000	0.42272	0.224000	0.20940	-0.250000	0.11733	TAC	T|0.997;C|0.003	0.003	strong		0.428	IQCH-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256969.1	NM_022784	
OR51T1	401665	hgsc.bcm.edu	37	11	4903219	4903219	+	Silent	SNP	C	C	T			TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr11:4903219C>T	ENST00000322049.1	+	1	90	c.90C>T	c.(88-90)tcC>tcT	p.S30S	MMP26_ENST00000380390.1_Intron|OR51T1_ENST00000380378.1_Silent_p.S57S|MMP26_ENST00000477339.1_Intron			Q8NGJ9	O51T1_HUMAN	olfactory receptor, family 51, subfamily T, member 1	30						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			NS(1)|endometrium(4)|kidney(2)|large_intestine(5)|lung(16)|ovary(2)|skin(3)|upper_aerodigestive_tract(1)	34		Medulloblastoma(188;0.0075)|all_neural(188;0.0577)|Breast(177;0.086)		Epithelial(150;4.77e-12)|BRCA - Breast invasive adenocarcinoma(625;0.00435)|LUSC - Lung squamous cell carcinoma(625;0.19)		TCTGGATCTCCATTCCAGTCT	0.448																																					p.S57S		Atlas-SNP	.											.	OR51T1	92	.	0			c.C171T						PASS	.						208.0	170.0	183.0					11																	4903219		2201	4298	6499	SO:0001819	synonymous_variant	401665	exon1			GATCTCCATTCCA	BK004283	CCDS31363.1	11p15.4	2012-08-09			ENSG00000176900	ENSG00000176900		"""GPCR / Class A : Olfactory receptors"""	15205	protein-coding gene	gene with protein product							Standard	NM_001004759		Approved		uc010qyp.2	Q8NGJ9	OTTHUMG00000066507	ENST00000322049.1:c.90C>T	11.37:g.4903219C>T		178.0	0.0	0		139.0	63.0	0.453237	NM_001004759	Q6IFH9	Silent	SNP	ENST00000322049.1	37																																																																																				.	.	none		0.448	OR51T1-001	KNOWN	basic|appris_candidate	protein_coding	protein_coding	OTTHUMT00000142180.1	NM_001004759	
ZFYVE16	9765	hgsc.bcm.edu	37	5	79741086	79741086	+	Silent	SNP	A	A	G	rs150392926	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr5:79741086A>G	ENST00000338008.5	+	6	2766	c.2586A>G	c.(2584-2586)ctA>ctG	p.L862L	ZFYVE16_ENST00000510158.1_Silent_p.L862L|ZFYVE16_ENST00000505560.1_Silent_p.L862L	NM_001284236.1|NM_014733.3	NP_001271165.1|NP_055548	Q7Z3T8	ZFY16_HUMAN	zinc finger, FYVE domain containing 16	862					BMP signaling pathway (GO:0030509)|endosomal transport (GO:0016197)|protein targeting to lysosome (GO:0006622)|regulation of endocytosis (GO:0030100)|signal transduction (GO:0007165)|vesicle organization (GO:0016050)	cytoplasm (GO:0005737)|early endosome (GO:0005769)|early endosome membrane (GO:0031901)|intracellular membrane-bounded organelle (GO:0043231)	1-phosphatidylinositol binding (GO:0005545)|metal ion binding (GO:0046872)|phosphatidylinositol-3,4,5-trisphosphate binding (GO:0005547)|protein transporter activity (GO:0008565)			breast(4)|cervix(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(4)|kidney(5)|large_intestine(14)|liver(1)|lung(6)|ovary(2)|prostate(2)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	51		Lung NSC(167;0.00428)|all_lung(232;0.00455)|Ovarian(174;0.0261)		OV - Ovarian serous cystadenocarcinoma(54;1.6e-46)|Epithelial(54;2.02e-41)|all cancers(79;5.05e-36)		TTCTAGGACTATGTTCCAAAG	0.318													a|||	10	0.00199681	0.0	0.0014	5008	,	,		18816	0.0		0.002	False		,,,				2504	0.0072				p.L862L	Melanoma(150;1452 1854 16018 17851 37292)	Atlas-SNP	.											.	ZFYVE16	100	.	0			c.A2586G						PASS	.	G	,	0,4406		0,0,2203	112.0	108.0	109.0		2586,2586	-4.7	0.0	5	dbSNP_134	109	14,8586	10.5+/-38.8	0,14,4286	no	coding-synonymous,coding-synonymous	ZFYVE16	NM_001105251.1,NM_014733.3	,	0,14,6489	GG,GA,AA		0.1628,0.0,0.1076	,	862/1540,862/1540	79741086	14,12992	2203	4300	6503	SO:0001819	synonymous_variant	9765	exon7			AGGACTATGTTCC	AB002303	CCDS4050.1	5q14.1	2012-09-20			ENSG00000039319	ENSG00000039319		"""Zinc fingers, FYVE domain containing"", ""Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"""	20756	protein-coding gene	gene with protein product	"""endofin"", ""protein phosphatase 1, regulatory subunit 69"""	608880				11546807	Standard	NM_014733		Approved	KIAA0305, PPP1R69	uc003kgq.4	Q7Z3T8	OTTHUMG00000108178	ENST00000338008.5:c.2586A>G	5.37:g.79741086A>G		75.0	0.0	0		97.0	53.0	0.546392	NM_001105251	O15023|Q5H9U2|Q7LAU7|Q86T69|Q8N5L3|Q8NEK3	Silent	SNP	ENST00000338008.5	37	CCDS4050.1																																																																																			A|0.999;G|0.001	0.001	strong		0.318	ZFYVE16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000226982.2	NM_014733	
TIMP4	7079	hgsc.bcm.edu	37	3	12198336	12198336	+	Missense_Mutation	SNP	C	C	G			TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr3:12198336C>G	ENST00000287814.4	-	3	846	c.336G>C	c.(334-336)aaG>aaC	p.K112N	SYN2_ENST00000432424.2_RNA	NM_003256.3	NP_003247.1	Q99727	TIMP4_HUMAN	TIMP metallopeptidase inhibitor 4	112	NTR. {ECO:0000255|PROSITE- ProRule:PRU00295}.				central nervous system development (GO:0007417)|negative regulation of endopeptidase activity (GO:0010951)|ovulation cycle (GO:0042698)|response to cytokine (GO:0034097)|response to drug (GO:0042493)|response to lipopolysaccharide (GO:0032496)|response to peptide hormone (GO:0043434)	extracellular space (GO:0005615)|sarcomere (GO:0030017)	metal ion binding (GO:0046872)|metalloendopeptidase inhibitor activity (GO:0008191)			central_nervous_system(1)|kidney(1)|large_intestine(2)|lung(5)|skin(1)|upper_aerodigestive_tract(1)	11						AGAGATACTGCTTCTGGCTGT	0.433																																					p.K112N	Melanoma(199;1446 2144 30617 38794 51714)	Atlas-SNP	.											.	TIMP4	21	.	0			c.G336C						PASS	.						122.0	111.0	115.0					3																	12198336		2203	4300	6503	SO:0001583	missense	7079	exon3			ATACTGCTTCTGG	U76456	CCDS2608.1	3p25	2005-10-31	2005-08-08		ENSG00000157150	ENSG00000157150			11823	protein-coding gene	gene with protein product		601915	"""tissue inhibitor of metalloproteinase 4"""			8939999, 9693046	Standard	NM_003256		Approved		uc003bwo.3	Q99727	OTTHUMG00000129763	ENST00000287814.4:c.336G>C	3.37:g.12198336C>G	ENSP00000287814:p.Lys112Asn	188.0	0.0	0		192.0	88.0	0.458333	NM_003256	B2R7K6	Missense_Mutation	SNP	ENST00000287814.4	37	CCDS2608.1	.	.	.	.	.	.	.	.	.	.	C	12.04	1.819542	0.32145	.	.	ENSG00000157150	ENST00000287814	D	0.94184	-3.37	4.85	1.79	0.24919	Tissue inhibitor of metalloproteinases-like, OB-fold (1);Netrin domain (1);	0.246504	0.42172	D	0.000755	D	0.92391	0.7585	M	0.74467	2.265	0.43156	D	0.994932	P	0.43857	0.819	P	0.47402	0.546	D	0.89472	0.3744	10	0.56958	D	0.05	.	5.3067	0.15807	0.1289:0.5526:0.0:0.3185	.	112	Q99727	TIMP4_HUMAN	N	112	ENSP00000287814:K112N	ENSP00000287814:K112N	K	-	3	2	TIMP4	12173336	0.131000	0.22433	1.000000	0.80357	0.952000	0.60782	-0.631000	0.05496	0.541000	0.28827	-0.150000	0.13652	AAG	.	.	none		0.433	TIMP4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251978.1	NM_003256	
PARP2	10038	hgsc.bcm.edu	37	14	20822331	20822331	+	Missense_Mutation	SNP	A	A	C			TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr14:20822331A>C	ENST00000250416.5	+	8	754	c.727A>C	c.(727-729)Aag>Cag	p.K243Q	PARP2_ENST00000429687.3_Missense_Mutation_p.K230Q|PARP2_ENST00000527915.1_Missense_Mutation_p.K243Q	NM_001042618.1|NM_005484.3	NP_001036083.1|NP_005475.2	Q9UGN5	PARP2_HUMAN	poly (ADP-ribose) polymerase 2	243	PARP alpha-helical. {ECO:0000255|PROSITE- ProRule:PRU00398}.				base-excision repair (GO:0006284)|DNA repair (GO:0006281)|extrinsic apoptotic signaling pathway (GO:0097191)|protein ADP-ribosylation (GO:0006471)	nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	DNA binding (GO:0003677)|NAD+ ADP-ribosyltransferase activity (GO:0003950)			central_nervous_system(2)|cervix(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(4)|lung(4)|ovary(1)|pancreas(1)	15	all_cancers(95;0.00092)	all_lung(585;0.235)	Epithelial(56;5.34e-07)|all cancers(55;3.7e-06)	GBM - Glioblastoma multiforme(265;0.00888)|READ - Rectum adenocarcinoma(17;0.0649)		GGAGTTAATAAAGTTGATCTG	0.388								Poly(ADP-ribose) polymerase (PARP) enzymes that bind to DNA																													p.K243Q		Atlas-SNP	.											PARP2_ENST00000250416,NS,carcinoma,0,2	PARP2	92	2	0			c.A727C						PASS	.						130.0	125.0	127.0					14																	20822331		1866	4111	5977	SO:0001583	missense	10038	exon8			TTAATAAAGTTGA	AF085734	CCDS41910.1, CCDS45077.1	14q11.2-q12	2010-02-16	2008-07-28	2004-08-26	ENSG00000129484	ENSG00000129484		"""Poly (ADP-ribose) polymerases"""	272	protein-coding gene	gene with protein product		607725	"""ADP-ribosyltransferase (NAD+; poly(ADP-ribose) polymerase)-like 2"", ""poly (ADP-ribose) polymerase family, member 2"""	ADPRTL2		10329013, 18353725	Standard	NM_005484		Approved		uc001vxc.3	Q9UGN5	OTTHUMG00000166106	ENST00000250416.5:c.727A>C	14.37:g.20822331A>C	ENSP00000250416:p.Lys243Gln	132.0	0.0	0		161.0	70.0	0.434783	NM_005484	Q8TEU4|Q9NUV2|Q9UMR4|Q9Y6C8	Missense_Mutation	SNP	ENST00000250416.5	37	CCDS41910.1	.	.	.	.	.	.	.	.	.	.	A	9.194	1.026692	0.19512	.	.	ENSG00000129484	ENST00000429687;ENST00000250416;ENST00000527915	T;T;T	0.15718	2.4;2.4;2.4	4.97	1.27	0.21489	Poly(ADP-ribose) polymerase, regulatory domain (4);	0.333967	0.32548	N	0.005946	T	0.09818	0.0241	N	0.25890	0.77	0.33351	D	0.571125	B;B	0.09022	0.0;0.002	B;B	0.04013	0.001;0.001	T	0.08493	-1.0719	10	0.41790	T	0.15	-3.5913	5.4142	0.16363	0.3821:0.4338:0.184:0.0	.	230;243	Q9UGN5-2;Q9UGN5	.;PARP2_HUMAN	Q	230;243;243	ENSP00000392972:K230Q;ENSP00000250416:K243Q;ENSP00000432283:K243Q	ENSP00000250416:K243Q	K	+	1	0	PARP2	19892171	0.812000	0.29077	0.992000	0.48379	0.704000	0.40688	0.898000	0.28404	0.424000	0.26061	0.477000	0.44152	AAG	.	.	none		0.388	PARP2-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000387847.2		
PRR27	401137	hgsc.bcm.edu	37	4	71024473	71024473	+	Silent	SNP	T	T	A	rs542201615		TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr4:71024473T>A	ENST00000344526.5	+	3	693	c.504T>A	c.(502-504)ccT>ccA	p.P168P	C4orf40_ENST00000502294.1_Silent_p.P168P|C4orf40_ENST00000502441.2_3'UTR	NM_214711.3	NP_999876.2	Q6MZM9	PRR27_HUMAN		168	Ala/Pro-rich.					extracellular vesicular exosome (GO:0070062)				breast(2)|central_nervous_system(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(1)|lung(3)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	12						GAGCTGAGCCTGCTGCAGAGG	0.627																																					p.P168P		Atlas-SNP	.											.	C4orf40	19	.	0			c.T504A						PASS	.																																			SO:0001819	synonymous_variant	401137	exon3			TGAGCCTGCTGCA																												ENST00000344526.5:c.504T>A	4.37:g.71024473T>A		151.0	0.0	0		125.0	20.0	0.16	NM_214711	A8MXP0|Q6MZR6	Silent	SNP	ENST00000344526.5	37	CCDS3535.1																																																																																			.	.	none		0.627	C4orf40-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251558.1		
GLB1L2	89944	hgsc.bcm.edu	37	11	134234269	134234269	+	Missense_Mutation	SNP	A	A	G	rs114723326	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr11:134234269A>G	ENST00000535456.2	+	8	969	c.781A>G	c.(781-783)Acc>Gcc	p.T261A	GLB1L2_ENST00000389881.3_Missense_Mutation_p.T261A|GLB1L2_ENST00000529077.1_3'UTR|GLB1L2_ENST00000339772.7_Missense_Mutation_p.T261A	NM_138342.3	NP_612351.2	Q8IW92	GLBL2_HUMAN	galactosidase, beta 1-like 2	261					carbohydrate metabolic process (GO:0005975)	extracellular region (GO:0005576)	beta-galactosidase activity (GO:0004565)			central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(6)|liver(1)|lung(20)|ovary(1)|pancreas(1)|prostate(3)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	41	all_hematologic(175;0.127)	all_cancers(12;2.85e-18)|all_epithelial(12;1.21e-12)|all_lung(97;0.000276)|Lung NSC(97;0.000518)|Breast(109;0.00122)|Medulloblastoma(222;0.0399)|all_neural(223;0.0412)|Esophageal squamous(93;0.0844)		Epithelial(10;1.37e-11)|all cancers(11;2.2e-10)|BRCA - Breast invasive adenocarcinoma(10;3.09e-10)|OV - Ovarian serous cystadenocarcinoma(99;0.000885)|Lung(977;0.223)		GCAGCTACTGACCACCTTTCT	0.557													A|||	117	0.0233626	0.0817	0.0086	5008	,	,		19623	0.0		0.003	False		,,,				2504	0.0				p.T261A		Atlas-SNP	.											.	GLB1L2	79	.	0			c.A781G						PASS	.	A	ALA/THR	254,4148	148.8+/-183.1	9,236,1956	286.0	251.0	263.0		781	4.0	0.0	11	dbSNP_132	263	6,8588	5.0+/-18.6	0,6,4291	yes	missense	GLB1L2	NM_138342.3	58	9,242,6247	GG,GA,AA		0.0698,5.7701,2.0006	benign	261/637	134234269	260,12736	2201	4297	6498	SO:0001583	missense	89944	exon8			CTACTGACCACCT		CCDS31724.1	11q25	2008-01-29			ENSG00000149328	ENSG00000149328			25129	protein-coding gene	gene with protein product						12975309	Standard	NM_138342		Approved		uc001qhp.3	Q8IW92	OTTHUMG00000167179	ENST00000535456.2:c.781A>G	11.37:g.134234269A>G	ENSP00000444628:p.Thr261Ala	100.0	0.0	0		106.0	46.0	0.433962	NM_138342	A6NCE6|Q6UX60|Q8NC62|Q8NCB3|Q8NCJ1|Q96HP3	Missense_Mutation	SNP	ENST00000535456.2	37	CCDS31724.1	40|40	0.018315018315018316|0.018315018315018316	38|38	0.07723577235772358|0.07723577235772358	2|2	0.0055248618784530384|0.0055248618784530384	0|0	0.0|0.0	0|0	0.0|0.0	A|A	5.513|5.513	0.279580|0.279580	0.10458|0.10458	0.057701|0.057701	6.98E-4|6.98E-4	ENSG00000149328|ENSG00000149328	ENST00000525089;ENST00000533324|ENST00000339772;ENST00000535456;ENST00000389881	.|D;D;D	.|0.97752	.|-4.52;-4.52;-4.52	3.97|3.97	3.97|3.97	0.46021|0.46021	.|Glycoside hydrolase, subgroup, catalytic domain (1);Glycoside hydrolase, superfamily (1);	.|0.599178	.|0.17894	.|N	.|0.158423	T|T	0.41789|0.41789	0.1174|0.1174	N|N	0.01649|0.01649	-0.78|-0.78	0.09310|0.09310	N|N	1|1	.|B	.|0.13145	.|0.007	.|B	.|0.15052	.|0.012	T|T	0.67035|0.67035	-0.5772|-0.5772	5|10	.|0.12430	.|T	.|0.62	-7.5496|-7.5496	11.2062|11.2062	0.48771|0.48771	1.0:0.0:0.0:0.0|1.0:0.0:0.0:0.0	.|.	.|261	.|Q8IW92	.|GLBL2_HUMAN	G|A	199;88|261	.|ENSP00000344659:T261A;ENSP00000444628:T261A;ENSP00000374531:T261A	.|ENSP00000344659:T261A	D|T	+|+	2|1	0|0	GLB1L2|GLB1L2	133739479|133739479	0.002000|0.002000	0.14202|0.14202	0.022000|0.022000	0.16811|0.16811	0.050000|0.050000	0.14768|0.14768	1.637000|1.637000	0.37155|0.37155	2.026000|2.026000	0.59711|0.59711	0.533000|0.533000	0.62120|0.62120	GAC|ACC	A|0.981;G|0.019	0.019	strong		0.557	GLB1L2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000393629.2	NM_138342	
C1QTNF9B	387911	hgsc.bcm.edu	37	13	24465537	24465537	+	Missense_Mutation	SNP	C	C	T	rs140860568	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr13:24465537C>T	ENST00000382140.2	-	5	953	c.893G>A	c.(892-894)gGg>gAg	p.G298E	C1QTNF9B-AS1_ENST00000435039.2_RNA|C1QTNF9B-AS1_ENST00000417034.1_RNA|C1QTNF9B_ENST00000382145.1_3'UTR|MIPEP_ENST00000469167.1_5'Flank|C1QTNF9B_ENST00000382137.3_Missense_Mutation_p.G298E|MIPEP_ENST00000382172.3_5'Flank|C1QTNF9B_ENST00000556521.1_5'UTR|C1QTNF9B-AS1_ENST00000382133.4_RNA			B2RNN3	C1T9B_HUMAN	C1q and tumor necrosis factor related protein 9B	298	C1q. {ECO:0000255|PROSITE- ProRule:PRU00368}.					collagen trimer (GO:0005581)|extracellular vesicular exosome (GO:0070062)				breast(1)|central_nervous_system(1)|large_intestine(3)|lung(1)	6						CATCTCATCCCCGAGCTTCAG	0.512													C|||	50	0.00998403	0.0023	0.0187	5008	,	,		16761	0.0		0.0308	False		,,,				2504	0.0031				p.G298E		Atlas-SNP	.											.	C1QTNF9B	27	.	0			c.G893A						PASS	.	C	GLU/GLY,,	34,4310		6,22,2144	92.0	91.0	91.0		893,,	3.1	1.0	13	dbSNP_134	91	276,8220		29,218,4001	no	missense,utr-5,utr-5	C1QTNF9B,C1QTNF9B-AS1	NM_001007537.1,NM_001014442.2,NM_001135816.1	98,,	35,240,6145	TT,TC,CC		3.2486,0.7827,2.4143	probably-damaging,,	298/334,,	24465537	310,12530	2172	4248	6420	SO:0001583	missense	387911	exon3			TCATCCCCGAGCT	BC110413	CCDS31947.1	13q12.12	2011-05-08			ENSG00000205863	ENSG00000205863			34072	protein-coding gene	gene with protein product		614148				17544811	Standard	NM_001007537		Approved	CTRP9B	uc010tcv.1	B2RNN3	OTTHUMG00000016570	ENST00000382140.2:c.893G>A	13.37:g.24465537C>T	ENSP00000371575:p.Gly298Glu	102.0	0.0	0		213.0	99.0	0.464789	NM_001007537	A2A3T6|B9EH31|Q0VGC5|Q5VX65|Q5VX66|Q8IUU4	Missense_Mutation	SNP	ENST00000382140.2	37	CCDS31947.1	31	0.014194139194139194	2	0.0040650406504065045	9	0.024861878453038673	0	0.0	20	0.026385224274406333	c	17.20	3.329762	0.60743	0.007827	0.032486	ENSG00000205863	ENST00000382137;ENST00000382140	D;D	0.82255	-1.59;-1.59	3.96	3.08	0.35506	Tumour necrosis factor-like (2);Complement C1q protein (4);	0.100850	0.64402	D	0.000002	T	0.80401	0.4616	M	0.82716	2.605	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.85108	0.0961	10	0.49607	T	0.09	.	13.6179	0.62120	0.0:0.8431:0.1569:0.0	.	298	B2RNN3	C1T9B_HUMAN	E	298	ENSP00000371572:G298E;ENSP00000371575:G298E	ENSP00000371572:G298E	G	-	2	0	C1QTNF9B	23363537	1.000000	0.71417	0.954000	0.39281	0.593000	0.36681	5.940000	0.70187	0.762000	0.33152	0.456000	0.33151	GGG	C|0.980;T|0.020	0.020	strong		0.512	C1QTNF9B-001	KNOWN	not_best_in_genome_evidence|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044162.3	NM_001007537	
LAMA3	3909	hgsc.bcm.edu	37	18	21494509	21494509	+	Missense_Mutation	SNP	C	C	T	rs147463397	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr18:21494509C>T	ENST00000313654.9	+	57	7706	c.7465C>T	c.(7465-7467)Cgg>Tgg	p.R2489W	LAMA3_ENST00000399516.3_Missense_Mutation_p.R2433W|LAMA3_ENST00000588770.1_3'UTR|LAMA3_ENST00000587184.1_Missense_Mutation_p.R824W|LAMA3_ENST00000269217.6_Missense_Mutation_p.R880W	NM_198129.1	NP_937762.1	Q16787	LAMA3_HUMAN	laminin, alpha 3	2489	Laminin G-like 1. {ECO:0000255|PROSITE- ProRule:PRU00122}.				cell adhesion (GO:0007155)|cell junction assembly (GO:0034329)|endodermal cell differentiation (GO:0035987)|epidermis development (GO:0008544)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|hemidesmosome assembly (GO:0031581)|regulation of cell adhesion (GO:0030155)|regulation of cell migration (GO:0030334)|regulation of embryonic development (GO:0045995)	basement membrane (GO:0005604)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|laminin-1 complex (GO:0005606)|laminin-5 complex (GO:0005610)	structural molecule activity (GO:0005198)			NS(2)|breast(4)|central_nervous_system(3)|cervix(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(2)|kidney(4)|large_intestine(24)|lung(54)|ovary(8)|prostate(6)|skin(7)|urinary_tract(4)	128	all_cancers(21;7.81e-05)|all_epithelial(16;4.45e-07)|Lung NSC(20;0.00156)|all_lung(20;0.00508)|Colorectal(14;0.0202)|Ovarian(20;0.17)					AGTTATGGATCGGGTGAAATT	0.488																																					p.R2489W		Atlas-SNP	.											.	LAMA3	397	.	0			c.C7465T						PASS	.	C	TRP/ARG,TRP/ARG,TRP/ARG,TRP/ARG	0,4406		0,0,2203	75.0	70.0	71.0		2638,7297,2470,7465	4.4	1.0	18	dbSNP_134	71	3,8597	3.0+/-9.4	0,3,4297	yes	missense,missense,missense,missense	LAMA3	NM_000227.3,NM_001127717.1,NM_001127718.1,NM_198129.1	101,101,101,101	0,3,6500	TT,TC,CC		0.0349,0.0,0.0231	probably-damaging,probably-damaging,probably-damaging,probably-damaging	880/1725,2433/3278,824/1669,2489/3334	21494509	3,13003	2203	4300	6503	SO:0001583	missense	3909	exon57			ATGGATCGGGTGA	L34155	CCDS11880.1, CCDS42419.1, CCDS45838.1, CCDS59307.1	18q11.2	2013-03-01	2002-08-29		ENSG00000053747	ENSG00000053747		"""Laminins"""	6483	protein-coding gene	gene with protein product		600805	"""laminin, alpha 3 (nicein (150kD), kalinin (165kD), BM600 (150kD), epilegrin)"""	LAMNA		8077230	Standard	NM_000227		Approved	nicein-150kDa, kalinin-165kDa, BM600-150kDa, epiligrin	uc002kuq.3	Q16787	OTTHUMG00000131874	ENST00000313654.9:c.7465C>T	18.37:g.21494509C>T	ENSP00000324532:p.Arg2489Trp	38.0	0.0	0		49.0	27.0	0.55102	NM_198129	B0YJ33|Q13679|Q13680|Q6VU67|Q6VU68|Q6VU69|Q76E14|Q96TG0	Missense_Mutation	SNP	ENST00000313654.9	37	CCDS42419.1	.	.	.	.	.	.	.	.	.	.	C	16.74	3.206989	0.58343	0.0	3.49E-4	ENSG00000053747	ENST00000313654;ENST00000399516;ENST00000269217	T;T;T	0.80566	-1.39;-1.39;-1.39	5.25	4.36	0.52297	Concanavalin A-like lectin/glucanase (1);Concanavalin A-like lectin/glucanase, subgroup (1);Laminin G domain (2);Laminin G, subdomain 2 (1);	.	.	.	.	D	0.88973	0.6583	M	0.73598	2.24	0.49915	D	0.999836	D;D;D;D	0.89917	1.0;1.0;1.0;1.0	D;D;D;D	0.97110	1.0;1.0;0.992;0.989	D	0.90115	0.4195	9	0.72032	D	0.01	.	15.1212	0.72443	0.1427:0.8573:0.0:0.0	.	824;880;2433;2489	Q6VU69;B0YJ33;Q6VU67;Q16787	.;.;.;LAMA3_HUMAN	W	2489;2433;880	ENSP00000324532:R2489W;ENSP00000382432:R2433W;ENSP00000269217:R880W	ENSP00000269217:R880W	R	+	1	2	LAMA3	19748507	1.000000	0.71417	1.000000	0.80357	0.795000	0.44927	2.974000	0.49272	1.179000	0.42884	0.561000	0.74099	CGG	C|1.000;T|0.000	0.000	strong		0.488	LAMA3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254824.3	NM_000227, NM_198129	
SLC35E4	339665	hgsc.bcm.edu	37	22	31032881	31032881	+	Silent	SNP	G	G	A	rs8136373	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr22:31032881G>A	ENST00000343605.4	+	1	1243	c.444G>A	c.(442-444)ctG>ctA	p.L148L	SLC35E4_ENST00000406566.1_Silent_p.L148L|SLC35E4_ENST00000300385.8_Silent_p.L148L	NM_001001479.2	NP_001001479.1	Q6ICL7	S35E4_HUMAN	solute carrier family 35, member E4	148	EamA.|Leu-rich.					integral component of membrane (GO:0016021)				autonomic_ganglia(1)|endometrium(1)|large_intestine(2)|lung(3)|ovary(1)|pancreas(1)|skin(1)	10						TGTTCACCCTGGCCCTGTCGG	0.677													G|||	440	0.0878594	0.2988	0.0303	5008	,	,		14087	0.0		0.0149	False		,,,				2504	0.0092				p.L148L		Atlas-SNP	.											.	SLC35E4	22	.	0			c.G444A						PASS	.	G		1219,3185	391.9+/-328.3	165,889,1148	65.0	36.0	46.0		444	5.2	1.0	22	dbSNP_116	46	171,8429	72.9+/-135.5	1,169,4130	no	coding-synonymous	SLC35E4	NM_001001479.2		166,1058,5278	AA,AG,GG		1.9884,27.6794,10.689		148/351	31032881	1390,11614	2202	4300	6502	SO:0001819	synonymous_variant	339665	exon1			CACCCTGGCCCTG		CCDS13882.1	22q12.2	2013-05-22			ENSG00000100036	ENSG00000100036		"""Solute carriers"""	17058	protein-coding gene	gene with protein product							Standard	NM_001001479		Approved		uc003ais.1	Q6ICL7	OTTHUMG00000151110	ENST00000343605.4:c.444G>A	22.37:g.31032881G>A		42.0	0.0	0		38.0	22.0	0.578947	NM_001001479	Q567P0	Silent	SNP	ENST00000343605.4	37	CCDS13882.1																																																																																			G|0.900;A|0.100	0.100	strong		0.677	SLC35E4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000321382.1	XM_290973	
IFNA10	3446	hgsc.bcm.edu	37	9	21206605	21206605	+	Missense_Mutation	SNP	C	C	G	rs28368148	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr9:21206605C>G	ENST00000357374.2	-	1	537	c.492G>C	c.(490-492)tgG>tgC	p.W164C		NM_002171.1	NP_002162.1	P01566	IFN10_HUMAN	interferon, alpha 10	164					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)			endometrium(1)|large_intestine(3)|liver(1)|lung(6)|prostate(2)|skin(1)|upper_aerodigestive_tract(2)	16				Lung(24;1.26e-23)|LUSC - Lung squamous cell carcinoma(38;1.4e-13)|OV - Ovarian serous cystadenocarcinoma(39;0.17)		TGACAACCTCCCAGGCACAAG	0.428													c|||	23	0.00459265	0.0008	0.0058	5008	,	,		18519	0.0		0.0129	False		,,,				2504	0.0051				p.W164C		Atlas-SNP	.											.	IFNA10	29	.	0			c.G492C						PASS	.	C	CYS/TRP	8,4398		0,8,2195	250.0	255.0	253.0		492	3.8	1.0	9	dbSNP_125	253	119,8481		1,117,4182	no	missense	IFNA10	NM_002171.1	215	1,125,6377	GG,GC,CC		1.3837,0.1816,0.9765	probably-damaging	164/190	21206605	127,12879	2203	4300	6503	SO:0001583	missense	3446	exon1			AACCTCCCAGGCA		CCDS6499.1	9p22	2010-08-24			ENSG00000186803	ENSG00000186803		"""Interferons"""	5418	protein-coding gene	gene with protein product		147577				1385305	Standard	NM_002171		Approved	IFN-alphaC	uc003zoq.1	P01566	OTTHUMG00000019658	ENST00000357374.2:c.492G>C	9.37:g.21206605C>G	ENSP00000369566:p.Trp164Cys	475.0	0.0	0		564.0	265.0	0.469858	NM_002171	Q5VV13	Missense_Mutation	SNP	ENST00000357374.2	37	CCDS6499.1	13	0.005952380952380952	2	0.0040650406504065045	3	0.008287292817679558	0	0.0	8	0.010554089709762533	-	15.33	2.801079	0.50315	0.001816	0.013837	ENSG00000186803	ENST00000357374	T	0.43294	0.95	3.75	3.75	0.43078	Four-helical cytokine-like, core (1);Four-helical cytokine, core (1);	0.000000	0.85682	D	0.000000	T	0.64472	0.2601	M	0.93678	3.445	0.58432	D	0.999991	D	0.89917	1.0	D	0.97110	1.0	T	0.77789	-0.2456	10	0.87932	D	0	.	12.9165	0.58209	0.0:1.0:0.0:0.0	rs28368148	164	P01566	IFN10_HUMAN	C	164	ENSP00000369566:W164C	ENSP00000369566:W164C	W	-	3	0	IFNA10	21196605	1.000000	0.71417	0.988000	0.46212	0.926000	0.56050	2.348000	0.44045	1.806000	0.52798	0.499000	0.49734	TGG	C|0.991;G|0.009	0.009	strong		0.428	IFNA10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051887.1	NM_002171	
TMEM132A	54972	hgsc.bcm.edu	37	11	60696399	60696399	+	Missense_Mutation	SNP	G	G	A	rs61751216	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr11:60696399G>A	ENST00000453848.2	+	4	991	c.833G>A	c.(832-834)cGg>cAg	p.R278Q	TMEM132A_ENST00000005286.4_Missense_Mutation_p.R278Q			Q24JP5	T132A_HUMAN	transmembrane protein 132A	278						endoplasmic reticulum (GO:0005783)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)				breast(1)|cervix(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(6)|lung(14)|ovary(3)|prostate(1)|skin(3)	32						CTCCTGCTTCGGCACAACTTC	0.637													G|||	50	0.00998403	0.003	0.013	5008	,	,		17378	0.0		0.0328	False		,,,				2504	0.0041				p.R278Q		Atlas-SNP	.											.	TMEM132A	135	.	0			c.G833A						PASS	.	G	GLN/ARG,GLN/ARG	27,4375		0,27,2174	39.0	39.0	39.0		833,833	2.8	0.8	11	dbSNP_129	39	347,8245		9,329,3958	yes	missense,missense	TMEM132A	NM_017870.3,NM_178031.2	43,43	9,356,6132	AA,AG,GG		4.0386,0.6134,2.8783	possibly-damaging,possibly-damaging	278/1025,278/1024	60696399	374,12620	2201	4296	6497	SO:0001583	missense	54972	exon4			TGCTTCGGCACAA	AK000546	CCDS7997.1, CCDS44618.1	11q12.2	2006-03-02	2006-03-02	2006-03-02	ENSG00000006118	ENSG00000006118			31092	protein-coding gene	gene with protein product			"""heat shock 70kDa protein 5 (glucose-regulated protein, 78kDa) binding protein 1"""	HSPA5BP1		12514190, 10997877	Standard	NM_017870		Approved	GBP, FLJ20539	uc001nqi.3	Q24JP5	OTTHUMG00000167803	ENST00000453848.2:c.833G>A	11.37:g.60696399G>A	ENSP00000405823:p.Arg278Gln	83.0	0.0	0		84.0	35.0	0.416667	NM_178031	Q69YU7|Q86VZ8|Q86W97|Q9H8K3|Q9HCI9|Q9NWY0	Missense_Mutation	SNP	ENST00000453848.2	37	CCDS44618.1	34	0.015567765567765568	3	0.006097560975609756	6	0.016574585635359115	0	0.0	25	0.032981530343007916	G	16.23	3.064526	0.55432	0.006134	0.040386	ENSG00000006118	ENST00000544065;ENST00000453848;ENST00000005286	T;T;T	0.13538	2.7;2.58;2.58	4.66	2.77	0.32553	.	0.000000	0.43110	D	0.000618	T	0.03739	0.0106	L	0.47716	1.5	0.19575	N	0.999969	D;D;D	0.60575	0.988;0.976;0.976	P;P;P	0.50934	0.654;0.465;0.465	T	0.04281	-1.0963	10	0.87932	D	0	.	7.0037	0.24823	0.3377:0.0:0.6623:0.0	rs61751216	267;278;278	Q24JP5-3;Q24JP5;Q24JP5-2	.;T132A_HUMAN;.	Q	16;278;278	ENSP00000442754:R16Q;ENSP00000405823:R278Q;ENSP00000005286:R278Q	ENSP00000005286:R278Q	R	+	2	0	TMEM132A	60452975	0.001000	0.12720	0.809000	0.32408	0.955000	0.61496	0.300000	0.19156	0.521000	0.28445	0.484000	0.47621	CGG	G|0.976;A|0.024	0.024	strong		0.637	TMEM132A-001	KNOWN	NAGNAG_splice_site|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000396352.1	NM_017870	
UGGT2	55757	hgsc.bcm.edu	37	13	96506633	96506633	+	Missense_Mutation	SNP	C	C	T	rs145358686	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr13:96506633C>T	ENST00000376747.3	-	35	4175	c.4105G>A	c.(4105-4107)Gga>Aga	p.G1369R		NM_020121.3	NP_064506.3	Q9NYU1	UGGG2_HUMAN	UDP-glucose glycoprotein glucosyltransferase 2	1369	Glucosyltransferase.				cellular protein metabolic process (GO:0044267)|post-translational protein modification (GO:0043687)|protein folding (GO:0006457)|protein N-linked glycosylation via asparagine (GO:0018279)|UDP-glucosylation (GO:0097359)	endoplasmic reticulum lumen (GO:0005788)	UDP-glucose:glycoprotein glucosyltransferase activity (GO:0003980)			NS(1)|breast(1)|central_nervous_system(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(17)|lung(20)|ovary(3)|pancreas(1)|prostate(4)|urinary_tract(2)	60						AAACGATATCCATCCATTTCC	0.388													C|||	10	0.00199681	0.0008	0.0029	5008	,	,		17239	0.0		0.006	False		,,,				2504	0.001				p.G1369R		Atlas-SNP	.											.	UGGT2	127	.	0			c.G4105A						PASS	.	C	ARG/GLY	3,4403	6.2+/-15.9	0,3,2200	111.0	106.0	108.0		4105	5.4	1.0	13	dbSNP_134	108	38,8562	25.7+/-73.6	0,38,4262	yes	missense	UGGT2	NM_020121.3	125	0,41,6462	TT,TC,CC		0.4419,0.0681,0.3152	probably-damaging	1369/1517	96506633	41,12965	2203	4300	6503	SO:0001583	missense	55757	exon35			GATATCCATCCAT	AF227906	CCDS9480.1	13q32.1	2009-07-23	2009-07-23	2009-07-23	ENSG00000102595	ENSG00000102595			15664	protein-coding gene	gene with protein product	"""UDP-glucose:glycoprotein glucosyltransferase 2"""	605898	"""UDP-glucose ceramide glucosyltransferase-like 2"""	UGCGL2		10694380	Standard	NM_020121		Approved	FLJ11485, HUGT2, FLJ10873, MGC150689, MGC87276, MGC117360	uc001vmt.3	Q9NYU1	OTTHUMG00000017230	ENST00000376747.3:c.4105G>A	13.37:g.96506633C>T	ENSP00000365938:p.Gly1369Arg	175.0	0.0	0		156.0	78.0	0.5	NM_020121	A6NKL4|Q08AD0|Q5JQR8|Q8N5K0|Q9UFC4	Missense_Mutation	SNP	ENST00000376747.3	37	CCDS9480.1	6	0.0027472527472527475	1	0.0020325203252032522	0	0.0	0	0.0	5	0.006596306068601583	C	31	5.075920	0.94000	6.81E-4	0.004419	ENSG00000102595	ENST00000376747	T	0.42513	0.97	5.37	5.37	0.77165	.	0.000000	0.85682	D	0.000000	T	0.70159	0.3192	H	0.95294	3.65	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	T	0.82500	-0.0426	10	0.87932	D	0	-18.4057	19.0987	0.93265	0.0:1.0:0.0:0.0	.	1369	Q9NYU1	UGGG2_HUMAN	R	1369	ENSP00000365938:G1369R	ENSP00000365938:G1369R	G	-	1	0	UGGT2	95304634	1.000000	0.71417	0.998000	0.56505	0.956000	0.61745	7.487000	0.81328	2.512000	0.84698	0.591000	0.81541	GGA	C|0.997;T|0.003	0.003	strong		0.388	UGGT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045507.1	NM_020121	
PANK4	55229	hgsc.bcm.edu	37	1	2445832	2445832	+	Missense_Mutation	SNP	T	T	C			TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr1:2445832T>C	ENST00000378466.3	-	11	1460	c.1448A>G	c.(1447-1449)aAg>aGg	p.K483R	PANK4_ENST00000435556.3_Missense_Mutation_p.K444R	NM_018216.1	NP_060686.1	Q9NVE7	PANK4_HUMAN	pantothenate kinase 4	483					coenzyme A biosynthetic process (GO:0015937)	cytoplasm (GO:0005737)	ATP binding (GO:0005524)|pantothenate kinase activity (GO:0004594)			breast(2)|cervix(2)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(2)|lung(4)|ovary(2)|prostate(1)|skin(1)|upper_aerodigestive_tract(4)	23	all_cancers(77;0.000158)|all_epithelial(69;8.01e-05)|all_lung(157;0.0212)|Lung NSC(156;0.0376)|Ovarian(185;0.0634)	all_epithelial(116;3.18e-20)|all_lung(118;1.67e-08)|Lung NSC(185;2.69e-06)|Breast(487;0.00147)|Renal(390;0.00183)|Hepatocellular(190;0.00826)|Myeloproliferative disorder(586;0.0122)|Ovarian(437;0.0308)|Lung SC(97;0.0847)|Medulloblastoma(700;0.123)		Epithelial(90;1.54e-37)|OV - Ovarian serous cystadenocarcinoma(86;6.95e-23)|GBM - Glioblastoma multiforme(42;2.81e-08)|Colorectal(212;4.25e-05)|COAD - Colon adenocarcinoma(227;0.000196)|Kidney(185;0.000342)|BRCA - Breast invasive adenocarcinoma(365;0.00445)|KIRC - Kidney renal clear cell carcinoma(229;0.00549)|STAD - Stomach adenocarcinoma(132;0.00644)|Lung(427;0.201)		GTTCCAGTACTTCTGCCGGAA	0.627																																					p.K483R		Atlas-SNP	.											.	PANK4	64	.	0			c.A1448G						PASS	.						72.0	75.0	74.0					1																	2445832		2203	4300	6503	SO:0001583	missense	55229	exon11			CAGTACTTCTGCC	AK001644	CCDS42.1	1p36.32	2008-02-05			ENSG00000157881	ENSG00000157881			19366	protein-coding gene	gene with protein product		606162				11479594	Standard	XR_241034		Approved	FLJ10782	uc001ajm.1	Q9NVE7	OTTHUMG00000000791	ENST00000378466.3:c.1448A>G	1.37:g.2445832T>C	ENSP00000367727:p.Lys483Arg	66.0	0.0	0		79.0	44.0	0.556962	NM_018216	B9DI84|Q53EU3|Q5TA84|Q7RTX3|Q9H3X5	Missense_Mutation	SNP	ENST00000378466.3	37	CCDS42.1	.	.	.	.	.	.	.	.	.	.	t	14.68	2.609185	0.46527	.	.	ENSG00000157881	ENST00000378466;ENST00000435556	T;T	0.18810	2.19;2.19	5.1	5.1	0.69264	Domain of unknown function DUF89 (2);	0.000000	0.85682	D	0.000000	T	0.32912	0.0845	L	0.33485	1.01	0.58432	D	0.999998	D;D	0.89917	1.0;1.0	D;D	0.81914	0.995;0.99	T	0.03503	-1.1030	10	0.22109	T	0.4	-33.6939	14.0447	0.64698	0.0:0.0:0.0:1.0	.	444;483	E9PHT6;Q9NVE7	.;PANK4_HUMAN	R	483;444	ENSP00000367727:K483R;ENSP00000421433:K444R	ENSP00000367727:K483R	K	-	2	0	PANK4	2435692	1.000000	0.71417	1.000000	0.80357	0.036000	0.12997	5.751000	0.68720	1.933000	0.56026	0.454000	0.30748	AAG	.	.	none		0.627	PANK4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000002082.1		
USP48	84196	hgsc.bcm.edu	37	1	22084201	22084201	+	Silent	SNP	A	A	G	rs150521027	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr1:22084201A>G	ENST00000308271.9	-	2	858	c.210T>C	c.(208-210)aaT>aaC	p.N70N	USP48_ENST00000400301.1_Silent_p.N70N|USP48_ENST00000529637.1_Silent_p.N70N|USP48_ENST00000421625.2_Silent_p.N70N	NM_032236.5	NP_115612.4	Q86UV5	UBP48_HUMAN	ubiquitin specific peptidase 48	70					ubiquitin-dependent protein catabolic process (GO:0006511)	cytoplasm (GO:0005737)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	ubiquitin-specific protease activity (GO:0004843)			NS(1)|endometrium(6)|kidney(2)|large_intestine(11)|lung(14)|ovary(2)|prostate(3)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	42		Colorectal(325;3.46e-05)|all_lung(284;4.29e-05)|Lung NSC(340;4.66e-05)|Renal(390;0.000219)|Breast(348;0.00222)|Ovarian(437;0.00308)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0182)|OV - Ovarian serous cystadenocarcinoma(117;4.74e-26)|COAD - Colon adenocarcinoma(152;1.3e-05)|GBM - Glioblastoma multiforme(114;1.86e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000614)|STAD - Stomach adenocarcinoma(196;0.00644)|KIRC - Kidney renal clear cell carcinoma(1967;0.00711)|Lung(427;0.0327)|READ - Rectum adenocarcinoma(331;0.0657)|LUSC - Lung squamous cell carcinoma(448;0.0753)		TATGAAAACTATTTTCATCTA	0.333													A|||	6	0.00119808	0.0	0.0	5008	,	,		19681	0.0		0.006	False		,,,				2504	0.0				p.N70N		Atlas-SNP	.											.	USP48	91	.	0			c.T210C						PASS	.	A	,	5,4401	9.9+/-24.2	0,5,2198	108.0	102.0	104.0		210,210	1.8	1.0	1	dbSNP_134	104	55,8545	35.9+/-90.5	0,55,4245	no	coding-synonymous,coding-synonymous	USP48	NM_001032730.1,NM_032236.5	,	0,60,6443	GG,GA,AA		0.6395,0.1135,0.4613	,	70/486,70/1036	22084201	60,12946	2203	4300	6503	SO:0001819	synonymous_variant	84196	exon2			AAAACTATTTTCA	AF502942	CCDS30623.1, CCDS44084.1	1p36.12	2008-02-05	2005-08-08	2004-04-07	ENSG00000090686	ENSG00000090686		"""Ubiquitin-specific peptidases"""	18533	protein-coding gene	gene with protein product			"""ubiquitin specific protease 31"", ""ubiquitin specific protease 48"""	USP31		12838346	Standard	XM_005246009		Approved	FLJ23277, FLJ11328, FLJ20103, FLJ23054, MGC14879	uc001bfb.3	Q86UV5	OTTHUMG00000007798	ENST00000308271.9:c.210T>C	1.37:g.22084201A>G		120.0	0.0	0		89.0	47.0	0.52809	NM_001032730	B7ZKS7|Q2M3I4|Q5SZI4|Q5T3T5|Q6NX53|Q8N3F6|Q96F64|Q96IQ3|Q9H5N3|Q9H5T7|Q9NUJ6|Q9NXR0	Silent	SNP	ENST00000308271.9	37	CCDS30623.1																																																																																			A|0.996;G|0.004	0.004	strong		0.333	USP48-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000021372.1	NM_032236	
TPR	7175	hgsc.bcm.edu	37	1	186314809	186314809	+	Missense_Mutation	SNP	G	G	A	rs200209324	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr1:186314809G>A	ENST00000367478.4	-	24	3412	c.3116C>T	c.(3115-3117)aCa>aTa	p.T1039I		NM_003292.2	NP_003283.2	P12270	TPR_HUMAN	translocated promoter region, nuclear basket protein	1039					carbohydrate metabolic process (GO:0005975)|cellular response to heat (GO:0034605)|cellular response to interferon-alpha (GO:0035457)|cytokine-mediated signaling pathway (GO:0019221)|glucose transport (GO:0015758)|hexose transport (GO:0008645)|MAPK import into nucleus (GO:0000189)|mitotic cell cycle (GO:0000278)|mitotic nuclear division (GO:0007067)|mitotic nuclear envelope disassembly (GO:0007077)|mitotic spindle assembly checkpoint (GO:0007094)|mRNA export from nucleus in response to heat stress (GO:0031990)|negative regulation of RNA export from nucleus (GO:0046832)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of translational initiation (GO:0045947)|nuclear pore organization (GO:0006999)|positive regulation of heterochromatin assembly (GO:0031453)|positive regulation of intracellular protein transport (GO:0090316)|positive regulation of mitotic cell cycle spindle assembly checkpoint (GO:0090267)|positive regulation of protein export from nucleus (GO:0046827)|positive regulation of protein import into nucleus (GO:0042307)|protein import into nucleus (GO:0006606)|regulation of glucose transport (GO:0010827)|regulation of mitotic sister chromatid separation (GO:0010965)|regulation of spindle assembly involved in mitosis (GO:1901673)|response to epidermal growth factor (GO:0070849)|RNA export from nucleus (GO:0006405)|RNA import into nucleus (GO:0006404)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)|viral process (GO:0016032)	cytoplasm (GO:0005737)|cytoplasmic dynein complex (GO:0005868)|extrinsic component of membrane (GO:0019898)|kinetochore (GO:0000776)|mitotic spindle (GO:0072686)|nuclear envelope (GO:0005635)|nuclear inclusion body (GO:0042405)|nuclear membrane (GO:0031965)|nuclear periphery (GO:0034399)|nuclear pore (GO:0005643)|nuclear pore nuclear basket (GO:0044615)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	chromatin binding (GO:0003682)|dynein complex binding (GO:0070840)|heat shock protein binding (GO:0031072)|mitogen-activated protein kinase binding (GO:0051019)|mRNA binding (GO:0003729)|nucleocytoplasmic transporter activity (GO:0005487)|poly(A) RNA binding (GO:0044822)|protein homodimerization activity (GO:0042803)|tubulin binding (GO:0015631)			autonomic_ganglia(1)|breast(5)|central_nervous_system(4)|cervix(2)|endometrium(9)|kidney(12)|large_intestine(23)|liver(1)|lung(45)|ovary(2)|pancreas(1)|prostate(6)|skin(3)|stomach(1)|urinary_tract(8)	123		Breast(1374;0.000659)|Lung SC(1967;0.0262)|Prostate(1639;0.157)		Colorectal(1306;1.12e-05)|KIRC - Kidney renal clear cell carcinoma(1967;0.00553)		ACTAGAAAGTGTTTTCTTCAA	0.348			T	NTRK1	papillary thyroid																																p.T1039I		Atlas-SNP	.		Dom	yes		1	1q25	7175	translocated promoter region		E	.	TPR	441	.	0			c.C3116T						PASS	.	G	ILE/THR	2,3686		0,2,1842	107.0	94.0	99.0		3116	4.3	1.0	1		99	16,8154		0,16,4069	yes	missense	TPR	NM_003292.2	89	0,18,5911	AA,AG,GG		0.1958,0.0542,0.1518	benign	1039/2364	186314809	18,11840	1844	4085	5929	SO:0001583	missense	7175	exon24			GAAAGTGTTTTCT	U69668	CCDS41446.1	1q25	2012-03-13	2012-03-13		ENSG00000047410	ENSG00000047410			12017	protein-coding gene	gene with protein product		189940	"""translocated promoter region (to activated MET oncogene)"""			1611909, 15229283	Standard	NM_003292		Approved		uc001grv.3	P12270	OTTHUMG00000035580	ENST00000367478.4:c.3116C>T	1.37:g.186314809G>A	ENSP00000356448:p.Thr1039Ile	64.0	0.0	0		72.0	35.0	0.486111	NM_003292	Q15655|Q5SWY0|Q99968	Missense_Mutation	SNP	ENST00000367478.4	37	CCDS41446.1	.	.	.	.	.	.	.	.	.	.	G	15.03	2.713644	0.48517	5.42E-4	0.001958	ENSG00000047410	ENST00000367478	T	0.23348	1.91	5.31	4.34	0.51931	Prefoldin (1);Tetratricopeptide, MLP1/MLP2-like (1);	0.083000	0.85682	D	0.000000	T	0.16769	0.0403	N	0.08118	0	0.28533	N	0.912504	P	0.35821	0.523	B	0.42798	0.398	T	0.07252	-1.0782	10	0.56958	D	0.05	.	9.3043	0.37865	0.0:0.3079:0.566:0.1261	.	1039	P12270	TPR_HUMAN	I	1039	ENSP00000356448:T1039I	ENSP00000356448:T1039I	T	-	2	0	TPR	184581432	1.000000	0.71417	1.000000	0.80357	0.991000	0.79684	3.135000	0.50546	2.630000	0.89119	0.650000	0.86243	ACA	G|0.998;A|0.002	0.002	strong		0.348	TPR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000086353.2	NM_003292	
SNW1	22938	hgsc.bcm.edu	37	14	78205189	78205189	+	Silent	SNP	T	T	C	rs147154490		TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr14:78205189T>C	ENST00000261531.7	-	5	527	c.465A>G	c.(463-465)gtA>gtG	p.V155V	SNW1_ENST00000555761.1_Silent_p.V155V|SLIRP_ENST00000557431.1_Intron|SNW1_ENST00000554775.1_5'UTR	NM_012245.2	NP_036377.1	Q13573	SNW1_HUMAN	SNW domain containing 1	155					cellular response to retinoic acid (GO:0071300)|gene expression (GO:0010467)|intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator (GO:0042771)|mRNA splicing, via spliceosome (GO:0000398)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|Notch signaling pathway (GO:0007219)|positive regulation by host of viral transcription (GO:0043923)|positive regulation of histone H3-K4 methylation (GO:0051571)|positive regulation of mRNA splicing, via spliceosome (GO:0048026)|positive regulation of neurogenesis (GO:0050769)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transforming growth factor beta receptor signaling pathway (GO:0030511)|positive regulation of vitamin D receptor signaling pathway (GO:0070564)|regulation of retinoic acid receptor signaling pathway (GO:0048385)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|regulation of vitamin D receptor signaling pathway (GO:0070562)|retinoic acid receptor signaling pathway (GO:0048384)|transcription initiation from RNA polymerase II promoter (GO:0006367)|viral process (GO:0016032)	catalytic step 2 spliceosome (GO:0071013)|chromatin (GO:0000785)|nuclear matrix (GO:0016363)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|spliceosomal complex (GO:0005681)	Notch binding (GO:0005112)|nuclear hormone receptor binding (GO:0035257)|poly(A) RNA binding (GO:0044822)|retinoic acid receptor binding (GO:0042974)|SMAD binding (GO:0046332)|transcription coactivator activity (GO:0003713)|transcription corepressor activity (GO:0003714)|vitamin D receptor binding (GO:0042809)			NS(1)|endometrium(3)|kidney(3)|large_intestine(6)|lung(6)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	24			Kidney(204;0.164)	BRCA - Breast invasive adenocarcinoma(234;0.0291)		CCTTCTGTGATACAGATTTTT	0.403													T|||	1	0.000199681	0.0	0.0	5008	,	,		18116	0.0		0.001	False		,,,				2504	0.0				p.V155V		Atlas-SNP	.											.	SNW1	44	.	0			c.A465G						PASS	.	T		0,4406		0,0,2203	90.0	93.0	92.0		465	-2.5	1.0	14	dbSNP_134	92	20,8580	14.6+/-50.1	0,20,4280	no	coding-synonymous	SNW1	NM_012245.2		0,20,6483	CC,CT,TT		0.2326,0.0,0.1538		155/537	78205189	20,12986	2203	4300	6503	SO:0001819	synonymous_variant	22938	exon5			CTGTGATACAGAT	AF045184	CCDS9867.1	14q22.1-q22.3	2005-09-13	2005-09-13	2005-09-13		ENSG00000100603			16696	protein-coding gene	gene with protein product		603055	"""SKI interacting protein"""	SKIIP		8973337, 9632709	Standard	NM_012245		Approved	NCoA-62, SKIP, Prp45, PRPF45, Bx42	uc001xuf.3	Q13573		ENST00000261531.7:c.465A>G	14.37:g.78205189T>C		140.0	0.0	0		168.0	70.0	0.416667	NM_012245	A8K8A9|Q13483|Q32N03|Q5D0D6	Silent	SNP	ENST00000261531.7	37	CCDS9867.1																																																																																			T|0.999;C|0.001	0.001	strong		0.403	SNW1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000413912.1	NM_012245	
PRDM16	63976	hgsc.bcm.edu	37	1	3102852	3102852	+	Silent	SNP	G	G	A	rs199614349	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr1:3102852G>A	ENST00000270722.5	+	2	250	c.201G>A	c.(199-201)ccG>ccA	p.P67P	PRDM16_ENST00000378391.2_Silent_p.P67P|PRDM16_ENST00000511072.1_Silent_p.P67P|PRDM16_ENST00000442529.2_Silent_p.P67P|PRDM16_ENST00000441472.2_Silent_p.P67P|PRDM16_ENST00000378398.3_Silent_p.P67P|PRDM16_ENST00000514189.1_Silent_p.P67P			Q9HAZ2	PRD16_HUMAN	PR domain containing 16	67					brown fat cell differentiation (GO:0050873)|negative regulation of granulocyte differentiation (GO:0030853)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|negative regulation of transforming growth factor beta receptor signaling pathway (GO:0030512)|neurogenesis (GO:0022008)|palate development (GO:0060021)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of cellular respiration (GO:0043457)|somatic stem cell maintenance (GO:0035019)|tongue development (GO:0043586)|transcription, DNA-templated (GO:0006351)|white fat cell differentiation (GO:0050872)	nucleus (GO:0005634)|transcriptional repressor complex (GO:0017053)	metal ion binding (GO:0046872)|sequence-specific DNA binding (GO:0043565)|transcription coactivator activity (GO:0003713)			breast(4)|central_nervous_system(1)|endometrium(5)|kidney(4)|large_intestine(7)|lung(22)|ovary(2)|pancreas(1)|prostate(2)|skin(7)|upper_aerodigestive_tract(1)|urinary_tract(3)	59	all_cancers(77;0.00208)|all_epithelial(69;0.000732)|Ovarian(185;0.0634)|Lung NSC(156;0.109)|all_lung(157;0.111)	all_epithelial(116;2.03e-21)|all_lung(118;7.55e-09)|Lung NSC(185;1.28e-06)|Breast(487;0.000792)|Renal(390;0.00137)|Hepatocellular(190;0.00515)|Myeloproliferative disorder(586;0.0267)|Ovarian(437;0.0365)|Lung SC(97;0.114)|Medulloblastoma(700;0.134)		Epithelial(90;5.59e-35)|OV - Ovarian serous cystadenocarcinoma(86;1.99e-20)|GBM - Glioblastoma multiforme(42;3.72e-11)|Colorectal(212;0.000425)|BRCA - Breast invasive adenocarcinoma(365;0.000946)|COAD - Colon adenocarcinoma(227;0.000968)|Kidney(185;0.00155)|STAD - Stomach adenocarcinoma(132;0.00644)|KIRC - Kidney renal clear cell carcinoma(229;0.0175)|Lung(427;0.137)		AGGGCTCGCCGTACGAGGCCC	0.672			T	EVI1	"""MDS, AML"""								G|||	6	0.00119808	0.0	0.0029	5008	,	,		14984	0.0		0.003	False		,,,				2504	0.001				p.P67P		Atlas-SNP	.		Dom	yes		1	1p36.23-p33	63976	PR domain containing 16		L	.	PRDM16	147	.	0			c.G201A						PASS	.	G	,	0,4074		0,0,2037	49.0	60.0	56.0		201,201	-2.7	1.0	1		56	24,8284		0,24,4130	no	coding-synonymous,coding-synonymous	PRDM16	NM_022114.3,NM_199454.2	,	0,24,6167	AA,AG,GG		0.2889,0.0,0.1938	,	67/1277,67/1258	3102852	24,12358	2037	4154	6191	SO:0001819	synonymous_variant	63976	exon2			CTCGCCGTACGAG	AF294278	CCDS41236.1, CCDS44048.1, CCDS41236.2, CCDS44048.2	1p36.23-p33	2013-01-08			ENSG00000142611	ENSG00000142611		"""Zinc fingers, C2H2-type"""	14000	protein-coding gene	gene with protein product	"""MDS1/EVI1-like"", ""PR-domain zinc finger protein 16"", ""transcription factor MEL1"""	605557				11050005	Standard	NM_199454		Approved	MEL1, PFM13, KIAA1675, MGC166915	uc001akf.3	Q9HAZ2	OTTHUMG00000000581	ENST00000270722.5:c.201G>A	1.37:g.3102852G>A		198.0	0.0	0		240.0	123.0	0.5125	NM_022114	A6NHQ8|B1AJP7|B1AJP8|B1AJP9|B1WB48|Q8WYJ9|Q9C0I8	Silent	SNP	ENST00000270722.5	37	CCDS41236.2																																																																																			G|0.989;A|0.011	0.011	strong		0.672	PRDM16-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000001382.3	NM_022114	
CC2D1A	54862	hgsc.bcm.edu	37	19	14024269	14024269	+	Missense_Mutation	SNP	C	C	T	rs61740117	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr19:14024269C>T	ENST00000318003.7	+	6	807	c.566C>T	c.(565-567)gCg>gTg	p.A189V	CC2D1A_ENST00000589606.1_Missense_Mutation_p.A189V	NM_017721.4	NP_060191.3	Q6P1N0	C2D1A_HUMAN	coiled-coil and C2 domain containing 1A	189					positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|nucleus (GO:0005634)	RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in negative regulation of transcription (GO:0001078)|signal transducer activity (GO:0004871)			NS(1)|breast(2)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(3)|lung(12)|prostate(2)|skin(2)	27			OV - Ovarian serous cystadenocarcinoma(19;3.49e-23)			ATTGACGAAGCGGACATCCCG	0.602													C|||	15	0.00299521	0.0	0.0029	5008	,	,		17181	0.0		0.0119	False		,,,				2504	0.001				p.A189V		Atlas-SNP	.											.	CC2D1A	67	.	0			c.C566T						PASS	.	C	VAL/ALA	7,4065		0,7,2029	35.0	44.0	41.0		566	-10.4	0.0	19	dbSNP_129	41	100,8246		0,100,4073	yes	missense	CC2D1A	NM_017721.4	64	0,107,6102	TT,TC,CC		1.1982,0.1719,0.8617	benign	189/952	14024269	107,12311	2036	4173	6209	SO:0001583	missense	54862	exon6			ACGAAGCGGACAT	AF536205	CCDS42512.1	19p13.12	2007-01-08				ENSG00000132024			30237	protein-coding gene	gene with protein product	"""mental retardation, nonsyndromic, autosomal recessive, 3"""	610055				12761501, 16033914	Standard	NM_017721		Approved	FLJ20241, MRT3	uc002mxo.2	Q6P1N0		ENST00000318003.7:c.566C>T	19.37:g.14024269C>T	ENSP00000313601:p.Ala189Val	87.0	0.0	0		107.0	56.0	0.523364	NM_017721	Q7Z435|Q86XV0|Q8NF89|Q9H603|Q9NXI1	Missense_Mutation	SNP	ENST00000318003.7	37	CCDS42512.1	10	0.004578754578754579	0	0.0	1	0.0027624309392265192	0	0.0	9	0.011873350923482849	C	10.62	1.400963	0.25291	0.001719	0.011982	ENSG00000132024	ENST00000318003;ENST00000254346;ENST00000389233	T	0.22539	1.95	5.2	-10.4	0.00318	Domain of unknown function DM14 (1);	0.466636	0.22488	N	0.059413	T	0.07279	0.0184	L	0.46157	1.445	0.24389	N	0.994752	P;P	0.37731	0.489;0.607	B;B	0.32724	0.151;0.143	T	0.01791	-1.1273	10	0.59425	D	0.04	-4.4191	6.3202	0.21213	0.5862:0.255:0.0806:0.0783	rs61740117	189;189	Q6P1N0-2;Q6P1N0	.;C2D1A_HUMAN	V	189;27;164	ENSP00000313601:A189V	ENSP00000254346:A27V	A	+	2	0	CC2D1A	13885269	0.983000	0.35010	0.037000	0.18230	0.014000	0.08584	0.328000	0.19681	-2.793000	0.00355	-1.555000	0.00892	GCG	C|0.995;T|0.005	0.005	strong		0.602	CC2D1A-001	KNOWN	NAGNAG_splice_site|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000457954.1	NM_017721	
SMU1	55234	hgsc.bcm.edu	37	9	33071879	33071879	+	Silent	SNP	T	T	C			TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr9:33071879T>C	ENST00000397149.3	-	3	299	c.249A>G	c.(247-249)gaA>gaG	p.E83E	SMU1_ENST00000536631.1_Intron	NM_018225.2	NP_060695.2	Q2TAY7	SMU1_HUMAN	smu-1 suppressor of mec-8 and unc-52 homolog (C. elegans)	83	CTLH. {ECO:0000255|PROSITE- ProRule:PRU00058}.					cytoplasm (GO:0005737)|nucleus (GO:0005634)				endometrium(2)|lung(4)|ovary(2)|prostate(1)	9			LUSC - Lung squamous cell carcinoma(29;0.0227)	GBM - Glioblastoma multiforme(74;0.11)		GCTCTATCAATTCCAGAACAA	0.368																																					p.E83E		Atlas-SNP	.											.	SMU1	29	.	0			c.A249G						PASS	.						74.0	72.0	73.0					9																	33071879		2203	4300	6503	SO:0001819	synonymous_variant	55234	exon3			TATCAATTCCAGA	AK001667	CCDS6534.1	9p12	2013-01-10			ENSG00000122692	ENSG00000122692		"""WD repeat domain containing"""	18247	protein-coding gene	gene with protein product	"""functional spliceosome-associated protein 57"""					11438655, 11410362	Standard	NM_018225		Approved	SMU-1, FLJ10805, BWD, fSAP57	uc003zsf.1	Q2TAY7	OTTHUMG00000019757	ENST00000397149.3:c.249A>G	9.37:g.33071879T>C		113.0	0.0	0		122.0	51.0	0.418033	NM_018225	B4E3L0|Q9BU59|Q9HA96|Q9NVD1	Silent	SNP	ENST00000397149.3	37	CCDS6534.1																																																																																			.	.	none		0.368	SMU1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052022.1	NM_018225	
AURKAIP1	54998	hgsc.bcm.edu	37	1	1309803	1309803	+	Silent	SNP	G	G	A	rs9554		TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr1:1309803G>A	ENST00000338370.3	-	2	475	c.75C>T	c.(73-75)gtC>gtT	p.V25V	AURKAIP1_ENST00000489799.1_5'UTR|AURKAIP1_ENST00000321751.5_Silent_p.V25V|AURKAIP1_ENST00000378853.3_Silent_p.V25V|AURKAIP1_ENST00000338338.5_Silent_p.V25V			Q9NWT8	AKIP_HUMAN	aurora kinase A interacting protein 1	25					negative regulation of mitosis (GO:0045839)|positive regulation of proteolysis (GO:0045862)	intracellular membrane-bounded organelle (GO:0043231)|mitochondrion (GO:0005739)|nucleus (GO:0005634)				kidney(1)|lung(2)	3	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)		Epithelial(90;5.82e-35)|OV - Ovarian serous cystadenocarcinoma(86;3.77e-21)|Colorectal(212;0.000155)|COAD - Colon adenocarcinoma(227;0.000193)|Kidney(185;0.00227)|BRCA - Breast invasive adenocarcinoma(365;0.00461)|STAD - Stomach adenocarcinoma(132;0.00644)|KIRC - Kidney renal clear cell carcinoma(229;0.0339)|Lung(427;0.145)		GCACTCCAGAGACGGGCCAAG	0.716																																					p.V25V		Atlas-SNP	.											.	AURKAIP1	12	.	0			c.C75T						PASS	.						2.0	4.0	3.0					1																	1309803		1684	3642	5326	SO:0001819	synonymous_variant	54998	exon3			TCCAGAGACGGGC		CCDS25.1	1p36.33	2014-02-12			ENSG00000175756	ENSG00000175756			24114	protein-coding gene	gene with protein product		609183				12244051	Standard	NM_017900		Approved	AKIP, AIP, FLJ20608	uc009vkb.1	Q9NWT8	OTTHUMG00000001413	ENST00000338370.3:c.75C>T	1.37:g.1309803G>A		11.0	0.0	0		10.0	9.0	0.9	NM_001127230	Q5TA36|Q8TBD3	Silent	SNP	ENST00000338370.3	37	CCDS25.1																																																																																			.	.	weak		0.716	AURKAIP1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000008273.1	NM_017900	
KRTAP5-1	387264	hgsc.bcm.edu	37	11	1605957	1605957	+	Missense_Mutation	SNP	C	C	T	rs151275365	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr11:1605957C>T	ENST00000382171.2	-	1	556	c.523G>A	c.(523-525)Ggg>Agg	p.G175R	KRTAP5-AS1_ENST00000424148.1_RNA|KRTAP5-AS1_ENST00000532922.1_RNA|KRTAP5-AS1_ENST00000524947.1_RNA|KRTAP5-AS1_ENST00000534077.1_RNA	NM_001005922.1	NP_001005922.1	Q6L8H4	KRA51_HUMAN	keratin associated protein 5-1	175	8 X 4 AA repeats of C-C-X-P.					keratin filament (GO:0045095)				endometrium(3)|kidney(1)|lung(9)|skin(2)|upper_aerodigestive_tract(1)	16		all_epithelial(84;0.00018)|Ovarian(85;0.0014)|Breast(177;0.00147)|Medulloblastoma(188;0.0109)|all_neural(188;0.0299)|Lung NSC(207;0.229)		BRCA - Breast invasive adenocarcinoma(625;0.000614)|Lung(200;0.0681)|LUSC - Lung squamous cell carcinoma(625;0.082)		CCACAGCCCCCCTTGGAGCCC	0.677																																					p.G175R		Atlas-SNP	.											.	KRTAP5-1	74	.	0			c.G523A						PASS	.	C	ARG/GLY	12,4390		0,12,2189	46.0	62.0	57.0		523	2.9	1.0	11	dbSNP_134	57	111,8487		1,109,4189	no	missense	KRTAP5-1	NM_001005922.1	125	1,121,6378	TT,TC,CC		1.291,0.2726,0.9462	possibly-damaging	175/279	1605957	123,12877	2201	4299	6500	SO:0001583	missense	387264	exon1			AGCCCCCCTTGGA	AB126070	CCDS31330.1	11p15.5	2008-02-05			ENSG00000205869	ENSG00000205869		"""Keratin associated proteins"""	23596	protein-coding gene	gene with protein product		148022	"""keratin, cuticle, ultrahigh sulphur 1-like"""	KRN1L		15144888	Standard	NM_001005922		Approved	KRTAP5.1	uc001ltu.1	Q6L8H4	OTTHUMG00000057557	ENST00000382171.2:c.523G>A	11.37:g.1605957C>T	ENSP00000371606:p.Gly175Arg	142.0	0.0	0		163.0	57.0	0.349693	NM_001005922		Missense_Mutation	SNP	ENST00000382171.2	37	CCDS31330.1	12	0.005494505494505495	0	0.0	0	0.0	0	0.0	12	0.0158311345646438	c	0.039	-1.291524	0.01375	0.002726	0.01291	ENSG00000205869	ENST00000382171	T	0.05199	3.48	2.91	2.91	0.33838	.	.	.	.	.	T	0.03263	0.0095	M	0.62266	1.93	0.26033	N	0.981718	P	0.40332	0.713	B	0.40375	0.327	T	0.17592	-1.0364	9	0.12103	T	0.63	.	5.9746	0.19371	0.0:0.8455:0.0:0.1545	.	175	Q6L8H4	KRA51_HUMAN	R	175	ENSP00000371606:G175R	ENSP00000371606:G175R	G	-	1	0	KRTAP5-1	1562533	0.000000	0.05858	0.998000	0.56505	0.319000	0.28217	-1.117000	0.03283	1.185000	0.42971	0.271000	0.19318	GGG	C|0.989;T|0.011	0.011	strong		0.677	KRTAP5-1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000127922.1	NM_001005922	
KIFC1	3833	hgsc.bcm.edu	37	6	33373341	33373341	+	Missense_Mutation	SNP	C	C	T	rs7770412	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr6:33373341C>T	ENST00000428849.2	+	7	1919	c.1469C>T	c.(1468-1470)gCa>gTa	p.A490V		NM_002263.3	NP_002254.2	Q9BW19	KIFC1_HUMAN	kinesin family member C1	490	Kinesin motor. {ECO:0000255|PROSITE- ProRule:PRU00283}.				ATP catabolic process (GO:0006200)|blood coagulation (GO:0007596)|metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)|mitotic sister chromatid segregation (GO:0000070)|spindle assembly (GO:0051225)	endosome (GO:0005768)|kinesin complex (GO:0005871)|membrane (GO:0016020)|microtubule (GO:0005874)|nucleus (GO:0005634)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)|minus-end-directed microtubule motor activity (GO:0008569)			endometrium(1)|kidney(1)|large_intestine(1)|lung(6)|prostate(3)|skin(1)	13						ATTCGCCGTGCAGGGCCAGGG	0.562													C|||	43	0.00858626	0.0098	0.0014	5008	,	,		19788	0.0099		0.0109	False		,,,				2504	0.0082				p.A490V		Atlas-SNP	.											.	KIFC1	47	.	0			c.C1469T						PASS	.	C	VAL/ALA	21,4385	25.3+/-52.1	0,21,2182	28.0	29.0	29.0		1469	5.2	1.0	6	dbSNP_116	29	72,8528	42.6+/-100.3	0,72,4228	yes	missense	KIFC1	NM_002263.3	64	0,93,6410	TT,TC,CC		0.8372,0.4766,0.7151	benign	490/674	33373341	93,12913	2203	4300	6503	SO:0001583	missense	3833	exon7			GCCGTGCAGGGCC	D14678	CCDS34430.1	6p21.32	2014-05-15	2003-01-09	2003-01-10	ENSG00000237649	ENSG00000237649		"""Kinesins"""	6389	protein-coding gene	gene with protein product		603763	"""kinesin-like 2"""	KNSL2		8276466	Standard	NM_002263		Approved	HSET	uc003oef.4	Q9BW19	OTTHUMG00000031209	ENST00000428849.2:c.1469C>T	6.37:g.33373341C>T	ENSP00000393963:p.Ala490Val	24.0	0.0	0		24.0	9.0	0.375	NM_002263	O60887|Q14834|Q4KMP0|Q5SU09|Q6GMS7|Q6P4A5|Q9UQP7	Missense_Mutation	SNP	ENST00000428849.2	37	CCDS34430.1	23	0.010531135531135532	8	0.016260162601626018	1	0.0027624309392265192	8	0.013986013986013986	6	0.0079155672823219	C	10.18	1.279858	0.23392	0.004766	0.008372	ENSG00000237649	ENST00000428849	T	0.75367	-0.93	5.22	5.22	0.72569	Kinesin, motor domain (4);	0.346115	0.29900	N	0.010904	T	0.41650	0.1168	N	0.20610	0.595	0.45502	D	0.998463	B;B	0.28400	0.21;0.21	B;B	0.26094	0.066;0.066	T	0.39143	-0.9628	10	0.22109	T	0.4	-17.1298	9.6556	0.39923	0.0:0.9081:0.0:0.0919	rs7770412	482;490	B4E063;Q9BW19	.;KIFC1_HUMAN	V	490	ENSP00000393963:A490V	ENSP00000393963:A490V	A	+	2	0	KIFC1	33481319	0.997000	0.39634	1.000000	0.80357	0.952000	0.60782	2.994000	0.49433	2.720000	0.93068	0.655000	0.94253	GCA	C|0.993;T|0.007	0.007	strong		0.562	KIFC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076417.1	NM_002263	
LRRC8B	23507	hgsc.bcm.edu	37	1	90049577	90049577	+	Silent	SNP	C	C	T	rs140158391		TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr1:90049577C>T	ENST00000330947.2	+	5	1728	c.1368C>T	c.(1366-1368)ccC>ccT	p.P456P	LRRC8B_ENST00000439853.1_Silent_p.P456P|RP5-1007M22.2_ENST00000443562.1_RNA|LRRC8B_ENST00000358200.4_Silent_p.P456P	NM_001134476.1	NP_001127948.1	Q6P9F7	LRC8B_HUMAN	leucine rich repeat containing 8 family, member B	456					ion transport (GO:0006811)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				breast(1)|central_nervous_system(1)|endometrium(6)|kidney(5)|large_intestine(2)|lung(5)|ovary(2)|prostate(2)|skin(1)|urinary_tract(1)	26		all_lung(203;0.17)		all cancers(265;0.00515)|Epithelial(280;0.0241)		TGAAGCTGCCCTCTGCAGTCT	0.473																																					p.P456P		Atlas-SNP	.											.	LRRC8B	49	.	0			c.C1368T						PASS	.	C	,	4,4402	8.1+/-20.4	0,4,2199	52.0	52.0	52.0		1368,1368	0.8	1.0	1	dbSNP_134	52	0,8600		0,0,4300	no	coding-synonymous,coding-synonymous	LRRC8B	NM_001134476.1,NM_015350.2	,	0,4,6499	TT,TC,CC		0.0,0.0908,0.0308	,	456/804,456/804	90049577	4,13002	2203	4300	6503	SO:0001819	synonymous_variant	23507	exon5			GCTGCCCTCTGCA	AF385436	CCDS724.1	1p22.2	2008-02-05			ENSG00000197147	ENSG00000197147			30692	protein-coding gene	gene with protein product	"""T cell activation leucine repeat rich protein"""	612888				9039502	Standard	NM_015350		Approved	TA-LRRP, KIAA0231	uc001dni.3	Q6P9F7	OTTHUMG00000010129	ENST00000330947.2:c.1368C>T	1.37:g.90049577C>T		50.0	0.0	0		64.0	4.0	0.0625	NM_015350	D3DT28|Q6UY21|Q8N106|Q92627	Silent	SNP	ENST00000330947.2	37	CCDS724.1																																																																																			C|1.000;T|0.000	0.000	weak		0.473	LRRC8B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000028008.1	NM_015350	
DSPP	1834	hgsc.bcm.edu	37	4	88537288	88537288	+	Silent	SNP	C	C	T	rs368208607		TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr4:88537288C>T	ENST00000282478.7	+	4	3507	c.3474C>T	c.(3472-3474)gaC>gaT	p.D1158D	RP11-742B18.1_ENST00000506480.1_RNA|DSPP_ENST00000399271.1_Silent_p.D1158D			Q9NZW4	DSPP_HUMAN	dentin sialophosphoprotein	1158	Asp/Ser-rich.				biomineral tissue development (GO:0031214)|cellular response to cell-matrix adhesion (GO:0071460)|extracellular matrix organization (GO:0030198)|multicellular organismal development (GO:0007275)|ossification (GO:0001503)|skeletal system development (GO:0001501)	cytoplasm (GO:0005737)|extracellular region (GO:0005576)|proteinaceous extracellular matrix (GO:0005578)	calcium ion binding (GO:0005509)|collagen binding (GO:0005518)|extracellular matrix structural constituent (GO:0005201)			breast(2)|central_nervous_system(1)|endometrium(9)|kidney(4)|large_intestine(8)|lung(13)|ovary(1)|skin(3)|stomach(3)|upper_aerodigestive_tract(2)|urinary_tract(1)	47		Hepatocellular(203;0.114)|all_hematologic(202;0.236)		OV - Ovarian serous cystadenocarcinoma(123;0.000508)		acagcagcgacagcagtgaca	0.557																																					p.D1158D		Atlas-SNP	.											.	DSPP	174	.	0			c.C3474T						PASS	.						46.0	59.0	54.0					4																	88537288		1591	2859	4450	SO:0001819	synonymous_variant	1834	exon5			CAGCGACAGCAGT	AF163151	CCDS43248.1	4q21.3	2008-02-05			ENSG00000152591	ENSG00000152591			3054	protein-coding gene	gene with protein product		125485		DFNA39, DGI1		8995371, 9533027	Standard	NM_014208		Approved	DMP3	uc003hqu.3	Q9NZW4	OTTHUMG00000161061	ENST00000282478.7:c.3474C>T	4.37:g.88537288C>T		217.0	0.0	0		175.0	9.0	0.0514286	NM_014208	A8MUI0|O95815	Silent	SNP	ENST00000282478.7	37	CCDS43248.1																																																																																			.	.	weak		0.557	DSPP-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000363616.3	NM_014208	
ZBED6CL	113763	hgsc.bcm.edu	37	7	150027802	150027802	+	Silent	SNP	C	C	T	rs75555338	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr7:150027802C>T	ENST00000343855.4	+	1	865	c.309C>T	c.(307-309)ctC>ctT	p.L103L	LRRC61_ENST00000323078.7_Intron|LRRC61_ENST00000493307.1_Intron|LRRC61_ENST00000359623.4_Intron	NM_138434.2	NP_612443.1	Q96FA7	ZB6CL_HUMAN	ZBED6 C-terminal like	103																	AGCAAGTCCTCGTGTACAAGG	0.567													C|||	12	0.00239617	0.0008	0.0014	5008	,	,		19715	0.0		0.0099	False		,,,				2504	0.0				p.L103L		Atlas-SNP	.											.	C7orf29	18	.	0			c.C309T						PASS	.	C	,,	7,4399	12.9+/-30.5	0,7,2196	74.0	75.0	75.0		,,309	-7.5	0.0	7	dbSNP_133	75	138,8462	68.4+/-130.8	2,134,4164	no	intron,intron,coding-synonymous	LRRC61,C7orf29	NM_001142928.1,NM_023942.2,NM_138434.2	,,	2,141,6360	TT,TC,CC		1.6047,0.1589,1.1149	,,	,,103/237	150027802	145,12861	2203	4300	6503	SO:0001819	synonymous_variant	113763	exon1			AGTCCTCGTGTAC	BC011406	CCDS5900.1	7q35	2013-05-03	2013-05-03	2013-05-03	ENSG00000188707	ENSG00000188707			21720	protein-coding gene	gene with protein product		615252	"""chromosome 7 open reading frame 29"""	C7orf29		23533661	Standard	NM_138434		Approved			Q96FA7	OTTHUMG00000158328	ENST00000343855.4:c.309C>T	7.37:g.150027802C>T		82.0	0.0	0		111.0	53.0	0.477477	NM_138434		Silent	SNP	ENST00000343855.4	37	CCDS5900.1																																																																																			C|0.990;T|0.010	0.010	strong		0.567	ZBED6CL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000350702.1	NM_138434	
CHL1	10752	hgsc.bcm.edu	37	3	361493	361493	+	Missense_Mutation	SNP	G	G	A	rs142251617	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr3:361493G>A	ENST00000256509.2	+	3	676	c.34G>A	c.(34-36)Gta>Ata	p.V12I	CHL1_ENST00000397491.2_Missense_Mutation_p.V12I	NM_001253387.1|NM_001253388.1|NM_006614.3	NP_001240316.1|NP_001240317.1|NP_006605.2	Q96FC9	DDX11_HUMAN	cell adhesion molecule L1-like	0	Helicase ATP-binding. {ECO:0000255|PROSITE-ProRule:PRU00541}.				activation of signaling protein activity involved in unfolded protein response (GO:0006987)|ATP catabolic process (GO:0006200)|cellular protein metabolic process (GO:0044267)|endoplasmic reticulum unfolded protein response (GO:0030968)|sister chromatid cohesion (GO:0007062)|viral process (GO:0016032)	midbody (GO:0030496)|nuclear chromatin (GO:0000790)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|spindle pole (GO:0000922)	4 iron, 4 sulfur cluster binding (GO:0051539)|ATP binding (GO:0005524)|ATP-dependent DNA helicase activity (GO:0004003)|DNA-dependent ATPase activity (GO:0008094)|double-stranded DNA binding (GO:0003690)|helicase activity (GO:0004386)|metal ion binding (GO:0046872)|RNA binding (GO:0003723)|single-stranded DNA binding (GO:0003697)			NS(1)|central_nervous_system(5)|endometrium(11)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(25)|lung(31)|ovary(1)|prostate(4)|skin(10)|stomach(1)	93		all_cancers(2;1.14e-06)|all_epithelial(2;0.00367)|all_lung(1;0.061)|Lung NSC(2;0.201)		Epithelial(13;5.36e-06)|all cancers(10;1.4e-05)|OV - Ovarian serous cystadenocarcinoma(96;0.00323)|COAD - Colon adenocarcinoma(1;0.00925)|Colorectal(20;0.0198)		AGGACTAATCGTATATCTAAT	0.348													G|||	66	0.0131789	0.0015	0.0634	5008	,	,		16221	0.001		0.0089	False		,,,				2504	0.0102				p.V12I		Atlas-SNP	.											.	CHL1	242	.	0			c.G34A						PASS	.	G	ILE/VAL	13,4391	20.2+/-43.8	0,13,2189	65.0	68.0	67.0		34	-9.8	0.0	3	dbSNP_134	67	106,8494	57.9+/-119.4	0,106,4194	yes	missense	CHL1	NM_006614.2	29	0,119,6383	AA,AG,GG		1.2326,0.2952,0.9151	benign	12/1225	361493	119,12885	2202	4300	6502	SO:0001583	missense	10752	exon1			CTAATCGTATATC	AF002246	CCDS2556.1, CCDS58812.1, CCDS74887.1	3p26	2013-05-01	2013-05-01		ENSG00000134121	ENSG00000134121		"""Immunoglobulin superfamily / I-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"", ""Fibronectin type III domain containing"""	1939	protein-coding gene	gene with protein product	"""neural cell adhesion molecule"", ""close homolog of L1"""	607416	"""cell adhesion molecule with homology to L1CAM (close homologue of L1)"", ""cell adhesion molecule with homology to L1CAM (close homolog of L1)"""			9799093	Standard	NM_006614		Approved	CALL, L1CAM2, FLJ44930, MGC132578	uc003bot.3	O00533	OTTHUMG00000090601	ENST00000256509.2:c.34G>A	3.37:g.361493G>A	ENSP00000256509:p.Val12Ile	43.0	0.0	0		41.0	18.0	0.439024	NM_001253388	Q13333|Q86VQ4|Q86W62|Q92498|Q92770|Q92998|Q92999	Missense_Mutation	SNP	ENST00000256509.2	37	CCDS2556.1	29	0.013278388278388278	3	0.006097560975609756	18	0.049723756906077346	1	0.0017482517482517483	7	0.009234828496042216	G	2.914	-0.224798	0.06022	0.002952	0.012326	ENSG00000134121	ENST00000256509;ENST00000397491;ENST00000427688;ENST00000421198;ENST00000435603;ENST00000449294	T;T;T;T;T;T	0.61627	0.34;0.34;1.06;0.43;0.31;0.09	4.91	-9.82	0.00484	.	2.380520	0.01454	N	0.015608	T	0.04861	0.0131	N	0.08118	0	0.09310	N	1	B;B;B	0.09022	0.0;0.001;0.002	B;B;B	0.04013	0.0;0.001;0.001	T	0.10941	-1.0608	10	0.11794	T	0.64	.	4.8623	0.13590	0.1328:0.4054:0.0618:0.4	.	12;12;12	B3KX75;O00533;O00533-2	.;CHL1_HUMAN;.	I	12	ENSP00000256509:V12I;ENSP00000380628:V12I;ENSP00000403311:V12I;ENSP00000413628:V12I;ENSP00000397445:V12I;ENSP00000390440:V12I	ENSP00000256509:V12I	V	+	1	0	CHL1	336493	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-2.238000	0.01199	-3.536000	0.00145	-0.238000	0.12139	GTA	G|0.990;A|0.010	0.010	strong		0.348	CHL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207155.2	NM_006614	
QRFP	347148	hgsc.bcm.edu	37	9	133768827	133768827	+	Silent	SNP	G	G	A	rs139926605	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr9:133768827G>A	ENST00000343079.1	-	1	398	c.399C>T	c.(397-399)ttC>ttT	p.F133F		NM_198180.1	NP_937823.1			pyroglutamylated RFamide peptide											cervix(1)|endometrium(3)|lung(1)|skin(2)	7	all_hematologic(7;0.0028)	Myeloproliferative disorder(178;0.204)		OV - Ovarian serous cystadenocarcinoma(145;6.17e-05)|Epithelial(140;0.000267)		ACCGCCGACCGAAGCGGAAGC	0.607													G|||	23	0.00459265	0.0068	0.0043	5008	,	,		18715	0.0		0.001	False		,,,				2504	0.0102				p.F133F		Atlas-SNP	.											.	QRFP	14	.	0			c.C399T						PASS	.	G		16,4388		0,16,2186	57.0	68.0	64.0		399	-7.2	0.6	9	dbSNP_134	64	10,8588		0,10,4289	no	coding-synonymous	QRFP	NM_198180.1		0,26,6475	AA,AG,GG		0.1163,0.3633,0.2		133/137	133768827	26,12976	2202	4299	6501	SO:0001819	synonymous_variant	347148	exon1			CCGACCGAAGCGG	AB109625	CCDS6936.1	9q34.12	2013-02-28			ENSG00000188710	ENSG00000188710		"""Endogenous ligands"""	29982	protein-coding gene	gene with protein product	"""prepro-QRFP"""	609795				12714592, 15808908	Standard	NM_198180		Approved	26RFa, P518	uc011mcb.2	P83859	OTTHUMG00000131663	ENST00000343079.1:c.399C>T	9.37:g.133768827G>A		68.0	0.0	0		79.0	40.0	0.506329	NM_198180		Silent	SNP	ENST00000343079.1	37	CCDS6936.1																																																																																			G|0.998;A|0.002	0.002	strong		0.607	QRFP-001	KNOWN	mRNA_start_NF|mRNA_end_NF|cds_end_NF|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254566.1	NM_198180	
VSIG4	11326	hgsc.bcm.edu	37	X	65253454	65253454	+	Missense_Mutation	SNP	C	C	A	rs41306131	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chrX:65253454C>A	ENST00000374737.4	-	2	382	c.274G>T	c.(274-276)Gtt>Ttt	p.V92F	VSIG4_ENST00000455586.2_Missense_Mutation_p.V92F|VSIG4_ENST00000412866.2_Missense_Mutation_p.V92F	NM_001257403.1|NM_007268.2	NP_001244332.1|NP_009199.1	Q9Y279	VSIG4_HUMAN	V-set and immunoglobulin domain containing 4	92	Ig-like 1.				complement activation, alternative pathway (GO:0006957)|negative regulation of interleukin-2 production (GO:0032703)|negative regulation of T cell proliferation (GO:0042130)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)				breast(2)|endometrium(1)|kidney(2)|large_intestine(2)|lung(14)|ovary(1)|prostate(2)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	29						TCTCCTGGAACCTTGTGGCTC	0.547													C|||	14	0.00370861	0.0	0.0058	3775	,	,		14684	0.0		0.007	False		,,,				2504	0.0031				p.V92F		Atlas-SNP	.											.	VSIG4	54	.	0			c.G274T						PASS	.	C	PHE/VAL,PHE/VAL,PHE/VAL,PHE/VAL	5,3830		0,4,1,1628,570	136.0	115.0	122.0		274,274,274,274	-0.5	0.1	X	dbSNP_127	122	55,6673		0,35,20,2393,1852	yes	missense,missense,missense,missense	VSIG4	NM_001100431.1,NM_001184830.1,NM_001184831.1,NM_007268.2	50,50,50,50	0,39,21,4021,2422	AA,AC,A,CC,C		0.8175,0.1304,0.568	probably-damaging,probably-damaging,probably-damaging,probably-damaging	92/306,92/322,92/228,92/400	65253454	60,10503	2203	4300	6503	SO:0001583	missense	11326	exon2			CTGGAACCTTGTG	AJ132502	CCDS14383.1, CCDS48132.1, CCDS55435.1	Xq12-q13.3	2013-01-29			ENSG00000155659	ENSG00000155659		"""Immunoglobulin superfamily / V-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	17032	protein-coding gene	gene with protein product		300353				10899594, 11004523, 17016555, 17016562	Standard	NM_007268		Approved	Z39IG	uc004dwh.2	Q9Y279	OTTHUMG00000021727	ENST00000374737.4:c.274G>T	X.37:g.65253454C>A	ENSP00000363869:p.Val92Phe	139.0	1.0	0.00719424		135.0	134.0	0.992593	NM_001100431	Q6UXI4	Missense_Mutation	SNP	ENST00000374737.4	37	CCDS14383.1	10|10	0.006027727546714889|0.006027727546714889	0|0	0.0|0.0	4|4	0.011049723756906077|0.011049723756906077	0|0	0.0|0.0	4|4	0.005305039787798408|0.005305039787798408	C|C	9.614|9.614	1.131982|1.131982	0.21041|0.21041	0.001304|0.001304	0.008175|0.008175	ENSG00000155659|ENSG00000155659	ENST00000427538|ENST00000374737;ENST00000455586;ENST00000412866	.|T;T;T	.|0.04156	.|3.69;3.69;3.69	4.93|4.93	-0.487|-0.487	0.12060|0.12060	.|Immunoglobulin subtype (1);Immunoglobulin V-set (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	.|0.656229	.|0.14136	.|N	.|0.339047	T|T	0.08358|0.08358	0.0208|0.0208	L|L	0.57536|0.57536	1.79|1.79	0.09310|0.09310	N|N	1|1	.|P;D;D;P;D	.|0.65815	.|0.825;0.994;0.995;0.889;0.995	.|P;P;D;P;D	.|0.69307	.|0.597;0.884;0.963;0.543;0.929	T|T	0.11275|0.11275	-1.0594|-1.0594	5|10	.|0.56958	.|D	.|0.05	-3.6037|-3.6037	4.5823|4.5823	0.12264|0.12264	0.0:0.4461:0.2494:0.3045|0.0:0.4461:0.2494:0.3045	rs41306131|rs41306131	.|92;92;82;92;92	.|C9J1L3;Q9Y279-2;C9JH67;Q9Y279-3;Q9Y279	.|.;.;.;.;VSIG4_HUMAN	V|F	18|92	.|ENSP00000363869:V92F;ENSP00000411581:V92F;ENSP00000394143:V92F	.|ENSP00000363869:V92F	G|V	-|-	2|1	0|0	VSIG4|VSIG4	65170179|65170179	0.000000|0.000000	0.05858|0.05858	0.076000|0.076000	0.20297|0.20297	0.004000|0.004000	0.04260|0.04260	-1.190000|-1.190000	0.03058|0.03058	0.038000|0.038000	0.15604|0.15604	-0.198000|-0.198000	0.12761|0.12761	GGT|GTT	C|0.994;A|0.006	0.006	strong		0.547	VSIG4-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000056986.1	NM_007268	
CPT1C	126129	hgsc.bcm.edu	37	19	50212024	50212024	+	Silent	SNP	C	C	T	rs61747405	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr19:50212024C>T	ENST00000392518.4	+	14	1866	c.1494C>T	c.(1492-1494)gaC>gaT	p.D498D	CPT1C_ENST00000598293.1_Silent_p.D498D|CPT1C_ENST00000354199.5_Silent_p.D498D|CPT1C_ENST00000405931.2_Silent_p.D487D|CPT1C_ENST00000323446.5_Silent_p.D498D	NM_001199752.1	NP_001186681.1	Q8TCG5	CPT1C_HUMAN	carnitine palmitoyltransferase 1C	498					carnitine metabolic process (GO:0009437)|fatty acid beta-oxidation (GO:0006635)	alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex (GO:0032281)|cell junction (GO:0030054)|endoplasmic reticulum membrane (GO:0005789)|mitochondrial outer membrane (GO:0005741)|synapse (GO:0045202)	carnitine O-palmitoyltransferase activity (GO:0004095)			breast(1)|central_nervous_system(3)|endometrium(3)|kidney(1)|lung(12)|ovary(1)|pancreas(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	27		all_lung(116;1.05e-05)|Lung NSC(112;3.77e-05)|all_neural(266;0.107)|Ovarian(192;0.231)		OV - Ovarian serous cystadenocarcinoma(262;0.0011)|GBM - Glioblastoma multiforme(134;0.00786)		ACTCAACAGACGGCCACTGCA	0.607													c|||	75	0.014976	0.0272	0.0101	5008	,	,		15016	0.001		0.0278	False		,,,				2504	0.0031				p.D498D		Atlas-SNP	.											.	CPT1C	93	.	0			c.C1494T						PASS	.	C	,,,	81,4325	72.5+/-110.5	1,79,2123	121.0	110.0	114.0		1461,1494,1494,1494	-4.4	0.7	19	dbSNP_129	114	206,8394	89.2+/-151.4	3,200,4097	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	CPT1C	NM_001136052.2,NM_001199752.1,NM_001199753.1,NM_152359.2	,,,	4,279,6220	TT,TC,CC		2.3953,1.8384,2.2067	,,,	487/793,498/804,498/804,498/804	50212024	287,12719	2203	4300	6503	SO:0001819	synonymous_variant	126129	exon14			AACAGACGGCCAC	AF357970	CCDS12779.1, CCDS46147.1	19q13.33	2014-03-14				ENSG00000169169			18540	protein-coding gene	gene with protein product		608846				12376098, 11001805	Standard	NM_001136052		Approved	FLJ23809, CPTIC, CPT1P	uc010eng.3	Q8TCG5		ENST00000392518.4:c.1494C>T	19.37:g.50212024C>T		91.0	0.0	0		108.0	63.0	0.583333	NM_001199752	A8K0Z8|Q5K6N5|Q8N6Q9|Q8NDS6|Q8TE84	Silent	SNP	ENST00000392518.4	37	CCDS12779.1																																																																																			C|0.978;T|0.022	0.022	strong		0.607	CPT1C-008	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000465873.1	NM_152359	
ZCCHC4	29063	hgsc.bcm.edu	37	4	25314478	25314478	+	Missense_Mutation	SNP	G	G	C	rs201763036	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr4:25314478G>C	ENST00000302874.4	+	1	71	c.47G>C	c.(46-48)aGc>aCc	p.S16T	ZCCHC4_ENST00000505451.1_3'UTR	NM_024936.2	NP_079212.2	Q9H5U6	ZCHC4_HUMAN	zinc finger, CCHC domain containing 4	16							methyltransferase activity (GO:0008168)|nucleic acid binding (GO:0003676)|zinc ion binding (GO:0008270)			endometrium(1)|large_intestine(3)|lung(2)|ovary(2)|pancreas(1)	9		Breast(46;0.0503)				GCAGAGGGCAGCGCAGGGTGC	0.642											OREG0016141	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	G|||	2	0.000399361	0.0	0.0	5008	,	,		14396	0.0		0.002	False		,,,				2504	0.0				p.S16T		Atlas-SNP	.											.	ZCCHC4	34	.	0			c.G47C						PASS	.	G	THR/SER	2,4098		0,2,2048	70.0	89.0	83.0		47	-5.7	0.0	4		83	6,8382		0,6,4188	yes	missense	ZCCHC4	NM_024936.2	58	0,8,6236	CC,CG,GG		0.0715,0.0488,0.0641	benign	16/514	25314478	8,12480	2050	4194	6244	SO:0001583	missense	29063	exon1			AGGGCAGCGCAGG	AF161537	CCDS43218.1	4p15.31	2014-02-18			ENSG00000168228	ENSG00000168228		"""Zinc fingers, CCHC domain containing"""	22917	protein-coding gene	gene with protein product	"""zinc finger, GRF-type containing 4"""	611792				11042152	Standard	NM_024936		Approved	HSPC052, FLJ23024, ZGRF4	uc003grl.4	Q9H5U6	OTTHUMG00000160563	ENST00000302874.4:c.47G>C	4.37:g.25314478G>C	ENSP00000303468:p.Ser16Thr	95.0	0.0	0	778	83.0	32.0	0.385542	NM_024936	B2RXF6|B4DRD8|B7ZW20|Q5IW78|Q96AN7	Missense_Mutation	SNP	ENST00000302874.4	37	CCDS43218.1	2	9.157509157509158E-4	0	0.0	0	0.0	0	0.0	2	0.002638522427440633	G	11.08	1.534797	0.27475	4.88E-4	7.15E-4	ENSG00000168228	ENST00000302874	T	0.30981	1.51	5.18	-5.71	0.02413	.	1.862370	0.01786	N	0.032033	T	0.14270	0.0345	N	0.19112	0.55	0.09310	N	1	B	0.06786	0.001	B	0.06405	0.002	T	0.16897	-1.0387	10	0.11182	T	0.66	-5.9509	1.3284	0.02130	0.2451:0.1002:0.2206:0.4341	.	16	Q9H5U6	ZCHC4_HUMAN	T	16	ENSP00000303468:S16T	ENSP00000303468:S16T	S	+	2	0	ZCCHC4	24923576	0.000000	0.05858	0.000000	0.03702	0.016000	0.09150	-1.725000	0.01863	-1.763000	0.01307	0.655000	0.94253	AGC	G|0.999;C|0.001	0.001	strong		0.642	ZCCHC4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000361151.1		
SLC47A2	146802	hgsc.bcm.edu	37	17	19607432	19607432	+	Silent	SNP	C	C	T	rs34169093	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr17:19607432C>T	ENST00000325411.5	-	11	1127	c.1077G>A	c.(1075-1077)gcG>gcA	p.A359A	SLC47A2_ENST00000350657.5_Silent_p.A337A|SLC47A2_ENST00000463318.1_5'UTR	NM_152908.3	NP_690872.2	Q86VL8	S47A2_HUMAN	solute carrier family 47 (multidrug and toxin extrusion), member 2	359					transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	antiporter activity (GO:0015297)|drug transmembrane transporter activity (GO:0015238)			endometrium(2)|kidney(3)|large_intestine(2)|lung(1)|ovary(1)	9	all_cancers(12;2.3e-05)|all_epithelial(12;0.0024)|Breast(13;0.245)				Aciclovir(DB00787)	GCACAGTATCCGCAGCCCCCA	0.617													C|||	311	0.0621006	0.1831	0.0187	5008	,	,		18054	0.0		0.0268	False		,,,				2504	0.0297				p.A359A		Atlas-SNP	.											.	SLC47A2	61	.	0			c.G1077A						PASS	.	C	,	663,3743	278.7+/-274.4	51,561,1591	50.0	49.0	50.0		969,1077	-0.3	0.0	17	dbSNP_126	50	237,8363	94.7+/-156.6	2,233,4065	no	coding-synonymous,coding-synonymous	SLC47A2	NM_001099646.1,NM_152908.3	,	53,794,5656	TT,TC,CC		2.7558,15.0477,6.9199	,	323/567,359/603	19607432	900,12106	2203	4300	6503	SO:0001819	synonymous_variant	146802	exon11			AGTATCCGCAGCC	AB250364	CCDS11211.1, CCDS58530.1	17p11.2	2013-07-17	2013-07-17		ENSG00000180638	ENSG00000180638		"""Solute carriers"""	26439	protein-coding gene	gene with protein product	"""multidrug and toxin extrusion 2"""	609833				16996621, 16807400	Standard	NM_152908		Approved	FLJ31196, MATE2, MATE2-K	uc002gwf.4	Q86VL8	OTTHUMG00000059464	ENST00000325411.5:c.1077G>A	17.37:g.19607432C>T		59.0	0.0	0		43.0	24.0	0.55814	NM_152908	A0JBX9|A0P8Z7|Q63HJ9|Q8IV44|Q96NA1	Silent	SNP	ENST00000325411.5	37	CCDS11211.1																																																																																			C|0.935;T|0.065	0.065	strong		0.617	SLC47A2-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000132242.2	NM_152908	
TOP3B	8940	hgsc.bcm.edu	37	22	22323003	22323003	+	Silent	SNP	C	C	A	rs114760416	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr22:22323003C>A	ENST00000398793.2	-	7	1160	c.726G>T	c.(724-726)gtG>gtT	p.V242V	TOP3B_ENST00000413067.2_5'UTR|TOP3B_ENST00000357179.5_Silent_p.V242V	NM_003935.3	NP_003926.1	O95985	TOP3B_HUMAN	topoisomerase (DNA) III beta	242					chromosome segregation (GO:0007059)|DNA topological change (GO:0006265)	condensed chromosome (GO:0000793)|nucleus (GO:0005634)	DNA binding (GO:0003677)|DNA topoisomerase activity (GO:0003916)|DNA topoisomerase type I activity (GO:0003917)|poly(A) RNA binding (GO:0044822)			breast(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(4)|lung(9)|ovary(1)	26	Colorectal(54;0.105)			READ - Rectum adenocarcinoma(21;0.145)		TGGCCTGCAGCACCCAGTAGG	0.532													C|||	4	0.000798722	0.0	0.0	5008	,	,		19610	0.0		0.004	False		,,,				2504	0.0				p.V242V		Atlas-SNP	.											.	TOP3B	107	.	0			c.G726T						PASS	.	C		2,4404	4.2+/-10.8	0,2,2201	122.0	119.0	120.0		726	4.0	1.0	22	dbSNP_132	120	16,8584	12.6+/-44.7	0,16,4284	no	coding-synonymous	TOP3B	NM_003935.3		0,18,6485	AA,AC,CC		0.186,0.0454,0.1384		242/863	22323003	18,12988	2203	4300	6503	SO:0001819	synonymous_variant	8940	exon7			CTGCAGCACCCAG	AF017146	CCDS13797.1	22q11.22	2011-05-24			ENSG00000100038	ENSG00000100038			11993	protein-coding gene	gene with protein product		603582				9786842, 9074928	Standard	XM_005261811		Approved		uc002zvs.3	O95985	OTTHUMG00000167438	ENST00000398793.2:c.726G>T	22.37:g.22323003C>A		109.0	0.0	0		104.0	44.0	0.423077	NM_003935	A0M8Q3|Q9BUP5	Silent	SNP	ENST00000398793.2	37	CCDS13797.1	4	0.0018315018315018315	0	0.0	0	0.0	0	0.0	4	0.005277044854881266	C	9.680	1.148957	0.21288	4.54E-4	0.00186	ENSG00000100038	ENST00000457270	.	.	.	5.04	4.01	0.46588	.	.	.	.	.	T	0.48095	0.1481	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.49908	-0.8889	4	.	.	.	.	6.9623	0.24603	0.0:0.7019:0.1436:0.1544	.	.	.	.	F	37	.	.	C	-	2	0	TOP3B	20653003	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	1.312000	0.33574	1.318000	0.45170	0.555000	0.69702	TGC	C|0.998;A|0.002	0.002	strong		0.532	TOP3B-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000320251.1	NM_003935	
ARHGAP8	23779	hgsc.bcm.edu	37	22	45258343	45258343	+	Silent	SNP	C	C	T	rs41278889	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr22:45258343C>T	ENST00000389774.2	+	13	1404	c.1263C>T	c.(1261-1263)caC>caT	p.H421H	ARHGAP8_ENST00000356099.6_Silent_p.H390H|ARHGAP8_ENST00000517296.3_Silent_p.H600H|ARHGAP8_ENST00000336963.4_3'UTR|PRR5-ARHGAP8_ENST00000361473.5_Silent_p.H521H|PRR5-ARHGAP8_ENST00000352766.7_Silent_p.H600H|ARHGAP8_ENST00000389773.5_Silent_p.H512H	NM_001017526.1	NP_001017526.1	P85298	RHG08_HUMAN	Rho GTPase activating protein 8	421					positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of Rho GTPase activity (GO:0032321)|regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)	Rho GTPase activator activity (GO:0005100)			breast(2)|central_nervous_system(1)|endometrium(2)|large_intestine(7)|lung(9)|prostate(1)|skin(7)	29		all_neural(38;0.00409)|Ovarian(80;0.00976)|Glioma(61;0.0649)		UCEC - Uterine corpus endometrioid carcinoma (28;0.0204)		CTGGGGAGCACGGCCTGGCAC	0.612													C|||	33	0.00658946	0.0212	0.0014	5008	,	,		17491	0.001		0.003	False		,,,				2504	0.0				p.H512H		Atlas-SNP	.											.	PRR5-ARHGAP8	53	.	0			c.C1536T						PASS	.	C	,,,	52,4354	53.6+/-89.4	1,50,2152	50.0	49.0	49.0		1263,,1536,1170	-6.1	0.0	22	dbSNP_127	49	21,8579	15.3+/-51.7	0,21,4279	no	coding-synonymous,utr-3,coding-synonymous,coding-synonymous	ARHGAP8,PRR5-ARHGAP8	NM_001017526.1,NM_001198726.1,NM_181334.4,NM_181335.2	,,,	1,71,6431	TT,TC,CC		0.2442,1.1802,0.5613	,,,	421/465,,512/556,390/434	45258343	73,12933	2203	4300	6503	SO:0001819	synonymous_variant	553158	exon15			GGAGCACGGCCTG	AF177331	CCDS14060.2, CCDS33664.1, CCDS56233.1	22q13.3	2010-05-11			ENSG00000241484	ENSG00000241484		"""Rho GTPase activating proteins"""	677	protein-coding gene	gene with protein product		609405				10591208	Standard	NM_001198726		Approved	FLJ20185, BPGAP1		P85298	OTTHUMG00000030234	ENST00000389774.2:c.1263C>T	22.37:g.45258343C>T		82.0	0.0	0		67.0	31.0	0.462687	NM_181334	A6ZJ79|A6ZJ80|O75983|O95695|Q96RW1|Q96RW2|Q9HA49|Q9HC46|Q9NSG0|Q9NVX8|Q9NXL1|Q9UH20	Silent	SNP	ENST00000389774.2	37	CCDS33664.1	10	0.004578754578754579	6	0.012195121951219513	1	0.0027624309392265192	1	0.0017482517482517483	2	0.002638522427440633	C	2.018	-0.425336	0.04701	0.011802	0.002442	ENSG00000248405	ENST00000515632	.	.	.	3.04	-6.08	0.02151	.	.	.	.	.	T	0.10937	0.0267	.	.	.	0.09310	N	1	.	.	.	.	.	.	T	0.23762	-1.0179	4	.	.	.	.	0.5	0.00578	0.2906:0.2175:0.2876:0.2043	rs41278889	.	.	.	M	461	.	.	T	+	2	0	PRR5-ARHGAP8	43637007	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-0.542000	0.06091	-1.256000	0.02478	-0.964000	0.02622	ACG	C|0.995;T|0.005	0.005	strong		0.612	ARHGAP8-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000075088.4	NM_017701	
SEZ6L2	26470	hgsc.bcm.edu	37	16	29899021	29899021	+	Missense_Mutation	SNP	C	C	T	rs117448844	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr16:29899021C>T	ENST00000308713.5	-	7	1684	c.1157G>A	c.(1156-1158)cGc>cAc	p.R386H	SEZ6L2_ENST00000350527.3_Missense_Mutation_p.R316H|SEZ6L2_ENST00000537485.1_Missense_Mutation_p.R342H|SEZ6L2_ENST00000346932.5_Missense_Mutation_p.R272H|SEZ6L2_ENST00000562159.1_5'Flank	NM_001114099.2|NM_201575.3	NP_001107571.1|NP_963869.2	Q6UXD5	SE6L2_HUMAN	seizure related 6 homolog (mouse)-like 2	386	CUB 2. {ECO:0000255|PROSITE- ProRule:PRU00059}.				adult locomotory behavior (GO:0008344)|cerebellar Purkinje cell layer development (GO:0021680)|regulation of protein kinase C signaling (GO:0090036)|synapse maturation (GO:0060074)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)				breast(2)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(10)|lung(16)|ovary(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	39						GTGCAGCCGGCGCCCCTCAGC	0.637													C|||	6	0.00119808	0.0	0.0043	5008	,	,		15751	0.0		0.003	False		,,,				2504	0.0				p.R386H		Atlas-SNP	.											SEZ6L2_ENST00000350527,NS,carcinoma,0,2	SEZ6L2	137	2	0			c.G1157A						PASS	.	C	HIS/ARG,HIS/ARG,HIS/ARG,HIS/ARG	4,4390	8.1+/-20.4	0,4,2193	78.0	72.0	74.0		947,815,947,1157	5.7	1.0	16	dbSNP_132	74	26,8574	19.8+/-62.0	0,26,4274	yes	missense,missense,missense,missense	SEZ6L2	NM_001114099.2,NM_001114100.2,NM_012410.3,NM_201575.3	29,29,29,29	0,30,6467	TT,TC,CC		0.3023,0.091,0.2309	benign,benign,benign,benign	316/841,272/810,316/854,386/911	29899021	30,12964	2197	4300	6497	SO:0001583	missense	26470	exon7			AGCCGGCGCCCCT	AY358404	CCDS10658.1, CCDS10659.1, CCDS45458.1, CCDS58447.1, CCDS73865.1	16p12.1	2008-02-05			ENSG00000174938	ENSG00000174938			30844	protein-coding gene	gene with protein product	"""type I transmembrane receptor (seizure related protein)"""					12975309	Standard	NM_012410		Approved	PSK-1, FLJ90517	uc010vec.2	Q6UXD5	OTTHUMG00000132112	ENST00000308713.5:c.1157G>A	16.37:g.29899021C>T	ENSP00000312550:p.Arg386His	137.0	0.0	0		114.0	62.0	0.54386	NM_001243332	B7Z1N0|F5H293|H7BXQ6|Q9BW82|Q9UJ45|Q9UJ46|Q9UJ47	Missense_Mutation	SNP	ENST00000308713.5	37	CCDS10659.1	4	0.0018315018315018315	0	0.0	3	0.008287292817679558	0	0.0	1	0.0013192612137203166	C	21.9	4.221861	0.79464	9.1E-4	0.003023	ENSG00000174938	ENST00000350527;ENST00000308713;ENST00000346932;ENST00000537485	T;T;T;T	0.50001	0.76;0.76;0.76;0.76	5.72	5.72	0.89469	CUB (4);	0.000000	0.56097	D	0.000031	T	0.13798	0.0334	N	0.02296	-0.605	0.35617	D	0.809155	B;B;B;B;B;B	0.24963	0.039;0.07;0.07;0.115;0.07;0.115	B;B;B;B;B;B	0.14023	0.01;0.003;0.002;0.006;0.003;0.006	T	0.30475	-0.9977	10	0.15066	T	0.55	.	8.9111	0.35555	0.0:0.8417:0.0:0.1583	.	342;386;272;316;386;316	F5H293;B7Z5L4;Q9BW82;Q6UXD5-2;Q6UXD5;Q6UXD5-3	.;.;.;.;SE6L2_HUMAN;.	H	316;386;272;342	ENSP00000310206:R316H;ENSP00000312550:R386H;ENSP00000319215:R272H;ENSP00000439412:R342H	ENSP00000312550:R386H	R	-	2	0	SEZ6L2	29806522	1.000000	0.71417	1.000000	0.80357	0.988000	0.76386	5.553000	0.67287	2.720000	0.93068	0.555000	0.69702	CGC	C|0.998;T|0.002	0.002	strong		0.637	SEZ6L2-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000255154.2	NM_012410	
ZNF57	126295	hgsc.bcm.edu	37	19	2917522	2917522	+	Silent	SNP	G	G	A	rs61754924	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr19:2917522G>A	ENST00000306908.5	+	4	1051	c.903G>A	c.(901-903)acG>acA	p.T301T	ZNF57_ENST00000523428.1_Silent_p.T269T|AC006277.2_ENST00000520090.2_RNA	NM_173480.2	NP_775751.1	Q68EA5	ZNF57_HUMAN	zinc finger protein 57	301					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)|kidney(2)|large_intestine(5)|lung(2)|ovary(1)|pancreas(1)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	18				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)|GBM - Glioblastoma multiforme(1328;0.00161)|STAD - Stomach adenocarcinoma(1328;0.18)		ATGAGAAGACGCACACGGGAG	0.488													G|||	130	0.0259585	0.0257	0.0288	5008	,	,		19252	0.0		0.0169	False		,,,				2504	0.0603				p.T301T	NSCLC(150;910 1964 4303 10464 26498)	Atlas-SNP	.											.	ZNF57	57	.	0			c.G903A						PASS	.	G		95,4311	77.3+/-115.6	0,95,2108	75.0	79.0	78.0		903	-4.5	0.0	19	dbSNP_129	78	209,8391	88.6+/-150.9	4,201,4095	no	coding-synonymous	ZNF57	NM_173480.2		4,296,6203	AA,AG,GG		2.4302,2.1562,2.3374		301/556	2917522	304,12702	2203	4300	6503	SO:0001819	synonymous_variant	126295	exon4			GAAGACGCACACG	M88368	CCDS12098.1	19p13.3	2013-01-08			ENSG00000171970	ENSG00000171970		"""Zinc fingers, C2H2-type"", ""-"""	13125	protein-coding gene	gene with protein product			"""zinc finger protein 424"""	ZNF424		1505991	Standard	NM_173480		Approved		uc002lwr.3	Q68EA5	OTTHUMG00000164485	ENST00000306908.5:c.903G>A	19.37:g.2917522G>A		47.0	0.0	0		50.0	22.0	0.44	NM_173480	Q8N6R9	Silent	SNP	ENST00000306908.5	37	CCDS12098.1																																																																																			G|0.973;A|0.027	0.027	strong		0.488	ZNF57-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000378969.1	NM_173480	
EMR1	2015	hgsc.bcm.edu	37	19	6906469	6906469	+	Silent	SNP	T	T	C	rs78491083	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr19:6906469T>C	ENST00000312053.4	+	9	1012	c.975T>C	c.(973-975)gaT>gaC	p.D325D	EMR1_ENST00000381407.5_Silent_p.D184D|EMR1_ENST00000450315.3_Silent_p.D148D|EMR1_ENST00000381404.4_Silent_p.D273D|EMR1_ENST00000250572.8_Silent_p.D325D	NM_001974.4	NP_001965.3	Q14246	EMR1_HUMAN	egf-like module containing, mucin-like, hormone receptor-like 1	325	Ser/Thr-rich.				cell adhesion (GO:0007155)|G-protein coupled receptor signaling pathway (GO:0007186)|neuropeptide signaling pathway (GO:0007218)	external side of plasma membrane (GO:0009897)|integral component of plasma membrane (GO:0005887)	calcium ion binding (GO:0005509)|G-protein coupled receptor activity (GO:0004930)			NS(2)|breast(1)|central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(11)|lung(31)|ovary(3)|prostate(1)|skin(8)	62	all_hematologic(4;0.166)					GTAAGGAAGATGTGATACCCG	0.383													T|||	20	0.00399361	0.0008	0.0058	5008	,	,		20677	0.0		0.0109	False		,,,				2504	0.0041				p.D325D		Atlas-SNP	.											EMR1,NS,carcinoma,+1,1	EMR1	153	1	0			c.T975C						PASS	.	T		11,4395	17.9+/-39.9	0,11,2192	143.0	136.0	138.0		975	-0.2	0.2	19	dbSNP_133	138	78,8522	46.3+/-105.2	1,76,4223	no	coding-synonymous	EMR1	NM_001974.3		1,87,6415	CC,CT,TT		0.907,0.2497,0.6843		325/887	6906469	89,12917	2203	4300	6503	SO:0001819	synonymous_variant	2015	exon9			GGAAGATGTGATA	X81479	CCDS12175.1, CCDS58643.1, CCDS58644.1, CCDS58645.1, CCDS58646.1	19p13.3	2014-08-08	2003-11-26					"""-"", ""GPCR / Class B : Orphans"""	3336	protein-coding gene	gene with protein product		600493	"""egf-like module containing, mucin-like, hormone receptor-like sequence 1"""	TM7LN3		7601460, 9500513	Standard	NM_001974		Approved		uc002mfw.4	Q14246		ENST00000312053.4:c.975T>C	19.37:g.6906469T>C		254.0	0.0	0		259.0	130.0	0.50193	NM_001256253	A6NHV2|B7Z486|B7Z489|E7EPX9|E9PD45|H9KV79|Q2I7G5|Q6ZMN0|Q8NGA7	Silent	SNP	ENST00000312053.4	37	CCDS12175.1																																																																																			T|0.994;C|0.006	0.006	strong		0.383	EMR1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000458485.1		
KIAA0895	23366	hgsc.bcm.edu	37	7	36396735	36396735	+	Missense_Mutation	SNP	G	G	C	rs199774798	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr7:36396735G>C	ENST00000297063.6	-	3	693	c.643C>G	c.(643-645)Cca>Gca	p.P215A	KIAA0895_ENST00000453212.1_Intron|KIAA0895_ENST00000436884.1_Missense_Mutation_p.P64A|KIAA0895_ENST00000480192.1_Intron|KIAA0895_ENST00000440378.1_Missense_Mutation_p.P164A|KIAA0895_ENST00000317020.6_Missense_Mutation_p.P164A|KIAA0895_ENST00000415803.2_Missense_Mutation_p.P202A|KIAA0895_ENST00000338533.5_Missense_Mutation_p.P202A	NM_001100425.1	NP_001093895.1	Q8NCT3	K0895_HUMAN	KIAA0895	215										breast(2)|endometrium(1)|kidney(1)|large_intestine(6)|liver(1)|lung(11)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	26						TTTGGCTTTGGAAGAGTGGAG	0.413													G|||	2	0.000399361	0.0008	0.0	5008	,	,		21233	0.0		0.001	False		,,,				2504	0.0				p.P215A		Atlas-SNP	.											.	KIAA0895	89	.	0			c.C643G						PASS	.	G	ALA/PRO,ALA/PRO,ALA/PRO,ALA/PRO,ALA/PRO	3,3749		0,3,1873	93.0	88.0	90.0		643,490,604,190,490	3.7	0.4	7		90	0,8236		0,0,4118	yes	missense,missense,missense,missense,missense	KIAA0895	NM_001100425.1,NM_001199706.1,NM_001199707.1,NM_001199708.1,NM_015314.2	27,27,27,27,27	0,3,5991	CC,CG,GG		0.0,0.08,0.025	benign,benign,benign,benign,benign	215/521,164/518,202/508,64/418,164/470	36396735	3,11985	1876	4118	5994	SO:0001583	missense	23366	exon3			GCTTTGGAAGAGT	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.643C>G	7.37:g.36396735G>C	ENSP00000297063:p.Pro215Ala	217.0	0.0	0		235.0	105.0	0.446809	NM_001100425	B4DF35|B7ZLT4|B9EGB9|O94969|Q0VGC1|Q7Z4L2	Missense_Mutation	SNP	ENST00000297063.6	37	CCDS43570.1	.	.	.	.	.	.	.	.	.	.	G	2.506	-0.314008	0.05422	8.0E-4	0.0	ENSG00000164542	ENST00000297063;ENST00000338533;ENST00000317020;ENST00000440378;ENST00000436884;ENST00000415803;ENST00000429651	.	.	.	5.65	3.69	0.42338	.	0.385185	0.30028	N	0.010586	T	0.24236	0.0587	N	0.15975	0.35	0.09310	N	1	B;B;B;B;B;B;B	0.06786	0.001;0.0;0.0;0.0;0.0;0.0;0.0	B;B;B;B;B;B;B	0.04013	0.001;0.0;0.0;0.001;0.001;0.001;0.0	T	0.13124	-1.0521	9	0.20046	T	0.44	-27.7009	11.557	0.50755	0.0:0.2899:0.5506:0.1596	.	164;164;64;202;215;202;164	B4DGN6;B7ZLT4;B4DF35;Q8NCT3-4;Q8NCT3;Q8NCT3-2;Q8NCT3-3	.;.;.;.;K0895_HUMAN;.;.	A	215;202;164;164;64;202;82	.	ENSP00000297063:P215A	P	-	1	0	KIAA0895	36363260	0.003000	0.15002	0.448000	0.26945	0.245000	0.25701	0.026000	0.13599	1.365000	0.46057	0.563000	0.77884	CCA	.	.	weak		0.413	KIAA0895-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000337717.1	NM_015314	
PTX4	390667	hgsc.bcm.edu	37	16	1537510	1537510	+	Silent	SNP	C	C	T	rs201970670	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr16:1537510C>T	ENST00000447419.2	-	2	628	c.603G>A	c.(601-603)ccG>ccA	p.P201P	PTX4_ENST00000440447.2_Intron|PTX4_ENST00000293922.1_Silent_p.P196P			Q96A99	PTX4_HUMAN	pentraxin 4, long	201						extracellular region (GO:0005576)	metal ion binding (GO:0046872)			breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(3)|lung(6)|ovary(1)|skin(2)|urinary_tract(1)	17						TCAGGGAGGTCGGGCCCAGCT	0.726													C|||	13	0.00259585	0.0	0.0058	5008	,	,		14445	0.0		0.0089	False		,,,				2504	0.0				p.P196P		Atlas-SNP	.											.	PTX4	46	.	0			c.G588A						PASS	.	C		12,4368		0,12,2178	11.0	13.0	13.0		588	-10.4	0.0	16		13	113,8431		0,113,4159	no	coding-synonymous	PTX4	NM_001013658.1		0,125,6337	TT,TC,CC		1.3226,0.274,0.9672		196/474	1537510	125,12799	2190	4272	6462	SO:0001819	synonymous_variant	390667	exon2			GGAGGTCGGGCCC		CCDS32362.1	16p13.3	2011-01-06	2010-03-30	2010-03-30	ENSG00000251692	ENSG00000251692			14171	protein-coding gene	gene with protein product		613442	"""chromosome 16 open reading frame 38"""	C16orf38			Standard	NM_001013658		Approved		uc010uvf.2	Q96A99		ENST00000447419.2:c.603G>A	16.37:g.1537510C>T		66.0	0.0	0		53.0	21.0	0.396226	NM_001013658		Silent	SNP	ENST00000447419.2	37																																																																																				C|0.997;T|0.003	0.003	strong		0.726	PTX4-001	KNOWN	not_organism_supported|basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000432526.1	NM_001013658	
TECPR1	25851	hgsc.bcm.edu	37	7	97852443	97852443	+	Silent	SNP	C	C	T	rs61745947	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr7:97852443C>T	ENST00000447648.2	-	21	3086	c.2787G>A	c.(2785-2787)gtG>gtA	p.V929V	TECPR1_ENST00000479975.1_5'UTR|TECPR1_ENST00000379795.3_Silent_p.V931V			Q7Z6L1	TCPR1_HUMAN	tectonin beta-propeller repeat containing 1	929					autophagic vacuole fusion (GO:0000046)|autophagy (GO:0006914)	autophagic vacuole membrane (GO:0000421)|cytoplasmic vesicle (GO:0031410)|integral component of membrane (GO:0016021)|lysosomal membrane (GO:0005765)	phosphatidylinositol-3-phosphate binding (GO:0032266)			central_nervous_system(2)|endometrium(8)|kidney(1)|large_intestine(1)|lung(9)|pancreas(1)|prostate(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	26						CGATGGGGGGCACCTCCAGCC	0.682													C|||	81	0.0161741	0.0008	0.0101	5008	,	,		10604	0.001		0.0219	False		,,,				2504	0.0511				p.V929V		Atlas-SNP	.											.	TECPR1	77	.	0			c.G2787A						PASS	.	C		16,4018		0,16,2001	20.0	26.0	24.0		2787	4.0	1.0	7	dbSNP_129	24	238,8088		4,230,3929	no	coding-synonymous	TECPR1	NM_015395.1		4,246,5930	TT,TC,CC		2.8585,0.3966,2.055		929/1166	97852443	254,12106	2017	4163	6180	SO:0001819	synonymous_variant	25851	exon21			GGGGGGCACCTCC		CCDS47648.1	7q21.3	2009-01-30			ENSG00000205356	ENSG00000205356			22214	protein-coding gene	gene with protein product		614781					Standard	NM_015395		Approved	DKFZP434B0335, FLJ23419, FLJ90593, KIAA1358	uc003upg.4	Q7Z6L1	OTTHUMG00000154273	ENST00000447648.2:c.2787G>A	7.37:g.97852443C>T		118.0	0.0	0		96.0	50.0	0.520833	NM_015395	A8KAD1|B3KPZ1|C9J024|F5GX57|Q96EB0|Q9P2I9|Q9UFR6	Silent	SNP	ENST00000447648.2	37	CCDS47648.1																																																																																			C|0.985;T|0.015	0.015	strong		0.682	TECPR1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000334661.1	NM_015395	
CCDC186	55088	hgsc.bcm.edu	37	10	115905428	115905428	+	Missense_Mutation	SNP	C	C	A	rs367843443		TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr10:115905428C>A	ENST00000369287.3	-	5	1247	c.981G>T	c.(979-981)aaG>aaT	p.K327N	C10orf118_ENST00000543782.1_5'Flank	NM_018017.2	NP_060487.2	Q7Z3E2	CC186_HUMAN		327										NS(1)|autonomic_ganglia(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(5)|lung(9)|ovary(2)	24		Colorectal(252;0.172)|Breast(234;0.188)		Epithelial(162;0.0161)|all cancers(201;0.0397)		TCTCTTTTTCCTTTCGAAGAT	0.368																																					p.K327N		Atlas-SNP	.											.	C10orf118	70	.	0			c.G981T						PASS	.	C	ASN/LYS	0,4406		0,0,2203	196.0	183.0	187.0		981	2.3	1.0	10		187	1,8599	1.2+/-3.3	0,1,4299	no	missense	C10orf118	NM_018017.2	94	0,1,6502	AA,AC,CC		0.0116,0.0,0.0077	probably-damaging	327/899	115905428	1,13005	2203	4300	6503	SO:0001583	missense	55088	exon5			TTTTTCCTTTCGA																												ENST00000369287.3:c.981G>T	10.37:g.115905428C>A	ENSP00000358293:p.Lys327Asn	144.0	0.0	0		156.0	91.0	0.583333	NM_018017	Q2M2V6|Q3ZB81|Q6NS91|Q7RTP1|Q8N117|Q8N3G3|Q8N6C2|Q9NWA3	Missense_Mutation	SNP	ENST00000369287.3	37	CCDS7587.1	.	.	.	.	.	.	.	.	.	.	C	21.0	4.075041	0.76415	0.0	1.16E-4	ENSG00000165813	ENST00000369287;ENST00000430353	T	0.53857	0.6	5.52	2.29	0.28610	.	0.099180	0.64402	D	0.000002	T	0.60248	0.2254	M	0.68593	2.085	0.80722	D	1	D	0.56746	0.977	P	0.55923	0.787	T	0.60900	-0.7171	10	0.72032	D	0.01	.	8.5338	0.33351	0.0:0.7277:0.0:0.2723	.	327	Q7Z3E2	CJ118_HUMAN	N	327;433	ENSP00000358293:K327N	ENSP00000358293:K327N	K	-	3	2	C10orf118	115895418	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	0.972000	0.29409	0.518000	0.28383	0.650000	0.86243	AAG	.	.	none		0.368	C10orf118-006	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050455.1		
CNTD2	79935	hgsc.bcm.edu	37	19	40732484	40732484	+	Missense_Mutation	SNP	G	G	T			TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr19:40732484G>T	ENST00000430325.2	-	1	113	c.65C>A	c.(64-66)gCc>gAc	p.A22D	CNTD2_ENST00000433940.1_Missense_Mutation_p.A22D|CNTD2_ENST00000513948.1_5'Flank	NM_024877.3	NP_079153.2	Q9H8S5	CNTD2_HUMAN	cyclin N-terminal domain containing 2	22					regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0000079)					lung(1)|prostate(1)	2						GGGCCTGGGGGCCCAGCGCCT	0.711																																					p.A22D		Atlas-SNP	.											.	CNTD2	22	.	0			c.C65A						PASS	.						7.0	10.0	9.0					19																	40732484		2153	4229	6382	SO:0001583	missense	79935	exon1			CTGGGGGCCCAGC	AK023327	CCDS12551.1, CCDS12551.2	19q13.2	2014-07-03				ENSG00000105219			25805	protein-coding gene	gene with protein product	"""cyclin P"""					11237006	Standard	NM_024877		Approved	FLJ13265, CCNP	uc010xvi.2	Q9H8S5		ENST00000430325.2:c.65C>A	19.37:g.40732484G>T	ENSP00000396755:p.Ala22Asp	69.0	0.0	0		73.0	40.0	0.547945	NM_024877	B4DX65	Missense_Mutation	SNP	ENST00000430325.2	37	CCDS12551.2	.	.	.	.	.	.	.	.	.	.	G	2.608	-0.291537	0.05568	.	.	ENSG00000105219	ENST00000430325;ENST00000433940	T	0.34859	1.34	2.44	-0.257	0.12979	.	3.315080	0.01764	N	0.030742	T	0.22085	0.0532	.	.	.	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.10268	-1.0637	9	0.22706	T	0.39	.	4.6612	0.12643	0.1483:0.0:0.6432:0.2085	.	22	B4DX65	.	D	22	ENSP00000396755:A22D	ENSP00000221818:A22D	A	-	2	0	CNTD2	45424324	0.011000	0.17503	0.000000	0.03702	0.002000	0.02628	0.152000	0.16302	-0.034000	0.13713	-1.134000	0.01955	GCC	.	.	none		0.711	CNTD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000360785.1	NM_024877	
NLRP8	126205	hgsc.bcm.edu	37	19	56467167	56467167	+	Silent	SNP	C	C	T	rs375534172		TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr19:56467167C>T	ENST00000291971.3	+	3	1814	c.1743C>T	c.(1741-1743)ttC>ttT	p.F581F	NLRP8_ENST00000590542.1_Silent_p.F581F	NM_176811.2	NP_789781.2	Q86W28	NALP8_HUMAN	NLR family, pyrin domain containing 8	581					neuron death (GO:0070997)	cytoplasm (GO:0005737)	ATP binding (GO:0005524)			breast(4)|central_nervous_system(2)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(14)|ovary(5)|skin(2)|stomach(3)|upper_aerodigestive_tract(2)	35		Colorectal(82;0.000147)|Ovarian(87;0.17)		GBM - Glioblastoma multiforme(193;0.0695)		AGGTGTCTTTCGGTAATAAGA	0.488																																					p.F581F		Atlas-SNP	.											.	NLRP8	225	.	0			c.C1743T						PASS	.	C		1,4405	2.1+/-5.4	0,1,2202	49.0	46.0	47.0		1743	-0.4	0.0	19		47	0,8600		0,0,4300	no	coding-synonymous	NLRP8	NM_176811.2		0,1,6502	TT,TC,CC		0.0,0.0227,0.0077		581/1049	56467167	1,13005	2203	4300	6503	SO:0001819	synonymous_variant	126205	exon3			GTCTTTCGGTAAT	AY154463	CCDS12937.1	19q13.43	2008-02-05	2006-12-08	2006-12-08		ENSG00000179709		"""Nucleotide-binding domain and leucine rich repeat containing"""	22940	protein-coding gene	gene with protein product	"""nucleotide-binding oligomerization domain, leucine rich repeat and pyrin domain containing 8"""	609659	"""NACHT, leucine rich repeat and PYD containing 8"""	NALP8		12563287	Standard	NM_176811		Approved	NOD16, PAN4, CLR19.2	uc002qmh.3	Q86W28		ENST00000291971.3:c.1743C>T	19.37:g.56467167C>T		115.0	0.0	0		150.0	58.0	0.386667	NM_176811	Q7RTR4	Silent	SNP	ENST00000291971.3	37	CCDS12937.1																																																																																			.	.	weak		0.488	NLRP8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000457462.1	NM_176811	
KBTBD6	89890	hgsc.bcm.edu	37	13	41705110	41705110	+	Missense_Mutation	SNP	T	T	C	rs200203929		TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr13:41705110T>C	ENST00000379485.1	-	1	1772	c.1538A>G	c.(1537-1539)aAt>aGt	p.N513S	KBTBD6_ENST00000499385.2_Missense_Mutation_p.N447S	NM_152903.4	NP_690867.3	Q86V97	KBTB6_HUMAN	kelch repeat and BTB (POZ) domain containing 6	513										NS(1)|breast(1)|endometrium(8)|kidney(4)|large_intestine(9)|lung(9)|ovary(1)|prostate(2)|skin(4)|urinary_tract(4)	43		Lung NSC(96;4.52e-06)|Breast(139;0.00123)|Prostate(109;0.0181)|Lung SC(185;0.0262)|Hepatocellular(98;0.114)		all cancers(112;4.08e-09)|Epithelial(112;4.74e-06)|OV - Ovarian serous cystadenocarcinoma(117;0.000131)|GBM - Glioblastoma multiforme(144;0.000876)|BRCA - Breast invasive adenocarcinoma(63;0.0673)		CTGAAAGTCATTGCGCTTCAG	0.448																																					p.N513S		Atlas-SNP	.											.	KBTBD6	83	.	0			c.A1538G						PASS	.						87.0	84.0	85.0					13																	41705110		2203	4300	6503	SO:0001583	missense	89890	exon1			AAGTCATTGCGCT	AK056633	CCDS9376.1	13q13.3	2013-01-08			ENSG00000165572	ENSG00000165572		"""BTB/POZ domain containing"""	25340	protein-coding gene	gene with protein product						12477932	Standard	NM_152903		Approved	DKFZp547E1912	uc001uxu.1	Q86V97	OTTHUMG00000016786	ENST00000379485.1:c.1538A>G	13.37:g.41705110T>C	ENSP00000368799:p.Asn513Ser	117.0	0.0	0		107.0	52.0	0.485981	NM_152903	Q5T6Y8|Q8N8L0|Q8NDM5|Q96MP6	Missense_Mutation	SNP	ENST00000379485.1	37	CCDS9376.1	.	.	.	.	.	.	.	.	.	.	t	0.006	-2.062628	0.00386	.	.	ENSG00000165572	ENST00000379485;ENST00000499385	T;T	0.64618	-0.11;-0.11	3.8	1.68	0.24146	Kelch-type beta propeller (1);	0.396703	0.27349	N	0.019776	T	0.25457	0.0619	N	0.01168	-0.975	0.23023	N	0.998416	B;B	0.06786	0.001;0.0	B;B	0.04013	0.001;0.0	T	0.20505	-1.0273	10	0.15066	T	0.55	.	5.5596	0.17135	0.0:0.6244:0.0:0.3756	.	447;513	F5GZN7;Q86V97	.;KBTB6_HUMAN	S	513;447	ENSP00000368799:N513S;ENSP00000444326:N447S	ENSP00000368799:N513S	N	-	2	0	KBTBD6	40603110	0.993000	0.37304	0.379000	0.26080	0.527000	0.34593	0.732000	0.26072	0.208000	0.20626	-0.464000	0.05259	AAT	T|0.999;C|0.001	0.001	weak		0.448	KBTBD6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044657.1	NM_152903	
PLK4	10733	hgsc.bcm.edu	37	4	128811038	128811038	+	Missense_Mutation	SNP	A	A	G			TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr4:128811038A>G	ENST00000270861.5	+	7	1751	c.1477A>G	c.(1477-1479)Act>Gct	p.T493A	PLK4_ENST00000514379.1_Missense_Mutation_p.T452A|PLK4_ENST00000507249.1_Missense_Mutation_p.T459A|PLK4_ENST00000515069.1_Intron|PLK4_ENST00000513090.1_Missense_Mutation_p.T461A|RNU6-583P_ENST00000516012.1_RNA	NM_014264.4	NP_055079.3	O00444	PLK4_HUMAN	polo-like kinase 4	493					centriole replication (GO:0007099)|de novo centriole assembly (GO:0098535)|G2/M transition of mitotic cell cycle (GO:0000086)|mitotic cell cycle (GO:0000278)|positive regulation of centriole replication (GO:0046601)|protein phosphorylation (GO:0006468)|trophoblast giant cell differentiation (GO:0060707)	centriole (GO:0005814)|centrosome (GO:0005813)|cytosol (GO:0005829)|deuterosome (GO:0098536)|nucleolus (GO:0005730)	ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)			central_nervous_system(1)|cervix(1)|endometrium(4)|kidney(1)|large_intestine(10)|lung(12)|prostate(1)|upper_aerodigestive_tract(1)	31						AAGAAAAACTACTGAATATGA	0.358																																					p.T493A	Colon(135;508 1718 19061 31832 42879)	Atlas-SNP	.											.	PLK4	65	.	0			c.A1477G						PASS	.						36.0	38.0	37.0					4																	128811038		2201	4296	6497	SO:0001583	missense	10733	exon7			AAAACTACTGAAT	Y13115	CCDS3735.1, CCDS54803.1, CCDS54804.1	4q27-q28	2013-01-18	2010-06-24	2004-01-28	ENSG00000142731	ENSG00000142731			11397	protein-coding gene	gene with protein product		605031	"""serine/threonine kinase 18"", ""polo-like kinase 4 (Drosophila)"""	STK18			Standard	NM_014264		Approved	Sak	uc003ifo.3	O00444	OTTHUMG00000133301	ENST00000270861.5:c.1477A>G	4.37:g.128811038A>G	ENSP00000270861:p.Thr493Ala	158.0	0.0	0		122.0	61.0	0.5	NM_014264	B2RAL0|B7Z837|B7Z8G7|Q8IYF0|Q96Q95|Q9UD84|Q9UDE2	Missense_Mutation	SNP	ENST00000270861.5	37	CCDS3735.1	.	.	.	.	.	.	.	.	.	.	A	0.176	-1.066534	0.01934	.	.	ENSG00000142731	ENST00000270861;ENST00000513090;ENST00000507249;ENST00000514379	T;T;T;T	0.32023	1.47;1.47;1.47;1.47	4.57	0.741	0.18336	.	0.520099	0.21520	N	0.073224	T	0.11110	0.0271	N	0.12182	0.205	0.09310	N	1	B;B	0.02656	0.0;0.0	B;B	0.06405	0.002;0.001	T	0.29336	-1.0015	10	0.06625	T	0.88	-2.5911	3.9503	0.09366	0.3168:0.399:0.2842:0.0	.	461;493	O00444-2;O00444	.;PLK4_HUMAN	A	493;461;459;452	ENSP00000270861:T493A;ENSP00000427554:T461A;ENSP00000423412:T459A;ENSP00000423582:T452A	ENSP00000270861:T493A	T	+	1	0	PLK4	129030488	0.335000	0.24748	0.921000	0.36526	0.022000	0.10575	0.100000	0.15231	0.787000	0.33731	0.482000	0.46254	ACT	.	.	none		0.358	PLK4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257095.3		
OR51B5	282763	hgsc.bcm.edu	37	11	5364431	5364431	+	Silent	SNP	G	G	A	rs58233587	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr11:5364431G>A	ENST00000300773.2	-	1	378	c.324C>T	c.(322-324)ctC>ctT	p.L108L	HBE1_ENST00000380237.1_Intron|AC104389.28_ENST00000415970.1_RNA|HBG2_ENST00000380252.1_Intron|HBG2_ENST00000380259.2_Intron	NM_001005567.2	NP_001005567.2	Q9H339	O51B5_HUMAN	olfactory receptor, family 51, subfamily B, member 5	108					detection of chemical stimulus involved in sensory perception of smell (GO:0050911)|sensory perception of smell (GO:0007608)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			NS(1)|central_nervous_system(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(4)|lung(13)|prostate(1)|skin(5)|upper_aerodigestive_tract(2)	28		Medulloblastoma(188;0.0075)|all_neural(188;0.0572)|Breast(177;0.0675)		Epithelial(150;3.05e-09)|BRCA - Breast invasive adenocarcinoma(625;0.135)		TGCCAGACTCGAGAAAGGAAA	0.493													G|||	486	0.0970447	0.3041	0.0476	5008	,	,		20358	0.0		0.0457	False		,,,				2504	0.0051				p.L108L		Atlas-SNP	.											OR51B5,NS,carcinoma,-1,1	OR51B5	60	1	0			c.C324T						PASS	.	G		1214,3188	413.5+/-336.5	164,886,1151	46.0	45.0	46.0		324	-8.8	0.1	11	dbSNP_129	46	454,8140	135.6+/-192.8	13,428,3856	no	coding-synonymous	OR51B5	NM_001005567.2		177,1314,5007	AA,AG,GG		5.2828,27.5784,12.8347		108/313	5364431	1668,11328	2201	4297	6498	SO:0001819	synonymous_variant	282763	exon5			AGACTCGAGAAAG	BK004430	CCDS31378.1	11p15.4	2012-08-09			ENSG00000242180	ENSG00000242180		"""GPCR / Class A : Olfactory receptors"""	19599	protein-coding gene	gene with protein product							Standard	NM_001005567		Approved		uc001maq.2	Q9H339	OTTHUMG00000066676	ENST00000300773.2:c.324C>T	11.37:g.5364431G>A		31.0	0.0	0		39.0	18.0	0.461538	NM_001005567	B2RN59	Silent	SNP	ENST00000300773.2	37	CCDS31378.1																																																																																			G|0.886;A|0.114	0.114	strong		0.493	OR51B5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000142975.1	NM_001005567	
MST1L	11223	hgsc.bcm.edu	37	1	17085592	17085592	+	RNA	SNP	G	G	A	rs371449598		TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr1:17085592G>A	ENST00000455405.2	-	0	0							Q2TV78	MST1L_HUMAN	macrophage stimulating 1-like							extracellular region (GO:0005576)	serine-type endopeptidase activity (GO:0004252)	p.Q376_R377delQR(1)|p.Q366_R367delQR(1)									GCGGACCAGCGCTGGCACTGG	0.706																																					p.R377C		Atlas-SNP	.											.	.	.	.	2	Deletion - In frame(2)	breast(2)	c.C1129T						PASS	.																																					11223	exon9			ACCAGCGCTGGCA	U28055, AF083416		1p36.33	2013-03-27	2012-11-09	2012-11-09	ENSG00000186715	ENSG00000186715			7390	other	unknown			"""macrophage stimulating, pseudogene 7"", ""macrophage stimulating, pseudogene 9"", ""macrophage stimulating 1 (hepatocyte growth factor-like) pseudogene 9"""	MSTP7, MSTP9, MST1P9		10728827	Standard	NM_001271733		Approved	D1F15S1A, MSPL7, MSPL-7	uc010ock.3	Q2TV78	OTTHUMG00000002578		1.37:g.17085592G>A		105.0	0.0	0		114.0	27.0	0.236842	NM_001271733	B7WPB1|Q13209	Missense_Mutation	SNP	ENST00000455405.2	37		.	.	.	.	.	.	.	.	.	.	.	12.29	1.894372	0.33442	.	.	ENSG00000186715	ENST00000389184;ENST00000334998;ENST00000442552	.	.	.	.	.	.	.	1.304990	0.05479	N	0.554513	T	0.47619	0.1455	.	.	.	.	.	.	D	0.76494	0.999	P	0.55785	0.784	T	0.38001	-0.9681	6	0.56958	D	0.05	.	2.8176	0.05461	3.0E-4:3.0E-4:0.4997:0.4997	.	377	Q2TV78-2	.	C	367;377;377	.	ENSP00000439273:R377C	R	-	1	0	MST1P9	16958179	0.833000	0.29383	0.000000	0.03702	0.000000	0.00434	0.760000	0.26475	-0.000000	0.14550	0.000000	0.15137	CGC	.	.	none		0.706	MST1L-002	KNOWN	basic	processed_transcript	pseudogene	OTTHUMT00000400328.1	NM_001271733	
SPHK1	8877	hgsc.bcm.edu	37	17	74383648	74383648	+	Missense_Mutation	SNP	C	C	T	rs56341546	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr17:74383648C>T	ENST00000545180.1	+	8	1945	c.1136C>T	c.(1135-1137)cCg>cTg	p.P379L	SPHK1_ENST00000323374.4_Missense_Mutation_p.P465L|SPHK1_ENST00000590959.1_Missense_Mutation_p.P393L|SPHK1_ENST00000592299.1_Missense_Mutation_p.P379L|SPHK1_ENST00000392496.3_Missense_Mutation_p.P379L			Q9NYA1	SPHK1_HUMAN	sphingosine kinase 1	379					'de novo' posttranslational protein folding (GO:0051084)|blood vessel development (GO:0001568)|brain development (GO:0007420)|calcium-mediated signaling (GO:0019722)|cellular protein metabolic process (GO:0044267)|cellular response to growth factor stimulus (GO:0071363)|cellular response to hydrogen peroxide (GO:0070301)|cellular response to starvation (GO:0009267)|cyclooxygenase pathway (GO:0019371)|female pregnancy (GO:0007565)|inflammatory response (GO:0006954)|intracellular signal transduction (GO:0035556)|lipid phosphorylation (GO:0046834)|negative regulation of apoptotic process (GO:0043066)|positive regulation of angiogenesis (GO:0045766)|positive regulation of cell growth (GO:0030307)|positive regulation of cell migration (GO:0030335)|positive regulation of fibroblast proliferation (GO:0048146)|positive regulation of mitotic cell cycle (GO:0045931)|positive regulation of neuron projection development (GO:0010976)|positive regulation of neurotransmitter secretion (GO:0001956)|positive regulation of NF-kappaB import into nucleus (GO:0042346)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of protein ubiquitination (GO:0031398)|positive regulation of smooth muscle contraction (GO:0045987)|protein folding (GO:0006457)|protein kinase C-activating G-protein coupled receptor signaling pathway (GO:0007205)|regulation of interleukin-1 beta production (GO:0032651)|regulation of tumor necrosis factor-mediated signaling pathway (GO:0010803)|response to amine (GO:0014075)|response to ATP (GO:0033198)|response to interleukin-1 (GO:0070555)|response to magnesium ion (GO:0032026)|response to progesterone (GO:0032570)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)|sphingoid catabolic process (GO:0046521)|sphingolipid biosynthetic process (GO:0030148)|sphingolipid metabolic process (GO:0006665)|sphingosine metabolic process (GO:0006670)	axon (GO:0030424)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|synaptic vesicle (GO:0008021)	ATP binding (GO:0005524)|calmodulin binding (GO:0005516)|D-erythro-sphingosine kinase activity (GO:0017050)|diacylglycerol kinase activity (GO:0004143)|DNA binding (GO:0003677)|magnesium ion binding (GO:0000287)|NAD+ kinase activity (GO:0003951)|protein phosphatase 2A binding (GO:0051721)|sphinganine kinase activity (GO:0008481)			cervix(1)|endometrium(2)|kidney(2)|large_intestine(1)|lung(4)|ovary(1)	11					Fingolimod(DB08868)	CAGATGCCACCGCCAGAAGAG	0.647													C|||	24	0.00479233	0.0	0.0043	5008	,	,		17320	0.0		0.0119	False		,,,				2504	0.0092				p.P465L	GBM(90;966 1307 27369 33775 44498)	Atlas-SNP	.											.	SPHK1	24	.	0			c.C1394T						PASS	.	C	LEU/PRO,LEU/PRO,LEU/PRO,LEU/PRO	6,4400		0,6,2197	27.0	30.0	29.0		1136,1136,1178,1394	0.9	0.0	17	dbSNP_129	29	52,8544		0,52,4246	yes	missense,missense,missense,missense	SPHK1	NM_001142601.1,NM_001142602.1,NM_021972.3,NM_182965.2	98,98,98,98	0,58,6443	TT,TC,CC		0.6049,0.1362,0.4461	benign,benign,benign,benign	379/385,379/385,393/399,465/471	74383648	58,12944	2203	4298	6501	SO:0001583	missense	8877	exon6			TGCCACCGCCAGA	BC030553	CCDS11744.1, CCDS45785.1, CCDS59297.1	17q25.2	2004-02-18				ENSG00000176170			11240	protein-coding gene	gene with protein product		603730				9726979	Standard	NM_182965		Approved	SPHK	uc002jrj.2	Q9NYA1		ENST00000545180.1:c.1136C>T	17.37:g.74383648C>T	ENSP00000440970:p.Pro379Leu	19.0	0.0	0		27.0	15.0	0.555556	NM_182965	Q8N632|Q96GK1|Q9HD92|Q9NY70|Q9NYL3	Missense_Mutation	SNP	ENST00000545180.1	37	CCDS45785.1	13	0.005952380952380952	0	0.0	4	0.011049723756906077	0	0.0	9	0.011873350923482849	C	12.92	2.081367	0.36758	0.001362	0.006049	ENSG00000176170	ENST00000545180;ENST00000323374;ENST00000392496;ENST00000543830	T;T;T	0.24350	1.96;1.86;1.96	4.64	0.926	0.19430	.	1.925830	0.02640	N	0.105239	T	0.14917	0.0360	L	0.32530	0.975	0.09310	N	1	B;B;B	0.06786	0.001;0.0;0.0	B;B;B	0.06405	0.002;0.0;0.0	T	0.23904	-1.0175	10	0.54805	T	0.06	0.009	4.5549	0.12131	0.1711:0.5944:0.0:0.2345	rs56341546;rs61751848	465;393;379	Q9NYA1-2;Q96GK1;Q9NYA1	.;.;SPHK1_HUMAN	L	379;465;379;378	ENSP00000440970:P379L;ENSP00000313681:P465L;ENSP00000376285:P379L	ENSP00000313681:P465L	P	+	2	0	SPHK1	71895243	0.000000	0.05858	0.005000	0.12908	0.032000	0.12392	0.093000	0.15086	0.480000	0.27534	0.558000	0.71614	CCG	C|0.994;T|0.006	0.006	strong		0.647	SPHK1-006	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000450113.1	NM_182965, NM_021972	
EP300	2033	hgsc.bcm.edu	37	22	41542753	41542753	+	Silent	SNP	A	A	G	rs61756763	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr22:41542753A>G	ENST00000263253.7	+	11	3283	c.2064A>G	c.(2062-2064)ctA>ctG	p.L688L		NM_001429.3	NP_001420.2	Q09472	EP300_HUMAN	E1A binding protein p300	688					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)			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						ATGGCCCTCTACCTGACCCAA	0.368			"""T,  N, F, Mis, O"""	"""MLL, RUNXBP2"""	"""colorectal, breast, pancreatic, AML, ALL, DLBCL"""				Rubinstein-Taybi syndrome				A|||	7	0.00139776	0.0	0.0	5008	,	,		16320	0.0		0.006	False		,,,				2504	0.001				p.L688L		Atlas-SNP	.		Rec	yes		22	22q13	2033	300 kd E1A-Binding protein gene		"""L, E"""	.	EP300	367	.	0			c.A2064G						PASS	.	A		4,4402	8.1+/-20.4	0,4,2199	95.0	93.0	93.0		2064	-11.5	0.3	22	dbSNP_129	93	41,8559	25.1+/-72.6	1,39,4260	no	coding-synonymous	EP300	NM_001429.3		1,43,6459	GG,GA,AA		0.4767,0.0908,0.346		688/2415	41542753	45,12961	2203	4300	6503	SO:0001819	synonymous_variant	2033	exon11	Familial Cancer Database	Broad Thumb-Hallux syndrome	CCCTCTACCTGAC	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.2064A>G	22.37:g.41542753A>G		32.0	0.0	0		43.0	24.0	0.55814	NM_001429	B1AKC2	Silent	SNP	ENST00000263253.7	37	CCDS14010.1																																																																																			A|0.997;G|0.003	0.003	strong		0.368	EP300-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000320600.1	NM_001429	
ZFP69B	65243	hgsc.bcm.edu	37	1	40929087	40929087	+	Silent	SNP	C	C	T	rs142494383	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr1:40929087C>T	ENST00000411995.2	+	6	1806	c.1431C>T	c.(1429-1431)tgC>tgT	p.C477C	ZFP69B_ENST00000361584.3_Silent_p.C375C|ZFP69B_ENST00000484445.1_3'UTR|RP1-228H13.5_ENST00000565390.1_RNA	NM_023070.2	NP_075558.2	Q9UJL9	ZF69B_HUMAN	ZFP69 zinc finger protein B	477					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)										CTTATGAATGCAGTCATTGTG	0.373													C|||	17	0.00339457	0.0023	0.0086	5008	,	,		21479	0.0		0.007	False		,,,				2504	0.001				p.C477C		Atlas-SNP	.											.	.	.	.	0			c.C1431T						PASS	.	C		9,4397		0,9,2194	92.0	89.0	90.0		1431	0.4	0.9	1	dbSNP_134	90	93,8507		0,93,4207	no	coding-synonymous	ZNF643	NM_023070.2		0,102,6401	TT,TC,CC		1.0814,0.2043,0.7843		477/535	40929087	102,12904	2203	4300	6503	SO:0001819	synonymous_variant	65243	exon5			TGAATGCAGTCAT	BC017498	CCDS452.1, CCDS452.2	1p34.2	2013-01-09	2012-11-27	2012-11-27	ENSG00000187801	ENSG00000187801		"""Zinc fingers, C2H2-type"", ""-"", ""-"", ""-"""	28053	protein-coding gene	gene with protein product			"""zinc finger protein 643"""	ZNF643			Standard	NM_023070		Approved	ZKSCAN23B, FLJ34293, ZSCAN54B	uc001cfn.2	Q9UJL9	OTTHUMG00000007302	ENST00000411995.2:c.1431C>T	1.37:g.40929087C>T		93.0	0.0	0		73.0	33.0	0.452055	NM_023070	Q5QPL4	Silent	SNP	ENST00000411995.2	37	CCDS452.2																																																																																			C|0.991;T|0.009	0.009	strong		0.373	ZFP69B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000019078.2	NM_023070	
SHMT2	6472	hgsc.bcm.edu	37	12	57624701	57624701	+	Missense_Mutation	SNP	C	C	T	rs73338162	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr12:57624701C>T	ENST00000328923.3	+	2	601	c.149C>T	c.(148-150)tCg>tTg	p.S50L	SHMT2_ENST00000557487.1_Missense_Mutation_p.S50L|SHMT2_ENST00000393827.4_5'UTR|SHMT2_ENST00000449049.3_Missense_Mutation_p.S29L|SHMT2_ENST00000414700.3_Missense_Mutation_p.S29L|SHMT2_ENST00000554600.1_3'UTR|SHMT2_ENST00000553474.1_Missense_Mutation_p.S29L|Y_RNA_ENST00000365197.1_RNA	NM_001166356.1|NM_005412.5	NP_001159828.1|NP_005403.2	P34897	GLYM_HUMAN	serine hydroxymethyltransferase 2 (mitochondrial)	50					glycine biosynthetic process from serine (GO:0019264)|L-serine biosynthetic process (GO:0006564)|one-carbon metabolic process (GO:0006730)|positive regulation of cell proliferation (GO:0008284)|protein homotetramerization (GO:0051289)|tetrahydrofolate interconversion (GO:0035999)	extracellular vesicular exosome (GO:0070062)|microtubule cytoskeleton (GO:0015630)|mitochondrial inner membrane (GO:0005743)|mitochondrial intermembrane space (GO:0005758)|mitochondrial matrix (GO:0005759)|mitochondrial nucleoid (GO:0042645)|mitochondrion (GO:0005739)	amino acid binding (GO:0016597)|chromatin binding (GO:0003682)|glycine hydroxymethyltransferase activity (GO:0004372)|L-allo-threonine aldolase activity (GO:0008732)|pyridoxal phosphate binding (GO:0030170)			breast(1)|central_nervous_system(1)|large_intestine(4)|liver(2)|lung(3)|ovary(1)|prostate(1)|stomach(1)|upper_aerodigestive_tract(1)	15					Glycine(DB00145)|Tetrahydrofolic acid(DB00116)	GAGAGCCTGTCGGACAGTGAT	0.622													C|||	118	0.0235623	0.0756	0.0144	5008	,	,		18639	0.0		0.008	False		,,,				2504	0.0				p.S50L	Esophageal Squamous(150;1369 2416 49071 49364)	Atlas-SNP	.											.	SHMT2	40	.	0			c.C149T						PASS	.	C	LEU/SER,LEU/SER,LEU/SER,LEU/SER,LEU/SER	343,4063	179.4+/-207.9	9,325,1869	101.0	84.0	90.0		149,86,86,86,149	3.9	0.5	12	dbSNP_130	90	72,8528	43.1+/-100.9	0,72,4228	yes	missense,missense,missense,missense,missense	SHMT2	NM_001166356.1,NM_001166357.1,NM_001166358.1,NM_001166359.1,NM_005412.5	145,145,145,145,145	9,397,6097	TT,TC,CC		0.8372,7.7848,3.1908	benign,benign,benign,benign,benign	50/495,29/484,29/484,29/484,50/505	57624701	415,12591	2203	4300	6503	SO:0001583	missense	6472	exon2			GCCTGTCGGACAG	AK223555	CCDS8934.1, CCDS53805.1, CCDS55837.1	12q12-q14	2006-03-27				ENSG00000182199	2.1.2.1		10852	protein-coding gene	gene with protein product		138450		SHMT		8999870	Standard	NM_005412		Approved		uc001snf.2	P34897		ENST00000328923.3:c.149C>T	12.37:g.57624701C>T	ENSP00000333667:p.Ser50Leu	225.0	1.0	0.00444444		241.0	108.0	0.448133	NM_005412	B7Z9F1|E7EQ19|E7EU43|O00740|Q8N1A5	Missense_Mutation	SNP	ENST00000328923.3	37	CCDS8934.1	52	0.023809523809523808	41	0.08333333333333333	5	0.013812154696132596	0	0.0	6	0.0079155672823219	C	16.72	3.201341	0.58234	0.077848	0.008372	ENSG00000182199	ENST00000328923;ENST00000557487;ENST00000556689;ENST00000414700;ENST00000557703;ENST00000553529;ENST00000554310;ENST00000557427;ENST00000553474;ENST00000555773;ENST00000554975;ENST00000449049;ENST00000556737	T;T;T;T;T;T;T;T;T;T;T;T;T	0.44881	0.91;0.91;0.91;0.91;0.91;0.91;0.91;0.91;0.91;0.91;0.91;0.91;0.91	4.81	3.92	0.45320	Pyridoxal phosphate-dependent transferase, major domain (1);	0.198794	0.43579	D	0.000549	T	0.01940	0.0061	L	0.37630	1.12	0.80722	D	1	B;B	0.24092	0.06;0.097	B;B	0.26202	0.067;0.052	T	0.01739	-1.1284	10	0.37606	T	0.19	-8.0204	12.6117	0.56554	0.0:0.9176:0.0:0.0824	.	50;50	Q8N1A5;P34897	.;GLYM_HUMAN	L	50;50;50;29;29;29;29;29;29;29;29;29;29	ENSP00000333667:S50L;ENSP00000452315:S50L;ENSP00000452035:S50L;ENSP00000406881:S29L;ENSP00000450452:S29L;ENSP00000452161:S29L;ENSP00000450893:S29L;ENSP00000452045:S29L;ENSP00000452419:S29L;ENSP00000451968:S29L;ENSP00000452404:S29L;ENSP00000413770:S29L;ENSP00000451495:S29L	ENSP00000333667:S50L	S	+	2	0	SHMT2	55910968	0.961000	0.32948	0.531000	0.27976	0.967000	0.64934	2.233000	0.43027	1.399000	0.46721	-0.137000	0.14449	TCG	C|0.970;T|0.030	0.030	strong		0.622	SHMT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000412525.2	NM_005412	
INHA	3623	hgsc.bcm.edu	37	2	220439634	220439634	+	Missense_Mutation	SNP	G	G	A	rs149916845	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr2:220439634G>A	ENST00000243786.2	+	2	667	c.487G>A	c.(487-489)Gtg>Atg	p.V163M	INHA_ENST00000489456.1_3'UTR	NM_002191.3	NP_002182.1	P05111	INHA_HUMAN	inhibin, alpha	163					cell cycle arrest (GO:0007050)|cell differentiation (GO:0030154)|cell surface receptor signaling pathway (GO:0007166)|cell-cell signaling (GO:0007267)|erythrocyte differentiation (GO:0030218)|hemoglobin biosynthetic process (GO:0042541)|male gonad development (GO:0008584)|negative regulation of B cell differentiation (GO:0045578)|negative regulation of cell cycle (GO:0045786)|negative regulation of follicle-stimulating hormone secretion (GO:0046882)|negative regulation of interferon-gamma biosynthetic process (GO:0045077)|negative regulation of macrophage differentiation (GO:0045650)|negative regulation of phosphorylation (GO:0042326)|nervous system development (GO:0007399)|ovarian follicle development (GO:0001541)|positive regulation of follicle-stimulating hormone secretion (GO:0046881)|regulation of cell cycle (GO:0051726)|regulation of cell proliferation (GO:0042127)|response to external stimulus (GO:0009605)|signal transduction (GO:0007165)|skeletal system development (GO:0001501)	extracellular region (GO:0005576)|inhibin A complex (GO:0043512)|inhibin-betaglycan-ActRII complex (GO:0034673)|neuronal cell body (GO:0043025)|photoreceptor inner segment (GO:0001917)|photoreceptor outer segment (GO:0001750)	cytokine activity (GO:0005125)|growth factor activity (GO:0008083)|hormone activity (GO:0005179)|receptor binding (GO:0005102)			large_intestine(2)|lung(5)|ovary(1)|skin(1)|urinary_tract(1)	10		Renal(207;0.0183)		Epithelial(149;4.58e-07)|all cancers(144;4.31e-05)|LUSC - Lung squamous cell carcinoma(224;0.008)|Lung(261;0.00802)		GGGAGGACCCGTGGCTGTGCC	0.667													G|||	4	0.000798722	0.0	0.0	5008	,	,		19117	0.0		0.004	False		,,,				2504	0.0				p.V163M		Atlas-SNP	.											INHA,NS,carcinoma,-1,1	INHA	30	1	0			c.G487A						PASS	.	G	MET/VAL	1,4405	2.1+/-5.4	0,1,2202	65.0	59.0	61.0		487	-0.8	0.0	2	dbSNP_134	61	16,8584	11.2+/-40.8	0,16,4284	yes	missense	INHA	NM_002191.3	21	0,17,6486	AA,AG,GG		0.186,0.0227,0.1307	benign	163/367	220439634	17,12989	2203	4300	6503	SO:0001583	missense	3623	exon2			GGACCCGTGGCTG		CCDS2444.1	2q35	2013-09-19			ENSG00000123999	ENSG00000123999			6065	protein-coding gene	gene with protein product		147380				3345731	Standard	NM_002191		Approved		uc002vmk.2	P05111	OTTHUMG00000059237	ENST00000243786.2:c.487G>A	2.37:g.220439634G>A	ENSP00000243786:p.Val163Met	133.0	0.0	0		147.0	74.0	0.503401	NM_002191	A8K8H5	Missense_Mutation	SNP	ENST00000243786.2	37	CCDS2444.1	3	0.0013736263736263737	0	0.0	0	0.0	0	0.0	3	0.00395778364116095	G	0.133	-1.111751	0.01813	2.27E-4	0.00186	ENSG00000123999	ENST00000243786	D	0.85556	-2.0	4.84	-0.764	0.11027	.	0.785011	0.12700	N	0.446402	T	0.65883	0.2734	N	0.05608	-0.01	0.09310	N	1	B	0.14012	0.009	B	0.09377	0.004	T	0.53809	-0.8386	10	0.40728	T	0.16	0.0079	5.5726	0.17204	0.3651:0.1689:0.4659:0.0	.	163	P05111	INHA_HUMAN	M	163	ENSP00000243786:V163M	ENSP00000243786:V163M	V	+	1	0	INHA	220147878	0.000000	0.05858	0.000000	0.03702	0.002000	0.02628	-0.549000	0.06041	0.025000	0.15241	-0.459000	0.05422	GTG	G|0.998;A|0.002	0.002	strong		0.667	INHA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000131425.1		
KIAA0195	9772	hgsc.bcm.edu	37	17	73493217	73493217	+	Silent	SNP	G	G	A	rs372068615		TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr17:73493217G>A	ENST00000314256.7	+	26	3739	c.3345G>A	c.(3343-3345)ctG>ctA	p.L1115L	AC100787.1_ENST00000579379.1_RNA|KIAA0195_ENST00000375248.5_Silent_p.L1125L|KIAA0195_ENST00000579208.1_Silent_p.L766L	NM_014738.4	NP_055553.3	Q12767	K0195_HUMAN	KIAA0195	1115						integral component of membrane (GO:0016021)|nucleus (GO:0005634)				breast(2)|endometrium(5)|kidney(2)|large_intestine(7)|lung(17)|ovary(5)|skin(2)|stomach(1)|urinary_tract(1)	42	all_cancers(13;3.15e-09)|all_epithelial(9;5.94e-10)|Breast(9;1.85e-09)|all_lung(278;0.246)		all cancers(21;5.01e-07)|Epithelial(20;5e-06)|Lung(188;0.0809)|LUSC - Lung squamous cell carcinoma(166;0.154)			TGGTCCAGCTGCCGCCACTCC	0.542																																					p.L1115L		Atlas-SNP	.											.	KIAA0195	102	.	0			c.G3345A						PASS	.	G		1,4405		0,1,2202	164.0	141.0	149.0		3345	2.8	1.0	17		149	0,8600		0,0,4300	no	coding-synonymous	KIAA0195	NM_014738.4		0,1,6502	AA,AG,GG		0.0,0.0227,0.0077		1115/1357	73493217	1,13005	2203	4300	6503	SO:0001819	synonymous_variant	9772	exon26			CCAGCTGCCGCCA		CCDS32732.1	17q25.1	2012-03-01			ENSG00000177728	ENSG00000177728			28983	protein-coding gene	gene with protein product						8724849	Standard	NM_014738		Approved	TMEM94	uc002jnz.4	Q12767		ENST00000314256.7:c.3345G>A	17.37:g.73493217G>A		138.0	0.0	0		144.0	62.0	0.430556	NM_014738	O75536|Q86XF1	Silent	SNP	ENST00000314256.7	37	CCDS32732.1																																																																																			.	.	weak		0.542	KIAA0195-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000447303.1	NM_014738	
KIF26A	26153	hgsc.bcm.edu	37	14	104640098	104640098	+	Silent	SNP	G	G	A	rs61745565	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr14:104640098G>A	ENST00000423312.2	+	10	1923	c.1923G>A	c.(1921-1923)gcG>gcA	p.A641A	KIF26A_ENST00000315264.7_Silent_p.A502A	NM_015656.1	NP_056471.1	Q9ULI4	KI26A_HUMAN	kinesin family member 26A	641	Kinesin motor. {ECO:0000255|PROSITE- ProRule:PRU00283}.				antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|blood coagulation (GO:0007596)|enteric nervous system development (GO:0048484)|metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)|negative regulation of signal transduction (GO:0009968)|regulation of cell growth by extracellular stimulus (GO:0001560)	cytosol (GO:0005829)|kinesin complex (GO:0005871)|microtubule (GO:0005874)	ATP binding (GO:0005524)|microtubule binding (GO:0008017)|microtubule motor activity (GO:0003777)			autonomic_ganglia(1)|endometrium(1)|kidney(1)|large_intestine(1)|lung(8)|pancreas(1)|prostate(2)|skin(4)|upper_aerodigestive_tract(2)	21		all_cancers(154;0.109)|Melanoma(154;0.0525)|all_epithelial(191;0.0767)	Epithelial(46;0.152)	Epithelial(152;0.161)		GTGAGGCGGCGGCTGGCAGGG	0.687													G|||	83	0.0165735	0.0015	0.0288	5008	,	,		15832	0.0		0.0388	False		,,,				2504	0.0225				p.A641A		Atlas-SNP	.											.	KIF26A	84	.	0			c.G1923A						PASS	.	G		24,3842		0,24,1909	17.0	24.0	22.0		1923	-2.2	0.0	14	dbSNP_129	22	289,7937		9,271,3833	no	coding-synonymous	KIF26A	NM_015656.1		9,295,5742	AA,AG,GG		3.5133,0.6208,2.5885		641/1883	104640098	313,11779	1933	4113	6046	SO:0001819	synonymous_variant	26153	exon10			GGCGGCGGCTGGC	AB033062	CCDS45171.1	14q32.33	2009-03-19			ENSG00000066735	ENSG00000066735		"""Kinesins"""	20226	protein-coding gene	gene with protein product		613231				10574462, 11416179	Standard	NM_015656		Approved	KIAA1236, DKFZP434N178	uc001yos.4	Q9ULI4	OTTHUMG00000154986	ENST00000423312.2:c.1923G>A	14.37:g.104640098G>A		23.0	0.0	0		64.0	64.0	1	NM_015656	Q8TAZ7|Q96GK3|Q9UFL3	Silent	SNP	ENST00000423312.2	37	CCDS45171.1																																																																																			G|0.981;A|0.019	0.019	strong		0.687	KIF26A-002	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000414356.1		
WFIKKN2	124857	hgsc.bcm.edu	37	17	48917384	48917384	+	Silent	SNP	G	G	A			TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr17:48917384G>A	ENST00000311378.4	+	2	1263	c.735G>A	c.(733-735)aaG>aaA	p.K245K	RP11-506D12.5_ENST00000572491.2_RNA|WFIKKN2_ENST00000426127.1_Silent_p.K152K	NM_175575.5	NP_783165.1	Q8TEU8	WFKN2_HUMAN	WAP, follistatin/kazal, immunoglobulin, kunitz and netrin domain containing 2	245	Ig-like C2-type.				muscle fiber development (GO:0048747)|negative regulation of DNA binding (GO:0043392)|negative regulation of protein binding (GO:0032091)|palate development (GO:0060021)|skeletal system development (GO:0001501)|transforming growth factor beta receptor signaling pathway (GO:0007179)	extracellular region (GO:0005576)	metalloendopeptidase inhibitor activity (GO:0008191)|serine-type endopeptidase inhibitor activity (GO:0004867)			cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(3)|lung(13)|ovary(4)|skin(1)	29			BRCA - Breast invasive adenocarcinoma(22;1.09e-08)			CCTGGGAGAAGCAGTTGGAGG	0.597																																					p.K245K		Atlas-SNP	.											.	WFIKKN2	69	.	0			c.G735A						PASS	.						107.0	103.0	104.0					17																	48917384		2203	4300	6503	SO:0001819	synonymous_variant	124857	exon2			GGAGAAGCAGTTG	AY358142	CCDS11575.1	17q21.33	2013-01-21			ENSG00000173714	ENSG00000173714		"""Immunoglobulin superfamily / I-set domain containing"", ""WAP four-disulfide core domain containing"""	30916	protein-coding gene	gene with protein product	"""WAP four-disulfide core domain 20B"""	610895				11928817, 12709070	Standard	NM_175575		Approved	WFIKKNRP, WFDC20B	uc002isv.4	Q8TEU8	OTTHUMG00000162274	ENST00000311378.4:c.735G>A	17.37:g.48917384G>A		105.0	0.0	0		113.0	46.0	0.40708	NM_175575	Q6UXZ9	Silent	SNP	ENST00000311378.4	37	CCDS11575.1																																																																																			.	.	none		0.597	WFIKKN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000368358.1	NM_175575	
BZRAP1	9256	hgsc.bcm.edu	37	17	56405046	56405046	+	Missense_Mutation	SNP	C	C	T	rs61743284	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr17:56405046C>T	ENST00000343736.4	-	1	399	c.236G>A	c.(235-237)gGa>gAa	p.G79E	BZRAP1_ENST00000355701.3_Missense_Mutation_p.G79E|BZRAP1-AS1_ENST00000578334.1_RNA|BZRAP1-AS1_ENST00000580633.1_RNA|BZRAP1-AS1_ENST00000580515.1_RNA|BZRAP1_ENST00000268893.6_Missense_Mutation_p.G79E|BZRAP1-AS1_ENST00000579527.1_RNA			O95153	RIMB1_HUMAN	benzodiazepine receptor (peripheral) associated protein 1	79						cytoplasm (GO:0005737)|mitochondrion (GO:0005739)	benzodiazepine receptor binding (GO:0030156)			cervix(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(11)|liver(2)|lung(16)|ovary(1)|prostate(1)|skin(6)|upper_aerodigestive_tract(2)|urinary_tract(1)	54	Medulloblastoma(34;0.127)|all_neural(34;0.237)					AGCCTCTGCTCCTTCAGGGTC	0.622													C|||	79	0.0157748	0.0015	0.013	5008	,	,		17888	0.0		0.0338	False		,,,				2504	0.0348				p.G79E		Atlas-SNP	.											.	BZRAP1	287	.	0			c.G236A						PASS	.	C	GLU/GLY,GLU/GLY	33,4373	38.4+/-70.7	0,33,2170	59.0	53.0	55.0		236,236	0.9	0.0	17	dbSNP_129	55	224,8376	92.6+/-154.6	3,218,4079	yes	missense,missense	BZRAP1	NM_004758.2,NM_024418.1	98,98	3,251,6249	TT,TC,CC		2.6047,0.749,1.976	possibly-damaging,possibly-damaging	79/1858,79/1798	56405046	257,12749	2203	4300	6503	SO:0001583	missense	9256	exon1			TCTGCTCCTTCAG	AB014512	CCDS11605.1, CCDS45742.1	17q22-q23	2014-01-09	2014-01-09						16831	protein-coding gene	gene with protein product		610764				9734811, 9915832	Standard	NM_004758		Approved	PRAX-1, KIAA0612, RIM-BP1, RIMBP1	uc002ivx.5	O95153		ENST00000343736.4:c.236G>A	17.37:g.56405046C>T	ENSP00000345824:p.Gly79Glu	88.0	0.0	0		76.0	37.0	0.486842	NM_024418	O75111|Q8N5W3	Missense_Mutation	SNP	ENST00000343736.4	37	CCDS11605.1	33	0.01510989010989011	0	0.0	4	0.011049723756906077	0	0.0	29	0.03825857519788918	C	9.261	1.043284	0.19748	0.00749	0.026047	ENSG00000005379	ENST00000355701;ENST00000343736;ENST00000268893	T;T;T	0.04917	3.64;3.65;3.53	5.19	0.886	0.19194	.	0.524608	0.17491	N	0.172355	T	0.01092	0.0036	L	0.44542	1.39	0.09310	N	1	B;P;B	0.39480	0.005;0.675;0.001	B;B;B	0.40940	0.006;0.344;0.003	T	0.29761	-1.0001	10	0.07482	T	0.82	.	6.3771	0.21513	0.0:0.6127:0.136:0.2513	.	79;79;79	B7ZVZ7;O95153-2;O95153	.;.;RIMB1_HUMAN	E	79	ENSP00000347929:G79E;ENSP00000345824:G79E;ENSP00000268893:G79E	ENSP00000268893:G79E	G	-	2	0	BZRAP1	53760045	0.807000	0.29009	0.014000	0.15608	0.004000	0.04260	0.719000	0.25881	-0.036000	0.13669	-1.598000	0.00824	GGA	C|0.982;T|0.018	0.018	strong		0.622	BZRAP1-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000443980.1	NM_004758	
EPYC	1833	hgsc.bcm.edu	37	12	91363909	91363909	+	Missense_Mutation	SNP	T	T	C			TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr12:91363909T>C	ENST00000261172.3	-	6	802	c.710A>G	c.(709-711)tAt>tGt	p.Y237C		NM_004950.4	NP_004941.2	Q99645	EPYC_HUMAN	epiphycan	237					female pregnancy (GO:0007565)	proteinaceous extracellular matrix (GO:0005578)	glycosaminoglycan binding (GO:0005539)			NS(1)|breast(1)|endometrium(1)|large_intestine(5)|lung(8)|skin(2)	18						ATGGAGATCATACATGTCCTG	0.408																																					p.Y237C		Atlas-SNP	.											.	EPYC	35	.	0			c.A710G						PASS	.						175.0	176.0	175.0					12																	91363909		2203	4300	6503	SO:0001583	missense	1833	exon6			AGATCATACATGT	AF031658	CCDS31870.1	12q21	2010-03-19	2006-11-21	2006-11-21	ENSG00000083782	ENSG00000083782		"""Proteoglycans / Extracellular Matrix : Small leucine-rich repeats"""	3053	protein-coding gene	gene with protein product	"""epiphycan proteoglycan"""	601657	"""dermatan sulphate proteoglycan 3"", ""dermatan sulfate proteoglycan 3"""	DSPG3		8975717	Standard	NM_004950		Approved	Pg-Lb, SLRR3B	uc001tbk.3	Q99645	OTTHUMG00000170072	ENST00000261172.3:c.710A>G	12.37:g.91363909T>C	ENSP00000261172:p.Tyr237Cys	85.0	0.0	0		91.0	47.0	0.516484	NM_004950	A8K3M7|Q8NEJ5	Missense_Mutation	SNP	ENST00000261172.3	37	CCDS31870.1	.	.	.	.	.	.	.	.	.	.	T	12.84	2.059179	0.36373	.	.	ENSG00000083782	ENST00000261172	T	0.02395	4.31	5.33	5.33	0.75918	.	0.379586	0.30556	N	0.009374	T	0.02012	0.0063	N	0.08118	0	0.29020	N	0.886362	P	0.44521	0.837	B	0.38562	0.276	T	0.42310	-0.9459	10	0.56958	D	0.05	.	11.9016	0.52687	0.0:0.0:0.1455:0.8545	.	237	Q99645	EPYC_HUMAN	C	237	ENSP00000261172:Y237C	ENSP00000261172:Y237C	Y	-	2	0	EPYC	89888040	0.977000	0.34250	1.000000	0.80357	0.979000	0.70002	1.131000	0.31406	2.016000	0.59253	0.383000	0.25322	TAT	.	.	none		0.408	EPYC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000407146.2	NM_004950	
KALRN	8997	hgsc.bcm.edu	37	3	124201699	124201699	+	Silent	SNP	C	C	T	rs61740058	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr3:124201699C>T	ENST00000240874.3	+	28	4387	c.4230C>T	c.(4228-4230)taC>taT	p.Y1410Y	KALRN_ENST00000360013.3_Silent_p.Y1410Y|KALRN_ENST00000460856.1_Silent_p.Y1401Y	NM_003947.4	NP_003938.1	O60229	KALRN_HUMAN	kalirin, RhoGEF kinase	1410	DH 1. {ECO:0000255|PROSITE- ProRule:PRU00062}.				apoptotic signaling pathway (GO:0097190)|intracellular signal transduction (GO:0035556)|nervous system development (GO:0007399)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of apoptotic process (GO:0043065)|positive regulation of GTPase activity (GO:0043547)|protein phosphorylation (GO:0006468)|regulation of small GTPase mediated signal transduction (GO:0051056)|signal transduction (GO:0007165)|small GTPase mediated signal transduction (GO:0007264)|vesicle-mediated transport (GO:0016192)	actin cytoskeleton (GO:0015629)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)	ATP binding (GO:0005524)|guanyl-nucleotide exchange factor activity (GO:0005085)|metal ion binding (GO:0046872)|protein serine/threonine kinase activity (GO:0004674)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)			NS(1)|breast(1)|central_nervous_system(1)|cervix(2)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(21)|lung(28)|ovary(4)|prostate(5)|skin(6)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(3)	83						TCTCTTCCTACCTAATTAAGC	0.527													C|||	38	0.00758786	0.0008	0.0144	5008	,	,		19189	0.0		0.0179	False		,,,				2504	0.0092				p.Y1410Y		Atlas-SNP	.											.	KALRN	556	.	0			c.C4230T						PASS	.	C	,	45,4361	46.7+/-81.2	0,45,2158	247.0	197.0	214.0		4230,4230	3.5	1.0	3	dbSNP_129	214	323,8277	113.7+/-173.7	7,309,3984	no	coding-synonymous,coding-synonymous	KALRN	NM_001024660.3,NM_003947.4	,	7,354,6142	TT,TC,CC		3.7558,1.0213,2.8295	,	1410/2987,1410/1664	124201699	368,12638	2203	4300	6503	SO:0001819	synonymous_variant	8997	exon28			TTCCTACCTAATT	U94190	CCDS3027.1, CCDS3028.1	3q21.2	2013-02-11	2005-03-11	2005-03-12	ENSG00000160145	ENSG00000160145		"""Rho guanine nucleotide exchange factors"", ""Immunoglobulin superfamily / I-set domain containing"", ""Fibronectin type III domain containing"""	4814	protein-coding gene	gene with protein product	"""serine/threonine kinase with Dbl and pleckstrin homology domains"""	604605	"""huntingtin-associated protein interacting protein (duo)"""	HAPIP		9285789, 10023074	Standard	NM_001024660		Approved	duo, Hs.8004, TRAD, DUET, Kalirin, ARHGEF24	uc003ehd.3	O60229	OTTHUMG00000125545	ENST00000240874.3:c.4230C>T	3.37:g.124201699C>T		210.0	0.0	0		169.0	88.0	0.52071	NM_003947	A8MSI4|C9JQ37|Q6ZN45|Q8TBQ5|Q9NSZ4|Q9Y2A5	Silent	SNP	ENST00000240874.3	37	CCDS3027.1	23	0.010531135531135532	0	0.0	8	0.022099447513812154	0	0.0	15	0.01978891820580475	C	8.830	0.939650	0.18281	0.010213	0.037558	ENSG00000160145	ENST00000354186	.	.	.	5.31	3.53	0.40419	.	.	.	.	.	T	0.25754	0.0627	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.27938	-1.0059	4	.	.	.	.	8.0382	0.30506	0.0:0.7055:0.0:0.2945	rs61740058	.	.	.	I	1379	.	.	T	+	2	0	KALRN	125684389	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	1.928000	0.40104	0.819000	0.34492	0.655000	0.94253	ACC	C|0.979;T|0.021	0.021	strong		0.527	KALRN-005	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000258843.4	NM_003947	
CPNE8	144402	hgsc.bcm.edu	37	12	39299249	39299249	+	Missense_Mutation	SNP	C	C	T			TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr12:39299249C>T	ENST00000331366.5	-	1	184	c.88G>A	c.(88-90)Gtg>Atg	p.V30M	RP11-396F22.1_ENST00000551152.1_RNA|CPNE8_ENST00000360449.3_Intron	NM_153634.2	NP_705898.1	Q86YQ8	CPNE8_HUMAN	copine VIII	30	C2 1. {ECO:0000255|PROSITE- ProRule:PRU00041}.					extracellular vesicular exosome (GO:0070062)				NS(1)|breast(1)|endometrium(1)|large_intestine(6)|lung(6)|pancreas(1)|prostate(2)|stomach(1)|upper_aerodigestive_tract(2)	21	Esophageal squamous(101;0.187)	Lung NSC(34;0.137)|Melanoma(24;0.152)|all_lung(34;0.157)				CTGCAGGACACGGACACCTCC	0.647																																					p.V30M		Atlas-SNP	.											.	CPNE8	66	.	0			c.G88A						PASS	.						62.0	50.0	54.0					12																	39299249		2195	4284	6479	SO:0001583	missense	144402	exon1			AGGACACGGACAC	AY177785	CCDS8733.1	12q12	2008-02-05				ENSG00000139117			23498	protein-coding gene	gene with protein product						12670487	Standard	NM_153634		Approved		uc001rls.1	Q86YQ8	OTTHUMG00000169396	ENST00000331366.5:c.88G>A	12.37:g.39299249C>T	ENSP00000329748:p.Val30Met	66.0	0.0	0		63.0	27.0	0.428571	NM_153634	Q2TB41|Q86VY2	Missense_Mutation	SNP	ENST00000331366.5	37	CCDS8733.1	.	.	.	.	.	.	.	.	.	.	C	23.1	4.377756	0.82682	.	.	ENSG00000139117	ENST00000331366	T	0.55234	0.53	4.53	4.53	0.55603	C2 membrane targeting protein (1);C2 calcium-dependent membrane targeting (2);C2 calcium/lipid-binding domain, CaLB (1);	0.102804	0.38959	N	0.001514	T	0.67126	0.2860	M	0.76938	2.355	0.80722	D	1	P	0.50710	0.938	P	0.54856	0.762	T	0.72798	-0.4184	10	0.72032	D	0.01	-11.5212	15.0267	0.71674	0.0:1.0:0.0:0.0	.	30	Q86YQ8	CPNE8_HUMAN	M	30	ENSP00000329748:V30M	ENSP00000329748:V30M	V	-	1	0	CPNE8	37585516	0.990000	0.36364	0.966000	0.40874	0.994000	0.84299	3.827000	0.55745	2.448000	0.82819	0.563000	0.77884	GTG	.	.	none		0.647	CPNE8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000403856.1	NM_153634	
SLC4A2	6522	hgsc.bcm.edu	37	7	150768280	150768280	+	Missense_Mutation	SNP	G	G	A	rs201086697		TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr7:150768280G>A	ENST00000485713.1	+	13	2911	c.1871G>A	c.(1870-1872)cGc>cAc	p.R624H	SLC4A2_ENST00000310317.5_Missense_Mutation_p.R542H|SLC4A2_ENST00000413384.2_Missense_Mutation_p.R624H|SLC4A2_ENST00000392826.2_Missense_Mutation_p.R615H|SLC4A2_ENST00000461735.1_Missense_Mutation_p.R610H	NM_001199692.1	NP_001186621.1	P04920	B3A2_HUMAN	solute carrier family 4 (anion exchanger), member 2	624					anion transport (GO:0006820)|bicarbonate transport (GO:0015701)|ion transport (GO:0006811)|transmembrane transport (GO:0055085)	basolateral plasma membrane (GO:0016323)|focal adhesion (GO:0005925)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)	anion transmembrane transporter activity (GO:0008509)|chloride transmembrane transporter activity (GO:0015108)|inorganic anion exchanger activity (GO:0005452)			NS(1)|central_nervous_system(2)|endometrium(3)|kidney(1)|large_intestine(2)|liver(2)|lung(14)|prostate(3)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	33			OV - Ovarian serous cystadenocarcinoma(82;0.0121)	UCEC - Uterine corpus endometrioid carcinoma (81;0.168)		GAGCTGCTGCGCTCTGTGGCC	0.652													G|||	1	0.000199681	0.0	0.0	5008	,	,		15698	0.0		0.0	False		,,,				2504	0.001				p.R624H		Atlas-SNP	.											SLC4A2,NS,carcinoma,0,1	SLC4A2	98	1	0			c.G1871A						PASS	.						24.0	24.0	24.0					7																	150768280		2203	4299	6502	SO:0001583	missense	6522	exon13			TGCTGCGCTCTGT		CCDS5917.1, CCDS56520.1, CCDS56521.1	7q36.1	2013-07-19	2013-07-19		ENSG00000164889	ENSG00000164889		"""Solute carriers"""	11028	protein-coding gene	gene with protein product	"""anion exchanger 2 type a"", ""anion exchanger 2 type b1"", ""anion exchanger 2 type b2"""	109280	"""erythrocyte membrane protein band 3-like 1"", ""solute carrier family 4, anion exchanger, member 2 (erythrocyte membrane protein band 3-like 1)"""	EPB3L1, AE2		8434259	Standard	NM_003040		Approved	HKB3, BND3L, NBND3	uc003wit.4	P04920	OTTHUMG00000158443	ENST00000485713.1:c.1871G>A	7.37:g.150768280G>A	ENSP00000419412:p.Arg624His	132.0	0.0	0		106.0	48.0	0.45283	NM_003040	B2R6T0|B4DIT0|D3DX05|F8W682|Q45EY5|Q969L3	Missense_Mutation	SNP	ENST00000485713.1	37	CCDS5917.1	.	.	.	.	.	.	.	.	.	.	G	13.93	2.382529	0.42207	.	.	ENSG00000164889	ENST00000485713;ENST00000413384;ENST00000310317;ENST00000392826;ENST00000461735	T;T;T;T;T	0.80214	-1.35;-1.35;-1.35;-1.35;-1.35	5.21	2.16	0.27623	Bicarbonate transporter, cytoplasmic (1);Phosphotransferase/anion transporter (1);	0.063739	0.64402	N	0.000005	T	0.67002	0.2847	L	0.38175	1.15	0.54753	D	0.999986	B;B;B	0.22480	0.07;0.031;0.031	B;B;B	0.18561	0.022;0.013;0.006	T	0.59925	-0.7362	10	0.46703	T	0.11	.	5.0009	0.14264	0.0834:0.1465:0.6191:0.151	.	615;610;624	F8W682;P04920-2;P04920	.;.;B3A2_HUMAN	H	624;624;542;615;610	ENSP00000419412:R624H;ENSP00000405600:R624H;ENSP00000311402:R542H;ENSP00000376571:R615H;ENSP00000419164:R610H	ENSP00000311402:R542H	R	+	2	0	SLC4A2	150399213	0.537000	0.26386	0.656000	0.29637	0.780000	0.44128	1.414000	0.34736	0.668000	0.31126	-0.145000	0.13849	CGC	.	.	weak		0.652	SLC4A2-002	KNOWN	alternative_5_UTR|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000351039.1	NM_003040	
CRYBG3	131544	hgsc.bcm.edu	37	3	97634465	97634465	+	Missense_Mutation	SNP	A	A	G	rs17302349	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr3:97634465A>G	ENST00000182096.4	+	14	2346	c.2282A>G	c.(2281-2283)tAt>tGt	p.Y761C		NM_153605.3	NP_705833.3	Q68DQ2	CRBG3_HUMAN	beta-gamma crystallin domain containing 3	2709							carbohydrate binding (GO:0030246)			breast(1)|cervix(1)|endometrium(5)|kidney(3)|large_intestine(9)|lung(10)|stomach(1)|upper_aerodigestive_tract(2)	32						TGGCTCCTCTATTACCAAGAA	0.438													A|||	18	0.00359425	0.0	0.0014	5008	,	,		18952	0.0		0.0169	False		,,,				2504	0.0				p.Y2709C		Atlas-SNP	.											.	CRYBG3	86	.	0			c.A8126G						PASS	.	A	CYS/TYR	13,3869		0,13,1928	131.0	124.0	127.0		8126	-0.7	0.7	3	dbSNP_123	127	101,8169		2,97,4036	no	missense	CRYBG3	XM_003118522.2	194	2,110,5964	GG,GA,AA		1.2213,0.3349,0.9381	benign	2709/2971	97634465	114,12038	1941	4135	6076	SO:0001583	missense	131544	exon17			TCCTCTATTACCA			3q11.2	2008-09-30			ENSG00000080200	ENSG00000080200			34427	protein-coding gene	gene with protein product							Standard	NM_153605		Approved	DKFZp667G2110	uc021xbn.2	Q68DQ2	OTTHUMG00000159187	ENST00000182096.4:c.2282A>G	3.37:g.97634465A>G	ENSP00000182096:p.Tyr761Cys	126.0	0.0	0		125.0	57.0	0.456	NM_153605	B4DLE8|F6VHI2|Q4G0V8|Q7Z4R9|Q86VD0|Q8N262|Q8N7F1|Q8NDQ8	Missense_Mutation	SNP	ENST00000182096.4	37		15	0.006868131868131868	0	0.0	1	0.0027624309392265192	0	0.0	14	0.018469656992084433	A	4.996	0.184921	0.09495	0.003349	0.012213	ENSG00000080200	ENST00000182096	D	0.85702	-2.02	5.87	-0.682	0.11339	Beta/gamma crystallin (4);Gamma-crystallin-related (1);	0.997902	0.08115	N	0.995570	T	0.66076	0.2753	L	0.60845	1.875	0.52501	D	0.999956	B	0.11235	0.004	B	0.09377	0.004	T	0.65919	-0.6051	10	0.51188	T	0.08	.	1.6488	0.02767	0.4574:0.1336:0.2803:0.1287	rs17302349;rs52818309;rs17302349	761	Q68DQ2	CRBG3_HUMAN	C	761	ENSP00000182096:Y761C	ENSP00000182096:Y761C	Y	+	2	0	CRYBG3	99117155	0.999000	0.42202	0.672000	0.29872	0.069000	0.16628	0.555000	0.23422	-0.105000	0.12132	-1.437000	0.01076	TAT	A|0.994;G|0.006	0.006	strong		0.438	CRYBG3-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000353751.1	NM_153605	
ANKRD52	283373	hgsc.bcm.edu	37	12	56638455	56638455	+	Silent	SNP	G	G	A	rs201117129	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr12:56638455G>A	ENST00000267116.7	-	24	2824	c.2703C>T	c.(2701-2703)aaC>aaT	p.N901N	ANKRD52_ENST00000548241.1_5'UTR	NM_173595.3	NP_775866.2	Q8NB46	ANR52_HUMAN	ankyrin repeat domain 52	901										endometrium(9)|kidney(2)|large_intestine(8)|lung(6)|ovary(2)|prostate(1)|skin(1)	29						CGGTCTGCCCGTTCTCAGCCG	0.647													G|||	3	0.000599042	0.0	0.0	5008	,	,		17818	0.0		0.003	False		,,,				2504	0.0				p.N901N		Atlas-SNP	.											.	ANKRD52	81	.	0			c.C2703T						PASS	.	G		1,4327		0,1,2163	43.0	47.0	45.0		2703	-4.6	0.9	12		45	36,8510		1,34,4238	no	coding-synonymous	ANKRD52	NM_173595.3		1,35,6401	AA,AG,GG		0.4212,0.0231,0.2874		901/1077	56638455	37,12837	2164	4273	6437	SO:0001819	synonymous_variant	283373	exon24			CTGCCCGTTCTCA	AK091555	CCDS44920.1	12q13.3	2013-01-10			ENSG00000139645	ENSG00000139645		"""Serine/threonine phosphatases / Protein phosphatase 6, regulatory subunits"", ""Ankyrin repeat domain containing"""	26614	protein-coding gene	gene with protein product	"""protein phosphatase 6 ankyrin repeat subunit C"""						Standard	NM_173595		Approved	FLJ34236, PP6-ARS-C	uc001skm.4	Q8NB46	OTTHUMG00000170329	ENST00000267116.7:c.2703C>T	12.37:g.56638455G>A		189.0	0.0	0		180.0	112.0	0.622222	NM_173595	A6NE79|B1Q2K2	Silent	SNP	ENST00000267116.7	37	CCDS44920.1																																																																																			G|0.998;A|0.002	0.002	strong		0.647	ANKRD52-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000408539.1	NM_173595	
MTRR	4552	hgsc.bcm.edu	37	5	7893005	7893005	+	Silent	SNP	C	C	T	rs34172797	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr5:7893005C>T	ENST00000264668.2	+	11	1647	c.1617C>T	c.(1615-1617)agC>agT	p.S539S	MTRR_ENST00000440940.2_Silent_p.S512S	NM_002454.2|NM_024010.2	NP_002445.2|NP_076915.2	Q9UBK8	MTRR_HUMAN	5-methyltetrahydrofolate-homocysteine methyltransferase reductase	539	FAD-binding FR-type. {ECO:0000255|PROSITE-ProRule:PRU00716}.				cellular nitrogen compound metabolic process (GO:0034641)|cobalamin metabolic process (GO:0009235)|DNA methylation (GO:0006306)|folic acid metabolic process (GO:0046655)|methionine biosynthetic process (GO:0009086)|methionine metabolic process (GO:0006555)|methylation (GO:0032259)|oxidation-reduction process (GO:0055114)|small molecule metabolic process (GO:0044281)|sulfur amino acid metabolic process (GO:0000096)|vitamin metabolic process (GO:0006766)|water-soluble vitamin metabolic process (GO:0006767)|xenobiotic metabolic process (GO:0006805)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|intermediate filament cytoskeleton (GO:0045111)|nucleus (GO:0005634)	[methionine synthase] reductase activity (GO:0030586)|flavin adenine dinucleotide binding (GO:0050660)|FMN binding (GO:0010181)|iron ion binding (GO:0005506)|NADP binding (GO:0050661)|oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, NAD(P)H as one donor, and incorporation of one atom of oxygen (GO:0016709)|oxidoreductase activity, oxidizing metal ions, NAD or NADP as acceptor (GO:0016723)			NS(1)|breast(3)|endometrium(2)|kidney(1)|large_intestine(4)|liver(1)|lung(14)|ovary(1)|prostate(3)|stomach(1)	31					Cyanocobalamin(DB00115)|Hydroxocobalamin(DB00200)|L-Methionine(DB00134)	ATGAAGACAGCGGGAAAGCCC	0.458													C|||	45	0.00898562	0.0045	0.0259	5008	,	,		18337	0.0		0.0189	False		,,,				2504	0.002				p.S539S		Atlas-SNP	.											.	MTRR	74	.	0			c.C1617T						PASS	.	C	,	66,4340	61.7+/-98.7	0,66,2137	84.0	71.0	75.0		1536,1617	0.2	0.0	5	dbSNP_126	75	207,8393	89.4+/-151.6	2,203,4095	no	coding-synonymous,coding-synonymous	MTRR	NM_002454.2,NM_024010.2	,	2,269,6232	TT,TC,CC		2.407,1.498,2.099	,	512/699,539/726	7893005	273,12733	2203	4300	6503	SO:0001819	synonymous_variant	4552	exon11			AGACAGCGGGAAA	AF025794	CCDS3874.1, CCDS47190.1	5p15.31	2011-05-12			ENSG00000124275	ENSG00000124275	1.16.1.8		7473	protein-coding gene	gene with protein product		602568				9501215	Standard	NM_024010		Approved	cblE	uc003jed.3	Q9UBK8	OTTHUMG00000090477	ENST00000264668.2:c.1617C>T	5.37:g.7893005C>T		82.0	0.0	0		81.0	39.0	0.481481	NM_024010	O60471|Q32MA9|Q7Z4M8	Silent	SNP	ENST00000264668.2	37	CCDS3874.1																																																																																			C|0.981;T|0.019	0.019	strong		0.458	MTRR-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000206931.1		
FAM86B1	85002	hgsc.bcm.edu	37	8	12044264	12044264	+	Missense_Mutation	SNP	C	C	T			TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr8:12044264C>T	ENST00000448228.2	-	4	368	c.319G>A	c.(319-321)Gcc>Acc	p.A107T	FAM86B1_ENST00000534520.1_Missense_Mutation_p.A107T|FAM86B1_ENST00000321602.8_Start_Codon_SNP_p.M1I|FAM86B1_ENST00000533852.2_Missense_Mutation_p.A141T|FAM86B1_ENST00000533513.1_Missense_Mutation_p.A141T	NM_001083537.1	NP_001077006.1	Q8N7N1	F86B1_HUMAN	family with sequence similarity 86, member B1	107										kidney(1)|prostate(1)|stomach(1)	3			STAD - Stomach adenocarcinoma(15;0.033)	COAD - Colon adenocarcinoma(149;0.0965)		TAGAGGGCGGCATCCCATGTG	0.612																																					p.A107T		Atlas-SNP	.											FAM86B1,NS,carcinoma,+2,1	FAM86B1	7	1	0			c.G319A						scavenged	.						1.0	1.0	1.0					8																	12044264		461	1070	1531	SO:0001583	missense	85002	exon4			GGGCGGCATCCCA	BC007983	CCDS59512.1	8p23.1	2014-02-12	2005-08-19		ENSG00000186523	ENSG00000186523			28268	protein-coding gene	gene with protein product						12477932	Standard	NM_001083537		Approved	MGC16279	uc010lse.3	Q8N7N1	OTTHUMG00000165298	ENST00000448228.2:c.319G>A	8.37:g.12044264C>T	ENSP00000407067:p.Ala107Thr	533.0	0.0	0		559.0	35.0	0.0626118	NM_001083537		Missense_Mutation	SNP	ENST00000448228.2	37	CCDS59512.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	-|-	11.97|11.97	1.796969|1.796969	0.31777|0.31777	.|.	.|.	ENSG00000186523|ENSG00000186523	ENST00000431227;ENST00000340537;ENST00000448228;ENST00000534520;ENST00000526708;ENST00000524571;ENST00000533513|ENST00000321602;ENST00000526802	T;T;T;T;T|T	0.36340|0.24350	1.26;2.52;1.26;1.56;4.06|1.86	1.17|1.17	1.17|1.17	0.20885|0.20885	.|.	10.022600|.	0.01570|.	U|.	0.020538|.	T|T	0.33731|0.33731	0.0873|0.0873	M|M	0.90309|0.90309	3.105|3.105	0.80722|0.80722	D|D	1|1	P;P|B;B	0.46457|0.15719	0.878;0.749|0.014;0.003	D;P|B;B	0.64144|0.08055	0.922;0.624|0.003;0.002	T|T	0.42050|0.42050	-0.9474|-0.9474	10|9	0.72032|0.87932	D|D	0.01|0	.|.	8.2654|8.2654	0.31810|0.31810	0.0:1.0:0.0:0.0|0.0:1.0:0.0:0.0	.|.	107;141|1;38	Q8N7N1;E9PN63|F6QN85;Q4KMP3	F86B1_HUMAN;.|.;.	T|I	141;107;107;107;141;79;141|1;102	ENSP00000342610:A107T;ENSP00000407067:A107T;ENSP00000431362:A107T;ENSP00000432790:A79T;ENSP00000435201:A141T|ENSP00000439686:M1I	ENSP00000342610:A107T|ENSP00000439686:M1I	A|M	-|-	1|3	0|0	FAM86B1|FAM86B1	12081673|12081673	1.000000|1.000000	0.71417|0.71417	0.088000|0.088000	0.20740|0.20740	0.049000|0.049000	0.14656|0.14656	6.283000|6.283000	0.72646|0.72646	0.950000|0.950000	0.37743|0.37743	0.173000|0.173000	0.16961|0.16961	GCC|ATG	.	.	none		0.612	FAM86B1-016	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000383317.1	NM_032916	
PPP2R1B	5519	hgsc.bcm.edu	37	11	111608216	111608216	+	IGR	SNP	T	T	A	rs61756429	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr11:111608216T>A	ENST00000527614.1	-	0	5587				PPP2R1B_ENST00000426998.2_Missense_Mutation_p.N559Y|PPP2R1B_ENST00000311129.5_Missense_Mutation_p.N623Y|PPP2R1B_ENST00000530787.1_5'Flank	NM_001177562.1|NM_002716.4	NP_001171033.1|NP_002707.3	P30154	2AAB_HUMAN	protein phosphatase 2, regulatory subunit A, beta						apoptotic process involved in morphogenesis (GO:0060561)|positive regulation of extrinsic apoptotic signaling pathway in absence of ligand (GO:2001241)	extracellular vesicular exosome (GO:0070062)|membrane raft (GO:0045121)				endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(2)|liver(1)|lung(10)|prostate(1)|urinary_tract(2)	22		all_cancers(61;2.34e-15)|all_epithelial(67;1.72e-09)|Melanoma(852;1.91e-06)|all_hematologic(158;0.000405)|Acute lymphoblastic leukemia(157;0.000967)|Breast(348;0.0112)|all_neural(223;0.0281)|Medulloblastoma(222;0.0425)		BRCA - Breast invasive adenocarcinoma(274;1.13e-06)|Epithelial(105;2.36e-06)|all cancers(92;3.78e-05)|OV - Ovarian serous cystadenocarcinoma(223;0.0761)		GGGAAGTGGTTCTTGTCAGCC	0.597													T|||	10	0.00199681	0.0	0.0043	5008	,	,		20031	0.0		0.007	False		,,,				2504	0.0				p.N623Y		Atlas-SNP	.											.	PPP2R1B	44	.	0			c.A1867T						PASS	.	T	TYR/ASN,TYR/ASN	13,4389	21.2+/-45.6	0,13,2188	155.0	128.0	137.0		1867,1675	4.1	1.0	11	dbSNP_129	137	86,8508	48.9+/-108.6	0,86,4211	yes	missense,missense	PPP2R1B	NM_181699.2,NM_181700.1	143,143	0,99,6399	AA,AT,TT		1.0007,0.2953,0.7618	possibly-damaging,possibly-damaging	623/668,559/604	111608216	99,12897	2201	4297	6498	SO:0001628	intergenic_variant	5519	exon15			AGTGGTTCTTGTC	AF087438	CCDS8348.1, CCDS8349.1, CCDS53706.1, CCDS53707.1, CCDS53708.1	11q23.1	2010-06-18	2010-04-14		ENSG00000137713	ENSG00000137713	3.1.3.16	"""Serine/threonine phosphatases / Protein phosphatase 2, regulatory subunits"""	9303	protein-coding gene	gene with protein product	"""PP2A-A-beta"", ""protein phosphatase 2A, regulatory subunit A, beta isoform"""	603113	"""protein phosphatase 2 (formerly 2A), regulatory subunit A (PR 65), beta isoform"", ""protein phosphatase 2 (formerly 2A), regulatory subunit A, beta isoform"""			2159327, 9795170	Standard	NM_181699		Approved	PR65B, PP2A-Abeta	uc001plw.1	P30154	OTTHUMG00000166741		11.37:g.111608216T>A		85.0	0.0	0		85.0	36.0	0.423529	NM_181699	A8MY67|B0YJ69|B4DGQ6|B4DK91|B4DWW5|F8W8G1|O75620|Q8NHV8	Missense_Mutation	SNP	ENST00000527614.1	37	CCDS8349.1	7	0.003205128205128205	0	0.0	2	0.0055248618784530384	0	0.0	5	0.006596306068601583	T	10.82	1.458179	0.26161	0.002953	0.010007	ENSG00000137713	ENST00000311129;ENST00000426998	.	.	.	5.25	4.13	0.48395	.	0.617749	0.15812	N	0.243438	T	0.27933	0.0688	N	0.08118	0	0.80722	D	1	P;D	0.54207	0.94;0.965	P;P	0.51135	0.459;0.66	T	0.18493	-1.0335	9	0.87932	D	0	-10.7806	7.9175	0.29827	0.0:0.0914:0.0:0.9086	rs61756429	559;623	B4DWW5;P30154-2	.;.	Y	623;559	.	ENSP00000311344:N623Y	N	-	1	0	PPP2R1B	111113426	1.000000	0.71417	0.991000	0.47740	0.214000	0.24535	1.866000	0.39489	1.132000	0.42129	0.496000	0.49642	AAC	T|0.992;A|0.008	0.008	strong		0.597	PPP2R1B-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000391298.1	NM_002716	
ZGPAT	84619	hgsc.bcm.edu	37	20	62339959	62339959	+	Silent	SNP	C	C	G	rs148155917		TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr20:62339959C>G	ENST00000328969.5	+	2	154	c.27C>G	c.(25-27)gcC>gcG	p.A9A	ZGPAT_ENST00000357119.4_Silent_p.A9A|ARFRP1_ENST00000359715.5_5'Flank|ZGPAT_ENST00000448100.2_Silent_p.A9A|RP4-583P15.15_ENST00000490623.2_5'Flank|ARFRP1_ENST00000440854.1_5'Flank|ZGPAT_ENST00000369967.3_Silent_p.A9A|ARFRP1_ENST00000607873.1_5'Flank|ARFRP1_ENST00000324228.2_5'Flank|ARFRP1_ENST00000609142.1_5'Flank|ZGPAT_ENST00000355969.6_Silent_p.A9A	NM_032527.4	NP_115916.3	Q8N5A5	ZGPAT_HUMAN	zinc finger, CCCH-type with G patch domain	9					negative regulation of epidermal growth factor-activated receptor activity (GO:0007175)|negative regulation of transcription, DNA-templated (GO:0045892)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	metal ion binding (GO:0046872)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)			endometrium(2)|kidney(1)|large_intestine(1)|lung(7)|ovary(2)|prostate(1)	14	all_cancers(38;1.13e-12)|all_epithelial(29;2.64e-14)|Lung NSC(23;4.79e-10)|all_lung(23;1.7e-09)					TGGAGTCGGCCTTGCAGACCT	0.687																																					p.A9A		Atlas-SNP	.											.	ZGPAT	57	.	0			c.C27G						PASS	.						22.0	24.0	24.0					20																	62339959		2194	4282	6476	SO:0001819	synonymous_variant	84619	exon2			GTCGGCCTTGCAG	AK027878	CCDS13534.1, CCDS13535.1, CCDS56203.1	20q13.3	2013-01-28	2004-12-01	2004-12-01	ENSG00000197114	ENSG00000197114		"""Zinc fingers, CCCH-type domain containing"", ""G patch domain containing"""	15948	protein-coding gene	gene with protein product			"""KIAA1847"""	KIAA1847		16952911	Standard	NM_181485		Approved	dJ583P15.3, MGC44880, FLJ14972, ZC3HDC9, ZC3H9, GPATC6, GPATCH6, ZIP	uc002ygk.3	Q8N5A5	OTTHUMG00000032998	ENST00000328969.5:c.27C>G	20.37:g.62339959C>G		109.0	0.0	0		111.0	57.0	0.513514	NM_032527	E1P5K1|Q4VXN9|Q5JWI9|Q5JWJ0|Q8NC55|Q8WUV4|Q96JI0|Q96JU4|Q9H401	Silent	SNP	ENST00000328969.5	37	CCDS13534.1																																																																																			C|1.000;T|0.000	.	alt		0.687	ZGPAT-006	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000080214.1	NM_181484	
EGFR	1956	hgsc.bcm.edu	37	7	55268916	55268916	+	Silent	SNP	C	C	T	rs2293347|rs587778251	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr7:55268916C>T	ENST00000275493.2	+	25	3159	c.2982C>T	c.(2980-2982)gaC>gaT	p.D994D	EGFR_ENST00000455089.1_Silent_p.D949D|EGFR_ENST00000442591.1_Intron|EGFR_ENST00000454757.2_Silent_p.D941D	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		135.0	0.0	0		158.0	72.0	0.455696	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	
KRT20	54474	hgsc.bcm.edu	37	17	39037000	39037000	+	Missense_Mutation	SNP	G	G	A	rs143378689	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr17:39037000G>A	ENST00000167588.3	-	3	537	c.496C>T	c.(496-498)Cgt>Tgt	p.R166C		NM_019010.2	NP_061883.1	P35900	K1C20_HUMAN	keratin 20	166	Coil 1B.|Rod.				apoptotic process (GO:0006915)|cellular response to stress (GO:0033554)|intermediate filament organization (GO:0045109)|regulation of protein secretion (GO:0050708)	cytoplasm (GO:0005737)|intermediate filament (GO:0005882)	structural constituent of cytoskeleton (GO:0005200)			NS(1)|endometrium(2)|kidney(1)|large_intestine(4)|lung(5)|skin(1)	14		Breast(137;0.000301)|Ovarian(249;0.15)				ACTGTTAGACGTATTCCTCTC	0.373													G|||	8	0.00159744	0.0	0.0014	5008	,	,		18332	0.0		0.007	False		,,,				2504	0.0				p.R166C		Atlas-SNP	.											.	KRT20	38	.	0			c.C496T						PASS	.	G	CYS/ARG	6,4400	11.4+/-27.6	0,6,2197	147.0	136.0	140.0		496	0.3	0.0	17	dbSNP_134	140	34,8566	23.4+/-69.3	0,34,4266	yes	missense	KRT20	NM_019010.2	180	0,40,6463	AA,AG,GG		0.3953,0.1362,0.3076	possibly-damaging	166/425	39037000	40,12966	2203	4300	6503	SO:0001583	missense	54474	exon3			TTAGACGTATTCC	BC031559	CCDS11379.1	17q21.2	2013-01-16			ENSG00000171431	ENSG00000171431		"""-"", ""Intermediate filaments type I, keratins (acidic)"""	20412	protein-coding gene	gene with protein product		608218				8359595, 12515621, 16831889	Standard	NM_019010		Approved	CK20, K20, MGC35423	uc002hvl.3	P35900	OTTHUMG00000133366	ENST00000167588.3:c.496C>T	17.37:g.39037000G>A	ENSP00000167588:p.Arg166Cys	93.0	0.0	0		80.0	38.0	0.475	NM_019010	B2R6W7	Missense_Mutation	SNP	ENST00000167588.3	37	CCDS11379.1	8	0.003663003663003663	0	0.0	1	0.0027624309392265192	0	0.0	7	0.009234828496042216	G	11.51	1.659928	0.29515	0.001362	0.003953	ENSG00000171431	ENST00000167588	D	0.91792	-2.91	5.45	0.338	0.15974	Filament (1);	0.496636	0.16942	N	0.193234	D	0.83529	0.5274	L	0.56199	1.76	0.19300	N	0.999978	B	0.29886	0.26	B	0.24974	0.057	T	0.77332	-0.2627	10	0.62326	D	0.03	.	8.0078	0.30336	0.0704:0.0844:0.6039:0.2414	.	166	P35900	K1C20_HUMAN	C	166	ENSP00000167588:R166C	ENSP00000167588:R166C	R	-	1	0	KRT20	36290526	0.000000	0.05858	0.000000	0.03702	0.006000	0.05464	0.030000	0.13688	0.242000	0.21303	0.591000	0.81541	CGT	G|0.996;A|0.004	0.004	strong		0.373	KRT20-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257202.2		
CDC42EP4	23580	hgsc.bcm.edu	37	17	71282132	71282132	+	Missense_Mutation	SNP	C	C	T	rs375486831		TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr17:71282132C>T	ENST00000335793.3	-	2	902	c.508G>A	c.(508-510)Gcg>Acg	p.A170T	CDC42EP4_ENST00000581014.1_Intron|CDC42EP4_ENST00000439510.2_Missense_Mutation_p.A100T			Q9H3Q1	BORG4_HUMAN	CDC42 effector protein (Rho GTPase binding) 4	170					positive regulation of pseudopodium assembly (GO:0031274)|regulation of cell shape (GO:0008360)|Rho protein signal transduction (GO:0007266)	actin cytoskeleton (GO:0015629)|cytoplasm (GO:0005737)|microtubule cytoskeleton (GO:0015630)|plasma membrane (GO:0005886)	GTP-Rho binding (GO:0017049)|poly(A) RNA binding (GO:0044822)			cervix(2)|endometrium(3)|large_intestine(1)|lung(7)|urinary_tract(1)	14			LUSC - Lung squamous cell carcinoma(166;0.0352)|Lung(188;0.0711)			TGTGGACCCGCGGCCCCATTC	0.662																																					p.A170T		Atlas-SNP	.											CDC42EP4,colon,carcinoma,0,1	CDC42EP4	19	1	0			c.G508A						PASS	.	C	THR/ALA	0,4406		0,0,2203	46.0	41.0	43.0		508	-5.5	0.0	17		43	1,8599	1.2+/-3.3	0,1,4299	no	missense	CDC42EP4	NM_012121.4	58	0,1,6502	TT,TC,CC		0.0116,0.0,0.0077	benign	170/357	71282132	1,13005	2203	4300	6503	SO:0001583	missense	23580	exon2			GACCCGCGGCCCC	AB042237	CCDS11695.1	17q24-q25	2008-07-18				ENSG00000179604			17147	protein-coding gene	gene with protein product	"""Cdc42 effector protein 4"", ""binder of Rho GTPases 4"""	605468				11035016, 10490598	Standard	NM_012121		Approved	CEP4, KAIA1777, BORG4, MGC3740, MGC17125	uc002jjo.3	Q9H3Q1		ENST00000335793.3:c.508G>A	17.37:g.71282132C>T	ENSP00000338258:p.Ala170Thr	110.0	0.0	0		141.0	68.0	0.482269	NM_012121	B3KUS7|O95828|Q96FT3	Missense_Mutation	SNP	ENST00000335793.3	37	CCDS11695.1	.	.	.	.	.	.	.	.	.	.	C	4.875	0.162607	0.09287	0.0	1.16E-4	ENSG00000179604	ENST00000335793;ENST00000439510	T;T	0.34275	1.37;1.37	4.5	-5.48	0.02592	.	1.452830	0.05166	N	0.498676	T	0.20292	0.0488	L	0.28115	0.83	0.09310	N	1	B;B	0.09022	0.002;0.0	B;B	0.01281	0.0;0.0	T	0.23726	-1.0180	10	0.12766	T	0.61	-1.5257	6.8507	0.24012	0.118:0.3419:0.0:0.5401	.	100;170	B3KUS7;Q9H3Q1	.;BORG4_HUMAN	T	170;100	ENSP00000338258:A170T;ENSP00000404270:A100T	ENSP00000338258:A170T	A	-	1	0	CDC42EP4	68793727	0.000000	0.05858	0.000000	0.03702	0.041000	0.13682	-0.321000	0.08018	-1.673000	0.01462	-0.678000	0.03780	GCG	.	.	weak		0.662	CDC42EP4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000441898.1	NM_012121	
ZNF189	7743	hgsc.bcm.edu	37	9	104162272	104162272	+	Missense_Mutation	SNP	A	A	G			TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr9:104162272A>G	ENST00000339664.2	+	2	269	c.140A>G	c.(139-141)tAt>tGt	p.Y47C	ZNF189_ENST00000259395.4_Missense_Mutation_p.Y5C|MRPL50_ENST00000539624.1_5'Flank|MRPL50_ENST00000374865.4_5'Flank|ZNF189_ENST00000374861.3_Missense_Mutation_p.Y33C	NM_001278240.1	NP_001265169.1	O75820	ZN189_HUMAN	zinc finger protein 189	47	KRAB. {ECO:0000255|PROSITE- ProRule:PRU00119}.				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)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(1)|central_nervous_system(1)|endometrium(2)|kidney(2)|large_intestine(2)|lung(10)|ovary(2)|prostate(3)|skin(2)|urinary_tract(1)	26		Acute lymphoblastic leukemia(62;0.0559)				ATGGAGAATTATGGAAACCTG	0.413																																					p.Y47C		Atlas-SNP	.											ZNF189,NS,carcinoma,+1,1	ZNF189	79	1	0			c.A140G						PASS	.						125.0	126.0	126.0					9																	104162272		2203	4300	6503	SO:0001583	missense	7743	exon2			AGAATTATGGAAA	AF025770	CCDS6754.1, CCDS6755.1, CCDS65096.1, CCDS75867.1	9q22-q31	2013-01-08			ENSG00000136870	ENSG00000136870		"""Zinc fingers, C2H2-type"", ""-"""	12980	protein-coding gene	gene with protein product		603132				9653648	Standard	NM_003452		Approved		uc004bbh.2	O75820	OTTHUMG00000020383	ENST00000339664.2:c.140A>G	9.37:g.104162272A>G	ENSP00000342019:p.Tyr47Cys	78.0	0.0	0		63.0	26.0	0.412698	NM_003452	O75802|Q5T7D7|Q5T7D8|Q5T7D9|Q9UBL4|Q9UPE9|Q9UPF0|Q9UPF1	Missense_Mutation	SNP	ENST00000339664.2	37	CCDS6754.1	.	.	.	.	.	.	.	.	.	.	A	17.28	3.348923	0.61183	.	.	ENSG00000136870	ENST00000374861;ENST00000339664;ENST00000259395	T;T;T	0.08193	4.26;4.26;3.12	4.79	3.61	0.41365	Krueppel-associated box (4);	0.191487	0.25958	N	0.027201	T	0.22627	0.0546	M	0.74467	2.265	0.34073	D	0.65865	P;D;D	0.63046	0.946;0.966;0.992	P;B;P	0.62184	0.749;0.338;0.899	T	0.29119	-1.0022	10	0.59425	D	0.04	.	9.0762	0.36522	0.8355:0.0:0.0:0.1645	.	32;33;47	B7ZLK9;Q5T7D8;O75820	.;.;ZN189_HUMAN	C	33;47;5	ENSP00000363995:Y33C;ENSP00000342019:Y47C;ENSP00000259395:Y5C	ENSP00000259395:Y5C	Y	+	2	0	ZNF189	103202093	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	4.826000	0.62715	0.924000	0.37069	0.528000	0.53228	TAT	.	.	none		0.413	ZNF189-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053447.1	NM_003452	
KIF16B	55614	hgsc.bcm.edu	37	20	16352344	16352344	+	Missense_Mutation	SNP	C	C	T	rs75989969	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr20:16352344C>T	ENST00000354981.2	-	21	3570	c.3413G>A	c.(3412-3414)aGt>aAt	p.S1138N	KIF16B_ENST00000378003.2_Missense_Mutation_p.S364N|KIF16B_ENST00000408042.1_Missense_Mutation_p.S1138N|KIF16B_ENST00000355755.3_Missense_Mutation_p.S1138N	NM_001199865.1|NM_024704.4	NP_001186794.1|NP_078980.3	Q96L93	KI16B_HUMAN	kinesin family member 16B	1138					ATP catabolic process (GO:0006200)|early endosome to late endosome transport (GO:0045022)|endoderm development (GO:0007492)|epidermal growth factor receptor signaling pathway (GO:0007173)|fibroblast growth factor receptor signaling pathway (GO:0008543)|formation of primary germ layer (GO:0001704)|Golgi to endosome transport (GO:0006895)|microtubule-based movement (GO:0007018)|receptor catabolic process (GO:0032801)|regulation of receptor recycling (GO:0001919)	early endosome (GO:0005769)|endosome (GO:0005768)|kinesin complex (GO:0005871)|membrane (GO:0016020)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|phosphatidylinositol-3,4,5-trisphosphate binding (GO:0005547)|phosphatidylinositol-3,4-bisphosphate binding (GO:0043325)|phosphatidylinositol-3,5-bisphosphate binding (GO:0080025)|phosphatidylinositol-3-phosphate binding (GO:0032266)|plus-end-directed microtubule motor activity (GO:0008574)			NS(2)|breast(1)|central_nervous_system(1)|cervix(1)|endometrium(3)|kidney(6)|large_intestine(15)|lung(24)|ovary(1)|prostate(15)|skin(3)|upper_aerodigestive_tract(2)	74						GCAGCCTTCACTAATCACACG	0.408													c|||	65	0.0129792	0.0454	0.0072	5008	,	,		20897	0.0		0.0	False		,,,				2504	0.0				p.S1138N		Atlas-SNP	.											.	KIF16B	305	.	0			c.G3413A						PASS	.	T	ASN/SER,ASN/SER,ASN/SER	148,4258	103.0+/-141.5	2,144,2057	143.0	118.0	126.0		3260,3413,3413	3.8	0.0	20	dbSNP_131	126	4,8596	3.7+/-12.6	0,4,4296	yes	missense,missense,missense	KIF16B	NM_001199865.1,NM_001199866.1,NM_024704.4	46,46,46	2,148,6353	TT,TC,CC		0.0465,3.3591,1.1687	benign,benign,benign	1087/1267,1138/1393,1138/1318	16352344	152,12854	2203	4300	6503	SO:0001583	missense	55614	exon21			CCTTCACTAATCA	AK000142	CCDS13122.1, CCDS56178.1	20p11.23	2008-03-03	2008-03-03	2008-03-03	ENSG00000089177	ENSG00000089177		"""Kinesins"""	15869	protein-coding gene	gene with protein product			"""chromosome 20 open reading frame 23"""	C20orf23		16084724, 16782399	Standard	NM_024704		Approved	FLJ20135, dJ971B4.1, SNX23	uc010gci.2	Q96L93	OTTHUMG00000031927	ENST00000354981.2:c.3413G>A	20.37:g.16352344C>T	ENSP00000347076:p.Ser1138Asn	123.0	0.0	0		155.0	80.0	0.516129	NM_001199866	A6NKJ9|A7E2A8|B1AKG3|B1AKT7|C9JDN5|C9JI52|C9JSM8|C9JWJ7|Q2TBF5|Q5HYC0|Q5HYK1|Q5JWW3|Q5TFK5|Q86VL9|Q86YS5|Q8IYU0|Q9BQJ8|Q9BQM0|Q9BQM1|Q9BQM5|Q9H5U0|Q9HCI2|Q9NXN9	Missense_Mutation	SNP	ENST00000354981.2	37	CCDS13122.1	30	0.013736263736263736	25	0.0508130081300813	5	0.013812154696132596	0	0.0	0	0.0	c	10.36	1.329121	0.24167	0.033591	4.65E-4	ENSG00000089177	ENST00000354981;ENST00000355755;ENST00000377997;ENST00000378003;ENST00000408042	T;T;T;T	0.70986	-0.53;-0.52;2.51;-0.47	5.8	3.8	0.43715	.	0.550979	0.21055	N	0.080929	T	0.16085	0.0387	L	0.29908	0.895	0.09310	N	1	B;B;B	0.02656	0.0;0.0;0.0	B;B;B	0.08055	0.003;0.001;0.0	T	0.07028	-1.0794	10	0.18710	T	0.47	.	8.6668	0.34125	0.0:0.6904:0.0:0.3096	.	1138;1138;1138	Q96L93-2;Q96L93-6;Q96L93	.;.;KI16B_HUMAN	N	1138;1138;982;364;1138	ENSP00000347076:S1138N;ENSP00000347995:S1138N;ENSP00000367242:S364N;ENSP00000384164:S1138N	ENSP00000347076:S1138N	S	-	2	0	KIF16B	16300344	0.000000	0.05858	0.000000	0.03702	0.004000	0.04260	0.629000	0.24538	0.743000	0.32719	-1.124000	0.02001	AGT	C|0.989;T|0.011	0.011	strong		0.408	KIF16B-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078104.2	NM_017683	
DOCK3	1795	hgsc.bcm.edu	37	3	51386357	51386357	+	Silent	SNP	C	C	T			TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr3:51386357C>T	ENST00000266037.9	+	39	4013	c.3990C>T	c.(3988-3990)ctC>ctT	p.L1330L		NM_004947.4	NP_004938.1	Q8IZD9	DOCK3_HUMAN	dedicator of cytokinesis 3	1330	DHR-2.				small GTPase mediated signal transduction (GO:0007264)	cytoplasm (GO:0005737)	guanyl-nucleotide exchange factor activity (GO:0005085)			breast(2)|cervix(1)|endometrium(10)|kidney(4)|lung(22)|prostate(5)|urinary_tract(1)	45				BRCA - Breast invasive adenocarcinoma(193;0.00105)|KIRC - Kidney renal clear cell carcinoma(197;0.00449)|Kidney(197;0.00518)		ACCAGAGCCTCAGCTGGATTC	0.562																																					p.L1330L		Atlas-SNP	.											.	DOCK3	397	.	0			c.C3990T						PASS	.						67.0	67.0	67.0					3																	51386357		1965	4145	6110	SO:0001819	synonymous_variant	1795	exon39			GAGCCTCAGCTGG	AB002297	CCDS46835.1	3p21	2008-02-01			ENSG00000088538	ENSG00000088538			2989	protein-coding gene	gene with protein product		603123	"""dedicator of cyto-kinesis 3"""			9205841	Standard	NM_004947		Approved	KIAA0299, MOCA, PBP	uc011bds.2	Q8IZD9	OTTHUMG00000156892	ENST00000266037.9:c.3990C>T	3.37:g.51386357C>T		114.0	0.0	0		120.0	63.0	0.525	NM_004947	O15017	Silent	SNP	ENST00000266037.9	37	CCDS46835.1																																																																																			.	.	none		0.562	DOCK3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000346478.5	NM_004947	
PER3	8863	hgsc.bcm.edu	37	1	7890153	7890153	+	Missense_Mutation	SNP	C	C	T	rs144178755	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr1:7890153C>T	ENST00000361923.2	+	18	3294	c.3119C>T	c.(3118-3120)aCt>aTt	p.T1040I	RP3-467L1.4_ENST00000451646.1_RNA|PER3_ENST00000377532.3_Missense_Mutation_p.T1049I	NM_016831.1	NP_058515.1	P56645	PER3_HUMAN	period circadian clock 3	1040	5 X 18 AA tandem repeats of S-[HP]-[AP]- T-[AT]-[GST]-[ATV]-L-S-[MT]-G-[LS]-P-P- [MRS]-[EKR]-[NST]-P.|Ser-rich.				circadian regulation of gene expression (GO:0032922)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|regulation of circadian sleep/wake cycle, sleep (GO:0045187)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	signal transducer activity (GO:0004871)			breast(4)|central_nervous_system(3)|cervix(2)|endometrium(2)|kidney(2)|large_intestine(9)|lung(8)|ovary(1)|pancreas(1)|prostate(2)|skin(3)|upper_aerodigestive_tract(2)	39	Ovarian(185;0.0634)|all_lung(157;0.178)	all_epithelial(116;9.35e-21)|all_lung(118;7.57e-07)|Lung NSC(185;4.52e-06)|Renal(390;0.000147)|Breast(487;0.00086)|Colorectal(325;0.000959)|Hepatocellular(190;0.00825)|Ovarian(437;0.0253)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0234)|all cancers(8;8.58e-70)|GBM - Glioblastoma multiforme(8;1.81e-35)|Colorectal(212;2.06e-07)|COAD - Colon adenocarcinoma(227;1.92e-05)|Kidney(185;7.18e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000472)|STAD - Stomach adenocarcinoma(132;0.00118)|KIRC - Kidney renal clear cell carcinoma(229;0.00122)|READ - Rectum adenocarcinoma(331;0.0649)		TCCCATCCTACTGCCACTGTT	0.547													C|||	2	0.000399361	0.0	0.0029	5008	,	,		18916	0.0		0.0	False		,,,				2504	0.0				p.T1040I		Atlas-SNP	.											.	PER3	95	.	0			c.C3119T						PASS	.	C	ILE/THR	0,4406		0,0,2203	142.0	115.0	124.0		3119	0.4	0.0	1	dbSNP_134	124	24,8576	17.3+/-56.4	0,24,4276	yes	missense	PER3	NM_016831.1	89	0,24,6479	TT,TC,CC		0.2791,0.0,0.1845	benign	1040/1202	7890153	24,12982	2203	4300	6503	SO:0001583	missense	8863	exon18			ATCCTACTGCCAC	BC026102	CCDS89.1, CCDS72695.1	1p36.23	2012-12-13	2012-12-13		ENSG00000049246	ENSG00000049246			8847	protein-coding gene	gene with protein product		603427	"""period (Drosophila) homolog 3"", ""period homolog 3 (Drosophila)"""			9427249	Standard	XM_005263520		Approved		uc001aoo.3	P56645	OTTHUMG00000001216	ENST00000361923.2:c.3119C>T	1.37:g.7890153C>T	ENSP00000355031:p.Thr1040Ile	97.0	0.0	0		141.0	74.0	0.524823	NM_016831	Q5H8X4|Q5H8X5|Q969K6|Q96S77|Q96S78|Q9C0J3|Q9NSP9|Q9UGU8	Missense_Mutation	SNP	ENST00000361923.2	37	CCDS89.1	1	4.578754578754579E-4	0	0.0	1	0.0027624309392265192	0	0.0	0	0.0	C	7.381	0.628779	0.14257	0.0	0.002791	ENSG00000049246	ENST00000377532;ENST00000361923;ENST00000539773	T;T	0.11495	2.77;2.83	1.61	0.359	0.16088	Period circadian-like, C-terminal (1);	7.092960	0.01606	U	0.022261	T	0.08891	0.0220	L	0.34521	1.04	0.09310	N	1	B;B;B;B;B	0.30889	0.075;0.054;0.299;0.248;0.054	B;B;B;B;B	0.27500	0.013;0.05;0.08;0.067;0.05	T	0.31166	-0.9953	10	0.52906	T	0.07	.	2.8786	0.05640	0.0:0.6047:0.0:0.3953	.	89;1040;1049;1049;1040	B4DR65;A2I2N5;A6H8X0;P56645-2;P56645	.;.;.;.;PER3_HUMAN	I	1049;1040;233	ENSP00000366755:T1049I;ENSP00000355031:T1040I	ENSP00000355031:T1040I	T	+	2	0	PER3	7812740	0.086000	0.21541	0.017000	0.16124	0.014000	0.08584	-0.079000	0.11357	0.692000	0.31613	0.305000	0.20034	ACT	C|0.998;T|0.002	0.002	strong		0.547	PER3-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000003607.1	NM_016831	
SLC25A10	1468	hgsc.bcm.edu	37	17	79686879	79686879	+	Missense_Mutation	SNP	G	G	A			TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr17:79686879G>A	ENST00000350690.5	+	10	810	c.724G>A	c.(724-726)Gtg>Atg	p.V242M	SLC25A10_ENST00000571730.1_Missense_Mutation_p.V397M|SLC25A10_ENST00000541223.1_Missense_Mutation_p.V397M|SLC25A10_ENST00000545862.1_Missense_Mutation_p.V199M|SLC25A10_ENST00000331531.5_Missense_Mutation_p.V251M	NM_001270953.1|NM_012140.4	NP_001257882.1|NP_036272.2	Q9UBX3	DIC_HUMAN	solute carrier family 25 (mitochondrial carrier; dicarboxylate transporter), member 10	242					carbohydrate metabolic process (GO:0005975)|cellular nitrogen compound metabolic process (GO:0034641)|dicarboxylic acid transport (GO:0006835)|gluconeogenesis (GO:0006094)|glucose metabolic process (GO:0006006)|ion transport (GO:0006811)|mitochondrial transport (GO:0006839)|small molecule metabolic process (GO:0044281)|sulfide oxidation, using sulfide:quinone oxidoreductase (GO:0070221)|sulfur amino acid catabolic process (GO:0000098)|sulfur amino acid metabolic process (GO:0000096)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|mitochondrial inner membrane (GO:0005743)|nucleus (GO:0005634)	dicarboxylic acid transmembrane transporter activity (GO:0005310)	p.V242L(1)		endometrium(1)|lung(9)|ovary(1)|prostate(1)|skin(2)	14	all_neural(118;0.0878)|Ovarian(332;0.12)|all_lung(278;0.23)		BRCA - Breast invasive adenocarcinoma(99;0.0117)|OV - Ovarian serous cystadenocarcinoma(97;0.0955)		Succinic acid(DB00139)	CCACTGCGCCGTGGAGACAGC	0.602																																					p.V251M		Atlas-SNP	.											SLC25A10,NS,carcinoma,0,1	SLC25A10	24	1	1	Substitution - Missense(1)	lung(1)	c.G751A						PASS	.						156.0	180.0	172.0					17																	79686879		2203	4300	6503	SO:0001583	missense	1468	exon10			TGCGCCGTGGAGA		CCDS11786.1, CCDS59301.1, CCDS74176.1	17q25.3	2013-07-15			ENSG00000183048	ENSG00000183048		"""Solute carriers"""	10980	protein-coding gene	gene with protein product		606794		DIC		9733776, 10072589	Standard	NM_001270953		Approved		uc031rew.1	Q9UBX3	OTTHUMG00000178173	ENST00000350690.5:c.724G>A	17.37:g.79686879G>A	ENSP00000345580:p.Val242Met	128.0	0.0	0		157.0	75.0	0.477707	NM_001270888	Q542Z3|Q96BA1|Q96IP1	Missense_Mutation	SNP	ENST00000350690.5	37	CCDS11786.1	.	.	.	.	.	.	.	.	.	.	G	10.33	1.320337	0.23994	.	.	ENSG00000183048	ENST00000541223;ENST00000331531;ENST00000350690;ENST00000545862	T;T;T;T	0.79352	-1.26;-1.26;-1.26;-1.26	4.36	-8.72	0.00845	Mitochondrial carrier domain (2);	0.647462	0.14300	N	0.328340	T	0.48696	0.1514	N	0.25286	0.73	0.09310	N	1	B;B;B	0.20988	0.018;0.05;0.025	B;B;B	0.20184	0.028;0.017;0.028	T	0.46373	-0.9196	10	0.14656	T	0.56	-2.2797	1.993	0.03450	0.3866:0.2096:0.2979:0.1059	.	397;251;242	B4DLN1;Q9UBX3-2;Q9UBX3	.;.;DIC_HUMAN	M	397;251;242;199	ENSP00000439565:V397M;ENSP00000328403:V251M;ENSP00000345580:V242M;ENSP00000446242:V199M	ENSP00000328403:V251M	V	+	1	0	SLC25A10	77297284	0.000000	0.05858	0.004000	0.12327	0.372000	0.29890	-1.990000	0.01479	-1.305000	0.02327	0.655000	0.94253	GTG	.	.	none		0.602	SLC25A10-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000440816.1		
ZKSCAN3	80317	hgsc.bcm.edu	37	6	28331573	28331573	+	Missense_Mutation	SNP	T	T	A	rs213227	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr6:28331573T>A	ENST00000377255.3	+	6	1035	c.738T>A	c.(736-738)caT>caA	p.H246Q	ZKSCAN3_ENST00000341464.5_Missense_Mutation_p.H98Q|ZKSCAN3_ENST00000252211.2_Missense_Mutation_p.H246Q	NM_001242894.1	NP_001229823.1	Q9BRR0	ZKSC3_HUMAN	zinc finger with KRAB and SCAN domains 3	246	KRAB.		H -> Q (in dbSNP:rs213227).		autophagy (GO:0006914)|lysosome organization (GO:0007040)|negative regulation of autophagy (GO:0010507)|negative regulation of cellular senescence (GO:2000773)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of transcription, DNA-templated (GO:0045893)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)			kidney(4)|large_intestine(3)|lung(8)|pancreas(1)|skin(2)|stomach(2)|urinary_tract(1)	21						AGGAGAACCATGGCAGCCTGG	0.463													T|||	244	0.048722	0.1278	0.0346	5008	,	,		18669	0.0119		0.0189	False		,,,				2504	0.0204				p.H246Q		Atlas-SNP	.											.	ZKSCAN3	50	.	0			c.T738A						PASS	.	T	GLN/HIS,GLN/HIS,GLN/HIS	459,3947		25,409,1769	81.0	74.0	76.0		738,294,738	0.5	0.0	6	dbSNP_79	76	135,8465		1,133,4166	yes	missense,missense,missense	ZKSCAN3	NM_001242894.1,NM_001242895.1,NM_024493.3	24,24,24	26,542,5935	AA,AT,TT		1.5698,10.4176,4.5671	benign,benign,benign	246/539,98/391,246/539	28331573	594,12412	2203	4300	6503	SO:0001583	missense	80317	exon5			GAACCATGGCAGC	U71601	CCDS4650.1, CCDS56408.1	6p22.1	2013-01-09	2007-02-20	2007-02-20		ENSG00000189298		"""Zinc fingers, C2H2-type"", ""-"", ""-"", ""-"""	13853	protein-coding gene	gene with protein product		612791	"""zinc finger protein 306"", ""zinc finger protein 309"""	ZNF306, ZNF309		10520746, 22531714	Standard	NM_024493		Approved	Zfp47, ZF47, ZSCAN35	uc003nle.4	Q9BRR0	OTTHUMG00000014521	ENST00000377255.3:c.738T>A	6.37:g.28331573T>A	ENSP00000366465:p.His246Gln	75.0	0.0	0		77.0	34.0	0.441558	NM_024493	B2R8W2|B3KVC0|H7BXX1|Q5VXH3|Q92972|Q9H4T3	Missense_Mutation	SNP	ENST00000377255.3	37	CCDS4650.1	90	0.04120879120879121	53	0.10772357723577236	14	0.03867403314917127	11	0.019230769230769232	12	0.0158311345646438	.	12.65	2.001597	0.35320	0.104176	0.015698	ENSG00000189298	ENST00000252211;ENST00000341464;ENST00000377255	T;T;T	0.01725	4.67;4.67;4.67	2.98	0.46	0.16684	Krueppel-associated box (3);	.	.	.	.	T	0.00468	0.0015	L	0.29908	0.895	0.80722	P	0.0	P	0.35821	0.523	B	0.33392	0.163	T	0.47983	-0.9074	8	0.25751	T	0.34	.	3.8184	0.08825	0.0:0.2424:0.4061:0.3515	rs213227;rs61181430;rs213227	246	Q9BRR0	ZKSC3_HUMAN	Q	246;98;246	ENSP00000252211:H246Q;ENSP00000341883:H98Q;ENSP00000366465:H246Q	ENSP00000252211:H246Q	H	+	3	2	ZKSCAN3	28439552	0.000000	0.05858	0.002000	0.10522	0.920000	0.55202	-0.612000	0.05616	0.086000	0.17137	0.460000	0.39030	CAT	T|0.958;A|0.042	0.042	strong		0.463	ZKSCAN3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040189.3	NM_024493	
LAMA2	3908	hgsc.bcm.edu	37	6	129833568	129833568	+	Missense_Mutation	SNP	C	C	A	rs145842163	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr6:129833568C>A	ENST00000421865.2	+	63	8967	c.8918C>A	c.(8917-8919)aCg>aAg	p.T2973K		NM_000426.3|NM_001079823.1	NP_000417|NP_001073291.1	P24043	LAMA2_HUMAN	laminin, alpha 2	2973	Laminin G-like 5. {ECO:0000255|PROSITE- ProRule:PRU00122}.				axon guidance (GO:0007411)|cell adhesion (GO:0007155)|extracellular matrix organization (GO:0030198)|muscle organ development (GO:0007517)|myelination in peripheral nervous system (GO:0022011)|positive regulation of synaptic transmission, cholinergic (GO:0032224)|regulation of cell adhesion (GO:0030155)|regulation of cell migration (GO:0030334)|regulation of embryonic development (GO:0045995)	basement membrane (GO:0005604)|dendritic spine (GO:0043197)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|laminin-1 complex (GO:0005606)|sarcolemma (GO:0042383)	structural molecule activity (GO:0005198)			NS(2)|biliary_tract(2)|breast(10)|central_nervous_system(1)|endometrium(18)|haematopoietic_and_lymphoid_tissue(2)|kidney(7)|large_intestine(35)|lung(84)|ovary(10)|prostate(4)|skin(9)|stomach(1)|upper_aerodigestive_tract(7)|urinary_tract(2)	194				OV - Ovarian serous cystadenocarcinoma(136;0.178)|all cancers(137;0.245)		ACAACTACAACGACTGGAGTT	0.363																																					p.T2973K		Atlas-SNP	.											.	LAMA2	481	.	0			c.C8918A						PASS	.	C	LYS/THR,LYS/THR	0,4406		0,0,2203	151.0	148.0	149.0		8918,8906	3.9	0.5	6	dbSNP_134	149	3,8597	3.0+/-9.4	0,3,4297	no	missense,missense	LAMA2	NM_000426.3,NM_001079823.1	78,78	0,3,6500	AA,AC,CC		0.0349,0.0,0.0231	probably-damaging,probably-damaging	2973/3123,2969/3119	129833568	3,13003	2203	4300	6503	SO:0001583	missense	3908	exon63			CTACAACGACTGG	Z26653	CCDS5138.1	6q22-q23	2014-09-17	2008-08-01		ENSG00000196569	ENSG00000196569		"""Laminins"""	6482	protein-coding gene	gene with protein product	"""merosin"", ""congenital muscular dystrophy"""	156225		LAMM		2185464, 8294519	Standard	NM_000426		Approved		uc003qbn.3	P24043	OTTHUMG00000015545	ENST00000421865.2:c.8918C>A	6.37:g.129833568C>A	ENSP00000400365:p.Thr2973Lys	149.0	0.0	0		172.0	78.0	0.453488	NM_000426	Q14736|Q5VUM2|Q93022	Missense_Mutation	SNP	ENST00000421865.2	37	CCDS5138.1	.	.	.	.	.	.	.	.	.	.	C	0.026	-1.373086	0.01214	0.0	3.49E-4	ENSG00000196569	ENST00000358023;ENST00000354729;ENST00000421865;ENST00000443169	T	0.76839	-1.05	5.73	3.93	0.45458	Concanavalin A-like lectin/glucanase (1);Concanavalin A-like lectin/glucanase, subgroup (1);Laminin G domain (2);Laminin G, subdomain 2 (1);	0.207503	0.48767	D	0.000175	T	0.47655	0.1457	N	0.17674	0.51	0.09310	N	1	P;P	0.47484	0.896;0.896	P;P	0.44696	0.458;0.458	T	0.37820	-0.9689	9	.	.	.	.	7.8481	0.29437	0.1468:0.7266:0.0:0.1266	.	2974;2973	A6NF00;P24043	.;LAMA2_HUMAN	K	2973;2972;2973;991	ENSP00000400365:T2973K	.	T	+	2	0	LAMA2	129875261	0.986000	0.35501	0.534000	0.28014	0.194000	0.23727	1.787000	0.38704	1.406000	0.46857	0.655000	0.94253	ACG	C|1.000;A|0.000	0.000	strong		0.363	LAMA2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042180.1		
ALPK2	115701	hgsc.bcm.edu	37	18	56204417	56204417	+	Missense_Mutation	SNP	G	G	A			TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr18:56204417G>A	ENST00000361673.3	-	5	3215	c.3002C>T	c.(3001-3003)gCg>gTg	p.A1001V	RP11-1151B14.4_ENST00000591360.1_RNA	NM_052947.3	NP_443179.3	Q86TB3	ALPK2_HUMAN	alpha-kinase 2	1001						nucleus (GO:0005634)	ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)			NS(1)|central_nervous_system(3)|cervix(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(13)|lung(33)|ovary(7)|prostate(1)|skin(10)|upper_aerodigestive_tract(2)	84						CTCCCTGGTCGCTTGAAAGCA	0.488																																					p.A1001V		Atlas-SNP	.											.	ALPK2	487	.	0			c.C3002T						PASS	.						111.0	96.0	101.0					18																	56204417		2203	4299	6502	SO:0001583	missense	115701	exon5			CTGGTCGCTTGAA	AY044450	CCDS11966.2	18q21.31	2013-01-11			ENSG00000198796	ENSG00000198796		"""Immunoglobulin superfamily / I-set domain containing"""	20565	protein-coding gene	gene with protein product	"""heart alpha-kinase"""					10021370	Standard	NM_052947		Approved	HAK	uc002lhj.4	Q86TB3	OTTHUMG00000132755	ENST00000361673.3:c.3002C>T	18.37:g.56204417G>A	ENSP00000354991:p.Ala1001Val	143.0	0.0	0		91.0	43.0	0.472527	NM_052947	Q6ZUX0|Q8NAT5|Q96L95	Missense_Mutation	SNP	ENST00000361673.3	37	CCDS11966.2	.	.	.	.	.	.	.	.	.	.	G	1.106	-0.659520	0.03454	.	.	ENSG00000198796	ENST00000361673	T	0.37752	1.18	5.08	-2.78	0.05859	.	4.754620	0.00550	N	0.000240	T	0.07098	0.0180	N	0.00289	-1.7	0.09310	N	1	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.39722	-0.9600	10	0.02654	T	1	-3.639	1.1061	0.01694	0.3981:0.281:0.1835:0.1373	.	1001;1001	Q86TB3-2;Q86TB3	.;ALPK2_HUMAN	V	1001	ENSP00000354991:A1001V	ENSP00000354991:A1001V	A	-	2	0	ALPK2	54355397	0.000000	0.05858	0.001000	0.08648	0.019000	0.09904	0.073000	0.14640	-0.244000	0.09639	-0.383000	0.06682	GCG	.	.	none		0.488	ALPK2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256126.1	NM_052947	
ABCC3	8714	hgsc.bcm.edu	37	17	48745035	48745035	+	Silent	SNP	A	A	C	rs11568601	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	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		71.0	0.0	0		54.0	24.0	0.444444	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	
AGTR1	185	hgsc.bcm.edu	37	3	148459129	148459129	+	Missense_Mutation	SNP	A	A	T	rs201745152		TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr3:148459129A>T	ENST00000497524.1	+	2	698	c.307A>T	c.(307-309)Att>Ttt	p.I103F	AGTR1_ENST00000404754.2_Missense_Mutation_p.I103F|AGTR1_ENST00000402260.1_Missense_Mutation_p.I103F|AGTR1_ENST00000475347.1_Missense_Mutation_p.I103F|AGTR1_ENST00000461609.1_Missense_Mutation_p.I103F|AGTR1_ENST00000542281.1_Missense_Mutation_p.I103F|AGTR1_ENST00000349243.3_Missense_Mutation_p.I103F|AGTR1_ENST00000418473.2_Missense_Mutation_p.I103F|AGTR1_ENST00000474935.1_Missense_Mutation_p.I103F	NM_009585.3	NP_033611.1	P30556	AGTR1_HUMAN	angiotensin II receptor, type 1	103					angiotensin-activated signaling pathway (GO:0038166)|calcium-mediated signaling (GO:0019722)|cell chemotaxis (GO:0060326)|G-protein coupled receptor signaling pathway (GO:0007186)|kidney development (GO:0001822)|low-density lipoprotein particle remodeling (GO:0034374)|phospholipase C-activating angiotensin-activated signaling pathway (GO:0086097)|phospholipase C-activating G-protein coupled receptor signaling pathway (GO:0007200)|positive regulation of cellular protein metabolic process (GO:0032270)|positive regulation of cholesterol esterification (GO:0010873)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|positive regulation of cytosolic calcium ion concentration involved in phospholipase C-activating G-protein coupled signaling pathway (GO:0051482)|positive regulation of inflammatory response (GO:0050729)|positive regulation of macrophage derived foam cell differentiation (GO:0010744)|positive regulation of NAD(P)H oxidase activity (GO:0033864)|positive regulation of phospholipase A2 activity (GO:0032430)|positive regulation of reactive oxygen species metabolic process (GO:2000379)|regulation of blood vessel size by renin-angiotensin (GO:0002034)|regulation of cell growth (GO:0001558)|regulation of cell proliferation (GO:0042127)|regulation of inflammatory response (GO:0050727)|regulation of renal sodium excretion (GO:0035813)|regulation of systemic arterial blood pressure by renin-angiotensin (GO:0003081)|regulation of vasoconstriction (GO:0019229)|regulation of vasodilation (GO:0042312)|renin-angiotensin regulation of aldosterone production (GO:0002018)|Rho protein signal transduction (GO:0007266)	integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	angiotensin type I receptor activity (GO:0001596)|angiotensin type II receptor activity (GO:0004945)|bradykinin receptor binding (GO:0031711)|protein heterodimerization activity (GO:0046982)			breast(4)|endometrium(3)|kidney(1)|large_intestine(5)|lung(13)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	30			LUSC - Lung squamous cell carcinoma(72;0.127)|Lung(72;0.152)		Azilsartan medoxomil(DB08822)|Candesartan(DB00796)|Eprosartan(DB00876)|Forasartan(DB01342)|Irbesartan(DB01029)|Losartan(DB00678)|Olmesartan(DB00275)|Saprisartan(DB01347)|Tasosartan(DB01349)|Telmisartan(DB00966)|Valsartan(DB00177)	CCTATGTAAGATTGCTTCAGC	0.458																																					p.I138F		Atlas-SNP	.											.	AGTR1	63	.	0			c.A412T						PASS	.						84.0	81.0	82.0					3																	148459129		2203	4300	6503	SO:0001583	missense	185	exon4			TGTAAGATTGCTT	M87290	CCDS3137.1	3q24	2012-08-08	2002-02-20		ENSG00000144891	ENSG00000144891		"""GPCR / Class A : Angiotensin receptors"""	336	protein-coding gene	gene with protein product		106165	"""angiotensin receptor 1B"""	AGTR1B		1550596	Standard	NM_009585		Approved	AT1, AT2R1, AGTR1A, AT2R1A, HAT1R, AG2S, AT2R1B, AT1B	uc003ewh.4	P30556	OTTHUMG00000159503	ENST00000497524.1:c.307A>T	3.37:g.148459129A>T	ENSP00000419422:p.Ile103Phe	28.0	0.0	0		42.0	17.0	0.404762	NM_031850	Q13725|Q8TBK4	Missense_Mutation	SNP	ENST00000497524.1	37	CCDS3137.1	.	.	.	.	.	.	.	.	.	.	A	12.88	2.069842	0.36566	.	.	ENSG00000144891	ENST00000497524;ENST00000349243;ENST00000542281;ENST00000418473;ENST00000404754;ENST00000475347;ENST00000474935;ENST00000461609;ENST00000402260	T;T;T;T;T;T;T;T;T	0.38077	1.16;1.16;1.16;1.16;1.16;1.16;1.16;1.16;1.16	5.48	5.48	0.80851	GPCR, rhodopsin-like superfamily (1);	0.326257	0.29616	N	0.011648	T	0.26195	0.0639	N	0.17345	0.48	0.36625	D	0.875957	B	0.29270	0.24	B	0.38921	0.285	T	0.31943	-0.9925	10	0.48119	T	0.1	-17.5731	6.1718	0.20421	0.5754:0.1271:0.0:0.2975	.	103	P30556	AGTR1_HUMAN	F	103	ENSP00000419422:I103F;ENSP00000273430:I103F;ENSP00000443186:I103F;ENSP00000398832:I103F;ENSP00000385612:I103F;ENSP00000419783:I103F;ENSP00000418084:I103F;ENSP00000418851:I103F;ENSP00000385641:I103F	ENSP00000273430:I103F	I	+	1	0	AGTR1	149941819	1.000000	0.71417	0.999000	0.59377	0.989000	0.77384	1.369000	0.34227	2.071000	0.62044	0.533000	0.62120	ATT	A|0.999;T|0.001	0.001	weak		0.458	AGTR1-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000355807.1		
KANK1	23189	hgsc.bcm.edu	37	9	738503	738503	+	Splice_Site	SNP	C	C	T			TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr9:738503C>T	ENST00000382303.1	+	12	4204	c.3552C>T	c.(3550-3552)gcC>gcT	p.A1184A	KANK1_ENST00000489369.1_3'UTR|KANK1_ENST00000382293.3_Splice_Site_p.A1026A|KANK1_ENST00000382297.2_Splice_Site_p.A1184A	NM_001256876.1	NP_001243805.1	Q14678	KANK1_HUMAN	KN motif and ankyrin repeat domains 1	1184	Interaction with KIF21A.				negative regulation of actin filament polymerization (GO:0030837)|negative regulation of cell migration (GO:0030336)|negative regulation of insulin receptor signaling pathway (GO:0046627)|negative regulation of lamellipodium morphogenesis (GO:2000393)|negative regulation of neuron projection development (GO:0010977)|negative regulation of Rho protein signal transduction (GO:0035024)|negative regulation of ruffle assembly (GO:1900028)|negative regulation of substrate adhesion-dependent cell spreading (GO:1900025)|positive regulation of catenin import into nucleus (GO:0035413)|positive regulation of Wnt signaling pathway (GO:0030177)|positive regulation of wound healing (GO:0090303)|regulation of establishment of cell polarity (GO:2000114)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|ruffle membrane (GO:0032587)	beta-catenin binding (GO:0008013)			autonomic_ganglia(1)|breast(1)|central_nervous_system(1)|cervix(1)|endometrium(7)|kidney(3)|large_intestine(9)|lung(8)|ovary(3)|pancreas(1)|prostate(3)|stomach(4)|upper_aerodigestive_tract(1)	43		Lung NSC(10;9.84e-12)|all_lung(10;1.02e-11)|Breast(48;0.128)		Epithelial(6;0.000153)|OV - Ovarian serous cystadenocarcinoma(1;0.000358)|Lung(218;0.0222)		TGTTAGATGCCGGTATGTTGG	0.517																																					p.A1184A		Atlas-SNP	.											.	KANK1	231	.	0			c.C3552T						PASS	.						103.0	78.0	87.0					9																	738503		2203	4300	6503	SO:0001630	splice_region_variant	23189	exon12			AGATGCCGGTATG	AL833161	CCDS6441.1, CCDS34976.1	9p24.3	2013-01-10	2008-01-29	2008-01-29	ENSG00000107104	ENSG00000107104		"""KN motif and ankyrin repeat domain containing"", ""Ankyrin repeat domain containing"""	19309	protein-coding gene	gene with protein product		607704	"""ankyrin repeat domain 15"""	ANKRD15		12133830, 17996375, 19554261	Standard	NM_015158		Approved	KIAA0172, KANK	uc003zgn.2	Q14678	OTTHUMG00000019434	ENST00000382303.1:c.3553+1C>T	9.37:g.738503C>T		134.0	0.0	0		118.0	52.0	0.440678	NM_001256876	A2A2W8|D3DRH3|Q5W0W0|Q8IY65|Q8WX74	Silent	SNP	ENST00000382303.1	37	CCDS34976.1																																																																																			.	.	none		0.517	KANK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051484.2	NM_015158	Silent
FKBP10	60681	hgsc.bcm.edu	37	17	39976713	39976713	+	Splice_Site	SNP	C	C	T	rs146422412	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr17:39976713C>T	ENST00000321562.4	+	7	1360	c.1256C>T	c.(1255-1257)tCg>tTg	p.S419L	FKBP10_ENST00000544340.1_Splice_Site_p.S192L	NM_021939.3	NP_068758.3	Q96AY3	FKB10_HUMAN	FK506 binding protein 10, 65 kDa	419	PPIase FKBP-type 4. {ECO:0000255|PROSITE- ProRule:PRU00277}.				chaperone-mediated protein folding (GO:0061077)|protein peptidyl-prolyl isomerization (GO:0000413)	endoplasmic reticulum membrane (GO:0005789)	calcium ion binding (GO:0005509)|FK506 binding (GO:0005528)|peptidyl-prolyl cis-trans isomerase activity (GO:0003755)			cervix(1)|endometrium(3)|large_intestine(1)|lung(5)|ovary(1)|prostate(1)|stomach(1)|upper_aerodigestive_tract(1)	14		Breast(137;0.00122)		BRCA - Breast invasive adenocarcinoma(366;0.148)		CTGTTCACCTCGTGGGTCCGG	0.632													C|||	3	0.000599042	0.0008	0.0	5008	,	,		12871	0.0		0.001	False		,,,				2504	0.001				p.S419L		Atlas-SNP	.											.	FKBP10	57	.	0			c.C1256T						PASS	.	C	LEU/SER	2,4404	4.2+/-10.8	0,2,2201	79.0	85.0	83.0		1256	4.9	1.0	17	dbSNP_134	83	9,8591	7.1+/-27.0	0,9,4291	yes	missense-near-splice	FKBP10	NM_021939.3	145	0,11,6492	TT,TC,CC		0.1047,0.0454,0.0846	probably-damaging	419/583	39976713	11,12995	2203	4300	6503	SO:0001630	splice_region_variant	60681	exon7			TCACCTCGTGGGT	AB045981	CCDS11409.1	17q21.2	2014-09-17	2002-08-29		ENSG00000141756	ENSG00000141756		"""EF-hand domain containing"""	18169	protein-coding gene	gene with protein product		607063	"""FK506 binding protein 10 (65 kDa)"""			11071917, 18786928	Standard	NM_021939		Approved	hFKBP65, FLJ22041, FKBP6, FLJ20683, FLJ23833	uc002hxv.2	Q96AY3	OTTHUMG00000133497	ENST00000321562.4:c.1256+1C>T	17.37:g.39976713C>T		72.0	0.0	0		91.0	43.0	0.472527	NM_021939	Q7Z3R4|Q9H3N3|Q9H6J3|Q9H6N5|Q9UF89	Missense_Mutation	SNP	ENST00000321562.4	37	CCDS11409.1	2|2	9.157509157509158E-4|9.157509157509158E-4	0|0	0.0|0.0	0|0	0.0|0.0	0|0	0.0|0.0	2|2	0.002638522427440633|0.002638522427440633	C|C	27.5|27.5	4.836108|4.836108	0.91117|0.91117	4.54E-4|4.54E-4	0.001047|0.001047	ENSG00000141756|ENSG00000141756	ENST00000455106|ENST00000269598;ENST00000321562;ENST00000414352;ENST00000544340	.|T;T	.|0.61980	.|0.06;0.06	4.89|4.89	4.89|4.89	0.63831|0.63831	.|Peptidyl-prolyl cis-trans isomerase, FKBP-type, domain (2);	.|0.000000	.|0.64402	.|D	.|0.000001	D|D	0.86016|0.86016	0.5832|0.5832	H|H	0.96333|0.96333	3.805|3.805	0.80722|0.80722	D|D	1|1	.|D;D	.|0.89917	.|0.99;1.0	.|P;D	.|0.91635	.|0.874;0.999	D|D	0.90651|0.90651	0.4582|0.4582	5|10	.|0.72032	.|D	.|0.01	-20.3857|-20.3857	18.0311|18.0311	0.89285|0.89285	0.0:1.0:0.0:0.0|0.0:1.0:0.0:0.0	.|.	.|192;419	.|Q9H6J3;Q96AY3	.|.;FKB10_HUMAN	C|L	223|307;419;419;192	.|ENSP00000317232:S419L;ENSP00000442009:S192L	.|ENSP00000269598:S307L	R|S	+|+	1|2	0|0	FKBP10|FKBP10	37230239|37230239	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.966000|0.966000	0.64601|0.64601	5.928000|5.928000	0.70088|0.70088	2.439000|2.439000	0.82584|0.82584	0.655000|0.655000	0.94253|0.94253	CGC|TCG	C|0.999;T|0.001	0.001	strong		0.632	FKBP10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257410.2	NM_021939	Missense_Mutation
SHROOM4	57477	hgsc.bcm.edu	37	X	50350751	50350751	+	Missense_Mutation	SNP	G	G	C	rs201290098		TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chrX:50350751G>C	ENST00000289292.7	-	6	3674	c.3391C>G	c.(3391-3393)Cag>Gag	p.Q1131E	SHROOM4_ENST00000460112.3_Missense_Mutation_p.Q1015E|SHROOM4_ENST00000376020.2_Missense_Mutation_p.Q1131E			Q9ULL8	SHRM4_HUMAN	shroom family member 4	1131	Gln-rich.			KQQ -> QQQQKQQE (in Ref. 1; BAA86516 and 3; AAI51241). {ECO:0000305}.	actin cytoskeleton organization (GO:0030036)|actin filament organization (GO:0007015)|brain development (GO:0007420)|cognition (GO:0050890)	apical plasma membrane (GO:0016324)|basal plasma membrane (GO:0009925)|cortical actin cytoskeleton (GO:0030864)|cytoplasm (GO:0005737)|cytoplasmic side of plasma membrane (GO:0009898)|myosin II complex (GO:0016460)|stress fiber (GO:0001725)	actin filament binding (GO:0051015)			breast(3)|central_nervous_system(1)|cervix(1)|endometrium(6)|kidney(5)|large_intestine(6)|liver(1)|lung(20)|ovary(1)|prostate(4)|skin(3)|upper_aerodigestive_tract(1)	52	Ovarian(276;0.236)					tcctcctcctgttgcttctgc	0.582																																					p.Q1131E		Atlas-SNP	.											.	SHROOM4	171	.	0			c.C3391G						PASS	.						15.0	14.0	15.0					X																	50350751		2199	4294	6493	SO:0001583	missense	57477	exon6			CCTCCTGTTGCTT	AB033028	CCDS35277.1	Xp11.22	2008-02-05			ENSG00000158352	ENSG00000158352			29215	protein-coding gene	gene with protein product		300579				10574462, 16615870	Standard	NR_027121		Approved	KIAA1202	uc004dpe.2	Q9ULL8	OTTHUMG00000021521	ENST00000289292.7:c.3391C>G	X.37:g.50350751G>C	ENSP00000289292:p.Gln1131Glu	66.0	0.0	0		52.0	6.0	0.115385	NM_020717	A7E2X9|D6RFW0|Q96LA0	Missense_Mutation	SNP	ENST00000289292.7	37	CCDS35277.1	.	.	.	.	.	.	.	.	.	.	G	0.015	-1.554911	0.00918	.	.	ENSG00000158352	ENST00000289292;ENST00000376020;ENST00000460112	T;T;T	0.06449	3.3;3.3;3.3	4.89	-0.0454	0.13851	.	1.383290	0.04423	N	0.367895	T	0.03827	0.0108	N	0.24115	0.695	0.09310	N	1	B	0.06786	0.001	B	0.06405	0.002	T	0.36456	-0.9747	10	0.02654	T	1	.	4.0399	0.09746	0.093:0.4322:0.3193:0.1556	.	1131	Q9ULL8	SHRM4_HUMAN	E	1131;1131;1015	ENSP00000289292:Q1131E;ENSP00000365188:Q1131E;ENSP00000421450:Q1015E	ENSP00000289292:Q1131E	Q	-	1	0	SHROOM4	50367491	0.000000	0.05858	0.001000	0.08648	0.009000	0.06853	0.374000	0.20501	-0.047000	0.13423	-0.434000	0.05882	CAG	.	.	weak		0.582	SHROOM4-001	KNOWN	NMD_exception|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056564.4	NM_020717	
ZNF230	7773	hgsc.bcm.edu	37	19	44514422	44514422	+	Splice_Site	SNP	C	C	T	rs146185685		TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr19:44514422C>T	ENST00000429154.2	+	5	459	c.231C>T	c.(229-231)ggC>ggT	p.G77G		NM_006300.3	NP_006291.2	Q9UIE0	ZN230_HUMAN	zinc finger protein 230	77					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			NS(1)|breast(1)|endometrium(2)|large_intestine(2)|lung(10)|skin(1)|stomach(3)|urinary_tract(2)	22		Prostate(69;0.0352)				TCCTTATAGGCGGCAAGACTA	0.428													c|||	1	0.000199681	0.0	0.0	5008	,	,		19264	0.0		0.0	False		,,,				2504	0.001				p.G77G	GBM(175;914 2069 22996 47111 52600)	Atlas-SNP	.											.	ZNF230	44	.	0			c.C231T						PASS	.	T		7,4399	12.9+/-30.5	0,7,2196	51.0	49.0	50.0		231	-2.3	0.0	19	dbSNP_134	50	0,8600		0,0,4300	yes	coding-synonymous-near-splice	ZNF230	NM_006300.3		0,7,6496	TT,TC,CC		0.0,0.1589,0.0538		77/475	44514422	7,12999	2203	4300	6503	SO:0001630	splice_region_variant	7773	exon5			TATAGGCGGCAAG	U95044	CCDS33044.1	19q13.31	2013-01-08				ENSG00000159882		"""Zinc fingers, C2H2-type"", ""-"""	13024	protein-coding gene	gene with protein product							Standard	NM_006300		Approved	FDZF2	uc002oyb.1	Q9UIE0		ENST00000429154.2:c.230-1C>T	19.37:g.44514422C>T		95.0	0.0	0		84.0	40.0	0.47619	NM_006300	O15322|Q504X7|Q86W84|Q9P1U6	Silent	SNP	ENST00000429154.2	37	CCDS33044.1																																																																																			C|1.000;T|0.000	0.000	weak		0.428	ZNF230-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000460456.1		Silent
CASZ1	54897	hgsc.bcm.edu	37	1	10720305	10720305	+	Missense_Mutation	SNP	A	A	G	rs138985539	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr1:10720305A>G	ENST00000377022.3	-	6	1111	c.794T>C	c.(793-795)gTg>gCg	p.V265A	CASZ1_ENST00000344008.5_Missense_Mutation_p.V265A|CASZ1_ENST00000478728.2_5'Flank	NM_001079843.2	NP_001073312.1	Q86V15	CASZ1_HUMAN	castor zinc finger 1	265					multicellular organismal development (GO:0007275)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|intracellular membrane-bounded organelle (GO:0043231)|nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			breast(1)|central_nervous_system(2)|cervix(1)|endometrium(9)|large_intestine(13)|lung(18)|ovary(2)|prostate(5)|skin(2)|urinary_tract(1)	54	Ovarian(185;0.203)|all_lung(157;0.204)	Lung NSC(185;4.96e-06)|all_lung(284;1.22e-05)|Renal(390;0.000147)|Breast(348;0.00093)|Colorectal(325;0.00212)|Hepatocellular(190;0.00913)|Ovarian(437;0.0229)|Myeloproliferative disorder(586;0.0255)	STAD - Stomach adenocarcinoma(5;0.0224)	UCEC - Uterine corpus endometrioid carcinoma (279;0.0265)|Colorectal(212;3.54e-08)|COAD - Colon adenocarcinoma(227;9.56e-06)|BRCA - Breast invasive adenocarcinoma(304;0.000219)|Kidney(185;0.00142)|KIRC - Kidney renal clear cell carcinoma(229;0.00381)|READ - Rectum adenocarcinoma(331;0.0419)|STAD - Stomach adenocarcinoma(132;0.0623)		CTCCTTGCCCACCCGCTCCTC	0.692													A|||	15	0.00299521	0.0	0.0072	5008	,	,		13239	0.0		0.005	False		,,,				2504	0.0051				p.V265A		Atlas-SNP	.											.	CASZ1	150	.	0			c.T794C						PASS	.	A	ALA/VAL,ALA/VAL	6,4396	11.4+/-27.6	0,6,2195	28.0	33.0	31.0		794,794	1.3	0.0	1	dbSNP_134	31	84,8516	48.1+/-107.5	0,84,4216	no	missense,missense	CASZ1	NM_001079843.1,NM_017766.3	64,64	0,90,6411	GG,GA,AA		0.9767,0.1363,0.6922	benign,benign	265/1760,265/1167	10720305	90,12912	2201	4300	6501	SO:0001583	missense	54897	exon6			TTGCCCACCCGCT	AK000328	CCDS120.2, CCDS41246.1	1p36.22	2013-01-07	2007-02-02		ENSG00000130940	ENSG00000130940		"""Zinc fingers, C2H2-type"""	26002	protein-coding gene	gene with protein product	"""zinc finger protein 693"", ""survival related gene"""	609895	"""castor homolog 1, zinc finger (Drosophila)"""			16631614, 21252912	Standard	NM_001079843		Approved	FLJ20321, ZNF693, castor, cst, SRG	uc001aro.4	Q86V15	OTTHUMG00000002035	ENST00000377022.3:c.794T>C	1.37:g.10720305A>G	ENSP00000366221:p.Val265Ala	31.0	0.0	0		23.0	11.0	0.478261	NM_001079843	Q078S9|Q2EN02|Q5T9S1|Q6ZNM8|Q8WX49|Q8WX50|Q9BT16|Q9NXC6	Missense_Mutation	SNP	ENST00000377022.3	37	CCDS41246.1	8	0.003663003663003663	0	0.0	4	0.011049723756906077	0	0.0	4	0.005277044854881266	A	0.003	-2.556568	0.00138	0.001363	0.009767	ENSG00000130940	ENST00000377022;ENST00000344008	.	.	.	4.38	1.3	0.21679	.	0.492755	0.20891	N	0.083835	T	0.05502	0.0145	N	0.02539	-0.55	0.09310	N	1	B;B;B;B	0.02656	0.0;0.0;0.0;0.0	B;B;B;B	0.04013	0.001;0.0;0.0;0.0	T	0.33803	-0.9854	9	0.02654	T	1	-4.3668	3.9612	0.09412	0.4216:0.0:0.4186:0.1597	.	289;265;265;265	B7Z1S3;B3KRV8;Q86V15-2;Q86V15	.;.;.;CASZ1_HUMAN	A	265	.	ENSP00000339445:V265A	V	-	2	0	CASZ1	10642892	0.454000	0.25728	0.020000	0.16555	0.084000	0.17831	0.831000	0.27476	0.082000	0.17018	-0.589000	0.04120	GTG	A|0.994;G|0.006	0.006	strong		0.692	CASZ1-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000005673.2	NM_017766	
GPBP1L1	60313	hgsc.bcm.edu	37	1	46105889	46105889	+	Missense_Mutation	SNP	G	G	A			TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr1:46105889G>A	ENST00000290795.3	-	7	1958	c.737C>T	c.(736-738)cCt>cTt	p.P246L	GPBP1L1_ENST00000355105.3_Missense_Mutation_p.P246L			Q9HC44	GPBL1_HUMAN	GC-rich promoter binding protein 1-like 1	246					positive regulation of transcription, DNA-templated (GO:0045893)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|sequence-specific DNA binding transcription factor activity (GO:0003700)		GPBP1L1/MAST2_ENST00000361297(2)	breast(1)|endometrium(2)|large_intestine(4)|lung(10)|ovary(1)|skin(2)|stomach(1)	21	Acute lymphoblastic leukemia(166;0.155)					TACCTTGGAAGGAGGTGGTAC	0.408																																					p.P246L		Atlas-SNP	.											.	GPBP1L1	43	.	0			c.C737T						PASS	.						114.0	110.0	111.0					1																	46105889		2203	4300	6503	SO:0001583	missense	60313	exon8			TTGGAAGGAGGTG		CCDS528.1	1p34.1	2008-02-05			ENSG00000159592	ENSG00000159592			28843	protein-coding gene	gene with protein product						12477932	Standard	NM_021639		Approved	SP192	uc001coq.3	Q9HC44	OTTHUMG00000040990	ENST00000290795.3:c.737C>T	1.37:g.46105889G>A	ENSP00000290795:p.Pro246Leu	78.0	0.0	0		93.0	45.0	0.483871	NM_021639	D3DQ10|Q9H751	Missense_Mutation	SNP	ENST00000290795.3	37	CCDS528.1	.	.	.	.	.	.	.	.	.	.	G	19.85	3.903432	0.72754	.	.	ENSG00000159592	ENST00000290795;ENST00000355105	T;T	0.28069	1.63;1.63	5.85	4.94	0.65067	.	0.053159	0.85682	D	0.000000	T	0.33469	0.0864	M	0.66939	2.045	0.58432	D	0.999999	P	0.35155	0.487	B	0.30943	0.122	T	0.25882	-1.0119	10	0.87932	D	0	-24.6457	15.1693	0.72858	0.0678:0.0:0.9322:0.0	.	246	Q9HC44	GPBL1_HUMAN	L	246	ENSP00000290795:P246L;ENSP00000347224:P246L	ENSP00000290795:P246L	P	-	2	0	GPBP1L1	45878476	1.000000	0.71417	1.000000	0.80357	0.977000	0.68977	9.439000	0.97543	1.478000	0.48253	0.655000	0.94253	CCT	.	.	none		0.408	GPBP1L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000098375.1	NM_021639	
SLC6A1	6529	hgsc.bcm.edu	37	3	11064091	11064091	+	Silent	SNP	G	G	A	rs6344	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr3:11064091G>A	ENST00000287766.4	+	7	1072	c.651G>A	c.(649-651)acG>acA	p.T217T	SLC6A1_ENST00000536032.1_Silent_p.T39T	NM_003042.3	NP_003033.3	P30531	SC6A1_HUMAN	solute carrier family 6 (neurotransmitter transporter), member 1	217					gamma-aminobutyric acid import (GO:0051939)|learning (GO:0007612)|negative regulation of synaptic transmission, GABAergic (GO:0032229)|neurotransmitter secretion (GO:0007269)|positive regulation of gamma-aminobutyric acid secretion (GO:0014054)|protein homooligomerization (GO:0051260)|response to calcium ion (GO:0051592)|response to cocaine (GO:0042220)|response to estradiol (GO:0032355)|response to lead ion (GO:0010288)|response to purine-containing compound (GO:0014074)|response to sucrose (GO:0009744)|response to toxic substance (GO:0009636)|synaptic transmission (GO:0007268)|transmembrane transport (GO:0055085)|transport (GO:0006810)	axon (GO:0030424)|cell surface (GO:0009986)|integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)	gamma-aminobutyric acid:sodium symporter activity (GO:0005332)|neurotransmitter:sodium symporter activity (GO:0005328)			breast(1)|endometrium(2)|large_intestine(6)|lung(6)|ovary(1)|prostate(4)|skin(5)|upper_aerodigestive_tract(1)	26		Ovarian(110;0.0392)		OV - Ovarian serous cystadenocarcinoma(96;0.00099)	Clobazam(DB00349)|Tiagabine(DB00906)	TGGCCATCACGCTGGCCATCG	0.552													G|||	9	0.00179712	0.0008	0.0058	5008	,	,		20511	0.0		0.004	False		,,,				2504	0.0				p.T217T		Atlas-SNP	.											.	SLC6A1	88	.	0			c.G651A						PASS	.						85.0	76.0	79.0					3																	11064091		2203	4300	6503	SO:0001819	synonymous_variant	6529	exon7			CATCACGCTGGCC		CCDS2603.1	3p25.3	2013-07-19	2013-07-19		ENSG00000157103	ENSG00000157103		"""Solute carriers"""	11042	protein-coding gene	gene with protein product	"""GABA transporter 1"""	137165	"""solute carrier family 6 (neurotransmitter transporter, GABA), member 1"""			8530094	Standard	NM_003042		Approved	GAT1, GABATR, GABATHG	uc010hdq.3	P30531	OTTHUMG00000044208	ENST00000287766.4:c.651G>A	3.37:g.11064091G>A		101.0	0.0	0		104.0	59.0	0.567308	NM_003042	Q8N4K8	Silent	SNP	ENST00000287766.4	37	CCDS2603.1																																																																																			A|0.000;G|0.954;T|0.046	0.000	strong		0.552	SLC6A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000102767.2	NM_003042	
PCOLCE2	26577	hgsc.bcm.edu	37	3	142548681	142548681	+	Missense_Mutation	SNP	C	C	T	rs140721173	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr3:142548681C>T	ENST00000295992.3	-	6	1024	c.718G>A	c.(718-720)Gtg>Atg	p.V240M	PCOLCE2_ENST00000485766.1_Intron	NM_013363.3	NP_037495.1	Q9UKZ9	PCOC2_HUMAN	procollagen C-endopeptidase enhancer 2	240	CUB 2. {ECO:0000255|PROSITE- ProRule:PRU00059}.				positive regulation of peptidase activity (GO:0010952)	extracellular vesicular exosome (GO:0070062)	collagen binding (GO:0005518)|heparin binding (GO:0008201)|peptidase activator activity (GO:0016504)			NS(1)|endometrium(1)|large_intestine(11)|lung(15)|ovary(2)|skin(1)|upper_aerodigestive_tract(1)	32						CTCTCAGACACAATTGGCCTA	0.313													C|||	4	0.000798722	0.0	0.0014	5008	,	,		16702	0.0		0.001	False		,,,				2504	0.002				p.V240M		Atlas-SNP	.											.	PCOLCE2	63	.	0			c.G718A						PASS	.	C	MET/VAL	1,4405	2.1+/-5.4	0,1,2202	75.0	78.0	77.0		718	3.5	1.0	3	dbSNP_134	77	8,8592	6.4+/-24.3	0,8,4292	yes	missense	PCOLCE2	NM_013363.3	21	0,9,6494	TT,TC,CC		0.093,0.0227,0.0692	possibly-damaging	240/416	142548681	9,12997	2203	4300	6503	SO:0001583	missense	26577	exon6			CAGACACAATTGG	AF098269	CCDS3127.1	3q21-q24	2008-07-18			ENSG00000163710	ENSG00000163710			8739	protein-coding gene	gene with protein product		607064				10873381	Standard	NM_013363		Approved	PCPE2	uc003evd.3	Q9UKZ9	OTTHUMG00000159312	ENST00000295992.3:c.718G>A	3.37:g.142548681C>T	ENSP00000295992:p.Val240Met	55.0	0.0	0		64.0	34.0	0.53125	NM_013363	B2RCH9|D3DNG4|Q9BRH3	Missense_Mutation	SNP	ENST00000295992.3	37	CCDS3127.1	2	9.157509157509158E-4	0	0.0	1	0.0027624309392265192	0	0.0	1	0.0013192612137203166	C	13.63	2.294192	0.40594	2.27E-4	9.3E-4	ENSG00000163710	ENST00000295992	T	0.30714	1.52	5.3	3.5	0.40072	CUB (5);	0.127288	0.51477	D	0.000085	T	0.37652	0.1011	M	0.69823	2.125	0.80722	D	1	P	0.48407	0.91	P	0.49561	0.615	T	0.10800	-1.0614	10	0.44086	T	0.13	-4.6795	6.5558	0.22460	0.125:0.5656:0.2418:0.0675	.	240	Q9UKZ9	PCOC2_HUMAN	M	240	ENSP00000295992:V240M	ENSP00000295992:V240M	V	-	1	0	PCOLCE2	144031371	0.876000	0.30132	0.999000	0.59377	0.724000	0.41520	-0.015000	0.12634	0.618000	0.30179	-0.226000	0.12346	GTG	C|0.999;T|0.001	0.001	strong		0.313	PCOLCE2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000354509.1	NM_013363	
OR5T2	219464	hgsc.bcm.edu	37	11	56000079	56000079	+	Missense_Mutation	SNP	C	C	T	rs77295387	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr11:56000079C>T	ENST00000313264.4	-	1	658	c.583G>A	c.(583-585)Gct>Act	p.A195T		NM_001004746.1	NP_001004746.1	Q8NGG2	OR5T2_HUMAN	olfactory receptor, family 5, subfamily T, member 2	195						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			endometrium(6)|kidney(1)|large_intestine(5)|lung(22)|ovary(2)|prostate(1)|skin(1)|stomach(3)	41	Esophageal squamous(21;0.00448)					TGTATAGTAGCATGTAAAATG	0.433													c|||	34	0.00678914	0.0015	0.0029	5008	,	,		23389	0.0		0.0268	False		,,,				2504	0.0031				p.A195T		Atlas-SNP	.											.	OR5T2	107	.	0			c.G583A						PASS	.	C	THR/ALA	21,4381	26.2+/-53.5	0,21,2180	193.0	169.0	177.0		583	4.1	0.1	11	dbSNP_131	177	237,8355	96.6+/-158.3	1,235,4060	yes	missense	OR5T2	NM_001004746.1	58	1,256,6240	TT,TC,CC		2.7584,0.4771,1.9855	probably-damaging	195/360	56000079	258,12736	2201	4296	6497	SO:0001583	missense	219464	exon1			TAGTAGCATGTAA	AB065838	CCDS31523.1	11q11	2012-08-09			ENSG00000181718	ENSG00000181718		"""GPCR / Class A : Olfactory receptors"""	15296	protein-coding gene	gene with protein product							Standard	NM_001004746		Approved		uc010rjc.2	Q8NGG2	OTTHUMG00000166851	ENST00000313264.4:c.583G>A	11.37:g.56000079C>T	ENSP00000323688:p.Ala195Thr	207.0	0.0	0		255.0	118.0	0.462745	NM_001004746	B9EGX5|Q6IFC8	Missense_Mutation	SNP	ENST00000313264.4	37	CCDS31523.1	21	0.009615384615384616	1	0.0020325203252032522	1	0.0027624309392265192	0	0.0	19	0.025065963060686015	C	12.15	1.852226	0.32699	0.004771	0.027584	ENSG00000181718	ENST00000313264	T	0.39056	1.1	5.07	4.13	0.48395	GPCR, rhodopsin-like superfamily (1);	0.184659	0.26013	U	0.026862	T	0.23054	0.0557	L	0.41356	1.27	0.09310	N	1	P	0.45986	0.87	P	0.53102	0.718	T	0.11155	-1.0599	10	0.49607	T	0.09	.	12.8779	0.57999	0.3516:0.6484:0.0:0.0	.	195	Q8NGG2	OR5T2_HUMAN	T	195	ENSP00000323688:A195T	ENSP00000323688:A195T	A	-	1	0	OR5T2	55756655	0.000000	0.05858	0.078000	0.20375	0.029000	0.11900	-0.966000	0.03825	1.207000	0.43291	0.478000	0.44815	GCT	C|0.981;T|0.019	0.019	strong		0.433	OR5T2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391598.1	NM_001004746	
BNIP1	662	hgsc.bcm.edu	37	5	172581387	172581387	+	Silent	SNP	A	A	G			TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr5:172581387A>G	ENST00000351486.5	+	3	271	c.240A>G	c.(238-240)gaA>gaG	p.E80E	BNIP1_ENST00000352523.6_Silent_p.E123E|BNIP1_ENST00000393770.4_Silent_p.E80E|BNIP1_ENST00000231668.9_Silent_p.E123E	NM_001205.2	NP_001196.2	Q12981	SEC20_HUMAN	BCL2/adenovirus E1B 19kDa interacting protein 1	80					apoptotic process (GO:0006915)|autophagy (GO:0006914)|endoplasmic reticulum membrane fusion (GO:0016320)|endoplasmic reticulum organization (GO:0007029)|execution phase of apoptosis (GO:0097194)|negative regulation of apoptotic process (GO:0043066)|vesicle-mediated transport (GO:0016192)	cytoplasm (GO:0005737)|endoplasmic reticulum (GO:0005783)|integral component of endoplasmic reticulum membrane (GO:0030176)|intracellular membrane-bounded organelle (GO:0043231)|mitochondrion (GO:0005739)|nuclear envelope (GO:0005635)|SNARE complex (GO:0031201)	SNAP receptor activity (GO:0005484)			breast(1)|kidney(2)|large_intestine(2)|lung(3)|ovary(1)|pancreas(1)|skin(1)	11	Renal(175;0.000159)|Lung NSC(126;0.00199)|all_lung(126;0.00351)	Medulloblastoma(196;0.0208)|all_neural(177;0.0416)	Kidney(164;3.85e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000183)			TACTCCAGGAAGTGGAGAATC	0.478																																					p.E123E		Atlas-SNP	.											.	BNIP1	30	.	0			c.A369G						PASS	.						68.0	66.0	67.0					5																	172581387		2203	4300	6503	SO:0001819	synonymous_variant	662	exon4			CCAGGAAGTGGAG	AF083957	CCDS4384.1, CCDS4385.1, CCDS4386.1, CCDS43400.1	5q33-q34	2008-02-05	2002-08-29		ENSG00000113734	ENSG00000113734			1082	protein-coding gene	gene with protein product		603291	"""BCL2/adenovirus E1B 19kD-interacting protein 1"""			7954800, 15272311	Standard	NM_013979		Approved	Nip1, SEC20	uc003mcj.4	Q12981	OTTHUMG00000130521	ENST00000351486.5:c.240A>G	5.37:g.172581387A>G		206.0	0.0	0		240.0	119.0	0.495833	NM_013979	D3DQM3|D3DQM4|D3DQM5|D3DQM6|O75622|O75623|O75624|Q6K044|Q96FG4	Silent	SNP	ENST00000351486.5	37	CCDS4384.1																																																																																			.	.	none		0.478	BNIP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252939.1	NM_013979	
C1orf106	55765	hgsc.bcm.edu	37	1	200867572	200867572	+	Missense_Mutation	SNP	T	T	A	rs41269923	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr1:200867572T>A	ENST00000367342.4	+	2	499	c.299T>A	c.(298-300)aTc>aAc	p.I100N	C1orf106_ENST00000413687.2_Missense_Mutation_p.I15N	NM_018265.3	NP_060735.3	Q3KP66	CA106_HUMAN	chromosome 1 open reading frame 106	100										endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(1)|lung(6)|ovary(1)|prostate(2)|skin(3)|stomach(1)|urinary_tract(2)	21						AGTGGCATCATCCTGCAGTCT	0.617													T|||	22	0.00439297	0.0	0.0101	5008	,	,		18319	0.0		0.0149	False		,,,				2504	0.0				p.I114N		Atlas-SNP	.											.	C1orf106	59	.	0			c.T341A						PASS	.	T	ASN/ILE,ASN/ILE	7,4399	12.9+/-30.5	0,7,2196	124.0	106.0	112.0		44,299	5.0	1.0	1	dbSNP_127	112	99,8501	55.2+/-116.2	1,97,4202	yes	missense,missense	C1orf106	NM_001142569.2,NM_018265.3	149,149	1,104,6398	AA,AT,TT		1.1512,0.1589,0.815	probably-damaging,probably-damaging	15/579,100/664	200867572	106,12900	2203	4300	6503	SO:0001583	missense	55765	exon2			GCATCATCCTGCA	AK001763	CCDS44292.1	1q32.1	2011-02-15			ENSG00000163362	ENSG00000163362			25599	protein-coding gene	gene with protein product						14702039	Standard	NM_018265		Approved	FLJ10901	uc001gvo.4	Q3KP66	OTTHUMG00000035789	ENST00000367342.4:c.299T>A	1.37:g.200867572T>A	ENSP00000356311:p.Ile100Asn	69.0	0.0	0		83.0	49.0	0.590361	NM_018265	B4E1K9|E9PFY0|Q9NV65|Q9NVI0	Missense_Mutation	SNP	ENST00000367342.4	37		12	0.005494505494505495	0	0.0	4	0.011049723756906077	0	0.0	8	0.010554089709762533	T	20.4	3.991502	0.74703	0.001589	0.011512	ENSG00000163362	ENST00000532631;ENST00000451872;ENST00000367342;ENST00000413687	T;T	0.58358	0.34;0.47	4.97	4.97	0.65823	.	0.128098	0.50627	D	0.000103	T	0.59582	0.2204	L	0.60455	1.87	0.42617	D	0.993332	D	0.71674	0.998	D	0.79784	0.993	T	0.67245	-0.5719	10	0.59425	D	0.04	-13.828	12.1482	0.54036	0.0:0.0:0.0:1.0	rs41269923	100	Q3KP66	CA106_HUMAN	N	15;15;100;15	ENSP00000356311:I100N;ENSP00000392105:I15N	ENSP00000356311:I100N	I	+	2	0	C1orf106	199134195	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	5.875000	0.69660	1.884000	0.54569	0.482000	0.46254	ATC	T|0.993;A|0.007	0.007	strong		0.617	C1orf106-001	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000087057.2	NM_018265	
ATM	472	hgsc.bcm.edu	37	11	108141988	108141988	+	Missense_Mutation	SNP	T	T	C	rs139552233	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr11:108141988T>C	ENST00000452508.2	+	21	3121	c.2932T>C	c.(2932-2934)Tct>Cct	p.S978P	ATM_ENST00000278616.4_Missense_Mutation_p.S978P			Q13315	ATM_HUMAN	ATM serine/threonine kinase	978					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)	p.S978P(1)		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)	CAATGTGTGTTCTTTGTATCG	0.313			"""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)			T|||	3	0.000599042	0.0	0.0	5008	,	,		16164	0.0		0.001	False		,,,				2504	0.002				p.S978P		Atlas-SNP	.	yes	Rec	yes	Ataxia-telangiectasia	11	11q22.3	472	ataxia telangiectasia mutated		"""L, O"""	ATM_ENST00000278616,colon,carcinoma,-2,5	ATM	1657	5	1	Substitution - Missense(1)	haematopoietic_and_lymphoid_tissue(1)	c.T2932C						scavenged	.	T	PRO/SER	0,4402		0,0,2201	90.0	88.0	89.0		2932	5.5	1.0	11	dbSNP_134	89	4,8592	3.7+/-12.6	0,4,4294	yes	missense	ATM	NM_000051.3	74	0,4,6495	CC,CT,TT		0.0465,0.0,0.0308	probably-damaging	978/3057	108141988	4,12994	2201	4298	6499	SO:0001583	missense	472	exon20	Familial Cancer Database	AT, Louis-Bar syndrome	GTGTGTTCTTTGT	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.2932T>C	11.37:g.108141988T>C	ENSP00000388058:p.Ser978Pro	79.0	1.0	0.0126582		75.0	35.0	0.466667	NM_000051	B2RNX5|O15429|Q12758|Q16551|Q93007|Q9NP02|Q9UCX7	Missense_Mutation	SNP	ENST00000452508.2	37	CCDS31669.1	1	4.578754578754579E-4	0	0.0	0	0.0	0	0.0	1	0.0013192612137203166	T	24.8	4.565967	0.86439	0.0	4.65E-4	ENSG00000149311	ENST00000527805;ENST00000278616;ENST00000452508	T;T;T	0.74106	-0.81;-0.81;-0.81	5.5	5.5	0.81552	Armadillo-type fold (1);	0.102849	0.64402	D	0.000001	D	0.85388	0.5685	M	0.70275	2.135	0.45567	D	0.998516	D	0.89917	1.0	D	0.87578	0.998	D	0.86822	0.2005	10	0.66056	D	0.02	.	15.8922	0.79309	0.0:0.0:0.0:1.0	.	978	Q13315	ATM_HUMAN	P	978	ENSP00000435747:S978P;ENSP00000278616:S978P;ENSP00000388058:S978P	ENSP00000278616:S978P	S	+	1	0	ATM	107647198	1.000000	0.71417	1.000000	0.80357	0.972000	0.66771	6.434000	0.73408	2.203000	0.70933	0.459000	0.35465	TCT	T|1.000;C|0.000	0.000	strong		0.313	ATM-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000389938.1	NM_000051	
RYR3	6263	hgsc.bcm.edu	37	15	33842400	33842400	+	Silent	SNP	A	A	T	rs41279202	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr15:33842400A>T	ENST00000389232.4	+	10	925	c.855A>T	c.(853-855)cgA>cgT	p.R285R	RYR3_ENST00000415757.3_Silent_p.R285R	NM_001036.3	NP_001027.3	Q15413	RYR3_HUMAN	ryanodine receptor 3	285	MIR 4. {ECO:0000255|PROSITE- ProRule:PRU00131}.				calcium ion transmembrane transport (GO:0070588)|calcium ion transport (GO:0006816)|cellular response to ATP (GO:0071318)|cellular response to caffeine (GO:0071313)|cellular response to calcium ion (GO:0071277)|cellular response to magnesium ion (GO:0071286)|ion transmembrane transport (GO:0034220)|negative regulation of cytosolic calcium ion concentration (GO:0051481)|protein homotetramerization (GO:0051289)|striated muscle contraction (GO:0006941)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|junctional membrane complex (GO:0030314)|perinuclear region of cytoplasm (GO:0048471)|sarcoplasmic reticulum membrane (GO:0033017)	calcium ion binding (GO:0005509)|calcium-induced calcium release activity (GO:0048763)|calcium-release channel activity (GO:0015278)|ryanodine-sensitive calcium-release channel activity (GO:0005219)			NS(3)|breast(9)|central_nervous_system(8)|cervix(2)|endometrium(29)|haematopoietic_and_lymphoid_tissue(2)|kidney(18)|large_intestine(55)|lung(148)|ovary(7)|pancreas(1)|prostate(13)|skin(4)|stomach(1)|upper_aerodigestive_tract(8)|urinary_tract(3)	311		all_lung(180;7.18e-09)		all cancers(64;8.95e-12)|GBM - Glioblastoma multiforme(186;0.00109)|BRCA - Breast invasive adenocarcinoma(123;0.0363)		AGGCTTTCCGACTCCGGCATC	0.483													A|||	68	0.0135783	0.0	0.0187	5008	,	,		17879	0.001		0.0447	False		,,,				2504	0.0092				p.R285R		Atlas-SNP	.											.	RYR3	760	.	0			c.A855T						PASS	.	A		34,4350	34.3+/-65.2	0,34,2158	40.0	42.0	41.0		855	-1.1	1.0	15	dbSNP_127	41	369,8219	120.2+/-179.5	8,353,3933	no	coding-synonymous	RYR3	NM_001036.3		8,387,6091	TT,TA,AA		4.2967,0.7755,3.1067		285/4871	33842400	403,12569	2192	4294	6486	SO:0001819	synonymous_variant	6263	exon10			TTTCCGACTCCGG		CCDS45210.1, CCDS58351.1	15q14-q15	2013-01-10				ENSG00000198838		"""Ion channels / Ryanodine receptors"", ""EF-hand domain containing"""	10485	protein-coding gene	gene with protein product		180903				8276408	Standard	NM_001036		Approved		uc001zhi.3	Q15413		ENST00000389232.4:c.855A>T	15.37:g.33842400A>T		66.0	0.0	0		103.0	46.0	0.446602	NM_001243996	O15175|Q15412	Silent	SNP	ENST00000389232.4	37	CCDS45210.1																																																																																			A|0.970;T|0.030	0.030	strong		0.483	RYR3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000417514.1		
TMEM216	51259	hgsc.bcm.edu	37	11	61161359	61161359	+	Missense_Mutation	SNP	T	T	C			TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr11:61161359T>C	ENST00000515837.2	+	3	1085	c.140T>C	c.(139-141)gTc>gCc	p.V47A	TMEM216_ENST00000334888.5_Missense_Mutation_p.V47A|TMEM216_ENST00000398979.3_5'UTR			Q9P0N5	TM216_HUMAN	transmembrane protein 216	47					cilium assembly (GO:0042384)|cilium morphogenesis (GO:0060271)	cilium (GO:0005929)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|integral component of membrane (GO:0016021)|TCTN-B9D complex (GO:0036038)				endometrium(1)|large_intestine(2)|lung(1)|prostate(2)	6						TTGGCAGGTGTCCTGCTACCA	0.433																																					p.V47A		Atlas-SNP	.											.	TMEM216	14	.	0			c.T140C						PASS	.						84.0	93.0	90.0					11																	61161359		1968	4156	6124	SO:0001583	missense	51259	exon3			CAGGTGTCCTGCT		CCDS53640.1	11q13.1	2014-09-17			ENSG00000187049	ENSG00000187049			25018	protein-coding gene	gene with protein product		613277	"""cerebello-oculo-renal syndrome 2"", ""Meckel syndrome, type 2"""	CORS2, MKS2		11042152, 20036350, 20512146	Standard	NM_016499		Approved	MGC13379, HSPC244, JBTS2	uc021qkf.1	Q9P0N5		ENST00000515837.2:c.140T>C	11.37:g.61161359T>C	ENSP00000440638:p.Val47Ala	200.0	0.0	0		231.0	91.0	0.393939	NM_001173990	A8MZ23|B7Z8N1	Missense_Mutation	SNP	ENST00000515837.2	37	CCDS53640.1	.	.	.	.	.	.	.	.	.	.	T	7.289	0.610705	0.14066	.	.	ENSG00000187049	ENST00000515837;ENST00000334888	D;D	0.88124	-2.34;-2.34	5.95	5.95	0.96441	.	.	.	.	.	T	0.77212	0.4097	N	0.14661	0.345	0.28495	N	0.914285	B	0.11235	0.004	B	0.12837	0.008	T	0.63229	-0.6684	9	0.15499	T	0.54	.	13.9469	0.64091	0.0:0.0:0.0:1.0	.	40	Q9P0N5	TM216_HUMAN	A	47	ENSP00000440638:V47A;ENSP00000334844:V47A	ENSP00000334844:V47A	V	+	2	0	TMEM216	60917935	0.988000	0.35896	0.929000	0.37066	0.003000	0.03518	3.612000	0.54142	2.279000	0.76181	0.533000	0.62120	GTC	.	.	none		0.433	TMEM216-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000398430.1	NM_016499	
UNC45A	55898	hgsc.bcm.edu	37	15	91496233	91496233	+	Missense_Mutation	SNP	G	G	A	rs149872991		TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr15:91496233G>A	ENST00000418476.2	+	18	2418	c.2378G>A	c.(2377-2379)cGg>cAg	p.R793Q	AC068831.6_ENST00000553321.1_RNA|UNC45A_ENST00000394275.2_Missense_Mutation_p.R778Q|RCCD1_ENST00000555155.1_5'Flank|RCCD1_ENST00000556618.1_5'Flank|RCCD1_ENST00000394258.2_5'Flank	NM_018671.3	NP_061141.2	Q9H3U1	UN45A_HUMAN	unc-45 homolog A (C. elegans)	793					cell differentiation (GO:0030154)|chaperone-mediated protein folding (GO:0061077)|muscle organ development (GO:0007517)	cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|nucleus (GO:0005634)				breast(1)|endometrium(4)|kidney(1)|large_intestine(5)|lung(7)|ovary(3)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	25	Lung NSC(78;0.0771)|all_lung(78;0.137)		Lung(145;0.189)			ATGATCCGCCGGGCAGCCACG	0.582													g|||	1	0.000199681	0.0	0.0	5008	,	,		22008	0.0		0.001	False		,,,				2504	0.0				p.R793Q		Atlas-SNP	.											.	UNC45A	57	.	0			c.G2378A						PASS	.		GLN/ARG,GLN/ARG	1,4395	2.1+/-5.4	0,1,2197	83.0	62.0	69.0		2333,2378	4.9	1.0	15	dbSNP_134	69	7,8589	5.7+/-21.5	0,7,4291	yes	missense,missense	UNC45A	NM_001039675.1,NM_018671.3	43,43	0,8,6488	AA,AG,GG		0.0814,0.0227,0.0616	benign,benign	778/930,793/945	91496233	8,12984	2198	4298	6496	SO:0001583	missense	55898	exon18			TCCGCCGGGCAGC		CCDS10367.1, CCDS42082.1	15q26.1	2008-02-05			ENSG00000140553	ENSG00000140553			30594	protein-coding gene	gene with protein product	"""smooth muscle cell associated protein-1"""	611219				12356907	Standard	XM_005254963		Approved	SMAP-1, GC-UNC45	uc002bqg.3	Q9H3U1	OTTHUMG00000141261	ENST00000418476.2:c.2378G>A	15.37:g.91496233G>A	ENSP00000407487:p.Arg793Gln	42.0	0.0	0		49.0	27.0	0.55102	NM_018671	A8K6F7|Q7L3Y6|Q9H3U8|Q9NSE8|Q9NSE9	Missense_Mutation	SNP	ENST00000418476.2	37	CCDS10367.1	.	.	.	.	.	.	.	.	.	.	g	15.13	2.742516	0.49151	2.27E-4	8.14E-4	ENSG00000140553	ENST00000394275;ENST00000418476	T;T	0.49720	0.77;0.77	4.88	4.88	0.63580	Armadillo-like helical (1);Armadillo-type fold (1);	0.457993	0.23413	N	0.048457	T	0.28830	0.0715	N	0.25992	0.78	0.37116	D	0.900608	P;P	0.48640	0.913;0.913	B;B	0.33799	0.17;0.17	T	0.30909	-0.9962	10	0.40728	T	0.16	-27.8398	10.8602	0.46823	0.0:0.0:0.7065:0.2935	.	793;778	Q9H3U1;A8K6F7	UN45A_HUMAN;.	Q	778;793	ENSP00000377816:R778Q;ENSP00000407487:R793Q	ENSP00000377816:R778Q	R	+	2	0	UNC45A	89297237	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	1.880000	0.39628	2.549000	0.85964	0.645000	0.84053	CGG	G|1.000;A|0.000	0.000	strong		0.582	UNC45A-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000280406.2	NM_018671	
IL1R1	3554	hgsc.bcm.edu	37	2	102781629	102781629	+	Silent	SNP	G	G	A	rs3917286	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr2:102781629G>A	ENST00000410023.1	+	5	669	c.351G>A	c.(349-351)gaG>gaA	p.E117E	IL1R1_ENST00000409589.1_Silent_p.E117E|IL1R1_ENST00000409288.1_Silent_p.E117E|IL1R1_ENST00000409929.1_Silent_p.E117E|IL1R1_ENST00000233946.3_Silent_p.E117E|IL1R1_ENST00000424272.1_Silent_p.E117E|IL1R1_ENST00000409329.1_Silent_p.E117E			P14778	IL1R1_HUMAN	interleukin 1 receptor, type I	117					cell surface receptor signaling pathway (GO:0007166)|immune response (GO:0006955)|interleukin-1-mediated signaling pathway (GO:0070498)|regulation of inflammatory response (GO:0050727)|response to interleukin-1 (GO:0070555)	cell surface (GO:0009986)|extracellular region (GO:0005576)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)	interleukin-1 receptor activity (GO:0004908)|interleukin-1, Type I, activating receptor activity (GO:0004909)|platelet-derived growth factor receptor binding (GO:0005161)|signal transducer activity (GO:0004871)|transmembrane signaling receptor activity (GO:0004888)			breast(2)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(4)|lung(4)|prostate(2)|skin(3)	19					Anakinra(DB00026)	TGGAGAATGAGCCTAACTTAT	0.313													G|||	225	0.0449281	0.0083	0.0072	5008	,	,		12413	0.0714		0.006	False		,,,				2504	0.1339				p.E117E		Atlas-SNP	.											.	IL1R1	52	.	0			c.G351A						PASS	.	G		47,4359	48.9+/-83.8	0,47,2156	50.0	51.0	50.0		351	-10.0	0.1	2	dbSNP_108	50	43,8555	27.4+/-76.7	0,43,4256	no	coding-synonymous	IL1R1	NM_000877.2		0,90,6412	AA,AG,GG		0.5001,1.0667,0.6921		117/570	102781629	90,12914	2203	4299	6502	SO:0001819	synonymous_variant	3554	exon4			GAATGAGCCTAAC	M27492	CCDS2055.1, CCDS74547.1	2q12	2013-01-29			ENSG00000115594	ENSG00000115594		"""Interleukins and interleukin receptors"", ""CD molecules"", ""Immunoglobulin superfamily / I-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	5993	protein-coding gene	gene with protein product		147810		IL1R, IL1RA		1833184, 10191101	Standard	XM_005263929		Approved	D2S1473, CD121A	uc002tbr.3	P14778	OTTHUMG00000130783	ENST00000410023.1:c.351G>A	2.37:g.102781629G>A		198.0	0.0	0		186.0	89.0	0.478495	NM_000877	Q587I7	Silent	SNP	ENST00000410023.1	37	CCDS2055.1																																																																																			G|0.984;A|0.016	0.016	strong		0.313	IL1R1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253299.1		
ZSCAN22	342945	hgsc.bcm.edu	37	19	58849789	58849789	+	Silent	SNP	G	G	A	rs368211476		TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr19:58849789G>A	ENST00000329665.4	+	3	720	c.573G>A	c.(571-573)ggG>ggA	p.G191G		NM_181846.2	NP_862829.1	P10073	ZSC22_HUMAN	zinc finger and SCAN domain containing 22	191					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(1)|endometrium(1)|kidney(1)|large_intestine(3)|lung(7)|pancreas(1)|prostate(2)	16		all_cancers(17;3.11e-12)|all_epithelial(17;9.43e-09)|Colorectal(82;0.000256)|Lung NSC(17;0.000607)|all_lung(17;0.0024)|all_neural(62;0.0412)|Ovarian(87;0.156)		UCEC - Uterine corpus endometrioid carcinoma (67;0.168)|GBM - Glioblastoma multiforme(193;0.0289)		GACTATCAGGGGAGATCTGGA	0.537													G|||	1	0.000199681	0.0	0.0	5008	,	,		20257	0.0		0.0	False		,,,				2504	0.001				p.G191G		Atlas-SNP	.											ZSCAN22,NS,carcinoma,+1,1	ZSCAN22	47	1	0			c.G573A						PASS	.						114.0	112.0	112.0					19																	58849789		2203	4300	6503	SO:0001819	synonymous_variant	342945	exon3			ATCAGGGGAGATC	M20675	CCDS12975.1	19q13.43	2013-01-08	2006-09-20	2006-09-20				"""-"", ""Zinc fingers, C2H2-type"""	4929	protein-coding gene	gene with protein product	"""oncogene HKR2"""	165260	"""zinc finger protein 50"", ""GLI-Kruppel family member HKR2"""	ZNF50, HKR2		2850480, 1505991	Standard	NM_181846		Approved		uc002qsc.2	P10073		ENST00000329665.4:c.573G>A	19.37:g.58849789G>A		113.0	0.0	0		121.0	59.0	0.487603	NM_181846	Q15922|Q7Z3L8	Silent	SNP	ENST00000329665.4	37	CCDS12975.1																																																																																			.	.	weak		0.537	ZSCAN22-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466765.1	NM_181846	
IL12B	3593	hgsc.bcm.edu	37	5	158750329	158750329	+	Missense_Mutation	SNP	C	C	T	rs3213096	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	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	45.0	0.0	0		65.0	34.0	0.523077	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	
ATAD5	79915	hgsc.bcm.edu	37	17	29221584	29221584	+	Missense_Mutation	SNP	A	A	G	rs114345202	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr17:29221584A>G	ENST00000321990.4	+	22	5678	c.5300A>G	c.(5299-5301)aAt>aGt	p.N1767S	TEFM_ENST00000579183.1_5'Flank	NM_024857.3	NP_079133.3	Q96QE3	ATAD5_HUMAN	ATPase family, AAA domain containing 5	1767					cellular response to DNA damage stimulus (GO:0006974)	nucleus (GO:0005634)	ATP binding (GO:0005524)			breast(3)|central_nervous_system(1)|cervix(1)|endometrium(8)|kidney(3)|large_intestine(18)|lung(13)|ovary(3)|pancreas(1)	51		all_hematologic(16;0.0202)|Acute lymphoblastic leukemia(14;0.0238)|Myeloproliferative disorder(56;0.0393)				TTTTACAGCAATGCTTGGAAG	0.368													A|||	27	0.00539137	0.0189	0.0029	5008	,	,		18155	0.0		0.0	False		,,,				2504	0.0				p.N1767S		Atlas-SNP	.											.	ATAD5	150	.	0			c.A5300G						PASS	.	A	SER/ASN	64,4342	59.3+/-96.0	0,64,2139	79.0	77.0	78.0		5300	-0.4	0.4	17	dbSNP_132	78	11,8589	8.4+/-32.0	0,11,4289	yes	missense	ATAD5	NM_024857.3	46	0,75,6428	GG,GA,AA		0.1279,1.4526,0.5767	benign	1767/1845	29221584	75,12931	2203	4300	6503	SO:0001583	missense	79915	exon22			ACAGCAATGCTTG		CCDS11260.1	17q11.2	2010-04-21	2007-02-08	2007-02-08	ENSG00000176208	ENSG00000176208		"""ATPases / AAA-type"""	25752	protein-coding gene	gene with protein product	"""enhanced level of genomic instability 1 homolog (S. cerevisiae)"""	609534	"""chromosome 17 open reading frame 41"""	C17orf41		15983387, 11468690, 19755857	Standard	NM_024857		Approved	FLJ12735, FRAG1, ELG1	uc002hfs.1	Q96QE3	OTTHUMG00000132794	ENST00000321990.4:c.5300A>G	17.37:g.29221584A>G	ENSP00000313171:p.Asn1767Ser	44.0	0.0	0		42.0	21.0	0.5	NM_024857	Q05DH0|Q69YR6|Q9H9I1	Missense_Mutation	SNP	ENST00000321990.4	37	CCDS11260.1	11	0.005036630036630037	9	0.018292682926829267	2	0.0055248618784530384	0	0.0	0	0.0	A	3.076	-0.190144	0.06299	0.014526	0.001279	ENSG00000176208	ENST00000321990	T	0.07800	3.16	5.59	-0.38	0.12490	.	0.706131	0.15070	N	0.282249	T	0.01061	0.0035	N	0.01267	-0.92	0.21256	N	0.999741	B	0.10296	0.003	B	0.08055	0.003	T	0.46062	-0.9218	10	0.21540	T	0.41	.	5.7512	0.18148	0.4172:0.0:0.441:0.1418	.	1767	Q96QE3	ATAD5_HUMAN	S	1767	ENSP00000313171:N1767S	ENSP00000313171:N1767S	N	+	2	0	ATAD5	26245710	0.924000	0.31332	0.415000	0.26534	0.785000	0.44390	0.700000	0.25601	-0.099000	0.12263	-0.334000	0.08254	AAT	A|0.994;G|0.006	0.006	strong		0.368	ATAD5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256206.2	NM_024857	
LILRB1	10859	hgsc.bcm.edu	37	19	55143395	55143395	+	Missense_Mutation	SNP	T	T	G	rs370374304		TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr19:55143395T>G	ENST00000396331.1	+	6	725	c.368T>G	c.(367-369)aTc>aGc	p.I123S	LILRB1_ENST00000396327.3_Missense_Mutation_p.I123S|LILRB1_ENST00000324602.7_Missense_Mutation_p.I123S|LILRB1_ENST00000427581.2_Missense_Mutation_p.I159S|LILRB1_ENST00000396321.2_Missense_Mutation_p.I123S|LILRB1_ENST00000418536.2_Missense_Mutation_p.I123S|LILRB1_ENST00000396315.1_Missense_Mutation_p.I123S|AC009892.1_ENST00000578908.1_RNA|LILRB1_ENST00000434867.2_Missense_Mutation_p.I123S|LILRB1_ENST00000396332.4_Missense_Mutation_p.I123S|LILRB1_ENST00000396317.1_Missense_Mutation_p.I123S|LILRB1_ENST00000448689.1_Missense_Mutation_p.I123S	NM_006669.3	NP_006660.3	Q8NHL6	LIRB1_HUMAN	leukocyte immunoglobulin-like receptor, subfamily B (with TM and ITIM domains), member 1	123	Ig-like C2-type 2.				cellular response to lipopolysaccharide (GO:0071222)|defense response to virus (GO:0051607)|dendritic cell differentiation (GO:0097028)|Fc receptor mediated inhibitory signaling pathway (GO:0002774)|immune response-inhibiting cell surface receptor signaling pathway (GO:0002767)|interferon-gamma production (GO:0032609)|interferon-gamma secretion (GO:0072643)|negative regulation of alpha-beta T cell activation (GO:0046636)|negative regulation of calcium ion transport (GO:0051926)|negative regulation of CD8-positive, alpha-beta T cell activation (GO:2001186)|negative regulation of cell cycle (GO:0045786)|negative regulation of cytokine secretion involved in immune response (GO:0002740)|negative regulation of dendritic cell apoptotic process (GO:2000669)|negative regulation of dendritic cell differentiation (GO:2001199)|negative regulation of endocytosis (GO:0045806)|negative regulation of interferon-beta secretion (GO:0035548)|negative regulation of interferon-gamma biosynthetic process (GO:0045077)|negative regulation of interferon-gamma production (GO:0032689)|negative regulation of interleukin-10 secretion (GO:2001180)|negative regulation of interleukin-12 secretion (GO:2001183)|negative regulation of mononuclear cell proliferation (GO:0032945)|negative regulation of natural killer cell mediated cytotoxicity (GO:0045953)|negative regulation of osteoclast development (GO:2001205)|negative regulation of serotonin secretion (GO:0014063)|negative regulation of T cell activation via T cell receptor contact with antigen bound to MHC molecule on antigen presenting cell (GO:2001189)|negative regulation of T cell mediated cytotoxicity (GO:0001915)|negative regulation of T cell proliferation (GO:0042130)|negative regulation of transforming growth factor-beta secretion (GO:2001202)|negative regulation of tumor necrosis factor biosynthetic process (GO:0042536)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cytolysis (GO:0045919)|positive regulation of defense response to virus by host (GO:0002230)|positive regulation of gamma-delta T cell activation involved in immune response (GO:2001193)|positive regulation of gene expression (GO:0010628)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|receptor internalization (GO:0031623)|regulation of immune response (GO:0050776)|response to virus (GO:0009615)|signal transduction (GO:0007165)|T cell proliferation involved in immune response (GO:0002309)	cytoplasm (GO:0005737)|external side of plasma membrane (GO:0009897)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	HLA-A specific inhibitory MHC class I receptor activity (GO:0030107)|HLA-B specific inhibitory MHC class I receptor activity (GO:0030109)|MHC class I protein binding (GO:0042288)|MHC class I receptor activity (GO:0032393)|protein homodimerization activity (GO:0042803)|protein phosphatase 1 binding (GO:0008157)|SH2 domain binding (GO:0042169)			NS(2)|breast(1)|central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(13)|lung(38)|ovary(1)|prostate(3)|skin(3)|upper_aerodigestive_tract(5)|urinary_tract(1)	74				GBM - Glioblastoma multiforme(193;0.0188)		GGAGCCTACATCAAACCCACC	0.587										HNSCC(37;0.09)			N|||	1	0.000199681	0.0008	0.0	5008	,	,		17815	0.0		0.0	False		,,,				2504	0.0				p.I123S		Atlas-SNP	.											.	LILRB1	140	.	0			c.T368G						PASS	.	G	SER/ILE,SER/ILE,SER/ILE,SER/ILE	0,4406		0,0,2203	72.0	75.0	74.0		368,368,368,368	-3.0	0.0	19		74	2,8598	818.7+/-406.8	0,2,4298	no	missense,missense,missense,missense	LILRB1	NM_001081637.1,NM_001081638.1,NM_001081639.1,NM_006669.3	142,142,142,142	0,2,6501	GG,GT,TT		0.0233,0.0,0.0154	benign,benign,benign,benign	123/653,123/652,123/652,123/651	55143395	2,13004	2203	4300	6503	SO:0001583	missense	10859	exon5			CCTACATCAAACC	AF009220	CCDS42614.1, CCDS42615.1, CCDS42616.1, CCDS42617.1, CCDS62803.1	19q13.4	2013-01-11						"""Leukocyte immunoglobulin-like receptors"", ""CD molecules"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	6605	protein-coding gene	gene with protein product		604811				9285411, 9382880	Standard	XM_006726246		Approved	LIR-1, ILT2, MIR-7, CD85, LIR1, CD85j	uc002qgm.3	Q8NHL6		ENST00000396331.1:c.368T>G	19.37:g.55143395T>G	ENSP00000379622:p.Ile123Ser	99.0	0.0	0		109.0	46.0	0.422018	NM_001081637	A2IXV4|A8MXT0|O75024|O75025|Q8NHJ9|Q8NHK0	Missense_Mutation	SNP	ENST00000396331.1	37	CCDS42617.1	.	.	.	.	.	.	.	.	.	.	g	0	-2.736760	0.00088	0.0	2.33E-4	ENSG00000104972	ENST00000396321;ENST00000418536;ENST00000448689;ENST00000396331;ENST00000396327;ENST00000324602;ENST00000434867;ENST00000396332;ENST00000427581;ENST00000396317;ENST00000396315	T;T;T;T;T;T;T;T;T;T;T	0.21191	2.02;2.02;2.02;2.02;2.02;2.02;2.02;2.02;2.02;2.02;2.02	1.57	-2.95	0.05564	Immunoglobulin-like fold (1);	1.339760	0.04742	N	0.422960	T	0.02929	0.0087	N	0.00121	-2.07	0.09310	N	1	B;B;B;B;B	0.02656	0.0;0.0;0.0;0.0;0.0	B;B;B;B;B	0.04013	0.0;0.001;0.0;0.0;0.0	T	0.35525	-0.9785	10	0.02654	T	1	.	2.0172	0.03500	0.3909:0.0:0.3453:0.2638	.	123;123;123;123;123	A8MVE2;Q8NHL6-3;A2IXV4;Q8NHL6-2;Q8NHL6	.;.;.;.;LIRB1_HUMAN	S	123;123;123;123;123;123;123;123;159;123;123	ENSP00000379614:I123S;ENSP00000391514:I123S;ENSP00000409968:I123S;ENSP00000379622:I123S;ENSP00000379618:I123S;ENSP00000315997:I123S;ENSP00000405243:I123S;ENSP00000379623:I123S;ENSP00000395004:I159S;ENSP00000379610:I123S;ENSP00000379608:I123S	ENSP00000315997:I123S	I	+	2	0	LILRB1	59835207	0.000000	0.05858	0.000000	0.03702	0.003000	0.03518	-5.408000	0.00124	-0.614000	0.05687	-3.867000	0.00017	ATC	.	.	weak		0.587	LILRB1-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000140796.4		
ABCA3	21	hgsc.bcm.edu	37	16	2327929	2327929	+	Silent	SNP	T	T	C	rs540282149	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr16:2327929T>C	ENST00000301732.5	-	31	5560	c.4860A>G	c.(4858-4860)caA>caG	p.Q1620Q	ABCA3_ENST00000382381.3_Silent_p.Q1562Q	NM_001089.2	NP_001080.2	Q99758	ABCA3_HUMAN	ATP-binding cassette, sub-family A (ABC1), member 3	1620					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)	GCGCCTCCTGTTGCCCTTCAC	0.672													T|||	2	0.000399361	0.0	0.0	5008	,	,		16834	0.0		0.0	False		,,,				2504	0.002				p.Q1620Q		Atlas-SNP	.											.	ABCA3	176	.	0			c.A4860G						PASS	.						28.0	29.0	28.0					16																	2327929		2198	4300	6498	SO:0001819	synonymous_variant	21	exon31			CTCCTGTTGCCCT	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.4860A>G	16.37:g.2327929T>C		78.0	0.0	0		98.0	44.0	0.44898	NM_001089	B2RU09|Q54A95|Q6P5P9|Q92473	Silent	SNP	ENST00000301732.5	37	CCDS10466.1																																																																																			.	.	none		0.672	ABCA3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250784.2	NM_001089	
CDH9	1007	hgsc.bcm.edu	37	5	26885964	26885964	+	Silent	SNP	T	T	G	rs35328154	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr5:26885964T>G	ENST00000231021.4	-	11	1813	c.1641A>C	c.(1639-1641)gcA>gcC	p.A547A		NM_016279.3	NP_057363.3	Q9ULB4	CADH9_HUMAN	cadherin 9, type 2 (T1-cadherin)	547	Cadherin 5. {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)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			breast(6)|endometrium(7)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(25)|lung(80)|ovary(5)|prostate(4)|skin(5)|upper_aerodigestive_tract(2)|urinary_tract(1)	137						TCATGATTCCTGCTGTATTAT	0.318													T|||	49	0.00978435	0.0	0.0187	5008	,	,		17688	0.0		0.0109	False		,,,				2504	0.0256				p.A547A	Melanoma(8;187 585 15745 40864 52829)	Atlas-SNP	.											.	CDH9	305	.	0			c.A1641C						PASS	.	T		7,4399	11.4+/-27.6	0,7,2196	55.0	58.0	57.0		1641	-4.3	1.0	5	dbSNP_126	57	82,8518	44.0+/-102.2	0,82,4218	no	coding-synonymous	CDH9	NM_016279.3		0,89,6414	GG,GT,TT		0.9535,0.1589,0.6843		547/790	26885964	89,12917	2203	4300	6503	SO:0001819	synonymous_variant	1007	exon11			GATTCCTGCTGTA	AB035302	CCDS3893.1	5p14	2010-01-26			ENSG00000113100	ENSG00000113100		"""Cadherins / Major cadherins"""	1768	protein-coding gene	gene with protein product		609974				2059658	Standard	NM_016279		Approved		uc003jgs.1	Q9ULB4	OTTHUMG00000090671	ENST00000231021.4:c.1641A>C	5.37:g.26885964T>G		67.0	0.0	0		60.0	28.0	0.466667	NM_016279	Q3B7I5	Silent	SNP	ENST00000231021.4	37	CCDS3893.1																																																																																			T|0.992;G|0.008	0.008	strong		0.318	CDH9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207352.1	NM_016279	
HSD3B2	3284	hgsc.bcm.edu	37	1	119964933	119964933	+	Missense_Mutation	SNP	T	T	C	rs75429891	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr1:119964933T>C	ENST00000543831.1	+	4	1058	c.809T>C	c.(808-810)aTc>aCc	p.I270T	HSD3B2_ENST00000369416.3_Missense_Mutation_p.I270T	NM_001166120.1	NP_001159592.1	P26439	3BHS2_HUMAN	hydroxy-delta-5-steroid dehydrogenase, 3 beta- and steroid delta-isomerase 2	270					androgen biosynthetic process (GO:0006702)|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 (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|mitochondrial inner membrane (GO:0005743)|mitochondrial intermembrane space (GO:0005758)|mitochondrial membrane (GO:0031966)|smooth endoplasmic reticulum membrane (GO:0030868)	3-beta-hydroxy-delta5-steroid dehydrogenase activity (GO:0003854)|steroid delta-isomerase activity (GO:0004769)			breast(1)|endometrium(2)|kidney(1)|large_intestine(1)|lung(19)|ovary(2)|skin(1)	27	all_neural(166;0.187)	all_lung(203;1.06e-06)|Lung NSC(69;7.5e-06)|all_epithelial(167;0.000284)		Lung(183;0.015)|LUSC - Lung squamous cell carcinoma(189;0.0836)	Corticotropin(DB01285)|Medroxyprogesterone Acetate(DB00603)|Trilostane(DB01108)	CTTAATTACATCCTGAGCAAA	0.498													T|||	2	0.000399361	0.0	0.0	5008	,	,		20150	0.0		0.002	False		,,,				2504	0.0				p.I270T		Atlas-SNP	.											.	HSD3B2	48	.	0			c.T809C						PASS	.	T	THR/ILE,THR/ILE	1,4405		0,1,2202	75.0	79.0	77.0		809,809	-8.0	0.0	1	dbSNP_131	77	6,8594		0,6,4294	no	missense,missense	HSD3B2	NM_000198.3,NM_001166120.1	89,89	0,7,6496	CC,CT,TT		0.0698,0.0227,0.0538	benign,benign	270/373,270/373	119964933	7,12999	2203	4300	6503	SO:0001583	missense	3284	exon4			ATTACATCCTGAG	BC038419	CCDS902.1	1p12	2014-06-03			ENSG00000203859	ENSG00000203859	1.1.1.145, 5.3.3.1	"""Short chain dehydrogenase/reductase superfamily / Extended SDR fold"""	5218	protein-coding gene	gene with protein product	"""short chain dehydrogenase/reductase family 11E, member 2"""	613890				1363812, 19027726	Standard	NM_000198		Approved	SDR11E2	uc001eht.3	P26439	OTTHUMG00000012526	ENST00000543831.1:c.809T>C	1.37:g.119964933T>C	ENSP00000445122:p.Ile270Thr	154.0	0.0	0		170.0	72.0	0.423529	NM_001166120	A2RRA5|Q16010|Q53GD4|Q6AI10|Q6LDB9|Q99890|Q9UD08	Missense_Mutation	SNP	ENST00000543831.1	37	CCDS902.1	0	0.0	0	0.0	0	0.0	0	0.0	0	0.0	-	0.003	-2.490832	0.00161	2.27E-4	6.98E-4	ENSG00000203859	ENST00000543831;ENST00000369416	D;D	0.88124	-2.34;-2.34	3.98	-7.97	0.01139	3-beta hydroxysteroid dehydrogenase/isomerase (1);NAD(P)-binding domain (1);	0.703655	0.13486	N	0.384300	T	0.28101	0.0693	N	0.00496	-1.435	0.09310	N	1	B	0.02656	0.0	B	0.04013	0.001	T	0.55976	-0.8055	9	.	.	.	-2.0251	7.6517	0.28352	0.592:0.2386:0.0:0.1694	.	270	P26439	3BHS2_HUMAN	T	270	ENSP00000445122:I270T;ENSP00000358424:I270T	.	I	+	2	0	HSD3B2	119766456	0.000000	0.05858	0.034000	0.17996	0.257000	0.26127	-0.688000	0.05150	-1.777000	0.01283	-0.782000	0.03352	ATC	T|1.000;C|0.000	0.000	strong		0.498	HSD3B2-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000034994.1	NM_000198	
MICAL3	57553	hgsc.bcm.edu	37	22	18379640	18379640	+	Silent	SNP	C	C	T	rs61739477	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr22:18379640C>T	ENST00000441493.2	-	8	1408	c.1056G>A	c.(1054-1056)ccG>ccA	p.P352P	MICAL3_ENST00000207726.7_Silent_p.P352P|MICAL3_ENST00000383094.3_Silent_p.P352P|MICAL3_ENST00000429452.1_Silent_p.P352P|MICAL3_ENST00000400561.2_Silent_p.P352P|MICAL3_ENST00000444520.1_Silent_p.P352P|MICAL3_ENST00000585038.1_Silent_p.P352P|MICAL3_ENST00000414725.2_Silent_p.P352P	NM_015241.2	NP_056056.2	Q7RTP6	MICA3_HUMAN	microtubule associated monooxygenase, calponin and LIM domain containing 3	352	Monooxygenase domain. {ECO:0000250}.				actin filament depolymerization (GO:0030042)|cytoskeleton organization (GO:0007010)|exocytosis (GO:0006887)|oxidation-reduction process (GO:0055114)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|nucleus (GO:0005634)	actin binding (GO:0003779)|FAD binding (GO:0071949)|oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, NAD(P)H as one donor, and incorporation of one atom of oxygen (GO:0016709)|zinc ion binding (GO:0008270)			large_intestine(1)|lung(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	4		all_epithelial(15;0.198)		Lung(27;0.0427)		AATCCAGAGACGGCAGCTGCT	0.582											OREG0026285	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	C|||	56	0.0111821	0.0	0.0029	5008	,	,		19187	0.0248		0.0149	False		,,,				2504	0.0143				p.P352P		Atlas-SNP	.											.	MICAL3	53	.	0			c.G1056A						PASS	.	C	,,	7,3129		0,7,1561	58.0	56.0	57.0		1056,1056,1056	-11.7	0.0	22	dbSNP_129	57	108,7056		1,106,3475	no	coding-synonymous,coding-synonymous,coding-synonymous	MICAL3	NM_001122731.1,NM_001136004.1,NM_015241.2	,,	1,113,5036	TT,TC,CC		1.5075,0.2232,1.1165	,,	352/967,352/1074,352/2003	18379640	115,10185	1568	3582	5150	SO:0001819	synonymous_variant	57553	exon8			CAGAGACGGCAGC	AB037785	CCDS46659.1, CCDS46660.1, CCDS46661.1	22q11.21	2013-03-26	2013-03-26		ENSG00000243156	ENSG00000243156			24694	protein-coding gene	gene with protein product		608882				12110185	Standard	NM_015241		Approved	KIAA0819	uc002zng.4	Q7RTP6	OTTHUMG00000150067	ENST00000441493.2:c.1056G>A	22.37:g.18379640C>T		64.0	0.0	0	725	67.0	34.0	0.507463	NM_015241	B2RXJ5|E9PEF0|O94909|Q5U4P4|Q6ICK4|Q96DF2|Q9P2I3	Silent	SNP	ENST00000441493.2	37	CCDS46659.1																																																																																			C|0.987;T|0.013	0.013	strong		0.582	MICAL3-010	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000447351.1		
VPS52	6293	hgsc.bcm.edu	37	6	33234454	33234454	+	Silent	SNP	G	G	A	rs34933266	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr6:33234454G>A	ENST00000445902.2	-	12	1379	c.1161C>T	c.(1159-1161)taC>taT	p.Y387Y	VPS52_ENST00000478934.1_5'UTR|VPS52_ENST00000436044.2_Silent_p.Y262Y|VPS52_ENST00000482399.1_3'UTR	NM_022553.4	NP_072047.4	Q8N1B4	VPS52_HUMAN	vacuolar protein sorting 52 homolog (S. cerevisiae)	387					ectodermal cell differentiation (GO:0010668)|embryonic ectodermal digestive tract development (GO:0048611)|protein transport (GO:0015031)	endosome (GO:0005768)|Golgi apparatus (GO:0005794)|membrane (GO:0016020)				endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(7)|liver(1)|lung(8)|ovary(4)|skin(1)|upper_aerodigestive_tract(1)	28						CTAGGAGGGCGTAGTGCTGGC	0.517													G|||	33	0.00658946	0.003	0.0014	5008	,	,		18785	0.0129		0.008	False		,,,				2504	0.0072				p.Y387Y		Atlas-SNP	.											.	VPS52	56	.	0			c.C1161T						PASS	.	G		13,3007		0,13,1497	61.0	64.0	63.0		1161	-5.7	1.0	6	dbSNP_126	63	31,5387		0,31,2678	no	coding-synonymous	VPS52	NM_022553.4		0,44,4175	AA,AG,GG		0.5722,0.4305,0.5215		387/724	33234454	44,8394	1510	2709	4219	SO:0001819	synonymous_variant	6293	exon12			GAGGGCGTAGTGC	AJ223319	CCDS4770.2	6p21.3	2010-02-17	2006-12-19	2003-09-05	ENSG00000223501	ENSG00000223501			10518	protein-coding gene	gene with protein product		603443	"""SAC2 suppressor of actin mutations 2-like (yeast)"", ""vacuolar protein sorting 52 (yeast)"""	SACM2L		9790748	Standard	NM_022553		Approved	ARE1	uc003odm.1	Q8N1B4	OTTHUMG00000031276	ENST00000445902.2:c.1161C>T	6.37:g.33234454G>A		86.0	0.0	0		83.0	45.0	0.542169	NM_022553	A2BF38|B0UZZ4|B4DNI9|Q53GR4|Q5JPA0|Q5SQW1|Q8IUN6|Q9NPT5	Silent	SNP	ENST00000445902.2	37	CCDS4770.2																																																																																			G|0.994;A|0.006	0.006	strong		0.517	VPS52-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076598.2	NM_022553	
SHANK2	22941	hgsc.bcm.edu	37	11	70331716	70331716	+	Missense_Mutation	SNP	G	G	C			TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr11:70331716G>C	ENST00000423696.2	-	15	3581	c.3545C>G	c.(3544-3546)gCa>gGa	p.A1182G	SHANK2_ENST00000449833.2_Missense_Mutation_p.A966G|SHANK2_ENST00000338508.4_Missense_Mutation_p.A1562G|SHANK2_ENST00000409161.1_Missense_Mutation_p.A965G			Q9UPX8	SHAN2_HUMAN	SH3 and multiple ankyrin repeat domains 2	1182					adult behavior (GO:0030534)|learning (GO:0007612)|long term synaptic depression (GO:0060292)|long-term synaptic potentiation (GO:0060291)|social behavior (GO:0035176)|synapse assembly (GO:0007416)|vocalization behavior (GO:0071625)	apical plasma membrane (GO:0016324)|brush border membrane (GO:0031526)|cell junction (GO:0030054)|ciliary membrane (GO:0060170)|cytoplasm (GO:0005737)|dendritic spine (GO:0043197)|growth cone (GO:0030426)|neuron projection (GO:0043005)|neuronal cell body (GO:0043025)|photoreceptor inner segment (GO:0001917)|photoreceptor outer segment (GO:0001750)|plasma membrane (GO:0005886)|postsynaptic density (GO:0014069)|postsynaptic membrane (GO:0045211)	GKAP/Homer scaffold activity (GO:0030160)|ionotropic glutamate receptor binding (GO:0035255)			NS(2)|breast(2)|central_nervous_system(1)|cervix(1)|endometrium(4)|kidney(2)|large_intestine(4)|lung(30)|ovary(3)|pancreas(2)|prostate(3)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	62			LUSC - Lung squamous cell carcinoma(11;4.72e-09)|STAD - Stomach adenocarcinoma(18;0.071)			TTGATAAAGTGCATTGCTTTT	0.552																																					p.A973G		Atlas-SNP	.											.	SHANK2	340	.	0			c.C2918G						PASS	.						147.0	145.0	145.0					11																	70331716		2200	4294	6494	SO:0001583	missense	22941	exon10			TAAAGTGCATTGC	AF141901		11q13.2	2013-01-10			ENSG00000162105	ENSG00000162105		"""Sterile alpha motif (SAM) domain containing"", ""Ankyrin repeat domain containing"""	14295	protein-coding gene	gene with protein product		603290	"""cortactin binding protein 1"""	CORTBP1		10506216	Standard	XM_005277930		Approved	CTTNBP1, ProSAP1, SHANK, SPANK-3	uc001oqc.3	Q9UPX8	OTTHUMG00000154615	ENST00000423696.2:c.3545C>G	11.37:g.70331716G>C	ENSP00000394536:p.Ala1182Gly	147.0	0.0	0		153.0	76.0	0.496732	NM_133266	C0SPG8|C0SPG9|Q3Y8G9|Q52LK2|Q9UKP1	Missense_Mutation	SNP	ENST00000423696.2	37		.	.	.	.	.	.	.	.	.	.	G	11.04	1.520786	0.27211	.	.	ENSG00000162105	ENST00000449833;ENST00000409161;ENST00000424924;ENST00000338508;ENST00000423696;ENST00000433693;ENST00000294018	T;T;T;T;T;T	0.19669	2.13;2.13;2.13;2.13;2.13;2.13	5.42	4.51	0.55191	.	0.353602	0.31872	N	0.006936	T	0.20333	0.0489	L	0.32530	0.975	0.80722	D	1	B;P;P	0.43287	0.437;0.802;0.573	B;B;B	0.43536	0.137;0.423;0.267	T	0.01561	-1.1324	10	0.37606	T	0.19	.	14.1457	0.65349	0.0721:0.0:0.9279:0.0	.	1182;1561;966	Q9UPX8;Q9UPX8-3;Q9UPX8-4	SHAN2_HUMAN;.;.	G	966;965;840;1562;1182;1200;1185	ENSP00000399423:A966G;ENSP00000386491:A965G;ENSP00000402944:A840G;ENSP00000345193:A1562G;ENSP00000394536:A1182G;ENSP00000294018:A1185G	ENSP00000294018:A1185G	A	-	2	0	SHANK2	70009364	1.000000	0.71417	0.013000	0.15412	0.999000	0.98932	6.103000	0.71492	1.294000	0.44707	0.655000	0.94253	GCA	.	.	none		0.552	SHANK2-203	KNOWN	basic	protein_coding	protein_coding		NM_012309	
THADA	63892	hgsc.bcm.edu	37	2	43571347	43571347	+	Silent	SNP	G	G	A	rs35422033	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr2:43571347G>A	ENST00000405006.4	-	30	4608	c.4257C>T	c.(4255-4257)gaC>gaT	p.D1419D	THADA_ENST00000485353.1_5'UTR|THADA_ENST00000405975.2_Silent_p.D1419D|THADA_ENST00000415080.2_Silent_p.D1100D|THADA_ENST00000330266.7_Intron	NM_001083953.1|NM_001271643.1	NP_001077422.1|NP_001258572.1	Q6YHU6	THADA_HUMAN	thyroid adenoma associated	1419										breast(1)|endometrium(9)|kidney(5)|large_intestine(9)|liver(1)|lung(28)|ovary(4)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(5)	66		Acute lymphoblastic leukemia(82;0.00361)|all_hematologic(82;0.00837)				CGTGTTTGGAGTCTGAGTAGG	0.398													G|||	91	0.0181709	0.0484	0.0187	5008	,	,		19017	0.0		0.006	False		,,,				2504	0.0082				p.D1419D		Atlas-SNP	.											.	THADA	131	.	0			c.C4257T						PASS	.	G	,	136,3678		3,130,1774	75.0	68.0	70.0		4257,4257	4.8	1.0	2	dbSNP_126	70	54,8200		0,54,4073	no	coding-synonymous,coding-synonymous	THADA	NM_001083953.1,NM_022065.4	,	3,184,5847	AA,AG,GG		0.6542,3.5658,1.5744	,	1419/1954,1419/1954	43571347	190,11878	1907	4127	6034	SO:0001819	synonymous_variant	63892	exon30			TTTGGAGTCTGAG	AY149629	CCDS46268.1, CCDS62901.1, CCDS62902.1	2p21	2008-02-05			ENSG00000115970	ENSG00000115970			19217	protein-coding gene	gene with protein product		611800				12063398, 11214970	Standard	NM_022065		Approved	FLJ21877, KIAA1767, GITA	uc002rsx.4	Q6YHU6	OTTHUMG00000152398	ENST00000405006.4:c.4257C>T	2.37:g.43571347G>A		167.0	0.0	0		166.0	87.0	0.524096	NM_001083953	A8K1V8|B7WNS6|Q3KR04|Q53RC6|Q53TB2|Q6YHU2|Q6ZU38|Q8IY32|Q8TAU8|Q96I88|Q9BZF7|Q9C096|Q9H6U0|Q9H6W7	Silent	SNP	ENST00000405006.4	37	CCDS46268.1	43	0.019688644688644688	31	0.06300813008130081	7	0.019337016574585635	0	0.0	5	0.006596306068601583	G	8.144	0.785827	0.16189	0.035658	0.006542	ENSG00000115970	ENST00000407351	.	.	.	4.8	4.8	0.61643	.	.	.	.	.	T	0.13543	0.0328	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.18650	-1.0330	4	.	.	.	-20.2203	8.2927	0.31967	0.0846:0.1598:0.7556:0.0	rs35422033	.	.	.	I	659	.	.	T	-	2	0	THADA	43424851	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	1.449000	0.35123	2.494000	0.84150	0.585000	0.79938	ACT	G|0.983;A|0.017	0.017	strong		0.398	THADA-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000326070.3	NM_022065	
S100P	6286	hgsc.bcm.edu	37	4	6698664	6698664	+	Silent	SNP	G	G	A	rs11737783	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr4:6698664G>A	ENST00000296370.3	+	2	1047	c.183G>A	c.(181-183)ctG>ctA	p.L61L	S100P_ENST00000513778.1_3'UTR	NM_005980.2	NP_005971.1	P25815	S100P_HUMAN	S100 calcium binding protein P	61	EF-hand 2. {ECO:0000255|PROSITE- ProRule:PRU00448}.				endothelial cell migration (GO:0043542)|response to organic substance (GO:0010033)	cell projection (GO:0042995)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|calcium-dependent protein binding (GO:0048306)|magnesium ion binding (GO:0000287)			prostate(1)	1		Myeloproliferative disorder(84;0.0255)		Colorectal(103;0.011)	Cromoglicic acid(DB01003)	TCAAGGACCTGGATGCCAATG	0.532													G|||	144	0.028754	0.0023	0.0331	5008	,	,		21956	0.001		0.0427	False		,,,				2504	0.0757				p.L61L		Atlas-SNP	.											.	S100P	7	.	0			c.G183A						PASS	.	G		34,4372	40.8+/-73.8	0,34,2169	242.0	226.0	231.0		183	-0.2	0.5	4	dbSNP_120	231	340,8260	116.3+/-176.0	1,338,3961	no	coding-synonymous	S100P	NM_005980.2		1,372,6130	AA,AG,GG		3.9535,0.7717,2.8756		61/96	6698664	374,12632	2203	4300	6503	SO:0001819	synonymous_variant	6286	exon2			GGACCTGGATGCC	X65614	CCDS3391.1	4p16	2013-01-10	2001-11-28		ENSG00000163993	ENSG00000163993		"""S100 calcium binding proteins"", ""EF-hand domain containing"""	10504	protein-coding gene	gene with protein product		600614	"""S100 calcium-binding protein P"""			8341667, 7759097	Standard	NM_005980		Approved		uc003gjl.3	P25815	OTTHUMG00000090491	ENST00000296370.3:c.183G>A	4.37:g.6698664G>A		213.0	0.0	0		172.0	80.0	0.465116	NM_005980	Q5J7W2	Silent	SNP	ENST00000296370.3	37	CCDS3391.1																																																																																			G|0.972;A|0.028	0.028	strong		0.532	S100P-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206979.1	NM_005980	
RNF112	7732	hgsc.bcm.edu	37	17	19319353	19319353	+	Silent	SNP	C	C	T			TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr17:19319353C>T	ENST00000461366.1	+	14	1976	c.1761C>T	c.(1759-1761)gcC>gcT	p.A587A	AC004448.2_ENST00000437646.1_lincRNA|CTB-187M2.2_ENST00000579897.1_RNA	NM_007148.4	NP_009079.2	Q9ULX5	RN112_HUMAN	ring finger protein 112	587						cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)|nucleus (GO:0005634)	GTP binding (GO:0005525)|GTPase activity (GO:0003924)|zinc ion binding (GO:0008270)			endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(1)|lung(2)|ovary(2)|prostate(1)|urinary_tract(1)	12						CTGGAGCTGCCGTGGGGGCCA	0.701																																					p.A587A		Atlas-SNP	.											.	RNF112	37	.	0			c.C1761T						PASS	.						3.0	4.0	4.0					17																	19319353		1690	3667	5357	SO:0001819	synonymous_variant	7732	exon14			AGCTGCCGTGGGG	AF054587	CCDS58529.1	17p11.2	2013-01-16	2008-06-13	2008-06-13	ENSG00000128482	ENSG00000128482		"""RING-type (C3HC4) zinc fingers"""	12968	protein-coding gene	gene with protein product		601237	"""zinc finger protein 179"""	ZNF179		8660987, 9806830	Standard	NM_007148		Approved	BFP	uc010vyw.2	Q9ULX5	OTTHUMG00000059601	ENST00000461366.1:c.1761C>T	17.37:g.19319353C>T		60.0	0.0	0		47.0	26.0	0.553191	NM_007148	O60633|Q7Z5V9	Silent	SNP	ENST00000461366.1	37	CCDS58529.1																																																																																			.	.	none		0.701	RNF112-001	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000132549.4	NM_007148	
SLURP1	57152	hgsc.bcm.edu	37	8	143823241	143823241	+	Missense_Mutation	SNP	G	G	A			TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr8:143823241G>A	ENST00000246515.1	-	2	183	c.158C>T	c.(157-159)aCg>aTg	p.T53M		NM_020427.2	NP_065160.1	P55000	SLUR1_HUMAN	secreted LY6/PLAUR domain containing 1	53	UPAR/Ly6.				cell activation (GO:0001775)|cell adhesion (GO:0007155)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)	cytokine activity (GO:0005125)			breast(1)|lung(7)|ovary(1)	9	all_cancers(97;3.96e-12)|all_epithelial(106;1.19e-08)|Lung NSC(106;0.000413)|all_lung(105;0.00106)|Medulloblastoma(13;0.00276)|all_neural(13;0.00559)|Ovarian(258;0.0254)|Acute lymphoblastic leukemia(118;0.155)					CGTCACCAGCGTGGTCATGCA	0.652																																					p.T53M		Atlas-SNP	.											SLURP1,NS,carcinoma,0,1	SLURP1	16	1	0			c.C158T						PASS	.						100.0	87.0	91.0					8																	143823241		2203	4299	6502	SO:0001583	missense	57152	exon2			ACCAGCGTGGTCA	AY579080	CCDS6387.1	8q24.3	2004-11-16			ENSG00000126233	ENSG00000126233			18746	protein-coding gene	gene with protein product	"""lymphocyte antigen 6-like secreted"", ""ARS component B"""	606119				11285253, 10211827	Standard	NM_020427		Approved	ARS, ANUP, MDM, ArsB, LY6LS	uc003ywy.3	P55000	OTTHUMG00000164685	ENST00000246515.1:c.158C>T	8.37:g.143823241G>A	ENSP00000246515:p.Thr53Met	56.0	0.0	0		53.0	26.0	0.490566	NM_020427	Q53YJ6|Q6PUA6|Q92483	Missense_Mutation	SNP	ENST00000246515.1	37	CCDS6387.1	.	.	.	.	.	.	.	.	.	.	G	13.36	2.212927	0.39102	.	.	ENSG00000126233	ENST00000246515	T	0.70749	-0.51	4.17	-1.92	0.07618	Ly-6 antigen / uPA receptor -like (1);CD59 antigen (1);	1.602070	0.04459	N	0.374005	T	0.66137	0.2759	M	0.78456	2.415	0.09310	N	1	B	0.34313	0.448	B	0.29440	0.102	T	0.55623	-0.8112	10	0.72032	D	0.01	-20.1734	3.9364	0.09307	0.2058:0.0:0.356:0.4382	.	53	P55000	SLUR1_HUMAN	M	53	ENSP00000246515:T53M	ENSP00000246515:T53M	T	-	2	0	SLURP1	143820243	0.000000	0.05858	0.001000	0.08648	0.057000	0.15508	-0.051000	0.11885	-0.259000	0.09432	-0.704000	0.03662	ACG	.	.	none		0.652	SLURP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000379741.1	NM_020427	
GCNT4	51301	hgsc.bcm.edu	37	5	74325101	74325101	+	Silent	SNP	C	C	T			TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr5:74325101C>T	ENST00000322348.4	-	1	1623	c.762G>A	c.(760-762)acG>acA	p.T254T		NM_016591.2	NP_057675.1	Q9P109	GCNT4_HUMAN	glucosaminyl (N-acetyl) transferase 4, core 2	254					carbohydrate metabolic process (GO:0005975)|cellular protein metabolic process (GO:0044267)|homeostasis of number of cells (GO:0048872)|inter-male aggressive behavior (GO:0002121)|kidney morphogenesis (GO:0060993)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)|protein O-linked glycosylation (GO:0006493)|thyroid hormone metabolic process (GO:0042403)|tissue morphogenesis (GO:0048729)	Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)	beta-1,3-galactosyl-O-glycosyl-glycoprotein beta-1,6-N-acetylglucosaminyltransferase activity (GO:0003829)|N-acetyllactosaminide beta-1,6-N-acetylglucosaminyltransferase activity (GO:0008109)			NS(1)|breast(1)|endometrium(1)|kidney(1)|large_intestine(7)|lung(3)|ovary(2)|skin(1)|stomach(2)	19		all_lung(232;0.0131)|Lung NSC(167;0.0282)|Ovarian(174;0.0798)		OV - Ovarian serous cystadenocarcinoma(47;8.44e-57)		GGGGTTTCACCGTCTCCAACA	0.378																																					p.T254T		Atlas-SNP	.											GCNT4,NS,carcinoma,-2,1	GCNT4	46	1	0			c.G762A						PASS	.						85.0	88.0	87.0					5																	74325101		2203	4300	6503	SO:0001819	synonymous_variant	51301	exon1			TTTCACCGTCTCC	AF132035	CCDS4026.1	5q12	2013-02-25	2010-03-16		ENSG00000176928	ENSG00000176928	2.4.1.102	"""Glucosaminyl (N-acetyl) transferase and xylosyltransferase family"""	17973	protein-coding gene	gene with protein product	"""core 2 beta-1,6-N-acetylglucosaminyltransferase 3"", ""beta-1,3-galactosyl-O-glycosyl-glycoprotein beta-1,6-N-acetylglucosaminyltransferase 4"""		"""glucosaminyl (N-acetyl) transferase 4, core 2 (beta-1,6-N-acetylglucosaminyltransferase)"""			10753916	Standard	NM_016591		Approved	C2GNT3	uc003kdn.3	Q9P109	OTTHUMG00000131272	ENST00000322348.4:c.762G>A	5.37:g.74325101C>T		103.0	0.0	0		106.0	52.0	0.490566	NM_016591		Silent	SNP	ENST00000322348.4	37	CCDS4026.1																																																																																			.	.	none		0.378	GCNT4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254040.1	NM_016591	
KLHL28	54813	hgsc.bcm.edu	37	14	45403616	45403616	+	Missense_Mutation	SNP	T	T	C	rs35728857	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr14:45403616T>C	ENST00000396128.4	-	3	1164	c.1045A>G	c.(1045-1047)Atc>Gtc	p.I349V	KLHL28_ENST00000355081.2_Missense_Mutation_p.I363V	NM_017658.3	NP_060128.2	Q9NXS3	KLH28_HUMAN	kelch-like family member 28	349			I -> V (in dbSNP:rs35728857).							breast(2)|endometrium(3)|large_intestine(3)|lung(10)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	22						TGTTTTCTGATAGTGACGCCA	0.388													T|||	6	0.00119808	0.0	0.0029	5008	,	,		19647	0.0		0.003	False		,,,				2504	0.001				p.I349V		Atlas-SNP	.											.	KLHL28	53	.	0			c.A1045G						PASS	.	T	VAL/ILE	6,4400	11.4+/-27.6	0,6,2197	116.0	108.0	111.0		1045	-1.1	1.0	14	dbSNP_126	111	36,8564	25.1+/-72.6	0,36,4264	yes	missense	KLHL28	NM_017658.3	29	0,42,6461	CC,CT,TT		0.4186,0.1362,0.3229	benign	349/572	45403616	42,12964	2203	4300	6503	SO:0001583	missense	54813	exon3			TTCTGATAGTGAC	AK000088	CCDS9680.1	14q21.1	2013-02-22	2013-02-22	2007-01-09	ENSG00000179454	ENSG00000179454		"""Kelch-like"", ""BTB/POZ domain containing"""	19741	protein-coding gene	gene with protein product			"""BTB (POZ) domain containing 5"", ""kelch-like 28 (Drosophila)"""	BTBD5			Standard	NM_017658		Approved	FLJ20081	uc001wvr.3	Q9NXS3	OTTHUMG00000140263	ENST00000396128.4:c.1045A>G	14.37:g.45403616T>C	ENSP00000379434:p.Ile349Val	155.0	0.0	0		140.0	65.0	0.464286	NM_017658	Q0VAL5	Missense_Mutation	SNP	ENST00000396128.4	37	CCDS9680.1	3	0.0013736263736263737	0	0.0	1	0.0027624309392265192	0	0.0	2	0.002638522427440633	T	10.34	1.322698	0.23994	0.001362	0.004186	ENSG00000179454	ENST00000396128;ENST00000355081	T;T	0.77229	-1.08;-1.08	5.38	-1.07	0.09968	Kelch-type beta propeller (1);	0.305531	0.37136	N	0.002234	T	0.48040	0.1478	N	0.12746	0.255	0.23515	N	0.997516	B	0.06786	0.001	B	0.14023	0.01	T	0.15407	-1.0438	10	0.14252	T	0.57	.	0.81	0.01091	0.3527:0.0965:0.2311:0.3196	rs35728857	349	Q9NXS3	KLH28_HUMAN	V	349;363	ENSP00000379434:I349V;ENSP00000347193:I363V	ENSP00000347193:I363V	I	-	1	0	KLHL28	44473366	1.000000	0.71417	0.992000	0.48379	0.986000	0.74619	1.815000	0.38981	0.060000	0.16281	0.455000	0.32223	ATC	T|0.997;C|0.003	0.003	strong		0.388	KLHL28-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276790.3		
E2F3	1871	hgsc.bcm.edu	37	6	20490428	20490428	+	Missense_Mutation	SNP	G	G	A	rs4134982	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr6:20490428G>A	ENST00000346618.3	+	7	1231	c.1165G>A	c.(1165-1167)Gat>Aat	p.D389N	E2F3_ENST00000535432.1_Missense_Mutation_p.D258N	NM_001949.4	NP_001940.1	O00716	E2F3_HUMAN	E2F transcription factor 3	389			D -> N (in dbSNP:rs4134982). {ECO:0000269|Ref.2}.		mitotic cell cycle (GO:0000278)|Notch signaling pathway (GO:0007219)|positive regulation of cell proliferation (GO:0008284)|positive regulation of transcription, DNA-templated (GO:0045893)|transcription initiation from RNA polymerase II promoter (GO:0006367)	cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|intracellular membrane-bounded organelle (GO:0043231)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	core promoter binding (GO:0001047)|sequence-specific DNA binding transcription factor activity (GO:0003700)			central_nervous_system(1)|kidney(1)|large_intestine(2)|lung(3)	7	all_cancers(95;0.154)|all_epithelial(95;0.0585)|Breast(50;0.146)|Ovarian(93;0.148)		OV - Ovarian serous cystadenocarcinoma(7;0.0068)|all cancers(50;0.0148)|Epithelial(50;0.0562)			AGGACATAGCGATTGCTCAGT	0.408													G|||	15	0.00299521	0.0	0.0043	5008	,	,		19775	0.0		0.0119	False		,,,				2504	0.0				p.D389N		Atlas-SNP	.											E2F3,NS,carcinoma,-2,1	E2F3	30	1	0			c.G1165A						PASS	.	G	ASN/ASP	12,4394	17.9+/-39.9	0,12,2191	75.0	75.0	75.0		1165	5.5	0.8	6	dbSNP_108	75	99,8501	54.0+/-114.7	0,99,4201	yes	missense	E2F3	NM_001949.4	23	0,111,6392	AA,AG,GG		1.1512,0.2724,0.8535	benign	389/466	20490428	111,12895	2203	4300	6503	SO:0001583	missense	1871	exon7			CATAGCGATTGCT	Y10479	CCDS4545.1, CCDS58999.1	6p22	2008-08-29			ENSG00000112242	ENSG00000112242			3115	protein-coding gene	gene with protein product		600427				8246996	Standard	NM_001949		Approved		uc003nda.2	O00716	OTTHUMG00000016389	ENST00000346618.3:c.1165G>A	6.37:g.20490428G>A	ENSP00000262904:p.Asp389Asn	176.0	0.0	0		137.0	57.0	0.416058	NM_001949	Q15000|Q68DT0|Q9BZ44	Missense_Mutation	SNP	ENST00000346618.3	37	CCDS4545.1	12	0.005494505494505495	1	0.0020325203252032522	3	0.008287292817679558	0	0.0	8	0.010554089709762533	G	9.602	1.129011	0.21041	0.002724	0.011512	ENSG00000112242	ENST00000346618;ENST00000535432	T;T	0.06933	3.24;3.26	5.49	5.49	0.81192	.	0.338236	0.35378	N	0.003255	T	0.02304	0.0071	N	0.21097	0.63	0.42665	D	0.993494	B	0.16396	0.017	B	0.08055	0.003	T	0.45760	-0.9239	10	0.27082	T	0.32	.	9.5533	0.39324	0.0743:0.1436:0.782:0.0	rs4134982;rs52820498;rs4134982	389	O00716	E2F3_HUMAN	N	389;258	ENSP00000262904:D389N;ENSP00000443418:D258N	ENSP00000262904:D389N	D	+	1	0	E2F3	20598407	1.000000	0.71417	0.808000	0.32385	0.973000	0.67179	3.942000	0.56614	2.746000	0.94184	0.561000	0.74099	GAT	G|0.993;A|0.007	0.007	strong		0.408	E2F3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000043828.1		
KDM5C	8242	hgsc.bcm.edu	37	X	53223819	53223819	+	Silent	SNP	C	C	T	rs76525703	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chrX:53223819C>T	ENST00000375401.3	-	23	4072	c.3540G>A	c.(3538-3540)acG>acA	p.T1180T	KDM5C_ENST00000404049.3_Silent_p.T1179T|KDM5C_ENST00000375379.3_Silent_p.T1180T|KDM5C_ENST00000452825.3_Silent_p.T1113T|KDM5C_ENST00000375383.3_Silent_p.T1139T	NM_001282622.1|NM_004187.3	NP_001269551.1|NP_004178.2	P41229	KDM5C_HUMAN	lysine (K)-specific demethylase 5C	1180					histone H3-K4 demethylation (GO:0034720)|negative regulation of transcription, DNA-templated (GO:0045892)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|histone demethylase activity (H3-K4 specific) (GO:0032453)|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)|zinc ion binding (GO:0008270)			autonomic_ganglia(1)|breast(4)|central_nervous_system(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(30)|large_intestine(9)|lung(17)|oesophagus(1)|ovary(6)|prostate(1)|salivary_gland(1)|skin(1)|upper_aerodigestive_tract(2)	82						TAGAGGAGGCCGTGCTCGATG	0.612			"""N, F, S"""		clear cell renal carcinoma								c|||	18	0.00476821	0.0136	0.0	3775	,	,		14232	0.0		0.0	False		,,,				2504	0.0				p.T1180T		Atlas-SNP	.		Rec	yes		X	Xp11.22-p11.21	8242	lysine (K)-specific demethylase 5C (JARID1C)		E	.	KDM5C	385	.	0			c.G3540A						PASS	.	C	,	37,3798		0,28,9,1604,562	221.0	158.0	179.0		3339,3540	-4.5	0.0	X	dbSNP_131	179	1,6727		0,0,1,2428,1871	no	coding-synonymous,coding-synonymous	KDM5C	NM_001146702.1,NM_004187.3	,	0,28,10,4032,2433	TT,TC,T,CC,C		0.0149,0.9648,0.3597	,	1113/1380,1180/1561	53223819	38,10525	2203	4300	6503	SO:0001819	synonymous_variant	8242	exon23			GGAGGCCGTGCTC	Z29650	CCDS14351.1, CCDS55417.1, CCDS65269.1	Xp11.22-p11.21	2014-01-31	2009-04-06	2009-04-06	ENSG00000126012	ENSG00000126012		"""Chromatin-modifying enzymes / K-demethylases"", ""Zinc fingers, PHD-type"""	11114	protein-coding gene	gene with protein product		314690	"""Jumonji, AT rich interactive domain 1C (RBP2-like)"", ""Smcy homolog, X-linked (mouse)"", ""jumonji, AT rich interactive domain 1C"", ""mental retardation, X-linked 13"""	SMCX, JARID1C, MRX13		7951230, 8162017, 19826449	Standard	NM_004187		Approved	DXS1272E, XE169	uc004drz.3	P41229	OTTHUMG00000021606	ENST00000375401.3:c.3540G>A	X.37:g.53223819C>T		245.0	1.0	0.00408163		279.0	278.0	0.996416	NM_004187	B0QZ44|B4E3I2|F5H3T1|Q5JUX3|Q5JUX4|Q5JUX5|Q7Z5S5	Silent	SNP	ENST00000375401.3	37	CCDS14351.1																																																																																			C|0.996;T|0.004	0.004	strong		0.612	KDM5C-005	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000056737.2	NM_004187	
AHNAK2	113146	hgsc.bcm.edu	37	14	105412335	105412335	+	Silent	SNP	C	C	T	rs202104959	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr14:105412335C>T	ENST00000333244.5	-	7	9572	c.9453G>A	c.(9451-9453)ccG>ccA	p.P3151P	AHNAK2_ENST00000557457.1_Intron	NM_138420.2	NP_612429.2	Q8IVF2	AHNK2_HUMAN	AHNAK nucleoprotein 2	3151						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)		p.P3151P(1)		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)			CCCCGAACGACGGCATCTTGA	0.602																																					p.P3151P		Atlas-SNP	.											AHNAK2_ENST00000333244,NS,carcinoma,0,2	AHNAK2	719	2	1	Substitution - coding silent(1)	endometrium(1)	c.G9453A						scavenged	.						198.0	138.0	157.0					14																	105412335		1921	4005	5926	SO:0001819	synonymous_variant	113146	exon7			GAACGACGGCATC	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.9453G>A	14.37:g.105412335C>T		291.0	0.0	0		21.0	4.0	0.190476	NM_138420	Q5BKX7|Q7Z343|Q7Z358|Q7Z394|Q7Z3G0|Q86WQ6|Q8IYY1|Q8N3G4|Q96EX9	Silent	SNP	ENST00000333244.5	37	CCDS45177.1																																																																																			C|0.963;T|0.037	0.037	strong		0.602	AHNAK2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000410300.1	NM_138420	
CNNM4	26504	hgsc.bcm.edu	37	2	97465379	97465379	+	Missense_Mutation	SNP	C	C	T	rs144495984		TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr2:97465379C>T	ENST00000377075.2	+	5	2040	c.1942C>T	c.(1942-1944)Ccc>Tcc	p.P648S	MIR3127_ENST00000583925.1_RNA|CNNM4_ENST00000540067.1_Missense_Mutation_p.P135S|CNNM4_ENST00000496186.1_3'UTR	NM_020184.3	NP_064569.3	Q6P4Q7	CNNM4_HUMAN	cyclin and CBS domain divalent metal cation transport mediator 4	648					biomineral tissue development (GO:0031214)|ion transport (GO:0006811)|response to stimulus (GO:0050896)|visual perception (GO:0007601)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	adenyl nucleotide binding (GO:0030554)			breast(2)|endometrium(4)|kidney(1)|large_intestine(1)|lung(9)|ovary(1)|prostate(2)	20						GACCTCGGTCCCCTCCGGTGA	0.602																																					p.P648S		Atlas-SNP	.											.	CNNM4	48	.	0			c.C1942T						PASS	.	C	SER/PRO	0,4340		0,0,2170	85.0	72.0	77.0		1942	-1.7	0.0	2	dbSNP_134	77	2,8374		0,2,4186	yes	missense	CNNM4	NM_020184.3	74	0,2,6356	TT,TC,CC		0.0239,0.0,0.0157	benign	648/776	97465379	2,12714	2170	4188	6358	SO:0001583	missense	26504	exon5			TCGGTCCCCTCCG	AB046812	CCDS2024.2	2q11.2	2014-08-08	2014-08-07		ENSG00000158158	ENSG00000158158			105	protein-coding gene	gene with protein product		607805	"""cyclin M4"""	ACDP4		21393841, 24194943	Standard	XM_005263914		Approved	KIAA1592	uc002swx.3	Q6P4Q7	OTTHUMG00000130532	ENST00000377075.2:c.1942C>T	2.37:g.97465379C>T	ENSP00000366275:p.Pro648Ser	161.0	0.0	0		174.0	84.0	0.482759	NM_020184	B7Z1U0|C7SQM3|C7SQM4|C7SQM5|Q53RE5|Q9H9G3|Q9HCI0|Q9NRN1	Missense_Mutation	SNP	ENST00000377075.2	37	CCDS2024.2	.	.	.	.	.	.	.	.	.	.	C	11.98	1.800104	0.31869	0.0	2.39E-4	ENSG00000158158	ENST00000377075;ENST00000540067	T	0.73047	-0.71	4.78	-1.71	0.08133	RmlC-like jelly roll fold (1);Cyclic nucleotide-binding domain (2);	0.773363	0.12569	N	0.457447	T	0.36082	0.0954	N	0.03281	-0.365	0.18873	N	0.999989	B;B	0.14438	0.01;0.0	B;B	0.17433	0.018;0.0	T	0.18053	-1.0349	10	0.17369	T	0.5	-9.342	0.8361	0.01140	0.2255:0.3422:0.2194:0.2129	.	135;648	B7Z1U0;Q6P4Q7	.;CNNM4_HUMAN	S	648;135	ENSP00000366275:P648S	ENSP00000366275:P648S	P	+	1	0	CNNM4	96829106	0.000000	0.05858	0.000000	0.03702	0.230000	0.25150	-1.945000	0.01537	-0.484000	0.06763	-0.291000	0.09656	CCC	C|1.000;T|0.000	0.000	weak		0.602	CNNM4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252954.1	NM_020184	
SLCO6A1	133482	hgsc.bcm.edu	37	5	101815888	101815888	+	Silent	SNP	T	T	C	rs150189521	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr5:101815888T>C	ENST00000506729.1	-	2	780	c.609A>G	c.(607-609)ggA>ggG	p.G203G	SLCO6A1_ENST00000379807.3_Silent_p.G203G|SLCO6A1_ENST00000389019.3_Silent_p.G203G|SLCO6A1_ENST00000514551.1_Intron|SLCO6A1_ENST00000513675.1_Silent_p.G203G|SLCO6A1_ENST00000379810.1_Silent_p.G203G			Q86UG4	SO6A1_HUMAN	solute carrier organic anion transporter family, member 6A1	203						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	transporter activity (GO:0005215)			breast(1)|central_nervous_system(1)|endometrium(2)|kidney(2)|large_intestine(17)|lung(22)|ovary(3)|prostate(4)|skin(6)|upper_aerodigestive_tract(1)|urinary_tract(1)	60		all_cancers(142;8e-09)|all_epithelial(76;2.83e-12)|Prostate(80;0.00125)|Colorectal(57;0.00342)|Ovarian(225;0.024)|Lung NSC(167;0.0259)|all_lung(232;0.0323)		Epithelial(69;1.47e-15)|COAD - Colon adenocarcinoma(37;0.0113)		TACCTTCAATTCCTACCTTAC	0.299													T|||	12	0.00239617	0.0008	0.0029	5008	,	,		18321	0.0		0.0089	False		,,,				2504	0.0				p.G203G		Atlas-SNP	.											.	SLCO6A1	153	.	0			c.A609G						PASS	.	T		8,4394	11.4+/-27.6	0,8,2193	66.0	68.0	68.0		609	0.4	0.0	5	dbSNP_134	68	81,8513	37.8+/-93.5	0,81,4216	no	coding-synonymous	SLCO6A1	NM_173488.3		0,89,6409	CC,CT,TT		0.9425,0.1817,0.6848		203/720	101815888	89,12907	2201	4297	6498	SO:0001819	synonymous_variant	133482	exon2			TTCAATTCCTACC	AF505657	CCDS34206.1, CCDS75282.1	5q21.2	2013-05-22			ENSG00000205359	ENSG00000205359		"""Solute carriers"""	23613	protein-coding gene	gene with protein product	"""cancer/testis antigen 48"""	613365					Standard	XM_005271874		Approved	OATP6A1, OATPY, MGC26949, CT48	uc003knp.3	Q86UG4	OTTHUMG00000162759	ENST00000506729.1:c.609A>G	5.37:g.101815888T>C		73.0	0.0	0		69.0	31.0	0.449275	NM_173488	A6NHC1|Q6ZMY5|Q86UV2|Q8IYU5	Silent	SNP	ENST00000506729.1	37	CCDS34206.1																																																																																			T|0.994;C|0.006	0.006	strong		0.299	SLCO6A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000370335.1	NM_173488	
KRT82	3888	hgsc.bcm.edu	37	12	52788814	52788814	+	Missense_Mutation	SNP	C	C	T	rs61730587	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr12:52788814C>T	ENST00000257974.2	-	9	1564	c.1487G>A	c.(1486-1488)cGg>cAg	p.R496Q	RP3-416H24.4_ENST00000547174.1_RNA	NM_033033.3	NP_149022.3	Q9NSB4	KRT82_HUMAN	keratin 82	496	Tail.					keratin filament (GO:0045095)	structural constituent of epidermis (GO:0030280)			endometrium(1)|kidney(2)|large_intestine(6)|liver(2)|lung(13)|ovary(1)|skin(3)|upper_aerodigestive_tract(1)	29				BRCA - Breast invasive adenocarcinoma(357;0.193)		GCTGGATTTCCGCCCGCTCCC	0.642													c|||	21	0.00419329	0.0023	0.0072	5008	,	,		16513	0.0		0.0089	False		,,,				2504	0.0041				p.R496Q		Atlas-SNP	.											KRT82,NS,carcinoma,-1,1	KRT82	45	1	0			c.G1487A						scavenged	.	T	GLN/ARG	14,4392	21.2+/-45.6	0,14,2189	48.0	48.0	48.0		1487	-0.4	0.0	12	dbSNP_129	48	113,8487	58.7+/-120.3	1,111,4188	yes	missense	KRT82	NM_033033.3	43	1,125,6377	TT,TC,CC		1.314,0.3177,0.9765	benign	496/514	52788814	127,12879	2203	4300	6503	SO:0001583	missense	3888	exon9			GATTTCCGCCCGC	Y19207	CCDS8826.1	12q13	2013-01-16	2006-07-17	2006-07-17		ENSG00000161850		"""-"", ""Intermediate filaments type II, keratins (basic)"""	6459	protein-coding gene	gene with protein product	"""hard keratin type II 2"""	601078	"""keratin, hair, basic, 2"""	KRTHB2		2431943, 16831889	Standard	NM_033033		Approved	Hb-2	uc001sai.1	Q9NSB4	OTTHUMG00000169636	ENST00000257974.2:c.1487G>A	12.37:g.52788814C>T	ENSP00000257974:p.Arg496Gln	138.0	1.0	0.00724638		125.0	65.0	0.52	NM_033033		Missense_Mutation	SNP	ENST00000257974.2	37	CCDS8826.1	11	0.005036630036630037	0	0.0	4	0.011049723756906077	0	0.0	7	0.009234828496042216	c	11.54	1.670563	0.29693	0.003177	0.01314	ENSG00000161850	ENST00000257974	D	0.82255	-1.59	4.59	-0.424	0.12321	.	0.753921	0.10873	N	0.624709	T	0.52933	0.1765	N	0.08118	0	0.09310	N	1	B	0.14438	0.01	B	0.04013	0.001	T	0.39800	-0.9596	10	0.25106	T	0.35	.	4.4613	0.11668	0.1481:0.4148:0.0:0.4371	rs61730587	496	Q9NSB4	KRT82_HUMAN	Q	496	ENSP00000257974:R496Q	ENSP00000257974:R496Q	R	-	2	0	KRT82	51075081	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	0.155000	0.16362	-0.326000	0.08564	-0.215000	0.12644	CGG	C|0.991;T|0.009	0.009	strong		0.642	KRT82-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000405189.1	NM_033033	
VSIG4	11326	hgsc.bcm.edu	37	X	65242157	65242157	+	Missense_Mutation	SNP	G	G	A	rs41307375	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chrX:65242157G>A	ENST00000374737.4	-	8	1256	c.1148C>T	c.(1147-1149)aCa>aTa	p.T383I	VSIG4_ENST00000455586.2_3'UTR|VSIG4_ENST00000412866.2_Missense_Mutation_p.T289I	NM_001257403.1|NM_007268.2	NP_001244332.1|NP_009199.1	Q9Y279	VSIG4_HUMAN	V-set and immunoglobulin domain containing 4	383					complement activation, alternative pathway (GO:0006957)|negative regulation of interleukin-2 production (GO:0032703)|negative regulation of T cell proliferation (GO:0042130)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)				breast(2)|endometrium(1)|kidney(2)|large_intestine(2)|lung(14)|ovary(1)|prostate(2)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	29						CAGAGGAACTGTGTCCAGCAG	0.507													G|||	14	0.00370861	0.0	0.0058	3775	,	,		15026	0.0		0.007	False		,,,				2504	0.0031				p.T383I		Atlas-SNP	.											.	VSIG4	54	.	0			c.C1148T						PASS	.	G	ILE/THR,,,ILE/THR	5,3830		0,4,1,1628,570	81.0	68.0	73.0		866,,,1148	2.7	0.0	X	dbSNP_127	73	55,6673		0,35,20,2393,1852	yes	missense,utr-3,utr-3,missense	VSIG4	NM_001100431.1,NM_001184830.1,NM_001184831.1,NM_007268.2	89,,,89	0,39,21,4021,2422	AA,AG,A,GG,G		0.8175,0.1304,0.568	probably-damaging,,,probably-damaging	289/306,,,383/400	65242157	60,10503	2203	4300	6503	SO:0001583	missense	11326	exon8			GGAACTGTGTCCA	AJ132502	CCDS14383.1, CCDS48132.1, CCDS55435.1	Xq12-q13.3	2013-01-29			ENSG00000155659	ENSG00000155659		"""Immunoglobulin superfamily / V-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	17032	protein-coding gene	gene with protein product		300353				10899594, 11004523, 17016555, 17016562	Standard	NM_007268		Approved	Z39IG	uc004dwh.2	Q9Y279	OTTHUMG00000021727	ENST00000374737.4:c.1148C>T	X.37:g.65242157G>A	ENSP00000363869:p.Thr383Ile	132.0	0.0	0		139.0	138.0	0.992806	NM_007268	Q6UXI4	Missense_Mutation	SNP	ENST00000374737.4	37	CCDS14383.1	10	0.006027727546714889	0	0.0	4	0.011049723756906077	0	0.0	4	0.005305039787798408	G	6.391	0.440248	0.12104	0.001304	0.008175	ENSG00000155659	ENST00000374737;ENST00000412866	T;T	0.29142	1.58;2.06	4.55	2.69	0.31865	.	0.562854	0.14925	N	0.290449	T	0.23532	0.0569	L	0.57536	1.79	0.09310	N	0.999995	P;B	0.35908	0.527;0.232	B;B	0.37989	0.262;0.082	T	0.13045	-1.0524	10	0.72032	D	0.01	-2.997	8.7467	0.34591	0.0:0.0:0.5888:0.4112	rs41307375	289;383	Q9Y279-3;Q9Y279	.;VSIG4_HUMAN	I	383;289	ENSP00000363869:T383I;ENSP00000394143:T289I	ENSP00000363869:T383I	T	-	2	0	VSIG4	65158882	0.010000	0.17322	0.007000	0.13788	0.011000	0.07611	0.952000	0.29149	0.423000	0.26033	0.513000	0.50165	ACA	G|0.994;A|0.006	0.006	strong		0.507	VSIG4-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000056986.1	NM_007268	
SLC38A8	146167	hgsc.bcm.edu	37	16	84050776	84050776	+	Missense_Mutation	SNP	T	T	C	rs142821762		TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr16:84050776T>C	ENST00000299709.3	-	7	921	c.922A>G	c.(922-924)Act>Gct	p.T308A		NM_001080442.1	NP_001073911.1	A6NNN8	S38A8_HUMAN	solute carrier family 38, member 8	308					amino acid transport (GO:0006865)|sodium ion transport (GO:0006814)	integral component of membrane (GO:0016021)				central_nervous_system(1)|endometrium(3)|kidney(3)|large_intestine(3)|lung(12)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	26						GGGTAGACAGTTACGATGGAG	0.537													T|||	1	0.000199681	0.0	0.0	5008	,	,		19595	0.0		0.001	False		,,,				2504	0.0				p.T308A		Atlas-SNP	.											.	SLC38A8	60	.	0			c.A922G						PASS	.	T	ALA/THR	0,4400		0,0,2200	113.0	88.0	97.0		922	4.8	0.2	16	dbSNP_134	97	8,8592	6.4+/-24.3	0,8,4292	yes	missense	SLC38A8	NM_001080442.1	58	0,8,6492	CC,CT,TT		0.093,0.0,0.0615	probably-damaging	308/436	84050776	8,12992	2200	4300	6500	SO:0001583	missense	146167	exon7			AGACAGTTACGAT		CCDS32495.1	16q23.3	2013-05-22				ENSG00000166558		"""Solute carriers"""	32434	protein-coding gene	gene with protein product		615585					Standard	XM_006721135		Approved		uc002fhg.1	A6NNN8		ENST00000299709.3:c.922A>G	16.37:g.84050776T>C	ENSP00000299709:p.Thr308Ala	56.0	0.0	0		77.0	51.0	0.662338	NM_001080442		Missense_Mutation	SNP	ENST00000299709.3	37	CCDS32495.1	.	.	.	.	.	.	.	.	.	.	T	19.79	3.893044	0.72524	0.0	9.3E-4	ENSG00000166558	ENST00000299709	T	0.02236	4.38	4.75	4.75	0.60458	.	0.110120	0.64402	D	0.000009	T	0.09642	0.0237	M	0.76838	2.35	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	T	0.36696	-0.9737	10	0.06099	T	0.92	-17.5765	13.2419	0.60002	0.0:0.0:0.0:1.0	.	308	A6NNN8	S38A8_HUMAN	A	308	ENSP00000299709:T308A	ENSP00000299709:T308A	T	-	1	0	SLC38A8	82608277	1.000000	0.71417	0.184000	0.23157	0.920000	0.55202	7.230000	0.78097	1.773000	0.52216	0.391000	0.25812	ACT	T|1.000;C|0.000	0.000	strong		0.537	SLC38A8-001	KNOWN	upstream_ATG|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000432623.1	NM_001080442	
TONSL	4796	hgsc.bcm.edu	37	8	145657840	145657840	+	Missense_Mutation	SNP	G	G	A	rs146566654	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr8:145657840G>A	ENST00000409379.3	-	23	3592	c.3563C>T	c.(3562-3564)gCt>gTt	p.A1188V	AC084125.4_ENST00000544423.1_RNA	NM_013432.4	NP_038460.4	Q96HA7	TONSL_HUMAN	tonsoku-like, DNA repair protein	1188					cytoplasmic sequestering of transcription factor (GO:0042994)|double-strand break repair via homologous recombination (GO:0000724)|regulation of RNA biosynthetic process (GO:2001141)|replication fork processing (GO:0031297)	cytoplasm (GO:0005737)|nuclear replication fork (GO:0043596)|nucleus (GO:0005634)	histone binding (GO:0042393)|transcription corepressor activity (GO:0003714)			biliary_tract(1)|central_nervous_system(1)|cervix(1)|endometrium(2)|kidney(2)|lung(14)|ovary(3)|prostate(1)|skin(1)	26						CAGGTGCTCAGCATCTGCACC	0.667													G|||	2	0.000399361	0.0	0.0	5008	,	,		15419	0.0		0.0	False		,,,				2504	0.002				p.A1188V		Atlas-SNP	.											.	TONSL	128	.	0			c.C3563T						PASS	.	G	VAL/ALA	1,4405	2.1+/-5.4	0,1,2202	49.0	56.0	54.0		3563	5.0	0.9	8	dbSNP_134	54	8,8592	6.4+/-24.3	0,8,4292	yes	missense	TONSL	NM_013432.4	64	0,9,6494	AA,AG,GG		0.093,0.0227,0.0692	possibly-damaging	1188/1379	145657840	9,12997	2203	4300	6503	SO:0001583	missense	4796	exon23			TGCTCAGCATCTG		CCDS34968.2	8q24.3	2013-01-10	2010-12-02	2010-11-30	ENSG00000160949	ENSG00000160949		"""Ankyrin repeat domain containing"""	7801	protein-coding gene	gene with protein product		604546	"""nuclear factor of kappa light polypeptide gene enhancer in B-cells inhibitor-like 2"""	NFKBIL2		7738005, 11246458	Standard	NM_013432		Approved	IKBR	uc011llg.2	Q96HA7	OTTHUMG00000153122	ENST00000409379.3:c.3563C>T	8.37:g.145657840G>A	ENSP00000386239:p.Ala1188Val	113.0	0.0	0		114.0	55.0	0.482456	NM_013432	B5MDP0|C9JKB1|C9JNV8|Q13006|Q9UGJ2	Missense_Mutation	SNP	ENST00000409379.3	37	CCDS34968.2	.	.	.	.	.	.	.	.	.	.	g	0.591	-0.833165	0.02713	2.27E-4	9.3E-4	ENSG00000160949	ENST00000409379;ENST00000422691	T	0.52526	0.66	4.99	4.99	0.66335	.	0.277567	0.33650	N	0.004684	T	0.44953	0.1318	L	0.51853	1.615	0.40916	D	0.984272	B	0.25390	0.125	B	0.22753	0.041	T	0.48175	-0.9058	10	0.66056	D	0.02	-9.63	15.8111	0.78565	0.0:0.0:1.0:0.0	.	1188	Q96HA7	TONSL_HUMAN	V	1188;1187	ENSP00000386239:A1188V	ENSP00000386239:A1188V	A	-	2	0	TONSL	145628648	0.970000	0.33590	0.868000	0.34077	0.114000	0.19823	2.838000	0.48199	2.324000	0.78689	0.456000	0.33151	GCT	G|1.000;A|0.000	0.000	strong		0.667	TONSL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000329668.2	NM_013432	
KANSL1	284058	hgsc.bcm.edu	37	17	44248783	44248783	+	Missense_Mutation	SNP	G	G	T	rs142096969	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr17:44248783G>T	ENST00000262419.6	-	2	1197	c.727C>A	c.(727-729)Caa>Aaa	p.Q243K	KANSL1_ENST00000572904.1_Missense_Mutation_p.Q243K|KANSL1_ENST00000576248.1_5'Flank|KANSL1_ENST00000574590.1_Missense_Mutation_p.Q243K|KANSL1_ENST00000393476.3_5'UTR|KANSL1_ENST00000432791.1_Missense_Mutation_p.Q243K|KANSL1_ENST00000575318.1_Missense_Mutation_p.Q243K	NM_001193466.1	NP_001180395	Q7Z3B3	KANL1_HUMAN	KAT8 regulatory NSL complex subunit 1	243					chromatin organization (GO:0006325)|histone H4-K16 acetylation (GO:0043984)|histone H4-K5 acetylation (GO:0043981)|histone H4-K8 acetylation (GO:0043982)	histone acetyltransferase complex (GO:0000123)|MLL1 complex (GO:0071339)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)		p.Q243E(2)									CTGCTTCCTTGAAGTGCCGGC	0.438													G|||	4	0.000798722	0.0	0.0043	5008	,	,		25143	0.0		0.001	False		,,,				2504	0.0				p.Q243K		Atlas-SNP	.											KIAA1267,NS,carcinoma,0,1	.	.	1	2	Substitution - Missense(2)	prostate(2)	c.C727A						PASS	.	G	LYS/GLN,LYS/GLN,LYS/GLN	1,4405	2.1+/-5.4	0,1,2202	97.0	122.0	114.0		727,727,727	6.0	1.0	17	dbSNP_134	114	21,8579	14.0+/-48.4	0,21,4279	yes	missense,missense,missense	KIAA1267	NM_001193465.1,NM_001193466.1,NM_015443.3	53,53,53	0,22,6481	TT,TG,GG		0.2442,0.0227,0.1692	benign,benign,benign	243/1105,243/1106,243/1106	44248783	22,12984	2203	4300	6503	SO:0001583	missense	284058	exon2			TTCCTTGAAGTGC	BX538006	CCDS11503.1, CCDS11503.2, CCDS74084.1	17q21.31	2012-02-20	2012-02-20	2012-02-20	ENSG00000120071	ENSG00000120071			24565	protein-coding gene	gene with protein product	"""centromere protein 36"""	612452	"""KIAA1267"""	KIAA1267		10574462	Standard	NM_015443		Approved	DKFZP727C091, MSL1v1, CENP-36, NSL1	uc002ikd.3	Q7Z3B3		ENST00000262419.6:c.727C>A	17.37:g.44248783G>T	ENSP00000262419:p.Gln243Lys	331.0	0.0	0		354.0	110.0	0.310734	NM_001193466	A8K5E4|Q6AW85|Q8IYH1|Q9BRH0|Q9NTE7|Q9UFT0|Q9ULF3	Missense_Mutation	SNP	ENST00000262419.6	37	CCDS11503.1	.	.	.	.	.	.	.	.	.	.	G	11.16	1.556207	0.27827	2.27E-4	0.002442	ENSG00000120071	ENST00000262419;ENST00000432791	T;T	0.12039	2.72;2.72	6.04	6.04	0.98038	.	0.144262	0.47852	D	0.000202	T	0.08980	0.0222	N	0.14661	0.345	0.80722	D	1	B;B	0.24426	0.103;0.07	B;B	0.25140	0.058;0.033	T	0.36016	-0.9765	10	0.17369	T	0.5	-9.4613	13.6782	0.62467	0.0:0.1543:0.8457:0.0	.	243;243	C9JHY2;Q7Z3B3	.;K1267_HUMAN	K	243	ENSP00000262419:Q243K;ENSP00000387393:Q243K	ENSP00000262419:Q243K	Q	-	1	0	KIAA1267	41604560	1.000000	0.71417	1.000000	0.80357	0.991000	0.79684	2.286000	0.43496	2.873000	0.98535	0.561000	0.74099	CAA	G|0.998;T|0.002	0.002	strong		0.438	KANSL1-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000440274.1	NM_015443	
RRP9	9136	hgsc.bcm.edu	37	3	51969389	51969389	+	Missense_Mutation	SNP	C	C	T			TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr3:51969389C>T	ENST00000232888.6	-	10	1013	c.940G>A	c.(940-942)Gag>Aag	p.E314K		NM_004704.3	NP_004695.1	O43818	U3IP2_HUMAN	ribosomal RNA processing 9, small subunit (SSU) processome component, homolog (yeast)	314					rRNA processing (GO:0006364)	nucleus (GO:0005634)|small nuclear ribonucleoprotein complex (GO:0030532)|small nucleolar ribonucleoprotein complex (GO:0005732)	poly(A) RNA binding (GO:0044822)			breast(3)|endometrium(1)|kidney(1)|large_intestine(7)|liver(1)|lung(6)|ovary(1)|skin(1)	21				BRCA - Breast invasive adenocarcinoma(193;8.04e-05)|Kidney(197;0.000553)|KIRC - Kidney renal clear cell carcinoma(197;0.000724)		TGGGACTCCTCGGGGATCTTC	0.652																																					p.E314K		Atlas-SNP	.											.	RRP9	40	.	0			c.G940A						PASS	.						40.0	40.0	40.0					3																	51969389		2203	4300	6503	SO:0001583	missense	9136	exon10			ACTCCTCGGGGAT	AJ001340	CCDS2837.1	3p21.31	2013-01-10	2008-02-26	2006-10-24	ENSG00000114767	ENSG00000114767		"""WD repeat domain containing"""	16829	protein-coding gene	gene with protein product			"""RNA, U3 small nucleolar interacting protein 2"""	RNU3IP2		9418896, 12032086	Standard	NM_004704		Approved	U3-55K	uc003dbw.2	O43818	OTTHUMG00000156930	ENST00000232888.6:c.940G>A	3.37:g.51969389C>T	ENSP00000232888:p.Glu314Lys	91.0	0.0	0		95.0	40.0	0.421053	NM_004704	B2R996|Q8IZ30	Missense_Mutation	SNP	ENST00000232888.6	37	CCDS2837.1	.	.	.	.	.	.	.	.	.	.	C	32	5.146212	0.94603	.	.	ENSG00000114767	ENST00000232888	T	0.80909	-1.43	4.36	4.36	0.52297	WD40/YVTN repeat-like-containing domain (1);WD40 repeat-like-containing domain (1);WD40-repeat-containing domain (1);	0.051372	0.85682	D	0.000000	D	0.90748	0.7096	M	0.90759	3.145	0.80722	D	1	D	0.89917	1.0	D	0.70227	0.968	D	0.91266	0.5040	10	0.38643	T	0.18	-33.3696	16.7078	0.85377	0.0:1.0:0.0:0.0	.	314	O43818	U3IP2_HUMAN	K	314	ENSP00000232888:E314K	ENSP00000232888:E314K	E	-	1	0	RRP9	51944429	1.000000	0.71417	0.936000	0.37596	0.950000	0.60333	7.083000	0.76859	2.278000	0.76064	0.561000	0.74099	GAG	.	.	none		0.652	RRP9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000346637.1	NM_004704	
FAM89A	375061	hgsc.bcm.edu	37	1	231155682	231155682	+	Missense_Mutation	SNP	C	C	T	rs141463019	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr1:231155682C>T	ENST00000366654.4	-	2	516	c.482G>A	c.(481-483)cGa>cAa	p.R161Q	MIR1182_ENST00000408363.1_RNA|FAM89A_ENST00000494111.1_5'UTR	NM_198552.2	NP_940954.1	Q96GI7	FA89A_HUMAN	family with sequence similarity 89, member A	161										endometrium(1)|upper_aerodigestive_tract(1)	2	Breast(184;0.0871)|Ovarian(103;0.183)	Prostate(94;0.178)				AGGAGGGCCTCGGTCCCTCCT	0.582													C|||	4	0.000798722	0.0015	0.0	5008	,	,		20019	0.0		0.002	False		,,,				2504	0.0				p.R161Q		Atlas-SNP	.											.	FAM89A	8	.	0			c.G482A						PASS	.	C	GLN/ARG	6,4400	11.4+/-27.6	0,6,2197	81.0	79.0	80.0		482	-0.1	0.0	1	dbSNP_134	80	16,8584	11.9+/-42.8	0,16,4284	yes	missense	FAM89A	NM_198552.2	43	0,22,6481	TT,TC,CC		0.186,0.1362,0.1692	benign	161/185	231155682	22,12984	2203	4300	6503	SO:0001583	missense	375061	exon2			GGGCCTCGGTCCC	BC009447	CCDS1590.1	1q42.2	2008-02-05	2005-09-13	2005-09-13	ENSG00000182118	ENSG00000182118			25057	protein-coding gene	gene with protein product			"""chromosome 1 open reading frame 153"""	C1orf153		12477932	Standard	NM_198552		Approved	MGC15887	uc001hui.2	Q96GI7	OTTHUMG00000037960	ENST00000366654.4:c.482G>A	1.37:g.231155682C>T	ENSP00000355614:p.Arg161Gln	75.0	0.0	0		91.0	47.0	0.516484	NM_198552		Missense_Mutation	SNP	ENST00000366654.4	37	CCDS1590.1	1	4.578754578754579E-4	0	0.0	0	0.0	0	0.0	1	0.0013192612137203166	C	17.03	3.285071	0.59867	0.001362	0.00186	ENSG00000182118	ENST00000366654	.	.	.	5.6	-0.0557	0.13808	.	1.086610	0.07184	N	0.854580	T	0.26159	0.0638	N	0.19112	0.55	0.09310	N	1	B	0.22346	0.068	B	0.12837	0.008	T	0.22871	-1.0204	9	0.19147	T	0.46	5.0E-4	9.7002	0.40182	0.0:0.4293:0.0:0.5707	.	161	Q96GI7	FA89A_HUMAN	Q	161	.	ENSP00000355614:R161Q	R	-	2	0	FAM89A	229222305	0.000000	0.05858	0.001000	0.08648	0.968000	0.65278	-0.990000	0.03732	0.163000	0.19507	0.453000	0.30009	CGA	C|0.999;T|0.001	0.001	strong		0.582	FAM89A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000092652.1	NM_198552	
ATG4B	23192	hgsc.bcm.edu	37	2	242606080	242606080	+	Missense_Mutation	SNP	G	G	A	rs35613684	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr2:242606080G>A	ENST00000404914.3	+	8	662	c.559G>A	c.(559-561)Gtt>Att	p.V187I	ATG4B_ENST00000402096.1_Missense_Mutation_p.V113I|ATG4B_ENST00000396411.3_Missense_Mutation_p.V113I|ATG4B_ENST00000405546.3_Missense_Mutation_p.V187I|ATG4B_ENST00000474739.2_Missense_Mutation_p.V173I	NM_013325.4|NM_178326.2	NP_037457.3|NP_847896.1	Q9Y4P1	ATG4B_HUMAN	autophagy related 4B, cysteine peptidase	187					autophagic vacuole assembly (GO:0000045)|autophagy (GO:0006914)|positive regulation of autophagy (GO:0010508)|positive regulation of protein catabolic process (GO:0045732)|protein transport (GO:0015031)|proteolysis (GO:0006508)	cytoplasm (GO:0005737)	cysteine-type peptidase activity (GO:0008234)|endopeptidase activity (GO:0004175)			breast(1)|endometrium(4)|kidney(1)|large_intestine(1)|lung(1)|prostate(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	11		all_cancers(19;1.09e-40)|all_epithelial(40;2.03e-18)|Breast(86;1.53e-05)|all_lung(227;0.00338)|Renal(207;0.00502)|Ovarian(221;0.00716)|Lung NSC(271;0.012)|Esophageal squamous(248;0.129)|Melanoma(123;0.144)|all_hematologic(139;0.158)|all_neural(83;0.243)|Hepatocellular(293;0.244)		Epithelial(32;2.44e-33)|all cancers(36;5.71e-31)|OV - Ovarian serous cystadenocarcinoma(60;3.75e-15)|Kidney(56;3.04e-09)|KIRC - Kidney renal clear cell carcinoma(57;3.23e-08)|BRCA - Breast invasive adenocarcinoma(100;1.65e-06)|Lung(119;0.000152)|LUSC - Lung squamous cell carcinoma(224;0.00154)|Colorectal(34;0.0129)|COAD - Colon adenocarcinoma(134;0.0848)		CAGGACCAGCGTTCCCTGTGC	0.567													G|||	7	0.00139776	0.0	0.0014	5008	,	,		18650	0.0		0.006	False		,,,				2504	0.0				p.V187I	Melanoma(78;458 1323 6342 12171 39523)	Atlas-SNP	.											.	ATG4B	35	.	0			c.G559A						PASS	.	G	ILE/VAL,ILE/VAL	7,4269		0,7,2131	33.0	36.0	35.0		559,559	-3.0	0.0	2	dbSNP_126	35	60,8384		2,56,4164	yes	missense,missense	ATG4B	NM_013325.4,NM_178326.2	29,29	2,63,6295	AA,AG,GG		0.7106,0.1637,0.5267	benign,benign	187/394,187/381	242606080	67,12653	2138	4222	6360	SO:0001583	missense	23192	exon8			ACCAGCGTTCCCT	AB023160	CCDS46564.1, CCDS46565.1	2q37.3	2014-02-12	2012-06-06	2005-09-11	ENSG00000168397	ENSG00000168397			20790	protein-coding gene	gene with protein product		611338	"""APG4 autophagy 4 homolog B (S. cerevisiae)"", ""ATG4 autophagy related 4 homolog B (S. cerevisiae)"""	APG4B		12446702	Standard	NM_013325		Approved	Apg4B, KIAA0943, DKFZp586D1822, AUTL1	uc002wbv.3	Q9Y4P1	OTTHUMG00000151514	ENST00000404914.3:c.559G>A	2.37:g.242606080G>A	ENSP00000384259:p.Val187Ile	153.0	0.0	0		131.0	65.0	0.496183	NM_178326	B7WNK2|Q53NU4|Q6ZUV8|Q8WYM9|Q96K07|Q96K96|Q96SZ1|Q9Y2F2	Missense_Mutation	SNP	ENST00000404914.3	37	CCDS46564.1	4	0.0018315018315018315	0	0.0	1	0.0027624309392265192	0	0.0	3	0.00395778364116095	G	12.75	2.032450	0.35893	0.001637	0.007106	ENSG00000168397	ENST00000405546;ENST00000337606;ENST00000402096;ENST00000404914;ENST00000474739;ENST00000396411;ENST00000400771;ENST00000429899;ENST00000311517;ENST00000428861	T;T;T;T;T;T;T;T	0.42513	0.97;0.97;0.97;0.97;0.97;0.97;0.97;0.97	5.79	-2.96	0.05547	.	1.522260	0.03648	N	0.240580	T	0.15609	0.0376	N	0.12920	0.275	0.09310	N	1	B;B;B;B;B	0.25235	0.121;0.067;0.055;0.009;0.007	B;B;B;B;B	0.20184	0.016;0.028;0.024;0.008;0.01	T	0.07328	-1.0778	10	0.21540	T	0.41	0.9712	3.7127	0.08425	0.1122:0.134:0.4743:0.2795	rs35613684	173;304;275;187;113	F5H7P2;B4DZK0;Q9Y4P1-2;Q9Y4P1;Q9Y4P1-4	.;.;.;ATG4B_HUMAN;.	I	187;304;113;187;173;113;136;113;113;24	ENSP00000383964:V187I;ENSP00000384661:V113I;ENSP00000384259:V187I;ENSP00000442378:V173I;ENSP00000379692:V113I;ENSP00000383582:V136I;ENSP00000410526:V113I;ENSP00000404783:V24I	ENSP00000309348:V113I	V	+	1	0	ATG4B	242254753	0.000000	0.05858	0.000000	0.03702	0.431000	0.31685	-0.503000	0.06383	-0.406000	0.07588	-1.053000	0.02334	GTT	G|0.998;A|0.002	0.002	strong		0.567	ATG4B-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000322967.3	NM_013325	
GPRC5C	55890	hgsc.bcm.edu	37	17	72436949	72436949	+	Missense_Mutation	SNP	T	T	C			TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr17:72436949T>C	ENST00000392627.1	+	2	2295	c.1169T>C	c.(1168-1170)aTg>aCg	p.M390T	GPRC5C_ENST00000342648.5_Missense_Mutation_p.M30T|GPRC5C_ENST00000392629.2_Missense_Mutation_p.M357T|GPRC5C_ENST00000481232.1_Intron	NM_022036.2	NP_071319.2	Q9NQ84	GPC5C_HUMAN	G protein-coupled receptor, class C, group 5, member C	345					G-protein coupled receptor signaling pathway (GO:0007186)	cytoplasmic vesicle (GO:0031410)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|mitochondrion (GO:0005739)|receptor complex (GO:0043235)|vesicle (GO:0031982)	G-protein coupled receptor activity (GO:0004930)			central_nervous_system(1)|large_intestine(3)|lung(9)|ovary(2)|pancreas(1)|prostate(1)	17						GCCTTTTCCATGGATGAGCCG	0.577																																					p.M390T		Atlas-SNP	.											.	GPRC5C	92	.	0			c.T1169C						PASS	.						84.0	82.0	83.0					17																	72436949		2203	4300	6503	SO:0001583	missense	55890	exon2			TTTCCATGGATGA	AF207989	CCDS11699.1, CCDS42378.1	17q25	2014-01-30	2014-01-30		ENSG00000170412	ENSG00000170412		"""GPCR / Class C : Orphans"""	13309	protein-coding gene	gene with protein product		605949	"""G protein-coupled receptor, family C, group 5, member C"""			10945465	Standard	NM_022036		Approved	RAIG-3	uc002jkr.3	Q9NQ84	OTTHUMG00000067613	ENST00000392627.1:c.1169T>C	17.37:g.72436949T>C	ENSP00000376403:p.Met390Thr	34.0	0.0	0		38.0	18.0	0.473684	NM_022036	B5BUN4|Q2NL85|Q9NZG5	Missense_Mutation	SNP	ENST00000392627.1	37	CCDS11699.1	.	.	.	.	.	.	.	.	.	.	T	12.94	2.089028	0.36855	.	.	ENSG00000170412	ENST00000392627;ENST00000342648;ENST00000262616;ENST00000392629;ENST00000392628	T	0.20463	2.07	5.42	5.42	0.78866	.	0.125962	0.85682	D	0.000000	T	0.26340	0.0643	L	0.59436	1.845	0.80722	D	1	B;B;B	0.25772	0.134;0.072;0.118	B;B;B	0.29267	0.075;0.046;0.1	T	0.04621	-1.0938	10	0.87932	D	0	-11.5631	14.6481	0.68774	0.0:0.0:0.0:1.0	.	345;345;357	A8MXZ4;Q9NQ84;Q9NQ84-2	.;GPC5C_HUMAN;.	T	345;390;56;357;345	ENSP00000376405:M357T	ENSP00000262616:M56T	M	+	2	0	GPRC5C	69948544	1.000000	0.71417	1.000000	0.80357	0.870000	0.49936	6.106000	0.71511	2.061000	0.61500	0.459000	0.35465	ATG	.	.	none		0.577	GPRC5C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000145094.2		
ARHGAP9	64333	hgsc.bcm.edu	37	12	57867907	57867907	+	Silent	SNP	G	G	A	rs61754174	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr12:57867907G>A	ENST00000356411.2	-	16	2031	c.1893C>T	c.(1891-1893)acC>acT	p.T631T	ARHGAP9_ENST00000550288.1_Silent_p.T691T|ARHGAP9_ENST00000550454.1_5'Flank|ARHGAP9_ENST00000393797.2_Silent_p.T702T|ARHGAP9_ENST00000424809.2_Silent_p.T612T|ARHGAP9_ENST00000430041.2_Silent_p.T428T|ARHGAP9_ENST00000393791.3_Silent_p.T612T			Q9BRR9	RHG09_HUMAN	Rho GTPase activating protein 9	631	Lipid binding.|Rho-GAP. {ECO:0000255|PROSITE- ProRule:PRU00172}.				positive regulation of GTPase activity (GO:0043547)|regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)	GTPase activator activity (GO:0005096)|phosphatidylinositol-3,4,5-trisphosphate binding (GO:0005547)			endometrium(1)|kidney(1)|large_intestine(10)|lung(16)|ovary(1)|prostate(1)	30			GBM - Glioblastoma multiforme(3;3.37e-34)			TCAGGGCTCCGGTGACCACAT	0.557													G|||	23	0.00459265	0.0	0.0115	5008	,	,		15812	0.0		0.0139	False		,,,				2504	0.001				p.T612T		Atlas-SNP	.											.	ARHGAP9	79	.	0			c.C1836T						PASS	.	G	,,	9,4397	15.5+/-35.6	0,9,2194	45.0	48.0	47.0		1284,1836,1836	-4.7	1.0	12	dbSNP_129	47	72,8528	42.6+/-100.3	0,72,4228	no	coding-synonymous,coding-synonymous,coding-synonymous	ARHGAP9	NM_001080156.1,NM_001080157.1,NM_032496.2	,,	0,81,6422	AA,AG,GG		0.8372,0.2043,0.6228	,,	428/548,612/641,612/732	57867907	81,12925	2203	4300	6503	SO:0001819	synonymous_variant	64333	exon15			GGCTCCGGTGACC	AB051853	CCDS8941.2, CCDS44928.1, CCDS44929.1	12q13.3	2013-01-10			ENSG00000123329	ENSG00000123329		"""Rho GTPase activating proteins"", ""Pleckstrin homology (PH) domain containing"""	14130	protein-coding gene	gene with protein product		610576				11396949	Standard	NM_032496		Approved	MGC1295, 10C	uc001soc.3	Q9BRR9	OTTHUMG00000150147	ENST00000356411.2:c.1893C>T	12.37:g.57867907G>A		74.0	0.0	0		56.0	23.0	0.410714	NM_001080157	B4DVI3|E9PDX9|Q8NAF3|Q8TCJ3|Q8WYR0|Q96EZ2|Q96S74	Silent	SNP	ENST00000356411.2	37																																																																																				G|0.994;A|0.006	0.006	strong		0.557	ARHGAP9-201	KNOWN	basic|appris_candidate	protein_coding	protein_coding		NM_032496	
MYH10	4628	hgsc.bcm.edu	37	17	8416982	8416982	+	Silent	SNP	C	C	T			TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr17:8416982C>T	ENST00000269243.4	-	21	2664	c.2526G>A	c.(2524-2526)aaG>aaA	p.K842K	MYH10_ENST00000379980.4_Silent_p.K858K|RNU7-43P_ENST00000516554.1_RNA|MYH10_ENST00000360416.3_Silent_p.K873K|MYH10_ENST00000396239.1_Silent_p.K863K	NM_005964.3	NP_005955.3	P35580	MYH10_HUMAN	myosin, heavy chain 10, non-muscle	842					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						GTAGAAGCGGCTTCACCTATG	0.443																																					p.K873K		Atlas-SNP	.											.	MYH10	148	.	0			c.G2619A						PASS	.						166.0	159.0	161.0					17																	8416982		2203	4300	6503	SO:0001819	synonymous_variant	4628	exon23			AAGCGGCTTCACC	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.2526G>A	17.37:g.8416982C>T		57.0	0.0	0		61.0	26.0	0.42623	NM_001256012	B2RWP9|D3DTS1|F8VTL3|Q12989|Q149N3|Q149N4|Q16087|Q4LE45|Q6PK16|Q9BWG0	Silent	SNP	ENST00000269243.4	37	CCDS11144.1																																																																																			.	.	none		0.443	MYH10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000227001.2		
FRMD7	90167	hgsc.bcm.edu	37	X	131212944	131212944	+	Silent	SNP	A	A	G	rs7051368	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chrX:131212944A>G	ENST00000298542.4	-	12	1276	c.1101T>C	c.(1099-1101)aaT>aaC	p.N367N	FRMD7_ENST00000464296.1_Silent_p.N352N|FRMD7_ENST00000370879.1_Silent_p.N247N	NM_194277.2	NP_919253.1	Q6ZUT3	FRMD7_HUMAN	FERM domain containing 7	367					regulation of neuron projection development (GO:0010975)	cytoskeleton (GO:0005856)|extracellular space (GO:0005615)|growth cone (GO:0030426)|neuron projection (GO:0043005)|neuronal cell body (GO:0043025)				breast(1)|endometrium(1)|kidney(2)|large_intestine(2)|lung(12)|prostate(2)|skin(2)|upper_aerodigestive_tract(2)	24	Acute lymphoblastic leukemia(192;0.000127)					cGTGCACTCCATTCACATTTT	0.483													A|||	179	0.0474172	0.0628	0.0231	3775	,	,		13883	0.0		0.0726	False		,,,				2504	0.0072				p.N367N		Atlas-SNP	.											.	FRMD7	69	.	0			c.T1101C						PASS	.	A		379,3456		11,295,62,1326,509	174.0	160.0	165.0		1101	-0.6	0.9	X	dbSNP_116	165	659,6069		23,440,173,1965,1699	no	coding-synonymous	FRMD7	NM_194277.2		34,735,235,3291,2208	GG,GA,G,AA,A		9.7949,9.8827,9.8268		367/715	131212944	1038,9525	2203	4300	6503	SO:0001819	synonymous_variant	90167	exon12			CACTCCATTCACA	AL161984	CCDS35397.1	Xq26.2	2014-09-17	2006-09-01	2006-09-01	ENSG00000165694	ENSG00000165694			8079	protein-coding gene	gene with protein product		300628	"""nystagmus 1, congenital"""	NYS, NYS1		2063919, 17013395	Standard	NM_194277		Approved	FLJ43346	uc004ewn.3	Q6ZUT3	OTTHUMG00000022421	ENST00000298542.4:c.1101T>C	X.37:g.131212944A>G		41.0	0.0	0		42.0	42.0	1	NM_194277	C0LLJ3|Q5JX99	Silent	SNP	ENST00000298542.4	37	CCDS35397.1																																																																																			A|0.911;G|0.089	0.089	strong		0.483	FRMD7-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000355031.1	NM_194277	
KRT72	140807	hgsc.bcm.edu	37	12	52992743	52992743	+	Missense_Mutation	SNP	C	C	T	rs142970524	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr12:52992743C>T	ENST00000537672.2	-	2	590	c.580G>A	c.(580-582)Ggg>Agg	p.G194R	KRT72_ENST00000398066.3_Missense_Mutation_p.G6R|KRT72_ENST00000354310.4_Missense_Mutation_p.G194R|KRT72_ENST00000293745.2_Missense_Mutation_p.G194R|RP11-641A6.2_ENST00000551089.1_RNA	NM_001146225.1	NP_001139697.1	Q14CN4	K2C72_HUMAN	keratin 72	194	Coil 1B.|Rod.					extracellular vesicular exosome (GO:0070062)|keratin filament (GO:0045095)	structural molecule activity (GO:0005198)			endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(6)|lung(14)|ovary(5)|pancreas(1)|prostate(3)|skin(3)|upper_aerodigestive_tract(2)	36				BRCA - Breast invasive adenocarcinoma(357;0.195)		AGCCTCACCCCGTCCCCAGAC	0.547																																					p.G194R		Atlas-SNP	.											.	KRT72	70	.	0			c.G580A						PASS	.	T	ARG/GLY,ARG/GLY,ARG/GLY	0,4406		0,0,2203	194.0	177.0	183.0		580,580,580	-4.3	1.0	12	dbSNP_134	183	10,8590	818.8+/-406.8	0,10,4290	yes	missense,missense,missense	KRT72	NM_001146225.1,NM_001146226.1,NM_080747.2	125,125,125	0,10,6493	TT,TC,CC		0.1163,0.0,0.0769	benign,benign,benign	194/512,194/470,194/512	52992743	10,12996	2203	4300	6503	SO:0001583	missense	140807	exon2			TCACCCCGTCCCC	AY033495	CCDS8833.1, CCDS53795.1	12q13.13	2013-06-25			ENSG00000170486	ENSG00000170486		"""-"", ""Intermediate filaments type II, keratins (basic)"""	28932	protein-coding gene	gene with protein product		608246				12648212, 11703281, 16831889	Standard	NM_080747		Approved	K6IRS2, KRT6IRS2, KRT6, K6irs	uc001saq.2	Q14CN4	OTTHUMG00000169744	ENST00000537672.2:c.580G>A	12.37:g.52992743C>T	ENSP00000441160:p.Gly194Arg	193.0	0.0	0		215.0	110.0	0.511628	NM_001146225	B4DEI8|H9KV51|Q8NA87|Q8WWY9|Q8WWZ0	Missense_Mutation	SNP	ENST00000537672.2	37	CCDS8833.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	3.962|3.962	-0.010160|-0.010160	0.07727|0.07727	0.0|0.0	0.001163|0.001163	ENSG00000170486|ENSG00000170486	ENST00000537672;ENST00000293745;ENST00000354310;ENST00000398066|ENST00000549979	D;D;D;D|.	0.86432|.	-2.12;-2.12;-2.12;-2.12|.	5.25|5.25	-4.29|-4.29	0.03721|0.03721	Filament (1);|.	0.000000|.	0.47852|.	N|.	0.000214|.	T|T	0.08846|0.08846	0.0219|0.0219	N|N	0.00191|0.00191	-1.88|-1.88	0.19575|0.19575	N|N	0.999963|0.999963	B;B|.	0.02656|.	0.0;0.0|.	B;B|.	0.04013|.	0.0;0.001|.	T|T	0.42396|0.42396	-0.9454|-0.9454	10|5	0.02654|.	T|.	1|.	.|.	16.5611|16.5611	0.84566|0.84566	0.0:0.0582:0.6555:0.2862|0.0:0.0582:0.6555:0.2862	.|.	194;194|.	B4DEI8;Q14CN4|.	.;K2C72_HUMAN|.	R|Q	194;194;194;6|190	ENSP00000441160:G194R;ENSP00000293745:G194R;ENSP00000346269:G194R;ENSP00000446151:G6R|.	ENSP00000293745:G194R|.	G|R	-|-	1|2	0|0	KRT72|KRT72	51279010|51279010	0.000000|0.000000	0.05858|0.05858	0.951000|0.951000	0.38953|0.38953	0.767000|0.767000	0.43475|0.43475	-0.184000|-0.184000	0.09698|0.09698	-0.750000|-0.750000	0.04740|0.04740	-0.361000|-0.361000	0.07541|0.07541	GGG|CGG	C|0.999;T|0.001	0.001	strong		0.547	KRT72-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000405693.1	NM_080747	
RELN	5649	hgsc.bcm.edu	37	7	103205779	103205779	+	Missense_Mutation	SNP	G	G	A	rs115913736	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr7:103205779G>A	ENST00000428762.1	-	34	5315	c.5156C>T	c.(5155-5157)tCg>tTg	p.S1719L	RELN_ENST00000343529.5_Missense_Mutation_p.S1719L|RELN_ENST00000424685.2_Missense_Mutation_p.S1719L	NM_005045.3	NP_005036.2	P78509	RELN_HUMAN	reelin	1719					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)		GAATCTTTCCGAGGTGTAAAT	0.463													G|||	17	0.00339457	0.0008	0.0	5008	,	,		19094	0.0		0.0089	False		,,,				2504	0.0072				p.S1719L	NSCLC(146;835 1944 15585 22231 52158)	Atlas-SNP	.											RELN,NS,lymphoid_neoplasm,+1,1	RELN	593	1	0			c.C5156T						PASS	.	G	LEU/SER,LEU/SER	3,4403	6.2+/-15.9	0,3,2200	129.0	114.0	119.0		5156,5156	5.2	0.9	7	dbSNP_132	119	70,8530	42.2+/-99.7	2,66,4232	yes	missense,missense	RELN	NM_005045.3,NM_173054.2	145,145	2,69,6432	AA,AG,GG		0.814,0.0681,0.5613	probably-damaging,probably-damaging	1719/3461,1719/3459	103205779	73,12933	2203	4300	6503	SO:0001583	missense	5649	exon34			CTTTCCGAGGTGT		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.5156C>T	7.37:g.103205779G>A	ENSP00000392423:p.Ser1719Leu	127.0	0.0	0		110.0	45.0	0.409091	NM_173054	A4D0P9|A4D0Q0|Q86UJ0|Q86UJ8|Q8NDV0|Q9UDQ2	Missense_Mutation	SNP	ENST00000428762.1	37	CCDS47680.1	8	0.003663003663003663	0	0.0	0	0.0	0	0.0	8	0.010554089709762533	G	23.4	4.410786	0.83340	6.81E-4	0.00814	ENSG00000189056	ENST00000428762;ENST00000343529;ENST00000424685;ENST00000448171	T;T;T	0.43688	1.75;0.94;1.75	6.02	5.15	0.70609	Neuraminidase (1);	0.066420	0.64402	N	0.000006	T	0.51261	0.1664	L	0.60455	1.87	0.54753	D	0.999988	D;D	0.76494	0.999;0.998	P;D	0.69307	0.889;0.963	T	0.56486	-0.7971	10	0.42905	T	0.14	.	15.254	0.73571	0.0668:0.0:0.9332:0.0	.	1719;1719	P78509-2;P78509	.;RELN_HUMAN	L	1719	ENSP00000392423:S1719L;ENSP00000345694:S1719L;ENSP00000388446:S1719L	ENSP00000345694:S1719L	S	-	2	0	RELN	102993015	1.000000	0.71417	0.913000	0.36048	0.978000	0.69477	9.139000	0.94554	1.569000	0.49696	0.655000	0.94253	TCG	G|0.994;A|0.006	0.006	strong		0.463	RELN-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000348148.1	NM_005045	
NUP37	79023	hgsc.bcm.edu	37	12	102494849	102494849	+	Silent	SNP	T	T	C	rs17438178	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr12:102494849T>C	ENST00000552283.1	-	4	454	c.315A>G	c.(313-315)agA>agG	p.R105R	NUP37_ENST00000543021.1_5'UTR|NUP37_ENST00000251074.1_Silent_p.R105R			Q8NFH4	NUP37_HUMAN	nucleoporin 37kDa	105					carbohydrate metabolic process (GO:0005975)|chromosome segregation (GO:0007059)|cytokine-mediated signaling pathway (GO:0019221)|glucose transport (GO:0015758)|hexose transport (GO:0008645)|mitotic cell cycle (GO:0000278)|mitotic nuclear division (GO:0007067)|mitotic nuclear envelope disassembly (GO:0007077)|mRNA transport (GO:0051028)|protein transport (GO:0015031)|regulation of glucose transport (GO:0010827)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)|viral process (GO:0016032)	cytosol (GO:0005829)|kinetochore (GO:0000776)|nuclear envelope (GO:0005635)|nuclear pore outer ring (GO:0031080)|nucleus (GO:0005634)				endometrium(3)|large_intestine(3)|lung(10)|ovary(1)	17						AAGTAAATAATCTAATTTTCA	0.308													T|||	110	0.0219649	0.0401	0.0058	5008	,	,		16106	0.0		0.0308	False		,,,				2504	0.0225				p.R105R		Atlas-SNP	.											.	NUP37	26	.	0			c.A315G						PASS	.	T		130,4262		4,122,2070	29.0	31.0	31.0		315	0.3	1.0	12	dbSNP_123	31	211,8361		2,207,4077	no	coding-synonymous	NUP37	NM_024057.2		6,329,6147	CC,CT,TT		2.4615,2.9599,2.6304		105/327	102494849	341,12623	2196	4286	6482	SO:0001819	synonymous_variant	79023	exon3			AAATAATCTAATT	AF514994	CCDS9089.1	12q23.2	2014-08-12			ENSG00000075188	ENSG00000075188		"""WD repeat domain containing"""	29929	protein-coding gene	gene with protein product		609264				12196509	Standard	NM_024057		Approved	MGC5585, FLJ22618	uc001tjc.3	Q8NFH4	OTTHUMG00000170478	ENST00000552283.1:c.315A>G	12.37:g.102494849T>C		163.0	0.0	0		144.0	62.0	0.430556	NM_024057	Q9H644	Silent	SNP	ENST00000552283.1	37	CCDS9089.1																																																																																			T|0.976;C|0.024	0.024	strong		0.308	NUP37-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000409330.1	NM_024057	
ZNF57	126295	hgsc.bcm.edu	37	19	2917509	2917509	+	Missense_Mutation	SNP	G	G	A	rs61754927	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr19:2917509G>A	ENST00000306908.5	+	4	1038	c.890G>A	c.(889-891)aGa>aAa	p.R297K	ZNF57_ENST00000523428.1_Missense_Mutation_p.R265K|AC006277.2_ENST00000520090.2_RNA	NM_173480.2	NP_775751.1	Q68EA5	ZNF57_HUMAN	zinc finger protein 57	297					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)|kidney(2)|large_intestine(5)|lung(2)|ovary(1)|pancreas(1)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	18				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)|GBM - Glioblastoma multiforme(1328;0.00161)|STAD - Stomach adenocarcinoma(1328;0.18)		GCTTTTCAAAGACATGAGAAG	0.488													G|||	130	0.0259585	0.0257	0.0288	5008	,	,		19431	0.0		0.0169	False		,,,				2504	0.0603				p.R297K	NSCLC(150;910 1964 4303 10464 26498)	Atlas-SNP	.											.	ZNF57	57	.	0			c.G890A						PASS	.	G	LYS/ARG	95,4311	76.8+/-115.0	0,95,2108	74.0	80.0	78.0		890	-4.1	0.0	19	dbSNP_129	78	208,8392	88.1+/-150.5	4,200,4096	yes	missense	ZNF57	NM_173480.2	26	4,295,6204	AA,AG,GG		2.4186,2.1562,2.3297	benign	297/556	2917509	303,12703	2203	4300	6503	SO:0001583	missense	126295	exon4			TTCAAAGACATGA	M88368	CCDS12098.1	19p13.3	2013-01-08			ENSG00000171970	ENSG00000171970		"""Zinc fingers, C2H2-type"", ""-"""	13125	protein-coding gene	gene with protein product			"""zinc finger protein 424"""	ZNF424		1505991	Standard	NM_173480		Approved		uc002lwr.3	Q68EA5	OTTHUMG00000164485	ENST00000306908.5:c.890G>A	19.37:g.2917509G>A	ENSP00000303696:p.Arg297Lys	44.0	0.0	0		48.0	20.0	0.416667	NM_173480	Q8N6R9	Missense_Mutation	SNP	ENST00000306908.5	37	CCDS12098.1	40	0.018315018315018316	17	0.034552845528455285	13	0.03591160220994475	0	0.0	10	0.013192612137203167	G	2.867	-0.234775	0.05983	0.021562	0.024186	ENSG00000171970	ENST00000306908;ENST00000395204;ENST00000523428	T;T	0.02197	4.4;4.4	2.25	-4.14	0.03892	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.00384	0.0012	L	0.31207	0.915	0.09310	N	1	B	0.33171	0.4	B	0.37943	0.261	T	0.41787	-0.9489	9	0.05721	T	0.95	.	0.9159	0.01304	0.2475:0.1759:0.3978:0.1788	rs61754927	297	Q68EA5	ZNF57_HUMAN	K	297;299;265	ENSP00000303696:R297K;ENSP00000430223:R265K	ENSP00000303696:R297K	R	+	2	0	ZNF57	2868509	0.000000	0.05858	0.001000	0.08648	0.558000	0.35554	-7.471000	0.00035	-1.087000	0.03081	0.511000	0.50034	AGA	G|0.974;A|0.026	0.026	strong		0.488	ZNF57-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000378969.1	NM_173480	
TRPC4	7223	hgsc.bcm.edu	37	13	38237564	38237564	+	Silent	SNP	A	A	G	rs75514550	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr13:38237564A>G	ENST00000379705.3	-	6	2534	c.1677T>C	c.(1675-1677)aaT>aaC	p.N559N	TRPC4_ENST00000379679.1_Silent_p.N386N|TRPC4_ENST00000338947.5_Silent_p.N386N|TRPC4_ENST00000379673.2_Silent_p.N559N|TRPC4_ENST00000358477.2_Silent_p.N559N|TRPC4_ENST00000355779.2_Silent_p.N559N|TRPC4_ENST00000447043.1_Silent_p.N559N|TRPC4_ENST00000494529.1_Intron|TRPC4_ENST00000426868.2_Intron|TRPC4_ENST00000379681.3_Silent_p.N559N			Q9UBN4	TRPC4_HUMAN	transient receptor potential cation channel, subfamily C, member 4	559					axon guidance (GO:0007411)|calcium ion import (GO:0070509)|calcium ion transmembrane transport (GO:0070588)|calcium ion transport (GO:0006816)|gamma-aminobutyric acid secretion (GO:0014051)|ion transmembrane transport (GO:0034220)|oligodendrocyte differentiation (GO:0048709)|transmembrane transport (GO:0055085)	basolateral plasma membrane (GO:0016323)|calcium channel complex (GO:0034704)|caveola (GO:0005901)|cell surface (GO:0009986)|cortical cytoskeleton (GO:0030863)|plasma membrane (GO:0005886)	beta-catenin binding (GO:0008013)|cadherin binding (GO:0045296)|inositol 1,4,5 trisphosphate binding (GO:0070679)|store-operated calcium channel activity (GO:0015279)			NS(2)|breast(4)|endometrium(3)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(26)|lung(30)|ovary(4)|prostate(1)|skin(4)|urinary_tract(2)	83				all cancers(112;1.92e-08)|Epithelial(112;5.04e-06)|OV - Ovarian serous cystadenocarcinoma(117;0.000677)|GBM - Glioblastoma multiforme(144;0.00623)|BRCA - Breast invasive adenocarcinoma(63;0.0126)		TTGAAAATGCATTATTCTGCT	0.348													A|||	34	0.00678914	0.0008	0.0187	5008	,	,		19000	0.0		0.0179	False		,,,				2504	0.002				p.N559N		Atlas-SNP	.											.	TRPC4	389	.	0			c.T1677C						PASS	.	A	,,,,,	11,4395	20.2+/-43.8	0,11,2192	79.0	74.0	75.0		1677,1677,1677,1158,1677,1677	2.2	1.0	13	dbSNP_132	75	165,8435	77.8+/-140.4	2,161,4137	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	TRPC4	NM_001135955.1,NM_001135956.1,NM_001135957.1,NM_001135958.1,NM_003306.1,NM_016179.2	,,,,,	2,172,6329	GG,GA,AA		1.9186,0.2497,1.3532	,,,,,	559/894,559/829,559/837,386/805,559/983,559/978	38237564	176,12830	2203	4300	6503	SO:0001819	synonymous_variant	7223	exon6			AAATGCATTATTC	U40983	CCDS9365.1, CCDS45035.1, CCDS45036.1, CCDS45038.1, CCDS45039.1	13q13.3	2013-01-10			ENSG00000133107	ENSG00000133107		"""Voltage-gated ion channels / Transient receptor potential cation channels"", ""Ankyrin repeat domain containing"""	12336	protein-coding gene	gene with protein product		603651				8646775, 16382100	Standard	NM_016179		Approved	HTRP4, TRP4	uc010abx.3	Q9UBN4	OTTHUMG00000016752	ENST00000379705.3:c.1677T>C	13.37:g.38237564A>G		168.0	0.0	0		148.0	91.0	0.614865	NM_003306	B1ALE0|B1ALE1|B1ALE2|Q15721|Q3SWS6|Q96P03|Q96P04|Q96P05|Q9UIB0|Q9UIB1|Q9UIB2	Silent	SNP	ENST00000379705.3	37	CCDS9365.1																																																																																			A|0.988;G|0.012	0.012	strong		0.348	TRPC4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044574.2	NM_003306	
TMPRSS11F	389208	hgsc.bcm.edu	37	4	68925094	68925094	+	Missense_Mutation	SNP	G	G	A	rs142412240	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr4:68925094G>A	ENST00000356291.2	-	9	1167	c.1108C>T	c.(1108-1110)Cca>Tca	p.P370S	UBA6-AS1_ENST00000500538.2_RNA|RP11-35D5.1_ENST00000600441.1_RNA	NM_207407.2	NP_997290.2	Q6ZWK6	TM11F_HUMAN	transmembrane protease, serine 11F	370	Peptidase S1. {ECO:0000255|PROSITE- ProRule:PRU00274}.					extracellular region (GO:0005576)|integral component of plasma membrane (GO:0005887)	serine-type endopeptidase activity (GO:0004252)			NS(1)|breast(1)|endometrium(2)|kidney(2)|large_intestine(7)|liver(1)|lung(18)|ovary(1)|pancreas(1)|prostate(1)|urinary_tract(4)	39						AACATTCCTGGAGTTATCAGG	0.393													G|||	2	0.000399361	0.0	0.0014	5008	,	,		18312	0.0		0.001	False		,,,				2504	0.0				p.P370S		Atlas-SNP	.											.	TMPRSS11F	79	.	0			c.C1108T						PASS	.	G	SER/PRO	1,4405	2.1+/-5.4	0,1,2202	216.0	188.0	197.0		1108	0.3	1.0	4	dbSNP_134	197	14,8586	10.5+/-38.8	0,14,4286	yes	missense	TMPRSS11F	NM_207407.2	74	0,15,6488	AA,AG,GG		0.1628,0.0227,0.1153	benign	370/439	68925094	15,12991	2203	4300	6503	SO:0001583	missense	389208	exon9			TTCCTGGAGTTAT	AK122625	CCDS3520.1	4q13.2	2010-04-13			ENSG00000198092	ENSG00000198092		"""Serine peptidases / Transmembrane"""	29994	protein-coding gene	gene with protein product							Standard	NM_207407		Approved	FLJ16046	uc003hdt.1	Q6ZWK6	OTTHUMG00000129307	ENST00000356291.2:c.1108C>T	4.37:g.68925094G>A	ENSP00000348639:p.Pro370Ser	177.0	0.0	0		201.0	87.0	0.432836	NM_207407	A8MXX2	Missense_Mutation	SNP	ENST00000356291.2	37	CCDS3520.1	1	4.578754578754579E-4	0	0.0	1	0.0027624309392265192	0	0.0	0	0.0	G	3.434	-0.115545	0.06881	2.27E-4	0.001628	ENSG00000198092	ENST00000356291	D	0.92545	-3.06	5.2	0.258	0.15578	Peptidase cysteine/serine, trypsin-like (1);Peptidase S1/S6, chymotrypsin/Hap (3);	1.014630	0.07912	N	0.974403	T	0.81754	0.4889	N	0.16903	0.455	0.29686	N	0.841319	B	0.02656	0.0	B	0.06405	0.002	T	0.68303	-0.5444	10	0.18276	T	0.48	.	4.0738	0.09894	0.2767:0.0:0.4486:0.2746	.	370	Q6ZWK6	TM11F_HUMAN	S	370	ENSP00000348639:P370S	ENSP00000348639:P370S	P	-	1	0	TMPRSS11F	68607689	0.878000	0.30173	0.997000	0.53966	0.986000	0.74619	0.300000	0.19156	0.093000	0.17368	0.591000	0.81541	CCA	G|0.999;A|0.001	0.001	strong		0.393	TMPRSS11F-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251439.1	NM_207407	
ZNF101	94039	hgsc.bcm.edu	37	19	19790690	19790690	+	Missense_Mutation	SNP	C	C	T	rs35358946	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr19:19790690C>T	ENST00000592502.1	+	4	1002	c.892C>T	c.(892-894)Cac>Tac	p.H298Y	ZNF101_ENST00000444249.2_3'UTR|ZNF101_ENST00000415784.2_Missense_Mutation_p.H178Y			Q8IZC7	ZN101_HUMAN	zinc finger protein 101	298					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			breast(2)|endometrium(1)|kidney(1)|large_intestine(6)|lung(4)|ovary(2)|prostate(1)	17						CAGTTCCCTTCACAGACATGA	0.453													C|||	29	0.00579073	0.0008	0.0115	5008	,	,		19424	0.0		0.007	False		,,,				2504	0.0133				p.H298Y		Atlas-SNP	.											.	ZNF101	43	.	0			c.C892T						PASS	.	C	TYR/HIS	8,4398	12.9+/-30.5	0,8,2195	48.0	46.0	47.0		892	0.2	0.0	19	dbSNP_126	47	63,8537	38.8+/-94.9	1,61,4238	yes	missense	ZNF101	NM_033204.2	83	1,69,6433	TT,TC,CC		0.7326,0.1816,0.5459	benign	298/437	19790690	71,12935	2203	4300	6503	SO:0001583	missense	94039	exon4			TCCCTTCACAGAC	AK097169	CCDS32971.1	19p13.11	2013-01-08	2004-02-10		ENSG00000181896	ENSG00000181896		"""Zinc fingers, C2H2-type"", ""-"""	12881	protein-coding gene	gene with protein product		603983	"""zinc finger protein 101 (Y2)"""			11441184	Standard	XM_005260165		Approved	HZF12, DKFZp570I0164	uc002nni.2	Q8IZC7	OTTHUMG00000167736	ENST00000592502.1:c.892C>T	19.37:g.19790690C>T	ENSP00000468049:p.His298Tyr	39.0	0.0	0		50.0	23.0	0.46	NM_033204	C9JU83|Q0VDG9	Missense_Mutation	SNP	ENST00000592502.1	37	CCDS32971.1	11	0.005036630036630037	0	0.0	4	0.011049723756906077	0	0.0	7	0.009234828496042216	C	4.392	0.072382	0.08436	0.001816	0.007326	ENSG00000181896	ENST00000318110;ENST00000415440;ENST00000415784	T;T	0.27557	1.66;1.66	0.235	0.235	0.15431	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (2);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.07098	0.0180	N	0.04245	-0.25	0.09310	N	0.999997	B	0.33940	0.433	B	0.29663	0.105	T	0.21042	-1.0257	8	.	.	.	.	3.123	0.06397	0.4753:0.5244:1.0E-4:1.0E-4	rs35358946;rs35358946	298	Q8IZC7	ZN101_HUMAN	Y	298;298;178	ENSP00000319716:H298Y;ENSP00000400952:H178Y	.	H	+	1	0	ZNF101	19651690	0.000000	0.05858	0.047000	0.18901	0.047000	0.14425	-0.669000	0.05262	0.308000	0.22923	0.313000	0.20887	CAC	C|0.994;T|0.006	0.006	strong		0.453	ZNF101-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000460559.1	NM_033204	
PHF2	5253	hgsc.bcm.edu	37	9	96411414	96411414	+	Silent	SNP	G	G	A	rs16912641	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr9:96411414G>A	ENST00000359246.4	+	5	889	c.522G>A	c.(520-522)ctG>ctA	p.L174L	PHF2_ENST00000375376.4_Intron	NM_005392.3	NP_005383.3	O75151	PHF2_HUMAN	PHD finger protein 2	174					liver development (GO:0001889)|negative regulation of chromatin silencing at rDNA (GO:0061188)|protein demethylation (GO:0006482)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleolus (GO:0005730)|nucleus (GO:0005634)	dioxygenase activity (GO:0051213)|histone demethylase activity (H3-K9 specific) (GO:0032454)|iron ion binding (GO:0005506)|methylated histone binding (GO:0035064)|zinc ion binding (GO:0008270)			breast(1)|central_nervous_system(2)|endometrium(6)|large_intestine(9)|lung(14)|ovary(2)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	40		Myeloproliferative disorder(762;0.0255)		OV - Ovarian serous cystadenocarcinoma(323;9.11e-28)		AGATGAAGCTGAAGGAGTTTG	0.572													G|||	177	0.0353435	0.0862	0.0101	5008	,	,		14042	0.0139		0.0298	False		,,,				2504	0.0123				p.L174L		Atlas-SNP	.											.	PHF2	113	.	0			c.G522A						PASS	.	G		330,3782		6,318,1732	110.0	71.0	84.0		522	3.7	1.0	9	dbSNP_123	84	140,7862		1,138,3862	no	coding-synonymous	PHF2	NM_005392.3		7,456,5594	AA,AG,GG		1.7496,8.0253,3.8798		174/1097	96411414	470,11644	2056	4001	6057	SO:0001819	synonymous_variant	5253	exon5			GAAGCTGAAGGAG	AF043725	CCDS35069.1	9q22	2013-01-28			ENSG00000197724	ENSG00000197724		"""Chromatin-modifying enzymes / K-demethylases"", ""Zinc fingers, PHD-type"""	8920	protein-coding gene	gene with protein product	"""jumonji C domain-containing histone demethylase 1E"", ""centromere protein 35"""	604351				10051327, 20129925	Standard	NM_005392		Approved	KIAA0662, JHDM1E, CENP-35	uc004aub.3	O75151	OTTHUMG00000020253	ENST00000359246.4:c.522G>A	9.37:g.96411414G>A		201.0	0.0	0		194.0	81.0	0.417526	NM_005392	Q4VXG0|Q8N3K2|Q9Y6N4	Silent	SNP	ENST00000359246.4	37	CCDS35069.1																																																																																			G|0.954;A|0.046	0.046	strong		0.572	PHF2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053162.1	NM_005392	
PHF2	5253	hgsc.bcm.edu	37	9	96436037	96436037	+	Missense_Mutation	SNP	G	G	A	rs41276200	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr9:96436037G>A	ENST00000359246.4	+	18	2886	c.2519G>A	c.(2518-2520)aGt>aAt	p.S840N	PHF2_ENST00000375376.4_Intron	NM_005392.3	NP_005383.3	O75151	PHF2_HUMAN	PHD finger protein 2	840				SGKSA -> NKGT (in Ref. 1; AAD21791). {ECO:0000305}.	liver development (GO:0001889)|negative regulation of chromatin silencing at rDNA (GO:0061188)|protein demethylation (GO:0006482)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleolus (GO:0005730)|nucleus (GO:0005634)	dioxygenase activity (GO:0051213)|histone demethylase activity (H3-K9 specific) (GO:0032454)|iron ion binding (GO:0005506)|methylated histone binding (GO:0035064)|zinc ion binding (GO:0008270)			breast(1)|central_nervous_system(2)|endometrium(6)|large_intestine(9)|lung(14)|ovary(2)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	40		Myeloproliferative disorder(762;0.0255)		OV - Ovarian serous cystadenocarcinoma(323;9.11e-28)		AGTGGCAAGAGTGCAGGCAAA	0.627													G|||	36	0.0071885	0.0	0.0029	5008	,	,		19197	0.0129		0.0169	False		,,,				2504	0.0041				p.S840N		Atlas-SNP	.											.	PHF2	113	.	0			c.G2519A						PASS	.	G	ASN/SER	11,4395	20.2+/-43.8	0,11,2192	88.0	74.0	78.0		2519	3.3	0.0	9	dbSNP_127	78	120,8480	62.4+/-124.4	2,116,4182	yes	missense	PHF2	NM_005392.3	46	2,127,6374	AA,AG,GG		1.3953,0.2497,1.0072	benign	840/1097	96436037	131,12875	2203	4300	6503	SO:0001583	missense	5253	exon18			GCAAGAGTGCAGG	AF043725	CCDS35069.1	9q22	2013-01-28			ENSG00000197724	ENSG00000197724		"""Chromatin-modifying enzymes / K-demethylases"", ""Zinc fingers, PHD-type"""	8920	protein-coding gene	gene with protein product	"""jumonji C domain-containing histone demethylase 1E"", ""centromere protein 35"""	604351				10051327, 20129925	Standard	NM_005392		Approved	KIAA0662, JHDM1E, CENP-35	uc004aub.3	O75151	OTTHUMG00000020253	ENST00000359246.4:c.2519G>A	9.37:g.96436037G>A	ENSP00000352185:p.Ser840Asn	119.0	0.0	0		150.0	75.0	0.5	NM_005392	Q4VXG0|Q8N3K2|Q9Y6N4	Missense_Mutation	SNP	ENST00000359246.4	37	CCDS35069.1	21	0.009615384615384616	1	0.0020325203252032522	1	0.0027624309392265192	6	0.01048951048951049	13	0.017150395778364115	G	10.03	1.237840	0.22711	0.002497	0.013953	ENSG00000197724	ENST00000359246	T	0.18502	2.21	5.18	3.32	0.38043	.	0.515497	0.21501	N	0.073536	T	0.02807	0.0084	N	0.11560	0.145	0.80722	D	1	B;B	0.13594	0.008;0.001	B;B	0.14578	0.011;0.003	T	0.22871	-1.0204	10	0.07990	T	0.79	-3.0171	3.472	0.07570	0.1562:0.0:0.4214:0.4224	rs41276200;rs61739260	259;840	Q8N359;O75151	.;PHF2_HUMAN	N	840	ENSP00000352185:S840N	ENSP00000352185:S840N	S	+	2	0	PHF2	95475858	0.998000	0.40836	0.019000	0.16419	0.398000	0.30690	2.824000	0.48088	1.149000	0.42402	0.561000	0.74099	AGT	G|0.990;A|0.010	0.010	strong		0.627	PHF2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053162.1	NM_005392	
DSEL	92126	hgsc.bcm.edu	37	18	65179657	65179657	+	Missense_Mutation	SNP	T	T	C	rs12953840	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr18:65179657T>C	ENST00000310045.7	-	2	3692	c.2219A>G	c.(2218-2220)tAt>tGt	p.Y740C	CTD-2541J13.2_ENST00000583493.1_RNA|CTD-2541J13.2_ENST00000581951.1_RNA	NM_032160.2	NP_115536.1	Q8IZU8	DSEL_HUMAN	dermatan sulfate epimerase-like	730					carbohydrate metabolic process (GO:0005975)|chondroitin sulfate metabolic process (GO:0030204)|dermatan sulfate biosynthetic process (GO:0030208)|glycosaminoglycan metabolic process (GO:0030203)|small molecule metabolic process (GO:0044281)	Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)	isomerase activity (GO:0016853)|sulfotransferase activity (GO:0008146)			NS(3)|breast(1)|central_nervous_system(1)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(25)|lung(23)|ovary(4)|pancreas(1)|prostate(2)|skin(3)|stomach(1)|upper_aerodigestive_tract(2)	74		Esophageal squamous(42;0.129)				GAATCCCAGATAATTGAATCT	0.403													T|||	4	0.000798722	0.0008	0.0029	5008	,	,		18544	0.0		0.001	False		,,,				2504	0.0				p.Y740C		Atlas-SNP	.											.	DSEL	196	.	0			c.A2219G						PASS	.	T	CYS/TYR	3,4403	6.2+/-15.9	0,3,2200	52.0	54.0	53.0		2219	5.1	1.0	18	dbSNP_121	53	30,8570	21.6+/-65.8	1,28,4271	yes	missense	DSEL	NM_032160.2	194	1,31,6471	CC,CT,TT		0.3488,0.0681,0.2537	probably-damaging	740/1223	65179657	33,12973	2203	4300	6503	SO:0001583	missense	92126	exon2			CCCAGATAATTGA	AF480435	CCDS11995.1	18q22.1	2007-01-29	2007-01-29	2007-01-29	ENSG00000171451	ENSG00000171451			18144	protein-coding gene	gene with protein product		611125	"""chromosome 18 open reading frame 4"""	C18orf4		16505484	Standard	NM_032160		Approved	NCAG1, FLJ11477	uc002lke.1	Q8IZU8	OTTHUMG00000132804	ENST00000310045.7:c.2219A>G	18.37:g.65179657T>C	ENSP00000310565:p.Tyr740Cys	99.0	0.0	0		102.0	43.0	0.421569	NM_032160	Q17RH1|Q6P5Z3	Missense_Mutation	SNP	ENST00000310045.7	37	CCDS11995.1	1	4.578754578754579E-4	0	0.0	1	0.0027624309392265192	0	0.0	0	0.0	T	15.14	2.743790	0.49151	6.81E-4	0.003488	ENSG00000171451	ENST00000310045;ENST00000397964	T	0.26373	1.74	5.09	5.09	0.68999	.	0.000000	0.64402	U	0.000002	T	0.44201	0.1282	M	0.70595	2.14	0.45806	D	0.99868	D	0.71674	0.998	P	0.60789	0.879	T	0.44406	-0.9330	10	0.87932	D	0	.	10.1284	0.42663	0.1494:0.0:0.0:0.8506	rs12953840;rs12953840	730	Q8IZU8	DSEL_HUMAN	C	740;730	ENSP00000310565:Y740C	ENSP00000310565:Y740C	Y	-	2	0	DSEL	63330637	1.000000	0.71417	0.986000	0.45419	0.966000	0.64601	5.986000	0.70563	2.060000	0.61445	0.374000	0.22700	TAT	T|0.998;C|0.002	0.002	strong		0.403	DSEL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256221.1	NM_032160	
OR10G3	26533	hgsc.bcm.edu	37	14	22038276	22038276	+	Silent	SNP	C	C	T	rs28436899	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr14:22038276C>T	ENST00000303532.1	-	1	599	c.600G>A	c.(598-600)acG>acA	p.T200T		NM_001005465.1	NP_001005465.1	Q8NGC4	O10G3_HUMAN	olfactory receptor, family 10, subfamily G, member 3	200						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			central_nervous_system(1)|endometrium(1)|kidney(2)|large_intestine(4)|lung(7)	15	all_cancers(95;0.000987)			GBM - Glioblastoma multiforme(265;0.0139)		TGTCTACAAACGTCACCAGCT	0.522													c|||	115	0.0229633	0.0794	0.013	5008	,	,		19542	0.0		0.0	False		,,,				2504	0.001				p.T200T		Atlas-SNP	.											.	OR10G3	40	.	0			c.G600A						PASS	.	T		261,4145	148.8+/-183.1	5,251,1947	196.0	188.0	191.0		600	-0.4	1.0	14	dbSNP_125	191	10,8590	7.1+/-27.0	0,10,4290	no	coding-synonymous	OR10G3	NM_001005465.1		5,261,6237	TT,TC,CC		0.1163,5.9237,2.0837		200/314	22038276	271,12735	2203	4300	6503	SO:0001819	synonymous_variant	26533	exon1			TACAAACGTCACC		CCDS32046.1	14q11.2	2013-09-24			ENSG00000169208	ENSG00000169208		"""GPCR / Class A : Olfactory receptors"""	8171	protein-coding gene	gene with protein product						8188290	Standard	NM_001005465		Approved		uc010tmb.2	Q8NGC4	OTTHUMG00000168886	ENST00000303532.1:c.600G>A	14.37:g.22038276C>T		243.0	1.0	0.00411523		239.0	132.0	0.552301	NM_001005465	Q6IET7|Q96R77	Silent	SNP	ENST00000303532.1	37	CCDS32046.1																																																																																			C|0.978;T|0.022	0.022	strong		0.522	OR10G3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000401521.1		
DND1	373863	hgsc.bcm.edu	37	5	140050907	140050907	+	Missense_Mutation	SNP	C	C	T	rs148639416	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr5:140050907C>T	ENST00000542735.1	-	4	1076	c.1033G>A	c.(1033-1035)Gct>Act	p.A345T	WDR55_ENST00000520764.1_3'UTR|WDR55_ENST00000358337.5_3'UTR	NM_194249.2	NP_919225.1	Q8IYX4	DND1_HUMAN	DND microRNA-mediated repression inhibitor 1	345					germ cell development (GO:0007281)|multicellular organismal development (GO:0007275)|negative regulation of gene silencing by miRNA (GO:0060965)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	AU-rich element binding (GO:0017091)|nucleotide binding (GO:0000166)			central_nervous_system(1)|prostate(4)	5			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			CCTGCCTCAGCCCCAGCAGAC	0.602																																					p.A345T		Atlas-SNP	.											.	DND1	15	.	0			c.G1033A						PASS	.						77.0	65.0	69.0					5																	140050907		1940	3940	5880	SO:0001583	missense	373863	exon4			CCTCAGCCCCAGC	AY321065	CCDS4236.1	5q31.3	2013-07-31	2013-07-31		ENSG00000256453	ENSG00000256453		"""RNA binding motif (RRM) containing"""	23799	protein-coding gene	gene with protein product		609385	"""dead end homolog 1 (zebrafish)"""			12932328	Standard	NM_194249		Approved	MGC34750, RBMS4	uc003lgt.3	Q8IYX4	OTTHUMG00000129499	ENST00000542735.1:c.1033G>A	5.37:g.140050907C>T	ENSP00000445366:p.Ala345Thr	490.0	0.0	0		764.0	132.0	0.172775	NM_194249		Missense_Mutation	SNP	ENST00000542735.1	37	CCDS4236.1	.	.	.	.	.	.	.	.	.	.	C	11.05	1.525451	0.27299	.	.	ENSG00000256453	ENST00000542735	T	0.34859	1.34	4.97	4.97	0.65823	.	0.357138	0.23704	N	0.045400	T	0.26268	0.0641	N	0.19112	0.55	0.27565	N	0.950072	B	0.26635	0.155	B	0.25759	0.063	T	0.24764	-1.0151	10	0.72032	D	0.01	-6.3441	13.9714	0.64242	0.0:1.0:0.0:0.0	.	345	Q8IYX4	DND1_HUMAN	T	345	ENSP00000445366:A345T	ENSP00000445366:A345T	A	-	1	0	DND1	140031091	0.814000	0.29104	1.000000	0.80357	0.382000	0.30200	0.973000	0.29422	2.750000	0.94351	0.551000	0.68910	GCT	.	.	weak		0.602	DND1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251669.2	NM_194249	
AKAP11	11215	hgsc.bcm.edu	37	13	42875258	42875258	+	Silent	SNP	T	T	C	rs61741710	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr13:42875258T>C	ENST00000025301.2	+	8	2551	c.2376T>C	c.(2374-2376)taT>taC	p.Y792Y		NM_016248.3	NP_057332.1	Q9UKA4	AKA11_HUMAN	A kinase (PRKA) anchor protein 11	792					intracellular signal transduction (GO:0035556)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)	protein kinase A binding (GO:0051018)|protein phosphatase 1 binding (GO:0008157)			breast(3)|central_nervous_system(4)|cervix(1)|endometrium(6)|kidney(3)|large_intestine(10)|liver(1)|lung(22)|ovary(1)|skin(3)|stomach(2)	56		Lung NSC(96;1.86e-05)|Prostate(109;0.0165)|Lung SC(185;0.0262)|Breast(139;0.0707)|Hepatocellular(98;0.114)		OV - Ovarian serous cystadenocarcinoma(117;0.000365)|GBM - Glioblastoma multiforme(144;0.00116)|BRCA - Breast invasive adenocarcinoma(63;0.19)		TTCTCCCATATCATATTTCAT	0.418													T|||	55	0.0109824	0.003	0.0029	5008	,	,		19247	0.001		0.0099	False		,,,				2504	0.0389				p.Y792Y		Atlas-SNP	.											.	AKAP11	146	.	0			c.T2376C						PASS	.	T		19,4387	26.2+/-53.5	0,19,2184	145.0	129.0	135.0		2376	0.9	0.3	13	dbSNP_129	135	84,8516	48.5+/-108.0	0,84,4216	no	coding-synonymous	AKAP11	NM_016248.3		0,103,6400	CC,CT,TT		0.9767,0.4312,0.7919		792/1902	42875258	103,12903	2203	4300	6503	SO:0001819	synonymous_variant	11215	exon8			CCCATATCATATT	AB014529	CCDS9383.1	13q	2012-04-17			ENSG00000023516	ENSG00000023516		"""A-kinase anchor proteins"", ""Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"""	369	protein-coding gene	gene with protein product	"""AKAP 220"", ""A-kinase anchoring protein, 220kDa"", ""protein kinase A anchoring protein 11"", ""protein phosphatase 1, regulatory subunit 44"""	604696				9734811, 8621616	Standard	NM_016248		Approved	KIAA0629, AKAP220, PRKA11, FLJ11304, DKFZp781I12161, PPP1R44	uc001uys.2	Q9UKA4	OTTHUMG00000016805	ENST00000025301.2:c.2376T>C	13.37:g.42875258T>C		106.0	0.0	0		117.0	58.0	0.495726	NM_016248	O75124|Q9NUK7	Silent	SNP	ENST00000025301.2	37	CCDS9383.1																																																																																			T|0.992;C|0.008	0.008	strong		0.418	AKAP11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044700.2	NM_016248	
ZNF37A	7587	hgsc.bcm.edu	37	10	38406359	38406359	+	Missense_Mutation	SNP	A	A	C	rs150470434	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr10:38406359A>C	ENST00000361085.5	+	7	625	c.280A>C	c.(280-282)Aat>Cat	p.N94H	ZNF37A_ENST00000351773.3_Missense_Mutation_p.N94H	NM_001178101.1|NM_003421.2	NP_001171572.1|NP_003412.1	P17032	ZN37A_HUMAN	zinc finger protein 37A	94					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)|breast(2)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(6)|lung(13)|prostate(1)	28						AATGAAGTTCAATGAGTTTAA	0.294													A|||	4	0.000798722	0.0	0.0	5008	,	,		18981	0.0		0.004	False		,,,				2504	0.0				p.N94H		Atlas-SNP	.											.	ZNF37A	118	.	0			c.A280C						PASS	.	A	HIS/ASN,HIS/ASN,HIS/ASN	0,4396		0,0,2198	65.0	77.0	73.0		280,280,280	-4.3	0.1	10	dbSNP_134	73	17,8563	9.8+/-36.6	0,17,4273	yes	missense,missense,missense	ZNF37A	NM_001007094.2,NM_001178101.1,NM_003421.2	68,68,68	0,17,6471	CC,CA,AA		0.1981,0.0,0.131	benign,benign,benign	94/562,94/562,94/562	38406359	17,12959	2198	4290	6488	SO:0001583	missense	7587	exon7			AAGTTCAATGAGT	X69115	CCDS31183.1	10p11.2	2013-01-08	2006-05-11		ENSG00000075407	ENSG00000075407		"""Zinc fingers, C2H2-type"", ""-"""	13102	protein-coding gene	gene with protein product			"""zinc finger protein 37a (KOX 21)"""			2014798, 8464732	Standard	NM_001178101		Approved	KOX21, ZNF37	uc001izl.3	P17032	OTTHUMG00000017990	ENST00000361085.5:c.280A>C	10.37:g.38406359A>C	ENSP00000354377:p.Asn94His	163.0	0.0	0		187.0	81.0	0.433155	NM_003421	B3KRQ3|D3DRZ3|Q96B88	Missense_Mutation	SNP	ENST00000361085.5	37	CCDS31183.1	2	9.157509157509158E-4	0	0.0	0	0.0	0	0.0	2	0.002638522427440633	A	0.012	-1.647092	0.00792	0.0	0.001981	ENSG00000075407	ENST00000351773;ENST00000361085	T;T	0.07021	3.23;3.23	2.16	-4.33	0.03677	.	.	.	.	.	T	0.02571	0.0078	N	0.02213	-0.635	0.09310	N	1	B	0.23442	0.085	B	0.28011	0.085	T	0.46816	-0.9164	9	0.19147	T	0.46	.	4.1301	0.10146	0.3936:0.0:0.4349:0.1715	.	94	P17032	ZN37A_HUMAN	H	94	ENSP00000329141:N94H;ENSP00000354377:N94H	ENSP00000329141:N94H	N	+	1	0	ZNF37A	38446365	0.000000	0.05858	0.149000	0.22428	0.397000	0.30659	-1.717000	0.01876	-0.782000	0.04541	-0.376000	0.06991	AAT	A|0.998;C|0.002	0.002	strong		0.294	ZNF37A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047624.2	NM_003421	
ITLN1	55600	hgsc.bcm.edu	37	1	160853312	160853312	+	Silent	SNP	C	C	T	rs79969862	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr1:160853312C>T	ENST00000326245.3	-	3	178	c.63G>A	c.(61-63)gaG>gaA	p.E21E	ITLN1_ENST00000487531.1_5'Flank	NM_017625.2	NP_060095.2	Q8WWA0	ITLN1_HUMAN	intelectin 1 (galactofuranose binding)	21					positive regulation of glucose import (GO:0046326)|positive regulation of protein phosphorylation (GO:0001934)|response to nematode (GO:0009624)	anchored component of membrane (GO:0031225)|brush border membrane (GO:0031526)|extracellular vesicular exosome (GO:0070062)|membrane raft (GO:0045121)|receptor complex (GO:0043235)	carbohydrate binding (GO:0030246)			breast(1)|central_nervous_system(1)|endometrium(4)|kidney(1)|large_intestine(1)|lung(6)|ovary(2)|pancreas(1)|skin(3)|upper_aerodigestive_tract(1)	21	all_cancers(52;2.99e-17)|all_hematologic(112;0.093)		BRCA - Breast invasive adenocarcinoma(70;0.00737)			AAGTATTAGCCTCATCTAGGG	0.463													C|||	89	0.0177716	0.0461	0.0043	5008	,	,		18185	0.0		0.0	False		,,,				2504	0.0256				p.E21E		Atlas-SNP	.											.	ITLN1	45	.	0			c.G63A						PASS	.	C		182,4224	117.1+/-155.0	5,172,2026	159.0	145.0	150.0		63	-3.0	0.0	1	dbSNP_132	150	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous	ITLN1	NM_017625.2		5,173,6325	TT,TC,CC		0.0116,4.1307,1.407		21/314	160853312	183,12823	2203	4300	6503	SO:0001819	synonymous_variant	55600	exon3			ATTAGCCTCATCT	AB036706	CCDS1211.1	1q21.3	2008-02-05			ENSG00000179914	ENSG00000179914			18259	protein-coding gene	gene with protein product		609873				11313366, 11181563	Standard	NM_017625		Approved	ITLN, FLJ20022, LFR, HL-1, hIntL	uc001fxc.3	Q8WWA0	OTTHUMG00000028604	ENST00000326245.3:c.63G>A	1.37:g.160853312C>T		155.0	0.0	0		139.0	49.0	0.352518	NM_017625	Q5IWS4|Q5VYI4|Q6YDJ3|Q9NP67	Silent	SNP	ENST00000326245.3	37	CCDS1211.1																																																																																			C|0.984;T|0.016	0.016	strong		0.463	ITLN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000071462.1	NM_017625	
SLC37A2	219855	hgsc.bcm.edu	37	11	124951719	124951719	+	Missense_Mutation	SNP	G	G	A	rs34485243	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr11:124951719G>A	ENST00000403796.2	+	9	1103	c.802G>A	c.(802-804)Ggc>Agc	p.G268S	SLC37A2_ENST00000407458.1_Missense_Mutation_p.G268S|SLC37A2_ENST00000298280.5_Missense_Mutation_p.G268S|SLC37A2_ENST00000308074.4_Missense_Mutation_p.G268S	NM_001145290.1	NP_001138762.1	Q8TED4	SPX2_HUMAN	solute carrier family 37 (glucose-6-phosphate transporter), member 2	268			G -> S (in dbSNP:rs34485243).		carbohydrate transport (GO:0008643)|transmembrane transport (GO:0055085)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)	transporter activity (GO:0005215)			NS(1)|breast(1)|central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(5)|lung(6)|ovary(2)|prostate(2)|skin(1)|stomach(2)|urinary_tract(1)	27	all_hematologic(175;0.215)	Breast(109;0.012)|Medulloblastoma(222;0.0523)|Lung NSC(97;0.152)|all_lung(97;0.159)|all_neural(223;0.224)		BRCA - Breast invasive adenocarcinoma(274;1.61e-06)|OV - Ovarian serous cystadenocarcinoma(99;0.0384)		CAGGGAGAGCGGCCTTGAGAC	0.592													G|||	170	0.0339457	0.1248	0.0058	5008	,	,		18150	0.0		0.001	False		,,,				2504	0.0				p.G268S	Melanoma(11;373 620 21213 26083 47768)	Atlas-SNP	.											.	SLC37A2	105	.	0			c.G802A						PASS	.	G	SER/GLY,SER/GLY	396,4006	198.7+/-222.5	15,366,1820	68.0	65.0	66.0		802,802	-8.0	0.0	11	dbSNP_126	66	2,8596	2.2+/-6.3	0,2,4297	yes	missense,missense	SLC37A2	NM_001145290.1,NM_198277.2	56,56	15,368,6117	AA,AG,GG		0.0233,8.9959,3.0615	benign,benign	268/502,268/506	124951719	398,12602	2201	4299	6500	SO:0001583	missense	219855	exon9			GAGAGCGGCCTTG	AK074100	CCDS31714.1, CCDS44757.1	11q24.2	2013-07-17	2013-07-17		ENSG00000134955	ENSG00000134955		"""Solute carriers"""	20644	protein-coding gene	gene with protein product			"""solute carrier family 37 (glycerol-3-phosphate transporter), member 2"""				Standard	NM_198277		Approved	FLJ00171	uc010sau.2	Q8TED4	OTTHUMG00000165879	ENST00000403796.2:c.802G>A	11.37:g.124951719G>A	ENSP00000384407:p.Gly268Ser	73.0	0.0	0		76.0	27.0	0.355263	NM_001145290	A8K2P9|Q6P599|Q7Z7P8|Q8TEM2	Missense_Mutation	SNP	ENST00000403796.2	37	CCDS44757.1	42	0.019230769230769232	39	0.07926829268292683	3	0.008287292817679558	0	0.0	0	0.0	G	1.561	-0.536711	0.04082	0.089959	2.33E-4	ENSG00000134955	ENST00000403796;ENST00000407458;ENST00000298280;ENST00000308074	T;T;T;T	0.31769	1.48;1.48;1.93;1.48	4.86	-7.96	0.01144	Major facilitator superfamily domain, general substrate transporter (1);Major facilitator superfamily domain (1);	1.505550	0.03203	N	0.175066	T	0.00328	0.0010	N	0.01473	-0.845	0.09310	N	1	B;B	0.10296	0.003;0.003	B;B	0.10450	0.005;0.003	T	0.15065	-1.0450	10	0.08599	T	0.76	-3.6249	6.3702	0.21477	0.2968:0.1007:0.5033:0.0992	rs34485243	268;268	Q8TED4-2;Q8TED4	.;SPX2_HUMAN	S	268	ENSP00000384407:G268S;ENSP00000385126:G268S;ENSP00000298280:G268S;ENSP00000311833:G268S	ENSP00000298280:G268S	G	+	1	0	SLC37A2	124456929	0.000000	0.05858	0.000000	0.03702	0.008000	0.06430	0.394000	0.20834	-1.389000	0.02090	-0.880000	0.02959	GGC	G|0.965;A|0.035	0.035	strong		0.592	SLC37A2-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000386837.1	XM_166184	
FBXO4	26272	hgsc.bcm.edu	37	5	41925431	41925431	+	Missense_Mutation	SNP	G	G	A	rs2231916		TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr5:41925431G>A	ENST00000281623.3	+	1	76	c.20G>A	c.(19-21)cGc>cAc	p.R7H	FBXO4_ENST00000509134.1_Missense_Mutation_p.R7H|FBXO4_ENST00000296812.2_Missense_Mutation_p.R7H	NM_012176.2	NP_036308.1	Q9UKT5	FBX4_HUMAN	F-box protein 4	7					positive regulation of protein ubiquitination (GO:0031398)|protein polyubiquitination (GO:0000209)|protein ubiquitination (GO:0016567)|SCF-dependent proteasomal ubiquitin-dependent protein catabolic process (GO:0031146)|telomere maintenance (GO:0000723)|ubiquitin-dependent protein catabolic process (GO:0006511)	cytoplasm (GO:0005737)|SCF ubiquitin ligase complex (GO:0019005)|ubiquitin ligase complex (GO:0000151)	protein homodimerization activity (GO:0042803)|ubiquitin-protein transferase activity (GO:0004842)			breast(2)|endometrium(1)|kidney(2)|large_intestine(6)|liver(1)|lung(11)|prostate(1)|stomach(1)|urinary_tract(2)	27		Lung NSC(810;4.15e-05)|Breast(839;0.00093)|Ovarian(839;0.00965)|Myeloproliferative disorder(839;0.0255)|all_neural(839;0.0604)				AGCGAGCCGCGCAGCGGAACA	0.706																																					p.R7H		Atlas-SNP	.											.	FBXO4	42	.	0			c.G20A						PASS	.						3.0	5.0	4.0					5																	41925431		1448	2780	4228	SO:0001583	missense	26272	exon1			AGCCGCGCAGCGG	AF129534	CCDS3938.1, CCDS3939.1, CCDS75238.1	5p12	2008-02-05	2004-06-15		ENSG00000151876	ENSG00000151876		"""F-boxes /  ""other"""""	13583	protein-coding gene	gene with protein product		609090	"""F-box only protein 4"""			10531035, 10531037	Standard	NM_033484		Approved	FBX4	uc003jmq.3	Q9UKT5	OTTHUMG00000094799	ENST00000281623.3:c.20G>A	5.37:g.41925431G>A	ENSP00000281623:p.Arg7His	16.0	0.0	0		20.0	10.0	0.5	NM_033484	Q68CU8|Q86VT8|Q9UK98	Missense_Mutation	SNP	ENST00000281623.3	37	CCDS3938.1	.	.	.	.	.	.	.	.	.	.	G	18.34	3.601780	0.66445	.	.	ENSG00000151876	ENST00000296812;ENST00000281623;ENST00000509134	T;T;T	0.65364	-0.15;-0.15;-0.15	4.14	4.14	0.48551	.	0.532611	0.20854	N	0.084478	T	0.41789	0.1174	N	0.14661	0.345	0.09310	N	1	B;B;B	0.10296	0.001;0.003;0.001	B;B;B	0.04013	0.0;0.001;0.001	T	0.24440	-1.0160	10	0.49607	T	0.09	-12.9866	8.033	0.30476	0.1107:0.0:0.8893:0.0	.	7;7;7	D6RAJ6;Q9UKT5;Q9UKT5-2	.;FBX4_HUMAN;.	H	7	ENSP00000296812:R7H;ENSP00000281623:R7H;ENSP00000421749:R7H	ENSP00000281623:R7H	R	+	2	0	FBXO4	41961188	0.010000	0.17322	0.037000	0.18230	0.752000	0.42762	1.241000	0.32743	2.311000	0.77944	0.563000	0.77884	CGC	.	.	alt		0.706	FBXO4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000211614.1		
MKI67	4288	hgsc.bcm.edu	37	10	129914162	129914162	+	Missense_Mutation	SNP	G	G	C	rs143381225	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr10:129914162G>C	ENST00000368654.3	-	7	885	c.510C>G	c.(508-510)gaC>gaG	p.D170E	MKI67_ENST00000368653.3_Intron	NM_002417.4	NP_002408.3	P46013	KI67_HUMAN	marker of proliferation Ki-67	170					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)				TGTCTTTTGAGTCATCTGCGG	0.413													G|||	4	0.000798722	0.0	0.0014	5008	,	,		18963	0.0		0.003	False		,,,				2504	0.0				p.D170E		Atlas-SNP	.											.	MKI67	363	.	0			c.C510G						PASS	.	G	,GLU/ASP	3,4403	6.2+/-15.9	0,3,2200	202.0	190.0	194.0		,510	2.6	0.0	10	dbSNP_134	194	21,8579	16.0+/-53.3	0,21,4279	yes	intron,missense	MKI67	NM_001145966.1,NM_002417.4	,45	0,24,6479	CC,CG,GG		0.2442,0.0681,0.1845	,possibly-damaging	,170/3257	129914162	24,12982	2203	4300	6503	SO:0001583	missense	4288	exon7			TTTTGAGTCATCT	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.510C>G	10.37:g.129914162G>C	ENSP00000357643:p.Asp170Glu	41.0	0.0	0		40.0	20.0	0.5	NM_002417	Q5VWH2	Missense_Mutation	SNP	ENST00000368654.3	37	CCDS7659.1	2	9.157509157509158E-4	0	0.0	0	0.0	0	0.0	2	0.002638522427440633	G	13.09	2.133471	0.37630	6.81E-4	0.002442	ENSG00000148773	ENST00000368654;ENST00000537609	T	0.21543	2.0	3.54	2.64	0.31445	.	1.326700	0.05140	N	0.494199	T	0.12263	0.0298	N	0.19112	0.55	0.09310	N	0.999994	P	0.37864	0.61	B	0.29353	0.101	T	0.20505	-1.0273	9	.	.	.	.	6.9772	0.24683	0.1232:0.0:0.8768:0.0	.	170	P46013	KI67_HUMAN	E	170	ENSP00000357643:D170E	.	D	-	3	2	MKI67	129804152	0.001000	0.12720	0.005000	0.12908	0.042000	0.13812	0.408000	0.21065	1.097000	0.41459	0.655000	0.94253	GAC	G|0.998;C|0.002	0.002	strong		0.413	MKI67-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000050999.1	NM_002417	
USP25	29761	hgsc.bcm.edu	37	21	17250244	17250244	+	Missense_Mutation	SNP	A	A	C	rs149241751		TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr21:17250244A>C	ENST00000285679.6	+	23	3298	c.2929A>C	c.(2929-2931)Aag>Cag	p.K977Q	USP25_ENST00000285681.2_Missense_Mutation_p.K1009Q|USP25_ENST00000351097.5_Missense_Mutation_p.K372Q|USP25_ENST00000400183.2_Missense_Mutation_p.K1047Q	NM_013396.3	NP_037528.3	Q9UHP3	UBP25_HUMAN	ubiquitin specific peptidase 25	977					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)		AATGGAAGAAAAGGATATACT	0.373													A|||	1	0.000199681	0.0	0.0	5008	,	,		15290	0.0		0.001	False		,,,				2504	0.0				p.K977Q		Atlas-SNP	.											.	USP25	156	.	0			c.A2929C						PASS	.	A	GLN/LYS	1,4405	2.1+/-5.4	0,1,2202	111.0	113.0	113.0		2929	4.5	1.0	21	dbSNP_134	113	14,8586	10.5+/-38.8	0,14,4286	yes	missense	USP25	NM_013396.3	53	0,15,6488	CC,CA,AA		0.1628,0.0227,0.1153	benign	977/1056	17250244	15,12991	2203	4300	6503	SO:0001583	missense	29761	exon23			GAAGAAAAGGATA	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.2929A>C	21.37:g.17250244A>C	ENSP00000285679:p.Lys977Gln	160.0	0.0	0		177.0	98.0	0.553672	NM_013396	C0LSZ0|Q6DHZ9|Q9H9W1	Missense_Mutation	SNP	ENST00000285679.6	37	CCDS33515.1	2	9.157509157509158E-4	0	0.0	0	0.0	0	0.0	2	0.002638522427440633	A	12.67	2.007030	0.35415	2.27E-4	0.001628	ENSG00000155313	ENST00000285681;ENST00000285679;ENST00000351097;ENST00000400183	T;T;T;T	0.29917	1.94;1.95;1.55;1.95	5.67	4.51	0.55191	.	0.131563	0.64402	D	0.000001	T	0.29458	0.0734	L	0.51422	1.61	0.41488	D	0.9882	B;P;B;P	0.50272	0.082;0.862;0.214;0.933	B;B;B;B	0.41917	0.059;0.37;0.127;0.323	T	0.05037	-1.0910	10	0.49607	T	0.09	-20.4276	11.8858	0.52602	0.8691:0.0:0.0:0.1309	.	1047;372;1009;977	Q9UHP3-3;Q96B65;Q9UHP3-1;Q9UHP3	.;.;.;UBP25_HUMAN	Q	1009;977;372;1047	ENSP00000285681:K1009Q;ENSP00000285679:K977Q;ENSP00000299574:K372Q;ENSP00000383044:K1047Q	ENSP00000285679:K977Q	K	+	1	0	USP25	16172115	1.000000	0.71417	0.999000	0.59377	0.173000	0.22820	8.932000	0.92897	0.970000	0.38263	-0.336000	0.08194	AAG	A|0.999;C|0.001	0.001	strong		0.373	USP25-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000157964.1		
SRRM1	10250	hgsc.bcm.edu	37	1	24979487	24979487	+	Missense_Mutation	SNP	C	C	T	rs144082896	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr1:24979487C>T	ENST00000323848.9	+	8	1319	c.1004C>T	c.(1003-1005)cCa>cTa	p.P335L	SRRM1_ENST00000479034.1_3'UTR|SRRM1_ENST00000374389.4_Missense_Mutation_p.P330L|SRRM1_ENST00000537199.1_Missense_Mutation_p.P204L|SRRM1_ENST00000447431.2_Missense_Mutation_p.P335L	NM_005839.3	NP_005830.2	Q8IYB3	SRRM1_HUMAN	serine/arginine repetitive matrix 1	335	Arg-rich.|Necessary for speckles and matrix localization.|Pro-rich.|Ser-rich.				gene expression (GO:0010467)|mRNA 3'-end processing (GO:0031124)|mRNA export from nucleus (GO:0006406)|mRNA splicing, via spliceosome (GO:0000398)|RNA splicing (GO:0008380)|RNA splicing, via transesterification reactions (GO:0000375)|termination of RNA polymerase II transcription (GO:0006369)|transcription from RNA polymerase II promoter (GO:0006366)	catalytic step 2 spliceosome (GO:0071013)|cytosol (GO:0005829)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	DNA binding (GO:0003677)|poly(A) RNA binding (GO:0044822)			breast(1)|central_nervous_system(3)|endometrium(3)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(12)|lung(9)|ovary(2)|prostate(1)|urinary_tract(2)	36		Colorectal(325;3.46e-05)|Renal(390;0.0007)|Lung NSC(340;0.000946)|all_lung(284;0.00125)|Ovarian(437;0.00764)|Breast(348;0.0148)|Myeloproliferative disorder(586;0.0255)|all_neural(195;0.19)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0422)|OV - Ovarian serous cystadenocarcinoma(117;1.01e-24)|Colorectal(126;5.95e-08)|COAD - Colon adenocarcinoma(152;3.24e-06)|GBM - Glioblastoma multiforme(114;0.000148)|BRCA - Breast invasive adenocarcinoma(304;0.00177)|KIRC - Kidney renal clear cell carcinoma(1967;0.00348)|STAD - Stomach adenocarcinoma(196;0.00483)|READ - Rectum adenocarcinoma(331;0.0649)|Lung(427;0.138)		ATGCCTCCTCCACCAAGGCAT	0.448													C|||	7	0.00139776	0.0	0.0	5008	,	,		17867	0.0		0.004	False		,,,				2504	0.0031				p.P335L	Ovarian(68;897 1494 3282 17478)	Atlas-SNP	.											.	SRRM1	81	.	0			c.C1004T						PASS	.	C	LEU/PRO	3,4403	6.2+/-15.9	0,3,2200	58.0	55.0	56.0		1004	5.4	1.0	1	dbSNP_134	56	33,8567	23.4+/-69.3	0,33,4267	yes	missense	SRRM1	NM_005839.3	98	0,36,6467	TT,TC,CC		0.3837,0.0681,0.2768	possibly-damaging	335/905	24979487	36,12970	2203	4300	6503	SO:0001583	missense	10250	exon8			CTCCTCCACCAAG	AF048977	CCDS255.1	1p36	2010-04-22			ENSG00000133226	ENSG00000133226			16638	protein-coding gene	gene with protein product	"""Ser/Arg-related nuclear matrix protein"", ""plenty of prolines 101-like"""	605975				9531537	Standard	NM_005839		Approved	SRM160, POP101, MGC39488	uc001bjm.3	Q8IYB3	OTTHUMG00000003320	ENST00000323848.9:c.1004C>T	1.37:g.24979487C>T	ENSP00000326261:p.Pro335Leu	232.0	0.0	0		237.0	100.0	0.421941	NM_005839	O60585|Q5VVN4	Missense_Mutation	SNP	ENST00000323848.9	37	CCDS255.1	4	0.0018315018315018315	0	0.0	1	0.0027624309392265192	0	0.0	3	0.00395778364116095	C	17.19	3.326020	0.60743	6.81E-4	0.003837	ENSG00000133226	ENST00000323848;ENST00000447431;ENST00000374389;ENST00000537199	T;T;T;T	0.53206	0.84;0.86;0.86;0.63	5.36	5.36	0.76844	.	0.000000	0.64402	D	0.000009	T	0.50120	0.1597	L	0.54323	1.7	0.53688	D	0.999977	P;P	0.50528	0.936;0.895	P;B	0.44477	0.451;0.264	T	0.50338	-0.8840	10	0.39692	T	0.17	.	19.065	0.93106	0.0:1.0:0.0:0.0	.	335;335	E9PCT1;Q8IYB3	.;SRRM1_HUMAN	L	335;335;330;204	ENSP00000326261:P335L;ENSP00000391430:P335L;ENSP00000363510:P330L;ENSP00000441776:P204L	ENSP00000326261:P335L	P	+	2	0	SRRM1	24852074	0.997000	0.39634	1.000000	0.80357	0.982000	0.71751	3.240000	0.51368	2.500000	0.84329	0.585000	0.79938	CCA	C|0.997;T|0.003	0.003	strong		0.448	SRRM1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000009292.2	NM_005839	
SLC29A3	55315	hgsc.bcm.edu	37	10	73122284	73122284	+	Silent	SNP	G	G	A	rs373404056		TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr10:73122284G>A	ENST00000373189.5	+	6	1399	c.1347G>A	c.(1345-1347)acG>acA	p.T449T		NM_001174098.1|NM_018344.5	NP_001167569.1|NP_060814.4	Q9BZD2	S29A3_HUMAN	solute carrier family 29 (equilibrative nucleoside transporter), member 3	449			T -> R (in HLAS; results in reduced nucleoside transport). {ECO:0000269|PubMed:19336477}.		transmembrane transport (GO:0055085)	endosome (GO:0005768)|integral component of membrane (GO:0016021)|lysosomal membrane (GO:0005765)	nucleoside transmembrane transporter activity (GO:0005337)			endometrium(3)|kidney(2)|large_intestine(3)|lung(4)|prostate(1)|skin(1)|urinary_tract(1)	15						CTGAGGCCACGGGAGTGGTGA	0.602																																					p.T449T	Esophageal Squamous(200;1319 2142 18949 31248 39672)	Atlas-SNP	.											SLC29A3,NS,carcinoma,+1,1	SLC29A3	51	1	0			c.G1347A						PASS	.	G	,	1,4405	2.1+/-5.4	0,1,2202	86.0	60.0	69.0		,1347	-11.1	0.0	10		69	0,8600		0,0,4300	no	utr-3,coding-synonymous	SLC29A3	NM_001174098.1,NM_018344.5	,	0,1,6502	AA,AG,GG		0.0,0.0227,0.0077	,	,449/476	73122284	1,13005	2203	4300	6503	SO:0001819	synonymous_variant	55315	exon6			GGCCACGGGAGTG	AF326987	CCDS7310.1	10q22.2	2013-07-17	2013-07-17		ENSG00000198246	ENSG00000198246		"""Solute carriers"""	23096	protein-coding gene	gene with protein product		612373	"""solute carrier family 29 (nucleoside transporters), member 3"""			11396612	Standard	NM_018344		Approved	ENT3, FLJ11160	uc001jrr.4	Q9BZD2	OTTHUMG00000018424	ENST00000373189.5:c.1347G>A	10.37:g.73122284G>A		137.0	0.0	0		144.0	79.0	0.548611	NM_018344	B2RB50|B4E2Z9|B7ZA37|Q0VAM9|Q5T465|Q7RTT8|Q8IVZ0|Q9BWI2|Q9NUS9	Silent	SNP	ENST00000373189.5	37	CCDS7310.1																																																																																			.	.	none		0.602	SLC29A3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048544.1	NM_018344	
COL23A1	91522	hgsc.bcm.edu	37	5	177674821	177674821	+	Missense_Mutation	SNP	T	T	C	rs200475672	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr5:177674821T>C	ENST00000390654.3	-	21	1581	c.1224A>G	c.(1222-1224)atA>atG	p.I408M		NM_173465.3	NP_775736.2	Q86Y22	CONA1_HUMAN	collagen, type XXIII, alpha 1	408	Gly-rich.				collagen catabolic process (GO:0030574)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)	collagen trimer (GO:0005581)|endoplasmic reticulum lumen (GO:0005788)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				breast(1)|central_nervous_system(1)|endometrium(4)|large_intestine(3)|lung(6)|ovary(1)|skin(2)|urinary_tract(1)	19	all_cancers(89;0.00188)|Renal(175;0.000159)|Lung NSC(126;0.00814)|all_lung(126;0.0129)	all_neural(177;0.00802)|Medulloblastoma(196;0.0145)|all_hematologic(541;0.248)	Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)	OV - Ovarian serous cystadenocarcinoma(192;0.153)|all cancers(165;0.172)		CTGGCTCCACTATGAGCTGAG	0.632													T|||	2	0.000399361	0.0	0.0	5008	,	,		17262	0.0		0.002	False		,,,				2504	0.0				p.I408M		Atlas-SNP	.											.	COL23A1	47	.	0			c.A1224G						PASS	.	T	MET/ILE	0,3916		0,0,1958	19.0	22.0	21.0		1224	3.6	1.0	5		21	4,8254		0,4,4125	yes	missense	COL23A1	NM_173465.3	10	0,4,6083	CC,CT,TT		0.0484,0.0,0.0329	probably-damaging	408/541	177674821	4,12170	1958	4129	6087	SO:0001583	missense	91522	exon21			CTCCACTATGAGC	AL137461	CCDS4436.1	5q35.3	2013-01-16			ENSG00000050767	ENSG00000050767		"""Collagens"""	22990	protein-coding gene	gene with protein product		610043				12644459	Standard	NM_173465		Approved	DKFZp434K0621	uc021yiz.1	Q86Y22	OTTHUMG00000130890	ENST00000390654.3:c.1224A>G	5.37:g.177674821T>C	ENSP00000375069:p.Ile408Met	157.0	0.0	0		146.0	68.0	0.465753	NM_173465	Q8IVR4|Q9NT93	Missense_Mutation	SNP	ENST00000390654.3	37	CCDS4436.1	.	.	.	.	.	.	.	.	.	.	T	7.999	0.754912	0.15846	0.0	4.84E-4	ENSG00000050767	ENST00000390654	D	0.93307	-3.2	4.76	3.57	0.40892	.	0.273854	0.26496	N	0.024047	D	0.89812	0.6823	L	0.47716	1.5	0.80722	D	1	P	0.44877	0.845	B	0.42522	0.39	D	0.86541	0.1828	10	0.48119	T	0.1	-4.3929	8.4416	0.32818	0.0:0.0:0.1982:0.8018	.	408	Q86Y22	CONA1_HUMAN	M	408	ENSP00000375069:I408M	ENSP00000375069:I408M	I	-	3	3	COL23A1	177607427	0.998000	0.40836	0.999000	0.59377	0.010000	0.07245	1.567000	0.36407	0.642000	0.30620	-0.460000	0.05396	ATA	.	.	weak		0.632	COL23A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253475.1	NM_173465	
GPR142	350383	hgsc.bcm.edu	37	17	72368383	72368383	+	Silent	SNP	C	C	A	rs144235997	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr17:72368383C>A	ENST00000335666.4	+	4	1081	c.1033C>A	c.(1033-1035)Cgg>Agg	p.R345R		NM_181790.1	NP_861455.1	Q7Z601	GP142_HUMAN	G protein-coupled receptor 142	345						cell junction (GO:0030054)|cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)			central_nervous_system(1)|endometrium(3)|large_intestine(3)|lung(21)|ovary(2)|prostate(1)|skin(4)	35						GAGGAGGGGCCGGAGTGGGCT	0.632													C|||	15	0.00299521	0.0	0.0086	5008	,	,		19090	0.0		0.008	False		,,,				2504	0.001				p.R345R		Atlas-SNP	.											GPR142,bladder,carcinoma,-2,1	GPR142	74	1	0			c.C1033A						PASS	.	C		2,4404	2.1+/-5.4	0,2,2201	93.0	75.0	81.0		1033	2.6	0.0	17	dbSNP_134	81	77,8523	44.9+/-103.4	0,77,4223	no	coding-synonymous	GPR142	NM_181790.1		0,79,6424	AA,AC,CC		0.8953,0.0454,0.6074		345/463	72368383	79,12927	2203	4300	6503	SO:0001819	synonymous_variant	350383	exon4			AGGGGCCGGAGTG	AY255622	CCDS11698.1	17q25.2	2012-08-21				ENSG00000257008		"""GPCR / Class A : Orphans"""	20088	protein-coding gene	gene with protein product		609046				14623098	Standard	NM_181790		Approved	PGR2	uc010wqy.2	Q7Z601		ENST00000335666.4:c.1033C>A	17.37:g.72368383C>A		183.0	0.0	0		145.0	69.0	0.475862	NM_181790	A4CYJ8|Q86SL3	Silent	SNP	ENST00000335666.4	37	CCDS11698.1																																																																																			C|0.994;A|0.006	0.006	strong		0.632	GPR142-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000442545.1	NM_181790	
ZNF57	126295	hgsc.bcm.edu	37	19	2917798	2917798	+	Silent	SNP	A	A	G	rs61755868	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr19:2917798A>G	ENST00000306908.5	+	4	1327	c.1179A>G	c.(1177-1179)aaA>aaG	p.K393K	ZNF57_ENST00000523428.1_Silent_p.K361K|AC006277.2_ENST00000520090.2_RNA	NM_173480.2	NP_775751.1	Q68EA5	ZNF57_HUMAN	zinc finger protein 57	393					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)|kidney(2)|large_intestine(5)|lung(2)|ovary(1)|pancreas(1)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	18				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)|GBM - Glioblastoma multiforme(1328;0.00161)|STAD - Stomach adenocarcinoma(1328;0.18)		AGCTCTATAAATGTGAACAAT	0.433													A|||	125	0.0249601	0.0219	0.0288	5008	,	,		22248	0.0		0.0169	False		,,,				2504	0.0603				p.K393K	NSCLC(150;910 1964 4303 10464 26498)	Atlas-SNP	.											.	ZNF57	57	.	0			c.A1179G						PASS	.	A		85,4321	71.4+/-109.4	0,85,2118	92.0	84.0	86.0		1179	-0.5	0.0	19	dbSNP_129	86	208,8392	88.6+/-150.9	4,200,4096	no	coding-synonymous	ZNF57	NM_173480.2		4,285,6214	GG,GA,AA		2.4186,1.9292,2.2528		393/556	2917798	293,12713	2203	4300	6503	SO:0001819	synonymous_variant	126295	exon4			CTATAAATGTGAA	M88368	CCDS12098.1	19p13.3	2013-01-08			ENSG00000171970	ENSG00000171970		"""Zinc fingers, C2H2-type"", ""-"""	13125	protein-coding gene	gene with protein product			"""zinc finger protein 424"""	ZNF424		1505991	Standard	NM_173480		Approved		uc002lwr.3	Q68EA5	OTTHUMG00000164485	ENST00000306908.5:c.1179A>G	19.37:g.2917798A>G		140.0	0.0	0		147.0	67.0	0.455782	NM_173480	Q8N6R9	Silent	SNP	ENST00000306908.5	37	CCDS12098.1																																																																																			A|0.975;G|0.025	0.025	strong		0.433	ZNF57-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000378969.1	NM_173480	
LNX1	84708	hgsc.bcm.edu	37	4	54373579	54373579	+	Missense_Mutation	SNP	G	G	A	rs147992678	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr4:54373579G>A	ENST00000263925.7	-	4	994	c.680C>T	c.(679-681)gCt>gTt	p.A227V	LNX1-AS1_ENST00000511989.1_RNA|LNX1-AS1_ENST00000514364.1_RNA|FIP1L1_ENST00000507166.1_Intron|LNX1_ENST00000306888.2_Missense_Mutation_p.A131V|LNX1-AS1_ENST00000510785.1_RNA	NM_001126328.2	NP_001119800.1	Q8TBB1	LNX1_HUMAN	ligand of numb-protein X 1, E3 ubiquitin protein ligase	227	Interaction with MAGEB18.				protein homooligomerization (GO:0051260)|protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:0042787)	cytoplasm (GO:0005737)	ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			autonomic_ganglia(1)|breast(1)|central_nervous_system(3)|endometrium(3)|large_intestine(11)|lung(6)|ovary(3)|urinary_tract(4)	32	all_neural(26;0.153)		GBM - Glioblastoma multiforme(3;8.2e-46)|LUSC - Lung squamous cell carcinoma(32;0.0134)			AACACTCAAAGCTCGATTTAT	0.448													G|||	5	0.000998403	0.0	0.0014	5008	,	,		18395	0.0		0.004	False		,,,				2504	0.0				p.A227V		Atlas-SNP	.											.	LNX1	139	.	0			c.C680T						PASS	.	G	VAL/ALA,VAL/ALA	2,4404	4.2+/-10.8	0,2,2201	89.0	88.0	88.0		680,392	4.9	0.2	4	dbSNP_134	88	18,8582	11.9+/-42.8	0,18,4282	yes	missense,missense	LNX1	NM_001126328.1,NM_032622.2	64,64	0,20,6483	AA,AG,GG		0.2093,0.0454,0.1538	probably-damaging,probably-damaging	227/729,131/633	54373579	20,12986	2203	4300	6503	SO:0001583	missense	84708	exon4			CTCAAAGCTCGAT	AF237782	CCDS3492.1, CCDS47057.1	4q12	2013-01-09	2012-02-23	2005-11-04	ENSG00000072201	ENSG00000072201		"""RING-type (C3HC4) zinc fingers"""	6657	protein-coding gene	gene with protein product		609732	"""ligand of numb-protein X"", ""ligand of numb-protein X 1"""	LNX		11521506, 11782429	Standard	NM_032622		Approved	MPDZ, PDZRN2	uc003hag.5	Q8TBB1	OTTHUMG00000102099	ENST00000263925.7:c.680C>T	4.37:g.54373579G>A	ENSP00000263925:p.Ala227Val	164.0	0.0	0		182.0	88.0	0.483516	NM_001126328	Q4W5K7|Q8N4C2|Q96MJ7|Q9BY20	Missense_Mutation	SNP	ENST00000263925.7	37	CCDS47057.1	4	0.0018315018315018315	0	0.0	1	0.0027624309392265192	0	0.0	3	0.00395778364116095	G	26.6	4.752364	0.89753	4.54E-4	0.002093	ENSG00000072201	ENST00000306888;ENST00000538207;ENST00000263925	T;T	0.09630	2.96;4.47	4.94	4.94	0.65067	.	0.000000	0.85682	D	0.000000	T	0.25344	0.0616	L	0.36672	1.1	0.80722	D	1	D;D	0.89917	1.0;0.998	D;P	0.87578	0.998;0.904	T	0.00780	-1.1569	10	0.45353	T	0.12	.	18.345	0.90318	0.0:0.0:1.0:0.0	.	227;131	Q8TBB1;Q8TBB1-2	LNX1_HUMAN;.	V	131;65;227	ENSP00000302879:A131V;ENSP00000263925:A227V	ENSP00000263925:A227V	A	-	2	0	LNX1	54068336	1.000000	0.71417	0.243000	0.24186	0.863000	0.49368	7.540000	0.82074	2.565000	0.86533	0.555000	0.69702	GCT	G|0.998;A|0.002	0.002	strong		0.448	LNX1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000219934.2		
PCSK9	255738	hgsc.bcm.edu	37	1	55505651	55505651	+	Silent	SNP	C	C	T	rs28385701	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr1:55505651C>T	ENST00000302118.5	+	1	431	c.141C>T	c.(139-141)tcC>tcT	p.S47S	PCSK9_ENST00000452118.2_Silent_p.S47S|PCSK9_ENST00000543384.1_5'Flank	NM_174936.3	NP_777596.2	Q8NBP7	PCSK9_HUMAN	proprotein convertase subtilisin/kexin type 9	47					apoptotic process (GO:0006915)|cellular response to insulin stimulus (GO:0032869)|cellular response to starvation (GO:0009267)|cholesterol homeostasis (GO:0042632)|cholesterol metabolic process (GO:0008203)|kidney development (GO:0001822)|lipoprotein metabolic process (GO:0042157)|liver development (GO:0001889)|low-density lipoprotein particle receptor catabolic process (GO:0032802)|lysosomal transport (GO:0007041)|negative regulation of low-density lipoprotein particle clearance (GO:0010989)|negative regulation of receptor recycling (GO:0001920)|neurogenesis (GO:0022008)|neuron differentiation (GO:0030182)|phospholipid metabolic process (GO:0006644)|positive regulation of neuron apoptotic process (GO:0043525)|positive regulation of receptor internalization (GO:0002092)|protein autoprocessing (GO:0016540)|proteolysis (GO:0006508)|regulation of low-density lipoprotein particle receptor catabolic process (GO:0032803)|regulation of neuron apoptotic process (GO:0043523)|regulation of receptor activity (GO:0010469)|triglyceride metabolic process (GO:0006641)	cell surface (GO:0009986)|cytoplasm (GO:0005737)|early endosome (GO:0005769)|endoplasmic reticulum (GO:0005783)|ER to Golgi transport vesicle (GO:0030134)|extracellular space (GO:0005615)|extrinsic component of external side of plasma membrane (GO:0031232)|Golgi apparatus (GO:0005794)|late endosome (GO:0005770)|lysosome (GO:0005764)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|rough endoplasmic reticulum (GO:0005791)	apolipoprotein binding (GO:0034185)|apolipoprotein receptor binding (GO:0034190)|low-density lipoprotein particle binding (GO:0030169)|low-density lipoprotein particle receptor binding (GO:0050750)|poly(A) RNA binding (GO:0044822)|protein self-association (GO:0043621)|serine-type endopeptidase activity (GO:0004252)|sodium channel inhibitor activity (GO:0019871)|very-low-density lipoprotein particle binding (GO:0034189)|very-low-density lipoprotein particle receptor binding (GO:0070326)			NS(2)|breast(2)|central_nervous_system(3)|endometrium(3)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(1)|liver(2)|lung(4)|ovary(3)|prostate(3)|skin(1)|urinary_tract(1)	32						CCTTGCGTTCCGAGGAGGACG	0.706													C|||	20	0.00399361	0.0	0.0043	5008	,	,		14828	0.0		0.0099	False		,,,				2504	0.0072				p.S47S	Pancreas(137;1454 1827 5886 22361 42375)	Atlas-SNP	.											.	PCSK9	76	.	0			c.C141T						PASS	.	C		8,4366		0,8,2179	35.0	28.0	30.0		141	-6.4	0.0	1	dbSNP_125	30	80,8460		0,80,4190	no	coding-synonymous	PCSK9	NM_174936.3		0,88,6369	TT,TC,CC		0.9368,0.1829,0.6814		47/693	55505651	88,12826	2187	4270	6457	SO:0001819	synonymous_variant	255738	exon1			GCGTTCCGAGGAG	AX207686	CCDS603.1	1p34.1-p32	2014-09-17	2003-05-13		ENSG00000169174	ENSG00000169174			20001	protein-coding gene	gene with protein product		607786	"""hypercholesterolemia, autosomal dominant 3"""	HCHOLA3		12552133, 12730697	Standard	NM_174936		Approved	NARC-1, FH3	uc001cyf.2	Q8NBP7	OTTHUMG00000008136	ENST00000302118.5:c.141C>T	1.37:g.55505651C>T		73.0	0.0	0		112.0	68.0	0.607143	NM_174936	A8T640|C0JYY9|Q5PSM5|Q5SZQ2	Silent	SNP	ENST00000302118.5	37	CCDS603.1																																																																																			C|0.993;T|0.007	0.007	strong		0.706	PCSK9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000022280.1	NM_174936	
IGSF3	3321	hgsc.bcm.edu	37	1	117156603	117156603	+	Missense_Mutation	SNP	A	A	T			TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr1:117156603A>T	ENST00000369486.3	-	4	1381	c.616T>A	c.(616-618)Tcc>Acc	p.S206T	IGSF3_ENST00000318837.6_Missense_Mutation_p.S206T|IGSF3_ENST00000369483.1_Missense_Mutation_p.S206T	NM_001007237.1	NP_001007238.1	O75054	IGSF3_HUMAN	immunoglobulin superfamily, member 3	206	Ig-like C2-type 2.				lacrimal gland development (GO:0032808)	cell surface (GO:0009986)|integral component of membrane (GO:0016021)				NS(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(9)|liver(1)|lung(31)|ovary(4)|prostate(1)|skin(4)|upper_aerodigestive_tract(2)	62	Lung SC(450;0.225)	all_cancers(81;1.24e-06)|all_epithelial(167;4.85e-07)|all_lung(203;1.66e-06)|Lung NSC(69;1.11e-05)		Lung(183;0.0142)|Colorectal(144;0.0929)|LUSC - Lung squamous cell carcinoma(189;0.108)|COAD - Colon adenocarcinoma(174;0.139)|all cancers(265;0.159)|Epithelial(280;0.166)		TCGCTGCTGGAGTGAAGCATG	0.617																																					p.S206T		Atlas-SNP	.											.	IGSF3	294	.	0			c.T616A						PASS	.						56.0	57.0	57.0					1																	117156603		2203	4300	6503	SO:0001583	missense	3321	exon4			TGCTGGAGTGAAG	AF031174	CCDS30813.1, CCDS30814.1	1p13	2013-01-29			ENSG00000143061	ENSG00000143061		"""Immunoglobulin superfamily / V-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	5950	protein-coding gene	gene with protein product		603491				9790749	Standard	NM_001007237		Approved	V8, EWI-3, MGC117164	uc031pnr.1	O75054	OTTHUMG00000022751	ENST00000369486.3:c.616T>A	1.37:g.117156603A>T	ENSP00000358498:p.Ser206Thr	161.0	0.0	0		174.0	89.0	0.511494	NM_001542	A6NJZ6|A6NMC7	Missense_Mutation	SNP	ENST00000369486.3	37	CCDS30813.1	.	.	.	.	.	.	.	.	.	.	A	13.46	2.243549	0.39697	.	.	ENSG00000143061	ENST00000369486;ENST00000369483;ENST00000318837	T;T;T	0.23552	1.9;1.9;1.9	5.02	5.02	0.67125	Immunoglobulin subtype (1);Immunoglobulin V-set (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	0.061231	0.64402	D	0.000002	T	0.13543	0.0328	L	0.27053	0.805	0.42061	D	0.991163	B;P	0.36183	0.387;0.542	P;B	0.45660	0.489;0.388	T	0.05451	-1.0884	10	0.66056	D	0.02	-47.2567	7.3497	0.26684	0.9046:0.0:0.0954:0.0	.	206;206	O75054;A6NJZ6	IGSF3_HUMAN;.	T	206	ENSP00000358498:S206T;ENSP00000358495:S206T;ENSP00000321184:S206T	ENSP00000321184:S206T	S	-	1	0	IGSF3	116958126	1.000000	0.71417	1.000000	0.80357	0.616000	0.37450	3.342000	0.52159	2.101000	0.63845	0.528000	0.53228	TCC	.	.	none		0.617	IGSF3-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000059040.1	NM_001542	
TTLL5	23093	hgsc.bcm.edu	37	14	76259376	76259376	+	Missense_Mutation	SNP	G	G	A			TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr14:76259376G>A	ENST00000298832.9	+	27	3309	c.3104G>A	c.(3103-3105)cGg>cAg	p.R1035Q	TTLL5_ENST00000556893.1_Missense_Mutation_p.R586Q|TTLL5_ENST00000557636.1_Missense_Mutation_p.R1050Q|TTLL5_ENST00000554510.1_Missense_Mutation_p.R544Q	NM_015072.4	NP_055887.3	Q6EMB2	TTLL5_HUMAN	tubulin tyrosine ligase-like family, member 5	1035					fertilization (GO:0009566)|protein polyglutamylation (GO:0018095)|sperm axoneme assembly (GO:0007288)|sperm motility (GO:0030317)|transcription, DNA-templated (GO:0006351)	centrosome (GO:0005813)|cilium (GO:0005929)|cytoplasm (GO:0005737)|nucleus (GO:0005634)	ligase activity (GO:0016874)			NS(2)|breast(2)|central_nervous_system(2)|endometrium(5)|haematopoietic_and_lymphoid_tissue(4)|kidney(1)|large_intestine(3)|lung(22)|ovary(2)|pancreas(1)|prostate(2)|skin(2)|urinary_tract(2)	50				BRCA - Breast invasive adenocarcinoma(234;0.029)		GAACTTCAGCGGCTAGCTGAG	0.473																																					p.R1035Q		Atlas-SNP	.											.	TTLL5	102	.	0			c.G3104A						PASS	.						101.0	91.0	94.0					14																	76259376		2203	4300	6503	SO:0001583	missense	23093	exon27			TTCAGCGGCTAGC	AF107885	CCDS32124.1	14q24.3	2014-09-09	2005-07-29	2005-07-29	ENSG00000119685	ENSG00000119685		"""Tubulin tyrosine ligase-like family"""	19963	protein-coding gene	gene with protein product		612268	"""KIAA0998"""	KIAA0998		15890843	Standard	NM_015072		Approved		uc001xrx.3	Q6EMB2	OTTHUMG00000171611	ENST00000298832.9:c.3104G>A	14.37:g.76259376G>A	ENSP00000298832:p.Arg1035Gln	118.0	0.0	0		124.0	64.0	0.516129	NM_015072	B9EGH8|B9EGH9|Q9BUB0|Q9H0G4|Q9H7W2|Q9P1V5|Q9UPZ4	Missense_Mutation	SNP	ENST00000298832.9	37	CCDS32124.1	.	.	.	.	.	.	.	.	.	.	G	15.49	2.848322	0.51164	.	.	ENSG00000119685	ENST00000418433;ENST00000286653;ENST00000557636;ENST00000298832;ENST00000393826;ENST00000556893;ENST00000554510	T;T;T;T	0.27104	3.83;3.91;1.69;1.7	5.41	5.41	0.78517	.	0.711361	0.13654	N	0.372060	T	0.34658	0.0905	N	0.19112	0.55	0.29768	N	0.835037	P;D;P;P	0.76494	0.698;0.999;0.917;0.572	B;D;B;B	0.79784	0.098;0.993;0.202;0.045	T	0.13656	-1.0501	10	0.38643	T	0.18	.	11.7839	0.52030	0.0831:0.0:0.9169:0.0	.	1050;109;586;1035	G3V2J9;F8W7N3;Q6EMB2-2;Q6EMB2	.;.;.;TTLL5_HUMAN	Q	722;109;1050;1035;586;586;544	ENSP00000450713:R1050Q;ENSP00000298832:R1035Q;ENSP00000452524:R586Q;ENSP00000451946:R544Q	ENSP00000286653:R109Q	R	+	2	0	TTLL5	75329129	1.000000	0.71417	0.999000	0.59377	0.894000	0.52154	3.531000	0.53546	2.538000	0.85594	0.563000	0.77884	CGG	.	.	none		0.473	TTLL5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000414453.1	NM_015072	
PGLYRP2	114770	hgsc.bcm.edu	37	19	15587103	15587103	+	Silent	SNP	C	C	T	rs35973013	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr19:15587103C>T	ENST00000340880.4	-	2	858	c.378G>A	c.(376-378)gcG>gcA	p.A126A	PGLYRP2_ENST00000292609.4_Silent_p.A126A	NM_052890.3	NP_443122.3	Q96PD5	PGRP2_HUMAN	peptidoglycan recognition protein 2	126					defense response to Gram-positive bacterium (GO:0050830)|detection of bacterium (GO:0016045)|growth of symbiont in host (GO:0044117)|innate immune response (GO:0045087)|negative regulation of interferon-gamma production (GO:0032689)|negative regulation of natural killer cell differentiation involved in immune response (GO:0032827)|pattern recognition receptor signaling pathway (GO:0002221)|peptide amidation (GO:0001519)|peptidoglycan catabolic process (GO:0009253)|regulation of inflammatory response (GO:0050727)	extracellular vesicular exosome (GO:0070062)|intracellular (GO:0005622)|membrane (GO:0016020)	N-acetylmuramoyl-L-alanine amidase activity (GO:0008745)|peptidoglycan binding (GO:0042834)|peptidoglycan receptor activity (GO:0016019)|zinc ion binding (GO:0008270)			endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(3)|lung(9)|ovary(3)|prostate(2)|skin(3)|stomach(2)|urinary_tract(1)	28						CCTCCAGCCCCGCCAGCAGAG	0.607													C|||	123	0.0245607	0.0477	0.0058	5008	,	,		19723	0.006		0.008	False		,,,				2504	0.0429				p.A126A		Atlas-SNP	.											.	PGLYRP2	116	.	0			c.G378A						PASS	.	C		193,4213	120.4+/-158.0	3,187,2013	100.0	86.0	91.0		378	-10.3	0.1	19	dbSNP_126	91	75,8525	44.0+/-102.2	0,75,4225	no	coding-synonymous	PGLYRP2	NM_052890.3		3,262,6238	TT,TC,CC		0.8721,4.3804,2.0606		126/577	15587103	268,12738	2203	4300	6503	SO:0001819	synonymous_variant	114770	exon2			CAGCCCCGCCAGC	AY358156	CCDS12330.2	19p13.12	2010-04-27			ENSG00000161031	ENSG00000161031	3.5.1.28		30013	protein-coding gene	gene with protein product	"""peptidoglycan recognition protein L precursor"", ""peptidoglycan recognition protein-like"", ""N-acetylmuramoyl-L-alanine amidase"""	608199				11461926, 12669421, 14506276	Standard	NM_052890		Approved	PGRP-L, PGLYRPL, TAGL-like, tagL, tagL-alpha, tagl-beta, PGRPL	uc002nbf.4	Q96PD5	OTTHUMG00000150690	ENST00000340880.4:c.378G>A	19.37:g.15587103C>T		146.0	0.0	0		155.0	86.0	0.554839	NM_052890	A8K050|A8K8C7|B2RMZ2|B7ZM33|Q68CK1|Q96N74|Q9UC60	Silent	SNP	ENST00000340880.4	37	CCDS12330.2																																																																																			C|0.981;T|0.019	0.019	strong		0.607	PGLYRP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000319626.1	NM_052890	
PHF21A	51317	hgsc.bcm.edu	37	11	45987091	45987091	+	Silent	SNP	A	A	T	rs151169176	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr11:45987091A>T	ENST00000418153.2	-	9	967	c.768T>A	c.(766-768)gcT>gcA	p.A256A	PHF21A_ENST00000323180.6_Silent_p.A257A|PHF21A_ENST00000257821.4_Silent_p.A257A|PHF21A_ENST00000527753.1_5'Flank			Q96BD5	PF21A_HUMAN	PHD finger protein 21A	256					blood coagulation (GO:0007596)|chromatin modification (GO:0016568)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|regulation of transcription, DNA-templated (GO:0006355)|suckling behavior (GO:0001967)|transcription, DNA-templated (GO:0006351)	histone deacetylase complex (GO:0000118)|nucleoplasm (GO:0005654)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)|zinc ion binding (GO:0008270)			central_nervous_system(2)|cervix(1)|endometrium(3)|large_intestine(10)|lung(9)|skin(2)|upper_aerodigestive_tract(2)	29						TAAGCTGAGGAGCTGCGAGCA	0.537											OREG0020936	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	A|||	15	0.00299521	0.0	0.0072	5008	,	,		19319	0.0		0.004	False		,,,				2504	0.0061				p.A257A		Atlas-SNP	.											.	PHF21A	107	.	0			c.T771A						PASS	.	A	,	6,4398	11.4+/-27.6	0,6,2196	72.0	57.0	62.0		768,771	3.7	1.0	11	dbSNP_134	62	61,8537	38.8+/-94.9	1,59,4239	no	coding-synonymous,coding-synonymous	PHF21A	NM_001101802.1,NM_016621.3	,	1,65,6435	TT,TA,AA		0.7095,0.1362,0.5153	,	256/681,257/635	45987091	67,12935	2202	4299	6501	SO:0001819	synonymous_variant	51317	exon9			CTGAGGAGCTGCG	AL359593	CCDS31474.1, CCDS44578.1	11p11.2	2013-01-28			ENSG00000135365	ENSG00000135365		"""Zinc fingers, PHD-type"""	24156	protein-coding gene	gene with protein product		608325				11214970, 12032298	Standard	NM_001101802		Approved	BHC80, KIAA1696, BM-006	uc001ncc.4	Q96BD5	OTTHUMG00000167038	ENST00000418153.2:c.768T>A	11.37:g.45987091A>T		186.0	0.0	0	935	230.0	128.0	0.556522	NM_016621	D3DQP5|Q6AWA2|Q9C0G7|Q9H8V9|Q9HAK6|Q9NZE9	Silent	SNP	ENST00000418153.2	37	CCDS44578.1																																																																																			A|0.994;T|0.006	0.006	strong		0.537	PHF21A-004	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000392583.1	NM_016621	
UMOD	7369	hgsc.bcm.edu	37	16	20352532	20352532	+	Silent	SNP	G	G	A	rs141800038	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr16:20352532G>A	ENST00000570689.1	-	7	1604	c.1458C>T	c.(1456-1458)taC>taT	p.Y486Y	UMOD_ENST00000396138.4_Silent_p.Y535Y|UMOD_ENST00000424589.1_Silent_p.Y519Y|UMOD_ENST00000396134.2_Silent_p.Y519Y|UMOD_ENST00000570331.1_5'UTR|UMOD_ENST00000396142.2_Silent_p.Y486Y|UMOD_ENST00000302509.4_Silent_p.Y486Y			P07911	UROM_HUMAN	uromodulin	486	ZP. {ECO:0000255|PROSITE- ProRule:PRU00375}.				cellular defense response (GO:0006968)|chemical homeostasis (GO:0048878)|excretion (GO:0007588)|heterophilic cell-cell adhesion (GO:0007157)|leukocyte cell-cell adhesion (GO:0007159)|metanephric ascending thin limb development (GO:0072218)|metanephric distal convoluted tubule development (GO:0072221)|metanephric thick ascending limb development (GO:0072233)|negative regulation of cell proliferation (GO:0008285)|neutrophil migration (GO:1990266)|regulation of ion homeostasis (GO:2000021)|response to organic substance (GO:0010033)	anchored component of membrane (GO:0031225)|apical plasma membrane (GO:0016324)|basolateral plasma membrane (GO:0016323)|cytoplasmic vesicle (GO:0031410)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|extrinsic component of membrane (GO:0019898)|Golgi apparatus (GO:0005794)|membrane raft (GO:0045121)|primary cilium (GO:0072372)|spindle pole (GO:0000922)	calcium ion binding (GO:0005509)|IgG binding (GO:0019864)			endometrium(5)|kidney(1)|large_intestine(7)|lung(20)|ovary(1)|skin(3)|upper_aerodigestive_tract(3)|urinary_tract(1)	41						TGGTGCCCACGTAGAGAAAAG	0.597													G|||	13	0.00259585	0.0	0.0	5008	,	,		16645	0.0		0.0099	False		,,,				2504	0.0031				p.Y486Y		Atlas-SNP	.											.	UMOD	128	.	0			c.C1458T						PASS	.	G	,	7,4399	12.9+/-30.5	0,7,2196	96.0	75.0	82.0		1458,1458	-4.3	0.9	16	dbSNP_134	82	90,8510	52.3+/-112.8	0,90,4210	no	coding-synonymous,coding-synonymous	UMOD	NM_001008389.1,NM_003361.2	,	0,97,6406	AA,AG,GG		1.0465,0.1589,0.7458	,	486/641,486/641	20352532	97,12909	2203	4300	6503	SO:0001819	synonymous_variant	7369	exon7			GCCCACGTAGAGA	M17778	CCDS10583.1, CCDS61876.1	16p12.3	2008-06-23	2008-06-23		ENSG00000169344	ENSG00000169344			12559	protein-coding gene	gene with protein product	"""Tamm-Horsfall glycoprotein"", ""uromucoid"""	191845	"""uromodulin (uromucoid, Tamm-Horsfall glycoprotein)"""			8382593	Standard	NM_003361		Approved		uc002dha.3	P07911	OTTHUMG00000131488	ENST00000570689.1:c.1458C>T	16.37:g.20352532G>A		73.0	0.0	0		66.0	37.0	0.560606	NM_003361	B3KP48|B3KRN9|E9PEA4|Q540J6|Q6ZS84|Q8IYG0	Silent	SNP	ENST00000570689.1	37	CCDS10583.1																																																																																			G|0.994;A|0.006	0.006	strong		0.597	UMOD-008	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000436862.1		
TSEN2	80746	hgsc.bcm.edu	37	3	12538040	12538040	+	Missense_Mutation	SNP	A	A	G			TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr3:12538040A>G	ENST00000284995.6	+	4	682	c.295A>G	c.(295-297)Atc>Gtc	p.I99V	TSEN2_ENST00000444864.1_Missense_Mutation_p.I99V|TSEN2_ENST00000314571.7_Missense_Mutation_p.I99V|TSEN2_ENST00000454502.2_Missense_Mutation_p.I99V|TSEN2_ENST00000402228.3_Missense_Mutation_p.I99V|TSEN2_ENST00000415684.1_Missense_Mutation_p.I99V|TSEN2_ENST00000383797.5_Missense_Mutation_p.I99V	NM_025265.3	NP_079541.1	Q8NCE0	SEN2_HUMAN	TSEN2 tRNA splicing endonuclease subunit	99					mRNA processing (GO:0006397)|tRNA splicing, via endonucleolytic cleavage and ligation (GO:0006388)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|nucleus (GO:0005634)|tRNA-intron endonuclease complex (GO:0000214)	lyase activity (GO:0016829)|nucleic acid binding (GO:0003676)|tRNA-intron endonuclease activity (GO:0000213)			central_nervous_system(2)|endometrium(2)|kidney(3)|large_intestine(5)|lung(7)	19						CATGCCTATCATCACATCAAA	0.368																																					p.I99V		Atlas-SNP	.											.	TSEN2	46	.	0			c.A295G						PASS	.						201.0	190.0	194.0					3																	12538040		2203	4300	6503	SO:0001583	missense	80746	exon4			CCTATCATCACAT	BC019582	CCDS2611.1, CCDS46757.1, CCDS46758.1, CCDS46759.1	3p25.2	2013-08-06	2013-08-06		ENSG00000154743	ENSG00000154743		"""tRNA splicing endonuclease subunits"""	28422	protein-coding gene	gene with protein product		608753	"""tRNA splicing endonuclease 2 homolog (SEN2, S. cerevisiae)"", ""tRNA splicing endonuclease 2 homolog (S. cerevisiae)"""			15109492	Standard	NM_025265		Approved	SEN2, SEN2L, MGC2776	uc003bxb.3	Q8NCE0	OTTHUMG00000129765	ENST00000284995.6:c.295A>G	3.37:g.12538040A>G	ENSP00000284995:p.Ile99Val	118.0	0.0	0		121.0	50.0	0.413223	NM_001145394	B7Z6K1|C9IZI7|G5E9Q3|Q8WTW7|Q9BPU7	Missense_Mutation	SNP	ENST00000284995.6	37	CCDS2611.1	.	.	.	.	.	.	.	.	.	.	A	13.07	2.128557	0.37533	.	.	ENSG00000154743	ENST00000446004;ENST00000314571;ENST00000454502;ENST00000383797;ENST00000402228;ENST00000284995;ENST00000444864;ENST00000537959;ENST00000415684	T;T;T;T;T;T;T;T	0.59364	0.29;0.3;0.39;0.29;0.35;0.35;0.27;0.3	5.12	1.92	0.25849	.	0.308783	0.32935	N	0.005479	T	0.48466	0.1501	M	0.71581	2.175	0.27073	N	0.963277	B;B;B;B	0.32283	0.362;0.03;0.066;0.003	B;B;B;B	0.33121	0.158;0.047;0.094;0.003	T	0.32693	-0.9897	10	0.30854	T	0.27	-16.8333	3.9504	0.09366	0.4827:0.3484:0.1689:0.0	.	99;99;99;99	G5E9Q3;Q8NCE0;Q8NCE0-3;C9IZI7	.;SEN2_HUMAN;.;.	V	99;99;99;99;99;99;99;72;99	ENSP00000406238:I99V;ENSP00000323188:I99V;ENSP00000392029:I99V;ENSP00000373307:I99V;ENSP00000385976:I99V;ENSP00000284995:I99V;ENSP00000407974:I99V;ENSP00000416510:I99V	ENSP00000284995:I99V	I	+	1	0	TSEN2	12513040	0.985000	0.35326	0.991000	0.47740	0.982000	0.71751	0.964000	0.29306	1.943000	0.56356	0.529000	0.55759	ATC	.	.	none		0.368	TSEN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251981.1	NM_025265	
BMP2K	55589	hgsc.bcm.edu	37	4	79832488	79832488	+	Silent	SNP	A	A	G	rs574665641	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr4:79832488A>G	ENST00000335016.5	+	16	2953	c.2787A>G	c.(2785-2787)gtA>gtG	p.V929V	PAQR3_ENST00000295462.3_Intron	NM_198892.1	NP_942595.1	Q9NSY1	BMP2K_HUMAN	BMP2 inducible kinase	929					regulation of bone mineralization (GO:0030500)	nucleus (GO:0005634)	ATP binding (GO:0005524)|phosphatase regulator activity (GO:0019208)|protein serine/threonine kinase activity (GO:0004674)			NS(1)|breast(1)|endometrium(4)|large_intestine(2)|lung(3)|prostate(1)|urinary_tract(1)	13						CCAAAAGTGTAGATGTATTTG	0.438													A|||	2	0.000399361	0.0	0.0	5008	,	,		21116	0.0		0.0	False		,,,				2504	0.002				p.V929V		Atlas-SNP	.											.	BMP2K	169	.	0			c.A2787G						PASS	.						60.0	54.0	56.0					4																	79832488		1946	4127	6073	SO:0001819	synonymous_variant	55589	exon16			AAGTGTAGATGTA	AB015331	CCDS34019.1, CCDS47083.1	4q21.21	2008-05-15			ENSG00000138756	ENSG00000138756			18041	protein-coding gene	gene with protein product							Standard	NM_017593		Approved	DKFZp434K0614, BIKe	uc003hlk.3	Q9NSY1	OTTHUMG00000160900	ENST00000335016.5:c.2787A>G	4.37:g.79832488A>G		289.0	1.0	0.00346021		306.0	155.0	0.506536	NM_198892	O94791|Q4W5H2|Q8IYF2|Q8N2G7|Q8NHG9|Q9NTG8	Silent	SNP	ENST00000335016.5	37	CCDS47083.1	.	.	.	.	.	.	.	.	.	.	A	5.217	0.225527	0.09916	.	.	ENSG00000138756	ENST00000502613	.	.	.	5.3	-4.97	0.03029	.	.	.	.	.	T	0.46964	0.1420	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.44892	-0.9298	4	.	.	.	-9.7415	5.8121	0.18471	0.1496:0.2279:0.5104:0.1121	.	.	.	.	G	622	.	.	R	+	1	2	BMP2K	80051512	0.006000	0.16342	0.843000	0.33291	0.837000	0.47467	-1.136000	0.03222	-0.932000	0.03742	0.397000	0.26171	AGA	.	.	none		0.438	BMP2K-201	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding		NM_017593	
EFCAB5	374786	hgsc.bcm.edu	37	17	28417576	28417576	+	Missense_Mutation	SNP	G	G	C	rs35724168	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr17:28417576G>C	ENST00000394835.3	+	20	4013	c.3821G>C	c.(3820-3822)aGg>aCg	p.R1274T	RP11-1148O4.2_ENST00000582938.1_RNA|EFCAB5_ENST00000320856.5_Missense_Mutation_p.R1150T|EFCAB5_ENST00000394832.2_Intron	NM_198529.3	NP_940931	A4FU69	EFCB5_HUMAN	EF-hand calcium binding domain 5	1274			R -> T (in dbSNP:rs35724168).				calcium ion binding (GO:0005509)			breast(7)|endometrium(2)|kidney(4)|large_intestine(11)|lung(14)|ovary(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	43						GGCCAAAATAGGATGTTGTTG	0.438													G|||	94	0.01877	0.0681	0.0029	5008	,	,		20188	0.0		0.002	False		,,,				2504	0.0				p.R1274T		Atlas-SNP	.											.	EFCAB5	122	.	0			c.G3821C						PASS	.	G	THR/ARG	165,3525		8,149,1688	140.0	137.0	138.0		3821	-0.0	0.1	17	dbSNP_126	138	12,8184		0,12,4086	yes	missense	EFCAB5	NM_198529.3	71	8,161,5774	CC,CG,GG		0.1464,4.4715,1.4891	benign	1274/1504	28417576	177,11709	1845	4098	5943	SO:0001583	missense	374786	exon20			AAAATAGGATGTT	AL833911	CCDS11254.2, CCDS54103.1	17q11.2	2013-01-10			ENSG00000176927	ENSG00000176927		"""EF-hand domain containing"""	24801	protein-coding gene	gene with protein product							Standard	NM_198529		Approved	FLJ46247	uc002het.3	A4FU69	OTTHUMG00000132753	ENST00000394835.3:c.3821G>C	17.37:g.28417576G>C	ENSP00000378312:p.Arg1274Thr	114.0	0.0	0		86.0	40.0	0.465116	NM_198529	B2RPN0|B4DS75|B4DZR5|F5GYL2|Q0VD68|Q6ZRM6|Q8NDG9	Missense_Mutation	SNP	ENST00000394835.3	37	CCDS11254.2	34	0.015567765567765568	32	0.06504065040650407	1	0.0027624309392265192	0	0.0	1	0.0013192612137203166	G	8.356	0.832049	0.16820	0.044715	0.001464	ENSG00000176927	ENST00000394835;ENST00000320856;ENST00000419434	T;T;T	0.10960	2.82;2.84;2.85	5.35	-0.00624	0.14014	.	0.653292	0.15652	N	0.251330	T	0.00580	0.0019	L	0.40543	1.245	0.09310	N	1	P;P	0.41848	0.763;0.763	B;B	0.36608	0.229;0.21	T	0.26121	-1.0112	10	0.66056	D	0.02	-6.6532	8.972	0.35912	0.523:0.0:0.477:0.0	rs35724168	1150;1274	E7EVS9;A4FU69	.;EFCB5_HUMAN	T	1274;1150;956	ENSP00000378312:R1274T;ENSP00000322003:R1150T;ENSP00000417009:R956T	ENSP00000322003:R1150T	R	+	2	0	EFCAB5	25441702	0.038000	0.19896	0.079000	0.20413	0.150000	0.21749	0.447000	0.21710	0.094000	0.17404	0.655000	0.94253	AGG	G|0.984;C|0.016	0.016	strong		0.438	EFCAB5-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256120.4	NM_198529	
FAT2	2196	hgsc.bcm.edu	37	5	150901209	150901209	+	Silent	SNP	G	G	T	rs142359154		TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr5:150901209G>T	ENST00000261800.5	-	18	10957	c.10945C>A	c.(10945-10947)Cgg>Agg	p.R3649R		NM_001447.2	NP_001438.1	Q9NYQ8	FAT2_HUMAN	FAT atypical cadherin 2	3649					epithelial cell migration (GO:0010631)|homophilic cell adhesion (GO:0007156)	cell-cell adherens junction (GO:0005913)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			NS(6)|breast(3)|central_nervous_system(3)|cervix(5)|endometrium(15)|haematopoietic_and_lymphoid_tissue(4)|kidney(8)|large_intestine(61)|liver(1)|lung(60)|ovary(6)|prostate(5)|skin(5)|stomach(2)|upper_aerodigestive_tract(11)|urinary_tract(1)	196		Medulloblastoma(196;0.0912)|all_hematologic(541;0.104)	KIRC - Kidney renal clear cell carcinoma(527;0.000785)|Kidney(363;0.00101)			TGCAGGTTCCGCCAGTGGTCA	0.607																																					p.R3649R		Atlas-SNP	.											.	FAT2	465	.	0			c.C10945A						PASS	.						34.0	30.0	32.0					5																	150901209		2203	4299	6502	SO:0001819	synonymous_variant	2196	exon18			GGTTCCGCCAGTG	AF231022	CCDS4317.1	5q33.1	2014-07-21	2013-05-31		ENSG00000086570	ENSG00000086570		"""Cadherins / Cadherin-related"""	3596	protein-coding gene	gene with protein product	"""cadherin-related family member 9"""	604269	"""FAT tumor suppressor (Drosophila) homolog 2"", ""FAT tumor suppressor homolog 2 (Drosophila)"""			9693030	Standard	NM_001447		Approved	MEGF1, CDHF8, HFAT2, CDHR9	uc003lue.4	Q9NYQ8	OTTHUMG00000130126	ENST00000261800.5:c.10945C>A	5.37:g.150901209G>T		53.0	0.0	0		89.0	44.0	0.494382	NM_001447	O75091|Q9NSR7	Silent	SNP	ENST00000261800.5	37	CCDS4317.1	.	.	.	.	.	.	.	.	.	.	G	8.154	0.788009	0.16258	.	.	ENSG00000086570	ENST00000520200	.	.	.	5.71	2.8	0.32819	.	.	.	.	.	T	0.68979	0.3060	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.65821	-0.6075	4	.	.	.	.	14.5588	0.68120	0.0:0.0:0.5656:0.4344	.	.	.	.	E	507	.	.	A	-	2	0	FAT2	150881402	1.000000	0.71417	1.000000	0.80357	0.958000	0.62258	2.794000	0.47853	0.264000	0.21851	-0.475000	0.04921	GCG	G|0.999;A|0.001	.	alt		0.607	FAT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252434.1	NM_001447	
MUC2	4583	hgsc.bcm.edu	37	11	1093778	1093778	+	Missense_Mutation	SNP	C	C	G			TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr11:1093778C>G	ENST00000441003.2	+	30	5624	c.5597C>G	c.(5596-5598)tCt>tGt	p.S1866C	MUC2_ENST00000333592.6_Missense_Mutation_p.S154C|MUC2_ENST00000361558.6_Intron	NM_002457.2	NP_002448.2	Q02817	MUC2_HUMAN	mucin 2, oligomeric mucus/gel-forming	4228					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)	CGGTCCACCTCTTCCCCTCTC	0.627																																					p.S1862C		Atlas-SNP	.											.	MUC2	614	.	0			c.C5585G						PASS	.						240.0	285.0	270.0					11																	1093778		2162	4255	6417	SO:0001583	missense	4583	exon31			CCACCTCTTCCCC	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.5597C>G	11.37:g.1093778C>G	ENSP00000415183:p.Ser1866Cys	81.0	0.0	0		87.0	4.0	0.045977	NM_002457	Q14878	Missense_Mutation	SNP	ENST00000441003.2	37		.	.	.	.	.	.	.	.	.	.	C	8.146	0.786373	0.16189	.	.	ENSG00000198788	ENST00000441003;ENST00000333592	T;T	0.12984	2.63;3.09	1.81	-0.426	0.12314	.	.	.	.	.	T	0.07503	0.0189	N	0.14661	0.345	0.09310	N	1	P	0.52463	0.953	B	0.43783	0.431	T	0.22487	-1.0215	9	0.59425	D	0.04	.	3.1045	0.06337	0.2592:0.5749:0.0:0.1658	.	1866	E7EUV1	.	C	1866;154	ENSP00000415183:S1866C;ENSP00000331373:S154C	ENSP00000331373:S154C	S	+	2	0	MUC2	1083778	0.000000	0.05858	0.002000	0.10522	0.152000	0.21847	-0.239000	0.08965	-0.281000	0.09141	0.305000	0.20034	TCT	.	.	none		0.627	MUC2-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000345894.2	NM_002457	
SLC39A5	283375	hgsc.bcm.edu	37	12	56630444	56630444	+	Missense_Mutation	SNP	G	G	C	rs74812296	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr12:56630444G>C	ENST00000266980.4	+	8	1414	c.1121G>C	c.(1120-1122)aGt>aCt	p.S374T	SLC39A5_ENST00000454355.2_Missense_Mutation_p.S374T|ANKRD52_ENST00000548241.1_5'Flank|SLC39A5_ENST00000419232.1_3'UTR	NM_001135195.1	NP_001128667.1	Q6ZMH5	S39A5_HUMAN	solute carrier family 39 (zinc transporter), member 5	374					cellular response to zinc ion starvation (GO:0034224)|G1 to G0 transition involved in cell differentiation (GO:0070315)|neural precursor cell proliferation (GO:0061351)|transmembrane transport (GO:0055085)|zinc ion transport (GO:0006829)	basolateral plasma membrane (GO:0016323)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)	metal ion transmembrane transporter activity (GO:0046873)			NS(1)|cervix(6)|endometrium(1)|large_intestine(5)|lung(6)|ovary(2)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	27						CAAGGCCACAGTCATGGGCAC	0.627													G|||	34	0.00678914	0.0015	0.0187	5008	,	,		20254	0.0		0.0179	False		,,,				2504	0.001				p.S374T		Atlas-SNP	.											.	SLC39A5	52	.	0			c.G1121C						PASS	.	G	THR/SER,THR/SER	12,4394	16.8+/-37.8	0,12,2191	109.0	96.0	101.0		1121,1121	5.0	1.0	12	dbSNP_131	101	168,8432	78.6+/-141.3	1,166,4133	yes	missense,missense	SLC39A5	NM_001135195.1,NM_173596.2	58,58	1,178,6324	CC,CG,GG		1.9535,0.2724,1.384	probably-damaging,probably-damaging	374/541,374/541	56630444	180,12826	2203	4300	6503	SO:0001583	missense	283375	exon10			GCCACAGTCATGG		CCDS8912.2	12q13.3	2013-07-17	2013-07-17		ENSG00000139540	ENSG00000139540		"""Solute carriers"""	20502	protein-coding gene	gene with protein product		608730	"""solute carrier family 39 (metal ion transporter), member 5"""				Standard	NM_173596		Approved		uc010sqj.2	Q6ZMH5	OTTHUMG00000156962	ENST00000266980.4:c.1121G>C	12.37:g.56630444G>C	ENSP00000266980:p.Ser374Thr	79.0	0.0	0		93.0	43.0	0.462366	NM_173596	B2R808|Q8N6Y3	Missense_Mutation	SNP	ENST00000266980.4	37	CCDS8912.2	22	0.010073260073260074	0	0.0	6	0.016574585635359115	0	0.0	16	0.021108179419525065	G	18.19	3.569542	0.65765	0.002724	0.019535	ENSG00000139540	ENST00000454355;ENST00000266980	T;T	0.51071	0.72;0.72	4.96	4.96	0.65561	.	0.188002	0.37393	N	0.002110	T	0.43122	0.1233	M	0.62088	1.915	0.38031	D	0.935152	D	0.69078	0.997	P	0.62885	0.908	T	0.50575	-0.8812	10	0.21540	T	0.41	-0.8511	12.2396	0.54534	0.0:0.2787:0.7213:0.0	.	374	Q6ZMH5	S39A5_HUMAN	T	374	ENSP00000405360:S374T;ENSP00000266980:S374T	ENSP00000266980:S374T	S	+	2	0	SLC39A5	54916711	1.000000	0.71417	0.997000	0.53966	0.987000	0.75469	3.606000	0.54095	2.746000	0.94184	0.655000	0.94253	AGT	G|0.987;C|0.013	0.013	strong		0.627	SLC39A5-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000346834.1	NM_173596	
PRRC2B	84726	hgsc.bcm.edu	37	9	134351655	134351655	+	Missense_Mutation	SNP	G	G	A			TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr9:134351655G>A	ENST00000357304.4	+	15	4194	c.4139G>A	c.(4138-4140)aGc>aAc	p.S1380N	PRRC2B_ENST00000458550.1_Intron|PRRC2B_ENST00000405995.1_Intron|PRRC2B_ENST00000372249.1_5'UTR	NM_013318.3	NP_037450.2	Q5JSZ5	PRC2B_HUMAN	proline-rich coiled-coil 2B	1380							poly(A) RNA binding (GO:0044822)			cervix(2)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(7)|lung(20)|ovary(2)	44						GCCTCCGAAAGCAGCGACTTC	0.662											OREG0019561	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.S1380N		Atlas-SNP	.											.	PRRC2B	266	.	0			c.G4139A						PASS	.						16.0	19.0	18.0					9																	134351655		1954	4134	6088	SO:0001583	missense	84726	exon15			CCGAAAGCAGCGA	AB011087	CCDS48044.1	9q34.13	2010-12-09	2010-12-09	2010-12-09	ENSG00000130723	ENSG00000130723			28121	protein-coding gene	gene with protein product			"""KIAA0515"", ""HLA-B associated transcript 2-like"", ""HLA-B associated transcript 2-like 1"""	KIAA0515, BAT2L, BAT2L1		9628581	Standard	NM_013318		Approved	MGC10526, LQFBS-1	uc004can.4	Q5JSZ5	OTTHUMG00000020827	ENST00000357304.4:c.4139G>A	9.37:g.134351655G>A	ENSP00000349856:p.Ser1380Asn	78.0	0.0	0	1610	94.0	50.0	0.531915	NM_013318	O60270|Q5JSZ7|Q66VZ2|Q68CR0|Q96EI9|Q9H683	Missense_Mutation	SNP	ENST00000357304.4	37	CCDS48044.1	.	.	.	.	.	.	.	.	.	.	G	18.55	3.647371	0.67358	.	.	ENSG00000130723	ENST00000357304;ENST00000418650	T	0.05447	3.44	5.93	5.93	0.95920	.	.	.	.	.	T	0.11537	0.0281	M	0.73962	2.25	0.80722	D	1	P;B;B	0.40970	0.734;0.347;0.236	B;B;B	0.35470	0.203;0.12;0.056	T	0.04565	-1.0942	9	0.33940	T	0.23	.	19.3291	0.94278	0.0:0.0:1.0:0.0	.	676;113;1380	Q5H9R5;Q5JSZ8;Q5JSZ5	.;.;PRC2B_HUMAN	N	1380;676	ENSP00000349856:S1380N	ENSP00000349856:S1380N	S	+	2	0	PRRC2B	133341476	1.000000	0.71417	1.000000	0.80357	0.980000	0.70556	4.145000	0.58065	2.814000	0.96858	0.655000	0.94253	AGC	.	.	none		0.662	PRRC2B-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding			
OR10G9	219870	hgsc.bcm.edu	37	11	123893757	123893757	+	Missense_Mutation	SNP	C	C	T			TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr11:123893757C>T	ENST00000375024.1	+	1	38	c.38C>T	c.(37-39)aCg>aTg	p.T13M		NM_001001953.1	NP_001001953.1	Q8NGN4	O10G9_HUMAN	olfactory receptor, family 10, subfamily G, member 9	13						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			breast(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(6)|lung(33)|prostate(2)|skin(4)|stomach(8)|urinary_tract(1)	61		Breast(109;0.00867)|Medulloblastoma(222;0.0523)|Lung NSC(97;0.118)|all_lung(97;0.126)|all_neural(223;0.22)		BRCA - Breast invasive adenocarcinoma(274;4.88e-06)|OV - Ovarian serous cystadenocarcinoma(99;0.0399)		TTCATCCTCACGGGCCTTCCC	0.562																																					p.T13M		Atlas-SNP	.											OR10G9,NS,carcinoma,0,2	OR10G9	80	2	0			c.C38T						scavenged	.						175.0	170.0	172.0					11																	123893757		2201	4299	6500	SO:0001583	missense	219870	exon1			TCCTCACGGGCCT	AB065756	CCDS31703.1	11q24.1	2012-08-09			ENSG00000236981	ENSG00000236981		"""GPCR / Class A : Olfactory receptors"""	15129	protein-coding gene	gene with protein product				OR10G10P			Standard	NM_001001953		Approved		uc010sad.2	Q8NGN4	OTTHUMG00000165967	ENST00000375024.1:c.38C>T	11.37:g.123893757C>T	ENSP00000364164:p.Thr13Met	308.0	0.0	0		387.0	29.0	0.0749354	NM_001001953		Missense_Mutation	SNP	ENST00000375024.1	37	CCDS31703.1	.	.	.	.	.	.	.	.	.	.	C	7.277	0.608309	0.14002	.	.	ENSG00000236981	ENST00000375024	T	0.00421	7.46	3.33	-4.34	0.03666	.	1.118960	0.06817	N	0.791372	T	0.00178	0.0005	N	0.04260	-0.245	0.09310	N	0.999992	B	0.06786	0.001	B	0.04013	0.001	T	0.29640	-1.0005	10	0.40728	T	0.16	.	9.7201	0.40297	0.0:0.2623:0.0:0.7377	.	13	Q8NGN4	O10G9_HUMAN	M	13	ENSP00000364164:T13M	ENSP00000364164:T13M	T	+	2	0	OR10G9	123398967	0.000000	0.05858	0.149000	0.22428	0.069000	0.16628	-0.761000	0.04751	-1.009000	0.03400	-0.766000	0.03442	ACG	.	.	none		0.562	OR10G9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000387269.1	NM_001001953	
OCA2	4948	hgsc.bcm.edu	37	15	28202804	28202804	+	Missense_Mutation	SNP	G	G	A	rs374415755		TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr15:28202804G>A	ENST00000354638.3	-	16	1869	c.1714C>T	c.(1714-1716)Cgc>Tgc	p.R572C	OCA2_ENST00000382996.2_Missense_Mutation_p.R572C|OCA2_ENST00000353809.5_Missense_Mutation_p.R548C	NM_000275.2	NP_000266.2	Q04671	P_HUMAN	oculocutaneous albinism II	572					cell proliferation (GO:0008283)|eye pigment biosynthetic process (GO:0006726)|melanin biosynthetic process (GO:0042438)|melanocyte differentiation (GO:0030318)|spermatid development (GO:0007286)|tyrosine transport (GO:0015828)	cytoplasm (GO:0005737)|endoplasmic reticulum membrane (GO:0005789)|endosome membrane (GO:0010008)|integral component of membrane (GO:0016021)|lysosomal membrane (GO:0005765)|melanosome membrane (GO:0033162)	L-tyrosine transmembrane transporter activity (GO:0005302)|transporter activity (GO:0005215)			NS(1)|breast(1)|central_nervous_system(1)|endometrium(7)|kidney(3)|large_intestine(11)|lung(48)|ovary(4)|pancreas(1)|prostate(1)|skin(3)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	85		all_lung(180;2.93e-12)|Breast(32;0.000315)|Colorectal(260;0.234)		all cancers(64;5.03e-07)|Epithelial(43;2.13e-06)|BRCA - Breast invasive adenocarcinoma(123;0.045)		AGCAGGCGGCGCACAGCTGTC	0.662									Oculocutaneous Albinism																												p.R572C		Atlas-SNP	.											OCA2,caecum,carcinoma,0,1	OCA2	173	1	0			c.C1714T						PASS	.	G	CYS/ARG	0,4402		0,0,2201	27.0	30.0	29.0		1714	3.8	0.2	15		29	2,8588		0,2,4293	no	missense	OCA2	NM_000275.2	180	0,2,6494	AA,AG,GG		0.0233,0.0,0.0154	probably-damaging	572/839	28202804	2,12990	2201	4295	6496	SO:0001583	missense	4948	exon16	Familial Cancer Database		GGCGGCGCACAGC		CCDS10020.1, CCDS73701.1	15q12	2013-01-08	2008-01-30		ENSG00000104044	ENSG00000104044			8101	protein-coding gene	gene with protein product	"""melanocyte-specific transporter protein"""	611409	"""oculocutaneous albinism II (pink-eye dilution (murine) homolog)"", ""eye color 3 (brown)"", ""eye color 2 (central brown)"", ""oculocutaneous albinism II (pink-eye dilution homolog, mouse)"""	D15S12, P, EYCL3, EYCL2			Standard	NM_000275		Approved	BEY2, EYCL, BEY, BEY1	uc001zbh.4	Q04671	OTTHUMG00000128871	ENST00000354638.3:c.1714C>T	15.37:g.28202804G>A	ENSP00000346659:p.Arg572Cys	29.0	0.0	0		55.0	27.0	0.490909	NM_000275	Q15211|Q15212|Q96EN1|Q9UMI5	Missense_Mutation	SNP	ENST00000354638.3	37	CCDS10020.1	.	.	.	.	.	.	.	.	.	.	G	15.27	2.784872	0.49997	0.0	2.33E-4	ENSG00000104044	ENST00000354638;ENST00000353809;ENST00000382996	D;D;D	0.91894	-2.92;-2.74;-2.93	5.8	3.79	0.43588	Divalent ion symporter (1);	0.118953	0.53938	D	0.000046	D	0.93700	0.7987	M	0.64997	1.995	0.51012	D	0.999906	D;D	0.89917	0.998;1.0	P;D	0.74023	0.827;0.982	D	0.92961	0.6389	10	0.87932	D	0	-7.3542	6.2138	0.20644	0.0936:0.0:0.6114:0.295	.	548;572	Q04671-2;Q04671	.;P_HUMAN	C	572;548;572	ENSP00000346659:R572C;ENSP00000261276:R548C;ENSP00000372457:R572C	ENSP00000261276:R548C	R	-	1	0	OCA2	25876399	1.000000	0.71417	0.234000	0.24042	0.118000	0.20060	5.943000	0.70211	1.468000	0.48064	-0.229000	0.12294	CGC	.	.	weak		0.662	OCA2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250823.1	NM_000275	
DUSP4	1846	hgsc.bcm.edu	37	8	29207692	29207692	+	Missense_Mutation	SNP	C	C	T	rs527419472		TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr8:29207692C>T	ENST00000240100.2	-	1	493	c.104G>A	c.(103-105)gGc>gAc	p.G35D	RP4-676L2.1_ENST00000567818.1_RNA|DUSP4_ENST00000240101.2_5'Flank	NM_001394.6	NP_001385.1	Q13115	DUS4_HUMAN	dual specificity phosphatase 4	35					endoderm formation (GO:0001706)|innate immune response (GO:0045087)|MAPK cascade (GO:0000165)|MyD88-dependent toll-like receptor signaling pathway (GO:0002755)|MyD88-independent toll-like receptor signaling pathway (GO:0002756)|neurotrophin TRK receptor signaling pathway (GO:0048011)|protein dephosphorylation (GO:0006470)|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)	nucleoplasm (GO:0005654)|nucleus (GO:0005634)	MAP kinase tyrosine/serine/threonine phosphatase activity (GO:0017017)|protein tyrosine phosphatase activity (GO:0004725)|protein tyrosine/serine/threonine phosphatase activity (GO:0008138)|protein tyrosine/threonine phosphatase activity (GO:0008330)			endometrium(1)|large_intestine(1)|lung(4)	6				KIRC - Kidney renal clear cell carcinoma(542;0.094)|Kidney(114;0.113)		CCCCAGGGTGCCGTGGCTGCC	0.682																																					p.G35D		Atlas-SNP	.											.	DUSP4	58	.	0			c.G104A						PASS	.						11.0	15.0	14.0					8																	29207692		1933	3796	5729	SO:0001583	missense	1846	exon1			AGGGTGCCGTGGC	U21108	CCDS6072.1, CCDS6073.1	8p12-p11	2011-06-09			ENSG00000120875	ENSG00000120875		"""Protein tyrosine phosphatases / Class I Cys-based PTPs : MAP kinase phosphatases"""	3070	protein-coding gene	gene with protein product	"""VH1 homologous phosphatase 2"", ""MAP kinase phosphatase 2"""	602747				7535768, 9205128	Standard	NM_001394		Approved	HVH2, MKP-2, TYP	uc003xhm.3	Q13115	OTTHUMG00000133395	ENST00000240100.2:c.104G>A	8.37:g.29207692C>T	ENSP00000240100:p.Gly35Asp	12.0	0.0	0		17.0	9.0	0.529412	NM_001394	B2RBU5|D3DSU4|G5E930|Q13524	Missense_Mutation	SNP	ENST00000240100.2	37	CCDS6072.1	.	.	.	.	.	.	.	.	.	.	C	10.20	1.284687	0.23392	.	.	ENSG00000120875	ENST00000240100	T	0.02552	4.25	3.26	3.26	0.37387	Rhodanese-like (3);	0.000000	0.51477	D	0.000081	T	0.01523	0.0049	N	0.08118	0	0.80722	D	1	P	0.37233	0.588	B	0.19946	0.027	T	0.65841	-0.6070	10	0.51188	T	0.08	.	12.7539	0.57323	0.0:1.0:0.0:0.0	.	35	Q13115	DUS4_HUMAN	D	35	ENSP00000240100:G35D	ENSP00000240100:G35D	G	-	2	0	DUSP4	29263611	0.826000	0.29277	1.000000	0.80357	0.425000	0.31504	-0.265000	0.08644	2.101000	0.63845	0.491000	0.48974	GGC	.	.	none		0.682	DUSP4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257249.1	NM_001394	
TTC24	164118	hgsc.bcm.edu	37	1	156551248	156551248	+	Missense_Mutation	SNP	G	G	A	rs192869620	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr1:156551248G>A	ENST00000368237.3	+	1	92	c.92G>A	c.(91-93)cGg>cAg	p.R31Q	TTC24_ENST00000368236.3_Missense_Mutation_p.R31Q			A2A3L6	TTC24_HUMAN	tetratricopeptide repeat domain 24	31										breast(1)|endometrium(2)|kidney(2)|large_intestine(3)|lung(10)|pancreas(1)|prostate(1)	20	all_hematologic(923;0.088)|Hepatocellular(266;0.158)					AAGTGGCTGCGGCAAGAAGCC	0.572													G|||	26	0.00519169	0.0	0.0173	5008	,	,		17596	0.0		0.0129	False		,,,				2504	0.001				p.R31Q		Atlas-SNP	.											TTC24,NS,carcinoma,0,2	TTC24	46	2	0			c.G92A						PASS	.						26.0	27.0	27.0					1																	156551248		692	1591	2283	SO:0001583	missense	164118	exon2			GGCTGCGGCAAGA		CCDS53379.1	1q22	2013-01-10			ENSG00000187862	ENSG00000187862		"""Tetratricopeptide (TTC) repeat domain containing"""	32348	protein-coding gene	gene with protein product							Standard	NM_001105669		Approved		uc021pbf.1	A2A3L6	OTTHUMG00000033202	ENST00000368237.3:c.92G>A	1.37:g.156551248G>A	ENSP00000357220:p.Arg31Gln	120.0	0.0	0		122.0	67.0	0.54918	NM_001105669	Q5T3H7	Missense_Mutation	SNP	ENST00000368237.3	37	CCDS53379.1	13	0.005952380952380952	0	0.0	7	0.019337016574585635	0	0.0	6	0.0079155672823219	G	2.638	-0.284842	0.05605	.	.	ENSG00000187862	ENST00000368236;ENST00000368237	T;T	0.76968	-1.06;-1.06	4.23	-1.72	0.08107	.	0.820698	0.10269	N	0.694981	T	0.19805	0.0476	N	0.02916	-0.46	0.09310	N	1	.	.	.	.	.	.	T	0.15321	-1.0441	8	0.11794	T	0.64	-1.6385	1.4317	0.02335	0.3363:0.1592:0.3497:0.1549	.	.	.	.	Q	31	ENSP00000357219:R31Q;ENSP00000357220:R31Q	ENSP00000357219:R31Q	R	+	2	0	TTC24	154817872	0.000000	0.05858	0.000000	0.03702	0.312000	0.27988	-0.224000	0.09164	-0.319000	0.08652	-0.672000	0.03802	CGG	G|0.994;A|0.006	0.006	strong		0.572	TTC24-006	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000158547.1	XM_089384	
RPL3L	6123	hgsc.bcm.edu	37	16	1996720	1996720	+	Missense_Mutation	SNP	C	C	T	rs147512517		TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr16:1996720C>T	ENST00000268661.7	-	7	951	c.857G>A	c.(856-858)cGc>cAc	p.R286H		NM_005061.2	NP_005052.1	Q92901	RL3L_HUMAN	ribosomal protein L3-like	286					cellular protein metabolic process (GO:0044267)|gene expression (GO:0010467)|mRNA metabolic process (GO:0016071)|nuclear-transcribed mRNA catabolic process, nonsense-mediated decay (GO:0000184)|RNA metabolic process (GO:0016070)|SRP-dependent cotranslational protein targeting to membrane (GO:0006614)|translation (GO:0006412)|translational elongation (GO:0006414)|translational initiation (GO:0006413)|translational termination (GO:0006415)|viral life cycle (GO:0019058)|viral process (GO:0016032)|viral transcription (GO:0019083)	cytosol (GO:0005829)|cytosolic large ribosomal subunit (GO:0022625)|membrane (GO:0016020)|ribosome (GO:0005840)	RNA binding (GO:0003723)|structural constituent of ribosome (GO:0003735)			NS(1)|endometrium(5)|kidney(2)|large_intestine(2)|lung(5)|prostate(1)|upper_aerodigestive_tract(1)	17						CCTGCCGATGCGGAAGATCTG	0.632																																					p.R286H		Atlas-SNP	.											RPL3L,caecum,carcinoma,-1,1	RPL3L	42	1	0			c.G857A						PASS	.	C	HIS/ARG	2,4394	4.2+/-10.8	0,2,2196	37.0	36.0	37.0		857	3.6	1.0	16	dbSNP_134	37	0,8598		0,0,4299	no	missense	RPL3L	NM_005061.2	29	0,2,6495	TT,TC,CC		0.0,0.0455,0.0154	probably-damaging	286/408	1996720	2,12992	2198	4299	6497	SO:0001583	missense	6123	exon7			CCGATGCGGAAGA	U65581	CCDS10450.1	16p13.3	2008-02-05			ENSG00000140986	ENSG00000140986		"""L ribosomal proteins"""	10351	protein-coding gene	gene with protein product						8921388	Standard	NM_005061		Approved		uc002cnh.3	Q92901	OTTHUMG00000128685	ENST00000268661.7:c.857G>A	16.37:g.1996720C>T	ENSP00000268661:p.Arg286His	47.0	0.0	0		32.0	15.0	0.46875	NM_005061		Missense_Mutation	SNP	ENST00000268661.7	37	CCDS10450.1	.	.	.	.	.	.	.	.	.	.	C	14.64	2.594823	0.46318	4.55E-4	0.0	ENSG00000140986	ENST00000268661	T	0.26067	1.76	4.55	3.59	0.41128	Translation elongation/initiation factor/Ribosomal, beta-barrel (1);	0.117044	0.64402	D	0.000012	T	0.63861	0.2547	H	0.97240	3.965	0.58432	D	0.999997	D	0.89917	1.0	D	0.97110	1.0	T	0.75428	-0.3321	10	0.87932	D	0	-32.639	11.9539	0.52970	0.0:0.9145:0.0:0.0855	.	286	Q92901	RL3L_HUMAN	H	286	ENSP00000268661:R286H	ENSP00000268661:R286H	R	-	2	0	RPL3L	1936721	0.990000	0.36364	0.987000	0.45799	0.039000	0.13416	2.583000	0.46094	1.037000	0.40024	-0.258000	0.10820	CGC	C|1.000;T|0.000	0.000	weak		0.632	RPL3L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250582.2	NM_005061	
FAM189A1	23359	hgsc.bcm.edu	37	15	29421059	29421059	+	Missense_Mutation	SNP	A	A	C	rs200682124	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr15:29421059A>C	ENST00000261275.4	-	8	935	c.936T>G	c.(934-936)agT>agG	p.S312R		NM_015307.1	NP_056122.1	O60320	F1891_HUMAN	family with sequence similarity 189, member A1	312	Pro-rich.					integral component of membrane (GO:0016021)				central_nervous_system(2)|endometrium(2)|kidney(1)|lung(1)|stomach(1)	7						GCTGACCTATACTTGTAACCT	0.557													A|||	9	0.00179712	0.0008	0.0029	5008	,	,		17039	0.0		0.004	False		,,,				2504	0.002				p.S312R		Atlas-SNP	.											.	FAM189A1	20	.	0			c.T936G						PASS	.	A	ARG/SER	0,1384		0,0,692	52.0	52.0	52.0		936	-6.1	0.0	15		52	8,3174		0,8,1583	yes	missense	FAM189A1	NM_015307.1	110	0,8,2275	CC,CA,AA		0.2514,0.0,0.1752	probably-damaging	312/540	29421059	8,4558	692	1591	2283	SO:0001583	missense	23359	exon8			ACCTATACTTGTA		CCDS45198.1	15q12	2014-02-12				ENSG00000104059			29075	protein-coding gene	gene with protein product	"""transmembrane protein 228"""					9628581	Standard	NM_015307		Approved	KIAA0574, TMEM228	uc010azk.1	O60320		ENST00000261275.4:c.936T>G	15.37:g.29421059A>C	ENSP00000261275:p.Ser312Arg	56.0	0.0	0		52.0	16.0	0.307692	NM_015307	A0PK09	Missense_Mutation	SNP	ENST00000261275.4	37	CCDS45198.1	.	.	.	.	.	.	.	.	.	.	A	11.14	1.551072	0.27739	0.0	0.002514	ENSG00000104059	ENST00000261275	T	0.04049	3.72	5.07	-6.1	0.02138	.	0.258929	0.41194	N	0.000939	T	0.05686	0.0149	M	0.68952	2.095	0.09310	N	1	B	0.29612	0.251	B	0.26202	0.067	T	0.07751	-1.0756	10	0.42905	T	0.14	-31.8889	14.1806	0.65572	0.4236:0.0:0.5764:0.0	.	312	O60320	F1891_HUMAN	R	312	ENSP00000261275:S312R	ENSP00000261275:S312R	S	-	3	2	FAM189A1	27208351	0.002000	0.14202	0.000000	0.03702	0.002000	0.02628	0.073000	0.14640	-1.192000	0.02691	0.533000	0.62120	AGT	.	.	weak		0.557	FAM189A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000417254.1	NM_015307	
SLC27A2	11001	hgsc.bcm.edu	37	15	50475035	50475035	+	Silent	SNP	C	C	T			TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr15:50475035C>T	ENST00000267842.5	+	1	643	c.411C>T	c.(409-411)aaC>aaT	p.N137N	SLC27A2_ENST00000380902.4_Silent_p.N137N	NM_003645.3	NP_003636.2	O14975	S27A2_HUMAN	solute carrier family 27 (fatty acid transporter), member 2	137					bile acid biosynthetic process (GO:0006699)|bile acid metabolic process (GO:0008206)|cellular lipid metabolic process (GO:0044255)|fatty acid alpha-oxidation (GO:0001561)|fatty acid beta-oxidation (GO:0006635)|long-chain fatty acid import (GO:0044539)|long-chain fatty acid metabolic process (GO:0001676)|methyl-branched fatty acid metabolic process (GO:0097089)|small molecule metabolic process (GO:0044281)|very long-chain fatty acid catabolic process (GO:0042760)	endoplasmic reticulum lumen (GO:0005788)|endoplasmic reticulum membrane (GO:0005789)|extracellular vesicular exosome (GO:0070062)|integral component of endoplasmic reticulum membrane (GO:0030176)|integral component of peroxisomal membrane (GO:0005779)|mitochondrion (GO:0005739)|peroxisomal membrane (GO:0005778)	ATP binding (GO:0005524)|enzyme binding (GO:0019899)|fatty acid transporter activity (GO:0015245)|long-chain fatty acid-CoA ligase activity (GO:0004467)|phytanate-CoA ligase activity (GO:0050197)|pristanate-CoA ligase activity (GO:0070251)|receptor binding (GO:0005102)|very long-chain fatty acid-CoA ligase activity (GO:0031957)			NS(1)|breast(2)|endometrium(3)|large_intestine(4)|lung(9)|ovary(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	25		all_lung(180;0.00177)		all cancers(107;1.16e-06)|GBM - Glioblastoma multiforme(94;0.000113)		TCAATTACAACATCCGCGCGA	0.657																																					p.N137N		Atlas-SNP	.											.	SLC27A2	50	.	0			c.C411T						PASS	.						99.0	107.0	104.0					15																	50475035		2196	4295	6491	SO:0001819	synonymous_variant	11001	exon1			TTACAACATCCGC	D88308	CCDS10133.1, CCDS53943.1	15q21.2	2013-05-22			ENSG00000140284	ENSG00000140284		"""Acyl-CoA synthetase family"", ""Solute carriers"""	10996	protein-coding gene	gene with protein product		603247		FACVL1		9730624	Standard	NM_003645		Approved	FATP2, hFACVL1, VLACS, VLCS, HsT17226, ACSVL1	uc001zxw.3	O14975	OTTHUMG00000131643	ENST00000267842.5:c.411C>T	15.37:g.50475035C>T		45.0	0.0	0		44.0	20.0	0.454545	NM_003645	A8K2J7|Q53FY6|Q6PF09	Silent	SNP	ENST00000267842.5	37	CCDS10133.1																																																																																			.	.	none		0.657	SLC27A2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254539.2	NM_003645	
PPEF2	5470	hgsc.bcm.edu	37	4	76797739	76797739	+	Nonsense_Mutation	SNP	G	G	A	rs149631239		TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr4:76797739G>A	ENST00000286719.7	-	11	1377	c.1021C>T	c.(1021-1023)Cag>Tag	p.Q341*		NM_006239.2	NP_006230.2	O14830	PPE2_HUMAN	protein phosphatase, EF-hand calcium binding domain 2	341	Catalytic.				detection of stimulus involved in sensory perception (GO:0050906)|negative regulation of MAPK cascade (GO:0043409)|negative regulation of peptidyl-threonine phosphorylation (GO:0010801)|protein dephosphorylation (GO:0006470)|regulation of JUN kinase activity (GO:0043506)|regulation of MAP kinase activity (GO:0043405)|visual perception (GO:0007601)	cilium (GO:0005929)|cytoplasm (GO:0005737)	calcium ion binding (GO:0005509)|Hsp70 protein binding (GO:0030544)|Hsp90 protein binding (GO:0051879)|iron ion binding (GO:0005506)|manganese ion binding (GO:0030145)|mitogen-activated protein kinase kinase kinase binding (GO:0031435)|protein serine/threonine phosphatase activity (GO:0004722)			breast(1)|central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(7)|lung(25)|ovary(2)|pancreas(1)|prostate(4)|skin(1)|upper_aerodigestive_tract(3)|urinary_tract(2)	50			Lung(101;0.0809)|LUSC - Lung squamous cell carcinoma(112;0.0934)			ATGGGTCCCTGTGCAGAGCTC	0.547													G|||	1	0.000199681	0.0008	0.0	5008	,	,		18236	0.0		0.0	False		,,,				2504	0.0				p.Q341X	NSCLC(105;1359 1603 15961 44567 47947)	Atlas-SNP	.											.	PPEF2	108	.	0			c.C1021T						PASS	.	G	stop/GLN	1,4405	2.1+/-5.4	0,1,2202	95.0	98.0	97.0		1021	0.9	0.0	4	dbSNP_134	97	9,8591	7.1+/-27.0	0,9,4291	yes	stop-gained	PPEF2	NM_006239.2		0,10,6493	AA,AG,GG		0.1047,0.0227,0.0769		341/754	76797739	10,12996	2203	4300	6503	SO:0001587	stop_gained	5470	exon11			GTCCCTGTGCAGA	AF023456	CCDS34013.1	4q21.1	2013-01-10			ENSG00000156194	ENSG00000156194		"""Serine/threonine phosphatases / Protein phosphatase, catalytic subunits"", ""EF-hand domain containing"""	9244	protein-coding gene	gene with protein product	"""protein phosphatase 7, catalytic subunit, beta isozyme"""	602256				9326663, 12051765	Standard	NM_006239		Approved	PPP7CB	uc003hix.3	O14830	OTTHUMG00000160915	ENST00000286719.7:c.1021C>T	4.37:g.76797739G>A	ENSP00000286719:p.Gln341*	312.0	0.0	0		289.0	144.0	0.49827	NM_006239	O14831	Nonsense_Mutation	SNP	ENST00000286719.7	37	CCDS34013.1	.	.	.	.	.	.	.	.	.	.	G	34	5.301613	0.95601	2.27E-4	0.001047	ENSG00000156194	ENST00000286719;ENST00000337500	.	.	.	3.63	0.893	0.19236	.	2.033460	0.02299	N	0.070992	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.06099	T	0.92	-0.1914	5.7028	0.17891	0.2626:0.4639:0.2735:0.0	.	.	.	.	X	341	.	ENSP00000286719:Q341X	Q	-	1	0	PPEF2	77016763	0.000000	0.05858	0.001000	0.08648	0.004000	0.04260	0.043000	0.13971	0.162000	0.19483	-0.339000	0.08088	CAG	G|0.999;A|0.001	0.001	strong		0.547	PPEF2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000362929.1	NM_006239	
LDLRAD1	388633	hgsc.bcm.edu	37	1	54483792	54483792	+	5'UTR	SNP	G	G	T	rs116802374	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr1:54483792G>T	ENST00000371360.1	-	0	11				LDLRAD1_ENST00000420619.1_Silent_p.R20R|LDLRAD1_ENST00000371362.3_5'UTR|LDLRAD1_ENST00000545928.1_5'UTR	NM_001010978.2	NP_001010978.2	Q5T700	LRAD1_HUMAN	low density lipoprotein receptor class A domain containing 1							integral component of membrane (GO:0016021)				large_intestine(3)|prostate(1)|skin(3)	7						TCATGTCTTCGGTTTCCTGCT	0.592													G|||	80	0.0159744	0.0	0.036	5008	,	,		18046	0.0		0.0288	False		,,,				2504	0.0266				p.R20R		Atlas-SNP	.											.	LDLRAD1	22	.	0			c.C58A						PASS	.	G		29,4377	34.3+/-65.2	0,29,2174	101.0	83.0	89.0			-2.3	0.0	1	dbSNP_132	89	215,8385	91.6+/-153.7	3,209,4088	no	utr-5	LDLRAD1	NM_001010978.2		3,238,6262	TT,TG,GG		2.5,0.6582,1.8761			54483792	244,12762	2203	4300	6503	SO:0001623	5_prime_UTR_variant	388633	exon1			GTCTTCGGTTTCC		CCDS30725.1, CCDS60145.1, CCDS60146.1, CCDS60147.1	1p32.3	2008-02-05	2005-10-07		ENSG00000203985	ENSG00000203985			32069	protein-coding gene	gene with protein product			"""low density lipoprotein receptor A domain containing 1"""				Standard	NM_001010978		Approved		uc001cwm.2	Q5T700	OTTHUMG00000008433	ENST00000371360.1:c.-7C>A	1.37:g.54483792G>T		96.0	0.0	0		116.0	52.0	0.448276	NM_001276392	A0PJY0|B7ZME3|Q5T6Z9	Silent	SNP	ENST00000371360.1	37	CCDS30725.1																																																																																			G|0.979;T|0.021	0.021	strong		0.592	LDLRAD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000023243.1	NM_001010978	
TRIM14	9830	hgsc.bcm.edu	37	9	100862339	100862339	+	Silent	SNP	C	C	A	rs35830621	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr9:100862339C>A	ENST00000341469.2	-	3	420	c.411G>T	c.(409-411)acG>acT	p.T137T	TRIM14_ENST00000342043.3_Silent_p.T137T|TRIM14_ENST00000375098.3_Silent_p.T137T	NM_014788.2	NP_055603.2	Q14142	TRI14_HUMAN	tripartite motif containing 14	137					innate immune response (GO:0045087)|negative regulation of viral transcription (GO:0032897)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)	cytoplasm (GO:0005737)|intracellular (GO:0005622)	zinc ion binding (GO:0008270)			central_nervous_system(1)|cervix(1)|endometrium(2)|kidney(1)|large_intestine(1)|lung(2)|upper_aerodigestive_tract(1)	9		Acute lymphoblastic leukemia(62;0.0559)				GGGTAAGCTGCGTGTTTTTAT	0.468													C|||	176	0.0351438	0.0711	0.0288	5008	,	,		19176	0.001		0.0527	False		,,,				2504	0.0082				p.T137T	Colon(14;460 597 13826 51781)	Atlas-SNP	.											.	TRIM14	24	.	0			c.G411T						PASS	.	C	,,	251,4155	145.7+/-180.5	6,239,1958	135.0	128.0	131.0		411,411,411	-9.1	0.0	9	dbSNP_126	131	465,8135	137.9+/-194.8	8,449,3843	no	coding-synonymous,coding-synonymous,coding-synonymous	TRIM14	NM_014788.2,NM_033219.1,NM_033220.1	,,	14,688,5801	AA,AC,CC		5.407,5.6968,5.5052	,,	137/443,137/443,137/443	100862339	716,12290	2203	4300	6503	SO:0001819	synonymous_variant	9830	exon3			AAGCTGCGTGTTT	AF220130	CCDS6734.1	9q31.1	2011-04-20	2011-01-25		ENSG00000106785	ENSG00000106785		"""Tripartite motif containing / Tripartite motif containing"""	16283	protein-coding gene	gene with protein product		606556	"""tripartite motif-containing 14"""			11331580	Standard	XM_005252320		Approved	KIAA0129	uc004ayd.2	Q14142	OTTHUMG00000020339	ENST00000341469.2:c.411G>T	9.37:g.100862339C>A		180.0	0.0	0		165.0	75.0	0.454545	NM_033219	A8K9W0|E7EQC4|F8W956|Q548W9|Q5TBQ8|Q6ZWL7|Q9BRD8|Q9C020	Silent	SNP	ENST00000341469.2	37	CCDS6734.1																																																																																			C|0.951;A|0.049	0.049	strong		0.468	TRIM14-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053350.1	NM_014788	
MYLK	4638	hgsc.bcm.edu	37	3	123419782	123419782	+	Missense_Mutation	SNP	G	G	A	rs3732485	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr3:123419782G>A	ENST00000475616.1	-	15	2532	c.2533C>T	c.(2533-2535)Cgc>Tgc	p.R845C	MYLK_ENST00000360772.3_Missense_Mutation_p.R845C|MYLK_ENST00000510775.1_5'Flank|MYLK_ENST00000346322.5_Missense_Mutation_p.R776C|MYLK_ENST00000359169.1_Missense_Mutation_p.R845C|MYLK_ENST00000360304.3_Missense_Mutation_p.R845C			Q15746	MYLK_HUMAN	myosin light chain kinase	845			R -> C (in dbSNP:rs3732485).		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)		GACCCATAGCGGTCACTACCA	0.627													G|||	226	0.0451278	0.0318	0.0101	5008	,	,		13765	0.0526		0.0189	False		,,,				2504	0.1074				p.R845C		Atlas-SNP	.											.	MYLK	224	.	0			c.C2533T						PASS	.	G	CYS/ARG,CYS/ARG,CYS/ARG,CYS/ARG	61,4341		0,61,2140	37.0	42.0	40.0		2533,2326,2533,2326	1.3	0.0	3	dbSNP_107	40	21,8569		0,21,4274	no	missense,missense,missense,missense	MYLK	NM_053025.3,NM_053026.3,NM_053027.3,NM_053028.3	180,180,180,180	0,82,6414	AA,AG,GG		0.2445,1.3857,0.6312	benign,benign,benign,benign	845/1915,776/1846,845/1864,776/1795	123419782	82,12910	2201	4295	6496	SO:0001583	missense	4638	exon18			CATAGCGGTCACT	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.2533C>T	3.37:g.123419782G>A	ENSP00000418335:p.Arg845Cys	23.0	0.0	0		43.0	22.0	0.511628	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	61	0.027930402930402932	16	0.032520325203252036	4	0.011049723756906077	24	0.04195804195804196	17	0.022427440633245383	G	6.688	0.495469	0.12762	0.013857	0.002445	ENSG00000065534	ENST00000360772;ENST00000360304;ENST00000359169;ENST00000346322;ENST00000475616	T;T;T;T;T	0.67698	-0.28;-0.23;-0.28;-0.22;-0.23	5.45	1.3	0.21679	.	.	.	.	.	T	0.14056	0.0340	N	0.17082	0.46	0.09310	N	0.999992	B;B;B;B;B	0.17268	0.001;0.002;0.021;0.005;0.0	B;B;B;B;B	0.06405	0.001;0.002;0.002;0.002;0.0	T	0.13926	-1.0491	9	0.45353	T	0.12	.	0.6904	0.00890	0.2428:0.1873:0.3784:0.1914	rs3732485;rs52814293;rs3732485	845;776;845;776;845	Q15746-6;Q15746-4;Q15746-3;Q15746-2;Q15746	.;.;.;.;MYLK_HUMAN	C	845;845;845;776;845	ENSP00000354004:R845C;ENSP00000353452:R845C;ENSP00000352088:R845C;ENSP00000320622:R776C;ENSP00000418335:R845C	ENSP00000320622:R776C	R	-	1	0	MYLK	124902472	0.005000	0.15991	0.002000	0.10522	0.625000	0.37756	-0.063000	0.11655	-0.056000	0.13221	-0.314000	0.08810	CGC	G|0.987;A|0.013	0.013	strong		0.627	MYLK-004	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000356464.1	NM_053025	
USPL1	10208	hgsc.bcm.edu	37	13	31231778	31231778	+	Missense_Mutation	SNP	G	G	C	rs17609459	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr13:31231778G>C	ENST00000255304.4	+	9	1906	c.1564G>C	c.(1564-1566)Gct>Cct	p.A522P		NM_005800.4	NP_005791.3	Q5W0Q7	USPL1_HUMAN	ubiquitin specific peptidase like 1	522			A -> P (in dbSNP:rs17609459).		Cajal body organization (GO:0030576)|cell proliferation (GO:0008283)|protein desumoylation (GO:0016926)	Cajal body (GO:0015030)|extracellular space (GO:0005615)	SUMO binding (GO:0032183)|SUMO-specific isopeptidase activity (GO:0070140)			breast(1)|endometrium(2)|kidney(1)|large_intestine(9)|lung(15)|pancreas(3)|skin(3)	34		Lung SC(185;0.0257)|Breast(139;0.203)		all cancers(112;0.0306)|Epithelial(112;0.131)|OV - Ovarian serous cystadenocarcinoma(117;0.134)		TGACCAACACGCTCTCAGTAA	0.403													G|||	62	0.0123802	0.0204	0.013	5008	,	,		20603	0.0		0.0199	False		,,,				2504	0.0061				p.A522P	Ovarian(60;318 1180 1554 28110 31601)	Atlas-SNP	.											.	USPL1	82	.	0			c.G1564C						PASS	.	G	PRO/ALA	101,4305	80.4+/-118.8	1,99,2103	135.0	131.0	133.0		1564	3.1	0.0	13	dbSNP_123	133	172,8428	79.5+/-142.1	4,164,4132	yes	missense	USPL1	NM_005800.4	27	5,263,6235	CC,CG,GG		2.0,2.2923,2.099	benign	522/1093	31231778	273,12733	2203	4300	6503	SO:0001583	missense	10208	exon9			CAACACGCTCTCA	X59131	CCDS9336.1	13q12-q14	2012-11-14	2005-11-24	2005-11-24	ENSG00000132952	ENSG00000132952			20294	protein-coding gene	gene with protein product			"""chromosome 13 open reading frame 22"""	C13orf22		22878415	Standard	NM_005800		Approved	bA121O19.1, D13S106E	uc001utc.2	Q5W0Q7	OTTHUMG00000016675	ENST00000255304.4:c.1564G>C	13.37:g.31231778G>C	ENSP00000255304:p.Ala522Pro	97.0	0.0	0		78.0	34.0	0.435897	NM_005800	Q14109|Q6AI45|Q8IY30|Q8IYE8	Missense_Mutation	SNP	ENST00000255304.4	37	CCDS9336.1	36	0.016483516483516484	13	0.026422764227642278	7	0.019337016574585635	0	0.0	16	0.021108179419525065	G	13.09	2.132849	0.37630	0.022923	0.02	ENSG00000132952	ENST00000255304	T	0.08102	3.13	5.79	3.06	0.35304	.	0.937697	0.09093	N	0.849598	T	0.03053	0.0090	L	0.54323	1.7	0.09310	N	1	B	0.24186	0.099	B	0.23852	0.049	T	0.40924	-0.9537	10	0.22109	T	0.4	-4.288	9.692	0.40134	0.0:0.1844:0.3512:0.4644	rs17609459;rs52830887;rs56453321;rs17609459	522	Q5W0Q7	USPL1_HUMAN	P	522	ENSP00000255304:A522P	ENSP00000255304:A522P	A	+	1	0	USPL1	30129778	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-0.189000	0.09629	0.341000	0.23771	-0.169000	0.13324	GCT	C|0.020;G|0.980	0.020	strong		0.403	USPL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044369.1	NM_005800	
MCM8	84515	hgsc.bcm.edu	37	20	5966626	5966626	+	Missense_Mutation	SNP	G	G	T	rs150257637		TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr20:5966626G>T	ENST00000378896.3	+	16	2389	c.2012G>T	c.(2011-2013)gGc>gTc	p.G671V	MCM8_ENST00000378886.2_Missense_Mutation_p.G711V|MCM8_ENST00000265187.4_Missense_Mutation_p.G655V|MCM8_ENST00000378883.1_Missense_Mutation_p.G624V	NM_001281520.1|NM_032485.4|NM_182802.1	NP_001268449.1|NP_115874.3|NP_877954.1	Q9UJA3	MCM8_HUMAN	minichromosome maintenance complex component 8	671					cellular response to DNA damage stimulus (GO:0006974)|DNA replication (GO:0006260)|DNA strand elongation involved in DNA replication (GO:0006271)|double-strand break repair via homologous recombination (GO:0000724)|female gamete generation (GO:0007292)|G1/S transition of mitotic cell cycle (GO:0000082)|male gamete generation (GO:0048232)|mitotic cell cycle (GO:0000278)	MCM8-MCM9 complex (GO:0097362)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	ATP binding (GO:0005524)|DNA binding (GO:0003677)|helicase activity (GO:0004386)			cervix(1)|endometrium(1)|kidney(1)|large_intestine(4)|lung(9)|prostate(2)|skin(3)|upper_aerodigestive_tract(2)	23						AAGTACATTGGCTATGCTCGG	0.448													G|||	1	0.000199681	0.0	0.0	5008	,	,		18852	0.0		0.001	False		,,,				2504	0.0				p.G671V		Atlas-SNP	.											.	MCM8	125	.	0			c.G2012T						PASS	.	G	VAL/GLY,VAL/GLY	1,4405	2.1+/-5.4	0,1,2202	135.0	121.0	126.0		2012,1964	5.3	1.0	20	dbSNP_134	126	5,8595	4.3+/-15.6	0,5,4295	yes	missense,missense	MCM8	NM_032485.4,NM_182802.1	109,109	0,6,6497	TT,TG,GG		0.0581,0.0227,0.0461	possibly-damaging,possibly-damaging	671/841,655/825	5966626	6,13000	2203	4300	6503	SO:0001583	missense	84515	exon16			ACATTGGCTATGC	AJ439063	CCDS13094.1, CCDS13095.1, CCDS63226.1, CCDS63227.1	20p12.3	2007-04-04	2007-04-04	2003-07-09	ENSG00000125885	ENSG00000125885			16147	protein-coding gene	gene with protein product	"""REC homolog (Drosophila)"""	608187	"""chromosome 20 open reading frame 154"""	C20orf154		12527764	Standard	NM_032485		Approved	MGC4816, MGC12866, MGC119522, MGC119523, dJ967N21.5, REC	uc002wmi.3	Q9UJA3	OTTHUMG00000031822	ENST00000378896.3:c.2012G>T	20.37:g.5966626G>T	ENSP00000368174:p.Gly671Val	115.0	0.0	0		156.0	70.0	0.448718	NM_032485	B2RBG7|D3DW08|E7EQU7|Q495R4|Q495R6|Q495R7|Q86US4|Q969I5	Missense_Mutation	SNP	ENST00000378896.3	37	CCDS13094.1	1	4.578754578754579E-4	0	0.0	0	0.0	0	0.0	1	0.0013192612137203166	G	20.9	4.060936	0.76074	2.27E-4	5.81E-4	ENSG00000125885	ENST00000378896;ENST00000378883;ENST00000378886;ENST00000265187	T;T;T;T	0.06068	3.35;3.35;3.35;3.35	5.33	5.33	0.75918	.	0.096141	0.64402	D	0.000001	T	0.10937	0.0267	L	0.39898	1.24	0.80722	D	1	P;P;B;P	0.47191	0.73;0.891;0.431;0.772	B;P;B;B	0.47346	0.219;0.544;0.219;0.326	T	0.12142	-1.0559	10	0.30078	T	0.28	-14.9313	19.4129	0.94683	0.0:0.0:1.0:0.0	.	624;711;655;671	Q9UJA3-2;E7EQU7;Q9UJA3-3;Q9UJA3	.;.;.;MCM8_HUMAN	V	671;624;711;655	ENSP00000368174:G671V;ENSP00000368161:G624V;ENSP00000368164:G711V;ENSP00000265187:G655V	ENSP00000265187:G655V	G	+	2	0	MCM8	5914626	1.000000	0.71417	1.000000	0.80357	0.991000	0.79684	9.648000	0.98483	2.652000	0.90054	0.655000	0.94253	GGC	G|0.999;T|0.001	0.001	strong		0.448	MCM8-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000077900.1	NM_032485	
SLCO1B7	338821	hgsc.bcm.edu	37	12	21174496	21174496	+	Missense_Mutation	SNP	C	C	T	rs12824121	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr12:21174496C>T	ENST00000421593.2	+	3	320	c.320C>T	c.(319-321)cCg>cTg	p.P107L	SLCO1B7_ENST00000554957.1_Missense_Mutation_p.P154L|LST3_ENST00000381541.3_Missense_Mutation_p.P154L|LST3_ENST00000540229.1_Intron|SLCO1B3_ENST00000553473.1_Intron	NM_001009562.4	NP_001009562.3	G3V0H7	SO1B7_HUMAN	solute carrier organic anion transporter family, member 1B7 (non-functional)	107						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	transporter activity (GO:0005215)			endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(7)|lung(25)|prostate(1)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(2)	46						AATAGAACACCGTCTGAGATA	0.254													C|||	21	0.00419329	0.0008	0.0029	5008	,	,		15614	0.0		0.0179	False		,,,				2504	0.0				p.P107L		Atlas-SNP	.											.	SLCO1B7	85	.	0			c.C320T						PASS	.	C	LEU/PRO	14,3786		0,14,1886	38.0	34.0	35.0		320	2.8	0.0	12	dbSNP_121	35	139,8183		1,137,4023	yes	missense	SLCO1B7	NM_001009562.4	98	1,151,5909	TT,TC,CC		1.6703,0.3684,1.2622		107/641	21174496	153,11969	1900	4161	6061	SO:0001583	missense	338821	exon3			GAACACCGTCTGA	AF401642	CCDS44843.1	12p12.3	2013-05-22			ENSG00000205754	ENSG00000205754		"""Solute carriers"""	32934	protein-coding gene	gene with protein product							Standard	NM_001009562		Approved	LST3, SLC21A21		G3V0H7	OTTHUMG00000169045	ENST00000421593.2:c.320C>T	12.37:g.21174496C>T	ENSP00000394168:p.Pro107Leu	119.0	0.0	0		105.0	46.0	0.438095	NM_001009562	Q71QF0	Missense_Mutation	SNP	ENST00000421593.2	37	CCDS44843.1	19	0.0086996336996337	0	0.0	1	0.0027624309392265192	0	0.0	18	0.023746701846965697	.	7.606	0.673791	0.14841	0.003684	0.016703	ENSG00000257046;ENSG00000205754;ENSG00000205754	ENST00000381541;ENST00000554957;ENST00000421593	T;T;T	0.37915	1.17;1.17;1.17	2.79	2.79	0.32731	.	1.095650	0.07077	U	0.836307	T	0.17152	0.0412	L	0.39147	1.195	0.09310	N	1	B;B	0.10296	0.002;0.003	B;B	0.13407	0.007;0.009	T	0.12941	-1.0528	10	0.37606	T	0.19	.	9.1237	0.36801	0.0:1.0:0.0:0.0	rs12824121;rs52800356;rs12824121	107;154	G3V0H7;F5H094	.;.	L	154;154;107	ENSP00000370952:P154L;ENSP00000452013:P154L;ENSP00000394168:P107L	ENSP00000370952:P154L	P	+	2	0	SLCO1B7;RP11-545J16.1	21065763	0.003000	0.15002	0.005000	0.12908	0.124000	0.20399	1.055000	0.30467	1.531000	0.49152	0.205000	0.17691	CCG	C|0.990;T|0.010	0.010	strong		0.254	SLCO1B7-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000402066.1	NM_001009562	
SLC25A6	293	hgsc.bcm.edu	37	X	1510877	1510877	+	Missense_Mutation	SNP	G	G	C			TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chrX:1510877G>C	ENST00000381401.5	-	1	740	c.26C>G	c.(25-27)gCc>gGc	p.A9G	SLC25A6_ENST00000475167.1_5'UTR	NM_001636.3	NP_001627.2	P12236	ADT3_HUMAN	solute carrier family 25 (mitochondrial carrier; adenine nucleotide translocator), member 6	9					active induction of host immune response by virus (GO:0046732)|ADP transport (GO:0015866)|apoptotic process (GO:0006915)|ATP transport (GO:0015867)|cellular protein metabolic process (GO:0044267)|energy reserve metabolic process (GO:0006112)|modulation by virus of host morphology or physiology (GO:0019048)|protein targeting to mitochondrion (GO:0006626)|regulation of insulin secretion (GO:0050796)|small molecule metabolic process (GO:0044281)|viral life cycle (GO:0019058)|viral process (GO:0016032)	integral component of membrane (GO:0016021)|mitochondrial inner membrane (GO:0005743)|mitochondrial inner membrane presequence translocase complex (GO:0005744)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	ATP:ADP antiporter activity (GO:0005471)			haematopoietic_and_lymphoid_tissue(1)|kidney(1)|lung(8)|upper_aerodigestive_tract(1)	11		all_cancers(21;4.28e-07)|all_epithelial(21;2.07e-08)|all_lung(23;2.81e-05)|Lung NSC(23;0.000693)|Lung SC(21;0.122)			Clodronate(DB00720)	GAAGTCTTTGGCGAAGGAGAT	0.692																																					p.A9G		Atlas-SNP	.											.	SLC25A6	27	.	0			c.C26G						PASS	.						36.0	37.0	36.0					X																	1510877		2202	4295	6497	SO:0001583	missense	293	exon1			TCTTTGGCGAAGG	AY007135	CCDS14114.1	Xp22.32 and Yp11.3	2013-05-22			ENSG00000169100	ENSG00000169100		"""Pseudoautosomal regions / PAR1"", ""Solute carriers"""	10992	protein-coding gene	gene with protein product		300151, 403000		ANT3			Standard	NM_001636		Approved	ANT3Y, MGC17525	uc004cpt.3	P12236	OTTHUMG00000021058	ENST00000381401.5:c.26C>G	X.37:g.1510877G>C	ENSP00000370808:p.Ala9Gly	81.0	0.0	0		63.0	28.0	0.444444	NM_001636	Q96C49	Missense_Mutation	SNP	ENST00000381401.5	37	CCDS14114.1	.	.	.	.	.	.	.	.	.	.	g	8.851	0.944558	0.18356	.	.	ENSG00000169100	ENST00000381401;ENST00000447786	T	0.79454	-1.27	1.54	1.54	0.23209	Mitochondrial carrier domain (2);	0.000000	0.41500	U	0.000862	T	0.69575	0.3126	L	0.52364	1.645	0.09310	N	1	B	0.09022	0.002	B	0.21708	0.036	T	0.61068	-0.7137	10	0.40728	T	0.16	.	10.0455	0.42184	0.0:0.0:1.0:0.0	.	9	P12236	ADT3_HUMAN	G	9	ENSP00000370808:A9G	ENSP00000370808:A9G	A	-	2	0	SLC25A6	1470877	0.997000	0.39634	0.724000	0.30704	0.047000	0.14425	1.204000	0.32296	0.807000	0.34208	0.281000	0.19383	GCC	.	.	none		0.692	SLC25A6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055596.1	NM_001636	
FBXO11	80204	hgsc.bcm.edu	37	2	48059539	48059539	+	Silent	SNP	A	A	G	rs141756242		TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr2:48059539A>G	ENST00000403359.3	-	11	1419	c.1347T>C	c.(1345-1347)aaT>aaC	p.N449N	FBXO11_ENST00000316377.4_Silent_p.N365N|FBXO11_ENST00000434523.2_5'UTR|FBXO11_ENST00000402508.1_Silent_p.N365N	NM_001190274.1	NP_001177203.1	Q86XK2	FBX11_HUMAN	F-box protein 11	449					cellular protein modification process (GO:0006464)|peptidyl-arginine N-methylation (GO:0035246)|protein ubiquitination (GO:0016567)|sensory perception of sound (GO:0007605)|ubiquitin-dependent protein catabolic process (GO:0006511)	chromosome (GO:0005694)|cytoplasm (GO:0005737)|nucleolus (GO:0005730)|nucleus (GO:0005634)|ubiquitin ligase complex (GO:0000151)	protein-arginine N-methyltransferase activity (GO:0016274)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)	p.0?(2)		endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(6)|lung(11)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)	26		Acute lymphoblastic leukemia(82;0.0299)|all_hematologic(82;0.0358)	Lung(47;0.101)|LUSC - Lung squamous cell carcinoma(58;0.151)			GATGAATATGATTCCGTCTAA	0.333			"""Mis, F, D"""		DLBCL								A|||	1	0.000199681	0.0	0.0014	5008	,	,		16143	0.0		0.0	False		,,,				2504	0.0				p.N449N		Atlas-SNP	.		Rec	yes		2	2p16.3	80204	F-box protein 11		L	.	FBXO11	127	.	2	Whole gene deletion(2)	haematopoietic_and_lymphoid_tissue(2)	c.T1347C						PASS	.	A	,	2,4402	4.2+/-10.8	0,2,2200	87.0	89.0	88.0		1347,1095	4.8	1.0	2	dbSNP_134	88	21,8577	16.0+/-53.3	0,21,4278	no	coding-synonymous,coding-synonymous	FBXO11	NM_001190274.1,NM_025133.4	,	0,23,6478	GG,GA,AA		0.2442,0.0454,0.1769	,	449/928,365/844	48059539	23,12979	2202	4299	6501	SO:0001819	synonymous_variant	80204	exon11			AATATGATTCCGT	AF174599	CCDS1837.1, CCDS54357.1	2p16.3	2014-01-29	2008-06-23	2008-06-23	ENSG00000138081	ENSG00000138081		"""Ubiquitin protein ligase E3 component n-recognins"", ""F-boxes /  ""other"""""	13590	protein-coding gene	gene with protein product	"""ubiquitin protein ligase E3 component n-recognin 6"""	607871	"""F-box only protein 11"""			10531035, 16487488, 18162545	Standard	NM_025133		Approved	FBX11, UBR6	uc002rwe.3	Q86XK2	OTTHUMG00000129130	ENST00000403359.3:c.1347T>C	2.37:g.48059539A>G		130.0	0.0	0		102.0	35.0	0.343137	NM_001190274	A1L491|Q52ZP1|Q53EP7|Q53RT5|Q8IXG3|Q96E90|Q9H6V8|Q9H9L1|Q9NR14|Q9UFK1|Q9UHI1|Q9UKC2	Silent	SNP	ENST00000403359.3	37	CCDS54357.1	.	.	.	.	.	.	.	.	.	.	A	7.851	0.724018	0.15439	4.54E-4	0.002442	ENSG00000138081	ENST00000493962	.	.	.	5.95	4.8	0.61643	.	.	.	.	.	T	0.63640	0.2528	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.61187	-0.7113	4	.	.	.	-19.7747	11.946	0.52928	0.9324:0.0:0.0676:0.0	.	.	.	.	P	241	.	.	S	-	1	0	FBXO11	47913043	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	3.794000	0.55492	1.076000	0.40961	0.460000	0.39030	TCA	A|0.998;G|0.002	0.002	strong		0.333	FBXO11-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000251181.3	NM_012167, NM_018693, NM_025133	
DDX55	57696	hgsc.bcm.edu	37	12	124102305	124102305	+	Splice_Site	SNP	T	T	A	rs147152712	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr12:124102305T>A	ENST00000238146.4	+	11	1100	c.1050T>A	c.(1048-1050)agT>agA	p.S350R	DDX55_ENST00000541259.1_Intron|DDX55_ENST00000538744.1_Splice_Site_p.S319R|SNORA9_ENST00000384170.1_RNA|DDX55_ENST00000421670.3_5'Flank	NM_020936.1	NP_065987.1	Q8NHQ9	DDX55_HUMAN	DEAD (Asp-Glu-Ala-Asp) box polypeptide 55	350	Helicase C-terminal. {ECO:0000255|PROSITE-ProRule:PRU00542}.					membrane (GO:0016020)	ATP binding (GO:0005524)|ATP-dependent helicase activity (GO:0008026)|poly(A) RNA binding (GO:0044822)			autonomic_ganglia(1)|breast(1)|endometrium(1)|large_intestine(3)|liver(1)|lung(4)|ovary(1)|prostate(1)|skin(1)	14	all_neural(191;0.101)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;0.000142)|Epithelial(86;0.000637)|all cancers(50;0.00772)		GTTCTCACAGTGCCTTCGTGC	0.582																																					p.S350R		Atlas-SNP	.											.	DDX55	51	.	0			c.T1050A						PASS	.	T	ARG/SER	1,4405	2.1+/-5.4	0,1,2202	90.0	79.0	83.0		1050	-6.2	0.9	12	dbSNP_134	83	9,8591	7.1+/-27.0	0,9,4291	yes	missense-near-splice	DDX55	NM_020936.1	110	0,10,6493	AA,AT,TT		0.1047,0.0227,0.0769	probably-damaging	350/601	124102305	10,12996	2203	4300	6503	SO:0001630	splice_region_variant	57696	exon11			TCACAGTGCCTTC	AB046815	CCDS9251.1	12q24.31	2003-06-13			ENSG00000111364	ENSG00000111364		"""DEAD-boxes"""	20085	protein-coding gene	gene with protein product						10997877	Standard	NM_020936		Approved	KIAA1595	uc001ufi.3	Q8NHQ9	OTTHUMG00000168695	ENST00000238146.4:c.1050-1T>A	12.37:g.124102305T>A		104.0	0.0	0		125.0	63.0	0.504	NM_020936	Q658L6|Q8IYH0|Q9HCH7	Missense_Mutation	SNP	ENST00000238146.4	37	CCDS9251.1	.	.	.	.	.	.	.	.	.	.	T	23.9	4.469762	0.84533	2.27E-4	0.001047	ENSG00000111364	ENST00000238146;ENST00000538744	T;D	0.92699	-0.93;-3.09	5.98	-6.16	0.02098	Helicase, C-terminal (3);	0.084790	0.85682	D	0.000000	D	0.90899	0.7140	L	0.33293	1	0.80722	D	1	P;D	0.58970	0.603;0.984	P;D	0.66847	0.516;0.947	D	0.88317	0.2960	9	.	.	.	.	15.8924	0.79309	0.0:0.5049:0.0:0.4951	.	350;350	B4DVE4;Q8NHQ9	.;DDX55_HUMAN	R	350;319	ENSP00000238146:S350R;ENSP00000443114:S319R	.	S	+	3	2	DDX55	122668258	0.229000	0.23729	0.920000	0.36463	0.971000	0.66376	-0.470000	0.06639	-0.950000	0.03659	-0.274000	0.10170	AGT	T|0.999;A|0.001	0.001	strong		0.582	DDX55-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000400616.2		Missense_Mutation
STRBP	55342	hgsc.bcm.edu	37	9	125895238	125895238	+	Missense_Mutation	SNP	C	C	T	rs79286922	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr9:125895238C>T	ENST00000348403.5	-	17	2212	c.1783G>A	c.(1783-1785)Gtt>Att	p.V595I	STRBP_ENST00000447404.2_Missense_Mutation_p.V595I|STRBP_ENST00000360998.3_Missense_Mutation_p.V581I	NM_018387.4	NP_060857.2	Q96SI9	STRBP_HUMAN	spermatid perinuclear RNA binding protein	595					cellular component movement (GO:0006928)|mechanosensory behavior (GO:0007638)|multicellular organismal development (GO:0007275)|spermatid development (GO:0007286)	cytoplasm (GO:0005737)|microtubule cytoskeleton (GO:0015630)|nucleus (GO:0005634)	DNA binding (GO:0003677)|double-stranded RNA binding (GO:0003725)|poly(A) RNA binding (GO:0044822)|single-stranded RNA binding (GO:0003727)			breast(1)|central_nervous_system(1)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(9)|lung(6)|prostate(1)|skin(2)	26						GTATTCACAACGCCCTTTGCC	0.438													C|||	28	0.00559105	0.0061	0.0072	5008	,	,		20536	0.0		0.0129	False		,,,				2504	0.002				p.V595I		Atlas-SNP	.											.	STRBP	73	.	0			c.G1783A						PASS	.	C	ILE/VAL,ILE/VAL	30,4376	36.0+/-67.5	0,30,2173	90.0	84.0	86.0		1741,1783	4.0	1.0	9	dbSNP_131	86	160,8440	76.3+/-139.0	1,158,4141	yes	missense,missense	STRBP	NM_001171137.1,NM_018387.4	29,29	1,188,6314	TT,TC,CC		1.8605,0.6809,1.4609	benign,benign	581/659,595/673	125895238	190,12816	2203	4300	6503	SO:0001583	missense	55342	exon17			TCACAACGCCCTT	AK002169	CCDS6851.1, CCDS55337.1	9q33.1-q33.3	2008-08-29	2001-11-28		ENSG00000165209	ENSG00000165209			16462	protein-coding gene	gene with protein product		611138	"""spermatid perinuclear RNA-binding protein"", ""interleukin enhancer binding factor 3-like"""	ILF3L			Standard	NM_018387		Approved	FLJ11307, SPNR	uc004bns.3	Q96SI9	OTTHUMG00000020636	ENST00000348403.5:c.1783G>A	9.37:g.125895238C>T	ENSP00000321347:p.Val595Ile	139.0	0.0	0		130.0	61.0	0.469231	NM_018387	Q32NB9|Q9BUE1|Q9BXG4|Q9H0B4|Q9H7V1|Q9NUK4	Missense_Mutation	SNP	ENST00000348403.5	37	CCDS6851.1	18	0.008241758241758242	5	0.01016260162601626	2	0.0055248618784530384	0	0.0	11	0.014511873350923483	C	15.15	2.746549	0.49257	0.006809	0.018605	ENSG00000165209	ENST00000447404;ENST00000348403;ENST00000360998	T;T;T	0.17054	2.56;2.56;2.3	5.96	4.03	0.46877	.	0.336970	0.34750	N	0.003716	T	0.05273	0.0140	N	0.24115	0.695	0.35920	D	0.831777	B;B	0.13145	0.004;0.007	B;B	0.08055	0.001;0.003	T	0.15752	-1.0426	10	0.30854	T	0.27	-1.5899	10.2451	0.43336	0.0:0.7752:0.0:0.2248	.	595;581	Q96SI9;Q96SI9-2	STRBP_HUMAN;.	I	595;595;581	ENSP00000415968:V595I;ENSP00000321347:V595I;ENSP00000354271:V581I	ENSP00000321347:V595I	V	-	1	0	STRBP	124935059	0.950000	0.32346	0.993000	0.49108	0.977000	0.68977	1.691000	0.37721	0.757000	0.33036	0.579000	0.79373	GTT	C|0.988;T|0.012	0.012	strong		0.438	STRBP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053982.1		
KDM5C	8242	hgsc.bcm.edu	37	X	53230909	53230909	+	Silent	SNP	C	C	T	rs74850270	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chrX:53230909C>T	ENST00000375401.3	-	14	2416	c.1884G>A	c.(1882-1884)caG>caA	p.Q628Q	KDM5C_ENST00000404049.3_Silent_p.Q627Q|KDM5C_ENST00000465402.1_5'UTR|KDM5C_ENST00000375379.3_Silent_p.Q628Q|KDM5C_ENST00000452825.3_Silent_p.Q561Q|KDM5C_ENST00000375383.3_Silent_p.Q587Q	NM_001282622.1|NM_004187.3	NP_001269551.1|NP_004178.2	P41229	KDM5C_HUMAN	lysine (K)-specific demethylase 5C	628	JmjC. {ECO:0000255|PROSITE- ProRule:PRU00538}.				histone H3-K4 demethylation (GO:0034720)|negative regulation of transcription, DNA-templated (GO:0045892)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|histone demethylase activity (H3-K4 specific) (GO:0032453)|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)|zinc ion binding (GO:0008270)			autonomic_ganglia(1)|breast(4)|central_nervous_system(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(30)|large_intestine(9)|lung(17)|oesophagus(1)|ovary(6)|prostate(1)|salivary_gland(1)|skin(1)|upper_aerodigestive_tract(2)	82						GCTCAATGCACTGGCGCCCAG	0.592			"""N, F, S"""		clear cell renal carcinoma								C|||	35	0.00927152	0.025	0.0029	3775	,	,		13930	0.0		0.0	False		,,,				2504	0.0				p.Q628Q		Atlas-SNP	.		Rec	yes		X	Xp11.22-p11.21	8242	lysine (K)-specific demethylase 5C (JARID1C)		E	.	KDM5C	385	.	0			c.G1884A						PASS	.	C	,	119,3716		1,96,21,1535,550	47.0	42.0	44.0		1683,1884	-0.3	1.0	X	dbSNP_131	44	1,6727		0,0,1,2428,1871	no	coding-synonymous,coding-synonymous	KDM5C	NM_001146702.1,NM_004187.3	,	1,96,22,3963,2421	TT,TC,T,CC,C		0.0149,3.103,1.136	,	561/1380,628/1561	53230909	120,10443	2203	4300	6503	SO:0001819	synonymous_variant	8242	exon14			AATGCACTGGCGC	Z29650	CCDS14351.1, CCDS55417.1, CCDS65269.1	Xp11.22-p11.21	2014-01-31	2009-04-06	2009-04-06	ENSG00000126012	ENSG00000126012		"""Chromatin-modifying enzymes / K-demethylases"", ""Zinc fingers, PHD-type"""	11114	protein-coding gene	gene with protein product		314690	"""Jumonji, AT rich interactive domain 1C (RBP2-like)"", ""Smcy homolog, X-linked (mouse)"", ""jumonji, AT rich interactive domain 1C"", ""mental retardation, X-linked 13"""	SMCX, JARID1C, MRX13		7951230, 8162017, 19826449	Standard	NM_004187		Approved	DXS1272E, XE169	uc004drz.3	P41229	OTTHUMG00000021606	ENST00000375401.3:c.1884G>A	X.37:g.53230909C>T		90.0	0.0	0		110.0	110.0	1	NM_004187	B0QZ44|B4E3I2|F5H3T1|Q5JUX3|Q5JUX4|Q5JUX5|Q7Z5S5	Silent	SNP	ENST00000375401.3	37	CCDS14351.1																																																																																			C|0.988;T|0.012	0.012	strong		0.592	KDM5C-005	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000056737.2	NM_004187	
TAS1R1	80835	hgsc.bcm.edu	37	1	6639073	6639073	+	Missense_Mutation	SNP	G	G	A	rs149418903	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr1:6639073G>A	ENST00000333172.6	+	6	2148	c.1955G>A	c.(1954-1956)cGc>cAc	p.R652H	ZBTB48_ENST00000377674.4_5'Flank|TAS1R1_ENST00000328191.4_3'UTR|TAS1R1_ENST00000351136.3_Missense_Mutation_p.R398H	NM_138697.3	NP_619642.2	Q7RTX1	TS1R1_HUMAN	taste receptor, type 1, member 1	652					detection of chemical stimulus involved in sensory perception of taste (GO:0050912)|sensory perception of umami taste (GO:0050917)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	protein heterodimerization activity (GO:0046982)|taste receptor activity (GO:0008527)			NS(2)|central_nervous_system(1)|endometrium(2)|large_intestine(7)|lung(13)|ovary(1)|skin(1)|urinary_tract(2)	29	Ovarian(185;0.0212)|all_lung(157;0.154)	all_cancers(23;8.73e-34)|all_epithelial(116;9.26e-22)|all_lung(118;7.57e-07)|Lung NSC(185;4.26e-06)|Breast(487;0.000353)|Renal(390;0.0007)|Colorectal(325;0.00104)|Hepatocellular(190;0.00308)|Myeloproliferative disorder(586;0.0255)|Ovarian(437;0.0443)		Colorectal(212;1.29e-07)|COAD - Colon adenocarcinoma(227;1.33e-05)|Kidney(185;4.89e-05)|KIRC - Kidney renal clear cell carcinoma(229;0.000896)|BRCA - Breast invasive adenocarcinoma(365;0.00108)|STAD - Stomach adenocarcinoma(132;0.0167)|READ - Rectum adenocarcinoma(331;0.0642)		CTGACAGTTCGCTCATTCCAA	0.522													G|||	4	0.000798722	0.0	0.0014	5008	,	,		22421	0.0		0.001	False		,,,				2504	0.002				p.R652H		Atlas-SNP	.											TAS1R1,colon,carcinoma,0,1	TAS1R1	76	1	0			c.G1955A						scavenged	.	G	HIS/ARG,HIS/ARG	0,4406		0,0,2203	129.0	128.0	128.0		1955,1193	4.8	1.0	1	dbSNP_134	128	14,8586	10.5+/-38.8	0,14,4286	yes	missense,missense	TAS1R1	NM_138697.3,NM_177540.2	29,29	0,14,6489	AA,AG,GG		0.1628,0.0,0.1076	probably-damaging,probably-damaging	652/842,398/588	6639073	14,12992	2203	4300	6503	SO:0001583	missense	80835	exon6			CAGTTCGCTCATT		CCDS81.1, CCDS82.1	1p36.23	2012-08-22	2003-03-24		ENSG00000173662	ENSG00000173662		"""Taste receptors / Type 1"", ""GPCR / Unclassified : Taste receptors"""	14448	protein-coding gene	gene with protein product		606225	"""G protein-coupled receptor 70"""	GPR70			Standard	NM_138697		Approved	T1R1, TR1	uc001ant.3	Q7RTX1	OTTHUMG00000001441	ENST00000333172.6:c.1955G>A	1.37:g.6639073G>A	ENSP00000331867:p.Arg652His	169.0	1.0	0.00591716		220.0	115.0	0.522727	NM_138697	B2RMX0|Q5SY22|Q5SY24|Q8NGZ7|Q8TDJ7|Q8TDJ8|Q8TDJ9|Q8TDK0	Missense_Mutation	SNP	ENST00000333172.6	37	CCDS81.1	.	.	.	.	.	.	.	.	.	.	G	29.7	5.031876	0.93575	0.0	0.001628	ENSG00000173662	ENST00000333172;ENST00000351136	D;D	0.88664	-2.41;-2.41	4.85	4.85	0.62838	GPCR, family 3, C-terminal (2);	0.000000	0.85682	D	0.000000	D	0.94532	0.8239	M	0.81614	2.55	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.91635	0.989;0.999	D	0.95172	0.8291	10	0.87932	D	0	.	17.1499	0.86775	0.0:0.0:1.0:0.0	.	398;652	Q7RTX1-2;Q7RTX1	.;TS1R1_HUMAN	H	652;398	ENSP00000331867:R652H;ENSP00000312558:R398H	ENSP00000331867:R652H	R	+	2	0	TAS1R1	6561660	0.885000	0.30320	0.994000	0.49952	0.998000	0.95712	2.584000	0.46102	2.505000	0.84491	0.655000	0.94253	CGC	G|0.999;A|0.001	0.001	strong		0.522	TAS1R1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000004211.1		
MICAL2	9645	hgsc.bcm.edu	37	11	12247813	12247813	+	Missense_Mutation	SNP	C	C	T			TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr11:12247813C>T	ENST00000256194.4	+	14	2072	c.1784C>T	c.(1783-1785)aCg>aTg	p.T595M	MICAL2_ENST00000379612.3_Missense_Mutation_p.T595M|MICAL2_ENST00000527546.1_Missense_Mutation_p.T595M|MICAL2_ENST00000537344.1_Missense_Mutation_p.T595M|MICAL2_ENST00000342902.5_Missense_Mutation_p.T595M	NM_001282663.1|NM_014632.2	NP_001269592.1|NP_055447.1	O94851	MICA2_HUMAN	microtubule associated monooxygenase, calponin and LIM domain containing 2	595	CH. {ECO:0000255|PROSITE- ProRule:PRU00044}.				actin filament depolymerization (GO:0030042)|cytoskeleton organization (GO:0007010)|heart development (GO:0007507)|heart looping (GO:0001947)|oxidation-reduction process (GO:0055114)|positive regulation of transcription via serum response element binding (GO:0010735)|sulfur oxidation (GO:0019417)	nucleus (GO:0005634)	actin binding (GO:0003779)|FAD binding (GO:0071949)|NADPH:sulfur oxidoreductase activity (GO:0043914)|oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, NAD(P)H as one donor, and incorporation of one atom of oxygen (GO:0016709)|zinc ion binding (GO:0008270)			breast(2)|central_nervous_system(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(6)|lung(12)|ovary(2)|prostate(2)|skin(3)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(4)	47				Epithelial(150;0.00552)		CCAGTGACCACGGGCAAAGAG	0.547																																					p.T595M		Atlas-SNP	.											MICAL2,NS,haematopoietic_neoplasm,0,1	MICAL2	114	1	0			c.C1784T						PASS	.						135.0	123.0	127.0					11																	12247813		2201	4294	6495	SO:0001583	missense	9645	exon14			TGACCACGGGCAA	AB018293	CCDS7809.1, CCDS60726.1, CCDS60727.1, CCDS60728.1	11p15.3	2014-08-12	2013-03-26		ENSG00000133816	ENSG00000133816			24693	protein-coding gene	gene with protein product		608881				12110185	Standard	XM_005253249		Approved	KIAA0750	uc001mjz.3	O94851	OTTHUMG00000165744	ENST00000256194.4:c.1784C>T	11.37:g.12247813C>T	ENSP00000256194:p.Thr595Met	95.0	0.0	0		124.0	5.0	0.0403226	NM_014632	B4DGZ0|B7Z849|D3DQW5|G3XAC8|Q5KTR3|Q5KTR4|Q7Z3A8	Missense_Mutation	SNP	ENST00000256194.4	37	CCDS7809.1	.	.	.	.	.	.	.	.	.	.	C	25.9	4.684033	0.88639	.	.	ENSG00000133816	ENST00000537344;ENST00000544073;ENST00000256194;ENST00000527546;ENST00000342902;ENST00000379612	D;D;D;D;D	0.95588	-3.75;-3.75;-3.75;-3.75;-3.75	5.28	5.28	0.74379	Calponin homology domain (5);	0.062767	0.64402	D	0.000008	D	0.98074	0.9365	M	0.88450	2.955	0.80722	D	1	D;D;D;D;D	0.89917	1.0;1.0;1.0;1.0;0.999	D;D;D;D;D	0.76575	0.98;0.979;0.984;0.983;0.988	D	0.99019	1.0817	10	0.87932	D	0	.	18.526	0.90973	0.0:1.0:0.0:0.0	.	595;595;595;595;595	G3XAC8;B7Z849;Q5KTR3;Q5KTR4;O94851	.;.;.;.;MICA2_HUMAN	M	595;128;595;595;595;595	ENSP00000441689:T595M;ENSP00000256194:T595M;ENSP00000433965:T595M;ENSP00000344894:T595M;ENSP00000368932:T595M	ENSP00000256194:T595M	T	+	2	0	MICAL2	12204389	1.000000	0.71417	0.968000	0.41197	0.895000	0.52256	7.818000	0.86416	2.466000	0.83321	0.563000	0.77884	ACG	.	.	none		0.547	MICAL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000385993.1	NM_014632	
GCNT1	2650	hgsc.bcm.edu	37	9	79118400	79118400	+	Missense_Mutation	SNP	C	C	T	rs147866228	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr9:79118400C>T	ENST00000376730.4	+	4	1586	c.1103C>T	c.(1102-1104)cCc>cTc	p.P368L	GCNT1_ENST00000444201.2_Missense_Mutation_p.P368L|GCNT1_ENST00000536223.1_Missense_Mutation_p.P368L|GCNT1_ENST00000442371.1_Missense_Mutation_p.P368L	NM_001097636.1|NM_001490.4	NP_001091105.1|NP_001481.2	Q02742	GCNT1_HUMAN	glucosaminyl (N-acetyl) transferase 1, core 2	368	Catalytic. {ECO:0000250}.				cell adhesion molecule production (GO:0060352)|cellular protein metabolic process (GO:0044267)|glycoprotein biosynthetic process (GO:0009101)|kidney morphogenesis (GO:0060993)|leukocyte tethering or rolling (GO:0050901)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)|response to insulin (GO:0032868)|tissue morphogenesis (GO:0048729)	extracellular space (GO:0005615)|Golgi cisterna (GO:0031985)|Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)|trans-Golgi network (GO:0005802)	beta-1,3-galactosyl-O-glycosyl-glycoprotein beta-1,6-N-acetylglucosaminyltransferase activity (GO:0003829)			breast(2)|central_nervous_system(1)|endometrium(4)|kidney(3)|large_intestine(6)|lung(11)|prostate(2)|urinary_tract(1)	30						AAGGGTGCTCCCTACCCGCCC	0.522													C|||	10	0.00199681	0.0015	0.0029	5008	,	,		13880	0.0		0.006	False		,,,				2504	0.0				p.P368L		Atlas-SNP	.											.	GCNT1	52	.	0			c.C1103T						PASS	.	C	LEU/PRO,LEU/PRO,LEU/PRO,LEU/PRO,LEU/PRO	6,4400	12.9+/-30.5	0,6,2197	110.0	92.0	98.0		1103,1103,1103,1103,1103	5.3	1.0	9	dbSNP_134	98	89,8511	50.6+/-110.7	0,89,4211	yes	missense,missense,missense,missense,missense	GCNT1	NM_001097633.1,NM_001097634.1,NM_001097635.1,NM_001097636.1,NM_001490.4	98,98,98,98,98	0,95,6408	TT,TC,CC		1.0349,0.1362,0.7304	probably-damaging,probably-damaging,probably-damaging,probably-damaging,probably-damaging	368/429,368/429,368/429,368/429,368/429	79118400	95,12911	2203	4300	6503	SO:0001583	missense	2650	exon4			GTGCTCCCTACCC	L41415	CCDS6653.1	9q13	2013-02-25	2010-03-16		ENSG00000187210	ENSG00000187210	2.4.1.102	"""Glucosaminyl (N-acetyl) transferase and xylosyltransferase family"""	4203	protein-coding gene	gene with protein product	"""core 2 beta1,6 N-acetylglucosaminyltransferase-I"", ""beta-1,3-galactosyl-O-glycosyl-glycoprotein beta-1,6-N--acetylglucosaminyltransferase"""	600391	"""glucosaminyl (N-acetyl) transferase 1, core 2 (beta-1,6-N-acetylglucosaminyltransferase)"""	NACGT2		8449405, 9915862	Standard	NM_001490		Approved	C2GNT, NAGCT2	uc004akf.4	Q02742	OTTHUMG00000020044	ENST00000376730.4:c.1103C>T	9.37:g.79118400C>T	ENSP00000365920:p.Pro368Leu	182.0	0.0	0		258.0	129.0	0.5	NM_001490	Q6DJZ4	Missense_Mutation	SNP	ENST00000376730.4	37	CCDS6653.1	8	0.003663003663003663	2	0.0040650406504065045	0	0.0	0	0.0	6	0.0079155672823219	c	14.65	2.600144	0.46423	0.001362	0.010349	ENSG00000187210	ENST00000536223;ENST00000442371;ENST00000444201;ENST00000376730	T;T;T;T	0.11169	2.8;2.8;2.8;2.8	6.17	5.28	0.74379	.	0.179527	0.50627	D	0.000111	T	0.28995	0.0720	M	0.82823	2.61	0.58432	D	0.999996	D	0.89917	1.0	D	0.97110	1.0	T	0.16070	-1.0415	9	.	.	.	1.2848	15.5517	0.76158	0.0:0.9345:0.0:0.0655	.	368	Q02742	GCNT1_HUMAN	L	368	ENSP00000440883:P368L;ENSP00000415454:P368L;ENSP00000390703:P368L;ENSP00000365920:P368L	.	P	+	2	0	GCNT1	78308220	0.432000	0.25554	0.987000	0.45799	0.047000	0.14425	2.020000	0.41010	1.635000	0.50512	0.655000	0.94253	CCC	C|0.994;T|0.006	0.006	strong		0.522	GCNT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052725.1	NM_001097634	
ELP6	54859	hgsc.bcm.edu	37	3	47545911	47545911	+	Missense_Mutation	SNP	G	G	A	rs377204125		TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr3:47545911G>A	ENST00000296149.4	-	4	402	c.232C>T	c.(232-234)Cgt>Tgt	p.R78C	ELP6_ENST00000446787.1_Missense_Mutation_p.R5C|ELP6_ENST00000439305.1_Missense_Mutation_p.R5C	NM_001031703.2	NP_001026873.2	Q0PNE2	ELP6_HUMAN	elongator acetyltransferase complex subunit 6	78					chromatin organization (GO:0006325)|positive regulation of cell migration (GO:0030335)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	Elongator holoenzyme complex (GO:0033588)											AGCTGCCCACGCTCCCGCGCC	0.542																																					p.R78C		Atlas-SNP	.											.	.	.	.	0			c.C232T						PASS	.	G	CYS/ARG	0,4072		0,0,2036	57.0	61.0	60.0		232	2.1	0.0	3		60	1,8375		0,1,4187	no	missense	C3orf75	NM_001031703.2	180	0,1,6223	AA,AG,GG		0.0119,0.0,0.0080	benign	78/267	47545911	1,12447	2036	4188	6224	SO:0001583	missense	54859	exon4			GCCCACGCTCCCG	AK000218	CCDS43082.1	3p21.31	2012-08-14	2012-08-08	2012-08-08	ENSG00000163832	ENSG00000163832		"""Elongator acetyltransferase complex subunits"""	25976	protein-coding gene	gene with protein product		615020	"""transmembrane protein 103"", ""chromosome 3 open reading frame 75"""	TMEM103, C3orf75		22854966	Standard	XM_005265241		Approved	FLJ20211	uc003crk.3	Q0PNE2	OTTHUMG00000133521	ENST00000296149.4:c.232C>T	3.37:g.47545911G>A	ENSP00000296149:p.Arg78Cys	25.0	0.0	0		33.0	13.0	0.393939	NM_001031703	Q9BW57|Q9NXJ3	Missense_Mutation	SNP	ENST00000296149.4	37	CCDS43082.1	.	.	.	.	.	.	.	.	.	.	G	12.69	2.012549	0.35511	0.0	1.19E-4	ENSG00000163832	ENST00000296149;ENST00000450051;ENST00000446787;ENST00000439305;ENST00000412761;ENST00000444760;ENST00000425291;ENST00000449409;ENST00000414236	.	.	.	6.06	2.13	0.27403	.	0.296215	0.40064	N	0.001181	T	0.27489	0.0675	L	0.41027	1.25	0.09310	N	0.999998	B;B;B	0.25351	0.061;0.124;0.052	B;B;B	0.23018	0.019;0.043;0.027	T	0.21381	-1.0247	9	0.56958	D	0.05	-0.5247	2.3576	0.04300	0.2284:0.1263:0.5154:0.1298	.	54;78;78	B4DP60;C9JAS1;Q0PNE2	.;.;CC075_HUMAN	C	78;54;5;5;5;5;5;5;5	.	ENSP00000296149:R78C	R	-	1	0	C3orf75	47520915	0.001000	0.12720	0.012000	0.15200	0.638000	0.38207	0.871000	0.28023	0.398000	0.25338	0.655000	0.94253	CGT	.	.	weak		0.542	ELP6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257493.1	NM_017713	
DUSP10	11221	hgsc.bcm.edu	37	1	221912334	221912334	+	Silent	SNP	T	T	G	rs35552569	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr1:221912334T>G	ENST00000366899.3	-	2	991	c.753A>C	c.(751-753)ccA>ccC	p.P251P	DUSP10_ENST00000323825.3_Intron|DUSP10_ENST00000544095.1_5'Flank|DUSP10_ENST00000468085.1_5'Flank	NM_007207.4	NP_009138.1	Q9Y6W6	DUS10_HUMAN	dual specificity phosphatase 10	251	Rhodanese. {ECO:0000255|PROSITE- ProRule:PRU00173}.				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 respiratory burst involved in inflammatory response (GO:0060266)|oligodendrocyte differentiation (GO:0048709)|protein dephosphorylation (GO:0006470)|regulation of adaptive immune response (GO:0002819)|response to lipopolysaccharide (GO:0032496)|response to stress (GO:0006950)	cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|nucleus (GO:0005634)	MAP kinase phosphatase activity (GO:0033549)|MAP kinase tyrosine/serine/threonine phosphatase activity (GO:0017017)|phosphatase activity (GO:0016791)|phosphoprotein phosphatase activity (GO:0004721)|protein tyrosine phosphatase activity (GO:0004725)|protein tyrosine/serine/threonine phosphatase activity (GO:0008138)			NS(1)|endometrium(6)|kidney(1)|large_intestine(6)|lung(16)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	36				GBM - Glioblastoma multiforme(131;0.0103)		CTATGTGAAGTGGCTGGGAGG	0.483													T|||	4	0.000798722	0.0	0.0	5008	,	,		21697	0.0		0.004	False		,,,				2504	0.0				p.P251P		Atlas-SNP	.											.	DUSP10	64	.	0			c.A753C						PASS	.	T	,	5,4401	9.9+/-24.2	0,5,2198	162.0	167.0	165.0		753,	-1.2	0.9	1	dbSNP_126	165	52,8548	32.8+/-85.7	1,50,4249	no	coding-synonymous,intron	DUSP10	NM_007207.4,NM_144729.2	,	1,55,6447	GG,GT,TT		0.6047,0.1135,0.4383	,	251/483,	221912334	57,12949	2203	4300	6503	SO:0001819	synonymous_variant	11221	exon2			GTGAAGTGGCTGG	AB026436	CCDS1528.1	1q41	2011-06-09			ENSG00000143507	ENSG00000143507		"""Protein tyrosine phosphatases / Class I Cys-based PTPs : MAP kinase phosphatases"""	3065	protein-coding gene	gene with protein product		608867				10391943, 10597297	Standard	NM_007207		Approved	MKP-5, MKP5	uc001hmy.2	Q9Y6W6	OTTHUMG00000037269	ENST00000366899.3:c.753A>C	1.37:g.221912334T>G		230.0	0.0	0		235.0	102.0	0.434043	NM_007207	D3DTB4|Q6GSI4|Q9H9Z5	Silent	SNP	ENST00000366899.3	37	CCDS1528.1																																																																																			T|0.997;G|0.003	0.003	strong		0.483	DUSP10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000090716.1	NM_007207	
SFTPA1	653509	hgsc.bcm.edu	37	10	81373810	81373810	+	Missense_Mutation	SNP	G	G	A	rs548998131		TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr10:81373810G>A	ENST00000398636.3	+	6	826	c.688G>A	c.(688-690)Gat>Aat	p.D230N	SFTPA1_ENST00000372313.5_Missense_Mutation_p.D171N|SFTPA1_ENST00000419470.2_Missense_Mutation_p.D245N|SFTPA1_ENST00000428376.2_Missense_Mutation_p.D230N|SFTPA1_ENST00000372308.3_Missense_Mutation_p.D230N	NM_001164644.1|NM_001164646.1|NM_005411.4	NP_001158116.1|NP_001158118.1|NP_005402.3	Q8IWL2	SFTA1_HUMAN	surfactant protein A1	230	C-type lectin. {ECO:0000255|PROSITE- ProRule:PRU00040}.				lipid transport (GO:0006869)|respiratory gaseous exchange (GO:0007585)	collagen trimer (GO:0005581)|extracellular region (GO:0005576)|proteinaceous extracellular matrix (GO:0005578)	carbohydrate binding (GO:0030246)|lipid transporter activity (GO:0005319)			endometrium(1)|lung(8)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	12	all_cancers(46;0.197)|Breast(12;0.000326)|Prostate(51;0.00985)|all_epithelial(25;0.0149)		Epithelial(14;0.00957)|all cancers(16;0.0179)|Colorectal(32;0.229)			GATGTACACAGATGGGCAGTG	0.572													g|||	1	0.000199681	0.0	0.0	5008	,	,		19728	0.0		0.001	False		,,,				2504	0.0				p.D245N		Atlas-SNP	.											.	SFTPA1	23	.	0			c.G733A						PASS	.						141.0	128.0	132.0					10																	81373810		2203	4296	6499	SO:0001583	missense	653509	exon6			TACACAGATGGGC	BC026229	CCDS44444.1, CCDS44445.1, CCDS44444.2	10q22.3	2012-11-02	2008-08-26			ENSG00000122852		"""Collectins"""	10798	protein-coding gene	gene with protein product	"""surfactant, pulmonary-associated protein A1A"""	178630	"""surfactant, pulmonary-associated protein A1"""	SFTP1			Standard	NM_001093770		Approved	SP-A, SP-A1, COLEC4	uc009xry.3	Q8IWL2		ENST00000398636.3:c.688G>A	10.37:g.81373810G>A	ENSP00000381633:p.Asp230Asn	419.0	0.0	0		432.0	218.0	0.50463	NM_001093770	A8K3T8|B7ZW50|E3VLD8|E3VLD9|E3VLE0|E3VLE1|G5E9J3|P07714|Q14DV4|Q5RIR5|Q5RIR7|Q6PIT0|Q8TC19	Missense_Mutation	SNP	ENST00000398636.3	37	CCDS44445.1	.	.	.	.	.	.	.	.	.	.	.	11.71	1.719016	0.30503	.	.	ENSG00000122852	ENST00000372308;ENST00000398636;ENST00000428376;ENST00000372313;ENST00000419470;ENST00000394569	T;T;T;T;T	0.56776	0.44;0.44;0.44;0.44;0.44	2.89	1.98	0.26296	C-type lectin fold (2);C-type lectin, conserved site (2);C-type lectin-like (2);C-type lectin (6);	0.072464	0.56097	N	0.000034	T	0.61714	0.2369	L	0.52823	1.66	0.40129	D	0.976696	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.97110	1.0;1.0;0.999	T	0.59337	-0.7473	10	0.40728	T	0.16	-9.4297	7.9528	0.30025	0.1308:0.0:0.8692:0.0	.	230;245;230	Q8IWL1;G5E9J3;Q8IWL2	SFPA2_HUMAN;.;SFTA1_HUMAN	N	230;230;230;171;245;230	ENSP00000361382:D230N;ENSP00000381633:D230N;ENSP00000411102:D230N;ENSP00000361387:D171N;ENSP00000397082:D245N	ENSP00000361382:D230N	D	+	1	0	SFTPA1	81043816	0.998000	0.40836	0.905000	0.35620	0.045000	0.14185	2.629000	0.46485	0.783000	0.33636	0.297000	0.19635	GAT	.	.	none		0.572	SFTPA1-203	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding		NM_005411	
MON2	23041	hgsc.bcm.edu	37	12	62965212	62965212	+	Missense_Mutation	SNP	C	C	T			TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr12:62965212C>T	ENST00000393632.2	+	30	4755	c.4364C>T	c.(4363-4365)tCt>tTt	p.S1455F	MON2_ENST00000280379.6_Missense_Mutation_p.S1456F|MON2_ENST00000393629.2_Missense_Mutation_p.S1449F|MON2_ENST00000393630.3_Missense_Mutation_p.S1456F|MON2_ENST00000546600.1_Missense_Mutation_p.S1455F|MON2_ENST00000552738.1_Missense_Mutation_p.S1426F	NM_015026.2	NP_055841.2	Q7Z3U7	MON2_HUMAN	MON2 homolog (S. cerevisiae)	1455					actin cytoskeleton organization (GO:0030036)|Golgi to endosome transport (GO:0006895)|positive regulation of GTPase activity (GO:0043547)|protein transport (GO:0015031)|vesicle-mediated transport (GO:0016192)	extracellular vesicular exosome (GO:0070062)|trans-Golgi network (GO:0005802)	ARF guanyl-nucleotide exchange factor activity (GO:0005086)			NS(1)|breast(3)|central_nervous_system(2)|cervix(2)|endometrium(5)|kidney(3)|large_intestine(15)|lung(21)|ovary(2)|pancreas(1)|prostate(1)|upper_aerodigestive_tract(1)	57			BRCA - Breast invasive adenocarcinoma(9;0.218)	GBM - Glioblastoma multiforme(28;0.128)		TCCTGCCCTTCTGAAAGCACA	0.383																																					p.S1455F		Atlas-SNP	.											.	MON2	160	.	0			c.C4364T						PASS	.						129.0	135.0	133.0					12																	62965212		2203	4300	6503	SO:0001583	missense	23041	exon30			GCCCTTCTGAAAG		CCDS31849.1, CCDS61175.1, CCDS61177.1, CCDS61178.1	12q14.1	2014-08-12	2006-04-04		ENSG00000061987	ENSG00000061987			29177	protein-coding gene	gene with protein product			"""MON2 homolog (yeast)"""			16301316, 24285343	Standard	NM_015026		Approved	KIAA1040	uc001sre.3	Q7Z3U7	OTTHUMG00000169992	ENST00000393632.2:c.4364C>T	12.37:g.62965212C>T	ENSP00000377252:p.Ser1455Phe	113.0	0.0	0		100.0	4.0	0.04	NM_015026	A5D8U7|A7E2Y0|B9EGP5|F8VWA6|F8W1Z6|Q86TA2|Q8N3I5|Q8NAI0|Q8NHE2|Q9UPW1	Missense_Mutation	SNP	ENST00000393632.2	37	CCDS31849.1	.	.	.	.	.	.	.	.	.	.	C	25.1	4.607945	0.87258	.	.	ENSG00000061987	ENST00000393632;ENST00000393630;ENST00000280379;ENST00000546600;ENST00000552738;ENST00000393629	T;T;T;T;T;T	0.64260	-0.09;-0.09;-0.09;-0.09;-0.09;-0.09	5.49	4.6	0.57074	.	0.000000	0.85682	D	0.000000	T	0.73289	0.3568	L	0.58810	1.83	0.80722	D	1	D;D;D;D;D	0.71674	0.997;0.994;0.996;0.984;0.998	P;D;D;P;D	0.65773	0.868;0.938;0.938;0.809;0.938	T	0.73294	-0.4028	9	.	.	.	-15.3521	14.0268	0.64590	0.0:0.9272:0.0:0.0728	.	1449;1426;1455;324;1455	B9EGP5;F8VWA6;F8W1Z6;Q7Z3U7-3;Q7Z3U7-4	.;.;.;.;.	F	1455;1456;1456;1455;1426;1449	ENSP00000377252:S1455F;ENSP00000377250:S1456F;ENSP00000280379:S1456F;ENSP00000447407:S1455F;ENSP00000449215:S1426F;ENSP00000377249:S1449F	.	S	+	2	0	MON2	61251479	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	7.814000	0.86154	1.316000	0.45131	0.650000	0.86243	TCT	.	.	none		0.383	MON2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000406767.3	NM_015026	
SPTA1	6708	hgsc.bcm.edu	37	1	158604391	158604391	+	Missense_Mutation	SNP	T	T	C	rs16830483	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr1:158604391T>C	ENST00000368147.4	-	39	5687	c.5507A>G	c.(5506-5508)aAt>aGt	p.N1836S		NM_003126.2	NP_003117.2	P02549	SPTA1_HUMAN	spectrin, alpha, erythrocytic 1	1836			N -> S (in dbSNP:rs16830483).		actin filament capping (GO:0051693)|actin filament organization (GO:0007015)|axon guidance (GO:0007411)|hemopoiesis (GO:0030097)|lymphocyte homeostasis (GO:0002260)|plasma membrane organization (GO:0007009)|porphyrin-containing compound biosynthetic process (GO:0006779)|positive regulation of protein binding (GO:0032092)|positive regulation of T cell proliferation (GO:0042102)|regulation of cell shape (GO:0008360)	actin cytoskeleton (GO:0015629)|cuticular plate (GO:0032437)|cytosol (GO:0005829)|intrinsic component of the cytoplasmic side of the plasma membrane (GO:0031235)|spectrin (GO:0008091)|spectrin-associated cytoskeleton (GO:0014731)	actin filament binding (GO:0051015)|calcium ion binding (GO:0005509)|structural constituent of cytoskeleton (GO:0005200)			NS(3)|breast(7)|cervix(1)|endometrium(22)|kidney(9)|large_intestine(29)|liver(2)|lung(183)|ovary(5)|prostate(18)|skin(11)|soft_tissue(1)|stomach(1)|upper_aerodigestive_tract(9)|urinary_tract(6)	307	all_hematologic(112;0.0378)					ATTCTTTTCATTGATCCAAGC	0.423													T|||	270	0.0539137	0.1407	0.0303	5008	,	,		22090	0.0		0.0229	False		,,,				2504	0.0409				p.N1836S		Atlas-SNP	.											.	SPTA1	720	.	0			c.A5507G						PASS	.	T	SER/ASN	544,3370		27,490,1440	197.0	180.0	185.0		5507	1.4	0.1	1	dbSNP_123	185	125,8155		2,121,4017	yes	missense	SPTA1	NM_003126.2	46	29,611,5457	CC,CT,TT		1.5097,13.8988,5.4863	benign	1836/2420	158604391	669,11525	1957	4140	6097	SO:0001583	missense	6708	exon39			TTTTCATTGATCC	M61877	CCDS41423.1	1q21	2014-06-23	2014-06-23		ENSG00000163554	ENSG00000163554		"""EF-hand domain containing"""	11272	protein-coding gene	gene with protein product	"""elliptocytosis 2"""	182860	"""spectrin, alpha, erythrocytic 1 (elliptocytosis 2)"""				Standard	NM_003126		Approved	EL2	uc001fst.1	P02549	OTTHUMG00000019636	ENST00000368147.4:c.5507A>G	1.37:g.158604391T>C	ENSP00000357129:p.Asn1836Ser	134.0	0.0	0		135.0	68.0	0.503704	NM_003126	Q15514|Q5VYL1|Q5VYL2|Q6LDY5	Missense_Mutation	SNP	ENST00000368147.4	37	CCDS41423.1	101	0.04624542124542125	75	0.1524390243902439	10	0.027624309392265192	0	0.0	16	0.021108179419525065	T	10.38	1.332942	0.24167	0.138988	0.015097	ENSG00000163554	ENST00000368148;ENST00000368147	T;T	0.48836	0.8;0.8	5.64	1.39	0.22231	.	1.056520	0.07576	N	0.919371	T	0.05273	0.0140	N	0.03016	-0.435	0.19575	N	0.999963	B	0.09022	0.002	B	0.12156	0.007	T	0.36648	-0.9739	10	0.06365	T	0.9	.	3.7159	0.08438	0.0:0.4471:0.1822:0.3708	rs16830483;rs52794569;rs61613472;rs16830483	1836	P02549	SPTA1_HUMAN	S	1836	ENSP00000357130:N1836S;ENSP00000357129:N1836S	ENSP00000357129:N1836S	N	-	2	0	SPTA1	156871015	0.982000	0.34865	0.086000	0.20670	0.956000	0.61745	0.751000	0.26348	0.447000	0.26695	-0.248000	0.11899	AAT	T|0.947;C|0.053	0.053	strong		0.423	SPTA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051851.3	NM_003126	
NPTXR	23467	hgsc.bcm.edu	37	22	39222627	39222627	+	Missense_Mutation	SNP	G	G	A	rs34637063	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr22:39222627G>A	ENST00000333039.2	-	3	1099	c.976C>T	c.(976-978)Cgg>Tgg	p.R326W		NM_014293.3	NP_055108	O95502	NPTXR_HUMAN	neuronal pentraxin receptor	326	Pentaxin.					integral component of membrane (GO:0016021)	metal ion binding (GO:0046872)	p.R326W(1)		central_nervous_system(2)|large_intestine(3)|lung(6)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	14	Melanoma(58;0.04)					GACCTGGACCGCAGCCACATG	0.632													G|||	8	0.00159744	0.0	0.0	5008	,	,		18002	0.0		0.006	False		,,,				2504	0.002				p.R326W	Pancreas(139;2521 3281 36965)	Atlas-SNP	.											NPTXR,colon,carcinoma,0,2	NPTXR	34	2	1	Substitution - Missense(1)	prostate(1)	c.C976T						scavenged	.	G	TRP/ARG	4,4402	8.1+/-20.4	0,4,2199	78.0	71.0	73.0		976	4.6	1.0	22	dbSNP_126	73	42,8558	27.9+/-77.7	2,38,4260	yes	missense	NPTXR	NM_014293.3	101	2,42,6459	AA,AG,GG		0.4884,0.0908,0.3537	probably-damaging	326/501	39222627	46,12960	2203	4300	6503	SO:0001583	missense	23467	exon3			TGGACCGCAGCCA	AF052163	CCDS33647.1	22q13.1	2007-01-25			ENSG00000221890	ENSG00000221890			7954	protein-coding gene	gene with protein product		609474				16497176	Standard	NM_014293		Approved		uc003awk.3	O95502	OTTHUMG00000150458	ENST00000333039.2:c.976C>T	22.37:g.39222627G>A	ENSP00000327545:p.Arg326Trp	91.0	1.0	0.010989		109.0	58.0	0.53211	NM_014293		Missense_Mutation	SNP	ENST00000333039.2	37	CCDS33647.1	6	0.0027472527472527475	0	0.0	0	0.0	0	0.0	6	0.0079155672823219	G	21.8	4.196556	0.79015	9.08E-4	0.004884	ENSG00000221890	ENST00000333039	T	0.61627	0.09	4.64	4.64	0.57946	Concanavalin A-like lectin/glucanase (1);Concanavalin A-like lectin/glucanase, subgroup (1);	0.277072	0.35067	N	0.003476	T	0.67230	0.2871	M	0.79123	2.44	0.37765	D	0.926466	D	0.89917	1.0	D	0.75484	0.986	T	0.78892	-0.2025	9	0.87932	D	0	-56.6397	11.0963	0.48145	0.0:0.0:0.6934:0.3066	rs34637063	326	O95502	NPTXR_HUMAN	W	326	ENSP00000327545:R326W	ENSP00000327545:R326W	R	-	1	2	NPTXR	37552573	1.000000	0.71417	1.000000	0.80357	0.883000	0.51084	5.441000	0.66569	2.861000	0.98227	0.655000	0.94253	CGG	G|0.996;A|0.004	0.004	strong		0.632	NPTXR-001	KNOWN	non_ATG_start|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318194.2	NM_014293	
DNAH14	127602	hgsc.bcm.edu	37	1	225237950	225237950	+	Missense_Mutation	SNP	A	A	G	rs78320839	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr1:225237950A>G	ENST00000445597.2	+	12	1864	c.1864A>G	c.(1864-1866)Atc>Gtc	p.I622V	DNAH14_ENST00000439375.2_Missense_Mutation_p.I651V|DNAH14_ENST00000430092.1_Missense_Mutation_p.I651V			Q0VDD8	DYH14_HUMAN	dynein, axonemal, heavy chain 14	622					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						CCAGCTGTCTATCTTCATTGA	0.343													A|||	43	0.00858626	0.0008	0.0101	5008	,	,		16907	0.0129		0.007	False		,,,				2504	0.0153				p.I651V		Atlas-SNP	.											.	DNAH14	300	.	0			c.A1951G						PASS	.	A	VAL/ILE	2,1382		0,2,690	169.0	139.0	148.0		1951	-4.1	0.0	1	dbSNP_131	148	58,3124		1,56,1534	yes	missense	DNAH14	NM_001373.1	29	1,58,2224	GG,GA,AA		1.8228,0.1445,1.3141	benign	651/4516	225237950	60,4506	692	1591	2283	SO:0001583	missense	127602	exon16			CTGTCTATCTTCA	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.1864A>G	1.37:g.225237950A>G	ENSP00000409472:p.Ile622Val	186.0	0.0	0		193.0	84.0	0.435233	NM_001373	A6NG62|A6NNL2|Q0VDD9|Q4VXC7|Q4VXG4|Q4VXG5|Q5VU33|Q5VU34	Missense_Mutation	SNP	ENST00000445597.2	37		20	0.009157509157509158	1	0.0020325203252032522	6	0.016574585635359115	9	0.015734265734265736	4	0.005277044854881266	A	14.53	2.563703	0.45694	0.001445	0.018228	ENSG00000185842	ENST00000445597;ENST00000430092;ENST00000439375	T;T;T	0.27890	2.61;1.64;1.64	5.49	-4.13	0.03904	.	.	.	.	.	T	0.06050	0.0157	N	0.08118	0	0.09310	N	0.999998	B	0.10296	0.003	B	0.12156	0.007	T	0.32134	-0.9918	9	0.21014	T	0.42	.	7.8316	0.29347	0.4385:0.1253:0.4362:0.0	.	651	Q0VDD8-4	.	V	622;651;651	ENSP00000409472:I622V;ENSP00000414402:I651V;ENSP00000392061:I651V	ENSP00000414402:I651V	I	+	1	0	DNAH14	223304573	0.000000	0.05858	0.005000	0.12908	0.439000	0.31926	-1.628000	0.02031	-0.704000	0.05042	0.338000	0.21704	ATC	A|0.991;G|0.009	0.009	strong		0.343	DNAH14-007	PUTATIVE	basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000331217.3	XM_059166	
ZNF268	10795	hgsc.bcm.edu	37	12	133780033	133780033	+	Silent	SNP	C	C	T	rs189953075	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr12:133780033C>T	ENST00000536435.2	+	6	2091	c.1761C>T	c.(1759-1761)acC>acT	p.T587T	ZNF268_ENST00000542986.2_3'UTR|ZNF268_ENST00000541009.2_3'UTR|ZNF268_ENST00000537565.1_Silent_p.T426T|ZNF268_ENST00000536899.2_3'UTR|ZNF268_ENST00000228289.5_Silent_p.T587T	NM_001165885.1|NM_003415.2	NP_001159357.1|NP_003406.1	Q14587	ZN268_HUMAN	zinc finger protein 268	587					cell differentiation (GO:0030154)|cellular response to tumor necrosis factor (GO:0071356)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cell cycle arrest (GO:0071157)|negative regulation of cell proliferation (GO:0008285)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cell differentiation (GO:0045597)|positive regulation of cell migration (GO:0030335)|positive regulation of cell proliferation (GO:0008284)|positive regulation of protein catabolic process (GO:0045732)|positive regulation of protein homodimerization activity (GO:0090073)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription from RNA polymerase II promoter during mitosis (GO:0046022)|regulation of mitotic cell cycle (GO:0007346)|regulation of protein heterodimerization activity (GO:0043497)|regulation of transcription, DNA-templated (GO:0006355)|release of cytoplasmic sequestered NF-kappaB (GO:0008588)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			NS(2)|breast(3)|endometrium(4)|kidney(2)|large_intestine(2)|liver(2)|lung(7)|ovary(1)|skin(1)	24	all_neural(191;0.0982)|Medulloblastoma(191;0.163)	all_cancers(7;0.000215)|all_epithelial(31;0.096)		OV - Ovarian serous cystadenocarcinoma(86;3.58e-08)|Epithelial(86;6.6e-07)|all cancers(50;2.28e-05)		ATGAATGCACCGACTGTGGAA	0.438													C|||	20	0.00399361	0.0151	0.0	5008	,	,		20480	0.0		0.0	False		,,,				2504	0.0				p.T587T		Atlas-SNP	.											.	ZNF268	71	.	0			c.C1761T						PASS	.	C	,,,,,,,,	8,1376		0,8,684	44.0	42.0	42.0		1761,1512,,,,,,1761,	-1.4	0.0	12		42	0,3182		0,0,1591	no	coding-synonymous,coding-synonymous,utr-3,utr-3,utr-3,utr-3,utr-3,coding-synonymous,utr-3	ZNF268	NM_001165881.2,NM_001165882.2,NM_001165883.1,NM_001165884.2,NM_001165885.1,NM_001165886.1,NM_001165887.1,NM_003415.2,NM_152943.2	,,,,,,,,	0,8,2275	TT,TC,CC		0.0,0.578,0.1752	,,,,,,,,	587/948,504/865,,,,,,587/948,	133780033	8,4558	692	1591	2283	SO:0001819	synonymous_variant	10795	exon6			ATGCACCGACTGT	X78926	CCDS45012.1, CCDS53851.1, CCDS53852.1, CCDS53853.1, CCDS53854.1, CCDS59239.1, CCDS59240.1	12q24.33	2013-01-08				ENSG00000090612		"""Zinc fingers, C2H2-type"", ""-"""	13061	protein-coding gene	gene with protein product		604753				7865130	Standard	NM_003415		Approved	HZF3	uc010tcf.2	Q14587	OTTHUMG00000167946	ENST00000536435.2:c.1761C>T	12.37:g.133780033C>T		2.0	0.0	0		6.0	5.0	0.833333	NM_001165881	Q8TDG8|Q96RH4|Q9BZJ9	Silent	SNP	ENST00000536435.2	37	CCDS45012.1																																																																																			C|0.997;T|0.003	0.003	strong		0.438	ZNF268-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000397191.2	NM_152943	
AKR1C2	1646	hgsc.bcm.edu	37	10	5043747	5043747	+	Missense_Mutation	SNP	C	C	G	rs142672563	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr10:5043747C>G	ENST00000380753.4	-	2	398	c.211G>C	c.(211-213)Gat>Cat	p.D71H	AKR1C2_ENST00000455190.1_Missense_Mutation_p.D71H|AKR1C2_ENST00000407674.1_Missense_Mutation_p.D71H|AKR1C2_ENST00000421196.3_Missense_Mutation_p.D71H	NM_205845.2	NP_995317.1	P52895	AK1C2_HUMAN	aldo-keto reductase family 1, member C2	71					cellular response to jasmonic acid stimulus (GO:0071395)|daunorubicin metabolic process (GO:0044597)|digestion (GO:0007586)|doxorubicin metabolic process (GO:0044598)|epithelial cell differentiation (GO:0030855)|G-protein coupled receptor signaling pathway (GO:0007186)|oxidation-reduction process (GO:0055114)|positive regulation of cell proliferation (GO:0008284)|positive regulation of protein kinase B signaling (GO:0051897)|progesterone metabolic process (GO:0042448)|prostaglandin metabolic process (GO:0006693)|response to prostaglandin (GO:0034694)|steroid metabolic process (GO:0008202)	cytoplasm (GO:0005737)	alditol:NADP+ 1-oxidoreductase activity (GO:0004032)|bile acid binding (GO:0032052)|carboxylic acid binding (GO:0031406)|ketosteroid monooxygenase activity (GO:0047086)|oxidoreductase activity, acting on NAD(P)H, quinone or similar compound as acceptor (GO:0016655)|phenanthrene 9,10-monooxygenase activity (GO:0018636)|prostaglandin F receptor activity (GO:0004958)|trans-1,2-dihydrobenzene-1,2-diol dehydrogenase activity (GO:0047115)			breast(1)|large_intestine(5)|lung(3)|skin(1)	10					Ursodeoxycholic acid(DB01586)	ACACTGCCATCTGCAATCTTG	0.443													C|||	13	0.00259585	0.0008	0.0043	5008	,	,		21249	0.0		0.001	False		,,,				2504	0.0082				p.D71H		Atlas-SNP	.											.	AKR1C2	68	.	0			c.G211C						PASS	.	C	HIS/ASP,HIS/ASP,HIS/ASP	0,4406		0,0,2203	133.0	114.0	120.0		211,211,211	2.3	1.0	10	dbSNP_134	120	11,8583	8.4+/-32.0	0,11,4286	no	missense,missense,missense	AKR1C2	NM_001135241.1,NM_001354.4,NM_205845.1	81,81,81	0,11,6489	GG,GC,CC		0.128,0.0,0.0846	probably-damaging,probably-damaging,probably-damaging	71/140,71/324,71/324	5043747	11,12989	2203	4297	6500	SO:0001583	missense	1646	exon4			TGCCATCTGCAAT	L32592	CCDS7062.1, CCDS44350.1	10p15-p14	2014-01-29	2012-12-04		ENSG00000151632	ENSG00000151632	1.3.1.20, 1.1.1.213	"""Aldo-keto reductases"""	385	protein-coding gene	gene with protein product	"""dihydrodiol dehydrogenase 2; bile acid binding protein; 3-alpha hydroxysteroid dehydrogenase, type III"""	600450	"""aldo-keto reductase family 1, member C2 (dihydrodiol dehydrogenase 2; bile acid binding protein; 3-alpha hydroxysteroid dehydrogenase, type III)"", ""testicular 17,20-desmolase deficiency"""	DDH2, TDD		9716498, 21802064	Standard	NM_001354		Approved	DD, BABP, DD2, HAKRD, MCDR2	uc001iht.3	P52895	OTTHUMG00000017584	ENST00000380753.4:c.211G>C	10.37:g.5043747C>G	ENSP00000370129:p.Asp71His	274.0	0.0	0		327.0	158.0	0.48318	NM_001354	A8K2N9|B4DKR9|Q14133|Q5SR16|Q7M4N1|Q96A71	Missense_Mutation	SNP	ENST00000380753.4	37	CCDS7062.1	4	0.0018315018315018315	1	0.0020325203252032522	3	0.008287292817679558	0	0.0	0	0.0	C	12.09	1.834056	0.32421	0.0	0.00128	ENSG00000151632	ENST00000380753;ENST00000421196;ENST00000407674;ENST00000455190	T;T;T;T	0.53206	0.63;0.63;0.63;0.63	2.35	2.35	0.29111	NADP-dependent oxidoreductase domain (3);	0.000000	0.56097	D	0.000030	T	0.53769	0.1817	M	0.72894	2.215	0.35214	D	0.775386	D;D;D	0.64830	0.989;0.994;0.988	D;P;P	0.65010	0.931;0.846;0.908	T	0.71735	-0.4503	10	0.87932	D	0	.	10.778	0.46361	0.0:1.0:0.0:0.0	.	71;71;71	B4DKR9;B4DK69;P52895	.;.;AK1C2_HUMAN	H	71	ENSP00000370129:D71H;ENSP00000392694:D71H;ENSP00000385221:D71H;ENSP00000408440:D71H	ENSP00000370129:D71H	D	-	1	0	AKR1C2	5033747	0.999000	0.42202	0.971000	0.41717	0.309000	0.27889	4.461000	0.60115	1.601000	0.50113	0.205000	0.17691	GAT	C|0.998;G|0.002	0.002	strong		0.443	AKR1C2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000046531.1	NM_001354	
NF1	4763	hgsc.bcm.edu	37	17	29679401	29679401	+	Silent	SNP	A	A	G	rs55865524	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr17:29679401A>G	ENST00000358273.4	+	51	7967	c.7584A>G	c.(7582-7584)caA>caG	p.Q2528Q	NF1_ENST00000417592.2_Intron|NF1_ENST00000356175.3_Silent_p.Q2507Q|NF1_ENST00000444181.2_Silent_p.Q321Q	NM_001042492.2	NP_001035957.1	P21359	NF1_HUMAN	neurofibromin 1	2528					actin cytoskeleton organization (GO:0030036)|adrenal gland development (GO:0030325)|artery morphogenesis (GO:0048844)|brain development (GO:0007420)|camera-type eye morphogenesis (GO:0048593)|cell communication (GO:0007154)|cerebral cortex development (GO:0021987)|cognition (GO:0050890)|collagen fibril organization (GO:0030199)|extracellular matrix organization (GO:0030198)|extrinsic apoptotic signaling pathway via death domain receptors (GO:0008625)|forebrain astrocyte development (GO:0021897)|forebrain morphogenesis (GO:0048853)|heart development (GO:0007507)|liver development (GO:0001889)|MAPK cascade (GO:0000165)|metanephros development (GO:0001656)|myelination in peripheral nervous system (GO:0022011)|negative regulation of angiogenesis (GO:0016525)|negative regulation of astrocyte differentiation (GO:0048712)|negative regulation of cell migration (GO:0030336)|negative regulation of cell-matrix adhesion (GO:0001953)|negative regulation of endothelial cell proliferation (GO:0001937)|negative regulation of fibroblast proliferation (GO:0048147)|negative regulation of MAP kinase activity (GO:0043407)|negative regulation of MAPK cascade (GO:0043409)|negative regulation of neuroblast proliferation (GO:0007406)|negative regulation of neurotransmitter secretion (GO:0046929)|negative regulation of oligodendrocyte differentiation (GO:0048715)|negative regulation of osteoclast differentiation (GO:0045671)|negative regulation of protein kinase activity (GO:0006469)|negative regulation of Rac protein signal transduction (GO:0035021)|negative regulation of Ras protein signal transduction (GO:0046580)|negative regulation of transcription factor import into nucleus (GO:0042992)|neural tube development (GO:0021915)|osteoblast differentiation (GO:0001649)|peripheral nervous system development (GO:0007422)|phosphatidylinositol 3-kinase signaling (GO:0014065)|pigmentation (GO:0043473)|positive regulation of adenylate cyclase activity (GO:0045762)|positive regulation of apoptotic process (GO:0043065)|positive regulation of endothelial cell proliferation (GO:0001938)|positive regulation of extrinsic apoptotic signaling pathway in absence of ligand (GO:2001241)|positive regulation of extrinsic apoptotic signaling pathway via death domain receptors (GO:1902043)|positive regulation of neuron apoptotic process (GO:0043525)|positive regulation of Ras GTPase activity (GO:0032320)|Ras protein signal transduction (GO:0007265)|regulation of angiogenesis (GO:0045765)|regulation of blood vessel endothelial cell migration (GO:0043535)|regulation of bone resorption (GO:0045124)|regulation of cell-matrix adhesion (GO:0001952)|regulation of glial cell differentiation (GO:0045685)|regulation of long-term neuronal synaptic plasticity (GO:0048169)|regulation of Ras GTPase activity (GO:0032318)|regulation of synaptic transmission, GABAergic (GO:0032228)|response to hypoxia (GO:0001666)|Schwann cell development (GO:0014044)|skeletal muscle tissue development (GO:0007519)|smooth muscle tissue development (GO:0048745)|spinal cord development (GO:0021510)|sympathetic nervous system development (GO:0048485)|visual learning (GO:0008542)|wound healing (GO:0042060)	axon (GO:0030424)|cytoplasm (GO:0005737)|dendrite (GO:0030425)|intrinsic component of the cytoplasmic side of the plasma membrane (GO:0031235)|membrane (GO:0016020)|nucleus (GO:0005634)	phosphatidylcholine binding (GO:0031210)|phosphatidylethanolamine binding (GO:0008429)|Ras GTPase activator activity (GO:0005099)	p.0?(8)|p.?(3)	NF1/ACCN1(2)	autonomic_ganglia(12)|breast(11)|central_nervous_system(72)|cervix(6)|endometrium(12)|haematopoietic_and_lymphoid_tissue(59)|kidney(9)|large_intestine(39)|liver(1)|lung(80)|ovary(20)|pancreas(2)|prostate(2)|skin(8)|soft_tissue(249)|stomach(2)|thyroid(1)|upper_aerodigestive_tract(5)|urinary_tract(9)	599		all_cancers(10;1.29e-12)|all_epithelial(10;0.00347)|all_hematologic(16;0.00556)|Acute lymphoblastic leukemia(14;0.00593)|Breast(31;0.014)|Myeloproliferative disorder(56;0.0255)|all_lung(9;0.0321)|Lung NSC(157;0.0659)		UCEC - Uterine corpus endometrioid carcinoma (4;4.38e-05)|all cancers(4;1.64e-26)|Epithelial(4;9.15e-23)|OV - Ovarian serous cystadenocarcinoma(4;3.58e-21)|GBM - Glioblastoma multiforme(4;0.00146)		ACATGGGGCAACCTTCTCAGG	0.413			"""D, Mis, N, F, S, O"""		"""neurofibroma, glioma"""	"""neurofibroma, glioma"""			Neurofibromatosis, type 1	TCGA GBM(6;<1E-08)|TSP Lung(7;0.0071)|TCGA Ovarian(3;0.0088)			G|||	5	0.000998403	0.0023	0.0029	5008	,	,		14500	0.0		0.0	False		,,,				2504	0.0				p.Q2528Q		Atlas-SNP	.	yes	Rec	yes	Neurofibromatosis type 1	17	17q12	4763	neurofibromatosis type 1 gene		O	.	NF1	1586	.	11	Whole gene deletion(8)|Unknown(3)	soft_tissue(7)|autonomic_ganglia(2)|lung(1)|central_nervous_system(1)	c.A7584G						PASS	.	G	,	4,4402	825.7+/-416.5	0,4,2199	56.0	53.0	54.0		7521,7584	4.9	1.0	17	dbSNP_129	54	8,8592	818.9+/-406.8	0,8,4292	no	coding-synonymous,coding-synonymous	NF1	NM_000267.3,NM_001042492.2	,	0,12,6491	GG,GA,AA		0.093,0.0908,0.0923	,	2507/2819,2528/2840	29679401	12,12994	2203	4300	6503	SO:0001819	synonymous_variant	4763	exon51	Familial Cancer Database	NF1, von Recklinghausen disease, incl.: Hereditary Spinal Neurofibromatosis, Neurofibromatosis-Noonan syndrome	GGGGCAACCTTCT		CCDS11264.1, CCDS42292.1, CCDS45645.1	17q11.2	2014-09-17	2008-07-31		ENSG00000196712	ENSG00000196712			7765	protein-coding gene	gene with protein product	"""neurofibromatosis"", ""von Recklinghausen disease"", ""Watson disease"""	613113				1715669	Standard	NM_000267		Approved		uc002hgg.3	P21359	OTTHUMG00000132871	ENST00000358273.4:c.7584A>G	17.37:g.29679401A>G		119.0	0.0	0		121.0	66.0	0.545455	NM_001042492	O00662|Q14284|Q14930|Q14931|Q9UMK3	Silent	SNP	ENST00000358273.4	37	CCDS42292.1																																																																																			A|0.999;G|0.001	0.001	strong		0.413	NF1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000256351.2	NM_000267	
CPNE7	27132	hgsc.bcm.edu	37	16	89657630	89657630	+	Missense_Mutation	SNP	C	C	G	rs377056293		TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr16:89657630C>G	ENST00000268720.5	+	15	1619	c.1489C>G	c.(1489-1491)Cgc>Ggc	p.R497G	CPNE7_ENST00000319518.8_Missense_Mutation_p.R422G	NM_014427.4	NP_055242.1	Q9UBL6	CPNE7_HUMAN	copine VII	497	VWFA. {ECO:0000255|PROSITE- ProRule:PRU00219}.				lipid metabolic process (GO:0006629)|transport (GO:0006810)	extracellular vesicular exosome (GO:0070062)	transporter activity (GO:0005215)			breast(1)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|lung(8)|ovary(2)	17		all_hematologic(23;0.0748)		all cancers(4;3.63e-08)|OV - Ovarian serous cystadenocarcinoma(4;1.7e-06)|BRCA - Breast invasive adenocarcinoma(80;0.0147)		CAAGGTGGCACGCGTGGCGGC	0.687																																					p.R497G		Atlas-SNP	.											.	CPNE7	56	.	0			c.C1489G						PASS	.						18.0	20.0	19.0					16																	89657630		2183	4285	6468	SO:0001583	missense	27132	exon15			GTGGCACGCGTGG	AJ133798	CCDS10980.1, CCDS10981.1	16q24.3	2008-07-03			ENSG00000178773	ENSG00000178773			2320	protein-coding gene	gene with protein product		605689					Standard	NM_014427		Approved		uc002fnq.3	Q9UBL6	OTTHUMG00000138051	ENST00000268720.5:c.1489C>G	16.37:g.89657630C>G	ENSP00000268720:p.Arg497Gly	70.0	0.0	0		73.0	34.0	0.465753	NM_014427		Missense_Mutation	SNP	ENST00000268720.5	37	CCDS10980.1	.	.	.	.	.	.	.	.	.	.	C	12.45	1.940346	0.34283	.	.	ENSG00000178773	ENST00000319518;ENST00000268720;ENST00000529800	T;T;T	0.22945	1.93;1.93;1.93	3.9	1.73	0.24493	von Willebrand factor, type A (2);Copine (1);	0.305959	0.32161	N	0.006489	T	0.27697	0.0681	M	0.77313	2.365	0.38493	D	0.948011	P;B	0.36660	0.564;0.049	B;B	0.37304	0.246;0.087	T	0.14392	-1.0474	10	0.59425	D	0.04	0.9483	6.5897	0.22639	0.295:0.6139:0.0:0.0911	.	422;497	Q9UBL6-2;Q9UBL6	.;CPNE7_HUMAN	G	422;497;142	ENSP00000317374:R422G;ENSP00000268720:R497G;ENSP00000435876:R142G	ENSP00000268720:R497G	R	+	1	0	CPNE7	88185131	0.518000	0.26234	0.988000	0.46212	0.873000	0.50193	2.044000	0.41241	0.759000	0.33084	0.556000	0.70494	CGC	.	.	alt		0.687	CPNE7-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000269929.2		
POP1	10940	hgsc.bcm.edu	37	8	99146261	99146261	+	Missense_Mutation	SNP	A	A	G			TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr8:99146261A>G	ENST00000401707.2	+	6	901	c.820A>G	c.(820-822)Aca>Gca	p.T274A	POP1_ENST00000349693.3_Missense_Mutation_p.T274A	NM_001145860.1|NM_001145861.1	NP_001139332.1|NP_001139333.1	Q99575	POP1_HUMAN	processing of precursor 1, ribonuclease P/MRP subunit (S. cerevisiae)	274					RNA phosphodiester bond hydrolysis (GO:0090501)|RNA phosphodiester bond hydrolysis, endonucleolytic (GO:0090502)|tRNA 5'-leader removal (GO:0001682)|tRNA catabolic process (GO:0016078)	extracellular space (GO:0005615)|nucleolar ribonuclease P complex (GO:0005655)|ribonuclease MRP complex (GO:0000172)	poly(A) RNA binding (GO:0044822)|ribonuclease MRP activity (GO:0000171)|ribonuclease P activity (GO:0004526)			autonomic_ganglia(1)|breast(3)|endometrium(4)|large_intestine(9)|lung(15)|ovary(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	36	Breast(36;1.78e-06)		OV - Ovarian serous cystadenocarcinoma(57;0.145)			TAACATAGACACAGGTAAACT	0.338																																					p.T274A		Atlas-SNP	.											POP1,NS,carcinoma,0,1	POP1	85	1	0			c.A820G						PASS	.						136.0	133.0	134.0					8																	99146261		2203	4300	6503	SO:0001583	missense	10940	exon6			ATAGACACAGGTA	D31765	CCDS6277.1	8q22.2	2012-05-21			ENSG00000104356	ENSG00000104356			30129	protein-coding gene	gene with protein product	"""processing of precursors 1"""	602486				10199568, 8918471	Standard	NM_015029		Approved		uc011lgv.2	Q99575	OTTHUMG00000164635	ENST00000401707.2:c.820A>G	8.37:g.99146261A>G	ENSP00000385787:p.Thr274Ala	70.0	0.0	0		73.0	39.0	0.534247	NM_001145860	A8K5W9|Q15037	Missense_Mutation	SNP	ENST00000401707.2	37	CCDS6277.1	.	.	.	.	.	.	.	.	.	.	A	7.548	0.662067	0.14645	.	.	ENSG00000104356	ENST00000401707;ENST00000349693	T;T	0.35236	1.32;1.32	5.51	0.307	0.15811	.	0.441525	0.24174	N	0.040879	T	0.15912	0.0383	N	0.13235	0.315	0.36378	D	0.861726	B	0.02656	0.0	B	0.04013	0.001	T	0.37407	-0.9707	10	0.05525	T	0.97	0.0715	9.807	0.40799	0.6459:0.0:0.3541:0.0	.	274	Q99575	POP1_HUMAN	A	274	ENSP00000385787:T274A;ENSP00000339529:T274A	ENSP00000339529:T274A	T	+	1	0	POP1	99215437	0.205000	0.23458	0.931000	0.37212	0.838000	0.47535	0.840000	0.27600	-0.165000	0.10908	0.260000	0.18958	ACA	.	.	none		0.338	POP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000379470.1	NM_015029	
TMEM101	84336	hgsc.bcm.edu	37	17	42092267	42092267	+	Silent	SNP	C	C	T	rs35301047	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr17:42092267C>T	ENST00000589334.1	-	2	369	c.54G>A	c.(52-54)ttG>ttA	p.L18L	TMEM101_ENST00000587529.1_Silent_p.L18L|TMEM101_ENST00000206380.3_Silent_p.L18L|TMEM101_ENST00000542039.1_Intron			Q96IK0	TM101_HUMAN	transmembrane protein 101	18					positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|signal transduction (GO:0007165)	integral component of membrane (GO:0016021)	signal transducer activity (GO:0004871)			central_nervous_system(1)|endometrium(1)|large_intestine(2)|lung(2)|upper_aerodigestive_tract(1)	7		Breast(137;0.0264)|Prostate(33;0.0861)		BRCA - Breast invasive adenocarcinoma(366;0.113)		GCACCGAACCCAACTGCATGA	0.612													C|||	43	0.00858626	0.025	0.0058	5008	,	,		18733	0.0		0.005	False		,,,				2504	0.001				p.L18L		Atlas-SNP	.											.	TMEM101	18	.	0			c.G54A						PASS	.	C		126,4280	93.9+/-132.6	1,124,2078	102.0	90.0	94.0		54	4.7	1.0	17	dbSNP_126	94	65,8535	40.3+/-97.0	1,63,4236	no	coding-synonymous	TMEM101	NM_032376.2		2,187,6314	TT,TC,CC		0.7558,2.8597,1.4686		18/258	42092267	191,12815	2203	4300	6503	SO:0001819	synonymous_variant	84336	exon1			CGAACCCAACTGC	AK172826	CCDS11474.1	17q21.31	2005-12-16							28653	protein-coding gene	gene with protein product						12761501	Standard	NM_032376		Approved	MGC4251, FLJ23987	uc002ieu.3	Q96IK0		ENST00000589334.1:c.54G>A	17.37:g.42092267C>T		223.0	0.0	0		243.0	102.0	0.419753	NM_032376	B2R9N6	Silent	SNP	ENST00000589334.1	37	CCDS11474.1																																																																																			C|0.988;T|0.012	0.012	strong		0.612	TMEM101-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000457665.1	NM_032376	
KAL1	3730	hgsc.bcm.edu	37	X	8538659	8538659	+	Missense_Mutation	SNP	A	A	C			TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chrX:8538659A>C	ENST00000262648.3	-	7	1092	c.943T>G	c.(943-945)Tgg>Ggg	p.W315G		NM_000216.2	NP_000207.2	P23352	KALM_HUMAN	Kallmann syndrome 1 sequence	315	Fibronectin type-III 2. {ECO:0000255|PROSITE-ProRule:PRU00316}.				axon guidance (GO:0007411)|cell adhesion (GO:0007155)|cellular component movement (GO:0006928)|chemotaxis (GO:0006935)	extracellular space (GO:0005615)|plasma membrane (GO:0005886)|proteinaceous extracellular matrix (GO:0005578)	extracellular matrix structural constituent (GO:0005201)|heparin binding (GO:0008201)|serine-type endopeptidase inhibitor activity (GO:0004867)			breast(3)|cervix(1)|endometrium(6)|kidney(1)|large_intestine(6)|liver(1)|lung(6)|ovary(3)|pancreas(1)|skin(3)|urinary_tract(1)	32						GGGAGATCCCAAACTATAGTG	0.542																																					p.W315G		Atlas-SNP	.											.	KAL1	78	.	0			c.T943G						PASS	.						81.0	60.0	67.0					X																	8538659		2203	4300	6503	SO:0001583	missense	3730	exon7			GATCCCAAACTAT		CCDS14130.1	Xp22.32	2013-02-11			ENSG00000011201	ENSG00000011201		"""WAP four-disulfide core domain containing"", ""Fibronectin type III domain containing"""	6211	protein-coding gene	gene with protein product	"""anosmin-1"", ""WAP four-disulfide core domain 19"""	300836		KAL, ADMLX		11463336	Standard	NM_000216		Approved	KALIG-1, WFDC19	uc004csf.3	P23352	OTTHUMG00000021107	ENST00000262648.3:c.943T>G	X.37:g.8538659A>C	ENSP00000262648:p.Trp315Gly	166.0	0.0	0		218.0	9.0	0.0412844	NM_000216	B2RPF8	Missense_Mutation	SNP	ENST00000262648.3	37	CCDS14130.1	.	.	.	.	.	.	.	.	.	.	A	12.48	1.950679	0.34377	.	.	ENSG00000011201	ENST00000262648	D	0.86297	-2.1	4.11	4.11	0.48088	Fibronectin, type III (4);Immunoglobulin-like fold (1);	0.125962	0.64402	D	0.000019	D	0.92034	0.7476	M	0.73962	2.25	0.80722	D	1	D	0.71674	0.998	D	0.69824	0.966	D	0.92526	0.6029	10	0.87932	D	0	-9.6393	11.7793	0.52003	1.0:0.0:0.0:0.0	.	315	P23352	KALM_HUMAN	G	315	ENSP00000262648:W315G	ENSP00000262648:W315G	W	-	1	0	KAL1	8498659	1.000000	0.71417	0.464000	0.27143	0.040000	0.13550	7.362000	0.79507	1.356000	0.45884	0.352000	0.21897	TGG	.	.	none		0.542	KAL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055692.1	NM_000216	
TMEM132D	121256	hgsc.bcm.edu	37	12	130387850	130387850	+	Missense_Mutation	SNP	T	T	A	rs142888394	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr12:130387850T>A	ENST00000422113.2	-	1	361	c.35A>T	c.(34-36)cAc>cTc	p.H12L		NM_133448.2	NP_597705.2	Q14C87	T132D_HUMAN	transmembrane protein 132D	12					negative regulation of phosphatase activity (GO:0010923)	integral component of membrane (GO:0016021)				NS(1)|breast(6)|cervix(2)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(33)|liver(1)|lung(69)|ovary(10)|pancreas(2)|prostate(2)|skin(7)|upper_aerodigestive_tract(5)|urinary_tract(2)	152	all_neural(191;0.101)|Medulloblastoma(191;0.163)	all_epithelial(31;0.0934)|Breast(359;0.133)		OV - Ovarian serous cystadenocarcinoma(86;0.000288)|Epithelial(86;0.0116)|all cancers(50;0.0246)		CGGCGACCAGTGGTGCCACAG	0.672													T|||	27	0.00539137	0.0008	0.0043	5008	,	,		12817	0.001		0.0099	False		,,,				2504	0.0123				p.H12L		Atlas-SNP	.											.	TMEM132D	299	.	0			c.A35T						PASS	.	T	LEU/HIS	8,4268		0,8,2130	30.0	29.0	29.0		35	-4.3	0.3	12	dbSNP_134	29	70,8242		1,68,4087	yes	missense	TMEM132D	NM_133448.2	99	1,76,6217	AA,AT,TT		0.8422,0.1871,0.6196	benign	12/1100	130387850	78,12510	2138	4156	6294	SO:0001583	missense	121256	exon1			GACCAGTGGTGCC	AB061814	CCDS9266.1	12q24.32-q24.33	2014-06-13			ENSG00000151952	ENSG00000151952			29411	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 153"""	611257				11853319, 12966072	Standard	NM_133448		Approved	KIAA1944, MOLT, PPP1R153	uc009zyl.1	Q14C87	OTTHUMG00000168400	ENST00000422113.2:c.35A>T	12.37:g.130387850T>A	ENSP00000408581:p.His12Leu	166.0	0.0	0		180.0	95.0	0.527778	NM_133448	Q14C96|Q76M59|Q8N1W9|Q8N3Q5|Q8TF57	Missense_Mutation	SNP	ENST00000422113.2	37	CCDS9266.1	10	0.004578754578754579	1	0.0020325203252032522	2	0.0055248618784530384	0	0.0	7	0.009234828496042216	T	4.656	0.122035	0.08931	0.001871	0.008422	ENSG00000151952	ENST00000422113	T	0.03553	3.89	5.2	-4.27	0.03744	.	0.452778	0.19129	N	0.121962	T	0.00637	0.0021	N	0.01352	-0.895	0.09310	N	0.999993	B	0.02656	0.0	B	0.04013	0.001	T	0.41016	-0.9532	9	.	.	.	-15.177	0.934	0.01340	0.4633:0.173:0.1254:0.2384	.	12	Q14C87	T132D_HUMAN	L	12	ENSP00000408581:H12L	.	H	-	2	0	TMEM132D	128953803	0.070000	0.21116	0.312000	0.25196	0.737000	0.42083	0.050000	0.14120	-0.792000	0.04480	0.482000	0.46254	CAC	T|0.996;A|0.004	0.004	strong		0.672	TMEM132D-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000399592.1	NM_133448	
C2orf43	60526	hgsc.bcm.edu	37	2	20974586	20974586	+	Missense_Mutation	SNP	C	C	T	rs114010802	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr2:20974586C>T	ENST00000237822.3	-	4	531	c.452G>A	c.(451-453)cGa>cAa	p.R151Q	C2orf43_ENST00000381090.3_Missense_Mutation_p.R151Q|C2orf43_ENST00000435420.2_Missense_Mutation_p.R103Q|C2orf43_ENST00000541941.1_Missense_Mutation_p.R21Q|C2orf43_ENST00000403006.2_Missense_Mutation_p.R21Q|C2orf43_ENST00000440866.2_Missense_Mutation_p.R151Q	NM_001282721.1|NM_021925.2	NP_001269650.1|NP_068744.1	Q9H6V9	CB043_HUMAN	chromosome 2 open reading frame 43	151										endometrium(1)|kidney(1)|large_intestine(1)|lung(2)|stomach(1)	6	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)					CTCAGGGACTCGCTTCAGCAT	0.483													C|||	20	0.00399361	0.0008	0.0043	5008	,	,		19497	0.0		0.0159	False		,,,				2504	0.0				p.R151Q		Atlas-SNP	.											.	C2orf43	28	.	0			c.G452A						PASS	.	C	GLN/ARG	10,4396	16.8+/-37.8	0,10,2193	169.0	155.0	160.0		452	-5.1	0.0	2	dbSNP_132	160	71,8529	42.6+/-100.3	0,71,4229	yes	missense	C2orf43	NM_021925.2	43	0,81,6422	TT,TC,CC		0.8256,0.227,0.6228	probably-damaging	151/326	20974586	81,12925	2203	4300	6503	SO:0001583	missense	60526	exon4			GGGACTCGCTTCA	AK025473	CCDS1702.1, CCDS62864.1, CCDS74488.1, CCDS74489.1	2p24.1	2014-02-07			ENSG00000118961	ENSG00000118961			26145	protein-coding gene	gene with protein product		613570				17135363, 24357060	Standard	NM_001282723		Approved	FLJ21820	uc002rec.3	Q9H6V9	OTTHUMG00000122097	ENST00000237822.3:c.452G>A	2.37:g.20974586C>T	ENSP00000237822:p.Arg151Gln	203.0	0.0	0		202.0	102.0	0.504951	NM_021925	B7ZA47|B7ZAJ5|D6W530|E7ESN0|Q53T37|Q53T58	Missense_Mutation	SNP	ENST00000237822.3	37	CCDS1702.1	17	0.007783882783882784	1	0.0020325203252032522	4	0.011049723756906077	0	0.0	12	0.0158311345646438	C	11.34	1.610511	0.28712	0.00227	0.008256	ENSG00000118961	ENST00000403006;ENST00000381090;ENST00000237822;ENST00000435420;ENST00000440866;ENST00000541941;ENST00000432947;ENST00000412261	T;T;T;T	0.71817	0.86;1.47;0.86;-0.6	5.73	-5.05	0.02955	.	0.589533	0.17377	N	0.176450	T	0.34832	0.0911	L	0.52759	1.655	0.24725	N	0.99312	P;P;B;B;P;P	0.45396	0.857;0.798;0.141;0.141;0.485;0.636	B;B;B;B;B;B	0.35859	0.176;0.179;0.013;0.013;0.212;0.206	T	0.45234	-0.9275	10	0.48119	T	0.1	-0.0561	5.7365	0.18069	0.3052:0.4799:0.0:0.2149	.	109;151;103;109;151;151	B4DS38;B4DRG3;B7ZAJ5;B4DWE2;Q9H6V9;B5MDU6	.;.;.;.;CB043_HUMAN;.	Q	21;151;151;103;151;21;21;103	ENSP00000384267:R21Q;ENSP00000388635:R103Q;ENSP00000440570:R21Q;ENSP00000396911:R21Q	ENSP00000237822:R151Q	R	-	2	0	C2orf43	20838067	0.000000	0.05858	0.001000	0.08648	0.035000	0.12851	-0.373000	0.07494	-1.306000	0.02324	-0.157000	0.13467	CGA	C|0.993;T|0.007	0.007	strong		0.483	C2orf43-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000242861.1	NM_021925	
FAM83E	54854	hgsc.bcm.edu	37	19	49107039	49107039	+	Silent	SNP	G	G	T	rs201027346	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr19:49107039G>T	ENST00000263266.3	-	4	1077	c.888C>A	c.(886-888)ccC>ccA	p.P296P	SPACA4_ENST00000321762.1_5'Flank	NM_017708.3	NP_060178.2	Q2M2I3	FA83E_HUMAN	family with sequence similarity 83, member E	296										NS(1)|endometrium(2)|large_intestine(1)|lung(3)|ovary(1)|urinary_tract(2)	10		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;0.000102)|all cancers(93;0.000117)|GBM - Glioblastoma multiforme(486;0.00627)|Epithelial(262;0.0158)		AGGGTTTCTGGGGGGGCGCAG	0.721																																					p.P296P		Atlas-SNP	.											.	FAM83E	34	.	0			c.C888A						PASS	.	G		0,3978		0,0,1989	12.0	13.0	13.0		888	1.2	0.0	19		13	2,8210		0,2,4104	no	coding-synonymous	FAM83E	NM_017708.3		0,2,6093	TT,TG,GG		0.0244,0.0,0.0164		296/479	49107039	2,12188	1989	4106	6095	SO:0001819	synonymous_variant	54854	exon4			TTTCTGGGGGGGC	AK000207	CCDS42587.1	19q13.33	2013-10-24			ENSG00000105523	ENSG00000105523			25972	protein-coding gene	gene with protein product							Standard	NM_017708		Approved	FLJ20200	uc002pjn.2	Q2M2I3	OTTHUMG00000183315	ENST00000263266.3:c.888C>A	19.37:g.49107039G>T		48.0	0.0	0		63.0	32.0	0.507937	NM_017708	Q9NXK1	Silent	SNP	ENST00000263266.3	37	CCDS42587.1																																																																																			G|0.999;T|0.001	0.001	weak		0.721	FAM83E-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466145.1	NM_017708	
MMP27	64066	hgsc.bcm.edu	37	11	102575442	102575442	+	Missense_Mutation	SNP	C	C	T	rs553456217		TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr11:102575442C>T	ENST00000260229.4	-	2	258	c.167G>A	c.(166-168)aGg>aAg	p.R56K		NM_022122.2	NP_071405.2	Q9H306	MMP27_HUMAN	matrix metallopeptidase 27	56					collagen catabolic process (GO:0030574)	proteinaceous extracellular matrix (GO:0005578)	calcium ion binding (GO:0005509)|metalloendopeptidase activity (GO:0004222)|zinc ion binding (GO:0008270)			NS(1)|breast(2)|central_nervous_system(1)|cervix(1)|endometrium(2)|kidney(1)|large_intestine(4)|liver(2)|lung(12)|ovary(2)|prostate(2)|skin(11)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	45	all_cancers(8;0.000843)|all_epithelial(12;0.00362)|Lung NSC(15;0.21)	all_hematologic(158;0.00092)|Acute lymphoblastic leukemia(157;0.000967)	Epithelial(9;0.0509)|Lung(13;0.0696)|LUSC - Lung squamous cell carcinoma(19;0.13)|all cancers(10;0.176)	BRCA - Breast invasive adenocarcinoma(274;0.0151)	Marimastat(DB00786)	TATGAGACTCCTATTCTTGCT	0.383																																					p.R56K		Atlas-SNP	.											.	MMP27	84	.	0			c.G167A						PASS	.						74.0	72.0	73.0					11																	102575442		2203	4299	6502	SO:0001583	missense	64066	exon2			AGACTCCTATTCT	AF195192	CCDS8319.1	11q24	2008-07-18	2005-08-08		ENSG00000137675	ENSG00000137675			14250	protein-coding gene	gene with protein product	"""matrix metalloprotease 27"""		"""matrix metalloproteinase 27"""			10419448	Standard	NM_022122		Approved		uc001phd.1	Q9H306	OTTHUMG00000168099	ENST00000260229.4:c.167G>A	11.37:g.102575442C>T	ENSP00000260229:p.Arg56Lys	80.0	0.0	0		91.0	38.0	0.417582	NM_022122	Q6UWK6	Missense_Mutation	SNP	ENST00000260229.4	37	CCDS8319.1	.	.	.	.	.	.	.	.	.	.	C	1.324	-0.598646	0.03744	.	.	ENSG00000137675	ENST00000260229	T	0.36340	1.26	5.55	1.43	0.22495	Peptidoglycan binding-like (2);Metallopeptidase, catalytic domain (1);	0.764123	0.12270	N	0.483911	T	0.13628	0.0330	N	0.08118	0	0.09310	N	1	B	0.02656	0.0	B	0.08055	0.003	T	0.29518	-1.0009	10	0.10111	T	0.7	.	2.5257	0.04690	0.1265:0.4691:0.1116:0.2928	.	56	Q9H306	MMP27_HUMAN	K	56	ENSP00000260229:R56K	ENSP00000260229:R56K	R	-	2	0	MMP27	102080652	0.000000	0.05858	0.610000	0.28997	0.014000	0.08584	-0.364000	0.07583	0.473000	0.27368	0.591000	0.81541	AGG	.	.	none		0.383	MMP27-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000398128.1	NM_022122	
FBXW5	54461	hgsc.bcm.edu	37	9	139835725	139835725	+	Missense_Mutation	SNP	C	C	T	rs374757784		TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr9:139835725C>T	ENST00000325285.3	-	8	1514	c.1435G>A	c.(1435-1437)Gtc>Atc	p.V479I	FBXW5_ENST00000483559.1_5'UTR	NM_018998.3	NP_061871.1	Q969U6	FBXW5_HUMAN	F-box and WD repeat domain containing 5	479					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)		TCCCTGCTGACGTCCAGGAAG	0.697																																					p.V479I		Atlas-SNP	.											.	FBXW5	36	.	0			c.G1435A						PASS	.	C	ILE/VAL	0,4404		0,0,2202	32.0	27.0	29.0		1435	4.2	1.0	9		29	1,8595	1.2+/-3.3	0,1,4297	no	missense	FBXW5	NM_018998.2	29	0,1,6499	TT,TC,CC		0.0116,0.0,0.0077	probably-damaging	479/567	139835725	1,12999	2202	4298	6500	SO:0001583	missense	54461	exon8			TGCTGACGTCCAG	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.1435G>A	9.37:g.139835725C>T	ENSP00000313034:p.Val479Ile	16.0	0.0	0		24.0	13.0	0.541667	NM_018998	B2RDZ6|Q59ET5|Q5SPZ8|Q5SPZ9|Q5SQ00|Q5SQ02|Q5SQ03|Q5SQ04|Q8WY79|Q96GJ6|Q9BSU8|Q9H6A8|Q9HBQ6|Q9NSZ3	Missense_Mutation	SNP	ENST00000325285.3	37	CCDS7014.1	.	.	.	.	.	.	.	.	.	.	C	20.5	4.002574	0.74932	0.0	1.16E-4	ENSG00000159069	ENST00000325285	T	0.65732	-0.17	4.24	4.24	0.50183	WD40/YVTN repeat-like-containing domain (1);Soluble quinoprotein glucose/sorbosone dehydrogenase (1);	0.000000	0.85682	D	0.000000	T	0.73118	0.3546	L	0.54323	1.7	0.80722	D	1	D;P	0.76494	0.999;0.751	D;B	0.72982	0.979;0.106	T	0.69401	-0.5155	10	0.21540	T	0.41	-10.464	16.8298	0.85941	0.0:1.0:0.0:0.0	.	344;479	Q59ET5;Q969U6	.;FBXW5_HUMAN	I	479	ENSP00000313034:V479I	ENSP00000313034:V479I	V	-	1	0	FBXW5	138955546	1.000000	0.71417	0.985000	0.45067	0.964000	0.63967	7.002000	0.76304	2.204000	0.70986	0.561000	0.74099	GTC	.	.	weak		0.697	FBXW5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055227.1	NM_018998	
TEKT5	146279	hgsc.bcm.edu	37	16	10788219	10788219	+	Missense_Mutation	SNP	G	G	A	rs141349037	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr16:10788219G>A	ENST00000283025.2	-	1	583	c.512C>T	c.(511-513)aCg>aTg	p.T171M	RP11-109M19.1_ENST00000576710.1_RNA	NM_144674.1	NP_653275.1	Q96M29	TEKT5_HUMAN	tektin 5	171						cilium (GO:0005929)|cytoplasm (GO:0005737)|microtubule (GO:0005874)|nucleus (GO:0005634)				breast(2)|cervix(1)|endometrium(2)|kidney(2)|large_intestine(9)|lung(9)|ovary(2)|prostate(2)|skin(1)|upper_aerodigestive_tract(4)	34						CCTCTTGACCGTCTCCAAGTT	0.597													G|||	3	0.000599042	0.0	0.0	5008	,	,		18281	0.0		0.002	False		,,,				2504	0.001				p.T171M		Atlas-SNP	.											.	TEKT5	66	.	0			c.C512T						PASS	.	G	MET/THR	1,4393	2.1+/-5.4	0,1,2196	140.0	152.0	148.0		512	-1.3	0.0	16	dbSNP_134	148	9,8591	7.1+/-27.0	0,9,4291	yes	missense	TEKT5	NM_144674.1	81	0,10,6487	AA,AG,GG		0.1047,0.0228,0.077	possibly-damaging	171/486	10788219	10,12984	2197	4300	6497	SO:0001583	missense	146279	exon1			TTGACCGTCTCCA		CCDS10542.1	16p13.13	2014-01-21			ENSG00000153060	ENSG00000153060			26554	protein-coding gene	gene with protein product							Standard	NM_144674		Approved	FLJ32871, CT149	uc002czz.1	Q96M29	OTTHUMG00000129750	ENST00000283025.2:c.512C>T	16.37:g.10788219G>A	ENSP00000283025:p.Thr171Met	77.0	0.0	0		80.0	26.0	0.325	NM_144674	A1L3Z3	Missense_Mutation	SNP	ENST00000283025.2	37	CCDS10542.1	1	4.578754578754579E-4	0	0.0	0	0.0	0	0.0	1	0.0013192612137203166	G	6.721	0.501787	0.12822	2.28E-4	0.001047	ENSG00000153060	ENST00000283025	T	0.02631	4.22	5.63	-1.29	0.09288	.	0.388807	0.24722	N	0.036122	T	0.03305	0.0096	L	0.59436	1.845	0.09310	N	1	B	0.31968	0.349	B	0.38020	0.263	T	0.35992	-0.9766	10	0.52906	T	0.07	-7.5255	1.0994	0.01680	0.2102:0.1177:0.3104:0.3617	.	171	Q96M29	TEKT5_HUMAN	M	171	ENSP00000283025:T171M	ENSP00000283025:T171M	T	-	2	0	TEKT5	10695720	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	0.881000	0.28173	-0.203000	0.10251	-0.143000	0.13931	ACG	G|0.999;A|0.001	0.001	strong		0.597	TEKT5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251963.1	NM_144674	
RGS7	6000	hgsc.bcm.edu	37	1	240975229	240975229	+	Silent	SNP	C	C	T			TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr1:240975229C>T	ENST00000407727.1	-	13	1070	c.1071G>A	c.(1069-1071)tcG>tcA	p.S357S	RGS7_ENST00000331110.7_Silent_p.S331S|RGS7_ENST00000348120.2_Silent_p.S304S|RGS7_ENST00000366563.1_Silent_p.S357S|RGS7_ENST00000401882.1_Silent_p.S304S|RGS7_ENST00000366565.1_Silent_p.S357S|RGS7_ENST00000366562.4_Silent_p.S357S|RGS7_ENST00000446183.2_Silent_p.S273S|RGS7_ENST00000366564.1_Silent_p.S357S			P49802	RGS7_HUMAN	regulator of G-protein signaling 7	357	RGS. {ECO:0000255|PROSITE- ProRule:PRU00171}.				G-protein coupled receptor signaling pathway (GO:0007186)|intracellular signal transduction (GO:0035556)|positive regulation of GTPase activity (GO:0043547)|termination of G-protein coupled receptor signaling pathway (GO:0038032)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|dendrite terminus (GO:0044292)|heterotrimeric G-protein complex (GO:0005834)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	G-protein beta-subunit binding (GO:0031681)|GTPase activator activity (GO:0005096)|signal transducer activity (GO:0004871)			breast(1)|endometrium(2)|kidney(4)|large_intestine(6)|lung(51)|ovary(4)|prostate(2)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	76		all_cancers(173;0.0131)	OV - Ovarian serous cystadenocarcinoma(106;0.027)			TTAAATTTTCCGAGCTGAATT	0.393																																					p.S357S		Atlas-SNP	.											RGS7_ENST00000366565,right_upper_lobe,carcinoma,-1,2	RGS7	308	2	0			c.G1071A						PASS	.						68.0	72.0	71.0					1																	240975229		2203	4299	6502	SO:0001819	synonymous_variant	6000	exon14			ATTTTCCGAGCTG	BC022009	CCDS31071.1, CCDS60457.1, CCDS60458.1, CCDS60459.1	1q43	2008-02-05	2007-08-14		ENSG00000182901	ENSG00000182901		"""Regulators of G-protein signaling"""	10003	protein-coding gene	gene with protein product		602517	"""regulator of G-protein signalling 7"""			8548815	Standard	XM_005273218		Approved		uc001hyv.2	P49802	OTTHUMG00000040107	ENST00000407727.1:c.1071G>A	1.37:g.240975229C>T		69.0	0.0	0		76.0	30.0	0.394737	NM_002924	Q5T3H4|Q8TD66|Q8TD67|Q8WW09|Q9UNU7|Q9Y6B9	Silent	SNP	ENST00000407727.1	37																																																																																				.	.	none		0.393	RGS7-204	KNOWN	basic	protein_coding	protein_coding		NM_002924	
COL3A1	1281	hgsc.bcm.edu	37	2	189862995	189862995	+	Silent	SNP	T	T	C	rs41263757	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr2:189862995T>C	ENST00000304636.3	+	28	2097	c.1927T>C	c.(1927-1929)Ttg>Ctg	p.L643L	COL3A1_ENST00000317840.5_Silent_p.L643L	NM_000090.3	NP_000081	P02461	CO3A1_HUMAN	collagen, type III, alpha 1	643	Triple-helical region.				aging (GO:0007568)|axon guidance (GO:0007411)|blood vessel development (GO:0001568)|cell-matrix adhesion (GO:0007160)|cellular response to amino acid stimulus (GO:0071230)|cerebral cortex development (GO:0021987)|collagen catabolic process (GO:0030574)|collagen fibril organization (GO:0030199)|digestive tract development (GO:0048565)|extracellular fibril organization (GO:0043206)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|heart development (GO:0007507)|integrin-mediated signaling pathway (GO:0007229)|negative regulation of immune response (GO:0050777)|negative regulation of neuron migration (GO:2001223)|peptide cross-linking (GO:0018149)|platelet activation (GO:0030168)|positive regulation of Rho protein signal transduction (GO:0035025)|response to cytokine (GO:0034097)|response to mechanical stimulus (GO:0009612)|response to radiation (GO:0009314)|skeletal system development (GO:0001501)|skin development (GO:0043588)|transforming growth factor beta receptor signaling pathway (GO:0007179)|wound healing (GO:0042060)	collagen type III trimer (GO:0005586)|endoplasmic reticulum lumen (GO:0005788)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)	extracellular matrix structural constituent (GO:0005201)|integrin binding (GO:0005178)|metal ion binding (GO:0046872)|platelet-derived growth factor binding (GO:0048407)			NS(2)|breast(1)|central_nervous_system(7)|cervix(1)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(17)|lung(60)|ovary(4)|pancreas(1)|prostate(5)|skin(10)|upper_aerodigestive_tract(3)|urinary_tract(3)	126			OV - Ovarian serous cystadenocarcinoma(117;0.0106)|Epithelial(96;0.141)		Collagenase(DB00048)	TTTCTAGGGCTTGCCTGGTAC	0.353													T|||	9	0.00179712	0.0	0.0014	5008	,	,		15368	0.0		0.008	False		,,,				2504	0.0				p.L643L		Atlas-SNP	.											.	COL3A1	292	.	0			c.T1927C						PASS	.	T		0,4406		0,0,2203	65.0	68.0	67.0		1927	-3.8	0.6	2	dbSNP_127	67	20,8580	14.0+/-48.4	0,20,4280	no	coding-synonymous	COL3A1	NM_000090.3		0,20,6483	CC,CT,TT		0.2326,0.0,0.1538		643/1467	189862995	20,12986	2203	4300	6503	SO:0001819	synonymous_variant	1281	exon28			TAGGGCTTGCCTG	X15332	CCDS2297.1	2q32.2	2014-09-17	2008-06-23		ENSG00000168542	ENSG00000168542		"""Collagens"""	2201	protein-coding gene	gene with protein product		120180	"""Ehlers-Danlos syndrome type IV, autosomal dominant"""	EDS4A		2780304, 2834369	Standard	NM_000090		Approved		uc002uqj.1	P02461	OTTHUMG00000132648	ENST00000304636.3:c.1927T>C	2.37:g.189862995T>C		76.0	0.0	0		102.0	47.0	0.460784	NM_000090	D2JYH5|D3DPH4|P78429|Q15112|Q16403|Q53S91|Q541P8|Q6LDB3|Q6LDJ2|Q6LDJ3|Q7KZ56|Q8N6U4|Q9UC88|Q9UC89|Q9UC90|Q9UC91|R4N3C5|V9GZI1	Silent	SNP	ENST00000304636.3	37	CCDS2297.1																																																																																			T|0.998;C|0.002	0.002	strong		0.353	COL3A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255899.3	NM_000090	
MUC16	94025	hgsc.bcm.edu	37	19	9091771	9091771	+	Missense_Mutation	SNP	C	C	T	rs375862521		TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr19:9091771C>T	ENST00000397910.4	-	1	247	c.44G>A	c.(43-45)cGc>cAc	p.R15H		NM_024690.2	NP_078966.2	Q8WXI7	MUC16_HUMAN	mucin 16, cell surface associated	15	Thr-rich.				cell adhesion (GO:0007155)|cellular protein metabolic process (GO:0044267)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	extracellular vesicular exosome (GO:0070062)|extrinsic component of membrane (GO:0019898)|Golgi lumen (GO:0005796)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|vesicle (GO:0031982)				NS(9)|autonomic_ganglia(1)|breast(26)|central_nervous_system(11)|cervix(1)|endometrium(46)|haematopoietic_and_lymphoid_tissue(5)|kidney(35)|large_intestine(91)|liver(1)|lung(278)|ovary(17)|pancreas(2)|prostate(17)|skin(18)|soft_tissue(1)|stomach(8)|upper_aerodigestive_tract(16)|urinary_tract(7)	590						CATCAAGGAGCGGGTGGGAGA	0.532																																					p.R15H		Atlas-SNP	.											MUC16_ENST00000397910,NS,carcinoma,0,2	MUC16	4315	2	0			c.G44A						scavenged	.	C	HIS/ARG	1,4003		0,1,2001	76.0	73.0	74.0		44	-2.7	0.0	19		74	0,8326		0,0,4163	no	missense	MUC16	NM_024690.2	29	0,1,6164	TT,TC,CC		0.0,0.025,0.0081	benign	15/14508	9091771	1,12329	2002	4163	6165	SO:0001583	missense	94025	exon1			AAGGAGCGGGTGG	AF414442	CCDS54212.1	19p13.2	2008-02-05	2006-03-14			ENSG00000181143		"""Mucins"""	15582	protein-coding gene	gene with protein product		606154				11369781	Standard	XM_006722941		Approved	CA125, FLJ14303	uc002mkp.3	Q8WXI7		ENST00000397910.4:c.44G>A	19.37:g.9091771C>T	ENSP00000381008:p.Arg15His	153.0	1.0	0.00653595		144.0	62.0	0.430556	NM_024690	Q6ZQW5|Q96RK2	Missense_Mutation	SNP	ENST00000397910.4	37	CCDS54212.1	.	.	.	.	.	.	.	.	.	.	c	0.061	-1.224947	0.01530	2.5E-4	0.0	ENSG00000181143	ENST00000397910	T	0.02916	4.11	1.35	-2.7	0.06004	.	.	.	.	.	T	0.01421	0.0046	N	0.08118	0	.	.	.	B	0.02656	0.0	B	0.01281	0.0	T	0.47018	-0.9149	8	0.87932	D	0	.	0.3222	0.00305	0.1936:0.1814:0.2537:0.3713	.	15	B5ME49	.	H	15	ENSP00000381008:R15H	ENSP00000381008:R15H	R	-	2	0	MUC16	8952771	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-3.995000	0.00317	-2.527000	0.00494	-2.577000	0.00169	CGC	.	.	weak		0.532	MUC16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402806.1	NM_024690	
LRGUK	136332	hgsc.bcm.edu	37	7	133884016	133884016	+	Silent	SNP	C	C	T	rs61749958		TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr7:133884016C>T	ENST00000285928.2	+	14	1659	c.1590C>T	c.(1588-1590)atC>atT	p.I530I		NM_144648.1	NP_653249.1	Q96M69	LRGUK_HUMAN	leucine-rich repeats and guanylate kinase domain containing	530	Guanylate kinase-like. {ECO:0000255|PROSITE-ProRule:PRU00100}.					cytoplasm (GO:0005737)|nucleus (GO:0005634)	ATP binding (GO:0005524)|kinase activity (GO:0016301)			breast(1)|endometrium(2)|kidney(2)|large_intestine(12)|lung(23)|ovary(1)|prostate(1)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	49						CTCGTTATATCCTGGTGGTGC	0.368																																					p.I530I		Atlas-SNP	.											.	LRGUK	113	.	0			c.C1590T						PASS	.	C		0,4406		0,0,2203	93.0	98.0	96.0		1590	5.2	1.0	7	dbSNP_129	96	2,8598	2.2+/-6.3	0,2,4298	no	coding-synonymous	LRGUK	NM_144648.1		0,2,6501	TT,TC,CC		0.0233,0.0,0.0154		530/826	133884016	2,13004	2203	4300	6503	SO:0001819	synonymous_variant	136332	exon14			TTATATCCTGGTG	AK057348	CCDS5830.1	7q33	2006-10-27			ENSG00000155530	ENSG00000155530			21964	protein-coding gene	gene with protein product							Standard	NM_144648		Approved	FLJ32786	uc003vrm.1	Q96M69	OTTHUMG00000155320	ENST00000285928.2:c.1590C>T	7.37:g.133884016C>T		158.0	0.0	0		180.0	80.0	0.444444	NM_144648	Q2M3I1	Silent	SNP	ENST00000285928.2	37	CCDS5830.1																																																																																			C|1.000;T|0.000	0.000	weak		0.368	LRGUK-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000339442.1	NM_144648	
EPPK1	83481	hgsc.bcm.edu	37	8	144944379	144944379	+	Missense_Mutation	SNP	A	A	G			TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr8:144944379A>G	ENST00000525985.1	-	2	3114	c.3043T>C	c.(3043-3045)Ttc>Ctc	p.F1015L				P58107	EPIPL_HUMAN	epiplakin 1	1015						cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)	poly(A) RNA binding (GO:0044822)			NS(1)|autonomic_ganglia(1)|breast(1)|central_nervous_system(5)|cervix(1)|endometrium(8)|kidney(4)|large_intestine(2)|lung(30)|ovary(2)|pancreas(1)|prostate(10)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	71	all_cancers(97;1.42e-10)|all_epithelial(106;1.99e-09)|Lung NSC(106;0.000126)|all_lung(105;0.000354)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155)		OV - Ovarian serous cystadenocarcinoma(54;2.46e-41)|Epithelial(56;2.88e-40)|all cancers(56;1.82e-35)|Colorectal(110;0.055)|BRCA - Breast invasive adenocarcinoma(115;0.105)			TTCCCAGAGAAGGGGTCTCTG	0.637																																					p.F1015L		Atlas-SNP	.											.	EPPK1	199	.	0			c.T3043C						PASS	.						14.0	17.0	16.0					8																	144944379		2067	4201	6268	SO:0001583	missense	83481	exon1			CAGAGAAGGGGTC	AB051895	CCDS75800.1	8q24.3	2014-09-17				ENSG00000261150			15577	protein-coding gene	gene with protein product	"""epidermal autoantigen 450K"""	607553				11278896, 15671067	Standard	NM_031308		Approved	EPIPL1	uc003zaa.1	P58107		ENST00000525985.1:c.3043T>C	8.37:g.144944379A>G	ENSP00000436337:p.Phe1015Leu	68.0	0.0	0		68.0	32.0	0.470588	NM_031308	Q76E58|Q9NSU9	Missense_Mutation	SNP	ENST00000525985.1	37		.	.	.	.	.	.	.	.	.	.	A	22.5	4.295045	0.81025	.	.	ENSG00000227184	ENST00000525985	T	0.67523	-0.27	4.67	3.52	0.40303	.	.	.	.	.	T	0.51890	0.1701	L	0.39898	1.24	0.24399	N	0.994711	B	0.16166	0.016	B	0.10450	0.005	T	0.35649	-0.9780	9	0.09843	T	0.71	.	8.3157	0.32100	0.9051:0.0:0.0949:0.0	.	1015	E9PPU0	.	L	1015	ENSP00000436337:F1015L	ENSP00000436337:F1015L	F	-	1	0	EPPK1	145016367	1.000000	0.71417	0.481000	0.27354	0.918000	0.54935	6.916000	0.75776	0.809000	0.34255	0.533000	0.62120	TTC	.	.	none		0.637	EPPK1-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000382675.1	NM_031308	
ATG2B	55102	hgsc.bcm.edu	37	14	96829302	96829302	+	Silent	SNP	C	C	T	rs72706804	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr14:96829302C>T	ENST00000359933.4	-	1	905	c.12G>A	c.(10-12)ccG>ccA	p.P4P	GSKIP_ENST00000556095.1_5'Flank|GSKIP_ENST00000554182.1_5'Flank|GSKIP_ENST00000555181.1_5'Flank	NM_018036.5	NP_060506	Q96BY7	ATG2B_HUMAN	autophagy related 2B	4					autophagic vacuole assembly (GO:0000045)|cellular response to nitrogen starvation (GO:0006995)|mitochondrion degradation (GO:0000422)|nucleophagy (GO:0044804)	extrinsic component of membrane (GO:0019898)|lipid particle (GO:0005811)|pre-autophagosomal structure (GO:0000407)				breast(3)|cervix(2)|endometrium(7)|kidney(4)|large_intestine(11)|liver(1)|lung(26)|ovary(1)|prostate(1)|skin(1)|urinary_tract(7)	64		all_cancers(154;0.0462)|all_epithelial(191;0.123)|Melanoma(154;0.155)		Epithelial(152;0.21)|COAD - Colon adenocarcinoma(157;0.244)		ACTCCGAAAACGGCCAAGGCA	0.672													C|||	38	0.00758786	0.0008	0.013	5008	,	,		15753	0.001		0.0239	False		,,,				2504	0.0031				p.P4P		Atlas-SNP	.											.	ATG2B	169	.	0			c.G12A						PASS	.	C		17,4211		0,17,2097	52.0	56.0	54.0		12	0.9	0.7	14	dbSNP_130	54	195,8315		0,195,4060	no	coding-synonymous	ATG2B	NM_018036.5		0,212,6157	TT,TC,CC		2.2914,0.4021,1.6643		4/2079	96829302	212,12526	2114	4255	6369	SO:0001819	synonymous_variant	55102	exon1			CGAAAACGGCCAA	AK001104	CCDS9944.2	14q32.31	2014-02-12	2012-06-06	2007-07-31	ENSG00000066739	ENSG00000066739			20187	protein-coding gene	gene with protein product			"""chromosome 14 open reading frame 103"", ""ATG2 autophagy related 2 homolog B (S. cerevisiae)"""	C14orf103		22350415	Standard	NM_018036		Approved	FLJ10242	uc001yfi.3	Q96BY7	OTTHUMG00000149933	ENST00000359933.4:c.12G>A	14.37:g.96829302C>T		132.0	0.0	0		142.0	63.0	0.443662	NM_018036	Q6ZRE7|Q96DQ3|Q9NW80	Silent	SNP	ENST00000359933.4	37	CCDS9944.2																																																																																			C|0.986;T|0.014	0.014	strong		0.672	ATG2B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000314037.1	NM_018036	
FLT3	2322	hgsc.bcm.edu	37	13	28624294	28624294	+	Missense_Mutation	SNP	G	G	A	rs1933437	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr13:28624294G>A	ENST00000241453.7	-	6	761	c.680C>T	c.(679-681)aCg>aTg	p.T227M	FLT3_ENST00000380982.4_Missense_Mutation_p.T227M|FLT3_ENST00000537084.1_Missense_Mutation_p.T227M	NM_004119.2	NP_004110.2	P36888	FLT3_HUMAN	fms-related tyrosine kinase 3	227			T -> M (in dbSNP:rs1933437). {ECO:0000269|PubMed:15489334, ECO:0000269|PubMed:17344846, ECO:0000269|PubMed:8394751, ECO:0000269|Ref.4}.		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)	CCTTATGTCCGTCCCAAATAA	0.398			"""Mis, O"""		"""AML, ALL"""								G|||	2798	0.558706	0.2844	0.6066	5008	,	,		21258	0.7688		0.5805	False		,,,				2504	0.6564				p.T227M		Atlas-SNP	.		Dom	yes		13	13q12	2322	fms-related tyrosine kinase 3		L	.	FLT3	15525	.	0			c.C680T						PASS	.	G	MET/THR	1513,2893	481.0+/-359.0	264,985,954	162.0	136.0	145.0		680	3.8	0.6	13	dbSNP_92	145	5288,3312	646.4+/-400.3	1636,2016,648	yes	missense	FLT3	NM_004119.2	81	1900,3001,1602	AA,AG,GG		38.5116,34.3395,47.7087	probably-damaging	227/994	28624294	6801,6205	2203	4300	6503	SO:0001583	missense	2322	exon6			ATGTCCGTCCCAA	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.680C>T	13.37:g.28624294G>A	ENSP00000241453:p.Thr227Met	199.0	1.0	0.00502513		160.0	160.0	1	NM_004119	A0AVG9|B7ZLT7|B7ZLT8|F5H0A0|Q13414	Missense_Mutation	SNP	ENST00000241453.7	37	CCDS31953.1	1241	0.5682234432234432	150	0.3048780487804878	220	0.6077348066298343	431	0.7534965034965035	440	0.5804749340369393	G	12.45	1.941805	0.34283	0.343395	0.614884	ENSG00000122025	ENST00000241453;ENST00000380982;ENST00000537084	T;T;T	0.79749	-1.23;-1.3;-1.03	5.63	3.85	0.44370	.	0.166014	0.42821	D	0.000648	T	0.00012	0.0000	L	0.29908	0.895	0.32868	P	0.491131	D;D	0.76494	0.999;0.999	P;P	0.60789	0.879;0.743	T	0.48547	-0.9026	9	0.41790	T	0.15	.	11.1573	0.48495	0.0:0.1387:0.7168:0.1445	rs1933437;rs52828701;rs57444997;rs1933437	227;227	P36888-2;P36888	.;FLT3_HUMAN	M	227	ENSP00000241453:T227M;ENSP00000370369:T227M;ENSP00000438139:T227M	ENSP00000241453:T227M	T	-	2	0	FLT3	27522294	1.000000	0.71417	0.599000	0.28851	0.006000	0.05464	3.696000	0.54757	0.687000	0.31509	-0.311000	0.09066	ACG	G|0.465;A|0.535	0.535	strong		0.398	FLT3-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000044319.2		
FASTKD3	79072	hgsc.bcm.edu	37	5	7867027	7867027	+	Silent	SNP	A	A	G	rs77130393	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr5:7867027A>G	ENST00000264669.5	-	2	1306	c.1170T>C	c.(1168-1170)aaT>aaC	p.N390N	MTRR_ENST00000341013.6_5'Flank|MTRR_ENST00000264668.2_5'Flank|FASTKD3_ENST00000513658.1_Intron|MTRR_ENST00000440940.2_5'Flank|MTRR_ENST00000502509.1_Intron	NM_024091.3	NP_076996.2	Q14CZ7	FAKD3_HUMAN	FAST kinase domains 3	390					cellular respiration (GO:0045333)	mitochondrion (GO:0005739)	poly(A) RNA binding (GO:0044822)|protein kinase activity (GO:0004672)			breast(4)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(8)|liver(2)|lung(11)|ovary(2)|pancreas(1)|prostate(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	39						CTGCCACTGCATTGAGGATGG	0.438													A|||	32	0.00638978	0.0	0.0173	5008	,	,		18240	0.0		0.0189	False		,,,				2504	0.001				p.N390N		Atlas-SNP	.											.	FASTKD3	88	.	0			c.T1170C						PASS	.	A		24,4382	30.8+/-60.4	0,24,2179	63.0	64.0	63.0		1170	-5.6	0.0	5	dbSNP_134	63	199,8401	87.1+/-149.5	1,197,4102	no	coding-synonymous	FASTKD3	NM_024091.3		1,221,6281	GG,GA,AA		2.314,0.5447,1.7146		390/663	7867027	223,12783	2203	4300	6503	SO:0001819	synonymous_variant	79072	exon2			CACTGCATTGAGG	AK026927	CCDS3873.1	5p15.31	2008-02-05			ENSG00000124279	ENSG00000124279			28758	protein-coding gene	gene with protein product						12477932	Standard	NM_024091		Approved	MGC5297, FLJ23274	uc003jeb.3	Q14CZ7	OTTHUMG00000131029	ENST00000264669.5:c.1170T>C	5.37:g.7867027A>G		165.0	0.0	0		151.0	68.0	0.450331	NM_024091	Q9BVD3	Silent	SNP	ENST00000264669.5	37	CCDS3873.1																																																																																			A|0.984;G|0.016	0.016	strong		0.438	FASTKD3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253673.1	NM_024091	
VEZF1	7716	hgsc.bcm.edu	37	17	56056607	56056607	+	Silent	SNP	C	C	T	rs73995411|rs57786397|rs369163670	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr17:56056607C>T	ENST00000581208.1	-	5	1084	c.1044G>A	c.(1042-1044)caG>caA	p.Q348Q	VEZF1_ENST00000584396.1_Silent_p.Q339Q	NM_007146.2	NP_009077.2	Q14119	VEZF1_HUMAN	vascular endothelial zinc finger 1	348	Poly-Gln.				angiogenesis (GO:0001525)|cellular defense response (GO:0006968)|endothelial cell development (GO:0001885)|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)			breast(1)|endometrium(1)|kidney(2)|lung(5)|ovary(1)	10						gttgttgttgctgctgctgct	0.463																																					p.Q348Q		Atlas-SNP	.											VEZF1,caecum,carcinoma,0,3	VEZF1	50	3	0			c.G1044A						scavenged	.	C		287,4119	132.9+/-169.3	3,281,1919	144.0	136.0	139.0		1044	-2.6	0.3	17	dbSNP_130	139	56,8544	29.6+/-80.5	0,56,4244	no	coding-synonymous	VEZF1	NM_007146.2		3,337,6163	TT,TC,CC		0.6512,6.5138,2.6372		348/522	56056607	343,12663	2203	4300	6503	SO:0001819	synonymous_variant	7716	exon5			TTGTTGCTGCTGC	D28118	CCDS32687.1	17q22	2012-10-05	2006-08-16	2006-08-16	ENSG00000136451	ENSG00000136451		"""Zinc fingers, C2H2-type"""	12949	protein-coding gene	gene with protein product		606747	"""zinc finger protein 161"""	ZNF161		8035792	Standard	XM_005257643		Approved	DB1	uc002ivf.1	Q14119	OTTHUMG00000178777	ENST00000581208.1:c.1044G>A	17.37:g.56056607C>T		123.0	0.0	0		193.0	9.0	0.0466321	NM_007146		Silent	SNP	ENST00000581208.1	37	CCDS32687.1																																																																																			C|0.969;T|0.031	0.031	strong		0.463	VEZF1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000443321.1		
KRTAP13-4	284827	hgsc.bcm.edu	37	21	31803054	31803054	+	Missense_Mutation	SNP	G	G	A	rs999597	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr21:31803054G>A	ENST00000334068.2	+	1	483	c.461G>A	c.(460-462)cGc>cAc	p.R154H		NM_181600.1	NP_853631.1	Q3LI77	KR134_HUMAN	keratin associated protein 13-4	154			R -> H (in dbSNP:rs999597).			intermediate filament (GO:0005882)				NS(1)|breast(1)|kidney(1)|large_intestine(2)|lung(9)|skin(1)	15						TGTGGATCTCGCTTCTATCAA	0.433													-|||	62	0.0123802	0.0053	0.0274	5008	,	,		17173	0.002		0.0298	False		,,,				2504	0.0041				p.R154H	NSCLC(196;2401 3038 18004 35753)	Atlas-SNP	.											.	KRTAP13-4	46	.	0			c.G461A						PASS	.		HIS/ARG	30,4376		1,28,2174	92.0	95.0	94.0		461	0.4	0.0	21	dbSNP_86	94	280,8320		4,272,4024	yes	missense	KRTAP13-4	NM_181600.1	29	5,300,6198	AA,AG,GG		3.2558,0.6809,2.3835	possibly-damaging	154/161	31803054	310,12696	2203	4300	6503	SO:0001583	missense	284827	exon1			GATCTCGCTTCTA	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.461G>A	21.37:g.31803054G>A	ENSP00000334834:p.Arg154His	84.0	0.0	0		94.0	46.0	0.489362	NM_181600	A2RRL3	Missense_Mutation	SNP	ENST00000334068.2	37	CCDS13592.1	37	0.01694139194139194	3	0.006097560975609756	8	0.022099447513812154	2	0.0034965034965034965	24	0.0316622691292876	-	14.66	2.600639	0.46423	0.006809	0.032558	ENSG00000186971	ENST00000334068	T	0.03152	4.03	4.67	0.445	0.16597	.	0.318065	0.22031	N	0.065594	T	0.01092	0.0036	L	0.40543	1.245	0.09310	N	1	P	0.45011	0.848	B	0.41946	0.371	T	0.41752	-0.9491	10	0.66056	D	0.02	.	5.1511	0.15009	0.2002:0.3157:0.4841:0.0	rs999597;rs52799706;rs999597	154	Q3LI77	KR134_HUMAN	H	154	ENSP00000334834:R154H	ENSP00000334834:R154H	R	+	2	0	KRTAP13-4	30724925	0.000000	0.05858	0.000000	0.03702	0.008000	0.06430	-0.844000	0.04345	-0.040000	0.13580	-0.364000	0.07487	CGC	G|0.979;A|0.021	0.021	strong		0.433	KRTAP13-4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000128222.1		
HIST1H2AC	8334	hgsc.bcm.edu	37	6	26124781	26124781	+	Silent	SNP	C	C	T	rs143405410	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr6:26124781C>T	ENST00000602637.1	+	1	351	c.321C>T	c.(319-321)ggC>ggT	p.G107G	HIST1H2AC_ENST00000377791.2_Silent_p.G107G|HIST1H2BC_ENST00000396984.1_5'Flank|HIST1H2BC_ENST00000314332.5_5'Flank			Q93077	H2A1C_HUMAN	histone cluster 1, H2ac	107						extracellular vesicular exosome (GO:0070062)|nucleosome (GO:0000786)|nucleus (GO:0005634)	DNA binding (GO:0003677)			NS(2)|endometrium(1)|haematopoietic_and_lymphoid_tissue(4)|lung(5)	12						CTCAGGGCGGCGTCCTTCCTA	0.577													C|||	3	0.000599042	0.0	0.0	5008	,	,		19312	0.0		0.003	False		,,,				2504	0.0				p.G107G		Atlas-SNP	.											HIST1H2AC,colon,carcinoma,0,1	HIST1H2AC	29	1	0			c.C321T						scavenged	.	C		2,4404		0,2,2201	93.0	92.0	92.0		321	0.6	1.0	6	dbSNP_134	92	26,8574		0,26,4274	no	coding-synonymous	HIST1H2AC	NM_003512.3		0,28,6475	TT,TC,CC		0.3023,0.0454,0.2153		107/131	26124781	28,12978	2203	4300	6503	SO:0001819	synonymous_variant	8334	exon1			GGGCGGCGTCCTT	Z80778	CCDS4585.1	6p22.1	2011-01-27	2006-10-11	2003-02-21	ENSG00000180573	ENSG00000180573		"""Histones / Replication-dependent"""	4733	protein-coding gene	gene with protein product		602794	"""H2A histone family, member L"", ""histone 1, H2ac"""	H2AFL		9119399, 12408966	Standard	NM_003512		Approved		uc003ngm.3	Q93077	OTTHUMG00000014428	ENST00000602637.1:c.321C>T	6.37:g.26124781C>T		169.0	1.0	0.00591716		190.0	95.0	0.5	NM_003512	B2R4F7|O00775|O00776|O00777|O00778|Q540R1	Silent	SNP	ENST00000602637.1	37	CCDS4585.1																																																																																			C|0.998;T|0.002	0.002	strong		0.577	HIST1H2AC-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000468023.1	NM_003512	
OR11A1	26531	hgsc.bcm.edu	37	6	29395180	29395180	+	Missense_Mutation	SNP	A	A	G	rs61978565	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr6:29395180A>G	ENST00000377149.1	-	5	711	c.239T>C	c.(238-240)aTg>aCg	p.M80T	OR11A1_ENST00000377147.2_Missense_Mutation_p.M80T|OR5V1_ENST00000377154.1_Intron|OR11A1_ENST00000377148.1_Missense_Mutation_p.M80T			Q9GZK7	O11A1_HUMAN	olfactory receptor, family 11, subfamily A, member 1	80						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)	p.M80T(1)		cervix(1)|large_intestine(1)|lung(12)|ovary(1)|pancreas(1)|prostate(2)|upper_aerodigestive_tract(1)	19						CATTTTTGGCATCACTGCGGA	0.483													A|||	219	0.04373	0.1384	0.0115	5008	,	,		19957	0.0119		0.0129	False		,,,				2504	0.0031				p.M80T		Atlas-SNP	.											OR11A1,NS,carcinoma,0,1	OR11A1	30	1	1	Substitution - Missense(1)	pancreas(1)	c.T239C						PASS	.	A	THR/MET	369,2651		26,317,1167	70.0	63.0	66.0		239	3.8	0.9	6	dbSNP_129	66	34,5384		0,34,2675	yes	missense	OR11A1	NM_013937.2	81	26,351,3842	GG,GA,AA		0.6275,12.2185,4.776	benign	80/316	29395180	403,8035	1510	2709	4219	SO:0001583	missense	26531	exon1			TTTGGCATCACTG		CCDS34363.1	6p22.2-p21.31	2014-02-19	2002-02-28		ENSG00000204694	ENSG00000204694		"""GPCR / Class A : Olfactory receptors"""	8176	protein-coding gene	gene with protein product			"""olfactory receptor, family 11, subfamily A, member 2"""	OR11A2			Standard	XM_005249001		Approved	hs6M1-18	uc003nmg.3	Q9GZK7	OTTHUMG00000031225	ENST00000377149.1:c.239T>C	6.37:g.29395180A>G	ENSP00000366354:p.Met80Thr	63.0	0.0	0		50.0	28.0	0.56	NM_013937	A2BF33|A6NFQ3|B0S7T2|Q5ST16|Q9GZK8	Missense_Mutation	SNP	ENST00000377149.1	37	CCDS34363.1	102	0.046703296703296704	74	0.15040650406504066	7	0.019337016574585635	10	0.017482517482517484	11	0.014511873350923483	A	8.985	0.976299	0.18736	0.122185	0.006275	ENSG00000204694	ENST00000377148;ENST00000377149;ENST00000377147	T;T;T	0.02974	4.09;4.09;4.09	3.78	3.78	0.43462	GPCR, rhodopsin-like superfamily (1);	0.297272	0.18047	U	0.153413	T	0.00524	0.0017	N	0.01209	-0.955	0.18873	N	0.999989	B	0.13594	0.008	B	0.14578	0.011	T	0.51028	-0.8757	10	0.56958	D	0.05	-9.2563	11.5265	0.50582	1.0:0.0:0.0:0.0	.	80	Q9GZK7	O11A1_HUMAN	T	80	ENSP00000366353:M80T;ENSP00000366354:M80T;ENSP00000366352:M80T	ENSP00000366352:M80T	M	-	2	0	OR11A1	29503159	0.000000	0.05858	0.925000	0.36789	0.702000	0.40608	0.971000	0.29396	1.569000	0.49696	0.333000	0.21579	ATG	A|0.957;G|0.043	0.043	strong		0.483	OR11A1-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000193778.1		
PGLYRP2	114770	hgsc.bcm.edu	37	19	15580694	15580694	+	Missense_Mutation	SNP	G	G	A	rs61734899	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr19:15580694G>A	ENST00000340880.4	-	4	1870	c.1390C>T	c.(1390-1392)Cac>Tac	p.H464Y	PGLYRP2_ENST00000292609.4_Missense_Mutation_p.H464Y	NM_052890.3	NP_443122.3	Q96PD5	PGRP2_HUMAN	peptidoglycan recognition protein 2	464					defense response to Gram-positive bacterium (GO:0050830)|detection of bacterium (GO:0016045)|growth of symbiont in host (GO:0044117)|innate immune response (GO:0045087)|negative regulation of interferon-gamma production (GO:0032689)|negative regulation of natural killer cell differentiation involved in immune response (GO:0032827)|pattern recognition receptor signaling pathway (GO:0002221)|peptide amidation (GO:0001519)|peptidoglycan catabolic process (GO:0009253)|regulation of inflammatory response (GO:0050727)	extracellular vesicular exosome (GO:0070062)|intracellular (GO:0005622)|membrane (GO:0016020)	N-acetylmuramoyl-L-alanine amidase activity (GO:0008745)|peptidoglycan binding (GO:0042834)|peptidoglycan receptor activity (GO:0016019)|zinc ion binding (GO:0008270)			endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(3)|lung(9)|ovary(3)|prostate(2)|skin(3)|stomach(2)|urinary_tract(1)	28						CCCACCCAGTGCCAGCCGCGT	0.716													G|||	124	0.0247604	0.0484	0.0058	5008	,	,		13687	0.006		0.008	False		,,,				2504	0.0429				p.H464Y		Atlas-SNP	.											.	PGLYRP2	116	.	0			c.C1390T						PASS	.	G	TYR/HIS	161,4189		2,157,2016	11.0	15.0	14.0		1390	2.9	1.0	19	dbSNP_129	14	65,8451		0,65,4193	yes	missense	PGLYRP2	NM_052890.3	83	2,222,6209	AA,AG,GG		0.7633,3.7011,1.7566	benign	464/577	15580694	226,12640	2175	4258	6433	SO:0001583	missense	114770	exon4			CCCAGTGCCAGCC	AY358156	CCDS12330.2	19p13.12	2010-04-27			ENSG00000161031	ENSG00000161031	3.5.1.28		30013	protein-coding gene	gene with protein product	"""peptidoglycan recognition protein L precursor"", ""peptidoglycan recognition protein-like"", ""N-acetylmuramoyl-L-alanine amidase"""	608199				11461926, 12669421, 14506276	Standard	NM_052890		Approved	PGRP-L, PGLYRPL, TAGL-like, tagL, tagL-alpha, tagl-beta, PGRPL	uc002nbf.4	Q96PD5	OTTHUMG00000150690	ENST00000340880.4:c.1390C>T	19.37:g.15580694G>A	ENSP00000345968:p.His464Tyr	33.0	0.0	0		47.0	17.0	0.361702	NM_052890	A8K050|A8K8C7|B2RMZ2|B7ZM33|Q68CK1|Q96N74|Q9UC60	Missense_Mutation	SNP	ENST00000340880.4	37	CCDS12330.2	34	0.015567765567765568	21	0.042682926829268296	3	0.008287292817679558	2	0.0034965034965034965	8	0.010554089709762533	G	12.80	2.046263	0.36085	0.037011	0.007633	ENSG00000161031	ENST00000340880;ENST00000292609	T;T	0.17213	2.29;2.29	5.04	2.91	0.33838	Peptidoglycan recognition protein family domain, metazoa/bacteria (1);N-acetylmuramoyl-L-alanine amidase domain (4);	0.380248	0.27554	N	0.018848	T	0.03564	0.0102	M	0.66378	2.025	0.35512	D	0.80071	B;B	0.09022	0.001;0.002	B;B	0.13407	0.008;0.009	T	0.08249	-1.0731	10	0.35671	T	0.21	-13.9263	4.8686	0.13620	0.1811:0.0:0.6507:0.1682	.	464;464	Q96PD5-2;Q96PD5	.;PGRP2_HUMAN	Y	464	ENSP00000345968:H464Y;ENSP00000292609:H464Y	ENSP00000292609:H464Y	H	-	1	0	PGLYRP2	15441694	1.000000	0.71417	1.000000	0.80357	0.957000	0.61999	0.700000	0.25601	0.540000	0.28808	-0.448000	0.05591	CAC	G|0.983;A|0.017	0.017	strong		0.716	PGLYRP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000319626.1	NM_052890	
KIF22	3835	hgsc.bcm.edu	37	16	29816237	29816237	+	Missense_Mutation	SNP	G	G	A	rs146561986	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr16:29816237G>A	ENST00000160827.4	+	12	1820	c.1780G>A	c.(1780-1782)Gat>Aat	p.D594N	AC009133.15_ENST00000566537.1_RNA|MAZ_ENST00000566906.2_5'Flank|MAZ_ENST00000563402.1_5'Flank|KIF22_ENST00000569382.2_Missense_Mutation_p.D540N|MAZ_ENST00000219782.6_5'Flank|KIF22_ENST00000400751.5_Missense_Mutation_p.D526N|MAZ_ENST00000545521.1_5'Flank|MAZ_ENST00000562337.1_5'Flank|KIF22_ENST00000561482.1_Missense_Mutation_p.D526N|MAZ_ENST00000322945.6_5'Flank	NM_001256269.1|NM_007317.2	NP_001243198.1|NP_015556.1	Q14807	KIF22_HUMAN	kinesin family member 22	594					antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|ATP catabolic process (GO:0006200)|blood coagulation (GO:0007596)|DNA repair (GO:0006281)|microtubule-based movement (GO:0007018)|mitotic nuclear division (GO:0007067)	chromatin (GO:0000785)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|focal adhesion (GO:0005925)|kinesin complex (GO:0005871)|kinetochore (GO:0000776)|microtubule (GO:0005874)|nucleus (GO:0005634)|spindle (GO:0005819)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|DNA binding (GO:0003677)|microtubule motor activity (GO:0003777)			endometrium(1)|large_intestine(1)|lung(11)|skin(1)	14						AAAAATACTGGATCTGCTGAA	0.617													G|||	5	0.000998403	0.0	0.0029	5008	,	,		19086	0.0		0.002	False		,,,				2504	0.001				p.D594N		Atlas-SNP	.											.	KIF22	29	.	0			c.G1780A						PASS	.	G	ASN/ASP	3,4391	6.2+/-15.9	0,3,2194	44.0	43.0	43.0		1780	1.4	0.4	16	dbSNP_134	43	23,8569	17.3+/-56.4	0,23,4273	yes	missense	KIF22	NM_007317.1	23	0,26,6467	AA,AG,GG		0.2677,0.0683,0.2002	benign	594/666	29816237	26,12960	2197	4296	6493	SO:0001583	missense	3835	exon12			ATACTGGATCTGC	D38751	CCDS10653.1, CCDS58444.1	16p11.2	2008-03-03	2003-01-09	2003-01-10	ENSG00000079616	ENSG00000079616		"""Kinesins"""	6391	protein-coding gene	gene with protein product		603213	"""kinesin-like 4"""	KNSL4		8599929, 11416179	Standard	NM_007317		Approved	Kid, OBP-1, OBP-2	uc002dts.4	Q14807	OTTHUMG00000097771	ENST00000160827.4:c.1780G>A	16.37:g.29816237G>A	ENSP00000160827:p.Asp594Asn	52.0	0.0	0		64.0	33.0	0.515625	NM_007317	B2R5M0|B7Z265|O60845|O94814|Q53F58|Q9BT46	Missense_Mutation	SNP	ENST00000160827.4	37	CCDS10653.1	3	0.0013736263736263737	0	0.0	2	0.0055248618784530384	0	0.0	1	0.0013192612137203166	G	15.07	2.723503	0.48728	6.83E-4	0.002677	ENSG00000079616	ENST00000160827;ENST00000400751	T;T	0.74106	-0.73;-0.81	5.64	1.38	0.22167	.	.	.	.	.	T	0.39911	0.1096	N	0.08118	0	0.80722	D	1	B;B	0.18166	0.002;0.026	B;B	0.18263	0.003;0.021	T	0.15521	-1.0434	9	0.39692	T	0.17	.	2.6855	0.05106	0.1508:0.2728:0.4355:0.1409	.	526;594	B7Z265;Q14807	.;KIF22_HUMAN	N	594;526	ENSP00000160827:D594N;ENSP00000383562:D526N	ENSP00000160827:D594N	D	+	1	0	KIF22	29723738	0.998000	0.40836	0.355000	0.25773	0.967000	0.64934	1.528000	0.35985	0.037000	0.15575	0.561000	0.74099	GAT	G|0.998;A|0.002	0.002	strong		0.617	KIF22-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000215012.2		
COMP	1311	hgsc.bcm.edu	37	19	18896823	18896823	+	Missense_Mutation	SNP	G	G	A			TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr19:18896823G>A	ENST00000222271.2	-	13	1485	c.1441C>T	c.(1441-1443)Cgg>Tgg	p.R481W	COMP_ENST00000542601.2_Missense_Mutation_p.R448W|COMP_ENST00000425807.1_Missense_Mutation_p.R428W	NM_000095.2	NP_000086.2	P49747	COMP_HUMAN	cartilage oligomeric matrix protein	481					apoptotic process (GO:0006915)|cell adhesion (GO:0007155)|extracellular matrix organization (GO:0030198)|growth plate cartilage development (GO:0003417)|limb development (GO:0060173)|negative regulation of apoptotic process (GO:0043066)|organ morphogenesis (GO:0009887)|skeletal system development (GO:0001501)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|proteinaceous extracellular matrix (GO:0005578)	calcium ion binding (GO:0005509)|collagen binding (GO:0005518)|extracellular matrix structural constituent (GO:0005201)|heparan sulfate proteoglycan binding (GO:0043395)|heparin binding (GO:0008201)|protease binding (GO:0002020)			breast(6)|cervix(1)|endometrium(2)|kidney(1)|large_intestine(3)|lung(12)|ovary(2)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	32						CAGTTGTCCCGACTGTCAGGG	0.701																																					p.R481W		Atlas-SNP	.											.	COMP	62	.	0			c.C1441T						PASS	.						46.0	37.0	40.0					19																	18896823		2203	4300	6503	SO:0001583	missense	1311	exon13			TGTCCCGACTGTC	L32137	CCDS12385.1	19p13.1	2008-02-05				ENSG00000105664			2227	protein-coding gene	gene with protein product	"""thrombospondin-5"""	600310	"""cartilage oligomeric matrix protein (pseudoachondroplasia, epiphyseal dysplasia 1, multiple)"""	PSACH, EDM1, EPD1		7713493, 8307576	Standard	NM_000095		Approved	MED, THBS5	uc002nke.3	P49747	OTTHUMG00000169318	ENST00000222271.2:c.1441C>T	19.37:g.18896823G>A	ENSP00000222271:p.Arg481Trp	58.0	0.0	0		49.0	22.0	0.44898	NM_000095	B4DKJ3|O14592|Q16388|Q16389|Q2NL86|Q8N4T2	Missense_Mutation	SNP	ENST00000222271.2	37	CCDS12385.1	.	.	.	.	.	.	.	.	.	.	G	18.61	3.660379	0.67586	.	.	ENSG00000105664	ENST00000542601;ENST00000222271;ENST00000425807;ENST00000454701	D;D;D	0.98362	-4.89;-4.89;-4.89	4.05	2.98	0.34508	.	0.243213	0.29133	U	0.013053	D	0.97901	0.9310	M	0.82716	2.605	0.37365	D	0.911397	P;P	0.47409	0.895;0.799	P;P	0.48114	0.469;0.567	D	0.98175	1.0454	10	0.72032	D	0.01	-29.5678	11.6098	0.51053	0.0:0.0:0.8201:0.1798	.	428;481	B4DKJ3;P49747	.;COMP_HUMAN	W	448;481;428;468	ENSP00000439156:R448W;ENSP00000222271:R481W;ENSP00000403792:R428W	ENSP00000222271:R481W	R	-	1	2	COMP	18757823	0.001000	0.12720	0.993000	0.49108	0.590000	0.36582	1.014000	0.29950	0.670000	0.31165	0.491000	0.48974	CGG	.	.	none		0.701	COMP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000403457.1	NM_000095	
ZHX2	22882	hgsc.bcm.edu	37	8	123964011	123964011	+	Silent	SNP	G	G	A	rs61752912	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr8:123964011G>A	ENST00000314393.4	+	3	1096	c.261G>A	c.(259-261)acG>acA	p.T87T		NM_014943.3	NP_055758.1	Q9Y6X8	ZHX2_HUMAN	zinc fingers and homeoboxes 2	87					mRNA catabolic process (GO:0006402)|negative regulation of neuron differentiation (GO:0045665)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|somatic stem cell maintenance (GO:0035019)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription corepressor activity (GO:0003714)			breast(1)|central_nervous_system(1)|endometrium(7)|kidney(1)|large_intestine(10)|lung(15)|ovary(1)|prostate(1)|skin(4)|stomach(3)|urinary_tract(1)	45	Lung NSC(37;2e-09)|Ovarian(258;0.0205)|Hepatocellular(40;0.105)		STAD - Stomach adenocarcinoma(47;0.00527)			CCTACTCCACGCAAAACCTGA	0.468													G|||	115	0.0229633	0.0424	0.0331	5008	,	,		20913	0.0		0.0298	False		,,,				2504	0.0061				p.T87T	Esophageal Squamous(94;1056 1388 11767 13799 49639)	Atlas-SNP	.											.	ZHX2	106	.	0			c.G261A						PASS	.	G		174,4232	114.6+/-152.6	5,164,2034	89.0	81.0	84.0		261	-6.5	0.7	8	dbSNP_129	84	278,8322	105.6+/-166.5	6,266,4028	no	coding-synonymous	ZHX2	NM_014943.3		11,430,6062	AA,AG,GG		3.2326,3.9492,3.4753		87/838	123964011	452,12554	2203	4300	6503	SO:0001819	synonymous_variant	22882	exon3			CTCCACGCAAAAC	AB020661	CCDS6336.1	8q24.13	2012-03-09	2004-01-23		ENSG00000178764	ENSG00000178764		"""Zinc fingers, C2H2-type"", ""Homeoboxes / ZF class"""	18513	protein-coding gene	gene with protein product		609185	"""zinc-fingers and homeoboxes 2"""			10048485, 12741956	Standard	XM_005250837		Approved	KIAA0854	uc003ypk.1	Q9Y6X8	OTTHUMG00000165077	ENST00000314393.4:c.261G>A	8.37:g.123964011G>A		41.0	0.0	0		52.0	18.0	0.346154	NM_014943		Silent	SNP	ENST00000314393.4	37	CCDS6336.1																																																																																			G|0.965;A|0.035	0.035	strong		0.468	ZHX2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000381709.1	NM_014943	
GLB1L2	89944	hgsc.bcm.edu	37	11	134239760	134239760	+	Silent	SNP	C	C	T	rs34063963	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr11:134239760C>T	ENST00000535456.2	+	11	1277	c.1089C>T	c.(1087-1089)gaC>gaT	p.D363D	GLB1L2_ENST00000389881.3_Silent_p.D363D|GLB1L2_ENST00000529077.1_3'UTR|GLB1L2_ENST00000339772.7_Silent_p.D363D	NM_138342.3	NP_612351.2	Q8IW92	GLBL2_HUMAN	galactosidase, beta 1-like 2	363					carbohydrate metabolic process (GO:0005975)	extracellular region (GO:0005576)	beta-galactosidase activity (GO:0004565)			central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(6)|liver(1)|lung(20)|ovary(1)|pancreas(1)|prostate(3)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	41	all_hematologic(175;0.127)	all_cancers(12;2.85e-18)|all_epithelial(12;1.21e-12)|all_lung(97;0.000276)|Lung NSC(97;0.000518)|Breast(109;0.00122)|Medulloblastoma(222;0.0399)|all_neural(223;0.0412)|Esophageal squamous(93;0.0844)		Epithelial(10;1.37e-11)|all cancers(11;2.2e-10)|BRCA - Breast invasive adenocarcinoma(10;3.09e-10)|OV - Ovarian serous cystadenocarcinoma(99;0.000885)|Lung(977;0.223)		AGCTTCGAGACTTCTTCGGCT	0.537													C|||	155	0.0309505	0.1112	0.0072	5008	,	,		20784	0.0		0.003	False		,,,				2504	0.0				p.D363D		Atlas-SNP	.											.	GLB1L2	79	.	0			c.C1089T						PASS	.	C		315,4087	171.6+/-201.8	8,299,1894	155.0	137.0	143.0		1089	-11.3	0.0	11	dbSNP_126	143	7,8587	5.7+/-21.5	0,7,4290	no	coding-synonymous	GLB1L2	NM_138342.3		8,306,6184	TT,TC,CC		0.0815,7.1558,2.4777		363/637	134239760	322,12674	2201	4297	6498	SO:0001819	synonymous_variant	89944	exon11			TCGAGACTTCTTC		CCDS31724.1	11q25	2008-01-29			ENSG00000149328	ENSG00000149328			25129	protein-coding gene	gene with protein product						12975309	Standard	NM_138342		Approved		uc001qhp.3	Q8IW92	OTTHUMG00000167179	ENST00000535456.2:c.1089C>T	11.37:g.134239760C>T		113.0	0.0	0		89.0	39.0	0.438202	NM_138342	A6NCE6|Q6UX60|Q8NC62|Q8NCB3|Q8NCJ1|Q96HP3	Silent	SNP	ENST00000535456.2	37	CCDS31724.1	63	0.028846153846153848	61	0.12398373983739837	2	0.0055248618784530384	0	0.0	0	0.0	C	4.109	0.018381	0.07959	0.071558	8.15E-4	ENSG00000149328	ENST00000525089;ENST00000533324	.	.	.	5.66	-11.3	0.00108	.	.	.	.	.	T	0.00210	0.0006	.	.	.	0.22918	N	0.998562	.	.	.	.	.	.	T	0.03576	-1.1023	4	.	.	.	-4.4127	1.5619	0.02596	0.3994:0.1015:0.2886:0.2106	rs34063963	.	.	.	F	302;191	.	.	L	+	1	0	GLB1L2	133744970	0.000000	0.05858	0.000000	0.03702	0.655000	0.38815	-4.333000	0.00251	-4.016000	0.00081	-0.181000	0.13052	CTT	C|0.976;T|0.024	0.024	strong		0.537	GLB1L2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000393629.2	NM_138342	
BAIAP3	8938	hgsc.bcm.edu	37	16	1384715	1384715	+	Missense_Mutation	SNP	T	T	C	rs200858324	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr16:1384715T>C	ENST00000324385.5	+	1	211	c.53T>C	c.(52-54)cTg>cCg	p.L18P	BAIAP3_ENST00000397489.1_5'UTR|BAIAP3_ENST00000397488.2_Intron|BAIAP3_ENST00000426824.3_Intron|BAIAP3_ENST00000562208.1_Intron|BAIAP3_ENST00000568887.1_Intron|BAIAP3_ENST00000421665.2_5'Flank	NM_003933.4	NP_003924.2	O94812	BAIP3_HUMAN	BAI1-associated protein 3	18					G-protein coupled receptor signaling pathway (GO:0007186)|neurotransmitter secretion (GO:0007269)		protein C-terminus binding (GO:0008022)			breast(2)|central_nervous_system(2)|cervix(1)|endometrium(5)|kidney(1)|large_intestine(1)|lung(25)|pancreas(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	42		Hepatocellular(780;0.0893)				GACCTGCACCTGGGCACCGCC	0.667													T|||	4	0.000798722	0.0	0.0	5008	,	,		13202	0.0		0.004	False		,,,				2504	0.0				p.L18P		Atlas-SNP	.											.	BAIAP3	88	.	0			c.T53C						PASS	.	T	PRO/LEU,,,	0,4224		0,0,2112	8.0	9.0	9.0		53,,,	-3.0	0.0	16		9	6,8358		0,6,4176	yes	missense,intron,intron,intron	BAIAP3	NM_003933.4,NM_001199097.1,NM_001199098.1,NM_001199099.1	98,,,	0,6,6288	CC,CT,TT		0.0717,0.0,0.0477	possibly-damaging,,,	18/1188,,,	1384715	6,12582	2112	4182	6294	SO:0001583	missense	8938	exon1			TGCACCTGGGCAC	AB017111	CCDS10434.1, CCDS55978.1, CCDS55979.1, CCDS58402.1, CCDS58403.1, CCDS66894.1	16p13.3	2008-07-04			ENSG00000007516	ENSG00000007516			948	protein-coding gene	gene with protein product		604009				9790924	Standard	NM_003933		Approved	BAP3, KIAA0734	uc002clk.2	O94812	OTTHUMG00000047833	ENST00000324385.5:c.53T>C	16.37:g.1384715T>C	ENSP00000324510:p.Leu18Pro	138.0	0.0	0		192.0	79.0	0.411458	NM_003933	A2A2B2|B2RCD7|B4DGS5|B4DIK3|B4DRK9|B4DRP1|E7EUB9|H3BUH8|H3BVI3|H7C2Q1|O94839|Q2M226|Q658J2|Q76N05|Q96RZ3|Q9UJK1	Missense_Mutation	SNP	ENST00000324385.5	37	CCDS10434.1	.	.	.	.	.	.	.	.	.	.	T	9.024	0.985626	0.18889	0.0	7.17E-4	ENSG00000007516	ENST00000324385	T	0.73258	-0.73	1.48	-2.96	0.05547	.	5.452210	0.01821	U	0.034057	T	0.44767	0.1309	N	0.08118	0	0.09310	N	0.999994	P;P	0.44734	0.842;0.617	B;B	0.32342	0.144;0.065	T	0.49021	-0.8982	10	0.56958	D	0.05	.	6.6146	0.22771	0.0:0.0:0.4668:0.5332	.	18;18	B4DGA2;O94812	.;BAIP3_HUMAN	P	18	ENSP00000324510:L18P	ENSP00000324510:L18P	L	+	2	0	BAIAP3	1324716	0.000000	0.05858	0.000000	0.03702	0.082000	0.17680	-2.273000	0.01164	-1.100000	0.03030	0.172000	0.16884	CTG	.	.	weak		0.667	BAIAP3-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000109056.3		
SPEN	23013	hgsc.bcm.edu	37	1	16255799	16255799	+	Missense_Mutation	SNP	G	G	A	rs115566585	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr1:16255799G>A	ENST00000375759.3	+	11	3268	c.3064G>A	c.(3064-3066)Gtg>Atg	p.V1022M		NM_015001.2	NP_055816.2	Q96T58	MINT_HUMAN	spen family transcriptional repressor	1022					negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|Notch signaling pathway (GO:0007219)|positive regulation of neurogenesis (GO:0050769)|positive regulation of transcription, DNA-templated (GO:0045893)|viral process (GO:0016032)	extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)|transcriptional repressor complex (GO:0017053)	nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)|RNA polymerase II transcription factor binding (GO:0001085)|RNA polymerase II transcription factor binding transcription factor activity involved in negative regulation of transcription (GO:0001191)|sequence-specific DNA binding transcription factor activity (GO:0003700)|single-stranded DNA binding (GO:0003697)|transcription corepressor activity (GO:0003714)			NS(1)|breast(13)|central_nervous_system(3)|cervix(5)|endometrium(16)|kidney(18)|large_intestine(27)|liver(2)|lung(37)|ovary(7)|prostate(7)|skin(7)|upper_aerodigestive_tract(5)|urinary_tract(1)	149		Colorectal(325;0.000258)|Breast(348;0.000278)|Lung NSC(340;0.000419)|Renal(390;0.000518)|all_lung(284;0.000567)|Ovarian(437;0.0129)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0185)|Colorectal(212;5.96e-07)|COAD - Colon adenocarcinoma(227;3.11e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000115)|Kidney(64;0.000212)|KIRC - Kidney renal clear cell carcinoma(64;0.003)|STAD - Stomach adenocarcinoma(313;0.013)|READ - Rectum adenocarcinoma(331;0.0681)		GCAGCCTGACGTGTCCTCTAG	0.423													G|||	12	0.00239617	0.0	0.0115	5008	,	,		20147	0.0		0.004	False		,,,				2504	0.0				p.V1022M		Atlas-SNP	.											.	SPEN	374	.	0			c.G3064A						PASS	.	G	MET/VAL	2,4404	2.1+/-5.4	0,2,2201	46.0	53.0	51.0		3064	-5.8	0.0	1	dbSNP_132	51	31,8569	18.5+/-59.3	0,31,4269	yes	missense	SPEN	NM_015001.2	21	0,33,6470	AA,AG,GG		0.3605,0.0454,0.2537	benign	1022/3665	16255799	33,12973	2203	4300	6503	SO:0001583	missense	23013	exon11			CCTGACGTGTCCT		CCDS164.1	1p36	2013-10-17	2013-10-17		ENSG00000065526	ENSG00000065526		"""RNA binding motif (RRM) containing"""	17575	protein-coding gene	gene with protein product		613484	"""SPEN homolog, transcriptional regulator (Drosophila)"", ""spen homolog, transcriptional regulator (Drosophila)"""			10451362, 11331609	Standard	NM_015001		Approved	KIAA0929, MINT, SHARP, RBM15C	uc001axk.1	Q96T58	OTTHUMG00000009376	ENST00000375759.3:c.3064G>A	1.37:g.16255799G>A	ENSP00000364912:p.Val1022Met	99.0	0.0	0		129.0	57.0	0.44186	NM_015001	Q9H9A8|Q9NWH5|Q9UQ01|Q9Y556	Missense_Mutation	SNP	ENST00000375759.3	37	CCDS164.1	5	0.0022893772893772895	0	0.0	4	0.011049723756906077	0	0.0	1	0.0013192612137203166	G	0.012	-1.676123	0.00751	4.54E-4	0.003605	ENSG00000065526	ENST00000375759	T	0.09445	2.98	5.13	-5.85	0.02311	.	.	.	.	.	T	0.02304	0.0071	N	0.03608	-0.345	0.09310	N	1	B	0.11235	0.004	B	0.06405	0.002	T	0.41233	-0.9520	9	0.42905	T	0.14	6.4781	3.6799	0.08306	0.2371:0.3302:0.3421:0.0907	.	1022	Q96T58	MINT_HUMAN	M	1022	ENSP00000364912:V1022M	ENSP00000364912:V1022M	V	+	1	0	SPEN	16128386	0.000000	0.05858	0.002000	0.10522	0.006000	0.05464	-1.308000	0.02730	-0.807000	0.04393	-0.150000	0.13652	GTG	G|0.998;A|0.002	0.002	strong		0.423	SPEN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000025993.1	NM_015001	
RPS15	6209	hgsc.bcm.edu	37	19	1440374	1440374	+	Silent	SNP	C	C	T	rs139332437	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr19:1440374C>T	ENST00000586686.2	+	4	390	c.351C>T	c.(349-351)ggC>ggT	p.G117G	RPS15_ENST00000589656.2_Silent_p.G113G|RPS15_ENST00000233609.4_Silent_p.G90G|RPS15_ENST00000591032.1_Silent_p.G84G|RPS15_ENST00000591804.2_Silent_p.G84G|RPS15_ENST00000593052.1_Silent_p.G124G|RPS15_ENST00000585665.1_Silent_p.G84G|RPS15_ENST00000586096.2_3'UTR|AC027307.3_ENST00000594262.1_5'Flank			P62841	RS15_HUMAN	ribosomal protein S15	117					cellular protein metabolic process (GO:0044267)|gene expression (GO:0010467)|mRNA metabolic process (GO:0016071)|nuclear-transcribed mRNA catabolic process, nonsense-mediated decay (GO:0000184)|osteoblast differentiation (GO:0001649)|ribosomal small subunit biogenesis (GO:0042274)|ribosomal small subunit export from nucleus (GO:0000056)|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)	cytosol (GO:0005829)|cytosolic small ribosomal subunit (GO:0022627)|focal adhesion (GO:0005925)|membrane (GO:0016020)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	DNA binding (GO:0003677)|poly(A) RNA binding (GO:0044822)|structural constituent of ribosome (GO:0003735)			endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(1)|lung(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	8		Acute lymphoblastic leukemia(61;3.02e-13)|all_hematologic(61;4.32e-09)|Hepatocellular(1079;0.137)		UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|OV - Ovarian serous cystadenocarcinoma(105;1.09e-113)|Epithelial(107;3.79e-112)|all cancers(105;1.67e-104)|BRCA - Breast invasive adenocarcinoma(158;0.00136)|STAD - Stomach adenocarcinoma(1328;0.18)		ACTACCTGGGCGAGTTCTCCA	0.632													C|||	5	0.000998403	0.0008	0.0	5008	,	,		15262	0.0		0.004	False		,,,				2504	0.0				p.G117G	Ovarian(170;79 2680 5719 44260)	Atlas-SNP	.											.	RPS15	11	.	0			c.C351T						PASS	.	C		4,4402	8.1+/-20.4	0,4,2199	39.0	40.0	40.0		351	2.3	1.0	19	dbSNP_134	40	27,8571	18.5+/-59.3	0,27,4272	no	coding-synonymous	RPS15	NM_001018.3		0,31,6471	TT,TC,CC		0.314,0.0908,0.2384		117/146	1440374	31,12973	2203	4299	6502	SO:0001819	synonymous_variant	6209	exon4			CCTGGGCGAGTTC		CCDS12067.1	19p13.3	2012-12-20			ENSG00000115268	ENSG00000115268		"""S ribosomal proteins"""	10388	protein-coding gene	gene with protein product	"""40S ribosomal protein S15"", ""homolog of rat insulinoma"", ""insulinoma protein"""	180535				2159154	Standard	NM_001018		Approved	RIG, MGC111130, S15	uc002lsp.1	P62841	OTTHUMG00000140099	ENST00000586686.2:c.351C>T	19.37:g.1440374C>T		186.0	0.0	0		170.0	87.0	0.511765	NM_001018	A5D8V9|P11174|Q3KRA1|Q9UDC2	Silent	SNP	ENST00000586686.2	37	CCDS12067.1																																																																																			C|0.998;T|0.002	0.002	strong		0.632	RPS15-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000449609.4	NM_001018	
C6orf132	647024	hgsc.bcm.edu	37	6	42074925	42074925	+	Missense_Mutation	SNP	G	G	A	rs568578371	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr6:42074925G>A	ENST00000341865.4	-	4	724	c.725C>T	c.(724-726)cCt>cTt	p.P242L		NM_001164446.1	NP_001157918.1	Q5T0Z8	CF132_HUMAN	chromosome 6 open reading frame 132	242										breast(1)	1						CACTGTGTGAGGAGATGCTGG	0.642													G|||	2	0.000399361	0.0	0.0014	5008	,	,		7599	0.0		0.001	False		,,,				2504	0.0				p.P242L		Atlas-SNP	.											.	C6orf132	48	.	0			c.C725T						PASS	.						6.0	7.0	6.0					6																	42074925		689	1585	2274	SO:0001583	missense	647024	exon4			GTGTGAGGAGATG		CCDS47428.1	6p21.1	2012-02-06			ENSG00000188112	ENSG00000188112			21288	protein-coding gene	gene with protein product							Standard	NM_001164446		Approved	bA7K24.2	uc003orw.2	Q5T0Z8	OTTHUMG00000014695	ENST00000341865.4:c.725C>T	6.37:g.42074925G>A	ENSP00000341368:p.Pro242Leu	3.0	0.0	0		8.0	4.0	0.5	NM_001164446	A6NI05	Missense_Mutation	SNP	ENST00000341865.4	37	CCDS47428.1	.	.	.	.	.	.	.	.	.	.	G	0.003	-2.525828	0.00147	.	.	ENSG00000188112	ENST00000341865	T	0.39997	1.05	3.67	0.7	0.18099	.	.	.	.	.	T	0.04815	0.0130	N	0.11560	0.145	0.19775	N	0.999957	.	.	.	.	.	.	T	0.39522	-0.9610	7	0.09843	T	0.71	.	3.0829	0.06269	0.2512:0.0:0.5395:0.2094	.	.	.	.	L	242	ENSP00000341368:P242L	ENSP00000341368:P242L	P	-	2	0	C6orf132	42182903	0.994000	0.37717	0.002000	0.10522	0.001000	0.01503	0.677000	0.25262	-0.119000	0.11830	-0.175000	0.13238	CCT	.	.	none		0.642	C6orf132-001	PUTATIVE	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000040548.2	NM_001164446	
TMEM9	252839	hgsc.bcm.edu	37	1	201115964	201115964	+	Silent	SNP	G	G	A	rs139286836	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr1:201115964G>A	ENST00000367330.1	-	3	687	c.171C>T	c.(169-171)caC>caT	p.H57H	TMEM9_ENST00000472411.1_5'Flank|TMEM9_ENST00000367332.1_Silent_p.H60H|TMEM9_ENST00000367334.5_Silent_p.H57H|TMEM9_ENST00000367333.2_Silent_p.H57H|TMEM9_ENST00000485839.2_Silent_p.H57H			Q9P0T7	TMEM9_HUMAN	transmembrane protein 9	57					transport (GO:0006810)	integral component of membrane (GO:0016021)|late endosome (GO:0005770)|lysosome (GO:0005764)				liver(1)|lung(1)|stomach(1)	3		Breast(1374;0.000301)				GCTCCACCACGTGCAGGCAGT	0.612													G|||	20	0.00399361	0.0	0.0144	5008	,	,		19530	0.0		0.005	False		,,,				2504	0.0051				p.H57H		Atlas-SNP	.											.	TMEM9	12	.	0			c.C171T						PASS	.	G		3,4403	6.2+/-15.9	0,3,2200	95.0	74.0	81.0		171	-1.5	1.0	1	dbSNP_134	81	83,8517	47.6+/-106.9	0,83,4217	no	coding-synonymous	TMEM9	NM_016456.3		0,86,6417	AA,AG,GG		0.9651,0.0681,0.6612		57/184	201115964	86,12920	2203	4300	6503	SO:0001819	synonymous_variant	252839	exon4			CACCACGTGCAGG		CCDS1408.1, CCDS73001.1	1q41	2008-02-05			ENSG00000116857	ENSG00000116857			18823	protein-coding gene	gene with protein product							Standard	NM_001288565		Approved	TMEM9A	uc001gvy.3	Q9P0T7	OTTHUMG00000035831	ENST00000367330.1:c.171C>T	1.37:g.201115964G>A		91.0	0.0	0		80.0	42.0	0.525	NM_016456	B1ALM6|Q96NQ9|Q9BQF5	Silent	SNP	ENST00000367330.1	37	CCDS1408.1																																																																																			G|0.994;A|0.006	0.006	strong		0.612	TMEM9-002	KNOWN	alternative_5_UTR|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000087160.1	NM_016456	
PARPBP	55010	hgsc.bcm.edu	37	12	102558369	102558369	+	Missense_Mutation	SNP	C	C	A	rs75438625	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr12:102558369C>A	ENST00000358383.5	+	5	694	c.649C>A	c.(649-651)Caa>Aaa	p.Q217K	PARPBP_ENST00000541394.1_Missense_Mutation_p.Q294K|PARPBP_ENST00000392911.2_Missense_Mutation_p.Q136K|PARPBP_ENST00000378128.3_Missense_Mutation_p.Q217K|PARPBP_ENST00000543784.1_Missense_Mutation_p.Q103K|PARPBP_ENST00000535811.1_Intron|PARPBP_ENST00000327680.2_Missense_Mutation_p.Q136K			Q9NWS1	PARI_HUMAN	PARP1 binding protein	217					DNA repair (GO:0006281)|negative regulation of double-strand break repair via homologous recombination (GO:2000042)	chromatin (GO:0000785)|cytoplasm (GO:0005737)|nucleus (GO:0005634)	DNA binding (GO:0003677)			endometrium(1)|lung(8)|urinary_tract(2)	11						TCGAGAGAAACAAATGTCTAT	0.383													C|||	163	0.0325479	0.1082	0.0058	5008	,	,		17316	0.0		0.005	False		,,,				2504	0.0112				p.Q217K		Atlas-SNP	.											.	PARPBP	40	.	0			c.C649A						PASS	.	C	LYS/GLN	318,4088	170.1+/-200.6	16,286,1901	143.0	152.0	149.0		649	4.9	1.0	12	dbSNP_131	149	21,8579	15.3+/-51.7	0,21,4279	yes	missense	C12orf48	NM_017915.3	53	16,307,6180	AA,AC,CC		0.2442,7.2174,2.6065	benign	217/580	102558369	339,12667	2203	4300	6503	SO:0001583	missense	55010	exon5			GAGAAACAAATGT	AK000648	CCDS9090.1, CCDS9090.2	12q23.2	2013-03-14	2012-01-24	2012-01-24		ENSG00000185480			26074	protein-coding gene	gene with protein product	"""PARP-1 binding protein"""	613687	"""chromosome 12 open reading frame 48"""	C12orf48		20931645	Standard	NM_017915		Approved	FLJ20641, PARI	uc001tjf.3	Q9NWS1		ENST00000358383.5:c.649C>A	12.37:g.102558369C>A	ENSP00000351153:p.Gln217Lys	81.0	0.0	0		90.0	30.0	0.333333	NM_017915	B4E0Y0|Q05C00|Q499L8|Q4FZA0|Q4KMW7|Q6NSC6|Q6PJA1|Q86W36	Missense_Mutation	SNP	ENST00000358383.5	37	CCDS9090.2	57	0.0260989010989011	52	0.10569105691056911	2	0.0055248618784530384	0	0.0	3	0.00395778364116095	C	4.014	-0.000060	0.07819	0.072174	0.002442	ENSG00000185480	ENST00000378128;ENST00000327680;ENST00000541394;ENST00000543784;ENST00000358383;ENST00000392911;ENST00000417507;ENST00000412715	T;T;T;T;T;T;T;T	0.41065	1.01;1.01;1.01;1.01;1.01;1.01;1.01;1.01	5.81	4.91	0.64330	.	0.653601	0.17239	N	0.181630	T	0.00440	0.0014	N	0.13043	0.29	0.26065	N	0.981294	B;B;B;B;B;B	0.16802	0.019;0.01;0.001;0.002;0.005;0.004	B;B;B;B;B;B	0.13407	0.009;0.006;0.003;0.003;0.004;0.006	T	0.05146	-1.0903	10	0.05721	T	0.95	0.0463	13.9017	0.63809	0.3925:0.6075:0.0:0.0	.	103;294;217;217;217;136	B4DT40;B4DZ31;Q9NWS1-6;Q9NWS1-7;Q9NWS1;Q9NWS1-2	.;.;.;.;PR1BP_HUMAN;.	K	217;136;294;103;217;136;184;184	ENSP00000367368:Q217K;ENSP00000332915:Q136K;ENSP00000440850:Q294K;ENSP00000444576:Q103K;ENSP00000351153:Q217K;ENSP00000376643:Q136K;ENSP00000411313:Q184K;ENSP00000393867:Q184K	ENSP00000332915:Q136K	Q	+	1	0	C12orf48	101082499	0.994000	0.37717	0.996000	0.52242	0.976000	0.68499	1.035000	0.30216	1.433000	0.47394	0.460000	0.39030	CAA	C|0.974;A|0.026	0.026	strong		0.383	PARPBP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000397030.2	NM_017915	
OSBPL9	114883	hgsc.bcm.edu	37	1	52250216	52250216	+	Silent	SNP	C	C	T	rs144748323		TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr1:52250216C>T	ENST00000428468.1	+	20	1793	c.1791C>T	c.(1789-1791)ttC>ttT	p.F597F	OSBPL9_ENST00000462759.1_Silent_p.F419F|OSBPL9_ENST00000453295.1_Silent_p.F580F|OSBPL9_ENST00000337809.4_Silent_p.F602F|OSBPL9_ENST00000371710.3_Silent_p.F615F|OSBPL9_ENST00000530544.1_Silent_p.F516F|OSBPL9_ENST00000435686.2_Silent_p.F432F|OSBPL9_ENST00000371714.1_Silent_p.F584F|OSBPL9_ENST00000531828.1_Silent_p.F432F|OSBPL9_ENST00000447887.1_Silent_p.F607F|OSBPL9_ENST00000486942.1_Silent_p.F419F|OSBPL9_ENST00000361556.5_Silent_p.F487F			Q96SU4	OSBL9_HUMAN	oxysterol binding protein-like 9	597					lipid transport (GO:0006869)	cytoplasm (GO:0005737)|endosome (GO:0005768)|Golgi apparatus (GO:0005794)|membrane (GO:0016020)	lipid binding (GO:0008289)			breast(1)|central_nervous_system(1)|endometrium(2)|kidney(4)|large_intestine(2)|lung(3)|pancreas(1)|prostate(3)|skin(1)	18						CTAAACCCTTCTATGGGGGCA	0.403																																					p.F607F		Atlas-SNP	.											.	OSBPL9	192	.	0			c.C1821T						PASS	.	T	,,,,,,	0,4406		0,0,2203	87.0	90.0	89.0		1791,1257,1257,1740,1461,1752,1821	2.7	1.0	1	dbSNP_134	89	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	OSBPL9	NM_024586.5,NM_148904.3,NM_148905.3,NM_148906.2,NM_148907.2,NM_148908.3,NM_148909.3	,,,,,,	0,1,6502	TT,TC,CC		0.0116,0.0,0.0077	,,,,,,	597/737,419/559,419/559,580/720,487/627,584/724,607/747	52250216	1,13005	2203	4300	6503	SO:0001819	synonymous_variant	114883	exon20			ACCCTTCTATGGG	AF392445	CCDS558.1, CCDS41332.1, CCDS41333.1, CCDS41334.1, CCDS41332.2, CCDS41332.3, CCDS41333.2, CCDS44145.1, CCDS55598.1	1p32.3	2013-01-10			ENSG00000117859	ENSG00000117859		"""Oxysterol binding proteins"", ""Pleckstrin homology (PH) domain containing"""	16386	protein-coding gene	gene with protein product		606737					Standard	NM_148904		Approved		uc001csu.3	Q96SU4	OTTHUMG00000008234	ENST00000428468.1:c.1791C>T	1.37:g.52250216C>T		94.0	0.0	0		141.0	74.0	0.524823	NM_148909	B1AKJ8|B3KPQ4|D3DQ31|Q5TFC0|Q6IA67|Q86YQ3|Q8NB17|Q8TAS8|Q96SK4|Q9H9X2	Silent	SNP	ENST00000428468.1	37	CCDS41332.3																																																																																			C|1.000;T|0.000	0.000	weak		0.403	OSBPL9-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000022584.4		
TBX6	6911	hgsc.bcm.edu	37	16	30100401	30100401	+	Missense_Mutation	SNP	C	C	T	rs56098093	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr16:30100401C>T	ENST00000395224.2	-	4	543	c.484G>A	c.(484-486)Ggc>Agc	p.G162S	TBX6_ENST00000553607.1_Missense_Mutation_p.G162S|TBX6_ENST00000279386.2_Missense_Mutation_p.G162S	NM_004608.3	NP_004599.2	O95947	TBX6_HUMAN	T-box 6	162			G -> S (in dbSNP:rs56098093).		anatomical structure morphogenesis (GO:0009653)|cell fate specification (GO:0001708)|mesoderm development (GO:0007498)|mesoderm formation (GO:0001707)|negative regulation of neuron maturation (GO:0014043)|negative regulation of neuron projection development (GO:0010977)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|signal transduction involved in regulation of gene expression (GO:0023019)|somite rostral/caudal axis specification (GO:0032525)	nucleus (GO:0005634)	DNA binding (GO:0003677)|RNA polymerase II activating transcription factor binding (GO:0001102)|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)			endometrium(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(1)|lung(2)|ovary(1)|pancreas(1)	9						TCTGCCTTGCCGCTGGGCTCC	0.647													C|||	4	0.000798722	0.0	0.0	5008	,	,		13926	0.0		0.004	False		,,,				2504	0.0				p.G162S		Atlas-SNP	.											.	TBX6	29	.	0			c.G484A						PASS	.	C	SER/GLY	5,4389	9.9+/-24.2	0,5,2192	47.0	52.0	50.0		484	5.8	1.0	16	dbSNP_129	50	52,8546	32.3+/-84.9	0,52,4247	yes	missense	TBX6	NM_004608.3	56	0,57,6439	TT,TC,CC		0.6048,0.1138,0.4387	probably-damaging	162/437	30100401	57,12935	2197	4299	6496	SO:0001583	missense	6911	exon4			CCTTGCCGCTGGG	AJ007989	CCDS10670.1	16p11.2	2008-02-05			ENSG00000149922	ENSG00000149922		"""T-boxes"""	11605	protein-coding gene	gene with protein product		602427				9888994, 9933572	Standard	NM_004608		Approved		uc010veh.2	O95947	OTTHUMG00000132115	ENST00000395224.2:c.484G>A	16.37:g.30100401C>T	ENSP00000378650:p.Gly162Ser	94.0	0.0	0		80.0	45.0	0.5625	NM_004608	Q8TAS4|Q9HA44	Missense_Mutation	SNP	ENST00000395224.2	37	CCDS10670.1	1	4.578754578754579E-4	0	0.0	0	0.0	0	0.0	1	0.0013192612137203166	C	36	5.633723	0.96682	0.001138	0.006048	ENSG00000149922	ENST00000395224;ENST00000279386;ENST00000553607	D;D;D	0.91237	-2.81;-2.81;-2.81	5.8	5.8	0.92144	p53-like transcription factor, DNA-binding (1);	0.000000	0.85682	D	0.000000	D	0.95287	0.8471	M	0.90977	3.165	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.91635	0.999;0.999	D	0.95019	0.8159	10	0.87932	D	0	.	18.8306	0.92137	0.0:1.0:0.0:0.0	rs56098093	162;162	O95947;Q9HA44	TBX6_HUMAN;.	S	162	ENSP00000378650:G162S;ENSP00000279386:G162S;ENSP00000461223:G162S	ENSP00000279386:G162S	G	-	1	0	TBX6	30007902	0.998000	0.40836	0.997000	0.53966	0.971000	0.66376	4.819000	0.62664	2.747000	0.94245	0.462000	0.41574	GGC	C|0.997;T|0.003	0.003	strong		0.647	TBX6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255157.2	NM_004608, NM_080758	
ITPR1	3708	hgsc.bcm.edu	37	3	4714929	4714929	+	Missense_Mutation	SNP	G	G	A			TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr3:4714929G>A	ENST00000443694.2	+	18	2269	c.2269G>A	c.(2269-2271)Gag>Aag	p.E757K	ITPR1_ENST00000357086.4_Missense_Mutation_p.E772K|ITPR1_ENST00000423119.2_Missense_Mutation_p.E772K|ITPR1_ENST00000302640.8_Missense_Mutation_p.E757K|ITPR1_ENST00000354582.6_Missense_Mutation_p.E772K|ITPR1_ENST00000544951.1_Intron|ITPR1_ENST00000456211.2_Missense_Mutation_p.E757K			Q14643	ITPR1_HUMAN	inositol 1,4,5-trisphosphate receptor, type 1	772					activation of phospholipase C activity (GO:0007202)|blood coagulation (GO:0007596)|calcium ion transport (GO:0006816)|endoplasmic reticulum calcium ion homeostasis (GO:0032469)|energy reserve metabolic process (GO:0006112)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|fibroblast growth factor receptor signaling pathway (GO:0008543)|innate immune response (GO:0045087)|inositol phosphate-mediated signaling (GO:0048016)|intrinsic apoptotic signaling pathway in response to endoplasmic reticulum stress (GO:0070059)|negative regulation of calcium-mediated signaling (GO:0050849)|neurotrophin TRK receptor signaling pathway (GO:0048011)|platelet activation (GO:0030168)|post-embryonic development (GO:0009791)|regulation of insulin secretion (GO:0050796)|release of sequestered calcium ion into cytosol (GO:0051209)|response to hypoxia (GO:0001666)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)|voluntary musculoskeletal movement (GO:0050882)	calcineurin complex (GO:0005955)|endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|nuclear inner membrane (GO:0005637)|nucleolus (GO:0005730)|platelet dense granule membrane (GO:0031088)|platelet dense tubular network (GO:0031094)|platelet dense tubular network membrane (GO:0031095)|postsynaptic density (GO:0014069)|sarcoplasmic reticulum (GO:0016529)	calcium channel inhibitor activity (GO:0019855)|calcium ion transmembrane transporter activity (GO:0015085)|inositol 1,4,5-trisphosphate-sensitive calcium-release channel activity (GO:0005220)|intracellular ligand-gated calcium channel activity (GO:0005218)|phosphatidylinositol binding (GO:0035091)			NS(1)|autonomic_ganglia(1)|breast(10)|endometrium(15)|kidney(6)|large_intestine(27)|liver(1)|lung(27)|ovary(6)|pancreas(1)|prostate(4)|skin(5)|urinary_tract(2)	106				Epithelial(13;0.0199)|OV - Ovarian serous cystadenocarcinoma(96;0.0361)|all cancers(10;0.0982)	Caffeine(DB00201)	CATGTCTGACGAGAACCTGCC	0.557																																					p.E772K		Atlas-SNP	.											ITPR1_ENST00000357086,NS,carcinoma,0,3	ITPR1	659	3	0			c.G2314A						scavenged	.						67.0	70.0	69.0					3																	4714929		2082	4212	6294	SO:0001583	missense	3708	exon21			TCTGACGAGAACC	D26070	CCDS46740.1, CCDS46740.2, CCDS54550.1, CCDS54551.1	3p26.1	2014-06-12	2011-04-28			ENSG00000150995		"""Ion channels / Inositol triphosphate receptors"""	6180	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 94"""	147265	"""spinocerebellar ataxia 15"", ""spinocerebellar ataxia 16"", ""spinocerebellar ataxia 29"""	SCA15, SCA16, SCA29		7945203, 7500840, 17590087, 17932120, 22986007	Standard	NM_001099952		Approved	Insp3r1, IP3R1, ACV, PPP1R94	uc003bqc.3	Q14643		ENST00000443694.2:c.2269G>A	3.37:g.4714929G>A	ENSP00000401671:p.Glu757Lys	91.0	1.0	0.010989		93.0	44.0	0.473118	NM_001099952	E7EPX7|E9PDE9|Q14660|Q99897	Missense_Mutation	SNP	ENST00000443694.2	37	CCDS54551.1	.	.	.	.	.	.	.	.	.	.	G	14.31	2.495999	0.44352	.	.	ENSG00000150995	ENST00000356617;ENST00000302640;ENST00000354582;ENST00000423119;ENST00000357086;ENST00000456211;ENST00000443694	D;D;D;D;D;D	0.91686	-2.89;-2.89;-2.88;-2.88;-2.89;-2.89	4.74	3.85	0.44370	.	0.000000	0.85682	D	0.000000	D	0.92763	0.7699	L	0.45051	1.395	0.80722	D	1	P;B;D	0.76494	0.603;0.443;0.999	B;B;D	0.63597	0.142;0.06;0.916	D	0.90586	0.4533	10	0.22706	T	0.39	.	14.273	0.66162	0.0:0.0:0.8496:0.1504	.	757;772;772	E7EPX7;Q14643;G5E9P1	.;ITPR1_HUMAN;.	K	772;757;772;772;772;757;757	ENSP00000306253:E757K;ENSP00000346595:E772K;ENSP00000405934:E772K;ENSP00000349597:E772K;ENSP00000397885:E757K;ENSP00000401671:E757K	ENSP00000306253:E757K	E	+	1	0	ITPR1	4689929	1.000000	0.71417	0.797000	0.32132	0.308000	0.27856	9.511000	0.98006	1.327000	0.45338	-0.282000	0.10007	GAG	.	.	none		0.557	ITPR1-004	KNOWN	non_canonical_conserved|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000337982.3	NM_002222	
ANKS1B	56899	hgsc.bcm.edu	37	12	99139552	99139552	+	Intron	SNP	C	C	T			TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr12:99139552C>T	ENST00000547776.2	-	25	3672				ANKS1B_ENST00000547446.1_Missense_Mutation_p.G384S|ANKS1B_ENST00000341752.7_Intron|ANKS1B_ENST00000549025.2_Missense_Mutation_p.G347S|ANKS1B_ENST00000333732.7_Missense_Mutation_p.G279S|ANKS1B_ENST00000550693.2_Missense_Mutation_p.G440S|ANKS1B_ENST00000546568.1_Missense_Mutation_p.G416S|ANKS1B_ENST00000547010.1_Intron|ANKS1B_ENST00000332712.7_Missense_Mutation_p.G440S|ANKS1B_ENST00000549558.2_Intron|ANKS1B_ENST00000329257.7_Intron|ANKS1B_ENST00000549493.2_Missense_Mutation_p.G500S	NM_152788.4	NP_690001.3	Q7Z6G8	ANS1B_HUMAN	ankyrin repeat and sterile alpha motif domain containing 1B							cell junction (GO:0030054)|cell projection (GO:0042995)|cytoplasm (GO:0005737)|nucleus (GO:0005634)|postsynaptic membrane (GO:0045211)	ephrin receptor binding (GO:0046875)			NS(1)|breast(1)|cervix(1)|endometrium(4)|kidney(6)|large_intestine(15)|lung(38)|pancreas(1)|prostate(2)|skin(1)	70		all_cancers(3;0.0197)|all_epithelial(3;0.0101)|Esophageal squamous(3;0.0559)|Breast(359;0.209)		OV - Ovarian serous cystadenocarcinoma(2;2.89e-08)|Epithelial(2;6.12e-08)|all cancers(2;4.07e-06)		GTATTAATGCCCCTCTTGGCT	0.537																																					p.G500S		Atlas-SNP	.											.	ANKS1B	180	.	0			c.G1498A						PASS	.						107.0	113.0	111.0					12																	99139552		1930	4139	6069	SO:0001627	intron_variant	56899	exon13			TAATGCCCCTCTT	AF145204	CCDS55864.1, CCDS55865.1, CCDS55866.1, CCDS55867.1, CCDS55868.1, CCDS55869.1, CCDS55870.1, CCDS55871.1, CCDS55872.1	12q23.1	2013-01-10						"""Sterile alpha motif (SAM) domain containing"", ""Ankyrin repeat domain containing"""	24600	protein-coding gene	gene with protein product		607815				10490826, 12415113	Standard	NM_020140		Approved	EB-1, AIDA-1, cajalin-2, ANKS2	uc001tge.2	Q7Z6G8		ENST00000547776.2:c.3672+5580G>A	12.37:g.99139552C>T		106.0	0.0	0		82.0	38.0	0.463415	NM_181670	A5PKY5|A7E259|A8K153|A8MSN4|B4DFP6|B4DH98|F8VPM3|F8VZR9|F8WC27|Q5XLJ0|Q6IVB5|Q6NUS4|Q7Z6G6|Q7Z6G7|Q8TAP3|Q9NRX7|Q9Y5K9	Missense_Mutation	SNP	ENST00000547776.2	37	CCDS55872.1	.	.	.	.	.	.	.	.	.	.	C	8.874	0.949903	0.18431	.	.	ENSG00000185046	ENST00000550693;ENST00000549025;ENST00000549493;ENST00000547446;ENST00000333732;ENST00000546568;ENST00000332712;ENST00000407362	T;T;T;T;T;T;T	0.68903	0.01;0.57;0.0;-0.36;-0.04;0.07;0.33	4.66	3.76	0.43208	.	.	.	.	.	T	0.57548	0.2061	N	0.04508	-0.205	0.34764	D	0.733028	B;D;D;D;D;B;B;D;B	0.89917	0.019;1.0;1.0;1.0;1.0;0.14;0.027;1.0;0.077	B;D;D;D;D;B;B;D;B	0.85130	0.016;0.997;0.994;0.997;0.994;0.076;0.042;0.997;0.09	T	0.57837	-0.7742	9	0.02654	T	1	.	12.6737	0.56882	0.0:0.9195:0.0:0.0805	.	384;279;280;440;389;464;416;500;347	F8VPM3;F8VR14;B7Z9I9;Q7Z6G8-5;B1VKB5;F8VQW6;Q7Z6G8-2;Q7Z6G8-3;F8VZR9	.;.;.;.;.;.;.;.;.	S	440;347;500;384;279;416;440;340	ENSP00000447999:G440S;ENSP00000447312:G347S;ENSP00000448203:G500S;ENSP00000450015:G384S;ENSP00000331256:G279S;ENSP00000448205:G416S;ENSP00000332683:G440S	ENSP00000332683:G440S	G	-	1	0	ANKS1B	97663683	1.000000	0.71417	1.000000	0.80357	0.990000	0.78478	4.436000	0.59948	1.060000	0.40578	0.549000	0.68633	GGC	.	.	none		0.537	ANKS1B-003	KNOWN	basic|appris_candidate_longest|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000408421.3	NM_020140	
DAB2	1601	hgsc.bcm.edu	37	5	39381651	39381651	+	Missense_Mutation	SNP	G	G	A			TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr5:39381651G>A	ENST00000320816.6	-	11	1876	c.1409C>T	c.(1408-1410)gCg>gTg	p.A470V	DAB2_ENST00000509337.1_Missense_Mutation_p.A449V|DAB2_ENST00000545653.1_Missense_Mutation_p.A449V|DAB2_ENST00000339788.6_Missense_Mutation_p.A252V	NM_001343.3	NP_001334.2	P98082	DAB2_HUMAN	Dab, mitogen-responsive phosphoprotein, homolog 2 (Drosophila)	470					activation of JUN kinase activity (GO:0007257)|apoptotic process (GO:0006915)|cell morphogenesis involved in differentiation (GO:0000904)|cell proliferation (GO:0008283)|cellular response to transforming growth factor beta stimulus (GO:0071560)|clathrin coat assembly (GO:0048268)|endoderm development (GO:0007492)|excretion (GO:0007588)|in utero embryonic development (GO:0001701)|leading edge cell differentiation (GO:0035026)|membrane organization (GO:0061024)|myeloid cell differentiation (GO:0030099)|negative regulation of androgen receptor signaling pathway (GO:0060766)|negative regulation of apoptotic process (GO:0043066)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of extrinsic apoptotic signaling pathway (GO:2001237)|negative regulation of protein binding (GO:0032091)|negative regulation of protein localization to plasma membrane (GO:1903077)|negative regulation of transcription, DNA-templated (GO:0045892)|pinocytosis (GO:0006907)|positive regulation of cell migration (GO:0030335)|positive regulation of clathrin-mediated endocytosis (GO:2000370)|positive regulation of early endosome to late endosome transport (GO:2000643)|positive regulation of endocytosis (GO:0045807)|positive regulation of epithelial to mesenchymal transition (GO:0010718)|positive regulation of integrin-mediated signaling pathway (GO:2001046)|positive regulation of pathway-restricted SMAD protein phosphorylation (GO:0010862)|positive regulation of proteasomal ubiquitin-dependent protein catabolic process (GO:0032436)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of receptor recycling (GO:0001921)|positive regulation of SMAD protein import into nucleus (GO:0060391)|positive regulation of substrate adhesion-dependent cell spreading (GO:1900026)|positive regulation of transcription elongation from RNA polymerase II promoter (GO:0032968)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of transforming growth factor beta receptor signaling pathway (GO:0030511)|positive regulation of Wnt signaling pathway, planar cell polarity pathway (GO:2000096)|protein transport (GO:0015031)|receptor-mediated endocytosis (GO:0006898)|Wnt signaling pathway (GO:0016055)	apical plasma membrane (GO:0016324)|clathrin coat of coated pit (GO:0030132)|clathrin-coated vesicle (GO:0030136)|coated pit (GO:0005905)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|intracellular membrane-bounded organelle (GO:0043231)|lysosomal membrane (GO:0005765)|nucleolus (GO:0005730)|plasma membrane (GO:0005886)	cargo receptor activity (GO:0038024)|clathrin adaptor activity (GO:0035615)|phosphatidylinositol-4,5-bisphosphate binding (GO:0005546)|protein C-terminus binding (GO:0008022)|SMAD binding (GO:0046332)			autonomic_ganglia(1)|breast(3)|central_nervous_system(1)|endometrium(1)|kidney(5)|large_intestine(9)|lung(19)|prostate(2)|skin(4)|upper_aerodigestive_tract(2)	47	all_lung(31;0.000197)		Epithelial(62;0.137)			TGTGGGTGACGCCTGGCCTGA	0.582																																					p.A470V		Atlas-SNP	.											.	DAB2	124	.	0			c.C1409T						PASS	.						129.0	126.0	127.0					5																	39381651		2203	4300	6503	SO:0001583	missense	1601	exon11			GGTGACGCCTGGC	U53446	CCDS34149.1, CCDS58946.1	5p13.1	2013-10-03	2013-03-08		ENSG00000153071	ENSG00000153071			2662	protein-coding gene	gene with protein product		601236	"""disabled (Drosophila) homolog 2 (mitogen-responsive phosphoprotein)"", ""disabled homolog 2, mitogen-responsive phosphoprotein (Drosophila)"""			8660969, 9620555	Standard	NM_001343		Approved	DOC-2	uc003jlx.3	P98082	OTTHUMG00000162043	ENST00000320816.6:c.1409C>T	5.37:g.39381651G>A	ENSP00000313391:p.Ala470Val	167.0	0.0	0		137.0	52.0	0.379562	NM_001343	A6NES5|Q13598|Q9BTY0|Q9UK04	Missense_Mutation	SNP	ENST00000320816.6	37	CCDS34149.1	.	.	.	.	.	.	.	.	.	.	G	8.024	0.760343	0.15914	.	.	ENSG00000153071	ENST00000320816;ENST00000339788;ENST00000545653;ENST00000509337	T;T;T;T	0.38240	1.24;1.15;1.21;1.21	5.96	-0.00481	0.14020	.	1.030630	0.07591	N	0.921918	T	0.12008	0.0292	N	0.02539	-0.55	0.09310	N	1	B;B	0.12013	0.005;0.005	B;B	0.06405	0.001;0.002	T	0.27938	-1.0059	10	0.02654	T	1	11.0513	6.3792	0.21525	0.5083:0.0:0.3716:0.12	.	470;449	P98082;P98082-3	DAB2_HUMAN;.	V	470;252;449;449	ENSP00000313391:A470V;ENSP00000345508:A252V;ENSP00000439919:A449V;ENSP00000426245:A449V	ENSP00000313391:A470V	A	-	2	0	DAB2	39417408	0.296000	0.24398	0.041000	0.18516	0.818000	0.46254	0.497000	0.22514	-0.303000	0.08856	-0.345000	0.07892	GCG	.	.	none		0.582	DAB2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000367014.1	NM_001343	
NOTCH4	4855	hgsc.bcm.edu	37	6	32163541	32163541	+	Silent	SNP	A	A	C	rs1044507	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr6:32163541A>C	ENST00000375023.3	-	30	5823	c.5685T>G	c.(5683-5685)tcT>tcG	p.S1895S	GPSM3_ENST00000375043.3_5'Flank|NOTCH4_ENST00000443903.2_3'UTR|GPSM3_ENST00000375040.3_5'Flank|GPSM3_ENST00000487761.1_5'Flank	NM_004557.3	NP_004548.3	Q99466	NOTC4_HUMAN	notch 4	1895					cell differentiation (GO:0030154)|cell fate determination (GO:0001709)|embryo development (GO:0009790)|endothelial cell morphogenesis (GO:0001886)|gene expression (GO:0010467)|hemopoiesis (GO:0030097)|mammary gland development (GO:0030879)|morphogenesis of a branching structure (GO:0001763)|negative regulation of cell differentiation (GO:0045596)|negative regulation of endothelial cell differentiation (GO:0045602)|Notch receptor processing (GO:0007220)|Notch signaling pathway (GO:0007219)|patterning of blood vessels (GO:0001569)|positive regulation of transcription of Notch receptor target (GO:0007221)|positive regulation of transcription, DNA-templated (GO:0045893)|transcription initiation from RNA polymerase II promoter (GO:0006367)	cell surface (GO:0009986)|cytosol (GO:0005829)|endoplasmic reticulum membrane (GO:0005789)|extracellular region (GO:0005576)|Golgi membrane (GO:0000139)|integral component of plasma membrane (GO:0005887)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|protein heterodimerization activity (GO:0046982)|receptor activity (GO:0004872)			NS(1)|autonomic_ganglia(1)|breast(4)|central_nervous_system(4)|cervix(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(11)|lung(47)|ovary(5)|prostate(4)|skin(10)|upper_aerodigestive_tract(1)|urinary_tract(1)	100						TCCGGCAATGAGAATAGGCCC	0.701													A|||	179	0.0357428	0.0144	0.0187	5008	,	,		13590	0.0278		0.0258	False		,,,				2504	0.0951				p.S1895S		Atlas-SNP	.											.	NOTCH4	201	.	0			c.T5685G						PASS	.	A		53,2953		0,53,1450	15.0	20.0	18.0		5685	-5.5	0.0	6	dbSNP_86	18	135,5251		3,129,2561	no	coding-synonymous	NOTCH4	NM_004557.3		3,182,4011	CC,CA,AA		2.5065,1.7631,2.2402		1895/2004	32163541	188,8204	1503	2693	4196	SO:0001819	synonymous_variant	4855	exon30			GCAATGAGAATAG		CCDS34420.1	6p21.3	2013-01-10	2010-06-24		ENSG00000204301	ENSG00000204301		"""Ankyrin repeat domain containing"""	7884	protein-coding gene	gene with protein product		164951	"""Notch (Drosophila) homolog 4"", ""Notch homolog 4 (Drosophila)"""	INT3		7835890	Standard	NM_004557		Approved		uc003obb.3	Q99466	OTTHUMG00000031044	ENST00000375023.3:c.5685T>G	6.37:g.32163541A>C		20.0	0.0	0		31.0	30.0	0.967742	NM_004557	B0V183|B0V1X5|O00306|Q5SSY7|Q99458|Q99940|Q9H3S8|Q9UII9|Q9UIJ0	Silent	SNP	ENST00000375023.3	37	CCDS34420.1																																																																																			A|0.974;C|0.026	0.026	strong		0.701	NOTCH4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076045.2		
RYR2	6262	hgsc.bcm.edu	37	1	237947171	237947171	+	Silent	SNP	G	G	A	rs41267517		TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr1:237947171G>A	ENST00000366574.2	+	90	12476	c.12159G>A	c.(12157-12159)gaG>gaA	p.E4053E	RYR2_ENST00000360064.6_Silent_p.E4059E|RYR2_ENST00000609119.1_3'UTR|RYR2_ENST00000542537.1_Silent_p.E4037E	NM_001035.2	NP_001026.2	Q92736	RYR2_HUMAN	ryanodine receptor 2 (cardiac)	4053					BMP signaling pathway (GO:0030509)|calcium ion transport (GO:0006816)|calcium ion transport into cytosol (GO:0060402)|calcium-mediated signaling (GO:0019722)|calcium-mediated signaling using intracellular calcium source (GO:0035584)|canonical Wnt signaling pathway (GO:0060070)|cardiac muscle contraction (GO:0060048)|cardiac muscle hypertrophy (GO:0003300)|cell communication by electrical coupling involved in cardiac conduction (GO:0086064)|cellular calcium ion homeostasis (GO:0006874)|cellular response to caffeine (GO:0071313)|cellular response to epinephrine stimulus (GO:0071872)|cytosolic calcium ion homeostasis (GO:0051480)|detection of calcium ion (GO:0005513)|embryonic heart tube morphogenesis (GO:0003143)|establishment of protein localization to endoplasmic reticulum (GO:0072599)|ion transmembrane transport (GO:0034220)|left ventricular cardiac muscle tissue morphogenesis (GO:0003220)|positive regulation of calcium-transporting ATPase activity (GO:1901896)|positive regulation of heart rate (GO:0010460)|positive regulation of ryanodine-sensitive calcium-release channel activity by adrenergic receptor signaling pathway involved in positive regulation of cardiac muscle contraction (GO:0086094)|positive regulation of sequestering of calcium ion (GO:0051284)|Purkinje myocyte to ventricular cardiac muscle cell signaling (GO:0086029)|regulation of cardiac muscle contraction (GO:0055117)|regulation of cardiac muscle contraction by regulation of the release of sequestered calcium ion (GO:0010881)|regulation of heart rate (GO:0002027)|release of sequestered calcium ion into cytosol (GO:0051209)|release of sequestered calcium ion into cytosol by sarcoplasmic reticulum (GO:0014808)|response to caffeine (GO:0031000)|response to hypoxia (GO:0001666)|response to redox state (GO:0051775)|sarcoplasmic reticulum calcium ion transport (GO:0070296)|transmembrane transport (GO:0055085)|type B pancreatic cell apoptotic process (GO:0097050)|ventricular cardiac muscle cell action potential (GO:0086005)	calcium channel complex (GO:0034704)|extracellular vesicular exosome (GO:0070062)|junctional sarcoplasmic reticulum membrane (GO:0014701)|membrane (GO:0016020)|plasma membrane (GO:0005886)|protein complex (GO:0043234)|sarcoplasmic reticulum (GO:0016529)|sarcoplasmic reticulum membrane (GO:0033017)|smooth endoplasmic reticulum (GO:0005790)|Z disc (GO:0030018)	calcium channel activity (GO:0005262)|calcium ion binding (GO:0005509)|calcium-induced calcium release activity (GO:0048763)|calcium-release channel activity (GO:0015278)|calmodulin binding (GO:0005516)|enzyme binding (GO:0019899)|identical protein binding (GO:0042802)|intracellular ligand-gated calcium channel activity (GO:0005218)|ion channel binding (GO:0044325)|protein kinase A catalytic subunit binding (GO:0034236)|protein kinase A regulatory subunit binding (GO:0034237)|ryanodine-sensitive calcium-release channel activity (GO:0005219)|suramin binding (GO:0043924)	p.E4051D(1)		NS(4)|breast(8)|central_nervous_system(11)|cervix(2)|endometrium(39)|haematopoietic_and_lymphoid_tissue(5)|kidney(17)|large_intestine(83)|liver(4)|lung(353)|ovary(18)|pancreas(5)|prostate(12)|skin(8)|stomach(1)|upper_aerodigestive_tract(12)|urinary_tract(4)	586	Ovarian(103;0.103)	all_cancers(173;0.000368)|Melanoma(53;0.0179)|all_epithelial(177;0.0225)	OV - Ovarian serous cystadenocarcinoma(106;0.00606)			AAGCGATGGAGAGCCATAAGC	0.448													G|||	1	0.000199681	0.0	0.0	5008	,	,		19393	0.0		0.001	False		,,,				2504	0.0				p.E4053E		Atlas-SNP	.											RYR2,NS,carcinoma,0,1	RYR2	1273	1	1	Substitution - Missense(1)	lung(1)	c.G12159A						PASS	.	G		1,3925		0,1,1962	45.0	44.0	44.0		12159	4.2	1.0	1	dbSNP_127	44	15,8295		0,15,4140	no	coding-synonymous	RYR2	NM_001035.2		0,16,6102	AA,AG,GG		0.1805,0.0255,0.1308		4053/4968	237947171	16,12220	1963	4155	6118	SO:0001819	synonymous_variant	6262	exon90			GATGGAGAGCCAT	X91869	CCDS55691.1	1q43	2014-09-17			ENSG00000198626	ENSG00000198626		"""Ion channels / Ryanodine receptors"", ""EF-hand domain containing"""	10484	protein-coding gene	gene with protein product		180902	"""arrhythmogenic right ventricular dysplasia 2"""	ARVD2		2380170, 8406504, 11159936	Standard	NM_001035		Approved	ARVC2, VTSIP	uc001hyl.1	Q92736	OTTHUMG00000039543	ENST00000366574.2:c.12159G>A	1.37:g.237947171G>A		94.0	0.0	0		110.0	44.0	0.4	NM_001035	Q15411|Q546N8|Q5T3P2	Silent	SNP	ENST00000366574.2	37	CCDS55691.1																																																																																			G|0.999;A|0.001	0.001	weak		0.448	RYR2-001	KNOWN	non_canonical_conserved|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000095402.2	NM_001035	
OR52W1	120787	hgsc.bcm.edu	37	11	6220596	6220596	+	Missense_Mutation	SNP	G	G	C			TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr11:6220596G>C	ENST00000311352.2	+	1	221	c.143G>C	c.(142-144)gGa>gCa	p.G48A	RP11-290F24.6_ENST00000600308.1_lincRNA	NM_001005178.1	NP_001005178.1	Q6IF63	O52W1_HUMAN	olfactory receptor, family 52, subfamily W, member 1	48						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			endometrium(2)|kidney(2)|large_intestine(1)|lung(6)	11		Medulloblastoma(188;0.00776)|all_neural(188;0.0652)|Breast(177;0.114)		Epithelial(150;2.13e-08)|BRCA - Breast invasive adenocarcinoma(625;0.135)		CTGGGCAATGGAGCACTGCCG	0.562																																					p.G48A		Atlas-SNP	.											.	OR52W1	33	.	0			c.G143C						PASS	.						58.0	51.0	53.0					11																	6220596		2201	4296	6497	SO:0001583	missense	120787	exon1			GCAATGGAGCACT	AB065511	CCDS31407.1	11p15.4	2012-08-09		2004-03-10	ENSG00000175485	ENSG00000175485		"""GPCR / Class A : Olfactory receptors"""	15239	protein-coding gene	gene with protein product				OR52W1P			Standard	NM_001005178		Approved		uc010qzz.2	Q6IF63	OTTHUMG00000165378	ENST00000311352.2:c.143G>C	11.37:g.6220596G>C	ENSP00000309673:p.Gly48Ala	172.0	0.0	0		165.0	81.0	0.490909	NM_001005178	Q8NH78	Missense_Mutation	SNP	ENST00000311352.2	37	CCDS31407.1	.	.	.	.	.	.	.	.	.	.	G	8.442	0.851009	0.17034	.	.	ENSG00000175485	ENST00000311352	T	0.02050	4.48	5.92	2.93	0.34026	GPCR, rhodopsin-like superfamily (1);	0.580151	0.13011	N	0.420892	T	0.02380	0.0073	L	0.41492	1.28	0.09310	N	1	B	0.12630	0.006	B	0.06405	0.002	T	0.44757	-0.9307	10	0.25106	T	0.35	.	7.8661	0.29539	0.0:0.307:0.328:0.365	.	48	Q6IF63	O52W1_HUMAN	A	48	ENSP00000309673:G48A	ENSP00000309673:G48A	G	+	2	0	OR52W1	6177172	0.000000	0.05858	0.759000	0.31340	0.903000	0.53119	-0.313000	0.08103	0.819000	0.34492	0.655000	0.94253	GGA	.	.	none		0.562	OR52W1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000383758.1	NM_001005178	
ANG	283	hgsc.bcm.edu	37	14	21161931	21161931	+	Missense_Mutation	SNP	A	A	G	rs121909541		TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr14:21161931A>G	ENST00000336811.6	+	2	808	c.208A>G	c.(208-210)Att>Gtt	p.I70V	RP11-903H12.3_ENST00000554286.1_RNA|RNASE4_ENST00000555597.1_Intron|ANG_ENST00000554073.1_Intron|RNASE4_ENST00000397995.2_Intron|AL163636.6_ENST00000553909.1_Intron|RNASE4_ENST00000304704.4_Intron|ANG_ENST00000397990.4_Missense_Mutation_p.I70V|RNASE4_ENST00000555835.1_Intron	NM_001145.4	NP_001136.1	P03950	ANGI_HUMAN	angiogenin, ribonuclease, RNase A family, 5	70			I -> V (in some ALS9 patients; pathogenicity uncertain; reduced ribonucleolytic activity; moderate reduction of thermal stability). {ECO:0000269|PubMed:16501576, ECO:0000269|PubMed:18087731}.		actin filament polymerization (GO:0030041)|activation of phospholipase A2 activity (GO:0032431)|activation of phospholipase C activity (GO:0007202)|activation of protein kinase B activity (GO:0032148)|angiogenesis (GO:0001525)|cell communication (GO:0007154)|cell death (GO:0008219)|cell migration (GO:0016477)|diacylglycerol biosynthetic process (GO:0006651)|homeostatic process (GO:0042592)|negative regulation of smooth muscle cell proliferation (GO:0048662)|negative regulation of translation (GO:0017148)|nucleic acid phosphodiester bond hydrolysis (GO:0090305)|oocyte maturation (GO:0001556)|ovarian follicle development (GO:0001541)|placenta development (GO:0001890)|positive regulation of endothelial cell proliferation (GO:0001938)|positive regulation of phosphorylation (GO:0042327)|positive regulation of protein secretion (GO:0050714)|response to hormone (GO:0009725)|response to hypoxia (GO:0001666)|RNA phosphodiester bond hydrolysis (GO:0090501)|rRNA transcription (GO:0009303)	angiogenin-PRI complex (GO:0032311)|basal lamina (GO:0005605)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|growth cone (GO:0030426)|neuronal cell body (GO:0043025)|nucleolus (GO:0005730)|nucleus (GO:0005634)	actin binding (GO:0003779)|copper ion binding (GO:0005507)|DNA binding (GO:0003677)|endonuclease activity (GO:0004519)|heparin binding (GO:0008201)|peptide binding (GO:0042277)|receptor binding (GO:0005102)|ribonuclease activity (GO:0004540)|rRNA binding (GO:0019843)			endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(1)|ovary(1)|prostate(1)	5	all_cancers(95;0.00387)	all_cancers(140;0.196)|all_epithelial(140;0.156)	Epithelial(56;5.13e-07)|all cancers(55;4.73e-06)	OV - Ovarian serous cystadenocarcinoma(311;3.25e-17)|GBM - Glioblastoma multiforme(265;5.56e-07)		CAACACATTTATTCATGGCAA	0.478													A|||	1	0.000199681	0.0	0.0	5008	,	,		21764	0.0		0.001	False		,,,				2504	0.0				p.I70V		Atlas-SNP	.											.	ANG	8	.	0			c.A208G	GRCh37	CM060832	ANG	M	rs121909541	PASS	.	A	VAL/ILE,VAL/ILE,,	2,4404	4.2+/-10.8	0,2,2201	118.0	100.0	106.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	208,208,,	-3.4	0.8	14	dbSNP_133	106	5,8595	4.3+/-15.6	0,5,4295	yes	missense,missense,intron,intron	ANG,RNASE4	NM_001097577.2,NM_001145.4,NM_002937.3,NM_194431.1	29,29,,	0,7,6496	GG,GA,AA		0.0581,0.0454,0.0538	benign,benign,,	70/148,70/148,,	21161931	7,12999	2203	4300	6503	SO:0001583	missense	283	exon2			ACATTTATTCATG		CCDS9554.1	14q11.1-q11.2	2014-09-17			ENSG00000214274	ENSG00000214274	3.1.27.-	"""Ribonucleases, RNase A"""	483	protein-coding gene	gene with protein product		105850				1978563	Standard	NM_001145		Approved	RNASE5	uc001vxw.4	P03950	OTTHUMG00000029576	ENST00000336811.6:c.208A>G	14.37:g.21161931A>G	ENSP00000336762:p.Ile70Val	172.0	0.0	0		163.0	85.0	0.521472	NM_001097577	Q05CV1|Q53X86|Q6P5T2|Q8WXE7	Missense_Mutation	SNP	ENST00000336811.6	37	CCDS9554.1	.	.	.	.	.	.	.	.	.	.	A	1.031	-0.681810	0.03353	4.54E-4	5.81E-4	ENSG00000214274	ENST00000336811;ENST00000397990	D;D	0.95788	-3.81;-3.81	4.73	-3.36	0.04913	Ribonuclease A, domain (4);	0.109560	0.31392	N	0.007721	D	0.88347	0.6412	N	0.25332	0.735	0.58432	A	0.999999	B	0.29508	0.246	B	0.30646	0.118	T	0.78914	-0.2016	9	0.15066	T	0.55	.	11.1811	0.48629	0.3918:0.0:0.6082:0.0	.	70	P03950	ANGI_HUMAN	V	70	ENSP00000336762:I70V;ENSP00000381077:I70V	ENSP00000336762:I70V	I	+	1	0	ANG	20231771	0.994000	0.37717	0.846000	0.33378	0.093000	0.18481	0.112000	0.15479	-0.882000	0.03987	-1.231000	0.01572	ATT	A|0.999;G|0.001	0.001	strong		0.478	ANG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000073731.3	NM_001097577	
FAM181B	220382	hgsc.bcm.edu	37	11	82444668	82444668	+	Missense_Mutation	SNP	C	C	G	rs144429777	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr11:82444668C>G	ENST00000329203.3	-	1	238	c.104G>C	c.(103-105)gGc>gCc	p.G35A		NM_175885.3	NP_787081.2	A6NEQ2	F181B_HUMAN	family with sequence similarity 181, member B	35										large_intestine(1)|lung(2)|prostate(1)	4						GAAACAGCAGCCCTTGTCCAG	0.721													C|||	17	0.00339457	0.0	0.0014	5008	,	,		7441	0.0		0.008	False		,,,				2504	0.0082				p.G35A		Atlas-SNP	.											.	FAM181B	14	.	0			c.G104C						PASS	.	C	ALA/GLY	3,4381		0,3,2189	11.0	13.0	12.0		104	4.0	1.0	11	dbSNP_134	12	28,8548		0,28,4260	yes	missense	FAM181B	NM_175885.3	60	0,31,6449	GG,GC,CC		0.3265,0.0684,0.2392	possibly-damaging	35/427	82444668	31,12929	2192	4288	6480	SO:0001583	missense	220382	exon1			CAGCAGCCCTTGT	AK095054, BC039262	CCDS31648.1	11q14.1	2011-11-30			ENSG00000182103	ENSG00000182103			28512	protein-coding gene	gene with protein product						12477932	Standard	NM_175885		Approved	LOC220382, MGC33846	uc001ozp.3	A6NEQ2	OTTHUMG00000166869	ENST00000329203.3:c.104G>C	11.37:g.82444668C>G	ENSP00000365295:p.Gly35Ala	21.0	0.0	0		27.0	21.0	0.777778	NM_175885	B2RWP1	Missense_Mutation	SNP	ENST00000329203.3	37	CCDS31648.1	.	.	.	.	.	.	.	.	.	.	C	11.54	1.668634	0.29604	6.84E-4	0.003265	ENSG00000182103	ENST00000329203	T	0.36340	1.26	4.04	4.04	0.47022	.	0.636557	0.14564	U	0.311877	T	0.47358	0.1441	L	0.44542	1.39	0.25758	N	0.984974	D	0.89917	1.0	D	0.66602	0.945	T	0.22173	-1.0224	9	.	.	.	.	10.1105	0.42559	0.0:0.9066:0.0:0.0934	.	35	A6NEQ2	F181B_HUMAN	A	35	ENSP00000365295:G35A	.	G	-	2	0	FAM181B	82122316	1.000000	0.71417	1.000000	0.80357	0.007000	0.05969	2.111000	0.41883	2.073000	0.62155	0.455000	0.32223	GGC	C|0.997;G|0.003	0.003	strong		0.721	FAM181B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391626.1	NM_175885	
FMN1	342184	hgsc.bcm.edu	37	15	33359093	33359093	+	Intron	SNP	T	T	C	rs74655292	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr15:33359093T>C	ENST00000559047.1	-	3	2043				FMN1_ENST00000559150.1_Intron|FMN1_ENST00000561249.1_Intron|FMN1_ENST00000558197.1_Silent_p.K331K|FMN1_ENST00000334528.9_Silent_p.K331K			Q68DA7	FMN1_HUMAN	formin 1						actin nucleation (GO:0045010)	actin filament (GO:0005884)|cell junction (GO:0030054)|cytoplasm (GO:0005737)|nucleus (GO:0005634)|plasma membrane (GO:0005886)				endometrium(3)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(3)|lung(14)|ovary(2)|prostate(1)|upper_aerodigestive_tract(3)	29		all_lung(180;1.14e-07)		all cancers(64;3.05e-15)|Epithelial(43;1.67e-10)|GBM - Glioblastoma multiforme(186;4.95e-05)|BRCA - Breast invasive adenocarcinoma(123;0.0262)		GATCAGTTGCTTTCTTCTCAC	0.522													T|||	29	0.00579073	0.0008	0.0202	5008	,	,		19662	0.0		0.0089	False		,,,				2504	0.0051				p.K331K		Atlas-SNP	.											.	FMN1	174	.	0			c.A993G						PASS	.	T		8,4060		0,8,2026	62.0	65.0	64.0		993	3.9	0.0	15	dbSNP_132	64	89,8257		0,89,4084	no	coding-synonymous	FMN1	NM_001103184.2		0,97,6110	CC,CT,TT		1.0664,0.1967,0.7814		331/1197	33359093	97,12317	2034	4173	6207	SO:0001627	intron_variant	342184	exon1			AGTTGCTTTCTTC	AH002864	CCDS45209.1, CCDS61581.1, CCDS61582.1	15q13.3	2013-06-13	2005-01-20	2005-01-22	ENSG00000248905	ENSG00000248905			3768	protein-coding gene	gene with protein product	"""limb deformity protein"""	136535	"""formin (limb deformity)"""	LD, FMN		1673046	Standard	NM_001277313		Approved	DKFZP686C2281, FLJ45135, MGC125288, MGC125289	uc031qrh.1	Q68DA7	OTTHUMG00000172201	ENST00000559047.1:c.2044-1818A>G	15.37:g.33359093T>C		206.0	0.0	0		228.0	106.0	0.464912	NM_001103184	Q3B7I6|Q3ZAR4|Q6ZSY1	Silent	SNP	ENST00000559047.1	37																																																																																				T|0.992;C|0.008	0.008	strong		0.522	FMN1-005	NOVEL	basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000417414.1	NM_001103184	
ZNF519	162655	hgsc.bcm.edu	37	18	14124427	14124427	+	Missense_Mutation	SNP	A	A	G	rs16941623	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr18:14124427A>G	ENST00000590202.1	-	2	204	c.52T>C	c.(52-54)Tgg>Cgg	p.W18R	ZNF519_ENST00000589498.1_Missense_Mutation_p.W18R|ZNF519_ENST00000589203.1_Intron	NM_145287.3	NP_660330.2	Q8TB69	ZN519_HUMAN	zinc finger protein 519	18	KRAB. {ECO:0000255|PROSITE- ProRule:PRU00119}.		W -> R (in dbSNP:rs16941623).		negative regulation of transcription during meiosis (GO:0051038)|spermatogenesis (GO:0007283)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			breast(2)|endometrium(1)|kidney(1)|large_intestine(4)|lung(9)|urinary_tract(1)	18						AGGCATTTCCACTCTTCTGGA	0.403													A|||	37	0.00738818	0.0272	0.0014	5008	,	,		15557	0.0		0.0	False		,,,				2504	0.0				p.W18R		Atlas-SNP	.											.	ZNF519	53	.	0			c.T52C						PASS	.	A	ARG/TRP	134,4272	97.6+/-136.3	2,130,2071	82.0	88.0	86.0		52		0.3	18	dbSNP_123	86	1,8599		0,1,4299	no	missense	ZNF519	NM_145287.3	101	2,131,6370	GG,GA,AA		0.0116,3.0413,1.038	probably-damaging	18/541	14124427	135,12871	2203	4300	6503	SO:0001583	missense	162655	exon2			ATTTCCACTCTTC	BC024227	CCDS32797.1	18p11.21	2014-06-18			ENSG00000175322	ENSG00000175322		"""Zinc fingers, C2H2-type"", ""-"""	30574	protein-coding gene	gene with protein product	"""similar to Zinc finger protein 85 (Zinc finger protein HPF4) (HTF1)"""					12477932	Standard	NM_145287		Approved	HsT2362, FLJ36809	uc002kst.2	Q8TB69	OTTHUMG00000182055	ENST00000590202.1:c.52T>C	18.37:g.14124427A>G	ENSP00000464872:p.Trp18Arg	96.0	0.0	0		114.0	61.0	0.535088	NM_145287		Missense_Mutation	SNP	ENST00000590202.1	37	CCDS32797.1	12	0.005494505494505495	11	0.022357723577235773	1	0.0027624309392265192	0	0.0	0	0.0	A	9.431	1.085594	0.20390	0.030413	1.16E-4	ENSG00000175322	ENST00000309305	.	.	.	.	.	.	Krueppel-associated box (4);	.	.	.	.	T	0.40196	0.1107	H	0.98155	4.16	0.09310	N	1	B	0.13594	0.008	B	0.04013	0.001	T	0.59705	-0.7404	6	0.87932	D	0	.	.	.	.	rs16941623;rs52802058;rs60926256;rs16941623	18	Q8TB69	ZN519_HUMAN	R	18	.	ENSP00000307908:W18R	W	-	1	0	ZNF519	14114427	0.444000	0.25649	0.272000	0.24630	0.274000	0.26718	1.863000	0.39459	0.077000	0.16863	0.076000	0.15429	TGG	A|0.988;G|0.012	0.012	strong		0.403	ZNF519-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000459037.1	NM_145287	
DPP10	57628	hgsc.bcm.edu	37	2	115822349	115822349	+	Intron	SNP	G	G	T	rs114821649	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr2:115822349G>T	ENST00000410059.1	+	2	540				DPP10_ENST00000409163.1_Intron	NM_001178037.1|NM_020868.3	NP_001171508.1|NP_065919	Q8N608	DPP10_HUMAN	dipeptidyl-peptidase 10 (non-functional)							integral component of membrane (GO:0016021)|membrane (GO:0016020)	serine-type peptidase activity (GO:0008236)			breast(4)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(8)|large_intestine(24)|liver(2)|lung(48)|ovary(6)|prostate(1)|skin(5)|soft_tissue(1)	101						TCATCACAGAGGTGGCTGAGG	0.428													G|||	16	0.00319489	0.0023	0.0014	5008	,	,		17880	0.0		0.0099	False		,,,				2504	0.002				p.E5D		Atlas-SNP	.											.	DPP10	415	.	0			c.G15T						PASS	.																																			SO:0001627	intron_variant	57628	exon1			CACAGAGGTGGCT	AY172661	CCDS33278.1, CCDS46400.1, CCDS54388.1, CCDS54389.1	2q14.1	2010-05-04	2010-05-04		ENSG00000175497	ENSG00000175497			20823	protein-coding gene	gene with protein product		608209	"""dipeptidylpeptidase 10"", ""dipeptidyl-peptidase 10"""			10819331, 12662155	Standard	NM_020868		Approved	DPRP3	uc002tle.3	Q8N608	OTTHUMG00000153294	ENST00000410059.1:c.61-244466G>T	2.37:g.115822349G>T		301.0	1.0	0.00332226		268.0	131.0	0.488806	NM_001178037	A8K1Q2|J3KPP2|J3KQ46|Q0GLB8|Q53QT3|Q53S86|Q53SL8|Q53SS4|Q6TTV4|Q86YR9|Q9P236	Missense_Mutation	SNP	ENST00000410059.1	37	CCDS46400.1	9	0.004120879120879121	1	0.0020325203252032522	1	0.0027624309392265192	0	0.0	7	0.009234828496042216	G	0.476	-0.882031	0.02530	.	.	ENSG00000175497	ENST00000393146	.	.	.	2.54	-1.69	0.08186	.	.	.	.	.	T	0.09905	0.0243	N	0.08118	0	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.18053	-1.0349	8	0.27785	T	0.31	.	1.6277	0.02726	0.2314:0.1609:0.448:0.1596	.	5	Q0GLB9	.	D	5	.	ENSP00000376854:E5D	E	+	3	2	DPP10	115538819	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-0.978000	0.03778	-0.884000	0.03976	-2.947000	0.00085	GAG	G|0.996;T|0.004	0.004	strong		0.428	DPP10-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000330580.4	NM_020868	
SPTA1	6708	hgsc.bcm.edu	37	1	158592781	158592781	+	Silent	SNP	G	G	A	rs75931146	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr1:158592781G>A	ENST00000368147.4	-	43	6292	c.6112C>T	c.(6112-6114)Cta>Tta	p.L2038L		NM_003126.2	NP_003117.2	P02549	SPTA1_HUMAN	spectrin, alpha, erythrocytic 1	2038					actin filament capping (GO:0051693)|actin filament organization (GO:0007015)|axon guidance (GO:0007411)|hemopoiesis (GO:0030097)|lymphocyte homeostasis (GO:0002260)|plasma membrane organization (GO:0007009)|porphyrin-containing compound biosynthetic process (GO:0006779)|positive regulation of protein binding (GO:0032092)|positive regulation of T cell proliferation (GO:0042102)|regulation of cell shape (GO:0008360)	actin cytoskeleton (GO:0015629)|cuticular plate (GO:0032437)|cytosol (GO:0005829)|intrinsic component of the cytoplasmic side of the plasma membrane (GO:0031235)|spectrin (GO:0008091)|spectrin-associated cytoskeleton (GO:0014731)	actin filament binding (GO:0051015)|calcium ion binding (GO:0005509)|structural constituent of cytoskeleton (GO:0005200)			NS(3)|breast(7)|cervix(1)|endometrium(22)|kidney(9)|large_intestine(29)|liver(2)|lung(183)|ovary(5)|prostate(18)|skin(11)|soft_tissue(1)|stomach(1)|upper_aerodigestive_tract(9)|urinary_tract(6)	307	all_hematologic(112;0.0378)					ACCTTCTGTAGAGGCAGCTGT	0.443													G|||	270	0.0539137	0.1407	0.0303	5008	,	,		18220	0.0		0.0229	False		,,,				2504	0.0409				p.L2038L		Atlas-SNP	.											.	SPTA1	720	.	0			c.C6112T						PASS	.	G		527,3225		26,475,1375	139.0	139.0	139.0		6112	2.9	0.3	1	dbSNP_132	139	125,8097		2,121,3988	no	coding-synonymous	SPTA1	NM_003126.2		28,596,5363	AA,AG,GG		1.5203,14.0458,5.4451		2038/2420	158592781	652,11322	1876	4111	5987	SO:0001819	synonymous_variant	6708	exon43			TCTGTAGAGGCAG	M61877	CCDS41423.1	1q21	2014-06-23	2014-06-23		ENSG00000163554	ENSG00000163554		"""EF-hand domain containing"""	11272	protein-coding gene	gene with protein product	"""elliptocytosis 2"""	182860	"""spectrin, alpha, erythrocytic 1 (elliptocytosis 2)"""				Standard	NM_003126		Approved	EL2	uc001fst.1	P02549	OTTHUMG00000019636	ENST00000368147.4:c.6112C>T	1.37:g.158592781G>A		162.0	0.0	0		167.0	70.0	0.419162	NM_003126	Q15514|Q5VYL1|Q5VYL2|Q6LDY5	Silent	SNP	ENST00000368147.4	37	CCDS41423.1																																																																																			G|0.961;A|0.039	0.039	strong		0.443	SPTA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051851.3	NM_003126	
AKAP11	11215	hgsc.bcm.edu	37	13	42875683	42875683	+	Missense_Mutation	SNP	A	A	G	rs41288309	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr13:42875683A>G	ENST00000025301.2	+	8	2976	c.2801A>G	c.(2800-2802)aAt>aGt	p.N934S		NM_016248.3	NP_057332.1	Q9UKA4	AKA11_HUMAN	A kinase (PRKA) anchor protein 11	934					intracellular signal transduction (GO:0035556)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)	protein kinase A binding (GO:0051018)|protein phosphatase 1 binding (GO:0008157)			breast(3)|central_nervous_system(4)|cervix(1)|endometrium(6)|kidney(3)|large_intestine(10)|liver(1)|lung(22)|ovary(1)|skin(3)|stomach(2)	56		Lung NSC(96;1.86e-05)|Prostate(109;0.0165)|Lung SC(185;0.0262)|Breast(139;0.0707)|Hepatocellular(98;0.114)		OV - Ovarian serous cystadenocarcinoma(117;0.000365)|GBM - Glioblastoma multiforme(144;0.00116)|BRCA - Breast invasive adenocarcinoma(63;0.19)		GCTAGTAGCAATAAGGACATG	0.358													A|||	50	0.00998403	0.0	0.0014	5008	,	,		19449	0.001		0.0099	False		,,,				2504	0.0389				p.N934S		Atlas-SNP	.											.	AKAP11	146	.	0			c.A2801G						PASS	.	A	SER/ASN	5,4401	8.1+/-20.4	0,5,2198	65.0	67.0	67.0		2801	-2.7	0.0	13	dbSNP_127	67	84,8516	48.1+/-107.5	0,84,4216	yes	missense	AKAP11	NM_016248.3	46	0,89,6414	GG,GA,AA		0.9767,0.1135,0.6843	benign	934/1902	42875683	89,12917	2203	4300	6503	SO:0001583	missense	11215	exon8			GTAGCAATAAGGA	AB014529	CCDS9383.1	13q	2012-04-17			ENSG00000023516	ENSG00000023516		"""A-kinase anchor proteins"", ""Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"""	369	protein-coding gene	gene with protein product	"""AKAP 220"", ""A-kinase anchoring protein, 220kDa"", ""protein kinase A anchoring protein 11"", ""protein phosphatase 1, regulatory subunit 44"""	604696				9734811, 8621616	Standard	NM_016248		Approved	KIAA0629, AKAP220, PRKA11, FLJ11304, DKFZp781I12161, PPP1R44	uc001uys.2	Q9UKA4	OTTHUMG00000016805	ENST00000025301.2:c.2801A>G	13.37:g.42875683A>G	ENSP00000025301:p.Asn934Ser	83.0	0.0	0		96.0	51.0	0.53125	NM_016248	O75124|Q9NUK7	Missense_Mutation	SNP	ENST00000025301.2	37	CCDS9383.1	8	0.003663003663003663	0	0.0	1	0.0027624309392265192	0	0.0	7	0.009234828496042216	A	2.918	-0.223797	0.06061	0.001135	0.009767	ENSG00000023516	ENST00000025301	T	0.12774	2.65	6.03	-2.7	0.06004	.	1.233830	0.05477	N	0.554106	T	0.04272	0.0118	N	0.04880	-0.145	0.09310	N	1	B	0.06786	0.001	B	0.06405	0.002	T	0.42292	-0.9460	10	0.13108	T	0.6	.	10.713	0.45995	0.4485:0.1412:0.4102:0.0	rs41288309;rs61756565	934	Q9UKA4	AKA11_HUMAN	S	934	ENSP00000025301:N934S	ENSP00000025301:N934S	N	+	2	0	AKAP11	41773683	0.000000	0.05858	0.039000	0.18376	0.069000	0.16628	-0.237000	0.08990	-0.478000	0.06823	-0.250000	0.11733	AAT	A|0.993;G|0.007	0.007	strong		0.358	AKAP11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044700.2	NM_016248	
PPARGC1B	133522	hgsc.bcm.edu	37	5	149212614	149212614	+	Silent	SNP	G	G	T	rs115557257	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr5:149212614G>T	ENST00000309241.5	+	5	1010	c.978G>T	c.(976-978)cgG>cgT	p.R326R	PPARGC1B_ENST00000360453.4_Silent_p.R287R|PPARGC1B_ENST00000403750.1_Silent_p.R262R|PPARGC1B_ENST00000394320.3_Silent_p.R326R	NM_133263.3	NP_573570.3	Q86YN6	PRGC2_HUMAN	peroxisome proliferator-activated receptor gamma, coactivator 1 beta	326					actin filament organization (GO:0007015)|bone trabecula formation (GO:0060346)|cellular lipid metabolic process (GO:0044255)|cellular response to reactive oxygen species (GO:0034614)|intracellular estrogen receptor signaling pathway (GO:0030520)|negative regulation of transcription, DNA-templated (GO:0045892)|ossification (GO:0001503)|positive regulation of alkaline phosphatase activity (GO:0010694)|positive regulation of bone resorption (GO:0045780)|positive regulation of osteoclast differentiation (GO:0045672)|positive regulation of phosphorylation (GO:0042327)|positive regulation of receptor activity (GO:2000273)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of transcription, DNA-templated (GO:0006355)|response to cAMP (GO:0051591)|response to glucocorticoid (GO:0051384)|small molecule metabolic process (GO:0044281)|transcription from mitochondrial promoter (GO:0006390)|transcription from RNA polymerase II promoter (GO:0006366)	mediator complex (GO:0016592)|mitochondrion (GO:0005739)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	AF-2 domain binding (GO:0050682)|estrogen receptor binding (GO:0030331)|ligand-dependent nuclear receptor transcription coactivator activity (GO:0030374)|nucleotide binding (GO:0000166)|receptor activator activity (GO:0030546)|RNA binding (GO:0003723)|RNA polymerase II transcription cofactor activity (GO:0001104)			NS(1)|breast(1)|endometrium(1)|kidney(3)|large_intestine(1)|liver(2)|lung(15)|ovary(3)|prostate(2)|stomach(1)	30			KIRC - Kidney renal clear cell carcinoma(527;0.000962)|Kidney(363;0.00147)			TCAGATCCCGGCCCTGGTCCC	0.622													G|||	44	0.00878594	0.0061	0.0202	5008	,	,		16385	0.0		0.0149	False		,,,				2504	0.0072				p.R326R		Atlas-SNP	.											.	PPARGC1B	74	.	0			c.G978T						PASS	.	G	,,	43,4363	45.3+/-79.5	0,43,2160	51.0	57.0	55.0		861,786,978	2.7	0.0	5	dbSNP_132	55	200,8400	87.4+/-149.7	2,196,4102	no	coding-synonymous,coding-synonymous,coding-synonymous	PPARGC1B	NM_001172698.1,NM_001172699.1,NM_133263.3	,,	2,239,6262	TT,TG,GG		2.3256,0.9759,1.8684	,,	287/985,262/960,326/1024	149212614	243,12763	2203	4300	6503	SO:0001819	synonymous_variant	133522	exon5			ATCCCGGCCCTGG	AF468496	CCDS4298.1, CCDS54933.1, CCDS54934.1	5q33.1	2013-02-12	2006-10-17		ENSG00000155846	ENSG00000155846		"""RNA binding motif (RRM) containing"""	30022	protein-coding gene	gene with protein product		608886	"""peroxisome proliferative activated receptor, gamma, coactivator 1, beta"""			11793024, 11854298	Standard	NM_133263		Approved	PERC, PGC1B	uc003lrc.3	Q86YN6	OTTHUMG00000130055	ENST00000309241.5:c.978G>T	5.37:g.149212614G>T		175.0	0.0	0		166.0	89.0	0.536145	NM_133263	A2RUM8|A2RUN0|B3KVW0|Q86YN3|Q86YN4|Q86YN5|Q8N1N9|Q8TDE4|Q8TDE5	Silent	SNP	ENST00000309241.5	37	CCDS4298.1	21	0.009615384615384616	3	0.006097560975609756	8	0.022099447513812154	0	0.0	10	0.013192612137203167	G	0.025	-1.378899	0.01204	0.009759	0.023256	ENSG00000155846	ENST00000434684	.	.	.	5.61	2.74	0.32292	.	.	.	.	.	T	0.14399	0.0348	.	.	.	0.09310	N	1	.	.	.	.	.	.	T	0.16660	-1.0395	4	.	.	.	-0.718	5.3707	0.16138	0.07:0.1258:0.5442:0.26	.	.	.	.	S	13	.	.	A	+	1	0	PPARGC1B	149192807	0.001000	0.12720	0.001000	0.08648	0.105000	0.19272	0.072000	0.14617	0.264000	0.21851	0.655000	0.94253	GCC	G|0.985;T|0.015	0.015	strong		0.622	PPARGC1B-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000252334.1	NM_133263	
TEX15	56154	hgsc.bcm.edu	37	8	30702739	30702739	+	Missense_Mutation	SNP	G	G	C	rs117362953	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr8:30702739G>C	ENST00000256246.2	-	1	3869	c.3795C>G	c.(3793-3795)gaC>gaG	p.D1265E		NM_031271.3	NP_112561.2	Q9BXT5	TEX15_HUMAN	testis expressed 15	1265					fertilization (GO:0009566)|homeostasis of number of cells within a tissue (GO:0048873)|male genitalia development (GO:0030539)|male meiosis (GO:0007140)|protein localization to chromosome (GO:0034502)|regulation of double-strand break repair via homologous recombination (GO:0010569)|regulation of protein localization (GO:0032880)|spermatogenesis (GO:0007283)|synaptonemal complex assembly (GO:0007130)			p.D1265D(1)		NS(2)|breast(3)|cervix(5)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(38)|lung(56)|ovary(5)|pancreas(1)|prostate(2)|skin(7)|upper_aerodigestive_tract(5)|urinary_tract(1)	138				KIRC - Kidney renal clear cell carcinoma(542;0.0918)|Kidney(114;0.111)		ATATAAGTACGTCAGTTTTCG	0.333													G|||	9	0.00179712	0.0	0.0	5008	,	,		19980	0.0		0.008	False		,,,				2504	0.001				p.D1265E		Atlas-SNP	.											TEX15,NS,carcinoma,0,1	TEX15	350	1	1	Substitution - coding silent(1)	prostate(1)	c.C3795G						PASS	.	G	GLU/ASP	3,4403	6.2+/-15.9	0,3,2200	96.0	92.0	94.0		3795	-2.4	0.0	8	dbSNP_132	94	39,8559	25.7+/-73.6	0,39,4260	yes	missense	TEX15	NM_031271.3	45	0,42,6460	CC,CG,GG		0.4536,0.0681,0.323	possibly-damaging	1265/2790	30702739	42,12962	2203	4299	6502	SO:0001583	missense	56154	exon1			AAGTACGTCAGTT	AF285605	CCDS6080.1	8p22	2009-03-25	2007-03-13			ENSG00000133863			11738	protein-coding gene	gene with protein product	"""cancer/testis antigen 42"""	605795	"""testis expressed sequence 15"""			11279525	Standard	NM_031271		Approved	CT42	uc003xil.3	Q9BXT5		ENST00000256246.2:c.3795C>G	8.37:g.30702739G>C	ENSP00000256246:p.Asp1265Glu	130.0	0.0	0		134.0	58.0	0.432836	NM_031271		Missense_Mutation	SNP	ENST00000256246.2	37	CCDS6080.1	8	0.003663003663003663	0	0.0	0	0.0	0	0.0	8	0.010554089709762533	G	10.11	1.259447	0.23051	6.81E-4	0.004536	ENSG00000133863	ENST00000256246	T	0.21932	1.98	5.92	-2.44	0.06502	.	0.178401	0.39759	N	0.001263	T	0.27313	0.0670	L	0.55481	1.735	0.09310	N	0.999999	D	0.89917	1.0	D	0.74674	0.984	T	0.19289	-1.0310	10	0.87932	D	0	.	12.5257	0.56085	0.5481:0.0:0.4519:0.0	.	1265	Q9BXT5	TEX15_HUMAN	E	1265	ENSP00000256246:D1265E	ENSP00000256246:D1265E	D	-	3	2	TEX15	30822281	0.000000	0.05858	0.001000	0.08648	0.010000	0.07245	-1.182000	0.03082	-0.565000	0.06061	-0.797000	0.03246	GAC	G|0.997;C|0.003	0.003	strong		0.333	TEX15-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000376193.1		
MICALL2	79778	hgsc.bcm.edu	37	7	1478525	1478525	+	Silent	SNP	C	C	T			TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr7:1478525C>T	ENST00000297508.7	-	10	2248	c.2073G>A	c.(2071-2073)gtG>gtA	p.V691V	MICALL2_ENST00000471899.1_5'UTR|MICALL2_ENST00000405088.4_Silent_p.V479V	NM_182924.3	NP_891554.1	Q8IY33	MILK2_HUMAN	MICAL-like 2	691	Mediates targeting to the cell plasma membrane. {ECO:0000250}.				actin cytoskeleton reorganization (GO:0031532)|actin filament polymerization (GO:0030041)|endocytic recycling (GO:0032456)|neuron projection development (GO:0031175)|substrate adhesion-dependent cell spreading (GO:0034446)|tight junction assembly (GO:0070830)	cell-cell junction (GO:0005911)|neuron projection (GO:0043005)|plasma membrane (GO:0005886)|recycling endosome (GO:0055037)|stress fiber (GO:0001725)|tight junction (GO:0005923)	actin filament binding (GO:0051015)|filamin binding (GO:0031005)|zinc ion binding (GO:0008270)			breast(3)|central_nervous_system(1)|endometrium(1)|kidney(2)|lung(8)|ovary(2)|skin(2)	19		Ovarian(82;0.0253)		UCEC - Uterine corpus endometrioid carcinoma (27;0.0178)|OV - Ovarian serous cystadenocarcinoma(56;6.01e-15)		TCCAGCTCTGCACTCGGGCTT	0.652																																					p.V691V		Atlas-SNP	.											.	MICALL2	63	.	0			c.G2073A						PASS	.						61.0	61.0	61.0					7																	1478525		2203	4300	6503	SO:0001819	synonymous_variant	79778	exon10			GCTCTGCACTCGG	BC037988	CCDS5324.1	7p22.3	2006-11-24			ENSG00000164877	ENSG00000164877			29672	protein-coding gene	gene with protein product	"""junctional Rab13-binding protein"""					12110185, 16525024	Standard	NM_182924		Approved	MGC46023, FLJ23471, MICAL-L2, JRAB	uc003skj.4	Q8IY33	OTTHUMG00000119021	ENST00000297508.7:c.2073G>A	7.37:g.1478525C>T		45.0	0.0	0		36.0	18.0	0.5	NM_182924	D3YTD2|Q7RTP4|Q7Z655|Q8TEQ4|Q9H5F9	Silent	SNP	ENST00000297508.7	37	CCDS5324.1																																																																																			.	.	none		0.652	MICALL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000239223.2	NM_182924	
STK32B	55351	hgsc.bcm.edu	37	4	5333091	5333091	+	Silent	SNP	G	G	A	rs16837029	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr4:5333091G>A	ENST00000282908.5	+	4	827	c.405G>A	c.(403-405)gaG>gaA	p.E135E	STK32B_ENST00000512636.1_Silent_p.E88E|STK32B_ENST00000510398.1_Silent_p.E88E	NM_018401.1	NP_060871.1			serine/threonine kinase 32B											breast(2)|central_nervous_system(1)|cervix(1)|endometrium(2)|kidney(1)|large_intestine(10)|lung(16)|prostate(1)|skin(2)|upper_aerodigestive_tract(3)	39						TGGCCCTGGAGTATCTTCAGA	0.577													G|||	422	0.0842652	0.2171	0.0245	5008	,	,		19648	0.0397		0.0328	False		,,,				2504	0.046				p.E135E		Atlas-SNP	.											.	STK32B	87	.	0			c.G405A						PASS	.	G		741,3665	304.9+/-288.7	63,615,1525	79.0	72.0	75.0		405	-1.6	0.9	4	dbSNP_123	75	222,8378	92.6+/-154.6	6,210,4084	no	coding-synonymous	STK32B	NM_018401.1		69,825,5609	AA,AG,GG		2.5814,16.818,7.4043		135/415	5333091	963,12043	2203	4300	6503	SO:0001819	synonymous_variant	55351	exon4			CCTGGAGTATCTT	AJ250839	CCDS3380.1	4p16	2009-09-30			ENSG00000152953	ENSG00000152953			14217	protein-coding gene	gene with protein product						10700184	Standard	XM_005247982		Approved	STKG6, YANK2, STK32, HSA250839	uc003gih.1	Q9NY57	OTTHUMG00000090423	ENST00000282908.5:c.405G>A	4.37:g.5333091G>A		70.0	0.0	0		52.0	28.0	0.538462	NM_018401		Silent	SNP	ENST00000282908.5	37	CCDS3380.1																																																																																			G|0.926;A|0.074	0.074	strong		0.577	STK32B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206854.4	NM_018401	
RTEL1	51750	hgsc.bcm.edu	37	20	62322290	62322290	+	Missense_Mutation	SNP	G	G	A	rs190887884	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr20:62322290G>A	ENST00000360203.5	+	27	2871	c.2546G>A	c.(2545-2547)gGc>gAc	p.G849D	RTEL1_ENST00000318100.4_Missense_Mutation_p.G849D|RTEL1_ENST00000370018.3_Missense_Mutation_p.G849D|RTEL1-TNFRSF6B_ENST00000482936.1_Missense_Mutation_p.G849D|RTEL1_ENST00000508582.2_Missense_Mutation_p.G873D|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	37.0	0.0	0		37.0	20.0	0.540541	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	
TRPV6	55503	hgsc.bcm.edu	37	7	142574544	142574544	+	Silent	SNP	G	G	A	rs138110961	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr7:142574544G>A	ENST00000359396.3	-	5	779	c.534C>T	c.(532-534)atC>atT	p.I178I	RP11-114L10.2_ENST00000438839.1_RNA	NM_018646.3	NP_061116	Q9H1D0	TRPV6_HUMAN	transient receptor potential cation channel, subfamily V, member 6	178					calcium ion transmembrane transport (GO:0070588)|calcium ion transport (GO:0006816)|ion transmembrane transport (GO:0034220)|regulation of calcium ion-dependent exocytosis (GO:0017158)|transmembrane transport (GO:0055085)	extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	calcium channel activity (GO:0005262)|calmodulin binding (GO:0005516)			breast(1)|endometrium(1)|kidney(2)|large_intestine(11)|lung(15)|ovary(3)|prostate(2)|skin(5)|upper_aerodigestive_tract(2)	42	Melanoma(164;0.059)					GCAGCCGCACGATCTCCTCAC	0.597													G|||	3	0.000599042	0.0	0.0029	5008	,	,		20351	0.0		0.001	False		,,,				2504	0.0				p.I178I		Atlas-SNP	.											.	TRPV6	108	.	0			c.C534T						PASS	.	G		1,4405	2.1+/-5.4	0,1,2202	101.0	86.0	91.0		534	-9.3	0.0	7	dbSNP_134	91	6,8594	5.0+/-18.6	0,6,4294	no	coding-synonymous	TRPV6	NM_018646.2		0,7,6496	AA,AG,GG		0.0698,0.0227,0.0538		178/726	142574544	7,12999	2203	4300	6503	SO:0001819	synonymous_variant	55503	exon5			CCGCACGATCTCC	AJ277909	CCDS5874.1	7q34	2013-01-10	2002-01-29	2002-02-01	ENSG00000165125	ENSG00000165125		"""Voltage-gated ion channels / Transient receptor potential cation channels"", ""Ankyrin repeat domain containing"""	14006	protein-coding gene	gene with protein product		606680	"""epithelial calcium channel 2"""	ECAC2		11097838, 11549322, 16382100, 16717058	Standard	NM_018646		Approved	CaT1	uc003wbx.2	Q9H1D0	OTTHUMG00000157158	ENST00000359396.3:c.534C>T	7.37:g.142574544G>A		152.0	0.0	0		167.0	86.0	0.51497	NM_018646	A4D2I8|Q8TDL3|Q8WXR8|Q96LC5|Q9H1D1|Q9H296	Silent	SNP	ENST00000359396.3	37	CCDS5874.1																																																																																			G|0.999;A|0.001	0.001	strong		0.597	TRPV6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347662.1	NM_014274	
OR2H1	26716	hgsc.bcm.edu	37	6	29429733	29429733	+	Missense_Mutation	SNP	G	G	A	rs61732185	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr6:29429733G>A	ENST00000377136.1	+	4	652	c.187G>A	c.(187-189)Gac>Aac	p.D63N	OR2H1_ENST00000442615.1_Missense_Mutation_p.D63N|OR2H1_ENST00000396792.2_Missense_Mutation_p.D63N|OR2H1_ENST00000377133.1_Missense_Mutation_p.D63N|OR2H1_ENST00000473369.1_Intron|OR2H1_ENST00000377132.1_Missense_Mutation_p.D63N			Q9GZK4	OR2H1_HUMAN	olfactory receptor, family 2, subfamily H, member 1	63			D -> N (in allele 6M1-16*02; dbSNP:rs61732185). {ECO:0000269|Ref.1}.			integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			large_intestine(5)|lung(12)	17						TTTCCTCTCTGACCTCTCCTT	0.532													G|||	174	0.0347444	0.1044	0.013	5008	,	,		20350	0.0119		0.0119	False		,,,				2504	0.0031				p.D63N		Atlas-SNP	.											.	OR2H1	38	.	0			c.G187A						PASS	.	G	ASN/ASP	301,2721		17,267,1227	137.0	134.0	135.0		187	0.4	1.0	6	dbSNP_129	135	33,5385		0,33,2676	yes	missense	OR2H1	NM_030883.3	23	17,300,3903	AA,AG,GG		0.6091,9.9603,3.9573	benign	63/317	29429733	334,8106	1511	2709	4220	SO:0001583	missense	26716	exon3			CTCTCTGACCTCT	AF044491	CCDS4660.1	6p22.1	2014-02-19	2002-02-28		ENSG00000204688	ENSG00000204688		"""GPCR / Class A : Olfactory receptors"""	8252	protein-coding gene	gene with protein product			"""olfactory receptor, family 2, subfamily H, member 8"""	OR2H6, OR2H8			Standard	NM_030883		Approved	OR6-2	uc003nmi.3	Q9GZK4	OTTHUMG00000031050	ENST00000377136.1:c.187G>A	6.37:g.29429733G>A	ENSP00000366340:p.Asp63Asn	230.0	1.0	0.00434783		253.0	120.0	0.474308	NM_030883	B0S7T4|O43629|O43661|O43662|Q5SUN6|Q9GZK9	Missense_Mutation	SNP	ENST00000377136.1	37	CCDS4660.1	88	0.040293040293040296	60	0.12195121951219512	8	0.022099447513812154	10	0.017482517482517484	10	0.013192612137203167	G	1.564	-0.535865	0.04082	0.099603	0.006091	ENSG00000204688	ENST00000377136;ENST00000377133;ENST00000442615;ENST00000377132;ENST00000396792	T;T;T;T;T	0.00940	5.52;5.52;5.52;5.52;5.52	2.88	0.407	0.16371	GPCR, rhodopsin-like superfamily (1);	0.156786	0.30126	N	0.010354	T	0.00039	0.0001	N	0.00003	-3.425	0.24176	N	0.995605	B	0.02656	0.0	B	0.01281	0.0	T	0.12604	-1.0541	10	0.02654	T	1	.	4.2744	0.10802	0.6269:0.1713:0.2018:0.0	rs61732185	63	Q9GZK4	OR2H1_HUMAN	N	63	ENSP00000366340:D63N;ENSP00000366337:D63N;ENSP00000393254:D63N;ENSP00000366336:D63N;ENSP00000380010:D63N	ENSP00000366336:D63N	D	+	1	0	OR2H1	29537712	0.036000	0.19791	0.986000	0.45419	0.919000	0.55068	1.592000	0.36676	0.072000	0.16694	-0.354000	0.07668	GAC	G|0.964;A|0.036	0.036	strong		0.532	OR2H1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000194014.3		
PRELID2	153768	hgsc.bcm.edu	37	5	145199531	145199531	+	Missense_Mutation	SNP	C	C	T	rs142301961		TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr5:145199531C>T	ENST00000334744.4	-	3	236	c.184G>A	c.(184-186)Gtg>Atg	p.V62M	PRELID2_ENST00000511435.1_Missense_Mutation_p.V62M|PRELID2_ENST00000505416.1_Missense_Mutation_p.V62M|PRELID2_ENST00000358004.2_Missense_Mutation_p.V62M|PRELID2_ENST00000394450.2_Missense_Mutation_p.V33M	NM_182960.2	NP_892005.1	Q8N945	PRLD2_HUMAN	PRELI domain containing 2	62	PRELI/MSF1. {ECO:0000255|PROSITE- ProRule:PRU00158}.				phospholipid transport (GO:0015914)	mitochondrial intermembrane space (GO:0005758)	phosphatidic acid transporter activity (GO:1990050)			endometrium(2)|large_intestine(1)|lung(2)|prostate(1)	6			KIRC - Kidney renal clear cell carcinoma(527;0.000785)|Kidney(363;0.00101)			TCTGGAACCACGTTCTGACAG	0.289													C|||	1	0.000199681	0.0	0.0	5008	,	,		16776	0.0		0.001	False		,,,				2504	0.0				p.V62M		Atlas-SNP	.											.	PRELID2	16	.	0			c.G184A						PASS	.	C	MET/VAL,MET/VAL,MET/VAL	1,4405	2.1+/-5.4	0,1,2202	88.0	95.0	93.0		97,184,184	5.3	1.0	5	dbSNP_134	93	10,8590	7.7+/-29.5	0,10,4290	yes	missense,missense,missense	PRELID2	NM_138492.4,NM_182960.2,NM_205846.1	21,21,21	0,11,6492	TT,TC,CC		0.1163,0.0227,0.0846	probably-damaging,probably-damaging,probably-damaging	33/149,62/190,62/178	145199531	11,12995	2203	4300	6503	SO:0001583	missense	153768	exon3			GAACCACGTTCTG	AK095695	CCDS34261.1, CCDS34262.1, CCDS43377.1	5q32	2012-04-23			ENSG00000186314	ENSG00000186314			28306	protein-coding gene	gene with protein product						12477932	Standard	NM_182960		Approved	MGC21644, FLJ38376	uc003lnq.1	Q8N945	OTTHUMG00000163384	ENST00000334744.4:c.184G>A	5.37:g.145199531C>T	ENSP00000335675:p.Val62Met	216.0	0.0	0		190.0	95.0	0.5	NM_182960	G5EA01|Q96EQ3	Missense_Mutation	SNP	ENST00000334744.4	37	CCDS34262.1	1	4.578754578754579E-4	0	0.0	0	0.0	0	0.0	1	0.0013192612137203166	C	21.1	4.095855	0.76870	2.27E-4	0.001163	ENSG00000186314	ENST00000358004;ENST00000334744;ENST00000394450;ENST00000505416;ENST00000511435	T;T;T;T;T	0.17528	2.27;2.27;2.27;2.27;2.27	5.3	5.3	0.74995	PRELI/MSF1 (2);	0.000000	0.64402	D	0.000014	T	0.40956	0.1138	M	0.67953	2.075	0.43480	D	0.995704	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.87578	0.995;0.992;0.998	T	0.07578	-1.0765	10	0.46703	T	0.11	-0.5438	16.2362	0.82377	0.0:1.0:0.0:0.0	.	62;62;62	D6RAB6;G5EA01;Q8N945	.;.;PRLD2_HUMAN	M	62;62;33;62;62	ENSP00000350694:V62M;ENSP00000335675:V62M;ENSP00000377965:V33M;ENSP00000424730:V62M;ENSP00000422789:V62M	ENSP00000335675:V62M	V	-	1	0	PRELID2	145179724	1.000000	0.71417	1.000000	0.80357	0.986000	0.74619	2.798000	0.47884	2.627000	0.88993	0.650000	0.86243	GTG	C|0.999;T|0.001	0.001	strong		0.289	PRELID2-004	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000372970.1	NM_182960	
DRC7	84229	hgsc.bcm.edu	37	16	57758727	57758727	+	Missense_Mutation	SNP	T	T	C	rs115241876	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr16:57758727T>C	ENST00000360716.3	+	13	1959	c.1738T>C	c.(1738-1740)Tca>Cca	p.S580P	CCDC135_ENST00000336825.8_Missense_Mutation_p.S515P|CCDC135_ENST00000394337.4_Missense_Mutation_p.S580P			Q8IY82	CC135_HUMAN		580					cell differentiation (GO:0030154)|spermatogenesis (GO:0007283)	cytoplasm (GO:0005737)|motile cilium (GO:0031514)				breast(1)|central_nervous_system(2)|cervix(2)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(3)|lung(12)|ovary(1)|prostate(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	30						CAGTGCAGAGTCAAACCCCCG	0.597													.|||	10	0.00199681	0.0	0.0058	5008	,	,		18147	0.0		0.005	False		,,,				2504	0.001				p.S580P		Atlas-SNP	.											.	CCDC135	97	.	0			c.T1738C						PASS	.	T	PRO/SER	2,4392		0,2,2195	49.0	43.0	45.0		1738	4.1	0.2	16	dbSNP_132	45	39,8559		1,37,4261	yes	missense	CCDC135	NM_032269.5	74	1,39,6456	CC,CT,TT		0.4536,0.0455,0.3156	possibly-damaging	580/875	57758727	41,12951	2197	4299	6496	SO:0001583	missense	84229	exon12			GCAGAGTCAAACC																												ENST00000360716.3:c.1738T>C	16.37:g.57758727T>C	ENSP00000353942:p.Ser580Pro	49.0	0.0	0		59.0	30.0	0.508475	NM_032269	A8K943|Q8NAA0|Q9H080	Missense_Mutation	SNP	ENST00000360716.3	37	CCDS10787.1	6	0.0027472527472527475	0	0.0	4	0.011049723756906077	0	0.0	2	0.002638522427440633	.	18.06	3.538954	0.65085	4.55E-4	0.004536	ENSG00000159625	ENST00000394337;ENST00000336825;ENST00000360716	T;T;T	0.10382	3.03;2.88;3.03	5.29	4.09	0.47781	.	0.814347	0.11090	N	0.600808	T	0.15609	0.0376	M	0.68317	2.08	0.09310	N	1	D;D	0.58970	0.984;0.966	P;P	0.56088	0.791;0.735	T	0.10132	-1.0643	10	0.37606	T	0.19	-14.6732	6.4912	0.22117	0.1385:0.0:0.2281:0.6334	.	515;580	Q8IY82-2;Q8IY82	.;CC135_HUMAN	P	580;515;580	ENSP00000377869:S580P;ENSP00000338938:S515P;ENSP00000353942:S580P	ENSP00000338938:S515P	S	+	1	0	CCDC135	56316228	0.001000	0.12720	0.236000	0.24074	0.737000	0.42083	0.422000	0.21296	2.004000	0.58718	0.533000	0.62120	TCA	T|0.997;C|0.003	0.003	strong		0.597	CCDC135-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000433323.2		
CHD6	84181	hgsc.bcm.edu	37	20	40079655	40079655	+	Missense_Mutation	SNP	G	G	C	rs41278126	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr20:40079655G>C	ENST00000373233.3	-	23	3791	c.3614C>G	c.(3613-3615)gCc>gGc	p.A1205G	CHD6_ENST00000309279.7_Missense_Mutation_p.A688G	NM_032221.3	NP_115597.3	Q8TD26	CHD6_HUMAN	chromodomain helicase DNA binding protein 6	1205					ATP catabolic process (GO:0006200)|chromatin modification (GO:0016568)|positive regulation of transcription from RNA polymerase II promoter in response to oxidative stress (GO:0036091)|transcription, DNA-templated (GO:0006351)	nucleoplasm (GO:0005654)	ATP binding (GO:0005524)|ATP-dependent helicase activity (GO:0008026)|chromatin binding (GO:0003682)|DNA binding (GO:0003677)|DNA-dependent ATPase activity (GO:0008094)|transcription cofactor binding (GO:0001221)			breast(8)|central_nervous_system(2)|cervix(2)|endometrium(5)|kidney(4)|large_intestine(24)|lung(53)|ovary(8)|prostate(5)|skin(8)|stomach(1)|urinary_tract(9)	129		Myeloproliferative disorder(115;0.00425)				GTTGCAGGTGGCTAGCCAATC	0.532													G|||	59	0.0117812	0.0008	0.0086	5008	,	,		19751	0.0		0.0457	False		,,,				2504	0.0061				p.A1205G		Atlas-SNP	.											.	CHD6	312	.	0			c.C3614G						PASS	.	G	GLY/ALA	46,4360	48.9+/-83.8	1,44,2158	174.0	139.0	151.0		3614	5.8	1.0	20	dbSNP_127	151	360,8240	121.0+/-180.1	12,336,3952	yes	missense	CHD6	NM_032221.3	60	13,380,6110	CC,CG,GG		4.186,1.044,3.1216	possibly-damaging	1205/2716	40079655	406,12600	2203	4300	6503	SO:0001583	missense	84181	exon23			CAGGTGGCTAGCC	AF525085	CCDS13317.1	20q12	2003-03-07			ENSG00000124177	ENSG00000124177			19057	protein-coding gene	gene with protein product						11889561	Standard	NM_032221		Approved	KIAA1335, FLJ22369, dJ620E11.1, CHD5, RIGB	uc002xka.1	Q8TD26	OTTHUMG00000032487	ENST00000373233.3:c.3614C>G	20.37:g.40079655G>C	ENSP00000362330:p.Ala1205Gly	181.0	0.0	0		215.0	105.0	0.488372	NM_032221	Q5JYQ0|Q5TGZ9|Q5TH00|Q5TH01|Q8IZR2|Q8WTY0|Q9H4H6|Q9H6D4|Q9NTT7|Q9P2L1	Missense_Mutation	SNP	ENST00000373233.3	37	CCDS13317.1	45|45	0.020604395604395604|0.020604395604395604	0|0	0.0|0.0	3|3	0.008287292817679558|0.008287292817679558	0|0	0.0|0.0	42|42	0.055408970976253295|0.055408970976253295	G|G	16.59|16.59	3.164784|3.164784	0.57476|0.57476	0.01044|0.01044	0.04186|0.04186	ENSG00000124177|ENSG00000124177	ENST00000373233;ENST00000309279|ENST00000440697	D;D|.	0.84800|.	-1.9;-1.9|.	5.78|5.78	5.78|5.78	0.91487|0.91487	.|.	0.199876|.	0.35739|.	N|.	0.003018|.	T|T	0.12518|0.12518	0.0304|0.0304	L|L	0.47716|0.47716	1.5|1.5	0.27988|0.27988	N|N	0.935797|0.935797	B|.	0.02656|.	0.0|.	B|.	0.04013|.	0.001|.	T|T	0.08973|0.08973	-1.0696|-1.0696	10|5	0.45353|.	T|.	0.12|.	-9.1677|-9.1677	20.0204|20.0204	0.97499|0.97499	0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0	rs41278126;rs61753662|rs41278126;rs61753662	1205|.	Q8TD26|.	CHD6_HUMAN|.	G|A	1205;688|391	ENSP00000362330:A1205G;ENSP00000308684:A688G|.	ENSP00000308684:A688G|.	A|P	-|-	2|1	0|0	CHD6|CHD6	39513069|39513069	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.989000|0.989000	0.77384|0.77384	6.429000|6.429000	0.73387|0.73387	2.729000|2.729000	0.93468|0.93468	0.650000|0.650000	0.86243|0.86243	GCC|CCA	G|0.971;C|0.029	0.029	strong		0.532	CHD6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079270.1		
DSPP	1834	hgsc.bcm.edu	37	4	88537324	88537324	+	Silent	SNP	C	C	T			TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr4:88537324C>T	ENST00000282478.7	+	4	3543	c.3510C>T	c.(3508-3510)gaC>gaT	p.D1170D	RP11-742B18.1_ENST00000506480.1_RNA|DSPP_ENST00000399271.1_Silent_p.D1170D			Q9NZW4	DSPP_HUMAN	dentin sialophosphoprotein	1170	Asp/Ser-rich.				biomineral tissue development (GO:0031214)|cellular response to cell-matrix adhesion (GO:0071460)|extracellular matrix organization (GO:0030198)|multicellular organismal development (GO:0007275)|ossification (GO:0001503)|skeletal system development (GO:0001501)	cytoplasm (GO:0005737)|extracellular region (GO:0005576)|proteinaceous extracellular matrix (GO:0005578)	calcium ion binding (GO:0005509)|collagen binding (GO:0005518)|extracellular matrix structural constituent (GO:0005201)			breast(2)|central_nervous_system(1)|endometrium(9)|kidney(4)|large_intestine(8)|lung(13)|ovary(1)|skin(3)|stomach(3)|upper_aerodigestive_tract(2)|urinary_tract(1)	47		Hepatocellular(203;0.114)|all_hematologic(202;0.236)		OV - Ovarian serous cystadenocarcinoma(123;0.000508)		acagcagcgacagcagcgata	0.567																																					p.D1170D		Atlas-SNP	.											DSPP,NS,carcinoma,0,2	DSPP	174	2	0			c.C3510T						PASS	.						44.0	63.0	56.0					4																	88537324		1605	2847	4452	SO:0001819	synonymous_variant	1834	exon5			CAGCGACAGCAGC	AF163151	CCDS43248.1	4q21.3	2008-02-05			ENSG00000152591	ENSG00000152591			3054	protein-coding gene	gene with protein product		125485		DFNA39, DGI1		8995371, 9533027	Standard	NM_014208		Approved	DMP3	uc003hqu.3	Q9NZW4	OTTHUMG00000161061	ENST00000282478.7:c.3510C>T	4.37:g.88537324C>T		236.0	0.0	0		183.0	11.0	0.0601093	NM_014208	A8MUI0|O95815	Silent	SNP	ENST00000282478.7	37	CCDS43248.1																																																																																			.	.	none		0.567	DSPP-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000363616.3	NM_014208	
FAM161A	84140	hgsc.bcm.edu	37	2	62053677	62053677	+	Silent	SNP	A	A	G	rs138464813	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr2:62053677A>G	ENST00000405894.3	-	6	1997	c.1896T>C	c.(1894-1896)atT>atC	p.I632I	FAM161A_ENST00000404929.1_Silent_p.I688I	NM_032180.2	NP_115556.2	Q3B820	F161A_HUMAN	family with sequence similarity 161, member A	632	Glu-rich.				cilium assembly (GO:0042384)|response to stimulus (GO:0050896)|visual perception (GO:0007601)	centrosome (GO:0005813)|ciliary basal body (GO:0036064)|cytoplasm (GO:0005737)|photoreceptor connecting cilium (GO:0032391)				breast(1)|endometrium(5)|large_intestine(8)|lung(4)|ovary(3)|pancreas(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	25						TGTTGGTATCAATAAAATAAT	0.328													A|||	6	0.00119808	0.0	0.0029	5008	,	,		19015	0.0		0.003	False		,,,				2504	0.001				p.I688I		Atlas-SNP	.											.	FAM161A	200	.	0			c.T2064C						PASS	.	A	,	3,3635		0,3,1816	107.0	98.0	101.0		2064,1896	3.0	1.0	2	dbSNP_134	101	33,8127		0,33,4047	yes	coding-synonymous,coding-synonymous	FAM161A	NM_001201543.1,NM_032180.2	,	0,36,5863	GG,GA,AA		0.4044,0.0825,0.3051	,	688/717,632/661	62053677	36,11762	1819	4080	5899	SO:0001819	synonymous_variant	84140	exon7			GGTATCAATAAAA		CCDS42687.2, CCDS56120.1	2p15	2011-03-15			ENSG00000170264	ENSG00000170264			25808	protein-coding gene	gene with protein product		613596	"""retinitis pigmentosa 28 (autosomal recessive)"""	RP28		10507729, 20705278, 20705279	Standard	NM_032180		Approved	FLJ13305	uc002sbm.4	Q3B820	OTTHUMG00000152165	ENST00000405894.3:c.1896T>C	2.37:g.62053677A>G		224.0	0.0	0		215.0	95.0	0.44186	NM_001201543	B4DJV7|Q9H8R2	Silent	SNP	ENST00000405894.3	37	CCDS42687.2																																																																																			A|0.998;G|0.002	0.002	strong		0.328	FAM161A-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000325537.2	NM_032180	
PEX26	55670	hgsc.bcm.edu	37	22	18561342	18561342	+	Missense_Mutation	SNP	A	A	G	rs201884779|rs267608189	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr22:18561342A>G	ENST00000329627.7	+	2	406	c.200A>G	c.(199-201)aAc>aGc	p.N67S	PEX26_ENST00000399744.3_Missense_Mutation_p.N67S|PEX26_ENST00000428061.2_Missense_Mutation_p.N67S|XXbac-B476C20.9_ENST00000426483.1_RNA|XXbac-B476C20.9_ENST00000607927.1_RNA	NM_017929.5	NP_060399.1	Q7Z412	PEX26_HUMAN	peroxisomal biogenesis factor 26	67					protein import into peroxisome matrix (GO:0016558)|protein import into peroxisome membrane (GO:0045046)	integral component of peroxisomal membrane (GO:0005779)|peroxisome (GO:0005777)	ATPase binding (GO:0051117)|protein C-terminus binding (GO:0008022)|protein complex binding (GO:0032403)			breast(1)|kidney(2)|large_intestine(3)|lung(4)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	13						AGTCTGGCCAACCACGCCGTG	0.677													A|||	3	0.000599042	0.0	0.0	5008	,	,		13652	0.0		0.003	False		,,,				2504	0.0				p.N67S		Atlas-SNP	.											.	PEX26	27	.	0			c.A200G						PASS	.	A	SER/ASN,SER/ASN,SER/ASN	0,4084		0,0,2042	6.0	7.0	7.0		200,200,200	-3.6	0.0	22		7	13,8139		0,13,4063	no	missense,missense,missense	PEX26	NM_001127649.2,NM_001199319.1,NM_017929.5	46,46,46	0,13,6105	GG,GA,AA		0.1595,0.0,0.1062	benign,benign,benign	67/306,67/257,67/306	18561342	13,12223	2042	4076	6118	SO:0001583	missense	55670	exon1			TGGCCAACCACGC	AB089678	CCDS13750.1, CCDS56221.1	22q11.21	2008-08-26	2008-08-26		ENSG00000215193	ENSG00000215193			22965	protein-coding gene	gene with protein product		608666	"""peroxisome biogenesis factor 26"""			12717447, 12851857	Standard	NM_017929		Approved	FLJ20695	uc002znp.4	Q7Z412	OTTHUMG00000149970	ENST00000329627.7:c.200A>G	22.37:g.18561342A>G	ENSP00000331106:p.Asn67Ser	31.0	0.0	0		26.0	11.0	0.423077	NM_001127649	F6UBB5|Q7Z413|Q7Z414|Q7Z415|Q7Z416|Q96B12|Q9NWQ0|Q9NXU0	Missense_Mutation	SNP	ENST00000329627.7	37	CCDS13750.1	.	.	.	.	.	.	.	.	.	.	A	5.785	0.329161	0.10956	0.0	0.001595	ENSG00000215193	ENST00000329627;ENST00000399744;ENST00000428061;ENST00000399746	D;D;D	0.92647	-3.08;-3.08;-3.08	5.21	-3.6	0.04570	.	1.979650	0.02715	U	0.113263	T	0.79975	0.4539	N	0.05199	-0.095	0.09310	N	1	B;B	0.06786	0.001;0.001	B;B	0.06405	0.001;0.002	T	0.73088	-0.4093	10	0.09843	T	0.71	2.4468	7.7401	0.28837	0.265:0.4559:0.2791:0.0	.	67;67	F6UBB5;Q7Z412	.;PEX26_HUMAN	S	67	ENSP00000331106:N67S;ENSP00000382648:N67S;ENSP00000412441:N67S	ENSP00000331106:N67S	N	+	2	0	PEX26	16941342	0.000000	0.05858	0.000000	0.03702	0.008000	0.06430	-1.459000	0.02370	-1.053000	0.03218	-0.435000	0.05868	AAC	A|0.994;G|0.006	0.006	weak		0.677	PEX26-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000314644.3	NM_017929	
NUDT19	390916	hgsc.bcm.edu	37	19	33200275	33200275	+	Missense_Mutation	SNP	A	A	T	rs371226805		TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr19:33200275A>T	ENST00000397061.3	+	2	899	c.899A>T	c.(898-900)gAt>gTt	p.D300V		NM_001105570.1	NP_001099040.1	A8MXV4	NUD19_HUMAN	nudix (nucleoside diphosphate linked moiety X)-type motif 19	300						mitochondrion (GO:0005739)|peroxisome (GO:0005777)	hydrolase activity (GO:0016787)|metal ion binding (GO:0046872)|receptor binding (GO:0005102)			endometrium(1)|large_intestine(1)|lung(4)|ovary(1)|upper_aerodigestive_tract(1)	8	Esophageal squamous(110;0.137)					TTAACTGCTGATGGGATGGTC	0.473																																					p.D300V		Atlas-SNP	.											.	NUDT19	15	.	0			c.A899T						PASS	.	A	VAL/ASP	0,3924		0,0,1962	145.0	132.0	136.0		899	4.9	1.0	19		136	3,8289		0,3,4143	no	missense	NUDT19	NM_001105570.1	152	0,3,6105	TT,TA,AA		0.0362,0.0,0.0246	probably-damaging	300/376	33200275	3,12213	1962	4146	6108	SO:0001583	missense	390916	exon2			CTGCTGATGGGAT		CCDS42543.1	19q13.11	2011-11-16			ENSG00000213965	ENSG00000213965		"""Nudix motif containing"""	32036	protein-coding gene	gene with protein product							Standard	NM_001105570		Approved	RP2	uc010edf.3	A8MXV4		ENST00000397061.3:c.899A>T	19.37:g.33200275A>T	ENSP00000380251:p.Asp300Val	96.0	0.0	0		107.0	55.0	0.514019	NM_001105570		Missense_Mutation	SNP	ENST00000397061.3	37	CCDS42543.1	.	.	.	.	.	.	.	.	.	.	A	19.01	3.743338	0.69418	0.0	3.62E-4	ENSG00000213965	ENST00000397061	T	0.53206	0.63	4.88	4.88	0.63580	.	0.252366	0.32719	U	0.005722	T	0.67655	0.2916	M	0.80746	2.51	0.80722	D	1	D	0.89917	1.0	D	0.74674	0.984	T	0.72384	-0.4310	10	0.87932	D	0	-10.9605	11.1678	0.48554	1.0:0.0:0.0:0.0	.	300	A8MXV4	NUD19_HUMAN	V	300	ENSP00000380251:D300V	ENSP00000380251:D300V	D	+	2	0	NUDT19	37892115	1.000000	0.71417	0.981000	0.43875	0.072000	0.16883	4.851000	0.62896	1.948000	0.56530	0.482000	0.46254	GAT	.	.	weak		0.473	NUDT19-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000450338.3	XM_372723	
NUP210L	91181	hgsc.bcm.edu	37	1	154115962	154115962	+	Silent	SNP	A	A	G			TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr1:154115962A>G	ENST00000368559.3	-	3	503	c.432T>C	c.(430-432)gaT>gaC	p.D144D	NUP210L_ENST00000271854.3_Silent_p.D144D	NM_207308.2	NP_997191.2	Q5VU65	P210L_HUMAN	nucleoporin 210kDa-like	144					Sertoli cell development (GO:0060009)|spermatid development (GO:0007286)	integral component of membrane (GO:0016021)				NS(1)|breast(6)|central_nervous_system(1)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(2)|kidney(4)|large_intestine(12)|lung(34)|ovary(4)|pancreas(1)|prostate(2)|skin(6)|urinary_tract(2)	80	all_lung(78;9.35e-31)|Lung NSC(65;1.33e-28)|Hepatocellular(266;0.0877)|Melanoma(130;0.128)		LUSC - Lung squamous cell carcinoma(543;0.151)|Colorectal(543;0.198)			CCAGTGGCGAATCATCTACAT	0.393																																					p.D144D		Atlas-SNP	.											.	NUP210L	181	.	0			c.T432C						PASS	.						125.0	126.0	126.0					1																	154115962		2069	4212	6281	SO:0001819	synonymous_variant	91181	exon3			TGGCGAATCATCT	AK125924	CCDS41399.1, CCDS53370.1	1q21.3	2008-02-05			ENSG00000143552	ENSG00000143552			29915	protein-coding gene	gene with protein product							Standard	NM_207308		Approved		uc001fdw.3	Q5VU65	OTTHUMG00000035852	ENST00000368559.3:c.432T>C	1.37:g.154115962A>G		197.0	0.0	0		199.0	105.0	0.527638	NM_001159484	E7EP56|Q5T4L7|Q6ZRN1|Q6ZRT4|Q6ZU81|Q8NDI6|Q9UF31	Silent	SNP	ENST00000368559.3	37	CCDS41399.1																																																																																			.	.	none		0.393	NUP210L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000087270.3	NM_207308	
EXD3	54932	hgsc.bcm.edu	37	9	140250749	140250749	+	Missense_Mutation	SNP	C	C	T	rs180687197	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr9:140250749C>T	ENST00000340951.4	-	8	923	c.728G>A	c.(727-729)cGt>cAt	p.R243H	EXD3_ENST00000342129.4_5'UTR	NM_017820.3	NP_060290.3	Q9NX53	MUT7B_HUMAN	exonuclease 3'-5' domain containing 3	0										NS(1)|central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(1)|lung(5)|prostate(2)	12						CTCCTGCAGACGCAAGACCTG	0.652													C|||	3	0.000599042	0.0008	0.0014	5008	,	,		16664	0.0		0.001	False		,,,				2504	0.0				p.R243H		Atlas-SNP	.											.	EXD3	86	.	0			c.G728A						PASS	.	C	HIS/ARG	1,4219		0,1,2109	28.0	33.0	31.0		728	1.4	0.0	9		31	7,8453		0,7,4223	yes	missense	EXD3	NM_017820.3	29	0,8,6332	TT,TC,CC		0.0827,0.0237,0.0631	benign	243/877	140250749	8,12672	2110	4230	6340	SO:0001583	missense	54932	exon8			TGCAGACGCAAGA		CCDS48066.1, CCDS75942.1	9q34.3	2009-03-04			ENSG00000187609	ENSG00000187609			26023	protein-coding gene	gene with protein product							Standard	XM_005266093		Approved	LOC54932, FLJ20433, mut-7	uc004cmp.2	Q8N9H8	OTTHUMG00000156149	ENST00000340951.4:c.728G>A	9.37:g.140250749C>T	ENSP00000340474:p.Arg243His	27.0	0.0	0		45.0	25.0	0.555556	NM_017820	Q6P1M1|Q8IXT8	Missense_Mutation	SNP	ENST00000340951.4	37	CCDS48066.1	2	9.157509157509158E-4	0	0.0	1	0.0027624309392265192	0	0.0	1	0.0013192612137203166	C	13.54	2.267912	0.40095	2.37E-4	8.27E-4	ENSG00000187609	ENST00000340951	T	0.63580	-0.05	2.34	1.41	0.22369	.	0.270733	0.24044	N	0.042075	T	0.43567	0.1253	L	0.35854	1.095	0.80722	D	1	B	0.30179	0.271	B	0.19148	0.024	T	0.31166	-0.9953	10	0.72032	D	0.01	.	5.0914	0.14710	0.0:0.6764:0.0:0.3236	.	243	Q8N9H8	MUT7_HUMAN	H	243	ENSP00000340474:R243H	ENSP00000340474:R243H	R	-	2	0	EXD3	139370570	0.005000	0.15991	0.019000	0.16419	0.567000	0.35839	1.383000	0.34385	0.294000	0.22547	0.306000	0.20318	CGT	C|0.999;T|0.001	0.001	strong		0.652	EXD3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000343182.1	NM_017820	
MAGEC1	9947	hgsc.bcm.edu	37	X	140993737	140993737	+	Missense_Mutation	SNP	C	C	T			TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chrX:140993737C>T	ENST00000285879.4	+	4	833	c.547C>T	c.(547-549)Cct>Tct	p.P183S	MAGEC1_ENST00000406005.2_Intron	NM_005462.4	NP_005453.2	O60732	MAGC1_HUMAN	melanoma antigen family C, 1	183										breast(3)|central_nervous_system(1)|cervix(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(2)|kidney(8)|large_intestine(22)|lung(60)|ovary(1)|pancreas(1)|prostate(1)|skin(7)|stomach(5)|upper_aerodigestive_tract(7)|urinary_tract(1)	127	Acute lymphoblastic leukemia(192;6.56e-05)					CCAGAGTTCCCCTGAGAGTAC	0.493										HNSCC(15;0.026)																											p.P183S		Atlas-SNP	.											.	MAGEC1	317	.	0			c.C547T						PASS	.						80.0	91.0	87.0					X																	140993737		2203	4298	6501	SO:0001583	missense	9947	exon4			AGTTCCCCTGAGA	AF064589	CCDS35417.1	Xq26	2009-03-18			ENSG00000155495	ENSG00000155495			6812	protein-coding gene	gene with protein product	"""cancer/testis antigen family 7, member 1"""	300223				9485030, 9618514	Standard	NM_005462		Approved	MAGE-C1, CT7, MGC39366, CT7.1	uc004fbt.3	O60732	OTTHUMG00000022569	ENST00000285879.4:c.547C>T	X.37:g.140993737C>T	ENSP00000285879:p.Pro183Ser	266.0	0.0	0		230.0	13.0	0.0565217	NM_005462	A0PK03|O75451|Q8TCV4	Missense_Mutation	SNP	ENST00000285879.4	37	CCDS35417.1	.	.	.	.	.	.	.	.	.	.	c	6.525	0.465191	0.12402	.	.	ENSG00000155495	ENST00000285879	T	0.03301	3.98	.	.	.	.	.	.	.	.	T	0.01976	0.0062	N	0.08118	0	0.09310	N	0.999996	B	0.17038	0.02	B	0.09377	0.004	T	0.45086	-0.9285	8	0.87932	D	0	.	3.8388	0.08905	0.0:0.6604:0.0:0.3396	.	183	O60732	MAGC1_HUMAN	S	183	ENSP00000285879:P183S	ENSP00000285879:P183S	P	+	1	0	MAGEC1	140821403	0.149000	0.22717	0.039000	0.18376	0.039000	0.13416	1.804000	0.38873	0.054000	0.16065	0.054000	0.15206	CCT	.	.	none		0.493	MAGEC1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000058604.1	NM_005462	
DMRT2	10655	hgsc.bcm.edu	37	9	1056569	1056569	+	Missense_Mutation	SNP	G	G	A	rs140004479	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr9:1056569G>A	ENST00000358146.2	+	3	982	c.982G>A	c.(982-984)Gtg>Atg	p.V328M	DMRT2_ENST00000259622.6_3'UTR|DMRT2_ENST00000382255.3_3'UTR|DMRT2_ENST00000302441.6_Missense_Mutation_p.V328M|DMRT2_ENST00000382251.3_Missense_Mutation_p.V328M			Q9Y5R5	DMRT2_HUMAN	doublesex and mab-3 related transcription factor 2	328					embryonic skeletal system development (GO:0048706)|positive regulation of myotome development (GO:2000287)|regulation of somitogenesis (GO:0014807)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	metal ion binding (GO:0046872)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)			large_intestine(1)|lung(1)|prostate(2)	4		all_lung(10;1.49e-09)|Lung NSC(10;1.86e-09)		Lung(218;0.0195)|GBM - Glioblastoma multiforme(50;0.0388)		TAATGTCAGCGTGGCCACAAC	0.458													G|||	7	0.00139776	0.0008	0.0014	5008	,	,		21074	0.0		0.005	False		,,,				2504	0.0				p.V328M		Atlas-SNP	.											.	DMRT2	70	.	0			c.G982A						PASS	.	G	,,MET/VAL	5,4401	9.9+/-24.2	0,5,2198	96.0	101.0	99.0		,,982	5.6	1.0	9	dbSNP_134	99	35,8565	23.4+/-69.3	0,35,4265	yes	utr-3,utr-3,missense	DMRT2	NM_001130865.2,NM_006557.6,NM_181872.4	,,21	0,40,6463	AA,AG,GG		0.407,0.1135,0.3076	,,probably-damaging	,,328/562	1056569	40,12966	2203	4300	6503	SO:0001583	missense	10655	exon4			GTCAGCGTGGCCA	AF130729	CCDS6444.1, CCDS6445.1	9p24.3	2008-07-21			ENSG00000173253	ENSG00000173253			2935	protein-coding gene	gene with protein product	"""terra-like protein"""	604935				10332030	Standard	NM_181872		Approved		uc003zha.3	Q9Y5R5	OTTHUMG00000019437	ENST00000358146.2:c.982G>A	9.37:g.1056569G>A	ENSP00000350865:p.Val328Met	99.0	0.0	0		129.0	75.0	0.581395	NM_181872	B1ANC0|B9EGJ1|Q9NPG6|Q9NQR6	Missense_Mutation	SNP	ENST00000358146.2	37	CCDS6444.1	3	0.0013736263736263737	0	0.0	0	0.0	0	0.0	3	0.00395778364116095	G	20.8	4.048378	0.75846	0.001135	0.00407	ENSG00000173253	ENST00000382251;ENST00000302441;ENST00000358146	T;T;T	0.38240	1.15;1.15;1.15	5.62	5.62	0.85841	.	0.121836	0.56097	D	0.000039	T	0.60483	0.2272	M	0.64404	1.975	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.91635	0.998;0.999	T	0.61579	-0.7034	10	0.87932	D	0	-22.0227	19.2806	0.94051	0.0:0.0:1.0:0.0	.	328;172	Q9Y5R5;Q5HYK2	DMRT2_HUMAN;.	M	328	ENSP00000371686:V328M;ENSP00000305785:V328M;ENSP00000350865:V328M	ENSP00000305785:V328M	V	+	1	0	DMRT2	1046569	1.000000	0.71417	0.999000	0.59377	0.993000	0.82548	9.230000	0.95299	2.665000	0.90641	0.650000	0.86243	GTG	G|0.997;A|0.003	0.003	strong		0.458	DMRT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051492.1	NM_006557	
SNRNP35	11066	hgsc.bcm.edu	37	12	123950408	123950408	+	Silent	SNP	A	A	G	rs28728202	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr12:123950408A>G	ENST00000526639.2	+	2	900	c.321A>G	c.(319-321)aaA>aaG	p.K107K	SNRNP35_ENST00000527158.2_Intron|SNRNP35_ENST00000412157.2_Silent_p.K112K|SNRNP35_ENST00000350887.5_Silent_p.K107K	NM_022717.3	NP_073208.1	Q16560	U1SBP_HUMAN	small nuclear ribonucleoprotein 35kDa (U11/U12)	107	RRM. {ECO:0000255|PROSITE- ProRule:PRU00176}.				mRNA processing (GO:0006397)|RNA splicing (GO:0008380)	nucleus (GO:0005634)|U12-type spliceosomal complex (GO:0005689)	nucleotide binding (GO:0000166)|RNA binding (GO:0003723)			NS(1)|large_intestine(1)|lung(4)|prostate(1)|skin(1)	8						CCGTGATCAAAGCTTACCGAG	0.532													A|||	8	0.00159744	0.0	0.0043	5008	,	,		18826	0.0		0.005	False		,,,				2504	0.0				p.K112K		Atlas-SNP	.											.	SNRNP35	28	.	0			c.A336G						PASS	.	A	,	6,4400	11.4+/-27.6	0,6,2197	107.0	105.0	106.0		321,336	-1.8	0.2	12	dbSNP_125	106	65,8535	38.8+/-94.9	0,65,4235	no	coding-synonymous,coding-synonymous	SNRNP35	NM_022717.2,NM_180699.2	,	0,71,6432	GG,GA,AA		0.7558,0.1362,0.5459	,	107/247,112/252	123950408	71,12935	2203	4300	6503	SO:0001819	synonymous_variant	11066	exon2			GATCAAAGCTTAC	BC054034	CCDS9249.1, CCDS45005.1	12q24.31	2013-02-12				ENSG00000184209		"""RNA binding motif (RRM) containing"""	30852	protein-coding gene	gene with protein product	"""U1 snRNP binding protein homolog"""					10520751, 8889548	Standard	XM_005253545		Approved	U1SNRNPBP	uc001ufb.1	Q16560		ENST00000526639.2:c.321A>G	12.37:g.123950408A>G		37.0	0.0	0		43.0	20.0	0.465116	NM_180699	A8K262|Q5XKN9	Silent	SNP	ENST00000526639.2	37	CCDS9249.1																																																																																			A|0.995;G|0.005	0.005	strong		0.532	SNRNP35-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000395197.2	NM_007020	
KLHL30	377007	hgsc.bcm.edu	37	2	239049537	239049537	+	Missense_Mutation	SNP	C	C	T	rs573206585		TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr2:239049537C>T	ENST00000409223.1	+	2	249	c.142C>T	c.(142-144)Cgc>Tgc	p.R48C	KLHL30_ENST00000305959.4_Missense_Mutation_p.R30C			Q0D2K2	KLH30_HUMAN	kelch-like family member 30	48	BTB. {ECO:0000255|PROSITE- ProRule:PRU00037}.									lung(4)	4		Breast(86;7.61e-05)|Renal(207;0.00183)|Ovarian(221;0.0481)|all_hematologic(139;0.158)|all_lung(227;0.198)|Melanoma(123;0.203)|Hepatocellular(293;0.244)		Epithelial(121;4.71e-24)|OV - Ovarian serous cystadenocarcinoma(60;3.02e-12)|Kidney(56;3.04e-09)|KIRC - Kidney renal clear cell carcinoma(57;5.63e-08)|BRCA - Breast invasive adenocarcinoma(100;0.000109)|Lung(119;0.0108)|LUSC - Lung squamous cell carcinoma(224;0.0253)		GCCATGCCACCGCGGCCTCCT	0.692													C|||	1	0.000199681	0.0	0.0	5008	,	,		17775	0.0		0.0	False		,,,				2504	0.001				p.R48C		Atlas-SNP	.											.	KLHL30	79	.	0			c.C142T						PASS	.						36.0	43.0	41.0					2																	239049537		2132	4219	6351	SO:0001583	missense	377007	exon2			TGCCACCGCGGCC		CCDS46555.1, CCDS46555.2	2q37.3	2013-02-22	2013-02-22		ENSG00000168427	ENSG00000168427		"""Kelch-like"", ""BTB/POZ domain containing"""	24770	protein-coding gene	gene with protein product			"""kelch-like 30 (Drosophila)"""				Standard	NM_198582		Approved	FLJ43374	uc002vxr.2	Q0D2K2	OTTHUMG00000152905	ENST00000409223.1:c.142C>T	2.37:g.239049537C>T	ENSP00000386389:p.Arg48Cys	102.0	0.0	0		68.0	44.0	0.647059	NM_198582	Q6ZUS1	Missense_Mutation	SNP	ENST00000409223.1	37	CCDS46555.2	.	.	.	.	.	.	.	.	.	.	C	24.7	4.563511	0.86335	.	.	ENSG00000168427	ENST00000409223;ENST00000305959	T;T	0.75477	-0.94;-0.94	5.75	5.75	0.90469	BTB/POZ-like (2);BTB/POZ (1);BTB/POZ fold (2);	0.000000	0.85682	D	0.000000	D	0.90511	0.7027	H	0.94771	3.58	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.92575	0.6069	10	0.87932	D	0	.	18.7132	0.91666	0.0:1.0:0.0:0.0	.	48	Q0D2K2	KLH30_HUMAN	C	48;30	ENSP00000386389:R48C;ENSP00000302386:R30C	ENSP00000302386:R30C	R	+	1	0	KLHL30	238714276	1.000000	0.71417	1.000000	0.80357	0.959000	0.62525	4.627000	0.61276	2.720000	0.93068	0.655000	0.94253	CGC	.	.	none		0.692	KLHL30-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000328518.1	NM_198582	
EXOC3L2	90332	hgsc.bcm.edu	37	19	45716364	45716364	+	Missense_Mutation	SNP	C	C	T	rs189063316	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr19:45716364C>T	ENST00000252482.3	-	9	1220	c.1193G>A	c.(1192-1194)cGg>cAg	p.R398Q	EXOC3L2_ENST00000413988.1_Missense_Mutation_p.R398Q|AC006126.3_ENST00000591569.1_Intron			Q2M3D2	EX3L2_HUMAN	exocyst complex component 3-like 2	398					exocytosis (GO:0006887)	exocyst (GO:0000145)				endometrium(1)|large_intestine(5)|lung(3)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)	12		all_neural(266;0.224)|Ovarian(192;0.231)		OV - Ovarian serous cystadenocarcinoma(262;0.00883)		AGACGGAGGCCGGGGCCGAGG	0.687													C|||	43	0.00858626	0.0	0.0043	5008	,	,		13018	0.0		0.0199	False		,,,				2504	0.0204				p.R398Q		Atlas-SNP	.											EXOC3L2,NS,lymphoid_neoplasm,0,1	EXOC3L2	30	1	0			c.G1193A						scavenged	.	C	GLN/ARG	13,4303		0,13,2145	8.0	10.0	9.0		1193	1.3	0.1	19		9	108,8370		1,106,4132	no	missense	EXOC3L2	NM_138568.3	43	1,119,6277	TT,TC,CC		1.2739,0.3012,0.9458	possibly-damaging	398/410	45716364	121,12673	2158	4239	6397	SO:0001583	missense	90332	exon10			GGAGGCCGGGGCC	AK093466	CCDS12657.1	19q13.32	2011-07-07			ENSG00000130201	ENSG00000130201			30162	protein-coding gene	gene with protein product						21566143	Standard	NM_138568		Approved	FLJ36147, XTP7	uc002pay.1	Q2M3D2	OTTHUMG00000155018	ENST00000252482.3:c.1193G>A	19.37:g.45716364C>T	ENSP00000252482:p.Arg398Gln	26.0	0.0	0		29.0	18.0	0.62069	NM_138568	Q8N9W2|Q96GV2	Missense_Mutation	SNP	ENST00000252482.3	37	CCDS12657.1	17	0.007783882783882784	0	0.0	3	0.008287292817679558	0	0.0	14	0.018469656992084433	C	15.67	2.903346	0.52333	0.003012	0.012739	ENSG00000130201	ENST00000252482;ENST00000413988	T;T	0.15718	2.4;2.4	3.52	1.26	0.21427	.	0.302293	0.21905	U	0.067396	T	0.03651	0.0104	L	0.27053	0.805	0.09310	N	1	P	0.34629	0.46	B	0.23419	0.046	T	0.24154	-1.0168	10	0.54805	T	0.06	.	4.0747	0.09899	0.0:0.6097:0.249:0.1413	.	398	Q2M3D2	EX3L2_HUMAN	Q	398	ENSP00000252482:R398Q;ENSP00000400713:R398Q	ENSP00000252482:R398Q	R	-	2	0	EXOC3L2	50408204	0.077000	0.21312	0.112000	0.21494	0.386000	0.30323	0.957000	0.29215	0.444000	0.26612	0.305000	0.20034	CGG	C|0.992;T|0.008	0.008	strong		0.687	EXOC3L2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000338073.1	NM_138568	
LYZL2	119180	hgsc.bcm.edu	37	10	30915078	30915078	+	Missense_Mutation	SNP	C	C	T			TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr10:30915078C>T	ENST00000375318.2	-	3	448	c.392G>A	c.(391-393)cGc>cAc	p.R131H		NM_183058.2	NP_898881.2	Q7Z4W2	LYZL2_HUMAN	lysozyme-like 2	85					cell wall macromolecule catabolic process (GO:0016998)	extracellular region (GO:0005576)	lysozyme activity (GO:0003796)			NS(2)|central_nervous_system(1)|large_intestine(1)|lung(14)|prostate(1)	19		Prostate(175;0.151)				CAGCTTTCCGCGTCTGCACCA	0.567																																					p.R131H		Atlas-SNP	.											.	LYZL2	33	.	0			c.G392A						PASS	.						173.0	144.0	154.0					10																	30915078		2203	4300	6503	SO:0001583	missense	119180	exon3			TTTCCGCGTCTGC	AF139543	CCDS7167.2	10p11.23	2009-12-04			ENSG00000151033	ENSG00000151033			29613	protein-coding gene	gene with protein product		612748					Standard	NM_183058		Approved		uc001ivk.3	Q7Z4W2	OTTHUMG00000017898	ENST00000375318.2:c.392G>A	10.37:g.30915078C>T	ENSP00000364467:p.Arg131His	164.0	0.0	0		210.0	93.0	0.442857	NM_183058	Q6NZ69	Missense_Mutation	SNP	ENST00000375318.2	37	CCDS7167.2	.	.	.	.	.	.	.	.	.	.	c	6.169	0.399451	0.11696	.	.	ENSG00000151033	ENST00000375318	T	0.69435	-0.4	2.27	-4.53	0.03462	.	1.768140	0.03329	N	0.193126	T	0.43211	0.1237	N	0.04148	-0.265	0.09310	N	1	B	0.02656	0.0	B	0.06405	0.002	T	0.39840	-0.9594	10	0.59425	D	0.04	-18.6248	8.4711	0.32986	0.0:0.4079:0.0:0.5921	.	131	Q7Z4W2-2	.	H	131	ENSP00000364467:R131H	ENSP00000364467:R131H	R	-	2	0	LYZL2	30955084	0.000000	0.05858	0.000000	0.03702	0.002000	0.02628	-2.771000	0.00779	-1.432000	0.01979	-2.148000	0.00335	CGC	.	.	none		0.567	LYZL2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047434.1	NM_183058	
SMARCA1	6594	hgsc.bcm.edu	37	X	128582381	128582381	+	Missense_Mutation	SNP	C	C	T			TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chrX:128582381C>T	ENST00000371122.4	-	24	3199	c.3070G>A	c.(3070-3072)Gag>Aag	p.E1024K	SMARCA1_ENST00000371123.1_Missense_Mutation_p.E1012K|SMARCA1_ENST00000371121.3_Missense_Mutation_p.E1012K	NM_003069.3	NP_003060.2	P28370	SMCA1_HUMAN	SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily a, member 1	1024					ATP catabolic process (GO:0006200)|ATP-dependent chromatin remodeling (GO:0043044)|brain development (GO:0007420)|chromatin remodeling (GO:0006338)|DNA strand renaturation (GO:0000733)|neuron differentiation (GO:0030182)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of neural precursor cell proliferation (GO:2000177)|transcription, DNA-templated (GO:0006351)	CERF complex (GO:0090537)|nuclear chromatin (GO:0000790)|nucleus (GO:0005634)|NURF complex (GO:0016589)	annealing helicase activity (GO:0036310)|ATP binding (GO:0005524)|chromatin binding (GO:0003682)|DNA binding (GO:0003677)|helicase activity (GO:0004386)			biliary_tract(1)|breast(1)|central_nervous_system(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(11)|liver(1)|lung(13)|ovary(5)|prostate(1)|skin(1)	45						TTTTCTTTCTCAATCAATGAA	0.323																																					p.E1024K		Atlas-SNP	.											.	SMARCA1	126	.	0			c.G3070A						PASS	.						125.0	117.0	120.0					X																	128582381		2203	4298	6501	SO:0001583	missense	6594	exon24			CTTTCTCAATCAA	M88163	CCDS14612.1, CCDS76018.1, CCDS76019.1	Xq25	2008-02-05			ENSG00000102038	ENSG00000102038			11097	protein-coding gene	gene with protein product		300012		SNF2L1, SNF2L		1408766, 14609955	Standard	XM_005262461		Approved	SNF2LB, NURF140, ISWI, SWI	uc004eun.4	P28370	OTTHUMG00000022370	ENST00000371122.4:c.3070G>A	X.37:g.128582381C>T	ENSP00000360163:p.Glu1024Lys	112.0	0.0	0		120.0	7.0	0.0583333	NM_003069	Q5JV41|Q5JV42	Missense_Mutation	SNP	ENST00000371122.4	37	CCDS14612.1	.	.	.	.	.	.	.	.	.	.	C	18.53	3.645013	0.67358	.	.	ENSG00000102038	ENST00000371121;ENST00000371123;ENST00000371122;ENST00000450039	D;D;D;D	0.91792	-2.91;-2.91;-2.9;-2.89	5.87	5.87	0.94306	SLIDE (1);Homeodomain-like (1);	0.000000	0.64402	D	0.000009	D	0.96436	0.8837	M	0.84773	2.715	0.80722	D	1	D;D;D;D	0.76494	0.992;0.999;0.99;0.992	D;D;D;D	0.79784	0.979;0.993;0.964;0.979	D	0.95323	0.8422	10	0.35671	T	0.21	-17.3926	19.3889	0.94570	0.0:1.0:0.0:0.0	.	1003;1024;1012;1024	E9PCY3;B7ZLQ5;P28370-2;P28370	.;.;.;SMCA1_HUMAN	K	1012;1012;1024;1003	ENSP00000360162:E1012K;ENSP00000360164:E1012K;ENSP00000360163:E1024K;ENSP00000404275:E1003K	ENSP00000360162:E1012K	E	-	1	0	SMARCA1	128410062	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	6.177000	0.71961	2.618000	0.88619	0.600000	0.82982	GAG	.	.	none		0.323	SMARCA1-004	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000058206.1	NM_003069	
SNX29	92017	hgsc.bcm.edu	37	16	12492322	12492322	+	Missense_Mutation	SNP	A	A	T			TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr16:12492322A>T	ENST00000566228.1	+	17	1988	c.1919A>T	c.(1918-1920)cAa>cTa	p.Q640L	SNX29_ENST00000306030.3_Missense_Mutation_p.Q255L|SNX29_ENST00000323433.4_Missense_Mutation_p.Q255L	NM_032167.3	NP_115543.3	Q8TEQ0	SNX29_HUMAN	sorting nexin 29	640						extracellular vesicular exosome (GO:0070062)	phosphatidylinositol binding (GO:0035091)			endometrium(1)|large_intestine(1)|lung(3)|ovary(1)|prostate(1)	7						GATTTGAGTCAAACGTCCGAA	0.463																																					p.Q640L		Atlas-SNP	.											.	SNX29	60	.	0			c.A1919T						PASS	.						136.0	132.0	133.0					16																	12492322		1866	4116	5982	SO:0001583	missense	92017	exon17			TGAGTCAAACGTC	AK074072	CCDS10553.2	16p13.13-p13.12	2011-08-16			ENSG00000048471	ENSG00000048471		"""Sorting nexins"""	30542	protein-coding gene	gene with protein product			"""RUN domain containing 2A"""	RUNDC2A		16782399	Standard	XM_005255682		Approved	FLJ12363	uc002dby.5	Q8TEQ0		ENST00000566228.1:c.1919A>T	16.37:g.12492322A>T	ENSP00000456480:p.Gln640Leu	145.0	0.0	0		180.0	80.0	0.444444	NM_032167	B5MDW2|Q8N2X2|Q9HA26	Missense_Mutation	SNP	ENST00000566228.1	37	CCDS10553.2	.	.	.	.	.	.	.	.	.	.	A	20.3	3.973375	0.74246	.	.	ENSG00000048471	ENST00000306030;ENST00000323433	.	.	.	5.62	5.62	0.85841	.	0.000000	0.85682	D	0.000000	T	0.49236	0.1545	L	0.40543	1.245	0.31498	N	0.665135	.	.	.	.	.	.	T	0.58470	-0.7631	7	0.44086	T	0.13	-15.7683	13.779	0.63071	1.0:0.0:0.0:0.0	.	.	.	.	L	255	.	ENSP00000306940:Q255L	Q	+	2	0	SNX29	12399823	1.000000	0.71417	1.000000	0.80357	0.939000	0.58152	6.483000	0.73617	2.129000	0.65627	0.533000	0.62120	CAA	.	.	none		0.463	SNX29-005	PUTATIVE	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000422622.1		
DST	667	hgsc.bcm.edu	37	6	56373536	56373536	+	Missense_Mutation	SNP	C	C	T	rs41271862	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr6:56373536C>T	ENST00000361203.3	-	70	18077	c.18070G>A	c.(18070-18072)Gac>Aac	p.D6024N	DST_ENST00000244364.6_Missense_Mutation_p.D3721N|DST_ENST00000370754.5_Missense_Mutation_p.D6313N|DST_ENST00000340834.4_5'UTR|DST_ENST00000370788.2_Missense_Mutation_p.D3938N|DST_ENST00000312431.6_3'UTR|DST_ENST00000421834.2_Missense_Mutation_p.D4047N|DST_ENST00000370769.4_Missense_Mutation_p.D6135N|DST_ENST00000446842.2_Missense_Mutation_p.D5809N			Q03001	DYST_HUMAN	dystonin	6020					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)			ACCATTTGGTCAAGCTTATCC	0.438													C|||	80	0.0159744	0.0	0.013	5008	,	,		21172	0.0		0.0557	False		,,,				2504	0.0153				p.D3721N		Atlas-SNP	.											.	DST	1427	.	0			c.G11161A						PASS	.	C	ASN/ASP	39,3815		0,39,1888	118.0	116.0	117.0		11161	5.5	1.0	6	dbSNP_127	117	407,7869		12,383,3743	yes	missense	DST	NM_015548.4	23	12,422,5631	TT,TC,CC		4.9178,1.0119,3.6768	probably-damaging	3721/5172	56373536	446,11684	1927	4138	6065	SO:0001583	missense	667	exon56			TTTGGTCAAGCTT	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.18070G>A	6.37:g.56373536C>T	ENSP00000354508:p.Asp6024Asn	165.0	0.0	0		175.0	81.0	0.462857	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		51	0.023351648351648352	0	0.0	4	0.011049723756906077	0	0.0	47	0.06200527704485488	C	20.9	4.070212	0.76301	0.010119	0.049178	ENSG00000151914	ENST00000244364;ENST00000370754;ENST00000370769;ENST00000421834;ENST00000446842;ENST00000370788;ENST00000361203;ENST00000537444	T;T;T;T;T;T;T	0.51071	1.26;1.26;1.26;1.26;1.26;1.26;0.72	5.54	5.54	0.83059	.	0.000000	0.56097	D	0.000022	T	0.57272	0.2042	L	0.53249	1.67	0.32212	N	0.576451	D;D;D;D;D	0.89917	0.999;1.0;1.0;0.999;0.963	D;D;D;D;P	0.97110	0.999;1.0;0.999;0.966;0.792	T	0.42430	-0.9452	9	0.23302	T	0.38	.	19.8426	0.96695	0.0:1.0:0.0:0.0	rs41271862	4047;6135;6313;6133;3721	Q5TBT1;E7ERU2;E9PEB9;Q03001;Q03001-8	.;.;.;DYST_HUMAN;.	N	3721;6313;6135;4047;5809;3938;6024;137	ENSP00000244364:D3721N;ENSP00000359790:D6313N;ENSP00000359805:D6135N;ENSP00000400883:D4047N;ENSP00000393645:D5809N;ENSP00000359824:D3938N;ENSP00000354508:D6024N	ENSP00000244364:D3721N	D	-	1	0	DST	56481495	1.000000	0.71417	0.999000	0.59377	0.976000	0.68499	6.039000	0.70972	2.765000	0.95021	0.557000	0.71058	GAC	C|0.967;T|0.033	0.033	strong		0.438	DST-004	NOVEL	not_organism_supported|basic|appris_candidate	protein_coding	protein_coding	OTTHUMT00000041021.3	NM_001723	
PKD1	5310	hgsc.bcm.edu	37	16	2161153	2161153	+	Missense_Mutation	SNP	C	C	T	rs147141131	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr16:2161153C>T	ENST00000262304.4	-	15	4223	c.4015G>A	c.(4015-4017)Gtg>Atg	p.V1339M	RP11-304L19.4_ENST00000568795.1_RNA|PKD1_ENST00000423118.1_Missense_Mutation_p.V1339M	NM_001009944.2	NP_001009944	P98161	PKD1_HUMAN	polycystic kidney disease 1 (autosomal dominant)	1339	PKD 8. {ECO:0000255|PROSITE- ProRule:PRU00151}.				anatomical structure morphogenesis (GO:0009653)|branching morphogenesis of an epithelial tube (GO:0048754)|calcium ion transmembrane transport (GO:0070588)|calcium-independent cell-matrix adhesion (GO:0007161)|cartilage condensation (GO:0001502)|cartilage development (GO:0051216)|cation transmembrane transport (GO:0098655)|cell cycle arrest (GO:0007050)|cell-matrix adhesion (GO:0007160)|cytoplasmic sequestering of transcription factor (GO:0042994)|detection of mechanical stimulus (GO:0050982)|digestive tract development (GO:0048565)|embryonic placenta development (GO:0001892)|genitalia development (GO:0048806)|heart development (GO:0007507)|homophilic cell adhesion (GO:0007156)|in utero embryonic development (GO:0001701)|JAK-STAT cascade (GO:0007259)|kidney development (GO:0001822)|liver development (GO:0001889)|lung epithelium development (GO:0060428)|mesonephric duct development (GO:0072177)|mesonephric tubule development (GO:0072164)|metanephric ascending thin limb development (GO:0072218)|metanephric collecting duct development (GO:0072205)|metanephric distal tubule morphogenesis (GO:0072287)|metanephric proximal tubule development (GO:0072237)|neural tube development (GO:0021915)|neuropeptide signaling pathway (GO:0007218)|nitrogen compound metabolic process (GO:0006807)|peptidyl-serine phosphorylation (GO:0018105)|placenta blood vessel development (GO:0060674)|positive regulation of cyclin-dependent protein serine/threonine kinase activity involved in G1/S transition of mitotic cell cycle (GO:0031659)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|positive regulation of protein binding (GO:0032092)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|protein export from nucleus (GO:0006611)|regulation of mitotic spindle organization (GO:0060236)|regulation of proteasomal protein catabolic process (GO:0061136)|response to fluid shear stress (GO:0034405)|skin development (GO:0043588)|spinal cord development (GO:0021510)	basolateral plasma membrane (GO:0016323)|cilium (GO:0005929)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|lateral plasma membrane (GO:0016328)|motile primary cilium (GO:0031512)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|polycystin complex (GO:0002133)	calcium channel activity (GO:0005262)|carbohydrate binding (GO:0030246)|cation channel activity (GO:0005261)|ion channel binding (GO:0044325)|protein domain specific binding (GO:0019904)|protein kinase binding (GO:0019901)			breast(1)|central_nervous_system(3)|cervix(1)|endometrium(7)|kidney(6)|lung(34)|prostate(4)|skin(10)|upper_aerodigestive_tract(3)|urinary_tract(3)	72						CACCCCCGCACGGTCGTGTTG	0.682																																					p.V1339M		Atlas-SNP	.											.	PKD1	184	.	0			c.G4015A						PASS	.	C	MET/VAL,MET/VAL	0,4374		0,0,2187	28.0	31.0	30.0		4015,4015	-0.2	0.0	16	dbSNP_134	30	4,8580	3.7+/-12.6	0,4,4288	no	missense,missense	PKD1	NM_000296.3,NM_001009944.2	21,21	0,4,6475	TT,TC,CC		0.0466,0.0,0.0309	benign,benign	1339/4303,1339/4304	2161153	4,12954	2187	4292	6479	SO:0001583	missense	5310	exon15			CCCGCACGGTCGT	L33243	CCDS32369.1, CCDS45385.1	16p13.3	2014-01-28			ENSG00000008710	ENSG00000008710		"""Voltage-gated ion channels / Transient receptor potential cation channels"""	9008	protein-coding gene	gene with protein product	"""polycystin 1"", ""transient receptor potential cation channel, subfamily P, member 1"""	601313					Standard	NM_001009944		Approved	PBP, Pc-1, TRPP1	uc002cos.1	P98161	OTTHUMG00000155795	ENST00000262304.4:c.4015G>A	16.37:g.2161153C>T	ENSP00000262304:p.Val1339Met	97.0	0.0	0		111.0	61.0	0.54955	NM_000296	Q15140|Q15141	Missense_Mutation	SNP	ENST00000262304.4	37	CCDS32369.1	.	.	.	.	.	.	.	.	.	.	c	10.06	1.246377	0.22796	0.0	4.66E-4	ENSG00000008710	ENST00000262304;ENST00000423118;ENST00000306101	T;T	0.62788	0.0;0.0	5.58	-0.241	0.13043	PKD/Chitinase domain (1);Polycystin cation channel (1);PKD domain (4);	0.716298	0.14231	N	0.332727	T	0.69178	0.3082	M	0.63428	1.95	0.09310	N	1	D;D	0.62365	0.991;0.984	P;P	0.61132	0.884;0.88	T	0.60571	-0.7237	10	0.41790	T	0.15	.	9.8488	0.41043	0.0:0.5988:0.0:0.4012	.	1339;1339	P98161-3;P98161	.;PKD1_HUMAN	M	1339;1339;1020	ENSP00000262304:V1339M;ENSP00000399501:V1339M	ENSP00000262304:V1339M	V	-	1	0	PKD1	2101154	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-1.106000	0.03319	-0.296000	0.08947	-0.401000	0.06369	GTG	C|0.999;T|0.001	0.001	strong		0.682	PKD1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000341688.1		
RIPK1	8737	hgsc.bcm.edu	37	6	3083369	3083369	+	Silent	SNP	T	T	C			TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr6:3083369T>C	ENST00000259808.4	+	5	808	c.510T>C	c.(508-510)aaT>aaC	p.N170N	RIPK1_ENST00000380409.2_Silent_p.N170N|RIPK1_ENST00000479389.1_3'UTR|RIPK1_ENST00000541791.1_Silent_p.N124N			Q13546	RIPK1_HUMAN	receptor (TNFRSF)-interacting serine-threonine kinase 1	170	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				activation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0006919)|activation of JUN kinase activity (GO:0007257)|amyloid fibril formation (GO:1990000)|apoptotic process (GO:0006915)|apoptotic signaling pathway (GO:0097190)|cellular protein catabolic process (GO:0044257)|cellular response to growth factor stimulus (GO:0071363)|cellular response to tumor necrosis factor (GO:0071356)|extrinsic apoptotic signaling pathway (GO:0097191)|innate immune response (GO:0045087)|MyD88-independent toll-like receptor signaling pathway (GO:0002756)|necroptotic process (GO:0070266)|necroptotic signaling pathway (GO:0097527)|negative regulation of extrinsic apoptotic signaling pathway (GO:2001237)|negative regulation of extrinsic apoptotic signaling pathway in absence of ligand (GO:2001240)|negative regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043124)|peptidyl-serine autophosphorylation (GO:0036289)|positive regulation of apoptotic process (GO:0043065)|positive regulation of extrinsic apoptotic signaling pathway (GO:2001238)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of interleukin-8 production (GO:0032757)|positive regulation of JNK cascade (GO:0046330)|positive regulation of macrophage differentiation (GO:0045651)|positive regulation of necroptotic process (GO:0060545)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of programmed cell death (GO:0043068)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of reactive oxygen species metabolic process (GO:2000379)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of tumor necrosis factor production (GO:0032760)|positive regulation of type I interferon production (GO:0032481)|protein autophosphorylation (GO:0046777)|protein heterooligomerization (GO:0051291)|protein homooligomerization (GO:0051260)|regulation of ATP:ADP antiporter activity (GO:0070926)|regulation of extrinsic apoptotic signaling pathway in absence of ligand (GO:2001239)|response to tumor necrosis factor (GO:0034612)|ripoptosome assembly (GO:0097343)|ripoptosome assembly involved in necroptotic process (GO:1901026)|T cell apoptotic process (GO:0070231)|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)	cytosol (GO:0005829)|death-inducing signaling complex (GO:0031264)|membrane raft (GO:0045121)|mitochondrion (GO:0005739)|receptor complex (GO:0043235)|ripoptosome (GO:0097342)	ATP binding (GO:0005524)|death domain binding (GO:0070513)|death receptor binding (GO:0005123)|identical protein binding (GO:0042802)|protein complex binding (GO:0032403)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)|ubiquitin protein ligase binding (GO:0031625)			breast(1)|endometrium(3)|kidney(2)|large_intestine(6)|lung(6)|prostate(1)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	23	Ovarian(93;0.0386)	all_hematologic(90;0.0895)				AACTGAATAATGAAGAGCACA	0.527																																					p.N170N		Atlas-SNP	.											.	RIPK1	56	.	0			c.T510C						PASS	.						133.0	117.0	123.0					6																	3083369		2203	4300	6503	SO:0001819	synonymous_variant	8737	exon4			GAATAATGAAGAG	U25994	CCDS4482.1	6p25.2	2008-02-05			ENSG00000137275	ENSG00000137275			10019	protein-coding gene	gene with protein product		603453				7538908, 8612133	Standard	XM_005249458		Approved	RIP	uc003mux.3	Q13546	OTTHUMG00000014134	ENST00000259808.4:c.510T>C	6.37:g.3083369T>C		67.0	0.0	0		108.0	69.0	0.638889	NM_003804	A0AV89|B2RAG1|B4E3F9|Q13180|Q59H33	Silent	SNP	ENST00000259808.4	37	CCDS4482.1																																																																																			.	.	none		0.527	RIPK1-005	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000039659.2	NM_003804	
PRSS53	339105	hgsc.bcm.edu	37	16	31096495	31096495	+	Missense_Mutation	SNP	G	G	C	rs72785539	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr16:31096495G>C	ENST00000280606.6	-	7	1123	c.970C>G	c.(970-972)Ctg>Gtg	p.L324V		NM_001039503.2	NP_001034592.1	Q2L4Q9	PRS53_HUMAN	protease, serine, 53	324	Peptidase S1 2. {ECO:0000255|PROSITE- ProRule:PRU00274}.					extracellular region (GO:0005576)	serine-type endopeptidase activity (GO:0004252)			large_intestine(1)|lung(3)	4						CCACAGGCCAGCTGTCCCTGG	0.637													G|||	4	0.000798722	0.0	0.0	5008	,	,		19514	0.0		0.004	False		,,,				2504	0.0				p.L324V		Atlas-SNP	.											.	PRSS53	29	.	0			c.C970G						PASS	.	G	VAL/LEU	2,4122		0,2,2060	21.0	26.0	25.0		970	4.6	0.9	16	dbSNP_130	25	24,8378		0,24,4177	yes	missense	PRSS53	NM_001039503.2	32	0,26,6237	CC,CG,GG		0.2856,0.0485,0.2076	possibly-damaging	324/554	31096495	26,12500	2062	4201	6263	SO:0001583	missense	339105	exon7			AGGCCAGCTGTCC		CCDS42153.1	16p11.2	2010-05-07			ENSG00000151006	ENSG00000151006		"""Serine peptidases / Serine peptidases"""	34407	protein-coding gene	gene with protein product	"""polyserase 3"""	610561				16566820	Standard	NM_001039503		Approved	POL3S	uc002eaq.3	Q2L4Q9	OTTHUMG00000047358	ENST00000280606.6:c.970C>G	16.37:g.31096495G>C	ENSP00000280606:p.Leu324Val	217.0	0.0	0		240.0	126.0	0.525	NM_001039503		Missense_Mutation	SNP	ENST00000280606.6	37	CCDS42153.1	2	9.157509157509158E-4	0	0.0	0	0.0	0	0.0	2	0.002638522427440633	G	13.86	2.364215	0.41902	4.85E-4	0.002856	ENSG00000151006	ENST00000280606	T	0.30448	1.53	5.75	4.61	0.57282	Peptidase cysteine/serine, trypsin-like (1);Peptidase S1/S6, chymotrypsin/Hap (3);	0.302705	0.17712	U	0.164555	T	0.28466	0.0704	L	0.49699	1.58	0.09310	N	1	P	0.43231	0.801	B	0.41374	0.355	T	0.17501	-1.0367	10	0.42905	T	0.14	.	9.359	0.38184	0.0858:0.0:0.7657:0.1485	.	324	Q2L4Q9	PRS53_HUMAN	V	324	ENSP00000280606:L324V	ENSP00000280606:L324V	L	-	1	2	PRSS53	31003996	0.998000	0.40836	0.950000	0.38849	0.578000	0.36192	3.172000	0.50832	2.720000	0.93068	0.655000	0.94253	CTG	G|0.999;C|0.001	0.001	strong		0.637	PRSS53-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000108580.4	NM_001081268	
TSHZ3	57616	hgsc.bcm.edu	37	19	31768890	31768890	+	Silent	SNP	G	G	A	rs138330927	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr19:31768890G>A	ENST00000240587.4	-	2	2136	c.1809C>T	c.(1807-1809)ccC>ccT	p.P603P		NM_020856.2	NP_065907.2	Q63HK5	TSH3_HUMAN	teashirt zinc finger homeobox 3	603					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)					AGTTTGTCTTGGGCATGGGGG	0.547													G|||	3	0.000599042	0.0	0.0	5008	,	,		17796	0.0		0.003	False		,,,				2504	0.0				p.P603P		Atlas-SNP	.											.	TSHZ3	549	.	0			c.C1809T						PASS	.	G		1,4405	2.1+/-5.4	0,1,2202	91.0	99.0	96.0		1809	3.1	1.0	19	dbSNP_134	96	6,8594	4.3+/-15.6	0,6,4294	no	coding-synonymous	TSHZ3	NM_020856.2		0,7,6496	AA,AG,GG		0.0698,0.0227,0.0538		603/1082	31768890	7,12999	2203	4300	6503	SO:0001819	synonymous_variant	57616	exon2			TGTCTTGGGCATG	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.1809C>T	19.37:g.31768890G>A		262.0	1.0	0.00381679		244.0	108.0	0.442623	NM_020856	Q9H0G6|Q9P254	Silent	SNP	ENST00000240587.4	37	CCDS12421.2																																																																																			G|0.999;A|0.001	0.001	strong		0.547	TSHZ3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000316743.2	NM_020856	
RIN2	54453	hgsc.bcm.edu	37	20	19915769	19915769	+	Silent	SNP	C	C	T	rs181853315	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr20:19915769C>T	ENST00000255006.6	+	3	380	c.231C>T	c.(229-231)atC>atT	p.I77I	RIN2_ENST00000440354.2_Silent_p.I28I|RIN2_ENST00000484638.1_3'UTR	NM_001242581.1|NM_018993.3	NP_001229510.1|NP_061866.1	Q8WYP3	RIN2_HUMAN	Ras and Rab interactor 2	28					endocytosis (GO:0006897)|positive regulation of Rab GTPase activity (GO:0032851)|regulation of catalytic activity (GO:0050790)|small GTPase mediated signal transduction (GO:0007264)	cytoplasm (GO:0005737)	GTPase activator activity (GO:0005096)|Rab guanyl-nucleotide exchange factor activity (GO:0017112)|small GTPase regulator activity (GO:0005083)			autonomic_ganglia(1)|breast(1)|endometrium(3)|kidney(3)|large_intestine(4)|lung(11)|ovary(1)|prostate(1)|urinary_tract(2)	27						CCTCGGAGATCGGAGAACTGA	0.527													C|||	9	0.00179712	0.0	0.0072	5008	,	,		17587	0.0		0.003	False		,,,				2504	0.001				p.I77I		Atlas-SNP	.											.	RIN2	126	.	0			c.C231T						PASS	.	C	,	7,3941		0,7,1967	70.0	67.0	68.0		231,84	4.8	1.0	20		68	83,8219		0,83,4068	no	coding-synonymous,coding-synonymous	RIN2	NM_001242581.1,NM_018993.3	,	0,90,6035	TT,TC,CC		0.9998,0.1773,0.7347	,	77/945,28/896	19915769	90,12160	1974	4151	6125	SO:0001819	synonymous_variant	54453	exon3			GGAGATCGGAGAA	AB060339	CCDS56182.1	20p11.22	2008-07-30			ENSG00000132669	ENSG00000132669			18750	protein-coding gene	gene with protein product		610222				11733506, 1849280, 16423831	Standard	NM_018993		Approved	RASSF4	uc002wro.2	Q8WYP3	OTTHUMG00000031996	ENST00000255006.6:c.231C>T	20.37:g.19915769C>T		87.0	0.0	0		84.0	40.0	0.47619	NM_001242581	Q00425|Q5TFT8|Q9BQL3|Q9H071	Silent	SNP	ENST00000255006.6	37	CCDS56182.1																																																																																			C|0.995;T|0.005	0.005	strong		0.527	RIN2-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078212.1		
POLD3	10714	hgsc.bcm.edu	37	11	74347275	74347275	+	Missense_Mutation	SNP	C	C	T	rs572105600		TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr11:74347275C>T	ENST00000263681.2	+	11	1282	c.1153C>T	c.(1153-1155)Cgc>Tgc	p.R385C	POLD3_ENST00000527458.1_Missense_Mutation_p.R346C|POLD3_ENST00000532497.1_Missense_Mutation_p.R279C	NM_006591.2	NP_006582.1	Q15054	DPOD3_HUMAN	polymerase (DNA-directed), delta 3, accessory subunit	385					base-excision repair (GO:0006284)|DNA repair (GO:0006281)|DNA strand elongation involved in DNA replication (GO:0006271)|DNA synthesis involved in DNA repair (GO:0000731)|mismatch repair (GO:0006298)|mitotic cell cycle (GO:0000278)|nucleotide-excision repair (GO:0006289)|nucleotide-excision repair, DNA gap filling (GO:0006297)|telomere maintenance (GO:0000723)|telomere maintenance via recombination (GO:0000722)|telomere maintenance via semi-conservative replication (GO:0032201)|transcription-coupled nucleotide-excision repair (GO:0006283)	delta DNA polymerase complex (GO:0043625)|mitochondrion (GO:0005739)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	DNA-directed DNA polymerase activity (GO:0003887)	p.R385G(2)		breast(2)|endometrium(2)|kidney(2)|large_intestine(3)|lung(6)|ovary(1)|skin(1)|stomach(1)	18	Breast(11;3.21e-06)					AAAACGAAAACGCGTACTAAA	0.358																																					p.R385C		Atlas-SNP	.											POLD3_ENST00000263681,NS,carcinoma,0,2	POLD3	87	2	2	Substitution - Missense(2)	endometrium(2)	c.C1153T						PASS	.						83.0	80.0	81.0					11																	74347275		2200	4293	6493	SO:0001583	missense	10714	exon11			CGAAAACGCGTAC	D26018	CCDS8233.1	11q14	2014-06-13			ENSG00000077514	ENSG00000077514		"""DNA polymerases"""	20932	protein-coding gene	gene with protein product	"""DNA polymerase delta subunit p66"", ""Pol delta C subunit (p66)"", ""protein phosphatase 1, regulatory subunit 128"""	611415				10219083	Standard	NM_006591		Approved	P66, KIAA0039, P68, PPP1R128	uc001ovf.2	Q15054	OTTHUMG00000165621	ENST00000263681.2:c.1153C>T	11.37:g.74347275C>T	ENSP00000263681:p.Arg385Cys	151.0	0.0	0		163.0	60.0	0.368098	NM_006591	B7ZAI6|Q32MZ9|Q32N00	Missense_Mutation	SNP	ENST00000263681.2	37	CCDS8233.1	.	.	.	.	.	.	.	.	.	.	C	18.46	3.629880	0.67015	.	.	ENSG00000077514	ENST00000263681;ENST00000527458;ENST00000532497	.	.	.	5.7	4.71	0.59529	.	0.000000	0.85682	D	0.000000	T	0.78272	0.4257	M	0.76328	2.33	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	T	0.80627	-0.1298	9	0.87932	D	0	-18.0768	14.9973	0.71443	0.1522:0.8478:0.0:0.0	.	385	Q15054	DPOD3_HUMAN	C	385;346;279	.	ENSP00000263681:R385C	R	+	1	0	POLD3	74024923	0.997000	0.39634	0.943000	0.38184	0.845000	0.48019	1.348000	0.33987	2.696000	0.92011	0.561000	0.74099	CGC	.	.	none		0.358	POLD3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000385376.1	NM_006591	
CFAP53	220136	hgsc.bcm.edu	37	18	47788544	47788544	+	Silent	SNP	T	T	G	rs112087763	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	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		74.0	0.0	0		100.0	52.0	0.52	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		
CREB3L3	84699	hgsc.bcm.edu	37	19	4159722	4159722	+	Silent	SNP	C	C	T	rs144868958	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr19:4159722C>T	ENST00000078445.2	+	4	666	c.519C>T	c.(517-519)tcC>tcT	p.S173S	CREB3L3_ENST00000602147.1_Silent_p.S173S|CREB3L3_ENST00000602257.1_Silent_p.S173S|CREB3L3_ENST00000595923.1_Silent_p.S172S|CREB3L3_ENST00000252587.3_Intron	NM_001271995.1|NM_001271996.1|NM_032607.1	NP_001258924.1|NP_001258925.1|NP_115996.1	Q68CJ9	CR3L3_HUMAN	cAMP responsive element binding protein 3-like 3	173					positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|response to unfolded protein (GO:0006986)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|nucleus (GO:0005634)	RNA polymerase II regulatory region sequence-specific DNA binding (GO:0000977)|RNA polymerase II transcription regulatory region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001228)			breast(2)|kidney(1)|large_intestine(3)|lung(12)|ovary(1)|skin(2)|urinary_tract(3)	24				UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|BRCA - Breast invasive adenocarcinoma(158;0.0232)|STAD - Stomach adenocarcinoma(1328;0.18)		TGGACCTGTCCCCACGATGCA	0.632													C|||	3	0.000599042	0.0	0.0014	5008	,	,		17296	0.0		0.002	False		,,,				2504	0.0				p.S173S		Atlas-SNP	.											.	CREB3L3	53	.	0			c.C519T						PASS	.	C		2,4404	4.2+/-10.8	0,2,2201	92.0	84.0	87.0		519	-6.4	0.0	19	dbSNP_134	87	22,8578	16.0+/-53.3	0,22,4278	no	coding-synonymous	CREB3L3	NM_032607.1		0,24,6479	TT,TC,CC		0.2558,0.0454,0.1845		173/462	4159722	24,12982	2203	4300	6503	SO:0001819	synonymous_variant	84699	exon4			CCTGTCCCCACGA		CCDS12121.1, CCDS62498.1, CCDS62499.1, CCDS62500.1	19p13.3	2013-01-10				ENSG00000060566		"""basic leucine zipper proteins"""	18855	protein-coding gene	gene with protein product		611998				11353085	Standard	NM_032607		Approved	CREB-H	uc002lzl.4	Q68CJ9		ENST00000078445.2:c.519C>T	19.37:g.4159722C>T		41.0	0.0	0		66.0	30.0	0.454545	NM_001271997	B2R7S6|B7ZL69|M0QYW7|Q6ZMC5|Q96TB9	Silent	SNP	ENST00000078445.2	37	CCDS12121.1																																																																																			C|0.998;T|0.002	0.002	strong		0.632	CREB3L3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000457922.1	NM_032607	
GPR35	2859	hgsc.bcm.edu	37	2	241569492	241569492	+	Silent	SNP	G	G	C	rs61734451	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr2:241569492G>C	ENST00000319838.5	+	6	1065	c.123G>C	c.(121-123)gcG>gcC	p.A41A	GPR35_ENST00000438013.2_Silent_p.A72A|GPR35_ENST00000430267.1_Silent_p.A41A|GPR35_ENST00000407714.1_Silent_p.A41A|GPR35_ENST00000403859.1_Silent_p.A41A	NM_001195381.1	NP_001182310.1	Q9HC97	GPR35_HUMAN	G protein-coupled receptor 35	41					G-protein coupled receptor signaling pathway (GO:0007186)	integral component of plasma membrane (GO:0005887)	G-protein coupled receptor activity (GO:0004930)			NS(2)|breast(1)|cervix(1)|endometrium(1)|lung(7)|ovary(1)|pancreas(1)|skin(2)|urinary_tract(1)	17		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;5.29e-32)|all cancers(36;1.38e-29)|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;5.02e-06)|Lung(119;0.00163)|Colorectal(34;0.00463)|LUSC - Lung squamous cell carcinoma(224;0.008)|COAD - Colon adenocarcinoma(134;0.031)		ACAGCCTGGCGCTCTGGGTGT	0.652													g|||	22	0.00439297	0.0008	0.0043	5008	,	,		17820	0.0		0.0139	False		,,,				2504	0.0041				p.A72A		Atlas-SNP	.											.	GPR35	43	.	0			c.G216C						PASS	.	G	,,	25,4381	31.7+/-61.6	0,25,2178	75.0	69.0	71.0		216,216,123	-3.3	1.0	2	dbSNP_129	71	145,8455	71.3+/-133.9	2,141,4157	no	coding-synonymous,coding-synonymous,coding-synonymous	GPR35	NM_001195381.1,NM_001195382.1,NM_005301.3	,,	2,166,6335	CC,CG,GG		1.686,0.5674,1.3071	,,	72/341,72/341,41/310	241569492	170,12836	2203	4300	6503	SO:0001819	synonymous_variant	2859	exon6			CCTGGCGCTCTGG		CCDS2541.1, CCDS56174.1	2q37.3	2012-08-21			ENSG00000178623	ENSG00000178623		"""GPCR / Class A : Orphans"""	4492	protein-coding gene	gene with protein product		602646				9479505	Standard	NM_005301		Approved		uc021vze.1	Q9HC97	OTTHUMG00000133356	ENST00000319838.5:c.123G>C	2.37:g.241569492G>C		79.0	0.0	0		80.0	36.0	0.45	NM_001195382	J3KR30|O43495|Q17R58|Q4VBN5|Q4ZFV2|Q6FHI8|Q86UH4	Silent	SNP	ENST00000319838.5	37	CCDS2541.1																																																																																			G|0.990;C|0.010	0.010	strong		0.652	GPR35-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000325631.1	NM_001195382	
TFR2	7036	hgsc.bcm.edu	37	7	100226937	100226937	+	Silent	SNP	G	G	A	rs368298121		TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr7:100226937G>A	ENST00000462107.1	-	11	1616	c.1329C>T	c.(1327-1329)tcC>tcT	p.S443S	TFR2_ENST00000431692.1_3'UTR|TFR2_ENST00000544242.1_5'UTR|TFR2_ENST00000223051.3_Silent_p.S443S			Q9UP52	TFR2_HUMAN	transferrin receptor 2	443					cellular iron ion homeostasis (GO:0006879)|iron ion transport (GO:0006826)|receptor-mediated endocytosis (GO:0006898)	cytoplasm (GO:0005737)|integral component of plasma membrane (GO:0005887)	transferrin receptor activity (GO:0004998)			central_nervous_system(1)|endometrium(1)|kidney(2)|large_intestine(6)|liver(1)|lung(8)|ovary(1)|pancreas(1)|prostate(1)|skin(1)	23	Lung NSC(181;0.0261)|all_lung(186;0.0392)|Esophageal squamous(72;0.0439)				Gallium nitrate(DB05260)	TCCCCACAGCGGATTTAGCTG	0.627																																					p.S443S		Atlas-SNP	.											TFR2,NS,carcinoma,-1,1	TFR2	53	1	0			c.C1329T						PASS	.	G	,	0,4406		0,0,2203	104.0	91.0	95.0		816,1329	-8.8	0.5	7		95	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous,coding-synonymous	TFR2	NM_001206855.1,NM_003227.3	,	0,1,6502	AA,AG,GG		0.0116,0.0,0.0077	,	272/631,443/802	100226937	1,13005	2203	4300	6503	SO:0001819	synonymous_variant	7036	exon10			CACAGCGGATTTA	AF053356	CCDS34707.1	7q22	2003-01-27			ENSG00000106327	ENSG00000106327			11762	protein-coding gene	gene with protein product		604720				9799793, 12130528	Standard	NM_003227		Approved	HFE3, TFRC2	uc003uvv.1	Q9UP52	OTTHUMG00000159598	ENST00000462107.1:c.1329C>T	7.37:g.100226937G>A		50.0	0.0	0		49.0	29.0	0.591837	NM_003227	A6NGM7|O75422|Q1HE13|Q9HA99|Q9NX67	Silent	SNP	ENST00000462107.1	37	CCDS34707.1																																																																																			.	.	weak		0.627	TFR2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000356392.3	NM_003227	
CAPN12	147968	hgsc.bcm.edu	37	19	39229075	39229075	+	Silent	SNP	C	C	T	rs201486563	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr19:39229075C>T	ENST00000328867.4	-	7	1181	c.873G>A	c.(871-873)acG>acA	p.T291T	CAPN12_ENST00000601953.1_Silent_p.T142T|CTD-2540F13.2_ENST00000602255.1_RNA	NM_144691.3	NP_653292.2	Q6ZSI9	CAN12_HUMAN	calpain 12	291	Calpain catalytic. {ECO:0000255|PROSITE- ProRule:PRU00239}.				proteolysis (GO:0006508)	cytoplasm (GO:0005737)	calcium ion binding (GO:0005509)|calcium-dependent cysteine-type endopeptidase activity (GO:0004198)			central_nervous_system(1)|cervix(1)|endometrium(3)|kidney(1)|large_intestine(2)|lung(6)|ovary(1)|pancreas(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	20	all_cancers(60;2.87e-05)|Ovarian(47;0.0454)		Lung(45;0.00416)|LUSC - Lung squamous cell carcinoma(53;0.00741)			TCCAGGCCCCCGTCCACTCCA	0.697													C|||	2	0.000399361	0.0008	0.0014	5008	,	,		14837	0.0		0.0	False		,,,				2504	0.0				p.T291T		Atlas-SNP	.											.	CAPN12	43	.	0			c.G873A						PASS	.	C		1,4399	2.1+/-5.4	0,1,2199	29.0	32.0	31.0		873	-7.4	0.5	19		31	1,8597	1.2+/-3.3	0,1,4298	no	coding-synonymous	CAPN12	NM_144691.3		0,2,6497	TT,TC,CC		0.0116,0.0227,0.0154		291/720	39229075	2,12996	2200	4299	6499	SO:0001819	synonymous_variant	147968	exon7			GGCCCCCGTCCAC	BC014027	CCDS12519.1	19q13.2	2014-08-12			ENSG00000182472	ENSG00000182472		"""EF-hand domain containing"""	13249	protein-coding gene	gene with protein product		608839					Standard	NM_144691		Approved		uc002ojd.1	Q6ZSI9	OTTHUMG00000182525	ENST00000328867.4:c.873G>A	19.37:g.39229075C>T		41.0	0.0	0		41.0	16.0	0.390244	NM_144691		Silent	SNP	ENST00000328867.4	37	CCDS12519.1																																																																																			C|1.000;T|0.000	0.000	strong		0.697	CAPN12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000462151.1		
SP140L	93349	hgsc.bcm.edu	37	2	231256814	231256814	+	Missense_Mutation	SNP	A	A	G	rs183267141	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr2:231256814A>G	ENST00000415673.2	+	12	1063	c.977A>G	c.(976-978)aAg>aGg	p.K326R	SP140L_ENST00000243810.6_Missense_Mutation_p.K326R|SP140L_ENST00000444636.1_Missense_Mutation_p.K326R|SP140L_ENST00000396563.4_Missense_Mutation_p.K291R	NM_138402.4	NP_612411.4	Q9H930	SP14L_HUMAN	SP140 nuclear body protein-like	326	SAND. {ECO:0000255|PROSITE- ProRule:PRU00185}.					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						ACCTTGGCAAAGTGTATACAG	0.502													A|||	8	0.00159744	0.0	0.0029	5008	,	,		19306	0.0		0.006	False		,,,				2504	0.0				p.K326R		Atlas-SNP	.											.	SP140L	68	.	0			c.A977G						PASS	.	A	ARG/LYS	1,3985		0,1,1992	106.0	112.0	110.0		977	-0.4	0.0	2		110	42,8344		0,42,4151	no	missense	SP140L	NM_138402.4	26	0,43,6143	GG,GA,AA		0.5008,0.0251,0.3476	benign	326/581	231256814	43,12329	1993	4193	6186	SO:0001583	missense	93349	exon12			TGGCAAAGTGTAT	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.977A>G	2.37:g.231256814A>G	ENSP00000397911:p.Lys326Arg	150.0	0.0	0		155.0	78.0	0.503226	NM_138402	Q2M375|Q4ZG65|Q9BSP3	Missense_Mutation	SNP	ENST00000415673.2	37	CCDS46538.1	5	0.0022893772893772895	0	0.0	1	0.0027624309392265192	0	0.0	4	0.005277044854881266	A	11.98	1.800033	0.31869	2.51E-4	0.005008	ENSG00000185404	ENST00000444636;ENST00000415673;ENST00000243810;ENST00000396563	T;T;T;T	0.74842	-0.88;-0.88;-0.88;-0.88	3.44	-0.423	0.12325	.	.	.	.	.	T	0.55386	0.1917	L	0.31420	0.93	0.09310	N	1	P;P	0.48230	0.811;0.907	P;P	0.49665	0.618;0.615	T	0.50651	-0.8803	9	0.35671	T	0.21	.	2.4941	0.04617	0.5579:0.0:0.2383:0.2038	.	291;326	Q9H930-2;Q9H930-4	.;.	R	326;326;326;291	ENSP00000395195:K326R;ENSP00000397911:K326R;ENSP00000243810:K326R;ENSP00000379811:K291R	ENSP00000243810:K326R	K	+	2	0	SP140L	230965058	0.259000	0.24043	0.000000	0.03702	0.011000	0.07611	0.573000	0.23699	-0.079000	0.12707	-0.326000	0.08463	AAG	A|0.997;G|0.003	0.003	strong		0.502	SP140L-009	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000374538.1	NM_138402	
CUL9	23113	hgsc.bcm.edu	37	6	43152366	43152366	+	Silent	SNP	C	C	A	rs41274928	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr6:43152366C>A	ENST00000252050.4	+	2	402	c.318C>A	c.(316-318)ggC>ggA	p.G106G	CUL9_ENST00000372647.2_Silent_p.G106G|CUL9_ENST00000354495.3_Silent_p.G106G	NM_015089.2	NP_055904.1	Q8IWT3	CUL9_HUMAN	cullin 9	106					microtubule cytoskeleton organization (GO:0000226)|protein ubiquitination (GO:0016567)|regulation of mitosis (GO:0007088)|ubiquitin-dependent protein catabolic process (GO:0006511)	cullin-RING ubiquitin ligase complex (GO:0031461)|cytoplasm (GO:0005737)	ATP binding (GO:0005524)|zinc ion binding (GO:0008270)			breast(3)|central_nervous_system(1)|cervix(1)|endometrium(11)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(18)|liver(1)|lung(30)|ovary(5)|prostate(3)|skin(7)|upper_aerodigestive_tract(1)|urinary_tract(4)	92						ATCCAGGAGGCCTGGATGAAG	0.607													C|||	248	0.0495208	0.1112	0.0288	5008	,	,		20915	0.003		0.0288	False		,,,				2504	0.0501				p.G106G		Atlas-SNP	.											.	CUL9	248	.	0			c.C318A						PASS	.	C		459,3947	217.1+/-235.6	32,395,1776	89.0	96.0	94.0		318	0.7	1.0	6	dbSNP_127	94	267,8333	101.9+/-163.1	2,263,4035	no	coding-synonymous	CUL9	NM_015089.2		34,658,5811	AA,AC,CC		3.1047,10.4176,5.582		106/2518	43152366	726,12280	2203	4300	6503	SO:0001819	synonymous_variant	23113	exon2			AGGAGGCCTGGAT	AB014608	CCDS4890.1	6p21.1	2011-05-24			ENSG00000112659	ENSG00000112659			15982	protein-coding gene	gene with protein product	"""parkin-like cytoplasmic p53 binding protein"", ""p53-associated parkin-like cytoplasmic protein"""	607489				17332328, 10521492, 12526791	Standard	NM_015089		Approved	H7AP1, KIAA0708, PARC	uc003ouk.3	Q8IWT3	OTTHUMG00000014723	ENST00000252050.4:c.318C>A	6.37:g.43152366C>A		154.0	0.0	0		185.0	84.0	0.454054	NM_015089	O75188|Q5TCY3|Q68CP2|Q68D92|Q8N3W9|Q9BU56	Silent	SNP	ENST00000252050.4	37	CCDS4890.1																																																																																			C|0.948;A|0.052	0.052	strong		0.607	CUL9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040582.2	NM_015089	
OR1M1	125963	hgsc.bcm.edu	37	19	9203994	9203994	+	Missense_Mutation	SNP	C	C	T	rs61738474	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr19:9203994C>T	ENST00000429566.3	+	1	140	c.74C>T	c.(73-75)aCg>aTg	p.T25M		NM_001004456.1	NP_001004456.1	Q8NGA1	OR1M1_HUMAN	olfactory receptor, family 1, subfamily M, member 1	25						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)	p.T25K(1)		breast(1)|endometrium(4)|large_intestine(3)|lung(17)|ovary(1)|prostate(1)|skin(4)|upper_aerodigestive_tract(1)	32						GAGCAGGAGACGCTTCTCTTT	0.522													c|||	58	0.0115815	0.0424	0.0029	5008	,	,		16171	0.0		0.0	False		,,,				2504	0.0				p.T25M		Atlas-SNP	.											OR1M1,NS,carcinoma,0,1	OR1M1	52	1	1	Substitution - Missense(1)	lung(1)	c.C74T						PASS	.	C	MET/THR	169,4237	111.6+/-149.8	6,157,2040	116.0	98.0	104.0		74	2.4	0.0	19	dbSNP_129	104	2,8598	2.2+/-6.3	0,2,4298	yes	missense	OR1M1	NM_001004456.1	81	6,159,6338	TT,TC,CC		0.0233,3.8357,1.3148	probably-damaging	25/314	9203994	171,12835	2203	4300	6503	SO:0001583	missense	125963	exon1			AGGAGACGCTTCT		CCDS32896.1	19p13.2	2013-09-20			ENSG00000170929	ENSG00000170929		"""GPCR / Class A : Olfactory receptors"""	8220	protein-coding gene	gene with protein product							Standard	NM_001004456		Approved	OR19-6	uc010xkj.2	Q8NGA1	OTTHUMG00000179930	ENST00000429566.3:c.74C>T	19.37:g.9203994C>T	ENSP00000401966:p.Thr25Met	178.0	0.0	0		185.0	75.0	0.405405	NM_001004456	B9EHA6|Q6IFJ3|Q96R91	Missense_Mutation	SNP	ENST00000429566.3	37	CCDS32896.1	32	0.014652014652014652	32	0.06504065040650407	0	0.0	0	0.0	0	0.0	c	11.15	1.552933	0.27739	0.038357	2.33E-4	ENSG00000170929	ENST00000305465;ENST00000429566	T	0.00428	7.44	3.49	2.44	0.29823	.	2.059810	0.02106	N	0.054364	T	0.00039	0.0001	N	0.11789	0.175	0.09310	N	1	D	0.54047	0.964	P	0.44477	0.451	T	0.48525	-0.9028	10	0.62326	D	0.03	.	5.4607	0.16615	0.0:0.6579:0.0:0.3421	rs61738474	25	Q8NGA1	OR1M1_HUMAN	M	28;25	ENSP00000401966:T25M	ENSP00000303195:T28M	T	+	2	0	OR1M1	9064994	0.000000	0.05858	0.001000	0.08648	0.003000	0.03518	-4.203000	0.00275	0.801000	0.34066	0.400000	0.26472	ACG	C|0.987;T|0.013	0.013	strong		0.522	OR1M1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000448993.1		
ROBO4	54538	hgsc.bcm.edu	37	11	124764176	124764176	+	Silent	SNP	T	T	C	rs11820142	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr11:124764176T>C	ENST00000306534.3	-	8	1724	c.1239A>G	c.(1237-1239)ccA>ccG	p.P413P	ROBO4_ENST00000526899.1_5'Flank|ROBO4_ENST00000533054.1_Silent_p.P268P	NM_019055.5	NP_061928.4	Q8WZ75	ROBO4_HUMAN	roundabout, axon guidance receptor, homolog 4 (Drosophila)	413	Fibronectin type-III 2. {ECO:0000255|PROSITE-ProRule:PRU00316}.				angiogenesis (GO:0001525)|cell differentiation (GO:0030154)|negative regulation of cell migration (GO:0030336)|regulation of cell migration (GO:0030334)	external side of plasma membrane (GO:0009897)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)	receptor activity (GO:0004872)			NS(2)|breast(1)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(11)|lung(42)|ovary(1)|prostate(4)|skin(5)|urinary_tract(3)	76	all_hematologic(175;0.215)	Medulloblastoma(222;0.0523)|Lung NSC(97;0.118)|all_lung(97;0.126)|Breast(109;0.171)|all_neural(223;0.224)		BRCA - Breast invasive adenocarcinoma(274;1.5e-06)|OV - Ovarian serous cystadenocarcinoma(99;0.0301)		AGTAGGAGCCTGGCATATGGG	0.597													T|||	125	0.0249601	0.0893	0.0086	5008	,	,		3618	0.0		0.001	False		,,,				2504	0.0				p.P413P		Atlas-SNP	.											.	ROBO4	130	.	0			c.A1239G						PASS	.	T		344,4058	179.4+/-207.9	9,326,1866	111.0	87.0	95.0		1239	1.1	1.0	11	dbSNP_120	95	2,8596	1.2+/-3.3	0,2,4297	no	coding-synonymous	ROBO4	NM_019055.5		9,328,6163	CC,CT,TT		0.0233,7.8146,2.6615		413/1008	124764176	346,12654	2201	4299	6500	SO:0001819	synonymous_variant	54538	exon8			GGAGCCTGGCATA	AF361473	CCDS8455.1, CCDS73409.1	11q24.2	2013-02-11	2011-12-09		ENSG00000154133	ENSG00000154133		"""Immunoglobulin superfamily / I-set domain containing"", ""Fibronectin type III domain containing"""	17985	protein-coding gene	gene with protein product	"""magic roundabout"""	607528	"""roundabout homolog 4 (Drosophila)"""			11076864	Standard	NM_019055		Approved	FLJ20798, MRB, ECSM4	uc001qbg.3	Q8WZ75	OTTHUMG00000165936	ENST00000306534.3:c.1239A>G	11.37:g.124764176T>C		100.0	0.0	0		110.0	55.0	0.5	NM_019055	A8K154|Q14DU7|Q8TEG1|Q96JV6|Q9H718|Q9NWJ8	Silent	SNP	ENST00000306534.3	37	CCDS8455.1																																																																																			T|0.971;C|0.029	0.029	strong		0.597	ROBO4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000387111.1	NM_019055	
CMTR2	55783	hgsc.bcm.edu	37	16	71317545	71317545	+	Missense_Mutation	SNP	T	T	C			TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr16:71317545T>C	ENST00000338099.5	-	3	2615	c.2279A>G	c.(2278-2280)gAa>gGa	p.E760G	CMTR2_ENST00000434935.2_Missense_Mutation_p.E760G			Q8IYT2	CMTR2_HUMAN	cap methyltransferase 2	760					7-methylguanosine mRNA capping (GO:0006370)|cap2 mRNA methylation (GO:0097310)	cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)|nucleus (GO:0005634)	mRNA (nucleoside-2'-O-)-methyltransferase activity (GO:0004483)										GATAATTTCTTCTCTCTCTCT	0.373																																					p.E760G		Atlas-SNP	.											.	FTSJD1	70	.	0			c.A2279G						PASS	.						37.0	41.0	40.0					16																	71317545		2198	4298	6496	SO:0001583	missense	55783	exon3			ATTTCTTCTCTCT	BC035005	CCDS10898.1	16q22.2	2013-07-23	2013-07-23	2013-07-23	ENSG00000180917	ENSG00000180917			25635	protein-coding gene	gene with protein product	"""adrift homolog (Drosophila)"""		"""FtsJ methyltransferase domain containing 1"""	FTSJD1		21310715	Standard	NM_018348		Approved	FLJ11171, AFT, MTr2	uc010cga.3	Q8IYT2	OTTHUMG00000137587	ENST00000338099.5:c.2279A>G	16.37:g.71317545T>C	ENSP00000337512:p.Glu760Gly	172.0	0.0	0		166.0	74.0	0.445783	NM_018348	B2RCD5|D3DWS1|Q8NE77|Q8NFR5|Q9H8Z4|Q9NUS3|Q9NXF5	Missense_Mutation	SNP	ENST00000338099.5	37	CCDS10898.1	.	.	.	.	.	.	.	.	.	.	T	15.55	2.866136	0.51588	.	.	ENSG00000180917	ENST00000338099;ENST00000434935	T;T	0.15603	2.41;2.41	5.08	5.08	0.68730	.	0.364292	0.26234	N	0.025558	T	0.11537	0.0281	N	0.14661	0.345	0.27675	N	0.946633	B	0.27498	0.18	B	0.25405	0.06	T	0.15867	-1.0422	10	0.66056	D	0.02	-4.0194	13.2858	0.60243	0.0:0.0:0.0:1.0	.	760	Q8IYT2	FTSJ1_HUMAN	G	760	ENSP00000337512:E760G;ENSP00000411148:E760G	ENSP00000337512:E760G	E	-	2	0	FTSJD1	69875046	1.000000	0.71417	0.981000	0.43875	0.796000	0.44982	3.431000	0.52814	2.213000	0.71641	0.477000	0.44152	GAA	.	.	none		0.373	CMTR2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000268984.2	NM_018348	
WDR49	151790	hgsc.bcm.edu	37	3	167217971	167217971	+	Missense_Mutation	SNP	G	G	T			TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr3:167217971G>T	ENST00000308378.3	-	14	2250	c.1945C>A	c.(1945-1947)Caa>Aaa	p.Q649K	WDR49_ENST00000479765.1_Intron|WDR49_ENST00000476376.1_Missense_Mutation_p.Q474K|WDR49_ENST00000453925.2_Missense_Mutation_p.Q614K	NM_178824.3	NP_849146.1	Q8IV35	WDR49_HUMAN	WD repeat domain 49	649										breast(1)|endometrium(1)|kidney(1)|large_intestine(8)|lung(28)|ovary(2)|prostate(1)|skin(3)|upper_aerodigestive_tract(3)|urinary_tract(2)	50						TCCAGAATTTGGGGACGCTCT	0.423																																					p.Q649K		Atlas-SNP	.											.	WDR49	188	.	0			c.C1945A						PASS	.						131.0	149.0	143.0					3																	167217971		2203	4300	6503	SO:0001583	missense	151790	exon14			GAATTTGGGGACG	AK097556	CCDS3201.1	3q26.1	2013-01-11			ENSG00000174776	ENSG00000174776		"""WD repeat domain containing"""	26587	protein-coding gene	gene with protein product						12477932	Standard	NM_178824		Approved	FLJ33620	uc003fev.1	Q8IV35	OTTHUMG00000158290	ENST00000308378.3:c.1945C>A	3.37:g.167217971G>T	ENSP00000311343:p.Gln649Lys	66.0	0.0	0		49.0	24.0	0.489796	NM_178824	Q8N297	Missense_Mutation	SNP	ENST00000308378.3	37	CCDS3201.1	.	.	.	.	.	.	.	.	.	.	G	0	-2.588097	0.00128	.	.	ENSG00000174776	ENST00000308378;ENST00000476376;ENST00000453925	T;T;T	0.47177	0.85;2.16;1.33	5.13	0.462	0.16695	.	0.427611	0.20451	N	0.092100	T	0.28632	0.0709	L	0.39898	1.24	0.09310	N	1	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.30794	-0.9966	10	0.02654	T	1	.	7.4361	0.27156	0.0:0.2474:0.2598:0.4928	.	614;649	E7EQK3;Q8IV35	.;WDR49_HUMAN	K	649;474;614	ENSP00000311343:Q649K;ENSP00000420508:Q474K;ENSP00000410863:Q614K	ENSP00000311343:Q649K	Q	-	1	0	WDR49	168700665	0.002000	0.14202	0.000000	0.03702	0.004000	0.04260	0.770000	0.26618	0.135000	0.18707	0.467000	0.42956	CAA	.	.	none		0.423	WDR49-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000350592.3	NM_178824	
ZC3H14	79882	hgsc.bcm.edu	37	14	89042232	89042232	+	Silent	SNP	G	G	A	rs147484262		TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr14:89042232G>A	ENST00000251038.5	+	8	1296	c.1071G>A	c.(1069-1071)aaG>aaA	p.K357K	ZC3H14_ENST00000393514.5_Silent_p.K357K|ZC3H14_ENST00000557605.1_3'UTR|ZC3H14_ENST00000557607.1_Silent_p.K202K|ZC3H14_ENST00000555755.1_Silent_p.K357K|ZC3H14_ENST00000336693.4_Silent_p.K323K|ZC3H14_ENST00000359301.3_Silent_p.K323K|ZC3H14_ENST00000302216.8_Silent_p.K357K|ZC3H14_ENST00000556945.1_Silent_p.K357K	NM_001160103.1|NM_001160104.1|NM_024824.4	NP_001153575.1|NP_001153576.1|NP_079100.2	Q6PJT7	ZC3HE_HUMAN	zinc finger CCCH-type containing 14	357						cytoplasm (GO:0005737)|nucleolus (GO:0005730)|nucleus (GO:0005634)	metal ion binding (GO:0046872)|poly(A) RNA binding (GO:0044822)			cervix(2)|endometrium(3)|kidney(2)|large_intestine(3)|lung(6)|ovary(2)|prostate(1)|skin(2)	21						TGATTTTGAAGGCTATATCTG	0.299													G|||	1	0.000199681	0.0	0.0	5008	,	,		18726	0.0		0.001	False		,,,				2504	0.0				p.K357K		Atlas-SNP	.											.	ZC3H14	71	.	0			c.G1071A						PASS	.	G	,,,,	0,4406		0,0,2203	99.0	102.0	101.0		1071,1071,1071,1071,969	3.7	1.0	14	dbSNP_134	101	4,8596	3.0+/-9.4	0,4,4296	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	ZC3H14	NM_001160103.1,NM_001160104.1,NM_024824.4,NM_207660.3,NM_207661.2	,,,,	0,4,6499	AA,AG,GG		0.0465,0.0,0.0308	,,,,	357/736,357/731,357/737,357/580,323/572	89042232	4,13002	2203	4300	6503	SO:0001819	synonymous_variant	79882	exon8			TTTGAAGGCTATA	AF155107	CCDS32133.1, CCDS32134.1, CCDS32135.1, CCDS32136.1, CCDS55938.1	14q31.3	2014-08-12			ENSG00000100722	ENSG00000100722		"""Zinc fingers, CCCH-type domain containing"""	20509	protein-coding gene	gene with protein product		613279				10508479	Standard	NM_024824		Approved	FLJ11806, UKp68, NY-REN-37	uc001xww.3	Q6PJT7	OTTHUMG00000170803	ENST00000251038.5:c.1071G>A	14.37:g.89042232G>A		82.0	0.0	0		76.0	40.0	0.526316	NM_001160104	A8MY46|B4DXU8|B4DZW7|B4E2H4|G3V5R4|Q6MZU4|Q6PJ32|Q6PUI6|Q6PUI8|Q86TQ5|Q86TW0|Q86TW1|Q8NCT6|Q8NCZ3|Q8TDE2|Q9HAC9|Q9Y5A0	Silent	SNP	ENST00000251038.5	37	CCDS32133.1	1	4.578754578754579E-4	0	0.0	0	0.0	0	0.0	1	0.0013192612137203166	G	8.970	0.972602	0.18736	0.0	4.65E-4	ENSG00000100722	ENST00000556000	.	.	.	5.77	3.71	0.42584	.	.	.	.	.	T	0.47948	0.1473	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.42766	-0.9432	4	.	.	.	-19.8172	4.4076	0.11416	0.4411:0.0:0.5589:0.0	.	.	.	.	K	273	.	.	R	+	2	0	ZC3H14	88111985	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	2.779000	0.47734	1.436000	0.47453	0.655000	0.94253	AGG	G|1.000;A|0.000	0.000	strong		0.299	ZC3H14-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000410387.1	NM_024824	
STAG1	10274	hgsc.bcm.edu	37	3	136062724	136062724	+	Missense_Mutation	SNP	C	C	G	rs34149860	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr3:136062724C>G	ENST00000383202.2	-	30	3652	c.3396G>C	c.(3394-3396)caG>caC	p.Q1132H	STAG1_ENST00000434713.2_Missense_Mutation_p.Q872H|STAG1_ENST00000236698.5_Missense_Mutation_p.Q1132H|STAG1_ENST00000536929.1_Missense_Mutation_p.Q716H	NM_005862.2	NP_005853.2	Q8WVM7	STAG1_HUMAN	stromal antigen 1	1132			Q -> H (in dbSNP:rs34149860).		chromosome segregation (GO:0007059)|mitotic cell cycle (GO:0000278)|mitotic nuclear division (GO:0007067)	cell junction (GO:0030054)|chromatin (GO:0000785)|chromosome (GO:0005694)|chromosome, centromeric region (GO:0000775)|cytosol (GO:0005829)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	chromatin binding (GO:0003682)			NS(2)|breast(4)|central_nervous_system(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(16)|lung(16)|ovary(2)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	58						GTTCTTGAATCTGGTCTCCCA	0.448													C|||	436	0.0870607	0.3124	0.0303	5008	,	,		20341	0.0		0.002	False		,,,				2504	0.0				p.Q1132H		Atlas-SNP	.											.	STAG1	135	.	0			c.G3396C						PASS	.	C	HIS/GLN	1218,3188	421.7+/-339.5	170,878,1155	100.0	99.0	99.0		3396	3.5	1.0	3	dbSNP_126	99	12,8588	8.4+/-32.0	0,12,4288	yes	missense	STAG1	NM_005862.2	24	170,890,5443	GG,GC,CC		0.1395,27.6441,9.4572	benign	1132/1259	136062724	1230,11776	2203	4300	6503	SO:0001583	missense	10274	exon30			TTGAATCTGGTCT	Z75330	CCDS3090.1	3q22.2-q22.3	2011-08-12			ENSG00000118007	ENSG00000118007			11354	protein-coding gene	gene with protein product		604358				9305759	Standard	XM_006713471		Approved	SA-1, SCC3A	uc003era.1	Q8WVM7	OTTHUMG00000159798	ENST00000383202.2:c.3396G>C	3.37:g.136062724C>G	ENSP00000372689:p.Gln1132His	155.0	0.0	0		164.0	73.0	0.445122	NM_005862	O00539|Q6P275	Missense_Mutation	SNP	ENST00000383202.2	37	CCDS3090.1	157	0.07188644688644688	145	0.29471544715447157	11	0.03038674033149171	0	0.0	1	0.0013192612137203166	C	8.880	0.951348	0.18431	0.276441	0.001395	ENSG00000118007	ENST00000383202;ENST00000236698;ENST00000434713;ENST00000536929	T;T;T;T	0.32272	1.87;1.9;1.85;1.46	5.48	3.45	0.39498	.	0.196262	0.47455	D	0.000221	T	0.00012	0.0000	N	0.11201	0.11	0.26204	P	0.9793941	B;B	0.06786	0.001;0.001	B;B	0.10450	0.005;0.002	T	0.34725	-0.9817	9	0.41790	T	0.15	.	9.8937	0.41304	0.0:0.7454:0.0:0.2546	rs34149860	1132;1132	Q6P275;Q8WVM7	.;STAG1_HUMAN	H	1132;1132;872;716	ENSP00000372689:Q1132H;ENSP00000236698:Q1132H;ENSP00000404396:Q872H;ENSP00000445787:Q716H	ENSP00000236698:Q1132H	Q	-	3	2	STAG1	137545414	1.000000	0.71417	1.000000	0.80357	0.981000	0.71138	1.602000	0.36783	1.316000	0.45131	-0.137000	0.14449	CAG	C|0.914;G|0.086	0.086	strong		0.448	STAG1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000357366.1	NM_005862	
LRRK1	79705	hgsc.bcm.edu	37	15	101593597	101593597	+	Silent	SNP	C	C	T	rs41418955	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr15:101593597C>T	ENST00000388948.3	+	26	4385	c.4026C>T	c.(4024-4026)ctC>ctT	p.L1342L	RP11-505E24.2_ENST00000559857.1_RNA|LRRK1_ENST00000284395.5_Silent_p.L1339L	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)			TCAGCAGCCTCAACACCGTGC	0.731													C|||	15	0.00299521	0.0	0.0043	5008	,	,		15960	0.0		0.0109	False		,,,				2504	0.001				p.L1342L		Atlas-SNP	.											.	LRRK1	310	.	0			c.C4026T						PASS	.	C		8,4328		0,8,2160	14.0	17.0	16.0		4026	3.0	1.0	15	dbSNP_127	16	75,8439		0,75,4182	no	coding-synonymous	LRRK1	NM_024652.3		0,83,6342	TT,TC,CC		0.8809,0.1845,0.6459		1342/2016	101593597	83,12767	2168	4257	6425	SO:0001819	synonymous_variant	79705	exon26			CAGCCTCAACACC	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.4026C>T	15.37:g.101593597C>T		20.0	0.0	0		21.0	12.0	0.571429	NM_024652		Silent	SNP	ENST00000388948.3	37	CCDS42086.1																																																																																			C|0.993;T|0.007	0.007	strong		0.731	LRRK1-003	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000384567.2	NM_024652	
PRKD3	23683	hgsc.bcm.edu	37	2	37518105	37518105	+	Silent	SNP	A	A	G	rs138302731	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr2:37518105A>G	ENST00000379066.1	-	4	1227	c.465T>C	c.(463-465)caT>caC	p.H155H	PRKD3_ENST00000234179.2_Silent_p.H155H			O94806	KPCD3_HUMAN	protein kinase D3	155					intracellular signal transduction (GO:0035556)|protein kinase C-activating G-protein coupled receptor signaling pathway (GO:0007205)|protein phosphorylation (GO:0006468)	cytoplasm (GO:0005737)|membrane (GO:0016020)|nucleus (GO:0005634)	ATP binding (GO:0005524)|metal ion binding (GO:0046872)|protein kinase C activity (GO:0004697)			breast(3)|central_nervous_system(2)|kidney(3)|large_intestine(8)|lung(9)|ovary(3)|prostate(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)	33		all_hematologic(82;0.21)				CATAGAGAGTATGTGGACGAA	0.388													A|||	2	0.000399361	0.0	0.0	5008	,	,		19716	0.0		0.0	False		,,,				2504	0.002				p.H155H	Melanoma(80;621 1355 8613 11814 51767)	Atlas-SNP	.											.	PRKD3	170	.	0			c.T465C						PASS	.	A		1,4405	2.1+/-5.4	0,1,2202	163.0	158.0	159.0		465	1.0	1.0	2	dbSNP_134	159	3,8597	2.2+/-6.3	0,3,4297	yes	coding-synonymous	PRKD3	NM_005813.3		0,4,6499	GG,GA,AA		0.0349,0.0227,0.0308		155/891	37518105	4,13002	2203	4300	6503	SO:0001819	synonymous_variant	23683	exon3			GAGAGTATGTGGA	AB015982	CCDS1789.1	2p21	2013-01-10	2004-10-28	2004-10-30	ENSG00000115825	ENSG00000115825		"""Pleckstrin homology (PH) domain containing"""	9408	protein-coding gene	gene with protein product		607077	"""protein kinase C, nu"""	PRKCN		10231560	Standard	NM_005813		Approved	EPK2	uc002rqd.3	O94806	OTTHUMG00000100961	ENST00000379066.1:c.465T>C	2.37:g.37518105A>G		91.0	0.0	0		91.0	43.0	0.472527	NM_005813	D6W587|Q53TR7|Q8NEL8	Silent	SNP	ENST00000379066.1	37	CCDS1789.1																																																																																			A|1.000;G|0.000	0.000	strong		0.388	PRKD3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000218570.3	NM_005813	
NBEAL1	65065	hgsc.bcm.edu	37	2	203922075	203922075	+	Silent	SNP	A	A	G	rs146121994	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr2:203922075A>G	ENST00000449802.1	+	6	747	c.414A>G	c.(412-414)gaA>gaG	p.E138E	NBEAL1_ENST00000478884.1_3'UTR	NM_001114132.1	NP_001107604.1	Q6ZS30	NBEL1_HUMAN	neurobeachin-like 1	138										NS(1)|breast(3)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(8)|liver(1)|lung(8)|ovary(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	37						AAGAGAAGGAAATGGCAGATC	0.313													A|||	7	0.00139776	0.0	0.0	5008	,	,		17801	0.0		0.006	False		,,,				2504	0.001				p.E138E		Atlas-SNP	.											.	NBEAL1	266	.	0			c.A414G						PASS	.	A		2,1382		0,2,690	169.0	146.0	153.0		414	2.5	1.0	2	dbSNP_134	153	29,3151		0,29,1561	no	coding-synonymous	NBEAL1	NM_001114132.1		0,31,2251	GG,GA,AA		0.9119,0.1445,0.6792		138/2695	203922075	31,4533	692	1590	2282	SO:0001819	synonymous_variant	65065	exon6			GAAGGAAATGGCA	AY172970	CCDS46495.1	2q33	2013-01-10			ENSG00000144426	ENSG00000144426		"""WD repeat domain containing"""	20681	protein-coding gene	gene with protein product		609816	"""amyotrophic lateral sclerosis 2 (juvenile) chromosome region, candidate 17"", ""amyotrophic lateral sclerosis 2 (juvenile) chromosome region, candidate 16"""	ALS2CR17, ALS2CR16		15193433	Standard	NM_001114132		Approved	MGC164581	uc002uzt.3	Q6ZS30	OTTHUMG00000154129	ENST00000449802.1:c.414A>G	2.37:g.203922075A>G		53.0	0.0	0		49.0	28.0	0.571429	NM_001114132	A6NHD5|Q6Y876|Q6ZP36|Q6ZQY5|Q8N8R4|Q96Q30|Q96Q31	Silent	SNP	ENST00000449802.1	37	CCDS46495.1																																																																																			A|0.997;G|0.003	0.003	strong		0.313	NBEAL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000333982.4		
RNF112	7732	hgsc.bcm.edu	37	17	19316656	19316656	+	Missense_Mutation	SNP	G	G	A			TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr17:19316656G>A	ENST00000461366.1	+	5	867	c.652G>A	c.(652-654)Gcc>Acc	p.A218T	RNF112_ENST00000580109.1_3'UTR|CTB-187M2.2_ENST00000579897.1_RNA	NM_007148.4	NP_009079.2	Q9ULX5	RN112_HUMAN	ring finger protein 112	218	GB1/RHD3-type G.					cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)|nucleus (GO:0005634)	GTP binding (GO:0005525)|GTPase activity (GO:0003924)|zinc ion binding (GO:0008270)			endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(1)|lung(2)|ovary(2)|prostate(1)|urinary_tract(1)	12						CAGGTGGGGCGCCAATGGCCT	0.642																																					p.A218T		Atlas-SNP	.											.	RNF112	37	.	0			c.G652A						PASS	.						20.0	24.0	23.0					17																	19316656		1952	4129	6081	SO:0001583	missense	7732	exon5			TGGGGCGCCAATG	AF054587	CCDS58529.1	17p11.2	2013-01-16	2008-06-13	2008-06-13	ENSG00000128482	ENSG00000128482		"""RING-type (C3HC4) zinc fingers"""	12968	protein-coding gene	gene with protein product		601237	"""zinc finger protein 179"""	ZNF179		8660987, 9806830	Standard	NM_007148		Approved	BFP	uc010vyw.2	Q9ULX5	OTTHUMG00000059601	ENST00000461366.1:c.652G>A	17.37:g.19316656G>A	ENSP00000454919:p.Ala218Thr	101.0	0.0	0		98.0	49.0	0.5	NM_007148	O60633|Q7Z5V9	Missense_Mutation	SNP	ENST00000461366.1	37	CCDS58529.1																																																																																			.	.	none		0.642	RNF112-001	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000132549.4	NM_007148	
GFM1	85476	hgsc.bcm.edu	37	3	158408032	158408032	+	Missense_Mutation	SNP	G	G	A	rs62288347	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr3:158408032G>A	ENST00000486715.1	+	16	2347	c.1990G>A	c.(1990-1992)Gta>Ata	p.V664I	GFM1_ENST00000264263.5_Missense_Mutation_p.V683I|RP11-379F4.7_ENST00000607624.1_lincRNA	NM_024996.5	NP_079272.4			G elongation factor, mitochondrial 1											breast(1)|central_nervous_system(1)|endometrium(1)|large_intestine(5)|lung(9)|ovary(3)|urinary_tract(2)	22			Lung(72;0.00309)|LUSC - Lung squamous cell carcinoma(72;0.0043)			TCAGGGACAAGTAATTGCAGG	0.393													G|||	35	0.00698882	0.0	0.0058	5008	,	,		17035	0.0		0.0258	False		,,,				2504	0.0051				p.V664I		Atlas-SNP	.											.	GFM1	83	.	0			c.G1990A						PASS	.	G	ILE/VAL	10,4396	19.1+/-41.9	0,10,2193	167.0	167.0	167.0		1990	5.8	0.4	3	dbSNP_129	167	175,8425	80.4+/-143.0	0,175,4125	yes	missense	GFM1	NM_024996.5	29	0,185,6318	AA,AG,GG		2.0349,0.227,1.4224	possibly-damaging	664/752	158408032	185,12821	2203	4300	6503	SO:0001583	missense	85476	exon16			GGACAAGTAATTG	AF309777	CCDS33885.1	3q25	2008-02-05			ENSG00000168827	ENSG00000168827			13780	protein-coding gene	gene with protein product		606639	"""G translation elongation factor, mitochondrial"""			11374907, 11735030	Standard	NM_024996		Approved	EFGM, GFM, EGF1	uc003fce.3	Q96RP9	OTTHUMG00000158804	ENST00000486715.1:c.1990G>A	3.37:g.158408032G>A	ENSP00000419038:p.Val664Ile	95.0	0.0	0		101.0	49.0	0.485149	NM_024996		Missense_Mutation	SNP	ENST00000486715.1	37	CCDS33885.1	27	0.012362637362637362	0	0.0	3	0.008287292817679558	0	0.0	24	0.0316622691292876	G	19.54	3.846986	0.71603	0.00227	0.020349	ENSG00000168827	ENST00000486715;ENST00000264263	T;T	0.60299	0.2;0.2	5.8	5.8	0.92144	Elongation factor G/III/V (1);Translation elongation factor EFG/EF2, C-terminal (3);	0.063724	0.64402	D	0.000007	T	0.31702	0.0805	N	0.26092	0.79	0.80722	D	1	P;P	0.41848	0.72;0.763	B;P	0.45946	0.365;0.498	T	0.48536	-0.9027	10	0.54805	T	0.06	-5.1032	20.0589	0.97667	0.0:0.0:1.0:0.0	rs62288347	683;664	Q96RP9-2;Q96RP9	.;EFGM_HUMAN	I	664;683	ENSP00000419038:V664I;ENSP00000264263:V683I	ENSP00000264263:V683I	V	+	1	0	GFM1	159890726	1.000000	0.71417	0.420000	0.26596	0.975000	0.68041	7.491000	0.81471	2.732000	0.93576	0.650000	0.86243	GTA	G|0.986;A|0.014	0.014	strong		0.393	GFM1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000352271.1	NM_024996	
CALCR	799	hgsc.bcm.edu	37	7	93108763	93108763	+	Silent	SNP	G	G	C	rs144326254	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr7:93108763G>C	ENST00000394441.1	-	3	423	c.108C>G	c.(106-108)ccC>ccG	p.P36P	CALCR_ENST00000359558.2_Silent_p.P54P|CALCR_ENST00000421592.1_Silent_p.P36P|CALCR_ENST00000360249.4_Silent_p.P36P|CALCR_ENST00000426151.1_Silent_p.P36P	NM_001164738.1	NP_001158210.1	P30988	CALCR_HUMAN	calcitonin receptor	54					adenylate cyclase-activating G-protein coupled receptor signaling pathway (GO:0007189)|G-protein coupled receptor signaling pathway (GO:0007186)|positive regulation of adenylate cyclase activity (GO:0045762)|positive regulation of cAMP biosynthetic process (GO:0030819)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|protein localization to plasma membrane (GO:0072659)|protein transport (GO:0015031)|receptor internalization (GO:0031623)|response to glucocorticoid (GO:0051384)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	calcitonin binding (GO:0032841)|calcitonin receptor activity (GO:0004948)|protein transporter activity (GO:0008565)|receptor activity (GO:0004872)			NS(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(7)|lung(27)|ovary(3)|pancreas(1)|skin(3)	45	all_cancers(62;3.18e-12)|all_epithelial(64;1.34e-11)|Breast(17;0.000675)|Lung NSC(181;0.207)		STAD - Stomach adenocarcinoma(171;0.000244)		Pramlintide(DB01278)|Salmon Calcitonin(DB00017)	GAAATGGCTTGGGCTCTATTG	0.418													G|||	27	0.00539137	0.0121	0.0072	5008	,	,		16950	0.0		0.006	False		,,,				2504	0.0				p.P54P		Atlas-SNP	.											.	CALCR	200	.	0			c.C162G						PASS	.	G	,,	35,4371	40.0+/-72.8	0,35,2168	179.0	168.0	171.0		162,108,108	-7.4	0.0	7	dbSNP_134	171	30,8570	21.6+/-65.8	0,30,4270	no	coding-synonymous,coding-synonymous,coding-synonymous	CALCR	NM_001164737.1,NM_001164738.1,NM_001742.3	,,	0,65,6438	CC,CG,GG		0.3488,0.7944,0.4998	,,	54/509,36/475,36/475	93108763	65,12941	2203	4300	6503	SO:0001819	synonymous_variant	799	exon5			TGGCTTGGGCTCT	L00587	CCDS5631.1, CCDS55125.1	7q21.3	2012-08-10			ENSG00000004948	ENSG00000004948		"""GPCR / Class B : Calcitonin receptors"""	1440	protein-coding gene	gene with protein product		114131				1331173	Standard	NM_001742		Approved	CTR	uc003umw.2	P30988	OTTHUMG00000023599	ENST00000394441.1:c.108C>G	7.37:g.93108763G>C		266.0	1.0	0.0037594		276.0	132.0	0.478261	NM_001164737	A4D1G6|F5H605|O14585|Q13941|Q5ZGL8|Q659U6|Q6DJU8|Q6T712	Silent	SNP	ENST00000394441.1	37	CCDS5631.1																																																																																			G|0.995;C|0.005	0.005	strong		0.418	CALCR-002	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254661.2	NM_001742	
EPHA10	284656	hgsc.bcm.edu	37	1	38184343	38184343	+	Missense_Mutation	SNP	T	T	C	rs201769517	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr1:38184343T>C	ENST00000373048.4	-	16	2901	c.2902A>G	c.(2902-2904)Atg>Gtg	p.M968V	EPHA10_ENST00000540011.1_3'UTR|EPHA10_ENST00000330210.7_Missense_Mutation_p.M463V|EPHA10_ENST00000446149.2_5'UTR|EPHA10_ENST00000427468.2_Missense_Mutation_p.M968V	NM_001099439.1	NP_001092909.1	Q5JZY3	EPHAA_HUMAN	EPH receptor A10	968	SAM. {ECO:0000255|PROSITE- ProRule:PRU00184}.				ephrin receptor signaling pathway (GO:0048013)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)	ATP binding (GO:0005524)|ephrin receptor activity (GO:0005003)|transmembrane-ephrin receptor activity (GO:0005005)			NS(2)|breast(4)|cervix(1)|endometrium(5)|kidney(4)|large_intestine(4)|lung(13)|prostate(3)|skin(8)|stomach(3)|upper_aerodigestive_tract(1)|urinary_tract(2)	50	Acute lymphoblastic leukemia(166;0.074)|all_hematologic(146;0.197)	Myeloproliferative disorder(586;0.0255)|all_neural(195;0.164)				TGGGCAGTCATCTCGGCCACG	0.662													T|||	4	0.000798722	0.0	0.0029	5008	,	,		17173	0.001		0.001	False		,,,				2504	0.0				p.M968V		Atlas-SNP	.											.	EPHA10	120	.	0			c.A2902G						PASS	.	T	VAL/MET	0,3998		0,0,1999	24.0	28.0	26.0		2902	3.7	1.0	1		26	4,8338		0,4,4167	no	missense	EPHA10	NM_001099439.1	21	0,4,6166	CC,CT,TT		0.048,0.0,0.0324	possibly-damaging	968/1009	38184343	4,12336	1999	4171	6170	SO:0001583	missense	284656	exon16			CAGTCATCTCGGC	AK090974	CCDS425.1, CCDS41305.1	1p34.3	2013-02-11			ENSG00000183317	ENSG00000183317		"""EPH receptors"", ""Sterile alpha motif (SAM) domain containing"", ""Fibronectin type III domain containing"""	19987	protein-coding gene	gene with protein product		611123				12477932	Standard	NM_001099439		Approved	FLJ16103, FLJ33655	uc009vvi.3	Q5JZY3	OTTHUMG00000004325	ENST00000373048.4:c.2902A>G	1.37:g.38184343T>C	ENSP00000362139:p.Met968Val	138.0	0.0	0		149.0	83.0	0.557047	NM_001099439	A4FU89|J3KPB5|Q6NW42	Missense_Mutation	SNP	ENST00000373048.4	37	CCDS41305.1	.	.	.	.	.	.	.	.	.	.	T	13.81	2.348125	0.41599	0.0	4.8E-4	ENSG00000183317	ENST00000330210;ENST00000427468;ENST00000373048	T;T;T	0.52295	0.67;0.67;0.67	4.88	3.67	0.42095	Sterile alpha motif domain (2);Sterile alpha motif/pointed domain (2);Sterile alpha motif, type 1 (1);	0.000000	0.47455	D	0.000232	T	0.54919	0.1888	L	0.56199	1.76	0.80722	D	1	P	0.52170	0.951	P	0.57679	0.825	T	0.53187	-0.8474	10	0.38643	T	0.18	.	10.8344	0.46679	0.0:0.0:0.158:0.842	.	968	Q5JZY3	EPHAA_HUMAN	V	463;968;968	ENSP00000330379:M463V;ENSP00000397746:M968V;ENSP00000362139:M968V	ENSP00000330379:M463V	M	-	1	0	EPHA10	37956930	1.000000	0.71417	1.000000	0.80357	0.831000	0.47069	4.864000	0.62990	1.969000	0.57287	0.402000	0.26972	ATG	T|0.998;C|0.002	0.002	strong		0.662	EPHA10-003	KNOWN	not_organism_supported|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000012497.2	NM_173641	
TMEM81	388730	hgsc.bcm.edu	37	1	205052998	205052998	+	Missense_Mutation	SNP	G	G	T	rs369137007		TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr1:205052998G>T	ENST00000367167.3	-	1	647	c.451C>A	c.(451-453)Cag>Aag	p.Q151K		NM_203376.1	NP_976310.1	Q6P7N7	TMM81_HUMAN	transmembrane protein 81	151	Ig-like.					integral component of membrane (GO:0016021)				endometrium(2)|kidney(1)|large_intestine(1)|lung(4)|skin(1)	9	all_cancers(21;0.144)|Breast(84;0.0437)		BRCA - Breast invasive adenocarcinoma(75;0.0923)			TCATACTCCTGAGCATATTTA	0.478																																					p.Q151K		Atlas-SNP	.											TMEM81,NS,carcinoma,+2,1	TMEM81	23	1	0			c.C451A						scavenged	.	G	LYS/GLN	0,4406		0,0,2203	77.0	84.0	82.0		451	2.8	0.0	1		82	1,8599	1.2+/-3.3	0,1,4299	no	missense	TMEM81	NM_203376.1	53	0,1,6502	TT,TG,GG		0.0116,0.0,0.0077	benign	151/256	205052998	1,13005	2203	4300	6503	SO:0001583	missense	388730	exon1			ACTCCTGAGCATA	BC061592	CCDS1450.1	1q32.1	2013-01-11			ENSG00000174529	ENSG00000174529		"""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	32349	protein-coding gene	gene with protein product							Standard	NM_203376		Approved	UNQ2788, MGC75217, HC3107, KVLA2788	uc001hbt.3	Q6P7N7	OTTHUMG00000037103	ENST00000367167.3:c.451C>A	1.37:g.205052998G>T	ENSP00000356135:p.Gln151Lys	155.0	1.0	0.00645161		138.0	61.0	0.442029	NM_203376	Q6UVZ4	Missense_Mutation	SNP	ENST00000367167.3	37	CCDS1450.1	.	.	.	.	.	.	.	.	.	.	G	3.064	-0.192683	0.06259	0.0	1.16E-4	ENSG00000174529	ENST00000367167	T	0.42900	0.96	5.93	2.81	0.32909	Immunoglobulin subtype (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	0.586479	0.17141	N	0.185438	T	0.23572	0.0570	L	0.43152	1.355	0.09310	N	1	B	0.21225	0.053	B	0.13407	0.009	T	0.28459	-1.0043	10	0.05436	T	0.98	-10.0286	1.3267	0.02127	0.183:0.1403:0.435:0.2417	.	151	Q6P7N7	TMM81_HUMAN	K	151	ENSP00000356135:Q151K	ENSP00000356135:Q151K	Q	-	1	0	TMEM81	203319621	0.004000	0.15560	0.012000	0.15200	0.685000	0.39939	1.419000	0.34793	0.793000	0.33875	0.655000	0.94253	CAG	.	.	none		0.478	TMEM81-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000090076.1	NM_203376	
SOX7	83595	hgsc.bcm.edu	37	8	10583616	10583616	+	Missense_Mutation	SNP	C	C	T	rs180762782	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr8:10583616C>T	ENST00000304501.1	-	2	877	c.799G>A	c.(799-801)Ggc>Agc	p.G267S	SOX7_ENST00000554914.1_Missense_Mutation_p.G319S|SOX7_ENST00000553390.1_Missense_Mutation_p.G319S	NM_031439.2	NP_113627.1	Q9BT81	SOX7_HUMAN	SRY (sex determining region Y)-box 7	267					endoderm formation (GO:0001706)|negative regulation of cell proliferation (GO:0008285)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043280)|regulation of canonical Wnt signaling pathway (GO:0060828)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription regulatory region DNA binding (GO:0044212)			breast(1)|endometrium(1)|kidney(1)|large_intestine(5)|lung(6)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	20				COAD - Colon adenocarcinoma(149;0.0732)		ATGGAGACGCCGGGGGACTGG	0.672													C|||	6	0.00119808	0.0	0.0	5008	,	,		13618	0.0		0.006	False		,,,				2504	0.0				p.G267S		Atlas-SNP	.											.	SOX7	50	.	0			c.G799A						PASS	.	C	SER/GLY	5,4381		0,5,2188	23.0	30.0	27.0		799	2.9	0.4	8		27	73,8499		0,73,4213	yes	missense	SOX7	NM_031439.2	56	0,78,6401	TT,TC,CC		0.8516,0.114,0.6019	benign	267/389	10583616	78,12880	2193	4286	6479	SO:0001583	missense	83595	exon2			AGACGCCGGGGGA	AJ409320	CCDS5977.1	8p22	2013-01-25			ENSG00000171056	ENSG00000171056		"""SRY (sex determining region Y)-boxes"""	18196	protein-coding gene	gene with protein product		612202				11691915	Standard	NM_031439		Approved		uc003wtf.3	Q9BT81	OTTHUMG00000090585	ENST00000304501.1:c.799G>A	8.37:g.10583616C>T	ENSP00000301921:p.Gly267Ser	65.0	0.0	0		78.0	34.0	0.435897	NM_031439	B4DKV0|Q53YD0	Missense_Mutation	SNP	ENST00000304501.1	37	CCDS5977.1	6	0.0027472527472527475	0	0.0	0	0.0	0	0.0	6	0.0079155672823219	C	6.489	0.458490	0.12342	0.00114	0.008516	ENSG00000171056;ENSG00000171056;ENSG00000258724	ENST00000304501;ENST00000553390;ENST00000554914	T;T;T	0.75477	-0.94;-0.94;-0.94	4.84	2.92	0.33932	.	0.176595	0.48286	N	0.000186	T	0.47192	0.1432	L	0.38531	1.155	0.20074	N	0.999936	P;B	0.52170	0.951;0.205	B;B	0.40134	0.32;0.023	T	0.49606	-0.8922	10	0.07644	T	0.81	.	7.2334	0.26055	0.0:0.6938:0.1419:0.1643	.	319;267	B4DKV0;Q9BT81	.;SOX7_HUMAN	S	267;319;319	ENSP00000301921:G267S;ENSP00000452017:G319S;ENSP00000451145:G319S	ENSP00000346908:G319S	G	-	1	0	SOX7;CTD-2135J3.4	10621026	0.000000	0.05858	0.377000	0.26055	0.354000	0.29330	-0.036000	0.12185	1.021000	0.39600	-0.379000	0.06801	GGC	C|0.997;T|0.003	0.003	strong		0.672	SOX7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207131.1		
ASAH2	56624	hgsc.bcm.edu	37	10	52005057	52005057	+	Silent	SNP	T	T	C	rs201282742		TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr10:52005057T>C	ENST00000395526.4	-	2	284	c.285A>G	c.(283-285)ctA>ctG	p.L95L	ASAH2_ENST00000447815.1_Silent_p.L95L|ASAH2_ENST00000329428.6_Silent_p.L76L	NM_019893.2	NP_063946.2	Q9NR71	ASAH2_HUMAN	N-acylsphingosine amidohydrolase (non-lysosomal ceramidase) 2	95					apoptotic process (GO:0006915)|ceramide metabolic process (GO:0006672)|glycosphingolipid metabolic process (GO:0006687)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)|sphingolipid metabolic process (GO:0006665)	integral component of membrane (GO:0016021)|mitochondrion (GO:0005739)|plasma membrane (GO:0005886)	ceramidase activity (GO:0017040)			large_intestine(1)|lung(9)|urinary_tract(1)	11						AGTTCTGAAATAGAGGAGACT	0.517																																					p.L95L		Atlas-SNP	.											.	ASAH2	69	.	0			c.A285G						PASS	.	T	,	0,4406		0,0,2203	176.0	181.0	179.0		285,285	-10.3	0.0	10		179	2,8598	2.2+/-6.3	0,2,4298	no	coding-synonymous,coding-synonymous	ASAH2	NM_001143974.1,NM_019893.2	,	0,2,6501	CC,CT,TT		0.0233,0.0,0.0154	,	95/746,95/781	52005057	2,13004	2203	4300	6503	SO:0001819	synonymous_variant	56624	exon2			CTGAAATAGAGGA	AF250847	CCDS7239.2, CCDS44398.1	10q11.23	2008-08-11			ENSG00000188611	ENSG00000188611			18860	protein-coding gene	gene with protein product		611202				10781606	Standard	NM_019893		Approved		uc001jjd.3	Q9NR71	OTTHUMG00000018223	ENST00000395526.4:c.285A>G	10.37:g.52005057T>C		195.0	0.0	0		173.0	85.0	0.491329	NM_019893	Q3KNU1|Q5SNT7|Q5SZP6|Q5SZP7|Q5T1D5|Q71ME6	Silent	SNP	ENST00000395526.4	37	CCDS7239.2																																																																																			T|0.999;C|0.001	0.001	weak		0.517	ASAH2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048061.3	NM_019893	
SLC46A1	113235	hgsc.bcm.edu	37	17	26731959	26731959	+	Silent	SNP	G	G	C	rs185900287	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr17:26731959G>C	ENST00000440501.1	-	2	851	c.756C>G	c.(754-756)gtC>gtG	p.V252V	CTD-2350C19.2_ENST00000580714.1_RNA|CTD-2350C19.1_ENST00000583956.1_RNA|SLC46A1_ENST00000321666.5_Silent_p.V252V|SLC46A1_ENST00000584729.1_5'UTR	NM_080669.4	NP_542400.2	Q96NT5	PCFT_HUMAN	solute carrier family 46 (folate transporter), member 1	252					cellular iron ion homeostasis (GO:0006879)|folic acid metabolic process (GO:0046655)|folic acid transport (GO:0015884)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)|vitamin metabolic process (GO:0006766)|water-soluble vitamin metabolic process (GO:0006767)	apical plasma membrane (GO:0016324)|brush border membrane (GO:0031526)|cell surface (GO:0009986)|cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	folic acid binding (GO:0005542)|folic acid transporter activity (GO:0008517)|heme transporter activity (GO:0015232)|methotrexate transporter activity (GO:0015350)			lung(5)	5	all_lung(13;0.000533)|Lung NSC(42;0.00171)			UCEC - Uterine corpus endometrioid carcinoma (53;0.153)	Folic Acid(DB00158)|Methotrexate(DB00563)|Sulfasalazine(DB00795)	CATAGAGCTGGACAATGGATC	0.542													G|||	4	0.000798722	0.0	0.0014	5008	,	,		18170	0.0		0.001	False		,,,				2504	0.002				p.V252V		Atlas-SNP	.											.	SLC46A1	17	.	0			c.C756G						PASS	.	G	,	0,3912		0,0,1956	120.0	126.0	124.0		756,756	4.4	0.4	17		124	17,8283		0,17,4133	no	coding-synonymous,coding-synonymous	SLC46A1	NM_001242366.1,NM_080669.4	,	0,17,6089	CC,CG,GG		0.2048,0.0,0.1392	,	252/432,252/460	26731959	17,12195	1956	4150	6106	SO:0001819	synonymous_variant	113235	exon2			GAGCTGGACAATG	AK054669	CCDS74019.1, CCDS74020.1	17q11.2	2014-09-17	2007-09-24			ENSG00000076351		"""Solute carriers"""	30521	protein-coding gene	gene with protein product	"""heme carrier protein 1"", ""proton-coupled folate transporter"""	611672	"""solute carrier family 46, member 1"""			16143108, 17129779	Standard	XM_005277786		Approved	HCP1, MGC9564, PCFT	uc002hbf.2	Q96NT5		ENST00000440501.1:c.756C>G	17.37:g.26731959G>C		101.0	0.0	0		129.0	72.0	0.55814	NM_001242366	Q1HE20|Q86T92|Q8TEG3|Q96FL0	Silent	SNP	ENST00000440501.1	37																																																																																				G|0.999;C|0.001	0.001	strong		0.542	SLC46A1-202	KNOWN	basic|appris_principal	protein_coding	protein_coding		NM_080669	
KRIT1	889	hgsc.bcm.edu	37	7	91864857	91864857	+	Missense_Mutation	SNP	T	T	C	rs140396626		TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr7:91864857T>C	ENST00000340022.2	-	8	1607	c.589A>G	c.(589-591)Act>Gct	p.T197A	KRIT1_ENST00000394503.2_Missense_Mutation_p.T197A|KRIT1_ENST00000394507.1_Missense_Mutation_p.T197A|KRIT1_ENST00000412043.2_Missense_Mutation_p.T197A|KRIT1_ENST00000394505.2_Missense_Mutation_p.T197A	NM_004912.3|NM_194455.1	NP_004903.2|NP_919437.1	O00522	KRIT1_HUMAN	KRIT1, ankyrin repeat containing	197					angiogenesis (GO:0001525)|cell redox homeostasis (GO:0045454)|negative regulation of angiogenesis (GO:0016525)|negative regulation of endothelial cell apoptotic process (GO:2000352)|negative regulation of endothelial cell migration (GO:0010596)|negative regulation of endothelial cell proliferation (GO:0001937)|positive regulation of protein binding (GO:0032092)|regulation of catalytic activity (GO:0050790)|regulation of establishment of cell polarity (GO:2000114)|small GTPase mediated signal transduction (GO:0007264)	cell-cell junction (GO:0005911)|cytoplasm (GO:0005737)|extracellular space (GO:0005615)|microtubule (GO:0005874)|plasma membrane (GO:0005886)	microtubule binding (GO:0008017)|phosphatidylinositol-4,5-bisphosphate binding (GO:0005546)|protein complex binding (GO:0032403)|small GTPase regulator activity (GO:0005083)			autonomic_ganglia(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(5)|lung(9)|ovary(2)|stomach(1)	22	all_cancers(62;1.04e-09)|all_epithelial(64;5.75e-09)|Breast(17;0.00206)|all_lung(186;0.0509)|Lung NSC(181;0.0692)		STAD - Stomach adenocarcinoma(171;6.16e-05)|Lung(22;0.123)|LUSC - Lung squamous cell carcinoma(200;0.225)			CCTGATTCAGTAGCATATGCA	0.378																																					p.T197A		Atlas-SNP	.											.	KRIT1	66	.	0			c.A589G						PASS	.	T	ALA/THR,ALA/THR,ALA/THR,ALA/THR,ALA/THR	0,4406		0,0,2203	185.0	179.0	181.0		589,589,589,589,589	1.4	1.0	7	dbSNP_134	181	2,8598	2.2+/-6.3	0,2,4298	yes	missense,missense,missense,missense,missense	KRIT1	NM_001013406.1,NM_004912.3,NM_194454.1,NM_194455.1,NM_194456.1	58,58,58,58,58	0,2,6501	CC,CT,TT		0.0233,0.0,0.0154	benign,benign,benign,benign,benign	197/689,197/737,197/737,197/737,197/737	91864857	2,13004	2203	4300	6503	SO:0001583	missense	889	exon9			ATTCAGTAGCATA	AJ294850	CCDS5624.1, CCDS34679.1	7q21.2	2014-09-17	2005-03-15	2005-03-17	ENSG00000001631	ENSG00000001631		"""Ankyrin repeat domain containing"""	1573	protein-coding gene	gene with protein product		604214	"""cerebral cavernous malformations 1"""	CCM1		7604043, 11342228	Standard	NM_194455		Approved	CAM	uc003ulu.1	O00522	OTTHUMG00000131187	ENST00000340022.2:c.589A>G	7.37:g.91864857T>C	ENSP00000344668:p.Thr197Ala	110.0	0.0	0		118.0	61.0	0.516949	NM_194456	A6NNU0|O43894|Q506L6|Q6U276|Q75N19|Q9H180|Q9H264|Q9HAX5	Missense_Mutation	SNP	ENST00000340022.2	37	CCDS5624.1	.	.	.	.	.	.	.	.	.	.	T	9.752	1.167806	0.21621	0.0	2.33E-4	ENSG00000001631	ENST00000394507;ENST00000340022;ENST00000412043;ENST00000394505;ENST00000394503;ENST00000415227;ENST00000458177	T;T;T;T;T;D	0.85258	1.03;1.03;1.03;1.03;-0.48;-1.96	5.21	1.36	0.22044	.	0.546663	0.21326	N	0.076374	T	0.64405	0.2595	N	0.12182	0.205	0.24873	N	0.992278	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.46707	-0.9172	10	0.09843	T	0.71	3.0499	4.3536	0.11167	0.1369:0.247:0.0:0.6161	.	197;197	A6NNU0;O00522	.;KRIT1_HUMAN	A	197	ENSP00000378015:T197A;ENSP00000344668:T197A;ENSP00000410909:T197A;ENSP00000378013:T197A;ENSP00000378011:T197A;ENSP00000391675:T197A	ENSP00000344668:T197A	T	-	1	0	KRIT1	91702793	1.000000	0.71417	0.997000	0.53966	0.996000	0.88848	1.687000	0.37680	-0.014000	0.14175	0.377000	0.23210	ACT	T|1.000;C|0.000	0.000	weak		0.378	KRIT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253910.1		
MYSM1	114803	hgsc.bcm.edu	37	1	59126851	59126851	+	Silent	SNP	A	A	G	rs376987710		TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr1:59126851A>G	ENST00000472487.1	-	19	2358	c.2319T>C	c.(2317-2319)tgT>tgC	p.C773C	MYSM1_ENST00000493821.1_5'UTR	NM_001085487.2	NP_001078956.1	Q5VVJ2	MYSM1_HUMAN	Myb-like, SWIRM and MPN domains 1	773					chromatin remodeling (GO:0006338)|monoubiquitinated histone H2A deubiquitination (GO:0035522)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)|histone binding (GO:0042393)|metal ion binding (GO:0046872)|metallopeptidase activity (GO:0008237)|protein complex binding (GO:0032403)|transcription coactivator activity (GO:0003713)|ubiquitin thiolesterase activity (GO:0004221)|ubiquitin-specific protease activity (GO:0004843)			breast(1)|endometrium(3)|kidney(1)|large_intestine(6)|lung(6)|prostate(1)|skin(2)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	24	all_cancers(7;9.36e-06)					CTTTCTGCAAACAAGTCAGGT	0.373																																					p.C773C		Atlas-SNP	.											.	MYSM1	50	.	0			c.T2319C						PASS	.	A		0,3664		0,0,1832	94.0	88.0	90.0		2319	4.1	1.0	1		90	2,8168		0,2,4083	no	coding-synonymous	MYSM1	NM_001085487.2		0,2,5915	GG,GA,AA		0.0245,0.0,0.0169		773/829	59126851	2,11832	1832	4085	5917	SO:0001819	synonymous_variant	114803	exon19			CTGCAAACAAGTC	AB067502	CCDS41343.1	1p32.1	2009-02-11	2009-02-11		ENSG00000162601	ENSG00000162601			29401	protein-coding gene	gene with protein product		612176				11572484, 17428495, 17707232	Standard	NM_001085487		Approved	KIAA1915	uc009wab.2	Q5VVJ2	OTTHUMG00000009533	ENST00000472487.1:c.2319T>C	1.37:g.59126851A>G		54.0	0.0	0		59.0	27.0	0.457627	NM_001085487	A8KA54|B3KX65|Q68DD3|Q6AI53|Q7Z3G8|Q96PX3	Silent	SNP	ENST00000472487.1	37	CCDS41343.1																																																																																			.	.	none		0.373	MYSM1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000026343.2	XM_055481	
ADAMTSL3	57188	hgsc.bcm.edu	37	15	84639314	84639314	+	Missense_Mutation	SNP	C	C	T			TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr15:84639314C>T	ENST00000286744.5	+	20	2793	c.2569C>T	c.(2569-2571)Ccc>Tcc	p.P857S	ADAMTSL3_ENST00000567476.1_Missense_Mutation_p.P857S|ADAMTSL3_ENST00000567716.1_3'UTR	NM_207517.2	NP_997400.2	P82987	ATL3_HUMAN	ADAMTS-like 3	857	TSP type-1 7. {ECO:0000255|PROSITE- ProRule:PRU00210}.					proteinaceous extracellular matrix (GO:0005578)	metallopeptidase activity (GO:0008237)|zinc ion binding (GO:0008270)			NS(2)|breast(7)|central_nervous_system(6)|endometrium(7)|haematopoietic_and_lymphoid_tissue(4)|kidney(3)|large_intestine(24)|lung(51)|ovary(7)|pancreas(2)|prostate(2)|skin(8)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(4)	130			BRCA - Breast invasive adenocarcinoma(143;0.211)			TCGGCGCATCCCCCTCAGTGA	0.522																																					p.P857S		Atlas-SNP	.											.	ADAMTSL3	290	.	0			c.C2569T						PASS	.						189.0	166.0	174.0					15																	84639314		2203	4300	6503	SO:0001583	missense	57188	exon20			CGCATCCCCCTCA	AF237652	CCDS10326.1, CCDS73773.1	15q25.2	2013-01-29			ENSG00000156218	ENSG00000156218		"""Immunoglobulin superfamily / I-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	14633	protein-coding gene	gene with protein product		609199				9628581, 10574462	Standard	NM_207517		Approved	KIAA1233, punctin-2	uc002bjz.4	P82987	OTTHUMG00000147363	ENST00000286744.5:c.2569C>T	15.37:g.84639314C>T	ENSP00000286744:p.Pro857Ser	97.0	0.0	0		102.0	58.0	0.568627	NM_207517	A1A566|A1A567|Q9ULI7	Missense_Mutation	SNP	ENST00000286744.5	37	CCDS10326.1	.	.	.	.	.	.	.	.	.	.	C	11.44	1.640716	0.29157	.	.	ENSG00000156218	ENST00000286744	T	0.51574	0.7	4.39	-0.603	0.11630	.	1.472120	0.04463	N	0.374714	T	0.33702	0.0872	L	0.44542	1.39	0.09310	N	1	B;B	0.13145	0.001;0.007	B;B	0.11329	0.006;0.005	T	0.10613	-1.0622	10	0.08599	T	0.76	.	3.5686	0.07909	0.2274:0.39:0.296:0.0866	.	857;857	P82987-2;P82987	.;ATL3_HUMAN	S	857	ENSP00000286744:P857S	ENSP00000286744:P857S	P	+	1	0	ADAMTSL3	82430318	0.000000	0.05858	0.000000	0.03702	0.244000	0.25665	0.095000	0.15127	0.064000	0.16427	0.650000	0.86243	CCC	.	.	none		0.522	ADAMTSL3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000304007.2	NM_207517	
FLT3	2322	hgsc.bcm.edu	37	13	28608459	28608459	+	Silent	SNP	T	T	C	rs34374211	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr13:28608459T>C	ENST00000241453.7	-	13	1764	c.1683A>G	c.(1681-1683)ctA>ctG	p.L561L	FLT3_ENST00000380982.4_Silent_p.L561L|FLT3_ENST00000537084.1_Silent_p.L561L	NM_004119.2	NP_004110.2	P36888	FLT3_HUMAN	fms-related tyrosine kinase 3	561					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)	p.L561L(5)		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)	TGTGACAAATTAGCAGGGTTA	0.378			"""Mis, O"""		"""AML, ALL"""								T|||	700	0.139776	0.236	0.0403	5008	,	,		20547	0.129		0.0308	False		,,,				2504	0.2035				p.L561L		Atlas-SNP	.		Dom	yes		13	13q12	2322	fms-related tyrosine kinase 3		L	FLT3,colon,carcinoma,-2,8	FLT3	15525	8	5	Substitution - coding silent(5)	haematopoietic_and_lymphoid_tissue(5)	c.A1683G						PASS	.	T		924,3482	354.9+/-312.8	106,712,1385	86.0	81.0	83.0		1683	-11.7	0.0	13	dbSNP_126	83	324,8276	113.7+/-173.7	10,304,3986	no	coding-synonymous	FLT3	NM_004119.2		116,1016,5371	CC,CT,TT		3.7674,20.9714,9.5956		561/994	28608459	1248,11758	2203	4300	6503	SO:0001819	synonymous_variant	2322	exon13			ACAAATTAGCAGG	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.1683A>G	13.37:g.28608459T>C		134.0	0.0	0		137.0	71.0	0.518248	NM_004119	A0AVG9|B7ZLT7|B7ZLT8|F5H0A0|Q13414	Silent	SNP	ENST00000241453.7	37	CCDS31953.1																																																																																			T|0.897;C|0.103	0.103	strong		0.378	FLT3-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000044319.2		
RRP1B	23076	hgsc.bcm.edu	37	21	45106786	45106786	+	Missense_Mutation	SNP	T	T	G	rs138939671	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr21:45106786T>G	ENST00000340648.4	+	12	1228	c.1111T>G	c.(1111-1113)Tta>Gta	p.L371V		NM_015056.2	NP_055871.1	Q14684	RRP1B_HUMAN	ribosomal RNA processing 1B	371					negative regulation of phosphatase activity (GO:0010923)|rRNA processing (GO:0006364)	cytosol (GO:0005829)|euchromatin (GO:0000791)|heterochromatin (GO:0000792)|nucleolus (GO:0005730)|nucleus (GO:0005634)|preribosome, small subunit precursor (GO:0030688)	poly(A) RNA binding (GO:0044822)			cervix(1)|endometrium(1)|kidney(3)|large_intestine(4)|lung(3)|ovary(1)|pancreas(1)|prostate(3)|skin(3)|stomach(1)	21				STAD - Stomach adenocarcinoma(101;0.178)		AAATAAACTTTTAGAGAAAAC	0.438													T|||	11	0.00219649	0.0008	0.0014	5008	,	,		18271	0.0		0.006	False		,,,				2504	0.0031				p.L371V		Atlas-SNP	.											.	RRP1B	51	.	0			c.T1111G						PASS	.	T	VAL/LEU	6,4400	11.4+/-27.6	0,6,2197	94.0	97.0	96.0		1111	-10.6	0.0	21	dbSNP_134	96	63,8537	38.8+/-94.9	0,63,4237	yes	missense	RRP1B	NM_015056.2	32	0,69,6434	GG,GT,TT		0.7326,0.1362,0.5305	possibly-damaging	371/759	45106786	69,12937	2203	4300	6503	SO:0001583	missense	23076	exon12			AAACTTTTAGAGA	AK124620	CCDS33577.1	21q22.3	2014-06-13	2013-07-02	2007-03-26	ENSG00000160208	ENSG00000160208			23818	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 136"""	610654	"""KIAA0179"", ""ribosomal RNA processing 1 homolog B (S. cerevisiae)"""	KIAA0179			Standard	NM_015056		Approved	Nnp1, RRP1, PPP1R136	uc002zdk.3	Q14684	OTTHUMG00000086872	ENST00000340648.4:c.1111T>G	21.37:g.45106786T>G	ENSP00000339145:p.Leu371Val	36.0	0.0	0		27.0	12.0	0.444444	NM_015056	Q8TBZ4	Missense_Mutation	SNP	ENST00000340648.4	37	CCDS33577.1	5	0.0022893772893772895	0	0.0	0	0.0	0	0.0	5	0.006596306068601583	T	3.798	-0.042253	0.07452	0.001362	0.007326	ENSG00000160208	ENST00000340648	T	0.01005	5.45	5.3	-10.6	0.00265	.	2.342010	0.01390	N	0.013218	T	0.00815	0.0027	M	0.71581	2.175	0.09310	N	1	B	0.15473	0.013	B	0.12156	0.007	T	0.49214	-0.8963	10	0.87932	D	0	-2.2485	1.3182	0.02111	0.1812:0.2897:0.2753:0.2539	.	371	Q14684	RRP1B_HUMAN	V	371	ENSP00000339145:L371V	ENSP00000339145:L371V	L	+	1	2	RRP1B	43931214	0.000000	0.05858	0.000000	0.03702	0.004000	0.04260	-3.909000	0.00337	-1.445000	0.01948	-1.275000	0.01399	TTA	T|0.996;G|0.004	0.004	strong		0.438	RRP1B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000195651.1	NM_015056	
ABCC3	8714	hgsc.bcm.edu	37	17	48761385	48761385	+	Missense_Mutation	SNP	A	A	G	rs150601692	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr17:48761385A>G	ENST00000285238.8	+	28	4110	c.4030A>G	c.(4030-4032)Aag>Gag	p.K1344E		NM_003786.3	NP_003777.2	O15438	MRP3_HUMAN	ATP-binding cassette, sub-family C (CFTR/MRP), member 3	1344	ABC transporter 2. {ECO:0000255|PROSITE- ProRule:PRU00434}.				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)	GGAGGCGGCAAAGGGTGAAAT	0.622													A|||	5	0.000998403	0.0	0.0	5008	,	,		20086	0.0		0.0	False		,,,				2504	0.0051				p.K1344E		Atlas-SNP	.											.	ABCC3	138	.	0			c.A4030G						PASS	.	A	GLU/LYS	1,4405	2.1+/-5.4	0,1,2202	54.0	48.0	50.0		4030	2.1	0.1	17	dbSNP_134	50	6,8594	5.0+/-18.6	0,6,4294	yes	missense	ABCC3	NM_003786.3	56	0,7,6496	GG,GA,AA		0.0698,0.0227,0.0538	benign	1344/1528	48761385	7,12999	2203	4300	6503	SO:0001583	missense	8714	exon28			GCGGCAAAGGGTG	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.4030A>G	17.37:g.48761385A>G	ENSP00000285238:p.Lys1344Glu	56.0	0.0	0		85.0	60.0	0.705882	NM_003786	B2RPA9|D3DTX9|O60265|O60922|O75621|O95078|O95289|O95290|Q86X85|Q9UN52	Missense_Mutation	SNP	ENST00000285238.8	37	CCDS32681.1	.	.	.	.	.	.	.	.	.	.	A	2.739	-0.262675	0.05754	2.27E-4	6.98E-4	ENSG00000108846	ENST00000285238	D	0.92752	-3.1	5.24	2.06	0.26882	ATPase, AAA+ type, core (1);ABC transporter-like (2);	0.385040	0.29473	N	0.012046	T	0.76744	0.4030	N	0.05259	-0.085	0.09310	N	1	B	0.06786	0.001	B	0.10450	0.005	T	0.62258	-0.6892	10	0.02654	T	1	-18.184	7.7134	0.28690	0.2169:0.1322:0.6509:0.0	.	1344	O15438	MRP3_HUMAN	E	1344	ENSP00000285238:K1344E	ENSP00000285238:K1344E	K	+	1	0	ABCC3	46116384	0.002000	0.14202	0.127000	0.21898	0.980000	0.70556	1.360000	0.34125	0.656000	0.30886	-0.242000	0.12053	AAG	A|0.999;G|0.001	0.001	strong		0.622	ABCC3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000368083.2	NM_020038	
SCN8A	6334	hgsc.bcm.edu	37	12	52162823	52162823	+	Missense_Mutation	SNP	C	C	T	rs117217073	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr12:52162823C>T	ENST00000354534.6	+	17	3254	c.3076C>T	c.(3076-3078)Cgt>Tgt	p.R1026C	SCN8A_ENST00000545061.1_Missense_Mutation_p.R1026C	NM_001177984.2|NM_014191.3	NP_001171455.1|NP_055006.1	Q9UQD0	SCN8A_HUMAN	sodium channel, voltage gated, type VIII, alpha subunit	1026					adult walking behavior (GO:0007628)|axon guidance (GO:0007411)|membrane depolarization during action potential (GO:0086010)|muscle organ development (GO:0007517)|myelination (GO:0042552)|nervous system development (GO:0007399)|neuromuscular process (GO:0050905)|neuronal action potential (GO:0019228)|peripheral nervous system development (GO:0007422)|response to toxic substance (GO:0009636)|sensory perception of sound (GO:0007605)|sodium ion transmembrane transport (GO:0035725)|sodium ion transport (GO:0006814)	axon initial segment (GO:0043194)|cytoplasmic vesicle (GO:0031410)|dendrite (GO:0030425)|integral component of membrane (GO:0016021)|neuronal cell body (GO:0043025)|node of Ranvier (GO:0033268)|plasma membrane (GO:0005886)|voltage-gated sodium channel complex (GO:0001518)|Z disc (GO:0030018)	ATP binding (GO:0005524)|voltage-gated sodium channel activity (GO:0005248)			breast(2)|central_nervous_system(1)|cervix(2)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(7)|lung(19)|ovary(8)|prostate(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	55				BRCA - Breast invasive adenocarcinoma(357;0.181)	Valproic Acid(DB00313)	CTTTAAGCAGCGTGAGGCTGA	0.512													C|||	24	0.00479233	0.0	0.0086	5008	,	,		22384	0.0		0.0169	False		,,,				2504	0.001				p.R1026C		Atlas-SNP	.											.	SCN8A	331	.	0			c.C3076T						PASS	.	C	CYS/ARG,CYS/ARG	8,4130		0,8,2061	73.0	75.0	74.0		3076,3076	4.6	1.0	12	dbSNP_132	74	131,8311		0,131,4090	yes	missense,missense	SCN8A	NM_001177984.1,NM_014191.2	180,180	0,139,6151	TT,TC,CC		1.5518,0.1933,1.1049	probably-damaging,probably-damaging	1026/1940,1026/1981	52162823	139,12441	2069	4221	6290	SO:0001583	missense	6334	exon17			AAGCAGCGTGAGG	AB027567	CCDS44891.1, CCDS53794.1	12q13.1	2012-02-26	2007-01-23			ENSG00000196876		"""Sodium channels"", ""Voltage-gated ion channels / Sodium channels"""	10596	protein-coding gene	gene with protein product		600702	"""sodium channel, voltage gated, type VIII, alpha polypeptide"""	MED		7670495, 9828131, 16382098	Standard	NM_014191		Approved	Nav1.6, NaCh6, PN4, CerIII	uc001ryw.4	Q9UQD0		ENST00000354534.6:c.3076C>T	12.37:g.52162823C>T	ENSP00000346534:p.Arg1026Cys	91.0	0.0	0		110.0	45.0	0.409091	NM_014191	B9VWG8|O95788|Q9NYX2|Q9UPB2	Missense_Mutation	SNP	ENST00000354534.6	37	CCDS44891.1	16	0.007326007326007326	0	0.0	2	0.0055248618784530384	0	0.0	14	0.018469656992084433	C	16.02	3.004177	0.54254	0.001933	0.015518	ENSG00000196876	ENST00000354534;ENST00000545061;ENST00000355133;ENST00000357961	D;D;D	0.84298	-1.83;-1.83;-1.83	4.55	4.55	0.56014	Sodium ion transport-associated (1);	0.110372	0.64402	D	0.000020	T	0.80944	0.4721	L	0.49778	1.585	0.48040	D	0.999573	D;D	0.89917	1.0;0.997	D;P	0.65987	0.94;0.849	D	0.84692	0.0723	10	0.87932	D	0	.	10.947	0.47306	0.3118:0.6882:0.0:0.0	.	1026;1026	F8VWM7;Q9UQD0	.;SCN8A_HUMAN	C	1026;1026;1026;939	ENSP00000346534:R1026C;ENSP00000440360:R1026C;ENSP00000347255:R1026C	ENSP00000346534:R1026C	R	+	1	0	SCN8A	50449090	0.999000	0.42202	1.000000	0.80357	0.704000	0.40688	1.398000	0.34554	2.816000	0.96949	0.563000	0.77884	CGT	C|0.991;T|0.009	0.009	strong		0.512	SCN8A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000404372.3	NM_014191	
PTPRG	5793	hgsc.bcm.edu	37	3	61989028	61989028	+	Missense_Mutation	SNP	A	A	G	rs140777402		TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr3:61989028A>G	ENST00000474889.1	+	4	753	c.376A>G	c.(376-378)Atc>Gtc	p.I126V	PTPRG_ENST00000295874.10_Missense_Mutation_p.I126V	NM_002841.3	NP_002832.3	P23470	PTPRG_HUMAN	protein tyrosine phosphatase, receptor type, G	126	Alpha-carbonic anhydrase.				brain development (GO:0007420)|negative regulation of epithelial cell migration (GO:0010633)|negative regulation of neuron projection development (GO:0010977)|peptidyl-tyrosine dephosphorylation (GO:0035335)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)	identical protein binding (GO:0042802)|protein tyrosine phosphatase activity (GO:0004725)|transmembrane receptor protein tyrosine phosphatase activity (GO:0005001)			NS(1)|breast(4)|central_nervous_system(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(2)|kidney(4)|large_intestine(12)|liver(2)|lung(15)|ovary(7)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	62				BRCA - Breast invasive adenocarcinoma(55;0.000376)|KIRC - Kidney renal clear cell carcinoma(10;0.0499)|Kidney(10;0.065)		CACAGTCGCCATCCTTCTGAA	0.428													A|||	1	0.000199681	0.0	0.0	5008	,	,		20437	0.0		0.001	False		,,,				2504	0.0				p.I126V		Atlas-SNP	.											PTPRG,NS,malignant_melanoma,-2,1	PTPRG	153	1	0			c.A376G						PASS	.	A	VAL/ILE	0,4406		0,0,2203	89.0	89.0	89.0		376	5.0	1.0	3	dbSNP_134	89	5,8595	3.7+/-12.6	0,5,4295	yes	missense	PTPRG	NM_002841.3	29	0,5,6498	GG,GA,AA		0.0581,0.0,0.0384	benign	126/1446	61989028	5,13001	2203	4300	6503	SO:0001583	missense	5793	exon4			GTCGCCATCCTTC	L09247	CCDS2895.1	3p21-p14	2013-02-11			ENSG00000144724	ENSG00000144724		"""Protein tyrosine phosphatases / Class I Cys-based PTPs : Transmembrane receptor-like"", ""Fibronectin type III domain containing"""	9671	protein-coding gene	gene with protein product		176886		PTPG		1711217	Standard	NM_002841		Approved	RPTPG	uc003dlb.3	P23470	OTTHUMG00000158660	ENST00000474889.1:c.376A>G	3.37:g.61989028A>G	ENSP00000418112:p.Ile126Val	103.0	0.0	0		87.0	40.0	0.45977	NM_002841	B2RU12|B7ZLX5|Q15623|Q59EE0|Q68DU5	Missense_Mutation	SNP	ENST00000474889.1	37	CCDS2895.1	1	4.578754578754579E-4	0	0.0	0	0.0	0	0.0	1	0.0013192612137203166	A	19.50	3.839240	0.71373	0.0	5.81E-4	ENSG00000144724	ENST00000474889;ENST00000295874	T;T	0.61742	0.08;0.08	6.16	5.0	0.66597	Carbonic anhydrase, alpha-class, catalytic domain (4);	0.052424	0.85682	D	0.000000	T	0.41213	0.1149	N	0.12637	0.245	0.53688	D	0.999973	B;B	0.25272	0.1;0.122	B;B	0.27380	0.047;0.079	T	0.43261	-0.9402	10	0.87932	D	0	.	12.6615	0.56815	0.9349:0.0:0.0651:0.0	.	126;126	P23470-2;P23470	.;PTPRG_HUMAN	V	126	ENSP00000418112:I126V;ENSP00000295874:I126V	ENSP00000295874:I126V	I	+	1	0	PTPRG	61964068	1.000000	0.71417	1.000000	0.80357	0.857000	0.48899	4.799000	0.62517	2.367000	0.80283	0.528000	0.53228	ATC	A|1.000;G|0.000	0.000	strong		0.428	PTPRG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000351674.1	NM_002841	
