#version 2.4
## 
## Oncotator v1.8.0.0 | Flat File Reference hg19 | GENCODE v19 EFFECT | UniProt_AAxform 2014_12 | ClinVar 12.03.20 | ESP 6500SI-V2 | ORegAnno UCSC Track | dbSNP build 142 | CCLE_By_GP 09292010 | COSMIC v62_291112 | 1000gp3 20130502 | UniProt_AA 2014_12 | dbNSFP v2.4 | ESP 6500SI-V2 | COSMIC_FusionGenes v62_291112 | gencode_xref_refseq metadata_v19 | CCLE_By_Gene 09292010 | ACHILLES_Lineage_Results 110303 | CGC full_2012-03-15 | UniProt 2014_12 | HumanDNARepairGenes 20110905 | HGNC Sept172014 | COSMIC_Tissue 291112 | Familial_Cancer_Genes 20110905 | TUMORScape 20100104 | Ensembl ICGC MUCOPA | TCGAScape 110405 | MutSig Published Results 20110905 
Hugo_Symbol	Entrez_Gene_Id	Center	NCBI_Build	Chromosome	Start_position	End_position	Strand	Variant_Classification	Variant_Type	Reference_Allele	Tumor_Seq_Allele1	Tumor_Seq_Allele2	dbSNP_RS	dbSNP_Val_Status	Tumor_Sample_Barcode	Matched_Norm_Sample_Barcode	Match_Norm_Seq_Allele1	Match_Norm_Seq_Allele2	Tumor_Validation_Allele1	Tumor_Validation_Allele2	Match_Norm_Validation_Allele1	Match_Norm_Validation_Allele2	Verification_Status	Validation_Status	Mutation_Status	Sequencing_Phase	Sequence_Source	Validation_Method	Score	BAM_file	Sequencer	Tumor_Sample_UUID	Matched_Norm_Sample_UUID	Genome_Change	Annotation_Transcript	Transcript_Strand	Transcript_Exon	Transcript_Position	cDNA_Change	Codon_Change	Protein_Change	Other_Transcripts	Refseq_mRNA_Id	Refseq_prot_Id	SwissProt_acc_Id	SwissProt_entry_Id	Description	UniProt_AApos	UniProt_Region	UniProt_Site	UniProt_Natural_Variations	UniProt_Experimental_Info	GO_Biological_Process	GO_Cellular_Component	GO_Molecular_Function	COSMIC_overlapping_mutations	COSMIC_fusion_genes	COSMIC_tissue_types_affected	COSMIC_total_alterations_in_gene	Tumorscape_Amplification_Peaks	Tumorscape_Deletion_Peaks	TCGAscape_Amplification_Peaks	TCGAscape_Deletion_Peaks	DrugBank	ref_context	gc_content	CCLE_ONCOMAP_overlapping_mutations	CCLE_ONCOMAP_total_mutations_in_gene	CGC_Mutation_Type	CGC_Translocation_Partner	CGC_Tumor_Types_Somatic	CGC_Tumor_Types_Germline	CGC_Other_Diseases	DNARepairGenes_Role	FamilialCancerDatabase_Syndromes	MUTSIG_Published_Results	OREGANNO_ID	OREGANNO_Values	i_1000gp3_AA	i_1000gp3_AC	i_1000gp3_AF	i_1000gp3_AFR_AF	i_1000gp3_AMR_AF	i_1000gp3_AN	i_1000gp3_CIEND	i_1000gp3_CIPOS	i_1000gp3_CS	i_1000gp3_DP	i_1000gp3_EAS_AF	i_1000gp3_END	i_1000gp3_EUR_AF	i_1000gp3_IMPRECISE	i_1000gp3_MC	i_1000gp3_MEINFO	i_1000gp3_MEND	i_1000gp3_MLEN	i_1000gp3_MSTART	i_1000gp3_NS	i_1000gp3_SAS_AF	i_1000gp3_SVLEN	i_1000gp3_SVTYPE	i_1000gp3_TSD	i_AAChange	i_ACHILLES_Lineage_Results_Top_Genes	i_Algorithm	i_BAM_File	i_CGC_Cancer Germline Mut	i_CGC_Cancer Molecular Genetics	i_CGC_Cancer Somatic Mut	i_CGC_Cancer Syndrome	i_CGC_Chr	i_CGC_Chr Band	i_CGC_GeneID	i_CGC_Name	i_CGC_Other Germline Mut	i_CGC_Tissue Type	i_COSMIC_Codon	i_COSMIC_Gene	i_COSMIC_Gene_Freq	i_COSMIC_Site_Freq	i_COSMIC_n_overlapping_mutations	i_COSMIC_overlapping_mutation_descriptions	i_COSMIC_overlapping_primary_sites	i_ChromChange	i_ClinVar_ASSEMBLY	i_ClinVar_HGMD_ID	i_ClinVar_SYM	i_ClinVar_TYPE	i_ClinVar_rs	i_Drug_Target	i_ESP_AA	i_ESP_AAC	i_ESP_AA_AC	i_ESP_AA_AGE	i_ESP_AA_GTC	i_ESP_AvgAAsampleReadDepth	i_ESP_AvgEAsampleReadDepth	i_ESP_AvgSampleReadDepth	i_ESP_CA	i_ESP_CDP	i_ESP_CG	i_ESP_CP	i_ESP_Chromosome	i_ESP_DBSNP	i_ESP_DP	i_ESP_EA_AC	i_ESP_EA_AGE	i_ESP_EA_GTC	i_ESP_EXOME_CHIP	i_ESP_FG	i_ESP_GL	i_ESP_GM	i_ESP_GS	i_ESP_GTC	i_ESP_GTS	i_ESP_GWAS_PUBMED	i_ESP_MAF	i_ESP_PH	i_ESP_PP	i_ESP_Position	i_ESP_TAC	i_ESP_TotalAAsamplesCovered	i_ESP_TotalEAsamplesCovered	i_ESP_TotalSamplesCovered	i_Ensembl_so_accession	i_Ensembl_so_term	i_Entrez_Gene_Id	i_Exon	i_Familial_Cancer_Genes_Reference	i_Familial_Cancer_Genes_Synonym	i_Genome_Plus_Minus_10_Bp	i_HGNC_Accession Numbers	i_HGNC_CCDS IDs	i_HGNC_Chromosome	i_HGNC_Date Modified	i_HGNC_Date Name Changed	i_HGNC_Date Symbol Changed	i_HGNC_Ensembl Gene ID	i_HGNC_Ensembl ID(supplied by Ensembl)	i_HGNC_Enzyme IDs	i_HGNC_Gene family description	i_HGNC_HGNC ID	i_HGNC_Locus Group	i_HGNC_Locus Type	i_HGNC_Name Synonyms	i_HGNC_OMIM ID(supplied by NCBI)	i_HGNC_Previous Names	i_HGNC_Previous Symbols	i_HGNC_Primary IDs	i_HGNC_Pubmed IDs	i_HGNC_Record Type	i_HGNC_RefSeq(supplied by NCBI)	i_HGNC_Secondary IDs	i_HGNC_Status	i_HGNC_Synonyms	i_HGNC_UCSC ID(supplied by UCSC)	i_HGNC_UniProt ID(supplied by UniProt)	i_HGNC_VEGA IDs	i_HGVS_coding_DNA_change	i_HGVS_genomic_change	i_HGVS_protein_change	i_NTotCov	i_NVarCov	i_ORegAnno_bin	i_TTotCov	i_TVarCov	i_Transcript_Id	i_UniProt_alt_uniprot_accessions	i_Variant_Classification	i_Variant_Type	i_annotation_transcript	i_build	i_ccds_id	i_dbNSFP_1000Gp1_AC	i_dbNSFP_1000Gp1_AF	i_dbNSFP_1000Gp1_AFR_AC	i_dbNSFP_1000Gp1_AFR_AF	i_dbNSFP_1000Gp1_AMR_AC	i_dbNSFP_1000Gp1_AMR_AF	i_dbNSFP_1000Gp1_ASN_AC	i_dbNSFP_1000Gp1_ASN_AF	i_dbNSFP_1000Gp1_EUR_AC	i_dbNSFP_1000Gp1_EUR_AF	i_dbNSFP_Ancestral_allele	i_dbNSFP_CADD_phred	i_dbNSFP_CADD_raw	i_dbNSFP_CADD_raw_rankscore	i_dbNSFP_ESP6500_AA_AF	i_dbNSFP_ESP6500_EA_AF	i_dbNSFP_Ensembl_geneid	i_dbNSFP_Ensembl_transcriptid	i_dbNSFP_FATHMM_pred	i_dbNSFP_FATHMM_rankscore	i_dbNSFP_FATHMM_score	i_dbNSFP_GERP++_NR	i_dbNSFP_GERP++_RS	i_dbNSFP_GERP++_RS_rankscore	i_dbNSFP_Interpro_domain	i_dbNSFP_LRT_Omega	i_dbNSFP_LRT_converted_rankscore	i_dbNSFP_LRT_pred	i_dbNSFP_LRT_score	i_dbNSFP_LR_pred	i_dbNSFP_LR_rankscore	i_dbNSFP_LR_score	i_dbNSFP_MutationAssessor_pred	i_dbNSFP_MutationAssessor_rankscore	i_dbNSFP_MutationAssessor_score	i_dbNSFP_MutationTaster_converted_rankscore	i_dbNSFP_MutationTaster_pred	i_dbNSFP_MutationTaster_score	i_dbNSFP_Polyphen2_HDIV_pred	i_dbNSFP_Polyphen2_HDIV_rankscore	i_dbNSFP_Polyphen2_HDIV_score	i_dbNSFP_Polyphen2_HVAR_pred	i_dbNSFP_Polyphen2_HVAR_rankscore	i_dbNSFP_Polyphen2_HVAR_score	i_dbNSFP_RadialSVM_pred	i_dbNSFP_RadialSVM_rankscore	i_dbNSFP_RadialSVM_score	i_dbNSFP_Reliability_index	i_dbNSFP_SIFT_converted_rankscore	i_dbNSFP_SIFT_pred	i_dbNSFP_SIFT_score	i_dbNSFP_SLR_test_statistic	i_dbNSFP_SiPhy_29way_logOdds	i_dbNSFP_SiPhy_29way_logOdds_rankscore	i_dbNSFP_SiPhy_29way_pi	i_dbNSFP_UniSNP_ids	i_dbNSFP_Uniprot_aapos	i_dbNSFP_Uniprot_acc	i_dbNSFP_Uniprot_id	i_dbNSFP_aaalt	i_dbNSFP_aapos	i_dbNSFP_aapos_FATHMM	i_dbNSFP_aapos_SIFT	i_dbNSFP_aaref	i_dbNSFP_cds_strand	i_dbNSFP_codonpos	i_dbNSFP_fold-degenerate	i_dbNSFP_genename	i_dbNSFP_hg18_pos(1-coor)	i_dbNSFP_phastCons100way_vertebrate	i_dbNSFP_phastCons100way_vertebrate_rankscore	i_dbNSFP_phastCons46way_placental	i_dbNSFP_phastCons46way_placental_rankscore	i_dbNSFP_phastCons46way_primate	i_dbNSFP_phastCons46way_primate_rankscore	i_dbNSFP_phyloP100way_vertebrate	i_dbNSFP_phyloP100way_vertebrate_rankscore	i_dbNSFP_phyloP46way_placental	i_dbNSFP_phyloP46way_placental_rankscore	i_dbNSFP_phyloP46way_primate	i_dbNSFP_phyloP46way_primate_rankscore	i_dbNSFP_refcodon	i_dbSNPPopFreq	i_dbSNP_AF	i_entrez_gene_id	i_gc_content_full	i_gencode_transcript_name	i_gencode_transcript_status	i_gencode_transcript_tags	i_gencode_transcript_type	i_gene_type	i_havana_transcript	i_refseq_mrna_id	i_secondary_variant_classification
PLOD1	5351	hgsc.bcm.edu	37	1	12023642	12023642	+	Missense_Mutation	SNP	A	A	C			TCGA-KR-A7K2-01A-12D-A33Q-10	TCGA-KR-A7K2-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cbf5cf66-d096-4a67-b0a1-7f985b2dcd42	6b5190db-85e5-485f-8174-2c1727487ef2	g.chr1:12023642A>C	ENST00000196061.4	+	11	1178	c.1151A>C	c.(1150-1152)gAc>gCc	p.D384A	PLOD1_ENST00000376369.3_Missense_Mutation_p.D431A	NM_000302.3	NP_000293.2	Q02809	PLOD1_HUMAN	procollagen-lysine, 2-oxoglutarate 5-dioxygenase 1	384					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)	GTGGATGCTGACGTGGCCCTG	0.627																																					p.D384A		Atlas-SNP	.											.	PLOD1	75	.	0			c.A1151C						.						57.0	44.0	48.0					1																	12023642		2202	4299	6501	SO:0001583	missense	5351	exon11			ATGCTGACGTGGC	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.1151A>C	chr1.hg19:g.12023642A>C	ENSP00000196061:p.Asp384Ala	61.0	0.0		49.0	12.0	NM_000302	B4DR87|Q96AV9|Q9H132	Missense_Mutation	SNP	ENST00000196061.4	hg19	CCDS142.1	.	.	.	.	.	.	.	.	.	.	A	18.46	3.629557	0.67015	.	.	ENSG00000083444	ENST00000376369;ENST00000196061	D;D	0.98120	-4.73;-4.73	5.01	5.01	0.66863	.	0.319876	0.33534	N	0.004811	D	0.98009	0.9344	M	0.77103	2.36	0.80722	D	1	D;B	0.62365	0.991;0.22	P;B	0.56127	0.792;0.115	D	0.98290	1.0513	10	0.59425	D	0.04	.	13.616	0.62108	1.0:0.0:0.0:0.0	.	431;384	B4DR87;Q02809	.;PLOD1_HUMAN	A	431;384	ENSP00000365548:D431A;ENSP00000196061:D384A	ENSP00000196061:D384A	D	+	2	0	PLOD1	11946229	1.000000	0.71417	0.945000	0.38365	0.862000	0.49288	9.205000	0.95048	1.879000	0.54435	0.529000	0.55759	GAC	.	.		0.627	PLOD1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000006865.1	NM_000302	
NCDN	23154	hgsc.bcm.edu	37	1	36024726	36024726	+	Missense_Mutation	SNP	A	A	T			TCGA-KR-A7K2-01A-12D-A33Q-10	TCGA-KR-A7K2-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cbf5cf66-d096-4a67-b0a1-7f985b2dcd42	6b5190db-85e5-485f-8174-2c1727487ef2	g.chr1:36024726A>T	ENST00000373243.2	+	2	435	c.52A>T	c.(52-54)Atg>Ttg	p.M18L	NCDN_ENST00000373253.3_Start_Codon_SNP_p.M1L|KIAA0319L_ENST00000325722.3_5'Flank|NCDN_ENST00000459931.1_3'UTR|NCDN_ENST00000356090.4_Missense_Mutation_p.M18L	NM_014284.2	NP_055099.1	Q9UBB6	NCDN_HUMAN	neurochondrin	18					bone resorption (GO:0045453)|neuron projection development (GO:0031175)|regulation of neuronal synaptic plasticity (GO:0048168)	cytosol (GO:0005829)|dendrite (GO:0030425)|membrane (GO:0016020)|neuronal cell body (GO:0043025)				breast(1)|endometrium(1)|kidney(1)|large_intestine(7)|lung(3)|pancreas(1)|skin(2)	16		Myeloproliferative disorder(586;0.0255)|all_neural(195;0.0887)				GGCGAGCATCATGGCCTCGGA	0.637																																					p.M18L		Atlas-SNP	.											.	NCDN	79	.	0			c.A52T						.						52.0	50.0	51.0					1																	36024726		2203	4300	6503	SO:0001583	missense	23154	exon2			AGCATCATGGCCT	AB011179	CCDS392.1, CCDS30672.1	1p34.3	2008-02-05			ENSG00000020129	ENSG00000020129			17597	protein-coding gene	gene with protein product		608458				15007648	Standard	NM_014284		Approved	NCDN-1, NCDN-2	uc001bza.3	Q9UBB6	OTTHUMG00000059204	ENST00000373243.2:c.52A>T	chr1.hg19:g.36024726A>T	ENSP00000362340:p.Met18Leu	166.0	0.0		138.0	68.0	NM_014284	D3DPR9|Q9UBY2|Q9Y4A6|Q9Y4D9	Missense_Mutation	SNP	ENST00000373243.2	hg19	CCDS392.1	.	.	.	.	.	.	.	.	.	.	A	14.82	2.648594	0.47258	.	.	ENSG00000020129	ENST00000373253;ENST00000356090;ENST00000373243;ENST00000437806	.	.	.	4.89	4.89	0.63831	.	0.400531	0.25275	N	0.031846	T	0.35624	0.0938	N	0.19112	0.55	0.34181	D	0.670955	B	0.29136	0.234	B	0.14578	0.011	T	0.49093	-0.8975	9	0.36615	T	0.2	.	13.3409	0.60545	1.0:0.0:0.0:0.0	.	18	Q9UBB6	NCDN_HUMAN	L	1;18;18;1	.	ENSP00000348394:M18L	M	+	1	0	NCDN	35797313	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	4.210000	0.58500	1.809000	0.52856	0.379000	0.24179	ATG	.	.		0.637	NCDN-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000131298.1	NM_014284	
CAPZA1	829	hgsc.bcm.edu	37	1	113212621	113212621	+	Missense_Mutation	SNP	T	T	G			TCGA-KR-A7K2-01A-12D-A33Q-10	TCGA-KR-A7K2-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cbf5cf66-d096-4a67-b0a1-7f985b2dcd42	6b5190db-85e5-485f-8174-2c1727487ef2	g.chr1:113212621T>G	ENST00000263168.3	+	10	1400	c.728T>G	c.(727-729)aTt>aGt	p.I243S	CAPZA1_ENST00000476936.1_3'UTR	NM_006135.2	NP_006126.1	P52907	CAZA1_HUMAN	capping protein (actin filament) muscle Z-line, alpha 1	243					actin cytoskeleton organization (GO:0030036)|actin filament capping (GO:0051693)|blood coagulation (GO:0007596)|cellular component movement (GO:0006928)|innate immune response (GO:0045087)|protein complex assembly (GO:0006461)	actin cytoskeleton (GO:0015629)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|F-actin capping protein complex (GO:0008290)|WASH complex (GO:0071203)	actin binding (GO:0003779)			breast(1)|kidney(2)|large_intestine(2)|lung(3)|prostate(1)	9	Lung SC(450;0.246)	all_cancers(81;1.44e-07)|all_epithelial(167;7.64e-07)|all_lung(203;2.16e-05)|Lung NSC(69;3.86e-05)		Lung(183;0.0234)|all cancers(265;0.0246)|Epithelial(280;0.0342)|Colorectal(144;0.0686)|COAD - Colon adenocarcinoma(174;0.111)|LUSC - Lung squamous cell carcinoma(189;0.133)		CAGACAGCAATTAGTGAAAAC	0.423																																					p.I243S		Atlas-SNP	.											.	CAPZA1	16	.	0			c.T728G						.						69.0	68.0	68.0					1																	113212621		2202	4300	6502	SO:0001583	missense	829	exon10			CAGCAATTAGTGA	U56637	CCDS30805.1	1p13.2	2014-05-09			ENSG00000116489	ENSG00000116489			1488	protein-coding gene	gene with protein product		601580				7665558, 9119363	Standard	NM_006135		Approved		uc001ecj.1	P52907	OTTHUMG00000011769	ENST00000263168.3:c.728T>G	chr1.hg19:g.113212621T>G	ENSP00000263168:p.Ile243Ser	142.0	0.0		125.0	62.0	NM_006135	Q53FQ6|Q6FHD5	Missense_Mutation	SNP	ENST00000263168.3	hg19	CCDS30805.1	.	.	.	.	.	.	.	.	.	.	T	26.7	4.761273	0.89932	.	.	ENSG00000116489	ENST00000263168	.	.	.	5.67	5.67	0.87782	.	0.000000	0.85682	D	0.000000	T	0.80929	0.4718	M	0.86178	2.8	0.80722	D	1	D	0.76494	0.999	D	0.97110	1.0	D	0.84490	0.0610	9	0.87932	D	0	-15.1678	15.8615	0.79026	0.0:0.0:0.0:1.0	.	243	P52907	CAZA1_HUMAN	S	243	.	ENSP00000263168:I243S	I	+	2	0	CAPZA1	113014144	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	7.979000	0.88103	2.285000	0.76669	0.528000	0.53228	ATT	.	.		0.423	CAPZA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000032567.2	NM_006135	
XPR1	9213	hgsc.bcm.edu	37	1	180794056	180794056	+	Silent	SNP	T	T	C			TCGA-KR-A7K2-01A-12D-A33Q-10	TCGA-KR-A7K2-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cbf5cf66-d096-4a67-b0a1-7f985b2dcd42	6b5190db-85e5-485f-8174-2c1727487ef2	g.chr1:180794056T>C	ENST00000367590.4	+	8	1129	c.931T>C	c.(931-933)Ttg>Ctg	p.L311L	AL590085.1_ENST00000579998.1_RNA|XPR1_ENST00000367589.3_Silent_p.L311L	NM_004736.3	NP_004727.2	Q9UBH6	XPR1_HUMAN	xenotropic and polytropic retrovirus receptor 1	311					G-protein coupled receptor signaling pathway (GO:0007186)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|receptor activity (GO:0004872)|transmembrane signaling receptor activity (GO:0004888)|virus receptor activity (GO:0001618)			breast(1)|endometrium(3)|kidney(2)|large_intestine(15)|lung(7)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(5)	35						GAGAAGCAATTTGTCTCATCA	0.378																																					p.L311L		Atlas-SNP	.											.	XPR1	76	.	0			c.T931C						.						129.0	119.0	122.0					1																	180794056		2203	4300	6503	SO:0001819	synonymous_variant	9213	exon8			AGCAATTTGTCTC	AF099082	CCDS1340.1, CCDS44284.1	1q25.1	2013-07-18	2010-04-23		ENSG00000143324	ENSG00000143324			12827	protein-coding gene	gene with protein product		605237	"""xenotropic and polytropic retrovirus receptor"""			9990033	Standard	NM_004736		Approved	SYG1, X3	uc001goi.3	Q9UBH6	OTTHUMG00000035116	ENST00000367590.4:c.931T>C	chr1.hg19:g.180794056T>C		53.0	0.0		111.0	16.0	NM_004736	O95719|Q7L8K9|Q8IW20|Q9NT19|Q9UFB9	Silent	SNP	ENST00000367590.4	hg19	CCDS1340.1																																																																																			.	.		0.378	XPR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000084996.2	NM_004736	
RYR2	6262	hgsc.bcm.edu	37	1	237670087	237670087	+	Silent	SNP	A	A	G			TCGA-KR-A7K2-01A-12D-A33Q-10	TCGA-KR-A7K2-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cbf5cf66-d096-4a67-b0a1-7f985b2dcd42	6b5190db-85e5-485f-8174-2c1727487ef2	g.chr1:237670087A>G	ENST00000366574.2	+	23	3008	c.2691A>G	c.(2689-2691)aaA>aaG	p.K897K	RYR2_ENST00000542537.1_Silent_p.K881K|RYR2_ENST00000360064.6_Silent_p.K895K	NM_001035.2	NP_001026.2	Q92736	RYR2_HUMAN	ryanodine receptor 2 (cardiac)	897	4 X approximate repeats.				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)			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)			TTATGAATAAAATTGAGCTTG	0.323																																					p.K897K		Atlas-SNP	.											.	RYR2	1273	.	0			c.A2691G						.						116.0	117.0	117.0					1																	237670087		1822	4080	5902	SO:0001819	synonymous_variant	6262	exon23			GAATAAAATTGAG	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.2691A>G	chr1.hg19:g.237670087A>G		40.0	0.0		86.0	25.0	NM_001035	Q15411|Q546N8|Q5T3P2	Silent	SNP	ENST00000366574.2	hg19	CCDS55691.1																																																																																			.	.		0.323	RYR2-001	KNOWN	non_canonical_conserved|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000095402.2	NM_001035	
GREB1	9687	hgsc.bcm.edu	37	2	11738866	11738866	+	Missense_Mutation	SNP	A	A	G			TCGA-KR-A7K2-01A-12D-A33Q-10	TCGA-KR-A7K2-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cbf5cf66-d096-4a67-b0a1-7f985b2dcd42	6b5190db-85e5-485f-8174-2c1727487ef2	g.chr2:11738866A>G	ENST00000381486.2	+	15	2513	c.2213A>G	c.(2212-2214)tAt>tGt	p.Y738C	GREB1_ENST00000234142.5_Missense_Mutation_p.Y738C	NM_014668.3	NP_055483.2	Q4ZG55	GREB1_HUMAN	growth regulation by estrogen in breast cancer 1	738						integral component of membrane (GO:0016021)				breast(3)|central_nervous_system(2)|endometrium(2)|kidney(4)|large_intestine(9)|lung(9)|ovary(1)	30	all_hematologic(175;0.127)|Acute lymphoblastic leukemia(172;0.155)			Epithelial(75;0.115)|OV - Ovarian serous cystadenocarcinoma(76;0.186)		GTGGAACAGTATGTTCTGAAG	0.448																																					p.Y738C	Ovarian(39;850 945 2785 23371 33093)	Atlas-SNP	.											GREB1_ENST00000381486,NS,carcinoma,0,1	GREB1	308	.	0			c.A2213G						.						197.0	200.0	199.0					2																	11738866		1985	4175	6160	SO:0001583	missense	9687	exon15			AACAGTATGTTCT		CCDS33146.1, CCDS33147.1, CCDS42655.1	2p25.1	2010-02-17	2009-09-10		ENSG00000196208	ENSG00000196208			24885	protein-coding gene	gene with protein product	"""gene regulated by estrogen in breast cancer"""	611736				11103799	Standard	NM_014668		Approved	KIAA0575	uc002rbk.1	Q4ZG55	OTTHUMG00000141276	ENST00000381486.2:c.2213A>G	chr2.hg19:g.11738866A>G	ENSP00000370896:p.Tyr738Cys	70.0	0.0		67.0	17.0	NM_014668	A6NHD0|A6NKN0|B5MDA9|O60321|Q7Z5S2|Q9H2Q6|Q9H2Q7|Q9H2Q8	Missense_Mutation	SNP	ENST00000381486.2	hg19	CCDS42655.1	.	.	.	.	.	.	.	.	.	.	A	14.44	2.536364	0.45176	.	.	ENSG00000196208	ENST00000381486;ENST00000234142;ENST00000432985	T;T;T	0.55930	2.81;2.81;0.49	5.04	5.04	0.67666	.	0.247626	0.35235	N	0.003342	T	0.67107	0.2858	M	0.65975	2.015	0.58432	D	0.999998	D;D	0.63046	0.992;0.992	P;P	0.59761	0.863;0.863	T	0.71842	-0.4470	10	0.87932	D	0	-44.4277	14.781	0.69766	1.0:0.0:0.0:0.0	.	372;738	C9JIG0;Q4ZG55	.;GREB1_HUMAN	C	738;738;372	ENSP00000370896:Y738C;ENSP00000234142:Y738C;ENSP00000403886:Y372C	ENSP00000234142:Y738C	Y	+	2	0	GREB1	11656317	1.000000	0.71417	0.007000	0.13788	0.004000	0.04260	7.021000	0.76425	1.900000	0.55004	0.460000	0.39030	TAT	.	.		0.448	GREB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000280490.1	NM_014668	
APOB	338	hgsc.bcm.edu	37	2	21229489	21229489	+	Silent	SNP	G	G	T	rs374560333		TCGA-KR-A7K2-01A-12D-A33Q-10	TCGA-KR-A7K2-10A-01D-A33Q-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cbf5cf66-d096-4a67-b0a1-7f985b2dcd42	6b5190db-85e5-485f-8174-2c1727487ef2	g.chr2:21229489G>T	ENST00000233242.1	-	26	10378	c.10251C>A	c.(10249-10251)acC>acA	p.T3417T		NM_000384.2	NP_000375	P04114	APOB_HUMAN	apolipoprotein B	3417	Heparin-binding.				artery morphogenesis (GO:0048844)|blood coagulation (GO:0007596)|cellular response to prostaglandin stimulus (GO:0071379)|cellular response to tumor necrosis factor (GO:0071356)|cholesterol efflux (GO:0033344)|cholesterol homeostasis (GO:0042632)|cholesterol metabolic process (GO:0008203)|cholesterol transport (GO:0030301)|fertilization (GO:0009566)|in utero embryonic development (GO:0001701)|leukocyte migration (GO:0050900)|lipoprotein biosynthetic process (GO:0042158)|lipoprotein catabolic process (GO:0042159)|lipoprotein metabolic process (GO:0042157)|lipoprotein transport (GO:0042953)|low-density lipoprotein particle clearance (GO:0034383)|low-density lipoprotein particle remodeling (GO:0034374)|nervous system development (GO:0007399)|phototransduction, visible light (GO:0007603)|positive regulation of cholesterol storage (GO:0010886)|positive regulation of lipid storage (GO:0010884)|positive regulation of macrophage derived foam cell differentiation (GO:0010744)|post-embryonic development (GO:0009791)|receptor-mediated endocytosis (GO:0006898)|regulation of cholesterol biosynthetic process (GO:0045540)|response to carbohydrate (GO:0009743)|response to lipopolysaccharide (GO:0032496)|response to selenium ion (GO:0010269)|response to virus (GO:0009615)|retinoid metabolic process (GO:0001523)|small molecule metabolic process (GO:0044281)|sperm motility (GO:0030317)|spermatogenesis (GO:0007283)|triglyceride catabolic process (GO:0019433)|triglyceride mobilization (GO:0006642)|very-low-density lipoprotein particle assembly (GO:0034379)	actin cytoskeleton (GO:0015629)|chylomicron (GO:0042627)|chylomicron remnant (GO:0034360)|clathrin-coated endocytic vesicle membrane (GO:0030669)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|early endosome (GO:0005769)|endocytic vesicle lumen (GO:0071682)|endoplasmic reticulum lumen (GO:0005788)|endoplasmic reticulum membrane (GO:0005789)|endosome lumen (GO:0031904)|endosome membrane (GO:0010008)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|intermediate-density lipoprotein particle (GO:0034363)|intracellular membrane-bounded organelle (GO:0043231)|low-density lipoprotein particle (GO:0034362)|mature chylomicron (GO:0034359)|plasma membrane (GO:0005886)|very-low-density lipoprotein particle (GO:0034361)	cholesterol transporter activity (GO:0017127)|heparin binding (GO:0008201)|lipase binding (GO:0035473)|low-density lipoprotein particle receptor binding (GO:0050750)|phospholipid binding (GO:0005543)			NS(5)|autonomic_ganglia(1)|breast(6)|central_nervous_system(4)|cervix(3)|endometrium(19)|kidney(10)|large_intestine(63)|liver(5)|lung(125)|ovary(16)|pancreas(1)|prostate(5)|skin(31)|stomach(1)|upper_aerodigestive_tract(4)|urinary_tract(6)	305	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)					TATTTTTCGTGGTTAAGCTCA	0.393																																					p.T3417T		Atlas-SNP	.											.	APOB	761	.	0			c.C10251A						.						175.0	173.0	174.0					2																	21229489		2203	4300	6503	SO:0001819	synonymous_variant	338	exon26			TTTCGTGGTTAAG	M14162	CCDS1703.1	2p24-p23	2013-05-29	2013-05-29		ENSG00000084674	ENSG00000084674		"""Apolipoproteins"""	603	protein-coding gene	gene with protein product		107730	"""apolipoprotein B (including Ag(x) antigen)"""				Standard	NM_000384		Approved		uc002red.3	P04114	OTTHUMG00000090785	ENST00000233242.1:c.10251C>A	chr2.hg19:g.21229489G>T		61.0	0.0		58.0	14.0	NM_000384	O00502|P78479|P78480|P78481|Q13779|Q13785|Q13786|Q13787|Q13788|Q4ZG63|Q53QC8|Q7Z600|Q9UMN0	Silent	SNP	ENST00000233242.1	hg19	CCDS1703.1																																																																																			.	.		0.393	APOB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207571.1		
CNGA3	1261	hgsc.bcm.edu	37	2	99012595	99012595	+	Missense_Mutation	SNP	A	A	G			TCGA-KR-A7K2-01A-12D-A33Q-10	TCGA-KR-A7K2-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cbf5cf66-d096-4a67-b0a1-7f985b2dcd42	6b5190db-85e5-485f-8174-2c1727487ef2	g.chr2:99012595A>G	ENST00000272602.2	+	7	1001	c.962A>G	c.(961-963)tAc>tGc	p.Y321C	CNGA3_ENST00000409937.1_Missense_Mutation_p.Y325C|CNGA3_ENST00000393504.1_Missense_Mutation_p.Y321C|CNGA3_ENST00000436404.2_Missense_Mutation_p.Y303C			Q16281	CNGA3_HUMAN	cyclic nucleotide gated channel alpha 3	321					cation transport (GO:0006812)|phototransduction, visible light (GO:0007603)|potassium ion transmembrane transport (GO:0071805)|regulation of membrane potential (GO:0042391)|response to cAMP (GO:0051591)|response to corticosteroid (GO:0031960)|response to magnesium ion (GO:0032026)|retinal cone cell development (GO:0046549)|signal transduction (GO:0007165)|transport (GO:0006810)|visual perception (GO:0007601)	cytoplasm (GO:0005737)|dendrite (GO:0030425)|integral component of plasma membrane (GO:0005887)|perikaryon (GO:0043204)|photoreceptor outer segment membrane (GO:0042622)|transmembrane transporter complex (GO:1902495)	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(1)|central_nervous_system(1)|endometrium(4)|kidney(1)|large_intestine(10)|lung(17)|ovary(5)|prostate(3)|skin(4)|upper_aerodigestive_tract(3)	49						GCCTGCATCTACTTTGCCATT	0.473																																					p.Y321C		Atlas-SNP	.											.	CNGA3	118	.	0			c.A962G						.						111.0	113.0	112.0					2																	99012595		2203	4300	6503	SO:0001583	missense	1261	exon8			GCATCTACTTTGC	S76069	CCDS2034.1, CCDS42719.1	2q11.2	2013-01-08			ENSG00000144191	ENSG00000144191		"""Voltage-gated ion channels / Cyclic nucleotide-regulated channels"""	2150	protein-coding gene	gene with protein product		600053		CNCG3, ACHM2		7532814, 9517456, 16382102	Standard	NM_001298		Approved	CCNC1, CCNCa, CNG3	uc002syt.3	Q16281	OTTHUMG00000130561	ENST00000272602.2:c.962A>G	chr2.hg19:g.99012595A>G	ENSP00000272602:p.Tyr321Cys	105.0	0.0		82.0	50.0	NM_001298	E9PF93|Q4VAP7|Q53RD2|Q6ZNA7|Q9UP64	Missense_Mutation	SNP	ENST00000272602.2	hg19	CCDS2034.1	.	.	.	.	.	.	.	.	.	.	A	13.45	2.240853	0.39598	.	.	ENSG00000144191	ENST00000393504;ENST00000436404;ENST00000272602;ENST00000409937	D;D;D;D	0.98777	-5.13;-5.13;-5.13;-5.13	4.99	4.99	0.66335	Ion transport (1);	0.116998	0.64402	D	0.000013	D	0.99312	0.9759	H	0.95850	3.73	0.53005	D	0.999966	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.87578	0.994;0.992;0.998	D	0.99215	1.0877	10	0.87932	D	0	.	9.6218	0.39725	0.8435:0.0:0.0:0.1565	.	325;303;321	E9PF93;Q4VAP7;Q16281	.;.;CNGA3_HUMAN	C	321;303;321;325	ENSP00000377140:Y321C;ENSP00000410070:Y303C;ENSP00000272602:Y321C;ENSP00000386761:Y325C	ENSP00000272602:Y321C	Y	+	2	0	CNGA3	98379027	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	3.464000	0.53057	2.098000	0.63641	0.460000	0.39030	TAC	.	.		0.473	CNGA3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000252986.1	NM_001298	
XIRP2	129446	hgsc.bcm.edu	37	2	168108386	168108386	+	Missense_Mutation	SNP	G	G	T			TCGA-KR-A7K2-01A-12D-A33Q-10	TCGA-KR-A7K2-10A-01D-A33Q-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cbf5cf66-d096-4a67-b0a1-7f985b2dcd42	6b5190db-85e5-485f-8174-2c1727487ef2	g.chr2:168108386G>T	ENST00000409195.1	+	9	10573	c.10484G>T	c.(10483-10485)gGa>gTa	p.G3495V	XIRP2_ENST00000420519.1_Intron|XIRP2_ENST00000409605.1_Intron|XIRP2_ENST00000295237.9_Missense_Mutation_p.G3495V|XIRP2_ENST00000409043.1_Intron|XIRP2_ENST00000409756.2_Intron|XIRP2_ENST00000409728.1_Intron|XIRP2_ENST00000409273.1_Missense_Mutation_p.G3273V	NM_152381.5	NP_689594.4	A4UGR9	XIRP2_HUMAN	xin actin-binding repeat containing 2	3320					actin cytoskeleton organization (GO:0030036)|cardiac muscle tissue morphogenesis (GO:0055008)|cell-cell junction organization (GO:0045216)|ventricular septum development (GO:0003281)	cell junction (GO:0030054)|Z disc (GO:0030018)				NS(3)|biliary_tract(2)|breast(5)|cervix(3)|endometrium(16)|haematopoietic_and_lymphoid_tissue(2)|kidney(18)|large_intestine(51)|lung(160)|ovary(7)|pancreas(3)|prostate(11)|skin(14)|stomach(5)|upper_aerodigestive_tract(8)|urinary_tract(7)	315						AAAGGCCTGGGATATGCAACC	0.383																																					p.G3495V		Atlas-SNP	.											.	XIRP2	914	.	0			c.G10484T						.						65.0	64.0	64.0					2																	168108386		1856	4083	5939	SO:0001583	missense	129446	exon9			GCCTGGGATATGC	AK056582	CCDS42768.1, CCDS42769.1, CCDS56143.1, CCDS56144.1, CCDS56145.1	2q31.1	2013-10-25	2007-06-27	2007-06-27	ENSG00000163092	ENSG00000163092			14303	protein-coding gene	gene with protein product	"""myomaxin"""	609778	"""cardiomyopathy associated 3"""	CMYA3		17046827, 12203715, 15454575	Standard	NM_001079810		Approved		uc002udx.3	A4UGR9	OTTHUMG00000154027	ENST00000409195.1:c.10484G>T	chr2.hg19:g.168108386G>T	ENSP00000386840:p.Gly3495Val	76.0	0.0		52.0	15.0	NM_152381	A0PJ94|B2BBS0|B2BBS1|B2BBS4|B3KVH0|J3KNB1|Q53R52|Q5MJ67|Q702N7|Q86T36|Q86T38|Q86T46|Q86T51|Q86T53|Q86T55|Q86T79|Q86TB6|Q8N1M9|Q8N3R5|Q8TBV6	Missense_Mutation	SNP	ENST00000409195.1	hg19	CCDS42769.1	.	.	.	.	.	.	.	.	.	.	G	12.52	1.961144	0.34565	.	.	ENSG00000163092	ENST00000409195;ENST00000295237;ENST00000409273;ENST00000413534	T;T;T	0.22743	2.01;2.01;1.94	5.94	5.07	0.68467	.	0.054870	0.64402	D	0.000001	T	0.46964	0.1420	M	0.74258	2.255	0.80722	D	1	D;D;D	0.89917	1.0;1.0;0.999	D;D;D	0.97110	0.999;1.0;0.985	T	0.50808	-0.8784	10	0.87932	D	0	-16.2881	14.0553	0.64764	0.073:0.0:0.927:0.0	.	3320;3320;3273	A4UGR9;A4UGR9-3;A4UGR9-2	XIRP2_HUMAN;.;.	V	3495;3495;3273;909	ENSP00000386840:G3495V;ENSP00000295237:G3495V;ENSP00000387255:G3273V	ENSP00000295237:G3495V	G	+	2	0	XIRP2	167816632	1.000000	0.71417	0.528000	0.27938	0.067000	0.16453	7.888000	0.87302	1.535000	0.49220	-0.142000	0.14014	GGA	.	.		0.383	XIRP2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000333547.1	NM_152381	
ABCB11	8647	hgsc.bcm.edu	37	2	169847362	169847362	+	Missense_Mutation	SNP	G	G	A			TCGA-KR-A7K2-01A-12D-A33Q-10	TCGA-KR-A7K2-10A-01D-A33Q-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cbf5cf66-d096-4a67-b0a1-7f985b2dcd42	6b5190db-85e5-485f-8174-2c1727487ef2	g.chr2:169847362G>A	ENST00000263817.6	-	9	981	c.857C>T	c.(856-858)tCa>tTa	p.S286L		NM_003742.2	NP_003733.2	O95342	ABCBB_HUMAN	ATP-binding cassette, sub-family B (MDR/TAP), member 11	286	ABC transmembrane type-1 1. {ECO:0000255|PROSITE-ProRule:PRU00441}.				bile acid and bile salt transport (GO:0015721)|bile acid biosynthetic process (GO:0006699)|bile acid metabolic process (GO:0008206)|canalicular bile acid transport (GO:0015722)|small molecule metabolic process (GO:0044281)|sodium ion transmembrane transport (GO:0035725)|transmembrane transport (GO:0055085)|transport (GO:0006810)	apical part of cell (GO:0045177)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|intercellular canaliculus (GO:0046581)|membrane (GO:0016020)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|ATPase activity, coupled to transmembrane movement of substances (GO:0042626)|bile acid-exporting ATPase activity (GO:0015432)|canalicular bile acid transmembrane transporter activity (GO:0015126)|sodium-exporting ATPase activity, phosphorylative mechanism (GO:0008554)|transporter activity (GO:0005215)			breast(3)|endometrium(2)|haematopoietic_and_lymphoid_tissue(4)|kidney(2)|large_intestine(16)|lung(26)|ovary(3)|stomach(1)	57					Adenosine triphosphate(DB00171)|Bosentan(DB00559)|Chlorpromazine(DB00477)|Cimetidine(DB00501)|Clofazimine(DB00845)|Cyclosporine(DB00091)|Daunorubicin(DB00694)|Dexamethasone(DB01234)|Digoxin(DB00390)|Doxorubicin(DB00997)|Ethinyl Estradiol(DB00977)|Fluorescein(DB00693)|Fusidic Acid(DB02703)|Glyburide(DB01016)|Ketoconazole(DB01026)|Novobiocin(DB01051)|Paclitaxel(DB01229)|Phenobarbital(DB01174)|Ponatinib(DB08901)|Pravastatin(DB00175)|Progesterone(DB00396)|Quinidine(DB00908)|Reserpine(DB00206)|Rifampicin(DB01045)|Rosuvastatin(DB01098)|Tamoxifen(DB00675)|Ursodeoxycholic acid(DB01586)|Verapamil(DB00661)|Vinblastine(DB00570)|Vincristine(DB00541)	TCTCATTGATGAAATGACTTC	0.393																																					p.S286L		Atlas-SNP	.											.	ABCB11	136	.	0			c.C857T						.						194.0	196.0	195.0					2																	169847362		1910	4121	6031	SO:0001583	missense	8647	exon9			ATTGATGAAATGA	AF091582	CCDS46444.1	2q24	2012-03-14			ENSG00000073734	ENSG00000073734		"""ATP binding cassette transporters / subfamily B"""	42	protein-coding gene	gene with protein product	"""ABC member 16, MDR/TAP subfamily"""	603201	"""progressive familial intrahepatic cholestasis 2"", ""bile salt export pump"""	BSEP, PFIC2		9806540	Standard	NM_003742		Approved	ABC16, SPGP, PFIC-2, PGY4	uc002ueo.1	O95342	OTTHUMG00000154039	ENST00000263817.6:c.857C>T	chr2.hg19:g.169847362G>A	ENSP00000263817:p.Ser286Leu	64.0	0.0		47.0	22.0	NM_003742	Q53TL2|Q9UNB2	Missense_Mutation	SNP	ENST00000263817.6	hg19	CCDS46444.1	.	.	.	.	.	.	.	.	.	.	G	21.2	4.117789	0.77323	.	.	ENSG00000073734	ENST00000263817	D	0.82344	-1.6	5.53	5.53	0.82687	ABC transporter, transmembrane domain, type 1 (1);ABC transporter, integral membrane type 1 (1);ABC transporter, transmembrane domain (1);	0.000000	0.85682	D	0.000000	D	0.88855	0.6550	M	0.87097	2.86	0.80722	D	1	B	0.28350	0.208	B	0.38264	0.269	D	0.87958	0.2728	10	0.72032	D	0.01	1.3303	19.8195	0.96586	0.0:0.0:1.0:0.0	.	286	O95342	ABCBB_HUMAN	L	286	ENSP00000263817:S286L	ENSP00000263817:S286L	S	-	2	0	ABCB11	169555608	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	7.923000	0.87546	2.756000	0.94617	0.655000	0.94253	TCA	.	.		0.393	ABCB11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000333616.2	NM_003742	
VIL1	7429	hgsc.bcm.edu	37	2	219305556	219305556	+	Missense_Mutation	SNP	C	C	T			TCGA-KR-A7K2-01A-12D-A33Q-10	TCGA-KR-A7K2-10A-01D-A33Q-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cbf5cf66-d096-4a67-b0a1-7f985b2dcd42	6b5190db-85e5-485f-8174-2c1727487ef2	g.chr2:219305556C>T	ENST00000248444.5	+	19	2429	c.2341C>T	c.(2341-2343)Ccc>Tcc	p.P781S	VIL1_ENST00000392114.2_Missense_Mutation_p.P470S	NM_007127.2	NP_009058.2	P09327	VILI_HUMAN	villin 1	781	HP. {ECO:0000255|PROSITE- ProRule:PRU00595}.|Headpiece.				actin filament capping (GO:0051693)|actin filament depolymerization (GO:0030042)|actin filament polymerization (GO:0030041)|actin filament severing (GO:0051014)|cellular response to epidermal growth factor stimulus (GO:0071364)|cellular response to hepatocyte growth factor stimulus (GO:0035729)|cytoplasmic actin-based contraction involved in cell motility (GO:0060327)|epidermal growth factor receptor signaling pathway (GO:0007173)|epithelial cell differentiation (GO:0030855)|positive regulation of actin filament bundle assembly (GO:0032233)|positive regulation of cell migration (GO:0030335)|positive regulation of epithelial cell migration (GO:0010634)|protein complex assembly (GO:0006461)|regulation of actin nucleation (GO:0051125)|regulation of cell shape (GO:0008360)|regulation of lamellipodium morphogenesis (GO:2000392)|regulation of wound healing (GO:0061041)|response to bacterium (GO:0009617)	actin filament bundle (GO:0032432)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|filopodium (GO:0030175)|filopodium tip (GO:0032433)|lamellipodium (GO:0030027)|microvillus (GO:0005902)|ruffle (GO:0001726)	actin filament binding (GO:0051015)|calcium ion binding (GO:0005509)|cysteine-type endopeptidase inhibitor activity involved in apoptotic process (GO:0043027)|identical protein binding (GO:0042802)|lysophosphatidic acid binding (GO:0035727)|phosphatidylinositol-4,5-bisphosphate binding (GO:0005546)|protein homodimerization activity (GO:0042803)			NS(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(4)|lung(20)|ovary(2)|prostate(3)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(1)	41		Renal(207;0.0474)		Epithelial(149;6.88e-07)|all cancers(144;0.00013)|LUSC - Lung squamous cell carcinoma(224;0.008)|Lung(261;0.00942)		AGAGGAGCTCCCCGAGGGTGT	0.537																																					p.P781S		Atlas-SNP	.											.	VIL1	65	.	0			c.C2341T						.						47.0	47.0	47.0					2																	219305556		2203	4300	6503	SO:0001583	missense	7429	exon19			GAGCTCCCCGAGG	X12901	CCDS2417.1	2q35	2012-10-02			ENSG00000127831	ENSG00000127831			12690	protein-coding gene	gene with protein product		193040		VIL		2846586	Standard	NM_007127		Approved	D2S1471	uc002via.3	P09327	OTTHUMG00000133112	ENST00000248444.5:c.2341C>T	chr2.hg19:g.219305556C>T	ENSP00000248444:p.Pro781Ser	86.0	0.0		86.0	39.0	NM_007127	B2R9A7|Q53S11|Q96AC8	Missense_Mutation	SNP	ENST00000248444.5	hg19	CCDS2417.1	.	.	.	.	.	.	.	.	.	.	C	21.2	4.105774	0.77096	.	.	ENSG00000127831	ENST00000248444;ENST00000392114	T;T	0.25749	1.78;1.9	5.85	5.85	0.93711	Villin headpiece (3);	0.000000	0.85682	D	0.000000	T	0.44973	0.1319	M	0.91140	3.18	0.80722	D	1	B	0.29162	0.235	B	0.29524	0.103	T	0.52419	-0.8578	10	0.87932	D	0	-12.1305	20.1729	0.98161	0.0:1.0:0.0:0.0	.	781	P09327	VILI_HUMAN	S	781;470	ENSP00000248444:P781S;ENSP00000375962:P470S	ENSP00000248444:P781S	P	+	1	0	VIL1	219013800	1.000000	0.71417	0.998000	0.56505	0.797000	0.45037	7.536000	0.82023	2.775000	0.95449	0.603000	0.83216	CCC	.	.		0.537	VIL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256778.3	NM_007127	
SPHKAP	80309	hgsc.bcm.edu	37	2	228882606	228882606	+	Silent	SNP	G	G	A			TCGA-KR-A7K2-01A-12D-A33Q-10	TCGA-KR-A7K2-10A-01D-A33Q-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cbf5cf66-d096-4a67-b0a1-7f985b2dcd42	6b5190db-85e5-485f-8174-2c1727487ef2	g.chr2:228882606G>A	ENST00000392056.3	-	7	3010	c.2964C>T	c.(2962-2964)agC>agT	p.S988S	SPHKAP_ENST00000344657.5_Silent_p.S988S	NM_001142644.1	NP_001136116.1	Q2M3C7	SPKAP_HUMAN	SPHK1 interactor, AKAP domain containing	988						extracellular vesicular exosome (GO:0070062)|mitochondrion (GO:0005739)|Z disc (GO:0030018)	protein kinase A binding (GO:0051018)	p.S988R(2)		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)		CAGCGGTCCCGCTCCCCTGGC	0.532																																					p.S988S		Atlas-SNP	.											SPHKAP_ENST00000392056,NS,carcinoma,0,2	SPHKAP	750	.	2	Substitution - Missense(2)	lung(2)	c.C2964T						.						74.0	69.0	70.0					2																	228882606		2203	4300	6503	SO:0001819	synonymous_variant	80309	exon7			GGTCCCGCTCCCC		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.2964C>T	chr2.hg19:g.228882606G>A		77.0	0.0		48.0	14.0	NM_030623	Q68DA3|Q68DR8|Q9C0I5	Silent	SNP	ENST00000392056.3	hg19	CCDS46537.1																																																																																			.	.		0.532	SPHKAP-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000331750.1	NM_030623	
MYH15	22989	hgsc.bcm.edu	37	3	108117574	108117574	+	Silent	SNP	C	C	T			TCGA-KR-A7K2-01A-12D-A33Q-10	TCGA-KR-A7K2-10A-01D-A33Q-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cbf5cf66-d096-4a67-b0a1-7f985b2dcd42	6b5190db-85e5-485f-8174-2c1727487ef2	g.chr3:108117574C>T	ENST00000273353.3	-	36	5159	c.5103G>A	c.(5101-5103)agG>agA	p.R1701R		NM_014981.1	NP_055796.1	Q9Y2K3	MYH15_HUMAN	myosin, heavy chain 15	1701						cytoplasm (GO:0005737)|myosin filament (GO:0032982)	ATP binding (GO:0005524)|motor activity (GO:0003774)			NS(1)|breast(3)|central_nervous_system(2)|cervix(4)|endometrium(10)|kidney(4)|large_intestine(14)|lung(47)|ovary(5)|pancreas(2)|prostate(6)|skin(2)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(2)	105						CTTGCAGGGACCTTAGATCCT	0.532																																					p.R1701R		Atlas-SNP	.											.	MYH15	223	.	0			c.G5103A						.						192.0	193.0	193.0					3																	108117574		1998	4187	6185	SO:0001819	synonymous_variant	22989	exon36			CAGGGACCTTAGA	AB023217	CCDS43127.1	3q13	2011-09-27	2006-09-29		ENSG00000144821	ENSG00000144821		"""Myosins / Myosin superfamily : Class II"""	31073	protein-coding gene	gene with protein product		609929	"""myosin, heavy polypeptide 15"""			15014174, 15042088	Standard	NM_014981		Approved	KIAA1000	uc003dxa.1	Q9Y2K3	OTTHUMG00000159226	ENST00000273353.3:c.5103G>A	chr3.hg19:g.108117574C>T		61.0	0.0		43.0	14.0	NM_014981		Silent	SNP	ENST00000273353.3	hg19	CCDS43127.1																																																																																			.	.		0.532	MYH15-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000353935.1	XM_036988	
RUVBL1	8607	hgsc.bcm.edu	37	3	127831762	127831762	+	Silent	SNP	C	C	T			TCGA-KR-A7K2-01A-12D-A33Q-10	TCGA-KR-A7K2-10A-01D-A33Q-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cbf5cf66-d096-4a67-b0a1-7f985b2dcd42	6b5190db-85e5-485f-8174-2c1727487ef2	g.chr3:127831762C>T	ENST00000322623.5	-	3	429	c.330G>A	c.(328-330)gaG>gaA	p.E110E	RUVBL1_ENST00000464873.1_Silent_p.E50E|RUVBL1_ENST00000417360.1_Silent_p.E110E	NM_003707.2	NP_003698.1	Q9Y265	RUVB1_HUMAN	RuvB-like AAA ATPase 1	110					CENP-A containing nucleosome assembly (GO:0034080)|chromatin organization (GO:0006325)|DNA duplex unwinding (GO:0032508)|DNA recombination (GO:0006310)|DNA repair (GO:0006281)|histone H2A acetylation (GO:0043968)|histone H4 acetylation (GO:0043967)|mitotic nuclear division (GO:0007067)|nucleosome assembly (GO:0006334)|regulation of growth (GO:0040008)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|spermatogenesis (GO:0007283)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|Ino80 complex (GO:0031011)|intracellular membrane-bounded organelle (GO:0043231)|membrane (GO:0016020)|MLL1 complex (GO:0071339)|NuA4 histone acetyltransferase complex (GO:0035267)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|Swr1 complex (GO:0000812)	ATP binding (GO:0005524)|DNA helicase activity (GO:0003678)			endometrium(1)|kidney(1)|large_intestine(9)|lung(9)|ovary(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	26				GBM - Glioblastoma multiforme(114;0.181)		CCATCAGCACCTCTGTCTTCT	0.527																																					p.E110E		Atlas-SNP	.											.	RUVBL1	38	.	0			c.G330A						.						161.0	146.0	151.0					3																	127831762		2203	4300	6503	SO:0001819	synonymous_variant	8607	exon3			CAGCACCTCTGTC	AF070735	CCDS3047.1	3q21	2013-09-12	2013-09-12		ENSG00000175792	ENSG00000175792		"""INO80 complex subunits"", ""ATPases / AAA-type"""	10474	protein-coding gene	gene with protein product	"""pontin"", ""INO80 complex subunit H"""	603449	"""RuvB (E coli homolog)-like 1"", ""RuvB-like 1 (E. coli)"", ""RuvB-like AAA ATPase"""			9774387, 9588198	Standard	NM_003707		Approved	TIP49, NMP238, RVB1, TIP49a, Pontin52, ECP54, TIH1, Rvb1, INO80H	uc003ekh.3	Q9Y265	OTTHUMG00000159658	ENST00000322623.5:c.330G>A	chr3.hg19:g.127831762C>T		120.0	0.0		59.0	11.0	NM_003707	B2R5S0|P82276|Q1KMR0|Q53HK5|Q53HL7|Q53Y27|Q9BSX9	Silent	SNP	ENST00000322623.5	hg19	CCDS3047.1																																																																																			.	.		0.527	RUVBL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000356728.2		
GRK7	131890	hgsc.bcm.edu	37	3	141497429	141497429	+	Silent	SNP	C	C	A			TCGA-KR-A7K2-01A-12D-A33Q-10	TCGA-KR-A7K2-10A-01D-A33Q-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cbf5cf66-d096-4a67-b0a1-7f985b2dcd42	6b5190db-85e5-485f-8174-2c1727487ef2	g.chr3:141497429C>A	ENST00000264952.2	+	1	440	c.303C>A	c.(301-303)acC>acA	p.T101T		NM_139209.2	NP_631948.1	Q8WTQ7	GRK7_HUMAN	G protein-coupled receptor kinase 7	101	RGS. {ECO:0000255|PROSITE- ProRule:PRU00171}.				protein autophosphorylation (GO:0046777)|signal transduction (GO:0007165)|termination of G-protein coupled receptor signaling pathway (GO:0038032)|visual perception (GO:0007601)	membrane (GO:0016020)	ATP binding (GO:0005524)|G-protein coupled receptor kinase activity (GO:0004703)|rhodopsin kinase activity (GO:0050254)			endometrium(2)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(3)|lung(14)|ovary(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)	26						AGGGACCCACCAAAGACAGCG	0.672																																					p.T101T		Atlas-SNP	.											.	GRK7	65	.	0			c.C303A						.						25.0	27.0	26.0					3																	141497429		2201	4298	6499	SO:0001819	synonymous_variant	131890	exon1			ACCCACCAAAGAC		CCDS3120.1	3q24	2004-02-04	2004-02-04	2004-02-04	ENSG00000114124	ENSG00000114124			17031	protein-coding gene	gene with protein product		606987		GPRK7		11717351, 11754336	Standard	NM_139209		Approved		uc011bnd.2	Q8WTQ7	OTTHUMG00000159068	ENST00000264952.2:c.303C>A	chr3.hg19:g.141497429C>A		94.0	0.0		68.0	20.0	NM_139209		Silent	SNP	ENST00000264952.2	hg19	CCDS3120.1																																																																																			.	.		0.672	GRK7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000353168.1	NM_139209	
GPR149	344758	hgsc.bcm.edu	37	3	154055628	154055628	+	Missense_Mutation	SNP	T	T	C			TCGA-KR-A7K2-01A-12D-A33Q-10	TCGA-KR-A7K2-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cbf5cf66-d096-4a67-b0a1-7f985b2dcd42	6b5190db-85e5-485f-8174-2c1727487ef2	g.chr3:154055628T>C	ENST00000389740.2	-	4	2155	c.2056A>G	c.(2056-2058)Aat>Gat	p.N686D		NM_001038705.1	NP_001033794.1	Q86SP6	GP149_HUMAN	G protein-coupled receptor 149	686					antral ovarian follicle growth (GO:0001547)|estrous cycle phase (GO:0060206)|negative regulation of ovulation (GO:0060280)|preantral ovarian follicle growth (GO:0001546)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)			autonomic_ganglia(1)|breast(1)|endometrium(4)|kidney(2)|large_intestine(6)|lung(22)|ovary(7)|prostate(1)|skin(1)|urinary_tract(2)	47			LUSC - Lung squamous cell carcinoma(72;0.114)|Lung(72;0.173)			ATGGAGATATTAATATCACCA	0.433																																					p.N686D		Atlas-SNP	.											.	GPR149	134	.	0			c.A2056G						.						260.0	239.0	246.0					3																	154055628		1914	4140	6054	SO:0001583	missense	344758	exon4			AGATATTAATATC	AY255534	CCDS43162.1	3q25.2	2012-08-21			ENSG00000174948	ENSG00000174948		"""GPCR / Class A : Orphans"""	23627	protein-coding gene	gene with protein product						12679517	Standard	NM_001038705		Approved	PGR10, IEDA	uc003faa.3	Q86SP6	OTTHUMG00000159131	ENST00000389740.2:c.2056A>G	chr3.hg19:g.154055628T>C	ENSP00000374390:p.Asn686Asp	91.0	0.0		113.0	60.0	NM_001038705		Missense_Mutation	SNP	ENST00000389740.2	hg19	CCDS43162.1	.	.	.	.	.	.	.	.	.	.	T	23.2	4.391436	0.83011	.	.	ENSG00000174948	ENST00000389740	.	.	.	5.8	5.8	0.92144	.	0.000000	0.85682	D	0.000000	T	0.61999	0.2392	N	0.24115	0.695	0.53688	D	0.999975	D	0.67145	0.996	P	0.60541	0.876	T	0.67090	-0.5758	9	0.87932	D	0	-21.6473	16.1538	0.81644	0.0:0.0:0.0:1.0	.	686	Q86SP6	GP149_HUMAN	D	686	.	ENSP00000374390:N686D	N	-	1	0	GPR149	155538322	1.000000	0.71417	0.985000	0.45067	0.656000	0.38851	7.706000	0.84615	2.213000	0.71641	0.528000	0.53228	AAT	.	.		0.433	GPR149-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000353430.1	XM_293580	
PDS5A	23244	hgsc.bcm.edu	37	4	39905761	39905761	+	Silent	SNP	T	T	C			TCGA-KR-A7K2-01A-12D-A33Q-10	TCGA-KR-A7K2-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cbf5cf66-d096-4a67-b0a1-7f985b2dcd42	6b5190db-85e5-485f-8174-2c1727487ef2	g.chr4:39905761T>C	ENST00000303538.8	-	12	1823	c.1284A>G	c.(1282-1284)aaA>aaG	p.K428K	PDS5A_ENST00000503396.1_Silent_p.K428K	NM_001100399.1	NP_001093869.1			PDS5, regulator of cohesion maintenance, homolog A (S. cerevisiae)											breast(2)|cervix(1)|endometrium(4)|kidney(4)|large_intestine(9)|lung(14)|prostate(3)|skin(1)|urinary_tract(1)	39						GAAGACAGTATTTCTTATAAA	0.373																																					p.K428K		Atlas-SNP	.											.	PDS5A	114	.	0			c.A1284G						.						71.0	62.0	65.0					4																	39905761		1858	4113	5971	SO:0001819	synonymous_variant	23244	exon12			ACAGTATTTCTTA	AF294791	CCDS47045.1, CCDS54759.1	4p14	2007-06-20			ENSG00000121892	ENSG00000121892			29088	protein-coding gene	gene with protein product		613200				11076961, 15855230	Standard	NM_001100399		Approved	KIAA0648, PIG54, SCC-112	uc003guv.4	Q29RF7	OTTHUMG00000160582	ENST00000303538.8:c.1284A>G	chr4.hg19:g.39905761T>C		48.0	0.0		56.0	32.0	NM_001100399		Silent	SNP	ENST00000303538.8	hg19	CCDS47045.1	.	.	.	.	.	.	.	.	.	.	T	9.138	1.013147	0.19277	.	.	ENSG00000121892	ENST00000513798	.	.	.	5.04	2.55	0.30701	.	.	.	.	.	T	0.57740	0.2074	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.50171	-0.8859	4	.	.	.	-16.4527	8.6341	0.33936	0.0:0.2974:0.0:0.7026	.	.	.	.	S	66	.	.	N	-	2	0	PDS5A	39582156	0.246000	0.23909	1.000000	0.80357	0.977000	0.68977	-0.288000	0.08377	0.338000	0.23692	-0.290000	0.09829	AAT	.	.		0.373	PDS5A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000361287.1	NM_015200	
GABRG1	2565	hgsc.bcm.edu	37	4	46066470	46066470	+	Missense_Mutation	SNP	C	C	G			TCGA-KR-A7K2-01A-12D-A33Q-10	TCGA-KR-A7K2-10A-01D-A33Q-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cbf5cf66-d096-4a67-b0a1-7f985b2dcd42	6b5190db-85e5-485f-8174-2c1727487ef2	g.chr4:46066470C>G	ENST00000295452.4	-	5	780	c.613G>C	c.(613-615)Gaa>Caa	p.E205Q		NM_173536.3	NP_775807.2	Q8N1C3	GBRG1_HUMAN	gamma-aminobutyric acid (GABA) A receptor, gamma 1	205					gamma-aminobutyric acid signaling pathway (GO:0007214)|synaptic transmission (GO:0007268)	cell junction (GO:0030054)|chloride channel complex (GO:0034707)|postsynaptic membrane (GO:0045211)|receptor complex (GO:0043235)	chloride channel activity (GO:0005254)|extracellular ligand-gated ion channel activity (GO:0005230)|GABA-A receptor activity (GO:0004890)			breast(2)|central_nervous_system(5)|endometrium(3)|kidney(4)|large_intestine(11)|liver(1)|lung(37)|ovary(2)|prostate(5)|skin(2)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	76				Lung(65;0.106)|LUSC - Lung squamous cell carcinoma(721;0.23)	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)|Ketazolam(DB01587)|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)	CTTGAAAATTCCAGTGGACAG	0.274																																					p.E205Q		Atlas-SNP	.											.	GABRG1	172	.	0			c.G613C						.						65.0	73.0	70.0					4																	46066470		2202	4287	6489	SO:0001583	missense	2565	exon5			AAAATTCCAGTGG	BC031087	CCDS3470.1	4p12	2012-06-22			ENSG00000163285	ENSG00000163285		"""GABA receptors"", ""Ligand-gated ion channels / GABA(A) receptors"""	4086	protein-coding gene	gene with protein product	"""GABA(A) receptor, gamma"""	137166				1321425	Standard	NM_173536		Approved		uc003gxb.3	Q8N1C3	OTTHUMG00000128609	ENST00000295452.4:c.613G>C	chr4.hg19:g.46066470C>G	ENSP00000295452:p.Glu205Gln	344.0	0.0		319.0	90.0	NM_173536	Q5H9T8	Missense_Mutation	SNP	ENST00000295452.4	hg19	CCDS3470.1	.	.	.	.	.	.	.	.	.	.	C	26.2	4.716852	0.89205	.	.	ENSG00000163285	ENST00000295452;ENST00000540030	T	0.79940	-1.32	5.8	5.8	0.92144	Neurotransmitter-gated ion-channel ligand-binding (3);	0.000000	0.85682	D	0.000000	D	0.83459	0.5259	L	0.37561	1.115	0.80722	D	1	D	0.57257	0.979	P	0.62740	0.906	T	0.77640	-0.2512	10	0.13108	T	0.6	.	19.0345	0.92971	0.0:1.0:0.0:0.0	.	205	Q8N1C3	GBRG1_HUMAN	Q	205	ENSP00000295452:E205Q	ENSP00000295452:E205Q	E	-	1	0	GABRG1	45761227	1.000000	0.71417	1.000000	0.80357	0.931000	0.56810	6.012000	0.70767	2.729000	0.93468	0.561000	0.74099	GAA	.	.		0.274	GABRG1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250470.1	NM_173536	
KDR	3791	hgsc.bcm.edu	37	4	55946235	55946235	+	Missense_Mutation	SNP	T	T	C			TCGA-KR-A7K2-01A-12D-A33Q-10	TCGA-KR-A7K2-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cbf5cf66-d096-4a67-b0a1-7f985b2dcd42	6b5190db-85e5-485f-8174-2c1727487ef2	g.chr4:55946235T>C	ENST00000263923.4	-	30	4239	c.3944A>G	c.(3943-3945)gAc>gGc	p.D1315G	RP11-530I17.1_ENST00000511222.1_RNA	NM_002253.2	NP_002244.1	P35968	VGFR2_HUMAN	kinase insert domain receptor (a type III receptor tyrosine kinase)	1315					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)	CACGGTGGTGTCTGTGTCATC	0.537			Mis		"""NSCLC, angiosarcoma"""					TSP Lung(20;0.16)																											p.D1315G		Atlas-SNP	.		Dom	yes		4	4q11-q12	3791	vascular endothelial growth factor receptor 2		E	.	KDR	307	.	0			c.A3944G						.						203.0	190.0	194.0					4																	55946235		2203	4300	6503	SO:0001583	missense	3791	exon30			GTGGTGTCTGTGT	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.3944A>G	chr4.hg19:g.55946235T>C	ENSP00000263923:p.Asp1315Gly	129.0	0.0		91.0	44.0	NM_002253	A2RRS0|B5A925|C5IFA0|O60723|Q14178	Missense_Mutation	SNP	ENST00000263923.4	hg19	CCDS3497.1	.	.	.	.	.	.	.	.	.	.	T	16.49	3.137104	0.56936	.	.	ENSG00000128052	ENST00000263923	T	0.76186	-1.0	5.62	5.62	0.85841	.	0.100113	0.64402	D	0.000002	T	0.73321	0.3572	L	0.31065	0.9	0.80722	D	1	D	0.65815	0.995	P	0.58928	0.848	T	0.68413	-0.5415	10	0.06757	T	0.87	.	15.8235	0.78678	0.0:0.0:0.0:1.0	.	1315	P35968	VGFR2_HUMAN	G	1315	ENSP00000263923:D1315G	ENSP00000263923:D1315G	D	-	2	0	KDR	55640992	1.000000	0.71417	0.982000	0.44146	0.923000	0.55619	7.698000	0.84413	2.149000	0.67028	0.528000	0.53228	GAC	.	.		0.537	KDR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250645.1		
NFKB1	4790	hgsc.bcm.edu	37	4	103518690	103518690	+	Silent	SNP	A	A	G			TCGA-KR-A7K2-01A-12D-A33Q-10	TCGA-KR-A7K2-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cbf5cf66-d096-4a67-b0a1-7f985b2dcd42	6b5190db-85e5-485f-8174-2c1727487ef2	g.chr4:103518690A>G	ENST00000505458.1	+	15	1783	c.1506A>G	c.(1504-1506)ctA>ctG	p.L502L	NFKB1_ENST00000600343.1_Silent_p.L322L|NFKB1_ENST00000394820.4_Silent_p.L502L|NFKB1_ENST00000226574.4_Silent_p.L503L			P19838	NFKB1_HUMAN	nuclear factor of kappa light polypeptide gene enhancer in B-cells 1	502	Interaction with CFLAR.				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)	ACCTCTTTCTAGAGAAGGCTA	0.483																																					p.L503L		Atlas-SNP	.											.	NFKB1	78	.	0			c.A1509G						.						101.0	93.0	96.0					4																	103518690		2203	4300	6503	SO:0001819	synonymous_variant	4790	exon15			CTTTCTAGAGAAG	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.1506A>G	chr4.hg19:g.103518690A>G		33.0	0.0		23.0	8.0	NM_003998	A8K5Y5|B3KVE8|Q68D84|Q86V43|Q8N4X7|Q9NZC0	Silent	SNP	ENST00000505458.1	hg19	CCDS54783.1																																																																																			.	.		0.483	NFKB1-003	KNOWN	alternative_5_UTR|non_canonical_polymorphism|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000363411.1		
CDH18	1016	hgsc.bcm.edu	37	5	19747162	19747162	+	Missense_Mutation	SNP	G	G	T			TCGA-KR-A7K2-01A-12D-A33Q-10	TCGA-KR-A7K2-10A-01D-A33Q-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cbf5cf66-d096-4a67-b0a1-7f985b2dcd42	6b5190db-85e5-485f-8174-2c1727487ef2	g.chr5:19747162G>T	ENST00000507958.1	-	6	1402	c.412C>A	c.(412-414)Cct>Act	p.P138T	CDH18_ENST00000274170.4_Missense_Mutation_p.P138T|CDH18_ENST00000511273.1_Missense_Mutation_p.P138T|CDH18_ENST00000502796.1_Missense_Mutation_p.P138T|CDH18_ENST00000382275.1_Missense_Mutation_p.P138T|CDH18_ENST00000506372.1_Missense_Mutation_p.P138T			Q13634	CAD18_HUMAN	cadherin 18, type 2	138	Cadherin 1. {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)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			breast(2)|endometrium(8)|haematopoietic_and_lymphoid_tissue(4)|kidney(8)|large_intestine(24)|lung(76)|ovary(5)|prostate(4)|skin(6)|upper_aerodigestive_tract(1)	138	Lung NSC(1;0.00734)|all_lung(1;0.0197)					GGCTCAAGAGGTTTGTTTGTA	0.433																																					p.P138T		Atlas-SNP	.											.	CDH18	561	.	0			c.C412A						.						228.0	206.0	213.0					5																	19747162		2203	4300	6503	SO:0001583	missense	1016	exon4			CAAGAGGTTTGTT	U59325	CCDS3889.1, CCDS54835.1, CCDS75229.1	5p14.3	2010-01-26			ENSG00000145526	ENSG00000145526		"""Cadherins / Major cadherins"""	1757	protein-coding gene	gene with protein product		603019				9030594, 10191097	Standard	NM_004934		Approved	CDH14, EY-CADHERIN	uc003jgd.3	Q13634	OTTHUMG00000090578	ENST00000507958.1:c.412C>A	chr5.hg19:g.19747162G>T	ENSP00000425093:p.Pro138Thr	105.0	0.0		106.0	54.0	NM_001167667	A8K0I2|B4DHG6|Q8N5Z2	Missense_Mutation	SNP	ENST00000507958.1	hg19	CCDS3889.1	.	.	.	.	.	.	.	.	.	.	G	16.69	3.194529	0.58017	.	.	ENSG00000145526	ENST00000382275;ENST00000507958;ENST00000542864;ENST00000274170;ENST00000506372;ENST00000502796;ENST00000515257;ENST00000511273	T;T;T;T;T;T;T	0.56275	0.47;0.47;0.47;0.47;0.47;0.47;0.47	5.04	5.04	0.67666	Cadherin (4);Cadherin-like (1);	0.058569	0.64402	D	0.000001	T	0.70002	0.3174	M	0.79343	2.45	0.53005	D	0.999961	P;D	0.52996	0.812;0.957	P;P	0.58820	0.773;0.846	T	0.72384	-0.4310	9	.	.	.	.	16.957	0.86262	0.0:0.0:1.0:0.0	.	138;138	B4DHG6;Q13634	.;CAD18_HUMAN	T	138;138;138;138;138;138;84;138	ENSP00000371710:P138T;ENSP00000425093:P138T;ENSP00000274170:P138T;ENSP00000424931:P138T;ENSP00000422138:P138T;ENSP00000427383:P84T;ENSP00000425854:P138T	.	P	-	1	0	CDH18	19782919	1.000000	0.71417	0.997000	0.53966	0.624000	0.37722	3.924000	0.56476	2.338000	0.79540	0.591000	0.81541	CCT	.	.		0.433	CDH18-005	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000366747.1	NM_004934	
FBN2	2201	hgsc.bcm.edu	37	5	127744387	127744387	+	Missense_Mutation	SNP	G	G	A			TCGA-KR-A7K2-01A-12D-A33Q-10	TCGA-KR-A7K2-10A-01D-A33Q-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cbf5cf66-d096-4a67-b0a1-7f985b2dcd42	6b5190db-85e5-485f-8174-2c1727487ef2	g.chr5:127744387G>A	ENST00000508053.1	-	14	2032	c.1058C>T	c.(1057-1059)aCa>aTa	p.T353I	FBN2_ENST00000262464.4_Missense_Mutation_p.T353I|FBN2_ENST00000508989.1_Missense_Mutation_p.T320I			P35556	FBN2_HUMAN	fibrillin 2	353	EGF-like 5; calcium-binding. {ECO:0000255|PROSITE-ProRule:PRU00076}.				anatomical structure morphogenesis (GO:0009653)|bone trabecula formation (GO:0060346)|embryonic limb morphogenesis (GO:0030326)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|positive regulation of bone mineralization (GO:0030501)|positive regulation of osteoblast differentiation (GO:0045669)|sequestering of TGFbeta in extracellular matrix (GO:0035583)	extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|microfibril (GO:0001527)|proteinaceous extracellular matrix (GO:0005578)	calcium ion binding (GO:0005509)|extracellular matrix structural constituent (GO:0005201)			NS(1)|autonomic_ganglia(1)|biliary_tract(1)|breast(1)|endometrium(15)|haematopoietic_and_lymphoid_tissue(4)|kidney(13)|large_intestine(37)|liver(1)|lung(89)|ovary(9)|pancreas(2)|prostate(6)|skin(10)|stomach(1)|upper_aerodigestive_tract(5)|urinary_tract(1)	197		all_cancers(142;0.0216)|Prostate(80;0.0551)	KIRC - Kidney renal clear cell carcinoma(527;0.0268)|Kidney(363;0.0488)	OV - Ovarian serous cystadenocarcinoma(64;0.0821)|Epithelial(69;0.146)		AGAGCCATCTGTTGAGGTTAC	0.448																																					p.T353I		Atlas-SNP	.											.	FBN2	858	.	0			c.C1058T						.						137.0	118.0	124.0					5																	127744387		2203	4300	6503	SO:0001583	missense	2201	exon8			CCATCTGTTGAGG	U03272	CCDS34222.1	5q23-q31	2008-08-01	2008-08-01			ENSG00000138829			3604	protein-coding gene	gene with protein product	"""fibrillin 5"""	612570	"""congenital contractural arachnodactyly"""	CCA		1852206, 8120105	Standard	NM_001999		Approved	DA9	uc003kuu.3	P35556		ENST00000508053.1:c.1058C>T	chr5.hg19:g.127744387G>A	ENSP00000424571:p.Thr353Ile	221.0	0.0		271.0	107.0	NM_001999	B4DU01|Q59ES6	Missense_Mutation	SNP	ENST00000508053.1	hg19	CCDS34222.1	.	.	.	.	.	.	.	.	.	.	G	13.27	2.188296	0.38609	.	.	ENSG00000138829	ENST00000262464;ENST00000508053;ENST00000508989	D;D;D	0.92446	-2.24;-2.24;-3.04	4.89	4.89	0.63831	EGF-like region, conserved site (1);EGF-like calcium-binding (2);Epidermal growth factor-like, type 3 (1);	0.142496	0.46758	D	0.000262	D	0.84942	0.5584	N	0.16478	0.41	0.36875	D	0.889126	B;B	0.26744	0.158;0.158	B;B	0.25405	0.06;0.041	D	0.84128	0.0410	10	0.35671	T	0.21	.	14.1899	0.65633	0.0:0.1504:0.8496:0.0	.	320;353	D6RJI3;P35556	.;FBN2_HUMAN	I	353;353;320	ENSP00000262464:T353I;ENSP00000424571:T353I;ENSP00000425596:T320I	ENSP00000262464:T353I	T	-	2	0	FBN2	127772286	0.983000	0.35010	1.000000	0.80357	0.610000	0.37248	3.218000	0.51192	2.647000	0.89833	0.555000	0.69702	ACA	.	.		0.448	FBN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000371618.2	NM_001999	
RREB1	6239	hgsc.bcm.edu	37	6	7231437	7231437	+	Silent	SNP	C	C	A			TCGA-KR-A7K2-01A-12D-A33Q-10	TCGA-KR-A7K2-10A-01D-A33Q-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cbf5cf66-d096-4a67-b0a1-7f985b2dcd42	6b5190db-85e5-485f-8174-2c1727487ef2	g.chr6:7231437C>A	ENST00000349384.6	+	10	3419	c.3105C>A	c.(3103-3105)ctC>ctA	p.L1035L	RREB1_ENST00000379938.2_Silent_p.L1035L|RREB1_ENST00000334984.6_Silent_p.L1035L|RREB1_ENST00000379933.3_Silent_p.L1035L	NM_001003698.3	NP_001003698.1	Q92766	RREB1_HUMAN	ras responsive element binding protein 1	1035	Pro-rich.				multicellular organismal development (GO:0007275)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of transcription, DNA-templated (GO:0045893)|Ras protein signal transduction (GO:0007265)|regulation of transcription, DNA-templated (GO:0006355)|transcription from RNA polymerase II promoter (GO:0006366)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|nuclear body (GO:0016604)|nucleolus (GO:0005730)|nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(3)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(5)|lung(18)|ovary(5)|pancreas(2)|prostate(3)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	58	Ovarian(93;0.0398)	all_hematologic(90;0.0384)|Prostate(151;0.191)				GCTCAGCCCTCCTGAGTGGCA	0.672																																					p.L1035L		Atlas-SNP	.											.	RREB1	242	.	0			c.C3105A						.						30.0	35.0	33.0					6																	7231437		2203	4296	6499	SO:0001819	synonymous_variant	6239	exon10			AGCCCTCCTGAGT	U26914	CCDS34335.1, CCDS34336.1, CCDS54963.1	6p25	2013-01-08			ENSG00000124782	ENSG00000124782		"""Zinc fingers, C2H2-type"""	10449	protein-coding gene	gene with protein product	"""hindsight homolog (drosophila)"""	602209				9367691, 18394891	Standard	NM_001003698		Approved	HNT	uc003mxb.3	Q92766	OTTHUMG00000014201	ENST00000349384.6:c.3105C>A	chr6.hg19:g.7231437C>A		41.0	0.0		47.0	12.0	NM_001003700	A2RRF5|E2GM80|E2GM81|O75567|O75568|Q5VYB2|Q6BEP5|Q6BEP6|Q6BEP8|Q86SU2|Q9Y474	Silent	SNP	ENST00000349384.6	hg19	CCDS34336.1																																																																																			.	.		0.672	RREB1-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000352985.1		
NOTCH4	4855	hgsc.bcm.edu	37	6	32163286	32163286	+	Silent	SNP	T	T	C			TCGA-KR-A7K2-01A-12D-A33Q-10	TCGA-KR-A7K2-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cbf5cf66-d096-4a67-b0a1-7f985b2dcd42	6b5190db-85e5-485f-8174-2c1727487ef2	g.chr6:32163286T>C	ENST00000375023.3	-	30	6078	c.5940A>G	c.(5938-5940)tcA>tcG	p.S1980S	GPSM3_ENST00000487761.1_5'Flank|GPSM3_ENST00000375043.3_5'UTR|GPSM3_ENST00000375040.3_5'Flank	NM_004557.3	NP_004548.3	Q99466	NOTC4_HUMAN	notch 4	1980					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						CAAGTTGAGGTGATCCCCGCT	0.552																																					p.S1980S		Atlas-SNP	.											.	NOTCH4	201	.	0			c.A5940G						.						95.0	112.0	106.0					6																	32163286		1509	2708	4217	SO:0001819	synonymous_variant	4855	exon30			TTGAGGTGATCCC		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.5940A>G	chr6.hg19:g.32163286T>C		84.0	0.0		61.0	7.0	NM_004557	B0V183|B0V1X5|O00306|Q5SSY7|Q99458|Q99940|Q9H3S8|Q9UII9|Q9UIJ0	Silent	SNP	ENST00000375023.3	hg19	CCDS34420.1																																																																																			.	.		0.552	NOTCH4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076045.2		
FIG4	9896	hgsc.bcm.edu	37	6	110098138	110098138	+	Silent	SNP	A	A	G			TCGA-KR-A7K2-01A-12D-A33Q-10	TCGA-KR-A7K2-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cbf5cf66-d096-4a67-b0a1-7f985b2dcd42	6b5190db-85e5-485f-8174-2c1727487ef2	g.chr6:110098138A>G	ENST00000230124.3	+	16	1888	c.1764A>G	c.(1762-1764)caA>caG	p.Q588Q	FIG4_ENST00000441478.2_Silent_p.Q311Q	NM_014845.5	NP_055660.1	Q92562	FIG4_HUMAN	FIG4 phosphoinositide 5-phosphatase	588					cell death (GO:0008219)|locomotory behavior (GO:0007626)|myelin assembly (GO:0032288)|negative regulation of myelination (GO:0031642)|neuron development (GO:0048666)|phosphatidylinositol biosynthetic process (GO:0006661)|phosphatidylinositol-3-phosphate biosynthetic process (GO:0036092)|phospholipid metabolic process (GO:0006644)|pigmentation (GO:0043473)|positive regulation of neuron projection development (GO:0010976)|small molecule metabolic process (GO:0044281)|vacuole organization (GO:0007033)	early endosome membrane (GO:0031901)|endosome membrane (GO:0010008)|Golgi membrane (GO:0000139)|late endosome membrane (GO:0031902)	phosphatidylinositol-3,5-bisphosphate 5-phosphatase activity (GO:0043813)|phosphatidylinositol-3-phosphatase activity (GO:0004438)|phosphatidylinositol-4-phosphate phosphatase activity (GO:0043812)			central_nervous_system(2)|cervix(1)|endometrium(4)|kidney(4)|large_intestine(3)|lung(14)|ovary(2)|prostate(2)	32		all_cancers(87;8.63e-07)|Acute lymphoblastic leukemia(125;2.66e-08)|all_hematologic(75;1.13e-06)|all_epithelial(87;0.000124)|all_lung(197;0.0187)|Colorectal(196;0.0492)|Lung SC(18;0.0548)		OV - Ovarian serous cystadenocarcinoma(136;0.0355)|Epithelial(106;0.038)|all cancers(137;0.0425)|BRCA - Breast invasive adenocarcinoma(108;0.079)		CCGATAGACAAGATTCCATTA	0.358																																					p.Q588Q		Atlas-SNP	.											.	FIG4	77	.	0			c.A1764G						.						57.0	62.0	60.0					6																	110098138		2203	4300	6503	SO:0001819	synonymous_variant	9896	exon16			TAGACAAGATTCC	D87464	CCDS5078.1	6q21	2014-09-17	2014-08-04	2007-07-30	ENSG00000112367	ENSG00000112367			16873	protein-coding gene	gene with protein product		609390	"""KIAA0274"", ""FIG4 homolog (S. cerevisiae)"", ""FIG4 homolog, SAC1 lipid phosphatase domain containing (S. cerevisiae)"""	KIAA0274		9039502, 11274189, 17572665	Standard	NM_014845		Approved	SAC3, hSac3, dJ249I4.1, ALS11, CMT4J	uc003ptt.2	Q92562	OTTHUMG00000015352	ENST00000230124.3:c.1764A>G	chr6.hg19:g.110098138A>G		98.0	0.0		98.0	4.0	NM_014845	Q53H49|Q5TCS6	Silent	SNP	ENST00000230124.3	hg19	CCDS5078.1	.	.	.	.	.	.	.	.	.	.	A	7.368	0.626218	0.14257	.	.	ENSG00000112367	ENST00000415980	.	.	.	5.35	2.95	0.34219	.	.	.	.	.	T	0.45418	0.1341	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.37220	-0.9715	4	.	.	.	-18.0992	9.7067	0.40220	0.8586:0.0:0.1414:0.0	.	.	.	.	G	61	.	.	R	+	1	2	FIG4	110204831	1.000000	0.71417	1.000000	0.80357	0.934000	0.57294	1.263000	0.33004	0.433000	0.26313	0.459000	0.35465	AGA	.	.		0.358	FIG4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041768.1	NM_014845	
ECT2L	345930	hgsc.bcm.edu	37	6	139134461	139134461	+	Missense_Mutation	SNP	A	A	T	rs369742195		TCGA-KR-A7K2-01A-12D-A33Q-10	TCGA-KR-A7K2-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cbf5cf66-d096-4a67-b0a1-7f985b2dcd42	6b5190db-85e5-485f-8174-2c1727487ef2	g.chr6:139134461A>T	ENST00000423192.1	+	2	211	c.50A>T	c.(49-51)aAg>aTg	p.K17M	ECT2L_ENST00000367682.2_Missense_Mutation_p.K17M|ECT2L_ENST00000541398.1_5'Flank			Q008S8	ECT2L_HUMAN	epithelial cell transforming 2 like	17							Rho guanyl-nucleotide exchange factor activity (GO:0005089)			breast(1)|central_nervous_system(1)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(3)|kidney(1)|large_intestine(7)|lung(12)|skin(1)|upper_aerodigestive_tract(1)	30						TTTAGCAACAAGTCATTAAAT	0.388			"""N, Splice, Mis"""		ETP ALL																																p.K17M		Atlas-SNP	.		Rec	yes		6	6q24.1	345930	epithelial cell transforming sequence 2 oncogene-like		L	.	ECT2L	75	.	0			c.A50T						.						78.0	72.0	73.0					6																	139134461		1828	4087	5915	SO:0001583	missense	345930	exon2			GCAACAAGTCATT		CCDS43508.1	6q24.1	2014-03-11	2014-03-11		ENSG00000203734	ENSG00000203734		"""Rho guanine nucleotide exchange factors"", ""F-boxes /  ""other"""""	21118	protein-coding gene	gene with protein product	"""lung specific F-box and DH domain containing protein"", ""F-box protein 49"""		"""chromosome 6 open reading frame 91"", ""epithelial cell transforming sequence 2 oncogene-like"""	C6orf91			Standard	NM_001077706		Approved	ARHGEF32, FBXO49, LFDH	uc021zfx.1	Q008S8	OTTHUMG00000015679	ENST00000423192.1:c.50A>T	chr6.hg19:g.139134461A>T	ENSP00000387388:p.Lys17Met	65.0	0.0		91.0	16.0	NM_001195037	B2RUV6|Q5JWK2|Q5JWK3|Q5JWK4	Missense_Mutation	SNP	ENST00000423192.1	hg19	CCDS43508.1	.	.	.	.	.	.	.	.	.	.	A	12.25	1.880305	0.33162	.	.	ENSG00000203734	ENST00000423192;ENST00000401414;ENST00000367682	T;T;T	0.63096	-0.02;0.76;-0.02	6.08	2.2	0.27929	.	.	.	.	.	T	0.24661	0.0598	N	0.14661	0.345	0.80722	D	1	B	0.23058	0.079	B	0.23716	0.048	T	0.09207	-1.0685	9	0.72032	D	0.01	-1.2885	7.498	0.27500	0.5852:0.2806:0.0:0.1341	.	17	Q008S8	ECT2L_HUMAN	M	17	ENSP00000387388:K17M;ENSP00000385187:K17M;ENSP00000356655:K17M	ENSP00000356655:K17M	K	+	2	0	ECT2L	139176154	0.942000	0.31987	0.971000	0.41717	0.099000	0.18886	0.780000	0.26760	0.137000	0.18759	-1.263000	0.01449	AAG	.	.		0.388	ECT2L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042441.3	NM_001077706	
C6orf120	387263	hgsc.bcm.edu	37	6	170102922	170102922	+	Missense_Mutation	SNP	T	T	A			TCGA-KR-A7K2-01A-12D-A33Q-10	TCGA-KR-A7K2-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cbf5cf66-d096-4a67-b0a1-7f985b2dcd42	6b5190db-85e5-485f-8174-2c1727487ef2	g.chr6:170102922T>A	ENST00000332290.2	+	1	666	c.367T>A	c.(367-369)Tcc>Acc	p.S123T	C6orf120_ENST00000439249.1_Missense_Mutation_p.S142T|WDR27_ENST00000333572.6_5'Flank|WDR27_ENST00000448612.1_5'Flank|WDR27_ENST00000423258.1_5'Flank|WDR27_ENST00000420344.2_5'Flank	NM_001029863.1	NP_001025034.1	Q7Z4R8	CF120_HUMAN	chromosome 6 open reading frame 120	123					apoptotic process (GO:0006915)	extracellular vesicular exosome (GO:0070062)				endometrium(1)|lung(2)	3		Breast(66;0.000338)		OV - Ovarian serous cystadenocarcinoma(33;9.65e-22)|BRCA - Breast invasive adenocarcinoma(81;1.29e-07)|GBM - Glioblastoma multiforme(31;0.0015)		TGGACACCCCTCCCACCTGGA	0.692																																					p.S123T		Atlas-SNP	.											.	C6orf120	5	.	0			c.T367A						.						28.0	29.0	29.0					6																	170102922		2203	4298	6501	SO:0001583	missense	387263	exon1			CACCCCTCCCACC	AF055030	CCDS34575.1	6q27	2012-06-21			ENSG00000185127	ENSG00000185127			21247	protein-coding gene	gene with protein product						8619474, 9110174, 22340178	Standard	NM_001029863		Approved	bA160E12.4	uc003qxb.3	Q7Z4R8	OTTHUMG00000016057	ENST00000332290.2:c.367T>A	chr6.hg19:g.170102922T>A	ENSP00000346931:p.Ser123Thr	44.0	0.0		35.0	14.0	NM_001029863	B4DHE9|E1P5C9	Missense_Mutation	SNP	ENST00000332290.2	hg19	CCDS34575.1	.	.	.	.	.	.	.	.	.	.	T	21.7	4.184594	0.78677	.	.	ENSG00000185127	ENST00000439249;ENST00000332290	.	.	.	5.48	5.48	0.80851	.	0.000000	0.85682	U	0.000000	T	0.76572	0.4006	M	0.85373	2.75	0.58432	D	0.999999	D;D	0.76494	0.999;0.999	D;D	0.70935	0.971;0.971	T	0.81088	-0.1091	9	0.66056	D	0.02	-20.1084	15.0314	0.71710	0.0:0.0:0.0:1.0	.	142;123	B4DJ79;Q7Z4R8	.;CF120_HUMAN	T	142;123	.	ENSP00000346931:S123T	S	+	1	0	C6orf120	169844847	1.000000	0.71417	0.095000	0.20976	0.031000	0.12232	5.941000	0.70195	2.195000	0.70347	0.533000	0.62120	TCC	.	.		0.692	C6orf120-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000043214.1	NM_001029863	
NPC1L1	29881	hgsc.bcm.edu	37	7	44555486	44555486	+	Missense_Mutation	SNP	A	A	T			TCGA-KR-A7K2-01A-12D-A33Q-10	TCGA-KR-A7K2-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cbf5cf66-d096-4a67-b0a1-7f985b2dcd42	6b5190db-85e5-485f-8174-2c1727487ef2	g.chr7:44555486A>T	ENST00000289547.4	-	19	3848	c.3793T>A	c.(3793-3795)Ttc>Atc	p.F1265I	NPC1L1_ENST00000546276.1_Missense_Mutation_p.F1192I|NPC1L1_ENST00000381160.3_Missense_Mutation_p.F1238I	NM_013389.2	NP_037521.2	Q9UHC9	NPCL1_HUMAN	NPC1-like 1	1265					cholesterol biosynthetic process (GO:0006695)|cholesterol transport (GO:0030301)|intestinal cholesterol absorption (GO:0030299)|lipoprotein metabolic process (GO:0042157)|response to drug (GO:0042493)|small molecule metabolic process (GO:0044281)|sterol transport (GO:0015918)	brush border membrane (GO:0031526)|cytoplasmic vesicle (GO:0031410)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	drug binding (GO:0008144)|hedgehog receptor activity (GO:0008158)|myosin V binding (GO:0031489)|Rab GTPase binding (GO:0017137)			breast(1)|central_nervous_system(2)|cervix(1)|endometrium(4)|large_intestine(7)|lung(27)|ovary(6)|prostate(2)|skin(2)|upper_aerodigestive_tract(3)|urinary_tract(2)	57					Ezetimibe(DB00973)	CGGAAGAAGAAGATCTGAATG	0.612																																					p.F1265I		Atlas-SNP	.											.	NPC1L1	141	.	0			c.T3793A						.						70.0	71.0	71.0					7																	44555486		2203	4300	6503	SO:0001583	missense	29881	exon19			AGAAGAAGATCTG		CCDS5491.1, CCDS43575.1, CCDS75587.1	7p13	2012-11-15	2012-11-15		ENSG00000015520	ENSG00000015520			7898	protein-coding gene	gene with protein product		608010	"""NPC1 (Niemann-Pick disease, type C1, gene)-like 1"""			10783261	Standard	NM_013389		Approved		uc003tlb.3	Q9UHC9	OTTHUMG00000023691	ENST00000289547.4:c.3793T>A	chr7.hg19:g.44555486A>T	ENSP00000289547:p.Phe1265Ile	90.0	0.0		75.0	55.0	NM_013389	A4D2J7|B7ZLE6|D3DVK9|Q17RV5|Q6R3Q4|Q9UHC8	Missense_Mutation	SNP	ENST00000289547.4	hg19	CCDS5491.1	.	.	.	.	.	.	.	.	.	.	A	26.1	4.708856	0.89018	.	.	ENSG00000015520	ENST00000289547;ENST00000381160;ENST00000546276	D;D;D	0.94966	-3.57;-3.57;-3.57	5.49	5.49	0.81192	.	0.000000	0.85682	D	0.000000	D	0.97639	0.9226	M	0.91972	3.26	0.51233	D	0.999915	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.91635	0.998;0.998;0.999	D	0.98419	1.0576	10	0.72032	D	0.01	-43.9093	13.5148	0.61535	1.0:0.0:0.0:0.0	.	1192;1238;1265	B7ZLE6;Q17RV5;D3DVK9	.;.;.	I	1265;1238;1192	ENSP00000289547:F1265I;ENSP00000370552:F1238I;ENSP00000438033:F1192I	ENSP00000289547:F1265I	F	-	1	0	NPC1L1	44522011	1.000000	0.71417	1.000000	0.80357	0.809000	0.45718	8.575000	0.90766	2.092000	0.63282	0.459000	0.35465	TTC	.	.		0.612	NPC1L1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000251256.1	NM_013389	
PCLO	27445	hgsc.bcm.edu	37	7	82451998	82451998	+	Missense_Mutation	SNP	C	C	A			TCGA-KR-A7K2-01A-12D-A33Q-10	TCGA-KR-A7K2-10A-01D-A33Q-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cbf5cf66-d096-4a67-b0a1-7f985b2dcd42	6b5190db-85e5-485f-8174-2c1727487ef2	g.chr7:82451998C>A	ENST00000333891.9	-	20	14941	c.14604G>T	c.(14602-14604)caG>caT	p.Q4868H	PCLO_ENST00000426442.2_5'UTR|PCLO_ENST00000423517.2_Missense_Mutation_p.Q4868H	NM_033026.5	NP_149015.2			piccolo presynaptic cytomatrix protein											breast(3)|central_nervous_system(3)|cervix(5)|endometrium(19)|haematopoietic_and_lymphoid_tissue(3)|kidney(19)|large_intestine(35)|lung(145)|ovary(7)|prostate(4)|upper_aerodigestive_tract(14)|urinary_tract(2)	259						TGGTGGGAACCTGCATGTCTG	0.413																																					p.Q4868H		Atlas-SNP	.											.	PCLO	1506	.	0			c.G14604T						.						208.0	203.0	205.0					7																	82451998		1956	4170	6126	SO:0001583	missense	27445	exon20			GGGAACCTGCATG	AB011131	CCDS47630.1, CCDS47631.1	7q11.23-q21.3	2013-01-07	2013-01-07		ENSG00000186472	ENSG00000186472			13406	protein-coding gene	gene with protein product	"""aczonin"""	604918	"""piccolo (presynaptic cytomatrix protein)"""			8900486, 9628581	Standard	NM_014510		Approved	KIAA0559, DKFZp779G1236, ACZ	uc003uhx.2	Q9Y6V0	OTTHUMG00000154853	ENST00000333891.9:c.14604G>T	chr7.hg19:g.82451998C>A	ENSP00000334319:p.Gln4868His	24.0	0.0		32.0	20.0	NM_014510		Missense_Mutation	SNP	ENST00000333891.9	hg19	CCDS47630.1	.	.	.	.	.	.	.	.	.	.	C	13.06	2.123340	0.37436	.	.	ENSG00000186472	ENST00000333891;ENST00000423517;ENST00000380195	T;T	0.18174	2.23;2.24	5.05	5.05	0.67936	.	.	.	.	.	T	0.32823	0.0842	L	0.29908	0.895	0.80722	D	1	D;D;D;D	0.89917	1.0;1.0;0.986;0.996	D;D;P;D	0.91635	0.999;0.999;0.814;0.986	T	0.10337	-1.0634	9	0.87932	D	0	.	18.7616	0.91853	0.0:1.0:0.0:0.0	.	4868;4868;289;356	Q9Y6V0-5;Q9Y6V0-6;Q9Y6V0-3;Q32P40	.;.;.;.	H	4868;4868;355	ENSP00000334319:Q4868H;ENSP00000388393:Q4868H	ENSP00000334319:Q4868H	Q	-	3	2	PCLO	82289934	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	4.304000	0.59104	2.500000	0.84329	0.655000	0.94253	CAG	.	.		0.413	PCLO-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000337368.5	NM_014510	
MDFIC	29969	hgsc.bcm.edu	37	7	114619638	114619638	+	Missense_Mutation	SNP	G	G	C	rs548881845	byFrequency	TCGA-KR-A7K2-01A-12D-A33Q-10	TCGA-KR-A7K2-10A-01D-A33Q-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cbf5cf66-d096-4a67-b0a1-7f985b2dcd42	6b5190db-85e5-485f-8174-2c1727487ef2	g.chr7:114619638G>C	ENST00000393486.1	+	4	885	c.295G>C	c.(295-297)Ggc>Cgc	p.G99R	MDFIC_ENST00000257724.3_Missense_Mutation_p.G208R	NM_001166345.1|NM_199072.4	NP_001159817.1|NP_951038.1			MyoD family inhibitor domain containing											breast(1)|endometrium(1)|kidney(1)|large_intestine(2)|lung(2)|ovary(1)	8						GATAAAGAACGGCCACACAGG	0.473																																					p.G208R		Atlas-SNP	.											.	MDFIC	30	.	0			c.G622C						.						85.0	81.0	83.0					7																	114619638		2203	4300	6503	SO:0001583	missense	29969	exon4			AAGAACGGCCACA	AF054589	CCDS34737.1, CCDS55155.1	7q31.1-q31.2	2006-01-11			ENSG00000135272	ENSG00000135272			28870	protein-coding gene	gene with protein product		614511				10671520	Standard	NM_199072		Approved	HIC	uc003vhf.3	Q9P1T7	OTTHUMG00000023647	ENST00000393486.1:c.295G>C	chr7.hg19:g.114619638G>C	ENSP00000377126:p.Gly99Arg	150.0	0.0		156.0	19.0	NM_199072		Missense_Mutation	SNP	ENST00000393486.1	hg19	CCDS55155.1	.	.	.	.	.	.	.	.	.	.	G	18.09	3.546299	0.65198	.	.	ENSG00000135272	ENST00000257724;ENST00000393486;ENST00000427207;ENST00000498196	.	.	.	5.98	3.14	0.36123	.	0.319263	0.28470	N	0.015223	T	0.67429	0.2892	M	0.77103	2.36	0.80722	D	1	D	0.54397	0.966	P	0.56474	0.799	T	0.67684	-0.5607	9	0.56958	D	0.05	0.0177	8.0155	0.30379	0.1349:0.0:0.7227:0.1424	.	99	Q9P1T7	MDFIC_HUMAN	R	208;99;85;44	.	ENSP00000257724:G208R	G	+	1	0	MDFIC	114406874	0.962000	0.33011	0.742000	0.31022	0.627000	0.37826	1.491000	0.35583	0.793000	0.33875	0.591000	0.81541	GGC	.	.		0.473	MDFIC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000059968.4	NM_199072	
ADAM28	10863	hgsc.bcm.edu	37	8	24157559	24157559	+	Missense_Mutation	SNP	A	A	G			TCGA-KR-A7K2-01A-12D-A33Q-10	TCGA-KR-A7K2-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cbf5cf66-d096-4a67-b0a1-7f985b2dcd42	6b5190db-85e5-485f-8174-2c1727487ef2	g.chr8:24157559A>G	ENST00000265769.4	+	2	229	c.119A>G	c.(118-120)cAt>cGt	p.H40R	ADAM28_ENST00000437154.2_Missense_Mutation_p.H40R|RP11-624C23.1_ENST00000523578.1_RNA|RP11-624C23.1_ENST00000518988.1_RNA|ADAM28_ENST00000540823.1_5'UTR|RP11-624C23.1_ENST00000519689.1_RNA|ADAM28_ENST00000397649.3_5'UTR|RP11-624C23.1_ENST00000523700.1_RNA	NM_014265.4	NP_055080.2	Q9UKQ2	ADA28_HUMAN	ADAM metallopeptidase domain 28	40					spermatogenesis (GO:0007283)	extracellular region (GO:0005576)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	metalloendopeptidase activity (GO:0004222)|metallopeptidase activity (GO:0008237)|zinc ion binding (GO:0008270)			central_nervous_system(1)|endometrium(5)|kidney(2)|large_intestine(10)|lung(7)|prostate(1)|skin(12)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	42		Prostate(55;0.0959)		Colorectal(74;0.0129)|COAD - Colon adenocarcinoma(73;0.0434)|BRCA - Breast invasive adenocarcinoma(99;0.175)		CATCCACTGCATAAAAGAGAG	0.343																																					p.H40R	NSCLC(193;488 2149 22258 34798 40734)	Atlas-SNP	.											.	ADAM28	100	.	0			c.A119G						.						98.0	103.0	101.0					8																	24157559		2203	4300	6503	SO:0001583	missense	10863	exon2			CACTGCATAAAAG	AJ242015	CCDS34865.1, CCDS47830.1	8p21.2	2005-11-29	2005-08-18		ENSG00000042980	ENSG00000042980		"""ADAM metallopeptidase domain containing"""	206	protein-coding gene	gene with protein product		606188	"""a disintegrin and metalloproteinase domain 28"""				Standard	XM_005273378		Approved	eMDCII, MDC-Lm, MDC-Ls, ADAM23	uc003xdy.3	Q9UKQ2	OTTHUMG00000163780	ENST00000265769.4:c.119A>G	chr8.hg19:g.24157559A>G	ENSP00000265769:p.His40Arg	28.0	0.0		23.0	17.0	NM_014265	B2RMV5|Q9Y339|Q9Y3S0	Missense_Mutation	SNP	ENST00000265769.4	hg19	CCDS34865.1	.	.	.	.	.	.	.	.	.	.	A	1.003	-0.690273	0.03303	.	.	ENSG00000042980	ENST00000265769;ENST00000437154	T;T	0.06142	3.34;3.34	4.31	1.8	0.24995	Peptidase M12B, propeptide (1);	.	.	.	.	T	0.03608	0.0103	N	0.13299	0.325	0.21897	N	0.999487	B;B	0.12013	0.001;0.005	B;B	0.15052	0.004;0.012	T	0.47935	-0.9078	9	0.19590	T	0.45	.	6.3711	0.21481	0.7939:0.0:0.2061:0.0	.	40;40	Q9UKQ2;Q9UKQ2-2	ADA28_HUMAN;.	R	40	ENSP00000265769:H40R;ENSP00000393699:H40R	ENSP00000265769:H40R	H	+	2	0	ADAM28	24213504	0.123000	0.22298	0.096000	0.21009	0.066000	0.16364	0.957000	0.29215	0.257000	0.21650	-0.736000	0.03550	CAT	.	.		0.343	ADAM28-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000375441.2	NM_021778	
CHD7	55636	hgsc.bcm.edu	37	8	61654307	61654307	+	Missense_Mutation	SNP	C	C	T			TCGA-KR-A7K2-01A-12D-A33Q-10	TCGA-KR-A7K2-10A-01D-A33Q-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cbf5cf66-d096-4a67-b0a1-7f985b2dcd42	6b5190db-85e5-485f-8174-2c1727487ef2	g.chr8:61654307C>T	ENST00000423902.2	+	2	795	c.316C>T	c.(316-318)Cac>Tac	p.H106Y	CHD7_ENST00000524602.1_Missense_Mutation_p.H106Y|CHD7_ENST00000525508.1_Missense_Mutation_p.H106Y	NM_017780.3	NP_060250.2	Q9P2D1	CHD7_HUMAN	chromodomain helicase DNA binding protein 7	106					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)			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)			CTCGCAGTATCACACCCCTCC	0.547																																					p.H106Y		Atlas-SNP	.											.	CHD7	534	.	0			c.C316T						.						52.0	58.0	56.0					8																	61654307		2161	4250	6411	SO:0001583	missense	55636	exon2			CAGTATCACACCC	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.316C>T	chr8.hg19:g.61654307C>T	ENSP00000392028:p.His106Tyr	82.0	0.0		119.0	29.0	NM_017780	D0VBA5|E9PNZ2|Q05DI5|Q2TAN4|Q66K35|Q7Z6C0|Q7Z7Q2|Q9NXA0|Q9NXA3	Missense_Mutation	SNP	ENST00000423902.2	hg19	CCDS47865.1	.	.	.	.	.	.	.	.	.	.	C	13.59	2.281219	0.40394	.	.	ENSG00000171316	ENST00000307121;ENST00000423902;ENST00000524602;ENST00000525508	T;T;T	0.52526	0.66;0.66;0.66	5.36	5.36	0.76844	.	0.000000	0.42294	D	0.000728	T	0.42404	0.1201	L	0.40543	1.245	0.47698	D	0.999493	D	0.53885	0.963	B	0.41036	0.346	T	0.29150	-1.0021	10	0.30854	T	0.27	-15.0176	19.0882	0.93215	0.0:1.0:0.0:0.0	.	106	Q9P2D1	CHD7_HUMAN	Y	106	ENSP00000392028:H106Y;ENSP00000437061:H106Y;ENSP00000436027:H106Y	ENSP00000307304:H106Y	H	+	1	0	CHD7	61816861	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	4.698000	0.61789	2.531000	0.85337	0.585000	0.79938	CAC	.	.		0.547	CHD7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000383468.2	XM_098762	
VPS13B	157680	hgsc.bcm.edu	37	8	100883103	100883103	+	Missense_Mutation	SNP	T	T	G			TCGA-KR-A7K2-01A-12D-A33Q-10	TCGA-KR-A7K2-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cbf5cf66-d096-4a67-b0a1-7f985b2dcd42	6b5190db-85e5-485f-8174-2c1727487ef2	g.chr8:100883103T>G	ENST00000358544.2	+	60	11669	c.11558T>G	c.(11557-11559)gTc>gGc	p.V3853G	VPS13B_ENST00000357162.2_Missense_Mutation_p.V3828G|VPS13B_ENST00000395996.1_3'UTR	NM_017890.4	NP_060360.3	Q7Z7G8	VP13B_HUMAN	vacuolar protein sorting 13 homolog B (yeast)	3853					protein transport (GO:0015031)					NS(1)|autonomic_ganglia(1)|breast(6)|central_nervous_system(4)|cervix(3)|endometrium(11)|haematopoietic_and_lymphoid_tissue(4)|kidney(10)|large_intestine(37)|lung(78)|ovary(8)|pancreas(3)|prostate(5)|skin(9)|upper_aerodigestive_tract(4)|urinary_tract(9)	193	Breast(36;3.73e-07)		OV - Ovarian serous cystadenocarcinoma(57;0.00636)			AACAGCCATGTCAAATATGTC	0.438																																					p.V3853G	Colon(161;2205 2542 7338 31318)	Atlas-SNP	.											.	VPS13B	811	.	0			c.T11558G						.						77.0	74.0	75.0					8																	100883103		2203	4300	6503	SO:0001583	missense	157680	exon60			GCCATGTCAAATA	AJ608772	CCDS6280.1, CCDS6281.1, CCDS6283.1, CCDS47903.1	8q22-q23	2014-09-17	2006-12-19	2005-04-08	ENSG00000132549	ENSG00000132549			2183	protein-coding gene	gene with protein product		607817	"""Cohen syndrome 1"""	CHS1, COH1		7920642, 15498460	Standard	NM_181661		Approved		uc003yiv.4	Q7Z7G8	OTTHUMG00000140383	ENST00000358544.2:c.11558T>G	chr8.hg19:g.100883103T>G	ENSP00000351346:p.Val3853Gly	176.0	0.0		345.0	73.0	NM_017890	C9JD30|Q709C6|Q709C7|Q7Z7G4|Q7Z7G5|Q7Z7G6|Q7Z7G7|Q8NB77|Q9NWV1|Q9Y4E7	Missense_Mutation	SNP	ENST00000358544.2	hg19	CCDS6280.1	.	.	.	.	.	.	.	.	.	.	T	20.3	3.961594	0.74016	.	.	ENSG00000132549	ENST00000357162;ENST00000358544	T;T	0.70749	-0.51;-0.51	5.73	5.73	0.89815	.	0.067596	0.64402	D	0.000012	T	0.66548	0.2800	L	0.32530	0.975	0.80722	D	1	P;D	0.61080	0.763;0.989	B;P	0.47299	0.387;0.543	T	0.67444	-0.5669	10	0.39692	T	0.17	.	16.0175	0.80455	0.0:0.0:0.0:1.0	.	3828;3853	Q7Z7G8-2;Q7Z7G8	.;VP13B_HUMAN	G	3828;3853	ENSP00000349685:V3828G;ENSP00000351346:V3853G	ENSP00000349685:V3828G	V	+	2	0	VPS13B	100952279	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	5.772000	0.68889	2.184000	0.69523	0.533000	0.62120	GTC	.	.		0.438	VPS13B-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000277138.1	NM_184042	
TMEM71	137835	hgsc.bcm.edu	37	8	133734323	133734323	+	Missense_Mutation	SNP	G	G	C			TCGA-KR-A7K2-01A-12D-A33Q-10	TCGA-KR-A7K2-10A-01D-A33Q-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cbf5cf66-d096-4a67-b0a1-7f985b2dcd42	6b5190db-85e5-485f-8174-2c1727487ef2	g.chr8:133734323G>C	ENST00000356838.3	-	7	800	c.658C>G	c.(658-660)Ctg>Gtg	p.L220V	TMEM71_ENST00000377901.4_Missense_Mutation_p.L176V|TMEM71_ENST00000523829.1_Missense_Mutation_p.L239V	NM_144649.2	NP_653250.2	Q6P5X7	TMM71_HUMAN	transmembrane protein 71	239						integral component of membrane (GO:0016021)				endometrium(2)|kidney(1)|large_intestine(3)|lung(6)|ovary(2)|skin(2)	16	all_neural(3;2.72e-06)|Medulloblastoma(3;7.08e-05)|Ovarian(258;0.00438)|Esophageal squamous(12;0.00507)|Acute lymphoblastic leukemia(118;0.155)		BRCA - Breast invasive adenocarcinoma(115;4.46e-05)			ACAGCAAGCAGGATTGCCTGA	0.348																																					p.L220V		Atlas-SNP	.											.	TMEM71	55	.	0			c.C658G						.						119.0	116.0	117.0					8																	133734323		2203	4300	6503	SO:0001583	missense	137835	exon7			CAAGCAGGATTGC	AK057631	CCDS6366.1, CCDS47921.1	8q24.22	2005-09-02				ENSG00000165071			26572	protein-coding gene	gene with protein product						12477932	Standard	NM_144649		Approved	FLJ33069	uc003ytn.3	Q6P5X7		ENST00000356838.3:c.658C>G	chr8.hg19:g.133734323G>C	ENSP00000349296:p.Leu220Val	415.0	1.0		710.0	308.0	NM_144649	Q3KRC2|Q8WVZ4|Q96LX9	Missense_Mutation	SNP	ENST00000356838.3	hg19	CCDS6366.1	.	.	.	.	.	.	.	.	.	.	G	13.17	2.156402	0.38119	.	.	ENSG00000165071	ENST00000523829;ENST00000356838;ENST00000377901	.	.	.	5.72	1.63	0.23807	.	0.581878	0.15507	N	0.258724	T	0.51770	0.1694	L	0.55481	1.735	0.09310	N	1	D;D;P	0.89917	1.0;1.0;0.946	D;D;B	0.83275	0.996;0.996;0.41	T	0.30679	-0.9970	9	0.87932	D	0	-0.0331	3.7446	0.08542	0.0873:0.3059:0.4493:0.1575	.	239;176;220	Q6P5X7;Q6P5X7-3;Q6P5X7-2	TMM71_HUMAN;.;.	V	239;220;176	.	ENSP00000349296:L220V	L	-	1	2	TMEM71	133803505	0.171000	0.23029	0.053000	0.19242	0.729000	0.41735	0.530000	0.23036	0.840000	0.34995	0.650000	0.86243	CTG	.	.		0.348	TMEM71-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000379591.1	NM_144649	
PSCA	8000	hgsc.bcm.edu	37	8	143763524	143763524	+	Silent	SNP	C	C	T			TCGA-KR-A7K2-01A-12D-A33Q-10	TCGA-KR-A7K2-10A-01D-A33Q-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cbf5cf66-d096-4a67-b0a1-7f985b2dcd42	6b5190db-85e5-485f-8174-2c1727487ef2	g.chr8:143763524C>T	ENST00000301258.4	+	3	402	c.319C>T	c.(319-321)Ctg>Ttg	p.L107L		NM_005672.4	NP_005663.2	O43653	PSCA_HUMAN	prostate stem cell antigen	116						anchored component of membrane (GO:0031225)|extracellular vesicular exosome (GO:0070062)|plasma membrane (GO:0005886)				endometrium(1)|large_intestine(1)	2	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)					ACTCGGCCTGCTGCTCTGGGG	0.697																																					p.L107L		Atlas-SNP	.											.	PSCA	9	.	0			c.C319T						.						21.0	24.0	23.0					8																	143763524		2121	4232	6353	SO:0001819	synonymous_variant	8000	exon3			GGCCTGCTGCTCT	AF043498	CCDS47925.1, CCDS47925.2	8q24.2	2004-02-03				ENSG00000167653			9500	protein-coding gene	gene with protein product		602470				9465086	Standard	NM_005672		Approved		uc022bcd.1	O43653		ENST00000301258.4:c.319C>T	chr8.hg19:g.143763524C>T		12.0	0.0		40.0	8.0	NM_005672	Q6UW92	Silent	SNP	ENST00000301258.4	hg19	CCDS47925.2																																																																																			.	.		0.697	PSCA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000367112.2	NM_005672	
GSN	2934	hgsc.bcm.edu	37	9	124065340	124065340	+	Nonsense_Mutation	SNP	C	C	G			TCGA-KR-A7K2-01A-12D-A33Q-10	TCGA-KR-A7K2-10A-01D-A33Q-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cbf5cf66-d096-4a67-b0a1-7f985b2dcd42	6b5190db-85e5-485f-8174-2c1727487ef2	g.chr9:124065340C>G	ENST00000373818.4	+	3	570	c.501C>G	c.(499-501)taC>taG	p.Y167*	GSN_ENST00000449733.1_Nonsense_Mutation_p.Y116*|GSN_ENST00000412819.1_Nonsense_Mutation_p.Y116*|GSN_ENST00000373808.2_Nonsense_Mutation_p.Y116*|GSN_ENST00000373823.3_Nonsense_Mutation_p.Y116*|GSN_ENST00000436847.1_Nonsense_Mutation_p.Y127*|GSN_ENST00000341272.2_Nonsense_Mutation_p.Y116*|GSN_ENST00000545652.1_Nonsense_Mutation_p.Y124*|GSN_ENST00000394353.2_Nonsense_Mutation_p.Y127*	NM_000177.4|NM_001258029.1	NP_000168.1|NP_001244958.1	P06396	GELS_HUMAN	gelsolin	167	Actin-severing. {ECO:0000255}.|Polyphosphoinositide binding. {ECO:0000250}.				actin filament polymerization (GO:0030041)|actin filament severing (GO:0051014)|aging (GO:0007568)|apoptotic process (GO:0006915)|barbed-end actin filament capping (GO:0051016)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|cellular response to cadmium ion (GO:0071276)|cilium morphogenesis (GO:0060271)|oligodendrocyte development (GO:0014003)|phosphatidylinositol-mediated signaling (GO:0048015)|regulation of cell adhesion (GO:0030155)|response to ethanol (GO:0045471)|response to folic acid (GO:0051593)|tissue regeneration (GO:0042246)|vesicle-mediated transport (GO:0016192)	actin cytoskeleton (GO:0015629)|blood microparticle (GO:0072562)|cytosol (GO:0005829)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|lamellipodium (GO:0030027)|perinuclear region of cytoplasm (GO:0048471)|protein complex (GO:0043234)|ruffle (GO:0001726)	calcium ion binding (GO:0005509)			NS(1)|autonomic_ganglia(1)|breast(2)|endometrium(6)|kidney(1)|large_intestine(1)|lung(8)|ovary(1)	21						GCCTGAAGTACAAGGTGGGTT	0.592																																					p.Y167X		Atlas-SNP	.											.	GSN	81	.	0			c.C501G						.						45.0	46.0	46.0					9																	124065340		2203	4300	6503	SO:0001587	stop_gained	2934	exon3			GAAGTACAAGGTG	X04412	CCDS6828.1, CCDS6829.1, CCDS48011.1, CCDS65118.1, CCDS75890.1, CCDS75891.1	9q33	2010-04-27	2010-04-27		ENSG00000148180	ENSG00000148180			4620	protein-coding gene	gene with protein product	"""amyloidosis, Finnish type"""	137350	"""gelsolin (amyloidosis, Finnish type)"""			1652889	Standard	NM_001127662		Approved	DKFZp313L0718	uc004blf.1	P06396	OTTHUMG00000020584	ENST00000373818.4:c.501C>G	chr9.hg19:g.124065340C>G	ENSP00000362924:p.Tyr167*	27.0	0.0		38.0	10.0	NM_000177	A2A418|A8MUD1|A8MYN7|B7Z373|B7Z5V1|F5H1A8|Q5T0I2|Q8WVV7	Nonsense_Mutation	SNP	ENST00000373818.4	hg19	CCDS6828.1	.	.	.	.	.	.	.	.	.	.	C	37	6.203764	0.97371	.	.	ENSG00000148180	ENST00000373823;ENST00000432226;ENST00000449773;ENST00000436847;ENST00000394353;ENST00000449733;ENST00000412819;ENST00000341272;ENST00000373808;ENST00000394352;ENST00000456109;ENST00000545652;ENST00000373818	.	.	.	5.91	4.02	0.46733	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-22.4785	10.3205	0.43762	0.0:0.8344:0.0:0.1656	.	.	.	.	X	116;116;127;127;127;116;116;116;116;100;90;124;167	.	ENSP00000340888:Y116X	Y	+	3	2	GSN	123105161	1.000000	0.71417	1.000000	0.80357	0.980000	0.70556	4.104000	0.57790	0.765000	0.33221	-0.150000	0.13652	TAC	.	.		0.592	GSN-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000053861.1	NM_000177	
SLC39A12	221074	hgsc.bcm.edu	37	10	18289660	18289660	+	Silent	SNP	T	T	C			TCGA-KR-A7K2-01A-12D-A33Q-10	TCGA-KR-A7K2-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cbf5cf66-d096-4a67-b0a1-7f985b2dcd42	6b5190db-85e5-485f-8174-2c1727487ef2	g.chr10:18289660T>C	ENST00000377369.2	+	11	1938	c.1665T>C	c.(1663-1665)gaT>gaC	p.D555D	SLC39A12_ENST00000377371.3_Silent_p.D554D|SLC39A12-AS1_ENST00000439319.1_RNA|SLC39A12-AS1_ENST00000445287.1_RNA|SLC39A12_ENST00000539911.1_Silent_p.D421D|SLC39A12_ENST00000377374.4_Silent_p.D518D	NM_001145195.1|NM_001282733.1|NM_001282734.1	NP_001138667.1|NP_001269662.1|NP_001269663.1	Q504Y0	S39AC_HUMAN	solute carrier family 39 (zinc transporter), member 12	555					regulation of microtubule polymerization (GO:0031113)|regulation of neuron projection development (GO:0010975)|signal transduction (GO:0007165)|zinc ion transmembrane import (GO:0071578)	integral component of membrane (GO:0016021)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|vesicle (GO:0031982)	zinc ion transmembrane transporter activity (GO:0005385)			NS(1)|breast(4)|central_nervous_system(1)|cervix(1)|kidney(3)|large_intestine(5)|lung(38)|ovary(3)|prostate(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	60						ATTTTGCAGATGGCCTAGCCA	0.433																																					p.D555D		Atlas-SNP	.											.	SLC39A12	181	.	0			c.T1665C						.						159.0	139.0	146.0					10																	18289660		2203	4300	6503	SO:0001819	synonymous_variant	221074	exon11			TGCAGATGGCCTA		CCDS7124.1, CCDS44362.1, CCDS60493.1, CCDS60494.1	10p12.33	2013-05-22			ENSG00000148482	ENSG00000148482		"""Solute carriers"""	20860	protein-coding gene	gene with protein product		608734	"""solute carrier family 39 (metal ion transporter), member 12"""			12659941	Standard	NM_152725		Approved	FLJ30499	uc001ipo.2	Q504Y0	OTTHUMG00000017759	ENST00000377369.2:c.1665T>C	chr10.hg19:g.18289660T>C		78.0	0.0		62.0	32.0	NM_001145195	B7ZL35|C9JJL4|Q49AN8|Q4G0L3|Q5VWV8|Q5VWV9|Q6NZY5|Q96NN4	Silent	SNP	ENST00000377369.2	hg19	CCDS44362.1																																																																																			.	.		0.433	SLC39A12-201	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding		NM_152725	
FRMPD2	143162	hgsc.bcm.edu	37	10	49447719	49447719	+	Silent	SNP	C	C	A			TCGA-KR-A7K2-01A-12D-A33Q-10	TCGA-KR-A7K2-10A-01D-A33Q-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cbf5cf66-d096-4a67-b0a1-7f985b2dcd42	6b5190db-85e5-485f-8174-2c1727487ef2	g.chr10:49447719C>A	ENST00000374201.3	-	7	1019	c.717G>T	c.(715-717)acG>acT	p.T239T	FRMPD2_ENST00000305531.3_Silent_p.T215T|FRMPD2_ENST00000407470.4_Silent_p.T208T	NM_001018071.3|NM_001042512.2	NP_001018081|NP_001035977.2	Q68DX3	FRPD2_HUMAN	FERM and PDZ domain containing 2	239			T -> M (in dbSNP:rs55802136).		tight junction assembly (GO:0070830)	basolateral plasma membrane (GO:0016323)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|tight junction (GO:0005923)	1-phosphatidylinositol binding (GO:0005545)			NS(2)|autonomic_ganglia(2)|breast(5)|cervix(1)|endometrium(3)|kidney(7)|large_intestine(15)|lung(24)|ovary(2)|prostate(1)|skin(3)|urinary_tract(1)	66				Kidney(211;0.201)		TCTGGGTCTCCGTGCTTCTTT	0.517																																					p.T239T		Atlas-SNP	.											.	FRMPD2	157	.	0			c.G717T						.						111.0	90.0	97.0					10																	49447719		2203	4300	6503	SO:0001819	synonymous_variant	143162	exon7			GGTCTCCGTGCTT	AK123038	CCDS31195.1	10q11	2010-10-13			ENSG00000170324	ENSG00000170324			28572	protein-coding gene	gene with protein product		613323	"""PDZ domain containing 5C"""	PDZD5C, PDZK5C			Standard	NM_001018071		Approved	MGC35285	uc001jdv.3	Q68DX3	OTTHUMG00000018171	ENST00000374201.3:c.717G>T	chr10.hg19:g.49447719C>A		49.0	0.0		45.0	21.0	NM_001018071	B7WNW0|B7ZML5|Q2VY07|Q6GMQ9|Q6ZN38|Q6ZWI2|Q8N5T9	Silent	SNP	ENST00000374201.3	hg19	CCDS31195.1																																																																																			.	.		0.517	FRMPD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047923.3	NM_152428	
NOX4	50507	hgsc.bcm.edu	37	11	89069106	89069106	+	Missense_Mutation	SNP	A	A	C			TCGA-KR-A7K2-01A-12D-A33Q-10	TCGA-KR-A7K2-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cbf5cf66-d096-4a67-b0a1-7f985b2dcd42	6b5190db-85e5-485f-8174-2c1727487ef2	g.chr11:89069106A>C	ENST00000263317.4	-	17	1761	c.1523T>G	c.(1522-1524)aTt>aGt	p.I508S	NOX4_ENST00000532825.1_Missense_Mutation_p.I444S|NOX4_ENST00000527956.1_Missense_Mutation_p.I484S|NOX4_ENST00000528341.1_Missense_Mutation_p.I483S|NOX4_ENST00000535633.1_Missense_Mutation_p.I484S|NOX4_ENST00000413594.2_Missense_Mutation_p.I529S|NOX4_ENST00000527626.1_Missense_Mutation_p.I321S|NOX4_ENST00000542487.1_Missense_Mutation_p.I484S|NOX4_ENST00000525196.1_Missense_Mutation_p.I272S|NOX4_ENST00000375979.3_Missense_Mutation_p.I201S|NOX4_ENST00000343727.5_Missense_Mutation_p.I484S|NOX4_ENST00000534731.1_Missense_Mutation_p.I468S|NOX4_ENST00000424319.1_Missense_Mutation_p.I484S|NOX4_ENST00000531342.1_Missense_Mutation_p.I161S			Q9NPH5	NOX4_HUMAN	NADPH oxidase 4	508	Mediates interaction with TLR4.				bone resorption (GO:0045453)|cardiac muscle cell differentiation (GO:0055007)|cell aging (GO:0007569)|cell morphogenesis (GO:0000902)|cellular response to cAMP (GO:0071320)|cellular response to gamma radiation (GO:0071480)|cellular response to glucose stimulus (GO:0071333)|cellular response to transforming growth factor beta stimulus (GO:0071560)|homocysteine metabolic process (GO:0050667)|inflammatory response (GO:0006954)|negative regulation of cell proliferation (GO:0008285)|oxidation-reduction process (GO:0055114)|positive regulation of apoptotic process (GO:0043065)|positive regulation of DNA biosynthetic process (GO:2000573)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of MAP kinase activity (GO:0043406)|positive regulation of protein kinase B signaling (GO:0051897)|positive regulation of reactive oxygen species metabolic process (GO:2000379)|positive regulation of smooth muscle cell migration (GO:0014911)|positive regulation of stress fiber assembly (GO:0051496)|reactive oxygen species metabolic process (GO:0072593)|response to hypoxia (GO:0001666)|superoxide anion generation (GO:0042554)	apical plasma membrane (GO:0016324)|endoplasmic reticulum (GO:0005783)|focal adhesion (GO:0005925)|integral component of membrane (GO:0016021)|mitochondrion (GO:0005739)|NADPH oxidase complex (GO:0043020)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)	electron carrier activity (GO:0009055)|flavin adenine dinucleotide binding (GO:0050660)|heme binding (GO:0020037)|modified amino acid binding (GO:0072341)|NAD(P)H oxidase activity (GO:0016174)|nucleotide binding (GO:0000166)|oxygen sensor activity (GO:0019826)|superoxide-generating NADPH oxidase activity (GO:0016175)			NS(2)|central_nervous_system(1)|endometrium(3)|kidney(3)|large_intestine(8)|lung(20)|ovary(2)|prostate(3)|skin(2)	44		Acute lymphoblastic leukemia(157;2.26e-05)|all_hematologic(158;0.011)				TTTTTCTCCAATTATCTTCTG	0.363																																					p.I508S		Atlas-SNP	.											.	NOX4	101	.	0			c.T1523G						.						61.0	62.0	62.0					11																	89069106		2201	4297	6498	SO:0001583	missense	50507	exon17			TCTCCAATTATCT	AF254621	CCDS8285.1, CCDS44695.1, CCDS44696.1, CCDS73361.1, CCDS73362.1	11q14.2-q21	2008-02-05			ENSG00000086991	ENSG00000086991			7891	protein-coding gene	gene with protein product		605261					Standard	NM_001143837		Approved	KOX-1, KOX	uc001pct.3	Q9NPH5	OTTHUMG00000167298	ENST00000263317.4:c.1523T>G	chr11.hg19:g.89069106A>C	ENSP00000263317:p.Ile508Ser	196.0	0.0		219.0	116.0	NM_016931	A8K715|B7Z520|E7EMD7|Q5K3R4|Q5K3R5|Q5K3R6|Q5K3R8|Q7Z7G3|Q86V92	Missense_Mutation	SNP	ENST00000263317.4	hg19	CCDS8285.1	.	.	.	.	.	.	.	.	.	.	A	9.882	1.201756	0.22121	.	.	ENSG00000086991	ENST00000424319;ENST00000535633;ENST00000343727;ENST00000534731;ENST00000525196;ENST00000263317;ENST00000532825;ENST00000527956;ENST00000542487;ENST00000527626;ENST00000528341;ENST00000413594;ENST00000531342;ENST00000375979	D;D;D;D;D;D;D;D;D;D;D;D;D;D	0.93859	-3.27;-3.27;-3.27;-3.27;-3.27;-3.27;-3.27;-3.27;-3.27;-3.3;-3.27;-3.27;-3.27;-3.27	4.33	4.33	0.51752	Ferric reductase, NAD binding (1);	0.420567	0.26421	N	0.024474	D	0.87038	0.6078	N	0.12853	0.265	0.46542	D	0.999093	B;B;B;B;B;B;B;B	0.33448	0.036;0.277;0.412;0.321;0.05;0.023;0.2;0.014	B;B;B;B;B;B;B;B	0.38921	0.03;0.164;0.164;0.285;0.047;0.006;0.069;0.065	D	0.84513	0.0623	9	.	.	.	-12.5691	13.8139	0.63278	1.0:0.0:0.0:0.0	.	444;321;483;272;161;201;468;508	E9PMY6;E9PR43;E9PPP2;E9PI95;Q9NPH5-3;Q9NPH5-4;Q9NPH5-6;Q9NPH5	.;.;.;.;.;.;.;NOX4_HUMAN	S	484;484;484;468;272;508;444;484;484;321;483;529;161;201	ENSP00000412446:I484S;ENSP00000440172:I484S;ENSP00000344747:I484S;ENSP00000436892:I468S;ENSP00000436716:I272S;ENSP00000263317:I508S;ENSP00000434924:I444S;ENSP00000433797:I484S;ENSP00000439373:I484S;ENSP00000436093:I321S;ENSP00000436970:I483S;ENSP00000405705:I529S;ENSP00000435039:I161S;ENSP00000365146:I201S	.	I	-	2	0	NOX4	88708754	1.000000	0.71417	1.000000	0.80357	0.982000	0.71751	4.663000	0.61532	1.729000	0.51567	0.460000	0.39030	ATT	.	.		0.363	NOX4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000394054.1	NM_016931	
GNPNAT1	64841	hgsc.bcm.edu	37	14	53245074	53245074	+	Silent	SNP	A	A	G			TCGA-KR-A7K2-01A-12D-A33Q-10	TCGA-KR-A7K2-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cbf5cf66-d096-4a67-b0a1-7f985b2dcd42	6b5190db-85e5-485f-8174-2c1727487ef2	g.chr14:53245074A>G	ENST00000216410.3	-	6	697	c.510T>C	c.(508-510)taT>taC	p.Y170Y	GNPNAT1_ENST00000554230.1_Silent_p.Y99Y|RP11-589M4.1_ENST00000555969.1_RNA|RP11-589M4.1_ENST00000555689.1_RNA|GNPNAT1_ENST00000554421.1_5'Flank	NM_198066.3	NP_932332.1	Q96EK6	GNA1_HUMAN	glucosamine-phosphate N-acetyltransferase 1	170	N-acetyltransferase. {ECO:0000255|PROSITE-ProRule:PRU00532}.				cellular protein metabolic process (GO:0044267)|dolichol-linked oligosaccharide biosynthetic process (GO:0006488)|glucosamine metabolic process (GO:0006041)|liver development (GO:0001889)|N-acetylglucosamine metabolic process (GO:0006044)|post-translational protein modification (GO:0043687)|protein N-linked glycosylation via asparagine (GO:0018279)|UDP-N-acetylglucosamine biosynthetic process (GO:0006048)	cytosol (GO:0005829)|endoplasmic reticulum-Golgi intermediate compartment (GO:0005793)|Golgi apparatus (GO:0005794)|late endosome (GO:0005770)|membrane (GO:0016020)	glucosamine 6-phosphate N-acetyltransferase activity (GO:0004343)|monosaccharide binding (GO:0048029)			liver(1)|lung(1)|prostate(1)|skin(1)	4	Breast(41;0.176)					CAGATACAGTATATCCAAACT	0.343																																					p.Y170Y		Atlas-SNP	.											.	GNPNAT1	14	.	0			c.T510C						.						53.0	55.0	54.0					14																	53245074		2203	4295	6498	SO:0001819	synonymous_variant	64841	exon6			TACAGTATATCCA	AK001469	CCDS9712.1	14q22.1	2011-11-16			ENSG00000100522	ENSG00000100522	2.3.1.4		19980	protein-coding gene	gene with protein product							Standard	NM_198066		Approved	Gpnat1, FLJ10607	uc001xab.3	Q96EK6	OTTHUMG00000152334	ENST00000216410.3:c.510T>C	chr14.hg19:g.53245074A>G		167.0	0.0		179.0	10.0	NM_198066		Silent	SNP	ENST00000216410.3	hg19	CCDS9712.1																																																																																			.	.		0.343	GNPNAT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276898.1		
CATSPER2	117155	hgsc.bcm.edu	37	15	43924421	43924421	+	Missense_Mutation	SNP	G	G	T	rs148790135		TCGA-KR-A7K2-01A-12D-A33Q-10	TCGA-KR-A7K2-10A-01D-A33Q-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cbf5cf66-d096-4a67-b0a1-7f985b2dcd42	6b5190db-85e5-485f-8174-2c1727487ef2	g.chr15:43924421G>T	ENST00000321596.5	-	12	1736	c.1537C>A	c.(1537-1539)Cgt>Agt	p.R513S	CATSPER2_ENST00000354127.4_Missense_Mutation_p.R511S|STRC_ENST00000541030.1_Intron|CATSPER2_ENST00000381761.1_Missense_Mutation_p.R517S|CATSPER2_ENST00000396879.1_Missense_Mutation_p.R511S|CATSPER2_ENST00000355438.2_3'UTR			Q96P56	CTSR2_HUMAN	cation channel, sperm associated 2	513					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)		AACTTCTTACGTTCCTCTAGG	0.453																																					p.R513S		Atlas-SNP	.											.	CATSPER2	49	.	0			c.C1537A						.						93.0	86.0	88.0					15																	43924421		2199	4297	6496	SO:0001583	missense	117155	exon12			TCTTACGTTCCTC	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.1537C>A	chr15.hg19:g.43924421G>T	ENSP00000321463:p.Arg513Ser	80.0	0.0		59.0	35.0	NM_172095	Q8NHT9|Q96P54|Q96P55	Missense_Mutation	SNP	ENST00000321596.5	hg19	CCDS10099.1	.	.	.	.	.	.	.	.	.	.	G	18.53	3.643235	0.67244	.	.	ENSG00000166762	ENST00000396879;ENST00000299989;ENST00000381761;ENST00000321596;ENST00000354127	D;D;D;D	0.99060	-5.35;-5.38;-5.32;-5.35	4.43	3.51	0.40186	.	0.000000	0.47093	D	0.000246	D	0.98972	0.9650	M	0.77616	2.38	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.91635	0.999;0.999	D	0.99572	1.0971	10	0.87932	D	0	.	8.2994	0.32006	0.1087:0.0:0.8913:0.0	.	517;513	F8W9H2;Q96P56	.;CTSR2_HUMAN	S	511;513;517;513;511	ENSP00000380088:R511S;ENSP00000371180:R517S;ENSP00000321463:R513S;ENSP00000339137:R511S	ENSP00000299989:R513S	R	-	1	0	CATSPER2	41711713	1.000000	0.71417	1.000000	0.80357	0.983000	0.72400	3.973000	0.56845	1.210000	0.43336	0.644000	0.83932	CGT	.	G|1.000;A|0.000		0.453	CATSPER2-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000133151.2	NM_054020	
ABCC1	4363	hgsc.bcm.edu	37	16	16139804	16139804	+	Silent	SNP	C	C	T			TCGA-KR-A7K2-01A-12D-A33Q-10	TCGA-KR-A7K2-10A-01D-A33Q-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cbf5cf66-d096-4a67-b0a1-7f985b2dcd42	6b5190db-85e5-485f-8174-2c1727487ef2	g.chr16:16139804C>T	ENST00000399410.3	+	9	1327	c.1152C>T	c.(1150-1152)taC>taT	p.Y384Y	ABCC1_ENST00000399408.2_Silent_p.Y384Y|ABCC1_ENST00000345148.5_Silent_p.Y384Y|ABCC1_ENST00000346370.5_Silent_p.Y384Y|ABCC1_ENST00000351154.5_Silent_p.Y384Y|ABCC1_ENST00000349029.5_Silent_p.Y384Y	NM_004996.3	NP_004987.2	P33527	MRP1_HUMAN	ATP-binding cassette, sub-family C (CFTR/MRP), member 1	384	ABC transmembrane type-1 1. {ECO:0000255|PROSITE-ProRule:PRU00441}.				arachidonic acid metabolic process (GO:0019369)|ATP catabolic process (GO:0006200)|cobalamin metabolic process (GO:0009235)|leukotriene metabolic process (GO:0006691)|response to drug (GO:0042493)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)|transport (GO:0006810)|vitamin metabolic process (GO:0006766)|water-soluble vitamin metabolic process (GO:0006767)	extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|ATPase activity, coupled to transmembrane movement of substances (GO:0042626)|transporter activity (GO:0005215)			breast(3)|endometrium(9)|kidney(3)|large_intestine(12)|lung(20)|ovary(5)|prostate(1)|skin(3)	56					Abiraterone(DB05812)|Aminohippurate(DB00345)|Amprenavir(DB00701)|Atazanavir(DB01072)|Atorvastatin(DB01076)|Colchicine(DB01394)|Conjugated Estrogens(DB00286)|Cyclosporine(DB00091)|Dactinomycin(DB00970)|Daunorubicin(DB00694)|Diclofenac(DB00586)|Docetaxel(DB01248)|Doxorubicin(DB00997)|Epirubicin(DB00445)|Erythromycin(DB00199)|Etoposide(DB00773)|Fluorescein(DB00693)|Glutathione(DB00143)|Glyburide(DB01016)|Ibuprofen(DB01050)|Idarubicin(DB01177)|Indinavir(DB00224)|Indomethacin(DB00328)|Irinotecan(DB00762)|Ivermectin(DB00602)|Lamivudine(DB00709)|Methotrexate(DB00563)|Mifepristone(DB00834)|Mitoxantrone(DB01204)|Ofloxacin(DB01165)|Paclitaxel(DB01229)|Phenobarbital(DB01174)|Probenecid(DB01032)|Progesterone(DB00396)|Rifampicin(DB01045)|Ritonavir(DB00503)|Rosuvastatin(DB01098)|Saquinavir(DB01232)|Saxagliptin(DB06335)|Sulfinpyrazone(DB01138)|Vandetanib(DB05294)|Vemurafenib(DB08881)|Verapamil(DB00661)|Vinblastine(DB00570)|Vincristine(DB00541)|Zoledronate(DB00399)	TGCACCAGTACTTCCACATCT	0.577											OREG0023639	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.Y384Y		Atlas-SNP	.											.	ABCC1	156	.	0			c.C1152T						.						77.0	79.0	79.0					16																	16139804		2124	4240	6364	SO:0001819	synonymous_variant	4363	exon9			CCAGTACTTCCAC	L05628	CCDS42122.1	16p13.1	2012-03-14			ENSG00000103222	ENSG00000103222		"""ATP binding cassette transporters / subfamily C"""	51	protein-coding gene	gene with protein product		158343	"""multidrug resistance associated protein 1"""	MRP, MRP1		8098549, 1360704	Standard	NM_004996		Approved	GS-X	uc010bvi.3	P33527	OTTHUMG00000048267	ENST00000399410.3:c.1152C>T	chr16.hg19:g.16139804C>T		86.0	0.0	708	101.0	12.0	NM_004996	A3RJX2|C9JPJ4|O14819|O43333|P78419|Q59GI9|Q9UQ97|Q9UQ99|Q9UQA0	Silent	SNP	ENST00000399410.3	hg19	CCDS42122.1																																																																																			.	.		0.577	ABCC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000109701.1	NM_004996	
MLKL	197259	hgsc.bcm.edu	37	16	74708937	74708937	+	Silent	SNP	A	A	C			TCGA-KR-A7K2-01A-12D-A33Q-10	TCGA-KR-A7K2-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cbf5cf66-d096-4a67-b0a1-7f985b2dcd42	6b5190db-85e5-485f-8174-2c1727487ef2	g.chr16:74708937A>C	ENST00000308807.7	-	10	1765	c.1302T>G	c.(1300-1302)ggT>ggG	p.G434G	MLKL_ENST00000306247.7_Silent_p.G226G	NM_152649.2	NP_689862.1			mixed lineage kinase domain-like											breast(1)|endometrium(2)|kidney(2)|large_intestine(3)|liver(2)|lung(6)|skin(1)|stomach(2)	19						GGCAGTCTTCACCCAGTGGCT	0.547																																					p.G434G		Atlas-SNP	.											.	MLKL	51	.	0			c.T1302G						.						50.0	52.0	51.0					16																	74708937		2198	4300	6498	SO:0001819	synonymous_variant	197259	exon10			GTCTTCACCCAGT	AK091708	CCDS32487.1, CCDS45528.1	16q22.3	2008-02-05				ENSG00000168404			26617	protein-coding gene	gene with protein product		615153				12477932	Standard	NM_152649		Approved	FLJ34389	uc002fdb.2	Q8NB16		ENST00000308807.7:c.1302T>G	chr16.hg19:g.74708937A>C		92.0	0.0		128.0	53.0	NM_152649		Silent	SNP	ENST00000308807.7	hg19	CCDS32487.1																																																																																			.	.		0.547	MLKL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000436403.3	NM_152649	
MNT	4335	hgsc.bcm.edu	37	17	2290484	2290484	+	Missense_Mutation	SNP	G	G	T			TCGA-KR-A7K2-01A-12D-A33Q-10	TCGA-KR-A7K2-10A-01D-A33Q-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cbf5cf66-d096-4a67-b0a1-7f985b2dcd42	6b5190db-85e5-485f-8174-2c1727487ef2	g.chr17:2290484G>T	ENST00000174618.4	-	6	1865	c.1460C>A	c.(1459-1461)cCc>cAc	p.P487H	MNT_ENST00000575374.1_5'Flank|RP1-59D14.1_ENST00000571775.1_RNA	NM_020310.2	NP_064706.1	Q99583	MNT_HUMAN	MAX network transcriptional repressor	487					cell aging (GO:0007569)|multicellular organismal development (GO:0007275)|negative regulation of apoptotic signaling pathway (GO:2001234)|negative regulation of cell proliferation (GO:0008285)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|regulation of cell cycle (GO:0051726)|transcription from RNA polymerase II promoter (GO:0006366)	nucleus (GO:0005634)	chromatin binding (GO:0003682)|RNA polymerase II regulatory region sequence-specific DNA binding (GO:0000977)|RNA polymerase II transcription regulatory region sequence-specific DNA binding transcription factor activity involved in negative regulation of transcription (GO:0001227)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription coactivator activity (GO:0003713)|transcription corepressor activity (GO:0003714)			endometrium(4)|large_intestine(5)|lung(1)|skin(1)|upper_aerodigestive_tract(1)	12				Colorectal(2;1.37e-05)|READ - Rectum adenocarcinoma(2;8.68e-05)		GTGCCCAATGGGGGGTGTGGC	0.682																																					p.P487H		Atlas-SNP	.											.	MNT	35	.	0			c.C1460A						.						23.0	25.0	24.0					17																	2290484		2201	4297	6498	SO:0001583	missense	4335	exon6			CCAATGGGGGGTG	Y13444	CCDS11018.1	17p13.3	2013-11-15	2013-11-15		ENSG00000070444	ENSG00000070444		"""MAX dimerization proteins"", ""Basic helix-loop-helix proteins"""	7188	protein-coding gene	gene with protein product	"""myc antagonist"", ""Max-interacting protein"""	603039	"""MAX binding protein"", ""MNT, MAX dimerization protein"""			9598315	Standard	NM_020310		Approved	ROX, MXD6, MAD6, bHLHd3	uc002fur.3	Q99583	OTTHUMG00000090603	ENST00000174618.4:c.1460C>A	chr17.hg19:g.2290484G>T	ENSP00000174618:p.Pro487His	37.0	0.0		32.0	11.0	NM_020310	A8K6D1|D3DTI7|Q1ED38	Missense_Mutation	SNP	ENST00000174618.4	hg19	CCDS11018.1	.	.	.	.	.	.	.	.	.	.	G	22.7	4.329680	0.81690	.	.	ENSG00000070444	ENST00000174618;ENST00000404961	D	0.87334	-2.24	4.91	4.91	0.64330	.	0.182095	0.38005	N	0.001842	D	0.87313	0.6146	N	0.24115	0.695	0.53688	D	0.99997	D	0.69078	0.997	P	0.58013	0.831	D	0.89619	0.3847	10	0.87932	D	0	-12.3015	17.0679	0.86564	0.0:0.0:1.0:0.0	.	487	Q99583	MNT_HUMAN	H	487	ENSP00000174618:P487H	ENSP00000174618:P487H	P	-	2	0	MNT	2237234	1.000000	0.71417	0.998000	0.56505	0.910000	0.53928	7.435000	0.80391	2.274000	0.75844	0.591000	0.81541	CCC	.	.		0.682	MNT-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207158.1	NM_020310	
KRTAP9-2	83899	hgsc.bcm.edu	37	17	39383271	39383271	+	Missense_Mutation	SNP	A	A	G			TCGA-KR-A7K2-01A-12D-A33Q-10	TCGA-KR-A7K2-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cbf5cf66-d096-4a67-b0a1-7f985b2dcd42	6b5190db-85e5-485f-8174-2c1727487ef2	g.chr17:39383271A>G	ENST00000377721.3	+	1	372	c.365A>G	c.(364-366)tAc>tGc	p.Y122C	KRTAP9-2_ENST00000455970.2_Missense_Mutation_p.Y106C	NM_031961.2	NP_114167.2	Q9BYQ4	KRA92_HUMAN	keratin associated protein 9-2	122	17 X 5 AA repeats of C-C-[RQVSGE]-[SPTQ]- [TASP].					keratin filament (GO:0045095)				large_intestine(1)|lung(6)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	11		Breast(137;0.000496)	STAD - Stomach adenocarcinoma(17;0.000397)			ACCTGCTACTACCCCACGACT	0.627																																					p.Y122C		Atlas-SNP	.											.	KRTAP9-2	24	.	0			c.A365G						.						162.0	155.0	157.0					17																	39383271		2203	4300	6503	SO:0001583	missense	83899	exon1			GCTACTACCCCAC	AJ406946	CCDS32651.1	17q21.2	2013-06-25			ENSG00000239886	ENSG00000239886		"""Keratin associated proteins"""	16926	protein-coding gene	gene with protein product						11279113	Standard	NM_031961		Approved	KAP9.2	uc002hwf.3	Q9BYQ4	OTTHUMG00000133609	ENST00000377721.3:c.365A>G	chr17.hg19:g.39383271A>G	ENSP00000366950:p.Tyr122Cys	140.0	0.0		131.0	70.0	NM_031961	Q17RK8|Q2TB15|Q6ISF6	Missense_Mutation	SNP	ENST00000377721.3	hg19	CCDS32651.1	.	.	.	.	.	.	.	.	.	.	.	11.10	1.539129	0.27475	.	.	ENSG00000239886	ENST00000377721;ENST00000455970	T;T	0.01335	5.0;5.0	2.68	0.349	0.16032	.	.	.	.	.	T	0.00845	0.0028	N	0.08118	0	0.09310	N	1	B	0.16166	0.016	B	0.12156	0.007	T	0.48281	-0.9049	9	0.42905	T	0.14	.	2.2922	0.04141	0.5096:0.0:0.27:0.2204	.	122	Q9BYQ4	KRA92_HUMAN	C	122;106	ENSP00000366950:Y122C;ENSP00000398325:Y106C	ENSP00000366950:Y122C	Y	+	2	0	KRTAP9-2	36636797	0.000000	0.05858	0.547000	0.28179	0.130000	0.20726	0.009000	0.13219	0.033000	0.15463	0.451000	0.29950	TAC	.	.		0.627	KRTAP9-2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000257717.1		
TIMP2	7077	hgsc.bcm.edu	37	17	76887017	76887017	+	Intron	SNP	C	C	A			TCGA-KR-A7K2-01A-12D-A33Q-10	TCGA-KR-A7K2-10A-01D-A33Q-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cbf5cf66-d096-4a67-b0a1-7f985b2dcd42	6b5190db-85e5-485f-8174-2c1727487ef2	g.chr17:76887017C>A	ENST00000262768.7	-	2	429				TIMP2_ENST00000536189.2_Intron|DDC8_ENST00000322630.2_Missense_Mutation_p.M523I	NM_003255.4	NP_003246.1	P16035	TIMP2_HUMAN	TIMP metallopeptidase inhibitor 2						aging (GO:0007568)|cellular response to organic substance (GO:0071310)|central nervous system development (GO:0007417)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|negative regulation of cell proliferation (GO:0008285)|negative regulation of endopeptidase activity (GO:0010951)|negative regulation of mitotic cell cycle (GO:0045930)|negative regulation of proteolysis (GO:0045861)|negative regulation of Ras protein signal transduction (GO:0046580)|positive regulation of adenylate cyclase activity (GO:0045762)|positive regulation of MAPK cascade (GO:0043410)|positive regulation of neuron differentiation (GO:0045666)|regulation of Rap protein signal transduction (GO:0032487)|response to cytokine (GO:0034097)|response to drug (GO:0042493)	basement membrane (GO:0005604)|cell surface (GO:0009986)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|growth cone (GO:0030426)|neuronal cell body (GO:0043025)	enzyme activator activity (GO:0008047)|metal ion binding (GO:0046872)|metalloendopeptidase inhibitor activity (GO:0008191)			central_nervous_system(2)	2			BRCA - Breast invasive adenocarcinoma(99;0.0101)|OV - Ovarian serous cystadenocarcinoma(97;0.194)			CTGGGTGTTCCATTTGTTCAA	0.498																																					p.M523I		Atlas-SNP	.											.	.	.	.	0			c.G1569T						.																																			SO:0001627	intron_variant	0	exon3			GTGTTCCATTTGT		CCDS11758.1	17q25	2008-07-18	2005-08-08		ENSG00000035862	ENSG00000035862			11821	protein-coding gene	gene with protein product		188825	"""tissue inhibitor of metalloproteinase 2"""			1427908	Standard	NM_003255		Approved	CSC-21K	uc002jwf.3	P16035	OTTHUMG00000154517	ENST00000262768.7:c.131-17016G>T	chr17.hg19:g.76887017C>A		49.0	0.0		40.0	22.0	NM_001243540	Q16121|Q93006|Q9UDF7	Missense_Mutation	SNP	ENST00000262768.7	hg19	CCDS11758.1	.	.	.	.	.	.	.	.	.	.	C	0.011	-1.722317	0.00700	.	.	ENSG00000178404	ENST00000322630	T	0.14766	2.48	4.17	-8.34	0.00988	.	1.631620	0.04027	N	0.300757	T	0.04724	0.0128	.	.	.	0.09310	N	0.999999	B	0.02656	0.0	B	0.01281	0.0	T	0.33111	-0.9881	9	0.13108	T	0.6	0.0396	1.5314	0.02536	0.3288:0.1842:0.333:0.154	.	523	Q96MC4	.	I	523	ENSP00000312767:M523I	ENSP00000312767:M523I	M	-	3	0	AC100788.1	74398612	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-2.020000	0.01441	-2.610000	0.00446	-0.181000	0.13052	ATG	.	.		0.498	TIMP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000335662.1	NM_003255	
PTPRM	5797	hgsc.bcm.edu	37	18	8143692	8143692	+	Missense_Mutation	SNP	C	C	T			TCGA-KR-A7K2-01A-12D-A33Q-10	TCGA-KR-A7K2-10A-01D-A33Q-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cbf5cf66-d096-4a67-b0a1-7f985b2dcd42	6b5190db-85e5-485f-8174-2c1727487ef2	g.chr18:8143692C>T	ENST00000332175.8	+	14	3252	c.2215C>T	c.(2215-2217)Cat>Tat	p.H739Y	PTPRM_ENST00000444013.1_Missense_Mutation_p.H526Y|PTPRM_ENST00000580170.1_Missense_Mutation_p.H739Y|PTPRM_ENST00000400060.4_Missense_Mutation_p.H739Y|PTPRM_ENST00000400053.4_Missense_Mutation_p.H677Y	NM_002845.3	NP_002836.3	P28827	PTPRM_HUMAN	protein tyrosine phosphatase, receptor type, M	739					homophilic cell adhesion (GO:0007156)|negative regulation of angiogenesis (GO:0016525)|negative regulation of endothelial cell migration (GO:0010596)|negative regulation of endothelial cell proliferation (GO:0001937)|neuron projection development (GO:0031175)|peptidyl-tyrosine dephosphorylation (GO:0035335)|positive regulation of vasodilation (GO:0045909)|protein dephosphorylation (GO:0006470)|response to drug (GO:0042493)|retina layer formation (GO:0010842)|retinal ganglion cell axon guidance (GO:0031290)|signal transduction (GO:0007165)	cell-cell adherens junction (GO:0005913)|cell-cell junction (GO:0005911)|cytoplasm (GO:0005737)|integral component of plasma membrane (GO:0005887)|lamellipodium (GO:0030027)|perinuclear region of cytoplasm (GO:0048471)	cadherin binding (GO:0045296)|identical protein binding (GO:0042802)|protein tyrosine phosphatase activity (GO:0004725)|transmembrane receptor protein tyrosine phosphatase activity (GO:0005001)			breast(3)|central_nervous_system(1)|cervix(3)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(32)|lung(25)|ovary(2)|prostate(4)|skin(2)|stomach(1)|upper_aerodigestive_tract(2)	90		Colorectal(10;0.234)				ACAGACAGACCATACAGTTAA	0.443																																					p.H739Y		Atlas-SNP	.											.	PTPRM	185	.	0			c.C2215T						.						151.0	148.0	149.0					18																	8143692		2203	4300	6503	SO:0001583	missense	5797	exon14			ACAGACCATACAG	X58288	CCDS11840.1, CCDS58613.1	18p11.2	2013-02-11			ENSG00000173482	ENSG00000173482		"""Protein tyrosine phosphatases / Class I Cys-based PTPs : Transmembrane receptor-like"", ""Immunoglobulin superfamily / I-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"", ""Fibronectin type III domain containing"""	9675	protein-coding gene	gene with protein product		176888		PTPRL1		1655529, 8404049	Standard	NM_002845		Approved	RPTPU, hR-PTPu	uc010dkv.3	P28827	OTTHUMG00000131575	ENST00000332175.8:c.2215C>T	chr18.hg19:g.8143692C>T	ENSP00000331418:p.His739Tyr	68.0	0.0		81.0	22.0	NM_001105244	A7MBN1|D3DUH8|J3QL11	Missense_Mutation	SNP	ENST00000332175.8	hg19	CCDS11840.1	.	.	.	.	.	.	.	.	.	.	C	29.2	4.982410	0.93044	.	.	ENSG00000173482	ENST00000332175;ENST00000400060;ENST00000400053;ENST00000444013	T;T;T;T	0.46819	1.18;1.19;1.0;0.86	5.92	5.92	0.95590	.	0.049790	0.85682	D	0.000000	T	0.65291	0.2677	L	0.51422	1.61	0.58432	D	0.999997	P;D;D	0.57899	0.754;0.981;0.981	B;D;D	0.67900	0.424;0.954;0.954	T	0.63019	-0.6730	10	0.56958	D	0.05	.	20.3206	0.98668	0.0:1.0:0.0:0.0	.	526;739;739	E7EVX9;A7MBN1;P28827	.;.;PTPRM_HUMAN	Y	739;739;677;526	ENSP00000331418:H739Y;ENSP00000382933:H739Y;ENSP00000382927:H677Y;ENSP00000387608:H526Y	ENSP00000331418:H739Y	H	+	1	0	PTPRM	8133692	1.000000	0.71417	0.997000	0.53966	0.964000	0.63967	7.478000	0.81082	2.809000	0.96659	0.655000	0.94253	CAT	.	.		0.443	PTPRM-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000254456.1		
DENND1C	79958	hgsc.bcm.edu	37	19	6472968	6472968	+	Missense_Mutation	SNP	C	C	G			TCGA-KR-A7K2-01A-12D-A33Q-10	TCGA-KR-A7K2-10A-01D-A33Q-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cbf5cf66-d096-4a67-b0a1-7f985b2dcd42	6b5190db-85e5-485f-8174-2c1727487ef2	g.chr19:6472968C>G	ENST00000381480.2	-	15	1202	c.1090G>C	c.(1090-1092)Gcc>Ccc	p.A364P	DENND1C_ENST00000543576.1_Missense_Mutation_p.A320P	NM_024898.2	NP_079174.2	Q8IV53	DEN1C_HUMAN	DENN/MADD domain containing 1C	364	dDENN. {ECO:0000255|PROSITE- ProRule:PRU00306}.				positive regulation of Rab GTPase activity (GO:0032851)	cytoplasmic vesicle (GO:0031410)	Rab guanyl-nucleotide exchange factor activity (GO:0017112)			endometrium(3)|kidney(3)|large_intestine(1)|lung(3)	10						GGCTTCTGGGCCAAGAAGACT	0.612																																					p.A364P		Atlas-SNP	.											.	DENND1C	93	.	0			c.G1090C						.						26.0	30.0	29.0					19																	6472968		1934	4130	6064	SO:0001583	missense	79958	exon15			TCTGGGCCAAGAA	AL713770	CCDS45938.1	19p13.3	2014-02-06	2005-08-17	2005-08-17	ENSG00000205744	ENSG00000205744		"""DENN/MADD domain containing"""	26225	protein-coding gene	gene with protein product		613634	"""family with sequence similarity 31, member C"""	FAM31C		12477932	Standard	XM_005259646		Approved	FLJ22757	uc002mfe.3	Q8IV53	OTTHUMG00000180853	ENST00000381480.2:c.1090G>C	chr19.hg19:g.6472968C>G	ENSP00000370889:p.Ala364Pro	29.0	0.0		35.0	6.0	NM_024898	B4E051|D3PFD4|Q8NDB1|Q9H5Z2	Missense_Mutation	SNP	ENST00000381480.2	hg19	CCDS45938.1	.	.	.	.	.	.	.	.	.	.	c	16.87	3.241085	0.58995	.	.	ENSG00000205744	ENST00000381480;ENST00000543576	T;T	0.44881	0.91;0.91	4.57	3.51	0.40186	dDENN (3);	0.575922	0.18100	N	0.151725	T	0.42988	0.1227	L	0.40543	1.245	0.22873	N	0.998626	P	0.41041	0.736	P	0.49451	0.611	T	0.23655	-1.0182	10	0.54805	T	0.06	-10.532	8.8932	0.35446	0.0:0.8922:0.0:0.1078	.	364	Q8IV53	DEN1C_HUMAN	P	364;320	ENSP00000370889:A364P;ENSP00000437805:A320P	ENSP00000370889:A364P	A	-	1	0	DENND1C	6423968	0.946000	0.32159	0.997000	0.53966	0.981000	0.71138	0.867000	0.27968	0.902000	0.36520	0.457000	0.33378	GCC	.	.		0.612	DENND1C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000453332.2	NM_024898	
ZNF792	126375	hgsc.bcm.edu	37	19	35449077	35449077	+	Missense_Mutation	SNP	G	G	A			TCGA-KR-A7K2-01A-12D-A33Q-10	TCGA-KR-A7K2-10A-01D-A33Q-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cbf5cf66-d096-4a67-b0a1-7f985b2dcd42	6b5190db-85e5-485f-8174-2c1727487ef2	g.chr19:35449077G>A	ENST00000404801.1	-	4	2068	c.1682C>T	c.(1681-1683)cCt>cTt	p.P561L	ZNF792_ENST00000605484.1_Missense_Mutation_p.P494L	NM_175872.4	NP_787068.3	Q3KQV3	ZN792_HUMAN	zinc finger protein 792	561					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			cervix(1)|endometrium(4)|kidney(1)|large_intestine(1)|lung(5)	12	all_lung(56;4.18e-08)|Lung NSC(56;6.62e-08)|Esophageal squamous(110;0.162)		LUSC - Lung squamous cell carcinoma(66;0.0849)			GCATTCGTAAGGCCTGTCTGG	0.522																																					p.P561L	GBM(1;7 183 21053 22581 22847)	Atlas-SNP	.											.	ZNF792	46	.	0			c.C1682T						.						123.0	94.0	104.0					19																	35449077		2203	4300	6503	SO:0001583	missense	126375	exon4			TCGTAAGGCCTGT	AK095770	CCDS12440.2	19q13.11	2013-01-08			ENSG00000180884	ENSG00000180884		"""Zinc fingers, C2H2-type"", ""-"""	24751	protein-coding gene	gene with protein product						8889548	Standard	NM_175872		Approved	FLJ38451	uc002nxh.1	Q3KQV3	OTTHUMG00000150339	ENST00000404801.1:c.1682C>T	chr19.hg19:g.35449077G>A	ENSP00000385099:p.Pro561Leu	148.0	0.0		173.0	75.0	NM_175872	B4E333|Q495L1|Q495L3|Q8N932	Missense_Mutation	SNP	ENST00000404801.1	hg19	CCDS12440.2	.	.	.	.	.	.	.	.	.	.	g	9.146	1.015163	0.19355	.	.	ENSG00000180884	ENST00000404801;ENST00000379189	T	0.17054	2.3	2.81	1.78	0.24846	Zinc finger, C2H2 (1);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.16085	0.0387	L	0.56769	1.78	0.09310	N	1	B	0.24721	0.11	B	0.23716	0.048	T	0.27606	-1.0069	9	0.72032	D	0.01	.	4.1938	0.10433	0.1364:0.2417:0.6219:0.0	.	561	Q3KQV3	ZN792_HUMAN	L	561;321	ENSP00000385099:P561L	ENSP00000368487:P321L	P	-	2	0	ZNF792	40140917	1.000000	0.71417	0.001000	0.08648	0.219000	0.24729	3.738000	0.55067	0.768000	0.33290	-0.253000	0.11424	CCT	.	.		0.522	ZNF792-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000317673.1	NM_175872	
ZNF512B	57473	hgsc.bcm.edu	37	20	62659867	62659867	+	Intron	SNP	G	G	A			TCGA-KR-A7K2-01A-12D-A33Q-10	TCGA-KR-A7K2-10A-01D-A33Q-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cbf5cf66-d096-4a67-b0a1-7f985b2dcd42	6b5190db-85e5-485f-8174-2c1727487ef2	g.chr20:62659867G>A	ENST00000450537.1	-	1	56				ZNF512B_ENST00000217130.3_Intron|PRPF6_ENST00000535781.1_Silent_p.L752L			Q96KM6	Z512B_HUMAN	zinc finger protein 512B						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)|cervix(2)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(3)|lung(16)|ovary(1)|prostate(4)|skin(1)	33	all_cancers(38;2.14e-11)|all_epithelial(29;3.41e-13)|Lung NSC(23;3.41e-09)|all_lung(23;1.06e-08)					GTGCGGGGCTGAAGAACATCG	0.632																																					p.L792L		Atlas-SNP	.											.	PRPF6	88	.	0			c.G2376A						.						75.0	71.0	73.0					20																	62659867		2203	4300	6503	SO:0001627	intron_variant	24148	exon18			GGGGCTGAAGAAC	AB033022	CCDS13548.1	20q13.33	2011-02-09			ENSG00000196700	ENSG00000196700			29212	protein-coding gene	gene with protein product						10574462	Standard	NM_020713		Approved	GM632, MGC149845, MGC149846	uc002yhl.2	Q96KM6	OTTHUMG00000033008	ENST00000450537.1:c.4+20190C>T	chr20.hg19:g.62659867G>A		44.0	0.0		40.0	14.0	NM_012469	Q08AK9|Q9ULM4	Silent	SNP	ENST00000450537.1	hg19	CCDS13548.1																																																																																			.	.		0.632	ZNF512B-202	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000080246.1	NM_020713	
MORC3	23515	hgsc.bcm.edu	37	21	37736428	37736428	+	Nonsense_Mutation	SNP	C	C	A			TCGA-KR-A7K2-01A-12D-A33Q-10	TCGA-KR-A7K2-10A-01D-A33Q-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cbf5cf66-d096-4a67-b0a1-7f985b2dcd42	6b5190db-85e5-485f-8174-2c1727487ef2	g.chr21:37736428C>A	ENST00000400485.1	+	14	1566	c.1490C>A	c.(1489-1491)tCa>tAa	p.S497*	MORC3_ENST00000487909.1_3'UTR|AP000692.9_ENST00000397184.2_RNA	NM_015358.2	NP_056173.1	Q14149	MORC3_HUMAN	MORC family CW-type zinc finger 3	497					cell aging (GO:0007569)|maintenance of protein location in nucleus (GO:0051457)|negative regulation of fibroblast proliferation (GO:0048147)|peptidyl-serine phosphorylation (GO:0018105)|post-embryonic development (GO:0009791)|protein phosphorylation (GO:0006468)|protein stabilization (GO:0050821)	PML body (GO:0016605)	zinc ion binding (GO:0008270)			breast(2)|endometrium(5)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(7)|lung(9)|ovary(2)|prostate(3)|upper_aerodigestive_tract(1)|urinary_tract(2)	35						ACTGCTCTTTCAACTCCAAGC	0.378																																					p.S497X		Atlas-SNP	.											.	MORC3	78	.	0			c.C1490A						.						126.0	114.0	118.0					21																	37736428		1857	4089	5946	SO:0001587	stop_gained	23515	exon14			CTCTTTCAACTCC	AK025327	CCDS42924.1	21q22.13	2005-06-15	2005-06-15	2005-06-15	ENSG00000159256	ENSG00000159256			23572	protein-coding gene	gene with protein product		610078	"""zinc finger, CW-type with coiled-coil domain 3"", ""zinc finger, CW type with coiled-coil domain 3"""	ZCWCC3		14607086	Standard	NM_015358		Approved	ZCW5, NXP2, KIAA0136	uc002yvi.3	Q14149	OTTHUMG00000086620	ENST00000400485.1:c.1490C>A	chr21.hg19:g.37736428C>A	ENSP00000383333:p.Ser497*	82.0	0.0		84.0	32.0	NM_015358	A8KA92|Q9UEZ2	Nonsense_Mutation	SNP	ENST00000400485.1	hg19	CCDS42924.1	.	.	.	.	.	.	.	.	.	.	C	20.2	3.951012	0.73787	.	.	ENSG00000159256	ENST00000400485	.	.	.	5.24	3.42	0.39159	.	1.062980	0.07374	N	0.886261	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.06494	T	0.89	-0.8832	9.18	0.37136	0.0:0.8287:0.0:0.1713	.	.	.	.	X	497	.	ENSP00000383333:S497X	S	+	2	0	MORC3	36658298	0.059000	0.20769	0.005000	0.12908	0.007000	0.05969	1.175000	0.31944	0.696000	0.31696	-0.258000	0.10820	TCA	.	.		0.378	MORC3-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000194640.1	NM_015358	
TYMP	1890	hgsc.bcm.edu	37	22	50968105	50968105	+	Missense_Mutation	SNP	G	G	A			TCGA-KR-A7K2-01A-12D-A33Q-10	TCGA-KR-A7K2-10A-01D-A33Q-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cbf5cf66-d096-4a67-b0a1-7f985b2dcd42	6b5190db-85e5-485f-8174-2c1727487ef2	g.chr22:50968105G>A	ENST00000252029.3	-	2	196	c.34C>T	c.(34-36)Cca>Tca	p.P12S	TYMP_ENST00000395681.1_Missense_Mutation_p.P12S|TYMP_ENST00000395678.3_Missense_Mutation_p.P12S|TYMP_ENST00000395680.1_Missense_Mutation_p.P12S	NM_001113755.2|NM_001113756.2|NM_001257988.1|NM_001257989.1|NM_001953.4	NP_001107227.1|NP_001107228.1|NP_001244917.1|NP_001244918.1|NP_001944.1	P19971	TYPH_HUMAN	thymidine phosphorylase	12					angiogenesis (GO:0001525)|cell differentiation (GO:0030154)|chemotaxis (GO:0006935)|DNA replication (GO:0006260)|mitochondrial genome maintenance (GO:0000002)|nucleobase-containing small molecule metabolic process (GO:0055086)|pyrimidine nucleobase metabolic process (GO:0006206)|pyrimidine nucleoside catabolic process (GO:0046135)|pyrimidine nucleoside salvage (GO:0043097)|pyrimidine nucleotide metabolic process (GO:0006220)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)	phosphorylase activity (GO:0004645)|platelet-derived growth factor receptor binding (GO:0005161)|pyrimidine-nucleoside phosphorylase activity (GO:0016154)|thymidine phosphorylase activity (GO:0009032)|transferase activity, transferring pentosyl groups (GO:0016763)			large_intestine(1)|lung(2)|ovary(1)|prostate(1)	5		all_cancers(38;4.58e-14)|all_epithelial(38;1.12e-12)|all_lung(38;3.07e-05)|Breast(42;6.27e-05)|Lung NSC(38;0.000813)|Ovarian(80;0.0221)|Hepatocellular(38;0.0691)|Lung SC(80;0.113)		BRCA - Breast invasive adenocarcinoma(115;0.206)|LUAD - Lung adenocarcinoma(64;0.247)	Capecitabine(DB01101)|Cidofovir(DB00369)|Floxuridine(DB00322)|Fluorouracil(DB00544)|Trifluridine(DB00432)	GGCGCGGGTGGGGCCCCGGTT	0.706																																					p.P12S		Atlas-SNP	.											.	TYMP	25	.	0			c.C34T						.						12.0	16.0	14.0					22																	50968105		2192	4291	6483	SO:0001583	missense	1890	exon2			CGGGTGGGGCCCC	M63193	CCDS14096.1, CCDS58811.1	22q13	2014-09-17	2008-01-21	2008-01-21	ENSG00000025708	ENSG00000025708	2.4.2.4		3148	protein-coding gene	gene with protein product	"""gliostatin"""	131222	"""endothelial cell growth factor 1 (platelet-derived)"""	MNGIE, ECGF1		1590793, 11733540	Standard	NM_001113755		Approved		uc003bme.5	P19971	OTTHUMG00000150249	ENST00000252029.3:c.34C>T	chr22.hg19:g.50968105G>A	ENSP00000252029:p.Pro12Ser	110.0	0.0		57.0	27.0	NM_001257989	A8MW15|H9KVA0|Q13390|Q8WVB7	Missense_Mutation	SNP	ENST00000252029.3	hg19	CCDS14096.1	.	.	.	.	.	.	.	.	.	.	G	18.37	3.609082	0.66558	.	.	ENSG00000025708	ENST00000395680;ENST00000395681;ENST00000252029;ENST00000395678;ENST00000425169	D;D;D;D;D	0.98666	-4.76;-4.75;-4.76;-4.76;-5.06	4.4	-3.91	0.04168	.	0.562517	0.13620	N	0.374461	D	0.92802	0.7711	N	0.08118	0	0.09310	N	1	B;B;B;B	0.14438	0.01;0.002;0.002;0.002	B;B;B;B	0.12156	0.007;0.001;0.002;0.002	D	0.86787	0.1983	10	0.87932	D	0	0.0036	4.9868	0.14194	0.5954:0.0:0.2412:0.1634	.	12;12;12;12	B4DVR2;B2RBL3;E5KRG5;P19971	.;.;.;TYPH_HUMAN	S	12	ENSP00000379037:P12S;ENSP00000379038:P12S;ENSP00000252029:P12S;ENSP00000379036:P12S;ENSP00000395875:P12S	ENSP00000252029:P12S	P	-	1	0	TYMP	49314971	0.000000	0.05858	0.000000	0.03702	0.053000	0.15095	-0.547000	0.06055	-0.481000	0.06792	0.462000	0.41574	CCA	.	.		0.706	TYMP-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000317081.1	NM_001953	
DMD	1756	hgsc.bcm.edu	37	X	32486815	32486815	+	Missense_Mutation	SNP	A	A	G			TCGA-KR-A7K2-01A-12D-A33Q-10	TCGA-KR-A7K2-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cbf5cf66-d096-4a67-b0a1-7f985b2dcd42	6b5190db-85e5-485f-8174-2c1727487ef2	g.chrX:32486815A>G	ENST00000357033.4	-	23	3168	c.2962T>C	c.(2962-2964)Tct>Cct	p.S988P	DMD_ENST00000378677.2_Missense_Mutation_p.S984P	NM_000109.3|NM_004006.2|NM_004011.3|NM_004012.3|NM_004014.2	NP_000100.2|NP_003997|NP_004002.2|NP_004003.1|NP_004005.1	P11532	DMD_HUMAN	dystrophin	988					cardiac muscle cell action potential (GO:0086001)|cardiac muscle contraction (GO:0060048)|cellular protein complex assembly (GO:0043623)|cellular protein localization (GO:0034613)|extracellular matrix organization (GO:0030198)|motile cilium assembly (GO:0044458)|muscle filament sliding (GO:0030049)|muscle organ development (GO:0007517)|negative regulation of peptidyl-cysteine S-nitrosylation (GO:1902083)|negative regulation of peptidyl-serine phosphorylation (GO:0033137)|peptide biosynthetic process (GO:0043043)|positive regulation of neuron differentiation (GO:0045666)|positive regulation of neuron projection development (GO:0010976)|positive regulation of sodium ion transmembrane transporter activity (GO:2000651)|regulation of cardiac muscle contraction by regulation of the release of sequestered calcium ion (GO:0010881)|regulation of cellular response to growth factor stimulus (GO:0090287)|regulation of heart rate (GO:0002027)|regulation of release of sequestered calcium ion into cytosol by sarcoplasmic reticulum (GO:0010880)|regulation of ryanodine-sensitive calcium-release channel activity (GO:0060314)|regulation of skeletal muscle contraction (GO:0014819)|regulation of skeletal muscle contraction by regulation of release of sequestered calcium ion (GO:0014809)|regulation of voltage-gated calcium channel activity (GO:1901385)	cell junction (GO:0030054)|cell surface (GO:0009986)|costamere (GO:0043034)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|dystrophin-associated glycoprotein complex (GO:0016010)|filopodium (GO:0030175)|filopodium membrane (GO:0031527)|membrane raft (GO:0045121)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)|protein complex (GO:0043234)|sarcolemma (GO:0042383)|syntrophin complex (GO:0016013)	actin binding (GO:0003779)|calcium ion binding (GO:0005509)|dystroglycan binding (GO:0002162)|myosin binding (GO:0017022)|nitric-oxide synthase binding (GO:0050998)|structural constituent of cytoskeleton (GO:0005200)|structural constituent of muscle (GO:0008307)|vinculin binding (GO:0017166)|zinc ion binding (GO:0008270)			NS(2)|breast(3)|central_nervous_system(1)|endometrium(11)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(17)|liver(1)|lung(25)|ovary(3)|pancreas(3)|prostate(2)|skin(1)|urinary_tract(2)	77		all_cancers(2;1.22e-16)|Acute lymphoblastic leukemia(2;4.65e-06)|all_hematologic(2;0.00108)|all_epithelial(3;0.00626)|all_neural(2;0.0189)|all_lung(315;0.182)|Glioma(3;0.203)				TCTTGCAGAGAACTTTGTAAA	0.333																																					p.S988P		Atlas-SNP	.											.	DMD	2127	.	0			c.T2962C						.						51.0	46.0	47.0					X																	32486815		2201	4297	6498	SO:0001583	missense	1756	exon23			GCAGAGAACTTTG	AF047505	CCDS14231.1, CCDS14232.1, CCDS14233.1, CCDS14234.1, CCDS48091.1, CCDS55394.1, CCDS55395.1, CCDS75965.1	Xp21.2	2014-09-17	2008-08-01		ENSG00000198947	ENSG00000198947			2928	protein-coding gene	gene with protein product	"""muscular dystrophy, Duchenne and Becker types"""	300377	"""dystrophin (muscular dystrophy, Duchenne and Becker types), includes DXS142, DXS164, DXS206, DXS230, DXS239, DXS268, DXS269, DXS270, DXS272"", ""mental retardation, X-linked 85"""	MRX85		3282674, 3607877, 23900271	Standard	NM_004019		Approved	BMD, DXS142, DXS164, DXS206, DXS230, DXS239, DXS268, DXS269, DXS270, DXS272	uc004dda.1	P11532	OTTHUMG00000021336	ENST00000357033.4:c.2962T>C	chrX.hg19:g.32486815A>G	ENSP00000354923:p.Ser988Pro	124.0	0.0		140.0	115.0	NM_004006	E9PDN1|Q02295|Q14169|Q14170|Q5JYU0|Q6NSJ9|Q7KZ48|Q8N754|Q9UCW3|Q9UCW4	Missense_Mutation	SNP	ENST00000357033.4	hg19	CCDS14233.1	.	.	.	.	.	.	.	.	.	.	A	15.65	2.895466	0.52121	.	.	ENSG00000198947	ENST00000534884;ENST00000378677;ENST00000357033;ENST00000542849;ENST00000535280	T;T	0.35789	1.29;1.29	5.12	3.86	0.44501	.	0.000000	0.33772	U	0.004578	T	0.43722	0.1260	L	0.34521	1.04	0.80722	D	1	D;D;D	0.71674	0.982;0.998;0.986	P;D;P	0.66847	0.802;0.947;0.875	T	0.23619	-1.0183	10	0.37606	T	0.19	.	10.9111	0.47110	0.8452:0.1548:0.0:0.0	.	980;988;984	P11532-4;P11532;E9PDN5	.;DMD_HUMAN;.	P	980;984;988;988;865	ENSP00000367948:S984P;ENSP00000354923:S988P	ENSP00000354923:S988P	S	-	1	0	DMD	32396736	1.000000	0.71417	0.999000	0.59377	0.729000	0.41735	3.240000	0.51368	1.789000	0.52484	0.437000	0.28790	TCT	.	.		0.333	DMD-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056182.2	NM_004006	
CSTF2	1478	hgsc.bcm.edu	37	X	100086583	100086583	+	Silent	SNP	A	A	G			TCGA-KR-A7K2-01A-12D-A33Q-10	TCGA-KR-A7K2-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cbf5cf66-d096-4a67-b0a1-7f985b2dcd42	6b5190db-85e5-485f-8174-2c1727487ef2	g.chrX:100086583A>G	ENST00000372972.2	+	9	985	c.969A>G	c.(967-969)ggA>ggG	p.G323G	CSTF2_ENST00000415585.2_Silent_p.G343G	NM_001325.2	NP_001316.1	P33240	CSTF2_HUMAN	cleavage stimulation factor, 3' pre-RNA, subunit 2, 64kDa	323	Gly/Pro-rich.				gene expression (GO:0010467)|mRNA 3'-end processing (GO:0031124)|mRNA cleavage (GO:0006379)|mRNA polyadenylation (GO:0006378)|mRNA splicing, via spliceosome (GO:0000398)|RNA splicing (GO:0008380)|termination of RNA polymerase II transcription (GO:0006369)|transcription from RNA polymerase II promoter (GO:0006366)	cleavage body (GO:0071920)|mRNA cleavage and polyadenylation specificity factor complex (GO:0005847)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)			central_nervous_system(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(1)|lung(6)|skin(2)|stomach(1)	13						GCTTGTTAGGAGATGCTCCGA	0.522																																					p.G323G		Atlas-SNP	.											.	CSTF2	47	.	0			c.A969G						.						119.0	100.0	106.0					X																	100086583		2203	4300	6503	SO:0001819	synonymous_variant	1478	exon9			GTTAGGAGATGCT	BC017712	CCDS14473.1	Xq22.1	2013-02-12	2002-08-29		ENSG00000101811	ENSG00000101811		"""RNA binding motif (RRM) containing"""	2484	protein-coding gene	gene with protein product		300907	"""cleavage stimulation factor, 3' pre-RNA, subunit 2, 64kD"""			1741396	Standard	XM_006724622		Approved		uc004egh.3	P33240	OTTHUMG00000022709	ENST00000372972.2:c.969A>G	chrX.hg19:g.100086583A>G		68.0	0.0		72.0	35.0	NM_001325	Q5H951|Q6LA74|Q8N502	Silent	SNP	ENST00000372972.2	hg19	CCDS14473.1																																																																																			.	.		0.522	CSTF2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000058926.1	NM_001325	
FAM127A	8933	hgsc.bcm.edu	37	X	134166686	134166686	+	Silent	SNP	C	C	A			TCGA-KR-A7K2-01A-12D-A33Q-10	TCGA-KR-A7K2-10A-01D-A33Q-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cbf5cf66-d096-4a67-b0a1-7f985b2dcd42	6b5190db-85e5-485f-8174-2c1727487ef2	g.chrX:134166686C>A	ENST00000257013.7	+	1	354	c.273C>A	c.(271-273)ctC>ctA	p.L91L	FAM127A_ENST00000464369.1_Intron	NM_001078171.1	NP_001071639.1	O15255	CXX1_HUMAN	family with sequence similarity 127, member A	0						plasma membrane (GO:0005886)				endometrium(3)|urinary_tract(1)	4	Acute lymphoblastic leukemia(192;0.000127)					GCCCCCTCCTCAATGATTACC	0.637																																					p.L91L		Atlas-SNP	.											.	FAM127A	21	.	0			c.C273A						.						42.0	45.0	44.0					X																	134166686		2187	4291	6478	SO:0001819	synonymous_variant	8933	exon1			CCTCCTCAATGAT	Y13374	CCDS43997.1	Xq26	2014-05-16	2006-11-16	2006-11-16	ENSG00000134590	ENSG00000134590			2569	protein-coding gene	gene with protein product		300213	"""CAAX box 1"""	CXX1		9403077, 15716091, 16093683	Standard	NM_001078171		Approved	Mart8, Mar8, MAR8C	uc004eyd.3	A6ZKI3	OTTHUMG00000022465	ENST00000257013.7:c.273C>A	chrX.hg19:g.134166686C>A		136.0	0.0		129.0	50.0	NM_001078171	Q6IBF1	Silent	SNP	ENST00000257013.7	hg19	CCDS43997.1																																																																																			.	.		0.637	FAM127A-002	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000058391.2	NM_001078171	
SSR4	6748	hgsc.bcm.edu	37	X	153060132	153060132	+	5'UTR	SNP	G	G	C			TCGA-KR-A7K2-01A-12D-A33Q-10	TCGA-KR-A7K2-10A-01D-A33Q-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cbf5cf66-d096-4a67-b0a1-7f985b2dcd42	6b5190db-85e5-485f-8174-2c1727487ef2	g.chrX:153060132G>C	ENST00000320857.3	+	0	1074				SSR4_ENST00000370087.1_5'UTR|SSR4_ENST00000370086.3_5'UTR|IDH3G_ENST00000427365.2_5'Flank|IDH3G_ENST00000370093.1_5'Flank|IDH3G_ENST00000370092.3_5'Flank|IDH3G_ENST00000217901.5_5'Flank|SSR4_ENST00000460616.1_3'UTR|SSR4_ENST00000370085.3_5'UTR|IDH3G_ENST00000497043.1_5'Flank	NM_001204526.1	NP_001191455.1	P51571	SSRD_HUMAN	signal sequence receptor, delta						cellular protein metabolic process (GO:0044267)|gene expression (GO:0010467)|SRP-dependent cotranslational protein targeting to membrane (GO:0006614)|translation (GO:0006412)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|Sec61 translocon complex (GO:0005784)				central_nervous_system(1)|endometrium(1)|lung(2)	4	all_hematologic(71;4.25e-06)|all_lung(58;3.83e-05)|Lung NSC(58;5.54e-05)|Acute lymphoblastic leukemia(192;6.56e-05)					CCTCTAGGCAGAGAAGAGGCG	0.647																																					p.R8T		Atlas-SNP	.											.	SSR4	15	.	0			c.G23C						.						56.0	43.0	47.0					X																	153060132		2202	4299	6501	SO:0001623	5_prime_UTR_variant	6748	exon2			TAGGCAGAGAAGA	BC032351	CCDS14731.1	Xq28	2011-08-31	2011-08-31		ENSG00000180879	ENSG00000180879			11326	protein-coding gene	gene with protein product	"""translocon-associated protein delta"""	300090				9286695	Standard	NM_001204526		Approved	TRAPD	uc022chw.1	P51571	OTTHUMG00000024212	ENST00000320857.3:c.-11G>C	chrX.hg19:g.153060132G>C		109.0	0.0		118.0	100.0	NM_001204526	A8K378|Q53XY1	Missense_Mutation	SNP	ENST00000320857.3	hg19	CCDS14731.1																																																																																			.	.		0.647	SSR4-005	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000061029.1	NM_006280	
KIAA1731	85459	hgsc.bcm.edu	37	11	93432956	93432959	+	Frame_Shift_Del	DEL	AAAC	AAAC	-	rs568540537		TCGA-KR-A7K2-01A-12D-A33Q-10	TCGA-KR-A7K2-10A-01D-A33Q-10	AAAC	AAAC	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cbf5cf66-d096-4a67-b0a1-7f985b2dcd42	6b5190db-85e5-485f-8174-2c1727487ef2	g.chr11:93432956_93432959delAAAC	ENST00000325212.6	+	15	5040_5043	c.4878_4881delAAAC	c.(4876-4881)ttaaacfs	p.LN1626fs	KIAA1731_ENST00000531700.1_Intron|KIAA1731_ENST00000344196.4_5'UTR|KIAA1731_ENST00000411936.1_Frame_Shift_Del_p.LN1626fs			Q9C0D2	K1731_HUMAN	KIAA1731	1626						centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)				breast(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)	11		Acute lymphoblastic leukemia(157;2.31e-05)|all_hematologic(158;0.00824)				AACTGTCTTTAAACAAACAAAGAA	0.392																																					p.1626_1627del		Atlas-Indel,Pindel	.											.	KIAA1731	173	.	0			c.4877_4880del						.																																			SO:0001589	frameshift_variant	85459	exon15			.	AB051518	CCDS44708.1	11q21	2014-03-11			ENSG00000166004	ENSG00000166004			29366	protein-coding gene	gene with protein product						20844083	Standard	NM_033395		Approved		uc009ywb.1	Q9C0D2	OTTHUMG00000167449	ENST00000325212.6:c.4878_4881delAAAC	chr11.hg19:g.93432960_93432963delAAAC	ENSP00000316681:p.Leu1626fs	76.0	0.0		50.0	12.0	NM_033395	C9J5H9|C9JQY8|Q8N7L4|Q8N919|Q8N9B0|Q96LT8	Frame_Shift_Del	DEL	ENST00000325212.6	hg19	CCDS44708.1																																																																																			.	.		0.392	KIAA1731-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000394640.1	NM_033395	
TAF1B	9014	hgsc.bcm.edu	37	2	9994549	9994563	+	Splice_Site	DEL	CGGTAAGTCACAAGT	CGGTAAGTCACAAGT	-	rs35681700		TCGA-KR-A7K2-01A-12D-A33Q-10	TCGA-KR-A7K2-10A-01D-A33Q-10	CGGTAAGTCACAAGT	CGGTAAGTCACAAGT	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cbf5cf66-d096-4a67-b0a1-7f985b2dcd42	6b5190db-85e5-485f-8174-2c1727487ef2	g.chr2:9994549_9994563delCGGTAAGTCACAAGT	ENST00000263663.5	+	5	586_587	c.398_399delCGGTAAGTCACAAGT	c.(397-399)acg>a	p.T133del	TAF1B_ENST00000396242.3_5'UTR|TAF1B_ENST00000402170.1_3'UTR	NM_005680.2	NP_005671	Q53T94	TAF1B_HUMAN	TATA box binding protein (TBP)-associated factor, RNA polymerase I, B, 63kDa	133	N-terminal cyclin fold.				gene expression (GO:0010467)|RNA polymerase I transcriptional preinitiation complex assembly at the promoter for the nuclear large rRNA transcript (GO:0001189)|termination of RNA polymerase I transcription (GO:0006363)|transcription elongation from RNA polymerase I promoter (GO:0006362)|transcription from RNA polymerase I promoter (GO:0006360)|transcription initiation from RNA polymerase I promoter (GO:0006361)|transcription, DNA-templated (GO:0006351)	extracellular vesicular exosome (GO:0070062)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|RNA polymerase I core factor complex (GO:0070860)	metal ion binding (GO:0046872)|RNA polymerase I CORE element sequence-specific DNA binding (GO:0001164)|RNA polymerase I CORE element sequence-specific DNA binding transcription factor recruiting transcription factor activity (GO:0001187)|sequence-specific DNA binding transcription factor activity (GO:0003700)|TBP-class protein binding (GO:0017025)			breast(2)|central_nervous_system(1)|endometrium(1)|kidney(1)|lung(4)|ovary(2)|pancreas(1)|prostate(1)|upper_aerodigestive_tract(1)	14	all_hematologic(175;0.127)|Acute lymphoblastic leukemia(172;0.155)					AGGAAACCTACGGTAAGTCACAAGTCTGAAAAGTT	0.391																																					p.133_133del		Atlas-Indel,Pindel	.											.	TAF1B	62	.	0			c.397_399del						.																																			SO:0001630	splice_region_variant	9014	exon5			.	L39061	CCDS33143.1	2p25	2008-06-02	2002-08-29		ENSG00000115750	ENSG00000115750			11533	protein-coding gene	gene with protein product		604904	"""TATA box binding protein (TBP)-associated factor, RNA polymerase I, B, 63kD"""			7801123	Standard	NM_005680		Approved	TAFI63, SL1, RAF1B, RAFI63	uc002qzz.3	Q53T94	OTTHUMG00000151673	ENST00000263663.5:c.399+1CGGTAAGTCACAAGT>-	chr2.hg19:g.9994549_9994563delCGGTAAGTCACAAGT		94.0	0.0		79.0	11.0	NM_005680	B4DI42|F8WD72|Q15574|Q8WVC3	In_Frame_Del	DEL	ENST00000263663.5	hg19	CCDS33143.1																																																																																			.	.		0.391	TAF1B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000323426.2	NM_005680	In_Frame_Del
GBP5	115362	hgsc.bcm.edu	37	1	89726418	89726419	+	Frame_Shift_Del	DEL	AC	AC	-			TCGA-KR-A7K2-01A-12D-A33Q-10	TCGA-KR-A7K2-10A-01D-A33Q-10	AC	AC	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cbf5cf66-d096-4a67-b0a1-7f985b2dcd42	6b5190db-85e5-485f-8174-2c1727487ef2	g.chr1:89726418_89726419delAC	ENST00000370459.3	-	11	1856_1857	c.1729_1730delGT	c.(1729-1731)gttfs	p.V577fs	GBP5_ENST00000471171.1_5'UTR|GBP5_ENST00000343435.5_Frame_Shift_Del_p.V577fs|RP4-620F22.2_ENST00000437128.1_RNA			Q96PP8	GBP5_HUMAN	guanylate binding protein 5	577	Required for tetramerization. {ECO:0000250}.					cytoplasm (GO:0005737)|membrane (GO:0016020)	GTP binding (GO:0005525)|GTPase activity (GO:0003924)|identical protein binding (GO:0042802)			breast(1)|endometrium(1)|large_intestine(6)|lung(14)|ovary(1)|prostate(1)	24				all cancers(265;0.00784)|Epithelial(280;0.0286)		ATCGTTATTAACAGTCCTCTGG	0.406																																					p.577_577del		Atlas-Indel,Pindel	.											.	GBP5	65	.	0			c.1730_1731del						.																																			SO:0001589	frameshift_variant	115362	exon12			.	AF430642	CCDS722.1	1p22.2	2008-02-05			ENSG00000154451	ENSG00000154451			19895	protein-coding gene	gene with protein product		611467					Standard	NM_052942		Approved		uc001dnd.3	Q96PP8	OTTHUMG00000010006	ENST00000370459.3:c.1729_1730delGT	chr1.hg19:g.89726418_89726419delAC	ENSP00000359488:p.Val577fs	51.0	0.0		50.0	15.0	NM_052942	B2RCE1|Q86TM5	Frame_Shift_Del	DEL	ENST00000370459.3	hg19	CCDS722.1																																																																																			.	.		0.406	GBP5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000027700.1	NM_052942	
PODXL	5420	hgsc.bcm.edu	37	7	131193753	131193756	+	Frame_Shift_Del	DEL	CTCT	CTCT	-			TCGA-KR-A7K2-01A-12D-A33Q-10	TCGA-KR-A7K2-10A-01D-A33Q-10	CTCT	CTCT	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cbf5cf66-d096-4a67-b0a1-7f985b2dcd42	6b5190db-85e5-485f-8174-2c1727487ef2	g.chr7:131193753_131193756delCTCT	ENST00000378555.3	-	5	1302_1305	c.1055_1058delAGAG	c.(1054-1059)cagagtfs	p.QS352fs	PODXL_ENST00000537928.1_Intron|PODXL_ENST00000541194.1_Frame_Shift_Del_p.QS354fs|PODXL_ENST00000322985.9_Frame_Shift_Del_p.QS320fs|PODXL_ENST00000465001.1_5'Flank			O00592	PODXL_HUMAN	podocalyxin-like	352					cell adhesion (GO:0007155)|cell migration (GO:0016477)|epithelial tube formation (GO:0072175)|glomerular visceral epithelial cell development (GO:0072015)|leukocyte migration (GO:0050900)|negative regulation of cell adhesion (GO:0007162)|negative regulation of cell-cell adhesion (GO:0022408)|positive regulation of cell migration (GO:0030335)|positive regulation of cell-cell adhesion mediated by integrin (GO:0033634)|regulation of microvillus assembly (GO:0032534)	apical plasma membrane (GO:0016324)|cell body (GO:0044297)|cytoplasm (GO:0005737)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|filopodium (GO:0030175)|integral component of plasma membrane (GO:0005887)|lamellipodium (GO:0030027)|microvillus membrane (GO:0031528)|plasma membrane (GO:0005886)|ruffle (GO:0001726)|slit diaphragm (GO:0036057)				NS(1)|breast(3)|endometrium(3)|kidney(3)|large_intestine(4)|lung(4)|pancreas(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)	24	Melanoma(18;0.162)					CTGCTTCTCACTCTGTGTCTGTGT	0.52																																					p.352_353del		Atlas-INDEL	.											.	PODXL	53	.	0			c.1056_1059del						.																																			SO:0001589	frameshift_variant	5420	exon5			.		CCDS34755.1, CCDS47714.1	7q32-q33	2008-07-18			ENSG00000128567	ENSG00000128567			9171	protein-coding gene	gene with protein product		602632					Standard	NM_001018111		Approved	PCLP, Gp200, PC	uc003vqx.4	O00592	OTTHUMG00000154918	ENST00000378555.3:c.1055_1058delAGAG	chr7.hg19:g.131193753_131193756delCTCT	ENSP00000367817:p.Gln352fs	164.0	0.0		145.0	18.0	NM_001018111	A6NHX8|Q52LZ7|Q53ER6	Frame_Shift_Del	DEL	ENST00000378555.3	hg19	CCDS34755.1																																																																																			.	.		0.520	PODXL-005	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000337627.2	NM_001018111	
MSMO1	6307	hgsc.bcm.edu	37	4	166259057	166259058	+	Frame_Shift_Ins	INS	-	-	A	rs148185089		TCGA-KR-A7K2-01A-12D-A33Q-10	TCGA-KR-A7K2-10A-01D-A33Q-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cbf5cf66-d096-4a67-b0a1-7f985b2dcd42	6b5190db-85e5-485f-8174-2c1727487ef2	g.chr4:166259057_166259058insA	ENST00000261507.6	+	3	545_546	c.372_373insA	c.(373-375)attfs	p.I125fs	MSMO1_ENST00000393766.2_5'UTR|MSMO1_ENST00000504317.1_Frame_Shift_Ins_p.I125fs	NM_006745.4	NP_006736.1	Q15800	MSMO1_HUMAN	methylsterol monooxygenase 1	125					cholesterol biosynthetic process (GO:0006695)|fatty acid biosynthetic process (GO:0006633)|fatty acid metabolic process (GO:0006631)|small molecule metabolic process (GO:0044281)|steroid metabolic process (GO:0008202)	endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	C-4 methylsterol oxidase activity (GO:0000254)|iron ion binding (GO:0005506)										AGTATTTCAATATTCCTTATGA	0.332																																					p.N124fs		Atlas-Indel,Pindel	.											.	.	.	.	0			c.372_373insA						.																																			SO:0001589	frameshift_variant	6307	exon3			.	U93162	CCDS3809.1, CCDS43280.1	4q32-q34	2013-03-04	2011-09-01	2011-09-01	ENSG00000052802	ENSG00000052802	1.14.13.72	"""Fatty acid hydroxylase domain containing"""	10545	protein-coding gene	gene with protein product		607545	"""sterol-C4-methyl oxidase-like"""	SC4MOL		8663358	Standard	NM_006745		Approved	DESP4, ERG25	uc003ire.3	Q15800	OTTHUMG00000161126	ENST00000261507.6:c.373dupA	chr4.hg19:g.166259058_166259058dupA	ENSP00000261507:p.Ile125fs	63.0	0.0		68.0	31.0	NM_006745	A8K8Q3|A8MYF6|D3DP32|Q32Q24	Frame_Shift_Ins	INS	ENST00000261507.6	hg19	CCDS3809.1																																																																																			.	.		0.332	MSMO1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000363880.1	NM_006745	
PODXL	5420	hgsc.bcm.edu	37	7	131193749	131193751	+	In_Frame_Del	DEL	CTC	CTC	-			TCGA-KR-A7K2-01A-12D-A33Q-10	TCGA-KR-A7K2-10A-01D-A33Q-10	CTC	CTC	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cbf5cf66-d096-4a67-b0a1-7f985b2dcd42	6b5190db-85e5-485f-8174-2c1727487ef2	g.chr7:131193749_131193751delCTC	ENST00000378555.3	-	5	1307_1309	c.1060_1062delGAG	c.(1060-1062)gagdel	p.E354del	PODXL_ENST00000537928.1_Intron|PODXL_ENST00000541194.1_In_Frame_Del_p.E356del|PODXL_ENST00000322985.9_In_Frame_Del_p.E322del|PODXL_ENST00000465001.1_5'Flank			O00592	PODXL_HUMAN	podocalyxin-like	354					cell adhesion (GO:0007155)|cell migration (GO:0016477)|epithelial tube formation (GO:0072175)|glomerular visceral epithelial cell development (GO:0072015)|leukocyte migration (GO:0050900)|negative regulation of cell adhesion (GO:0007162)|negative regulation of cell-cell adhesion (GO:0022408)|positive regulation of cell migration (GO:0030335)|positive regulation of cell-cell adhesion mediated by integrin (GO:0033634)|regulation of microvillus assembly (GO:0032534)	apical plasma membrane (GO:0016324)|cell body (GO:0044297)|cytoplasm (GO:0005737)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|filopodium (GO:0030175)|integral component of plasma membrane (GO:0005887)|lamellipodium (GO:0030027)|microvillus membrane (GO:0031528)|plasma membrane (GO:0005886)|ruffle (GO:0001726)|slit diaphragm (GO:0036057)				NS(1)|breast(3)|endometrium(3)|kidney(3)|large_intestine(4)|lung(4)|pancreas(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)	24	Melanoma(18;0.162)					CGAGCTGCTTCTCACTCTGTGTC	0.532																																					p.354_355del		Atlas-INDEL	.											.	PODXL	53	.	0			c.1061_1063del						.																																			SO:0001651	inframe_deletion	5420	exon5			.		CCDS34755.1, CCDS47714.1	7q32-q33	2008-07-18			ENSG00000128567	ENSG00000128567			9171	protein-coding gene	gene with protein product		602632					Standard	NM_001018111		Approved	PCLP, Gp200, PC	uc003vqx.4	O00592	OTTHUMG00000154918	ENST00000378555.3:c.1060_1062delGAG	chr7.hg19:g.131193749_131193751delCTC	ENSP00000367817:p.Glu354del	165.0	0.0		147.0	19.0	NM_001018111	A6NHX8|Q52LZ7|Q53ER6	In_Frame_Del	DEL	ENST00000378555.3	hg19	CCDS34755.1																																																																																			.	.		0.532	PODXL-005	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000337627.2	NM_001018111	
PODXL	5420	hgsc.bcm.edu	37	7	131193749	131193756	+	Frame_Shift_Del	DEL	CTCACTCT	CTCACTCT	-			TCGA-KR-A7K2-01A-12D-A33Q-10	TCGA-KR-A7K2-10A-01D-A33Q-10	CTCACTCT	CTCACTCT	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cbf5cf66-d096-4a67-b0a1-7f985b2dcd42	6b5190db-85e5-485f-8174-2c1727487ef2	g.chr7:131193749_131193756delCTCACTCT	ENST00000378555.3	-	5	1302_1309	c.1055_1062delAGAGTGAG	c.(1054-1062)cagagtgagfs	p.QSE352fs	PODXL_ENST00000537928.1_Intron|PODXL_ENST00000541194.1_Frame_Shift_Del_p.QSE354fs|PODXL_ENST00000322985.9_Frame_Shift_Del_p.QSE320fs|PODXL_ENST00000465001.1_5'Flank			O00592	PODXL_HUMAN	podocalyxin-like	352					cell adhesion (GO:0007155)|cell migration (GO:0016477)|epithelial tube formation (GO:0072175)|glomerular visceral epithelial cell development (GO:0072015)|leukocyte migration (GO:0050900)|negative regulation of cell adhesion (GO:0007162)|negative regulation of cell-cell adhesion (GO:0022408)|positive regulation of cell migration (GO:0030335)|positive regulation of cell-cell adhesion mediated by integrin (GO:0033634)|regulation of microvillus assembly (GO:0032534)	apical plasma membrane (GO:0016324)|cell body (GO:0044297)|cytoplasm (GO:0005737)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|filopodium (GO:0030175)|integral component of plasma membrane (GO:0005887)|lamellipodium (GO:0030027)|microvillus membrane (GO:0031528)|plasma membrane (GO:0005886)|ruffle (GO:0001726)|slit diaphragm (GO:0036057)				NS(1)|breast(3)|endometrium(3)|kidney(3)|large_intestine(4)|lung(4)|pancreas(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)	24	Melanoma(18;0.162)					CGAGCTGCTTCTCACTCTGTGTCTGTGT	0.524																																					p.352_355del		Pindel	.											.	PODXL	53	.	0			c.1056_1063del						.																																			SO:0001589	frameshift_variant	5420	exon5			.		CCDS34755.1, CCDS47714.1	7q32-q33	2008-07-18			ENSG00000128567	ENSG00000128567			9171	protein-coding gene	gene with protein product		602632					Standard	NM_001018111		Approved	PCLP, Gp200, PC	uc003vqx.4	O00592	OTTHUMG00000154918	ENST00000378555.3:c.1055_1062delAGAGTGAG	chr7.hg19:g.131193749_131193756delCTCACTCT	ENSP00000367817:p.Gln352fs	165.0	0.0		151.0	19.0	NM_001018111	A6NHX8|Q52LZ7|Q53ER6	Frame_Shift_Del	DEL	ENST00000378555.3	hg19	CCDS34755.1																																																																																			.	.		0.524	PODXL-005	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000337627.2	NM_001018111	
