#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
KIAA2013	90231	hgsc.bcm.edu	37	1	11985677	11985677	+	Silent	SNP	G	G	T			TCGA-WJ-A86L-01A-12D-A45V-10	TCGA-WJ-A86L-10A-01D-A38X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	80e4fac9-c066-47a9-9fc0-2a42eef954cd	cebd5a99-cbde-441d-b98a-b84cf1825d65	g.chr1:11985677G>T	ENST00000376572.3	-	1	803	c.618C>A	c.(616-618)atC>atA	p.I206I	KIAA2013_ENST00000376576.3_Silent_p.I206I	NM_138346.2	NP_612355.1	Q8IYS2	K2013_HUMAN	KIAA2013	206						integral component of membrane (GO:0016021)|membrane (GO:0016020)				endometrium(1)|lung(3)|ovary(1)|prostate(1)|skin(1)	7	Ovarian(185;0.249)	Renal(390;0.000469)|Lung NSC(185;0.00149)|all_lung(284;0.00189)|Breast(348;0.00586)|Colorectal(325;0.0062)|Myeloproliferative disorder(586;0.0393)|Hepatocellular(190;0.0556)|Ovarian(437;0.0731)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0228)|Colorectal(212;4.88e-06)|COAD - Colon adenocarcinoma(227;0.000241)|BRCA - Breast invasive adenocarcinoma(304;0.000293)|Kidney(185;0.000722)|KIRC - Kidney renal clear cell carcinoma(229;0.00258)|STAD - Stomach adenocarcinoma(313;0.0072)|READ - Rectum adenocarcinoma(331;0.0649)		TGTTGAGCTGGATGCGCTGCA	0.701																																					p.I206I		Atlas-SNP	.											.	KIAA2013	25	.	0			c.C618A						.						9.0	12.0	11.0					1																	11985677		2083	4103	6186	SO:0001819	synonymous_variant	90231	exon1			GAGCTGGATGCGC	AB095933	CCDS141.1	1p36.22	2011-02-09			ENSG00000116685	ENSG00000116685			28513	protein-coding gene	gene with protein product						12477932	Standard	NM_138346		Approved	MGC33867, RP5-1077B9.1	uc001atk.3	Q8IYS2	OTTHUMG00000002391	ENST00000376572.3:c.618C>A	chr1.hg19:g.11985677G>T		73.0	0.0		85.0	26.0	NM_138346	Q5JXC1|Q8IVF8|Q8NDI7|Q9BSY1	Silent	SNP	ENST00000376572.3	hg19	CCDS141.1																																																																																			.	.		0.701	KIAA2013-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000006858.1	NM_138346	
TIE1	7075	hgsc.bcm.edu	37	1	43774664	43774664	+	Silent	SNP	C	C	T			TCGA-WJ-A86L-01A-12D-A45V-10	TCGA-WJ-A86L-10A-01D-A38X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	80e4fac9-c066-47a9-9fc0-2a42eef954cd	cebd5a99-cbde-441d-b98a-b84cf1825d65	g.chr1:43774664C>T	ENST00000372476.3	+	8	1129	c.1050C>T	c.(1048-1050)atC>atT	p.I350I	TIE1_ENST00000441333.2_Intron|TIE1_ENST00000433781.2_5'UTR	NM_001253357.1|NM_005424.4	NP_001240286.1|NP_005415.1	P35590	TIE1_HUMAN	tyrosine kinase with immunoglobulin-like and EGF-like domains 1	350					angiogenesis (GO:0001525)|in utero embryonic development (GO:0001701)|mesoderm development (GO:0007498)|negative regulation of angiogenesis (GO:0016525)|negative regulation of cell migration (GO:0030336)|peptidyl-tyrosine phosphorylation (GO:0018108)|plasma membrane fusion (GO:0045026)|response to retinoic acid (GO:0032526)|signal transduction (GO:0007165)|vasculogenesis (GO:0001570)	integral component of plasma membrane (GO:0005887)	ATP binding (GO:0005524)|transmembrane receptor protein tyrosine kinase activity (GO:0004714)			breast(1)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(3)|kidney(3)|large_intestine(8)|lung(28)|ovary(3)|prostate(2)|salivary_gland(1)|skin(10)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(4)	70	Acute lymphoblastic leukemia(166;0.155)	Myeloproliferative disorder(586;0.0505)				CAGACCGGATCCCCCAGATCC	0.597																																					p.I350I		Atlas-SNP	.											.	TIE1	132	.	0			c.C1050T						.						75.0	64.0	68.0					1																	43774664		2203	4300	6503	SO:0001819	synonymous_variant	7075	exon8			CCGGATCCCCCAG	BC038239	CCDS482.1	1p34-p33	2013-02-11	2004-12-13	2004-12-14	ENSG00000066056	ENSG00000066056	2.7.10.1	"""Immunoglobulin superfamily / Immunoglobulin-like domain containing"", ""Fibronectin type III domain containing"""	11809	protein-coding gene	gene with protein product		600222	"""tyrosine kinase with immunoglobulin and epidermal growth factor homology domains 1"""	TIE		1312667	Standard	NM_005424		Approved	JTK14	uc001ciu.3	P35590	OTTHUMG00000007282	ENST00000372476.3:c.1050C>T	chr1.hg19:g.43774664C>T		203.0	0.0		320.0	15.0	NM_005424	B5A949|B5A950	Silent	SNP	ENST00000372476.3	hg19	CCDS482.1																																																																																			.	.		0.597	TIE1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000019011.1	NM_005424	
CYP4A11	1579	hgsc.bcm.edu	37	1	47401258	47401258	+	Missense_Mutation	SNP	A	A	G			TCGA-WJ-A86L-01A-12D-A45V-10	TCGA-WJ-A86L-10A-01D-A38X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	80e4fac9-c066-47a9-9fc0-2a42eef954cd	cebd5a99-cbde-441d-b98a-b84cf1825d65	g.chr1:47401258A>G	ENST00000310638.4	-	5	603	c.572T>C	c.(571-573)tTg>tCg	p.L191S	CYP4A11_ENST00000457840.2_Missense_Mutation_p.L87S|CYP4A11_ENST00000462347.1_Missense_Mutation_p.L191S|CYP4A11_ENST00000496519.1_5'Flank|CYP4A11_ENST00000371905.1_Missense_Mutation_p.L191S|CYP4A11_ENST00000371904.4_Missense_Mutation_p.L191S	NM_000778.3	NP_000769.2	Q02928	CP4AB_HUMAN	cytochrome P450, family 4, subfamily A, polypeptide 11	191					arachidonic acid metabolic process (GO:0019369)|cellular lipid metabolic process (GO:0044255)|epoxygenase P450 pathway (GO:0019373)|fatty acid metabolic process (GO:0006631)|leukotriene B4 catabolic process (GO:0036101)|leukotriene metabolic process (GO:0006691)|long-chain fatty acid metabolic process (GO:0001676)|omega-hydroxylase P450 pathway (GO:0097267)|oxidation-reduction process (GO:0055114)|positive regulation of icosanoid secretion (GO:0032305)|pressure natriuresis (GO:0003095)|renal water homeostasis (GO:0003091)|small molecule metabolic process (GO:0044281)|sodium ion homeostasis (GO:0055078)|xenobiotic metabolic process (GO:0006805)	apical plasma membrane (GO:0016324)|cytoplasm (GO:0005737)|endoplasmic reticulum membrane (GO:0005789)|extracellular vesicular exosome (GO:0070062)|intracellular membrane-bounded organelle (GO:0043231)	alkane 1-monooxygenase activity (GO:0018685)|arachidonic acid epoxygenase activity (GO:0008392)|arachidonic acid omega-hydroxylase activity (GO:0052869)|heme binding (GO:0020037)|iron ion binding (GO:0005506)|leukotriene-B4 20-monooxygenase activity (GO:0050051)			endometrium(2)|kidney(5)|large_intestine(6)|lung(6)|ovary(5)|prostate(3)|skin(6)|soft_tissue(1)|upper_aerodigestive_tract(2)	36					Cisplatin(DB00515)|Clofibrate(DB00636)|Dexamethasone(DB01234)|Estrone(DB00655)|Ethanol(DB00898)|Lansoprazole(DB00448)|Pegvisomant(DB00082)|Pentamidine(DB00738)|Phenobarbital(DB01174)|Rifampicin(DB01045)|Tretinoin(DB00755)	CAGGGTCATCAAGGAGACGTG	0.567																																					p.L191S		Atlas-SNP	.											.	CYP4A11	77	.	0			c.T572C						.						109.0	91.0	97.0					1																	47401258		2203	4300	6503	SO:0001583	missense	1579	exon5			GTCATCAAGGAGA	L04751	CCDS543.1	1p33	2008-02-05	2003-01-14		ENSG00000187048	ENSG00000187048		"""Cytochrome P450s"""	2642	protein-coding gene	gene with protein product		601310	"""cytochrome P450, subfamily IVA, polypeptide 11"""	CYP4A2		7679927	Standard	NM_000778		Approved	CYP4AII	uc001cqp.4	Q02928	OTTHUMG00000008020	ENST00000310638.4:c.572T>C	chr1.hg19:g.47401258A>G	ENSP00000311095:p.Leu191Ser	409.0	1.0		388.0	158.0	NM_000778	Q06766|Q16865|Q16866|Q5VSP8|Q86SU6|Q8IWY5	Missense_Mutation	SNP	ENST00000310638.4	hg19	CCDS543.1	.	.	.	.	.	.	.	.	.	.	N	19.75	3.885441	0.72410	.	.	ENSG00000187048	ENST00000310638;ENST00000371904;ENST00000371905;ENST00000457840	T;T;T;T	0.68903	-0.36;-0.36;-0.36;-0.36	5.14	3.99	0.46301	.	0.225843	0.37577	N	0.002028	T	0.72220	0.3433	M	0.74647	2.275	0.44728	D	0.997729	P	0.45011	0.848	P	0.48524	0.58	T	0.74318	-0.3704	10	0.59425	D	0.04	.	12.36	0.55197	0.8587:0.1413:0.0:0.0	.	191	Q02928	CP4AB_HUMAN	S	191;191;191;87	ENSP00000311095:L191S;ENSP00000360971:L191S;ENSP00000360972:L191S;ENSP00000406272:L87S	ENSP00000311095:L191S	L	-	2	0	CYP4A11	47173845	1.000000	0.71417	0.993000	0.49108	0.954000	0.61252	7.088000	0.76901	0.885000	0.36088	0.528000	0.53228	TTG	.	.		0.567	CYP4A11-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000022022.1	NM_000778	
LMO4	8543	hgsc.bcm.edu	37	1	87797781	87797781	+	Missense_Mutation	SNP	G	G	T			TCGA-WJ-A86L-01A-12D-A45V-10	TCGA-WJ-A86L-10A-01D-A38X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	80e4fac9-c066-47a9-9fc0-2a42eef954cd	cebd5a99-cbde-441d-b98a-b84cf1825d65	g.chr1:87797781G>T	ENST00000370544.5	+	2	863	c.83G>T	c.(82-84)gGc>gTc	p.G28V	LMO4_ENST00000489303.1_3'UTR|LMO4_ENST00000370542.1_Missense_Mutation_p.G28V	NM_006769.3	NP_006760.1	P61968	LMO4_HUMAN	LIM domain only 4	28	LIM zinc-binding 1. {ECO:0000255|PROSITE- ProRule:PRU00125}.				negative regulation of protein complex assembly (GO:0031333)|neural tube closure (GO:0001843)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of cell activation (GO:0050865)|regulation of cell fate specification (GO:0042659)|spinal cord association neuron differentiation (GO:0021527)|spinal cord motor neuron differentiation (GO:0021522)|thymus development (GO:0048538)|transcription from RNA polymerase II promoter (GO:0006366)|ventral spinal cord interneuron differentiation (GO:0021514)|ventricular septum development (GO:0003281)	transcription factor complex (GO:0005667)	enhancer sequence-specific DNA binding (GO:0001158)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription factor binding (GO:0008134)|zinc ion binding (GO:0008270)			NS(1)|endometrium(2)|kidney(3)|large_intestine(2)|lung(1)	9		Lung NSC(277;0.179)		all cancers(265;0.00456)|Epithelial(280;0.0148)|BRCA - Breast invasive adenocarcinoma(282;0.153)		GGCTGCGGGGGCAAGATTGCG	0.682																																					p.G28V		Atlas-SNP	.											.	LMO4	21	.	0			c.G83T						.						35.0	38.0	37.0					1																	87797781		2202	4300	6502	SO:0001583	missense	8543	exon2			GCGGGGGCAAGAT	U24576	CCDS713.1	1p22.3	2008-02-05			ENSG00000143013	ENSG00000143013			6644	protein-coding gene	gene with protein product		603129					Standard	NM_006769		Approved		uc001dmi.3	P61968	OTTHUMG00000010248	ENST00000370544.5:c.83G>T	chr1.hg19:g.87797781G>T	ENSP00000359575:p.Gly28Val	110.0	0.0		87.0	43.0	NM_006769	D3DT23|O00158|O88894	Missense_Mutation	SNP	ENST00000370544.5	hg19	CCDS713.1	.	.	.	.	.	.	.	.	.	.	G	23.2	4.389354	0.82902	.	.	ENSG00000143013	ENST00000370544;ENST00000370542	D;D	0.87491	-2.26;-2.26	5.57	5.57	0.84162	Zinc finger, LIM-type (5);	0.000000	0.85682	D	0.000000	D	0.89206	0.6649	M	0.70903	2.155	0.80722	D	1	D	0.54047	0.964	P	0.52386	0.697	D	0.88314	0.2958	10	0.44086	T	0.13	.	19.5493	0.95311	0.0:0.0:1.0:0.0	.	28	P61968	LMO4_HUMAN	V	28	ENSP00000359575:G28V;ENSP00000359573:G28V	ENSP00000359573:G28V	G	+	2	0	LMO4	87570369	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	7.750000	0.85110	2.621000	0.88768	0.650000	0.86243	GGC	.	.		0.682	LMO4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000028264.2	NM_006769	
PHGDH	26227	hgsc.bcm.edu	37	1	120286648	120286648	+	Missense_Mutation	SNP	C	C	G			TCGA-WJ-A86L-01A-12D-A45V-10	TCGA-WJ-A86L-10A-01D-A38X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	80e4fac9-c066-47a9-9fc0-2a42eef954cd	cebd5a99-cbde-441d-b98a-b84cf1825d65	g.chr1:120286648C>G	ENST00000369409.4	+	12	1723	c.1587C>G	c.(1585-1587)ttC>ttG	p.F529L	PHGDH_ENST00000482968.1_3'UTR|PHGDH_ENST00000369407.3_Missense_Mutation_p.F495L	NM_006623.3	NP_006614.2	O43175	SERA_HUMAN	phosphoglycerate dehydrogenase	529					brain development (GO:0007420)|cellular amino acid biosynthetic process (GO:0008652)|cellular nitrogen compound metabolic process (GO:0034641)|G1 to G0 transition (GO:0070314)|gamma-aminobutyric acid metabolic process (GO:0009448)|glial cell development (GO:0021782)|glutamine metabolic process (GO:0006541)|glycine metabolic process (GO:0006544)|L-serine biosynthetic process (GO:0006564)|neural tube development (GO:0021915)|neuron projection development (GO:0031175)|regulation of gene expression (GO:0010468)|small molecule metabolic process (GO:0044281)|spinal cord development (GO:0021510)|taurine metabolic process (GO:0019530)|threonine metabolic process (GO:0006566)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)	electron carrier activity (GO:0009055)|NAD binding (GO:0051287)|phosphoglycerate dehydrogenase activity (GO:0004617)			breast(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(3)|lung(5)|ovary(1)|upper_aerodigestive_tract(2)	18	all_cancers(5;1.18e-09)|all_epithelial(5;2.16e-10)|Melanoma(3;1.93e-05)|all_neural(166;0.219)	all_lung(203;3.66e-05)|Lung NSC(69;0.000202)|all_epithelial(167;0.0347)		Lung(183;0.0111)|LUSC - Lung squamous cell carcinoma(189;0.0593)		CTGAAGCCTTCCAGTTCCACT	0.542											OREG0013728	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.F529L		Atlas-SNP	.											.	PHGDH	51	.	0			c.C1587G						.						122.0	109.0	113.0					1																	120286648		2203	4300	6503	SO:0001583	missense	26227	exon12			AGCCTTCCAGTTC	BC011262	CCDS904.1	1p12	2008-02-05			ENSG00000092621	ENSG00000092621	1.1.1.95		8923	protein-coding gene	gene with protein product		606879					Standard	NM_006623		Approved	SERA, PGDH, PDG	uc001ehz.3	O43175	OTTHUMG00000012100	ENST00000369409.4:c.1587C>G	chr1.hg19:g.120286648C>G	ENSP00000358417:p.Phe529Leu	94.0	0.0	1502	94.0	40.0	NM_006623	B2RD08|Q5SZU3|Q9BQ01	Missense_Mutation	SNP	ENST00000369409.4	hg19	CCDS904.1	.	.	.	.	.	.	.	.	.	.	C	15.11	2.735718	0.49045	.	.	ENSG00000092621	ENST00000369409;ENST00000537497;ENST00000369407	D;D	0.90444	-2.66;-2.67	5.94	5.03	0.67393	.	0.145791	0.64402	D	0.000006	T	0.75671	0.3881	L	0.29908	0.895	0.35803	D	0.823254	B;B;P;P	0.42692	0.07;0.07;0.655;0.787	B;B;B;B	0.41236	0.021;0.021;0.231;0.351	T	0.74325	-0.3702	10	0.14656	T	0.56	-10.1735	11.1037	0.48190	0.0:0.9153:0.0:0.0847	.	495;495;402;529	B3KSC3;Q5SZU1;F5H634;O43175	.;.;.;SERA_HUMAN	L	529;402;495	ENSP00000358417:F529L;ENSP00000358415:F495L	ENSP00000358415:F495L	F	+	3	2	PHGDH	120088171	1.000000	0.71417	1.000000	0.80357	0.728000	0.41692	1.254000	0.32897	1.523000	0.49018	0.650000	0.86243	TTC	.	.		0.542	PHGDH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000033464.1	NM_006623	
NBPF10	100132406	hgsc.bcm.edu	37	1	145304611	145304611	+	Missense_Mutation	SNP	C	C	T			TCGA-WJ-A86L-01A-12D-A45V-10	TCGA-WJ-A86L-10A-01D-A38X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	80e4fac9-c066-47a9-9fc0-2a42eef954cd	cebd5a99-cbde-441d-b98a-b84cf1825d65	g.chr1:145304611C>T	ENST00000369339.3	+	7	984	c.731C>T	c.(730-732)tCc>tTc	p.S244F	RP11-458D21.5_ENST00000468030.1_3'UTR|NBPF10_ENST00000369338.1_Missense_Mutation_p.S244F|NBPF10_ENST00000342960.5_Missense_Mutation_p.S515F			Q6P3W6	NBPFA_HUMAN	neuroblastoma breakpoint family, member 10	515	NBPF 1. {ECO:0000255|PROSITE- ProRule:PRU00647}.					cytoplasm (GO:0005737)	poly(A) RNA binding (GO:0044822)			NS(3)|breast(1)|central_nervous_system(3)|endometrium(12)|kidney(23)|lung(15)|ovary(1)|prostate(7)|skin(6)|urinary_tract(2)	73	all_hematologic(923;0.032)			Colorectal(1306;1.36e-07)|KIRC - Kidney renal clear cell carcinoma(1967;0.00258)		ATTGGCTCATCCTCTCATGTT	0.428																																					p.S515F		Atlas-SNP	.											.	NBPF10	221	.	0			c.C1544T						.																																			SO:0001583	missense	100132406	exon10			GCTCATCCTCTCA	BC021111		1q21.1	2013-01-17			ENSG00000163386	ENSG00000271425		"""neuroblastoma breakpoint family"""	31992	protein-coding gene	gene with protein product		614000				16079250	Standard	NM_001039703		Approved	AG1		Q6P3W6	OTTHUMG00000013757	ENST00000369339.3:c.731C>T	chr1.hg19:g.145304611C>T	ENSP00000358345:p.Ser244Phe	194.0	0.0		462.0	75.0	NM_001039703	Q5RHC0|Q9NWN6	Missense_Mutation	SNP	ENST00000369339.3	hg19		.	.	.	.	.	.	.	.	.	.	.	9.728	1.161525	0.21538	.	.	ENSG00000163386	ENST00000448873;ENST00000369338;ENST00000369334;ENST00000342960;ENST00000449032	T;T	0.04406	3.68;3.63	0.745	0.745	0.18359	.	.	.	.	.	T	0.05502	0.0145	L	0.58810	1.83	0.09310	N	1	P;D;D;P	0.61080	0.676;0.969;0.989;0.952	P;P;D;P	0.64042	0.485;0.805;0.921;0.583	T	0.30679	-0.9970	9	0.62326	D	0.03	.	4.8431	0.13500	0.0:1.0:0.0:0.0	.	190;480;446;244	Q4VC10;Q3BBV7;Q5U227;A8MQ30	.;.;.;.	F	440;244;244;515;4	ENSP00000358344:S244F;ENSP00000345684:S515F	ENSP00000345684:S515F	S	+	2	0	NBPF10	144015968	0.000000	0.05858	0.007000	0.13788	0.035000	0.12851	-0.959000	0.03853	0.682000	0.31407	0.162000	0.16502	TCC	.	.		0.428	NBPF10-001	KNOWN	not_best_in_genome_evidence|basic	protein_coding	protein_coding	OTTHUMT00000038550.3	NM_001039703	
CD1A	909	hgsc.bcm.edu	37	1	158225110	158225110	+	Missense_Mutation	SNP	C	C	G			TCGA-WJ-A86L-01A-12D-A45V-10	TCGA-WJ-A86L-10A-01D-A38X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	80e4fac9-c066-47a9-9fc0-2a42eef954cd	cebd5a99-cbde-441d-b98a-b84cf1825d65	g.chr1:158225110C>G	ENST00000289429.5	+	2	828	c.295C>G	c.(295-297)Cgt>Ggt	p.R99G		NM_001763.2	NP_001754.2	P06126	CD1A_HUMAN	CD1a molecule	99					antigen processing and presentation (GO:0019882)|immune response (GO:0006955)	endosome (GO:0005768)|integral component of plasma membrane (GO:0005887)				NS(1)|central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(5)|lung(14)|pancreas(2)|prostate(4)|skin(2)|urinary_tract(1)	32	all_hematologic(112;0.0378)				Antithymocyte globulin(DB00098)	TGAGGGAATTCGTAGATACGC	0.468																																					p.R99G		Atlas-SNP	.											CD1A,right_lower_lobe,carcinoma,0,1	CD1A	88	.	0			c.C295G						.						88.0	84.0	85.0					1																	158225110		2203	4300	6503	SO:0001583	missense	909	exon2			GGAATTCGTAGAT	M28825	CCDS1174.1	1q23.1	2014-01-14	2006-03-28		ENSG00000158477	ENSG00000158477		"""CD molecules"", ""Immunoglobulin superfamily / C1-set domain containing"""	1634	protein-coding gene	gene with protein product		188370	"""CD1A antigen, a polypeptide"", ""CD1a antigen"""	CD1		2447586, 2784820	Standard	NM_001763		Approved		uc001frt.3	P06126	OTTHUMG00000017512	ENST00000289429.5:c.295C>G	chr1.hg19:g.158225110C>G	ENSP00000289429:p.Arg99Gly	77.0	0.0		141.0	34.0	NM_001763	D3DVD7|Q13962|Q5TDJ8|Q9UMM4|Q9Y5M5	Missense_Mutation	SNP	ENST00000289429.5	hg19	CCDS1174.1	.	.	.	.	.	.	.	.	.	.	C	10.31	1.314224	0.23908	.	.	ENSG00000158477	ENST00000289429	T	0.06528	3.29	4.07	-0.567	0.11763	MHC class I, alpha chain, alpha1/alpha2 (1);MHC classes I/II-like antigen recognition protein (1);MHC class I-like antigen recognition (1);	1.769060	0.03408	N	0.204308	T	0.02727	0.0082	L	0.42245	1.32	0.09310	N	1	B	0.30455	0.28	B	0.35278	0.199	T	0.46992	-0.9151	10	0.66056	D	0.02	0.0237	6.903	0.24293	0.4838:0.3544:0.1618:0.0	.	99	P06126	CD1A_HUMAN	G	99	ENSP00000289429:R99G	ENSP00000289429:R99G	R	+	1	0	CD1A	156491734	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-0.176000	0.09811	0.106000	0.17784	-0.203000	0.12734	CGT	.	.		0.468	CD1A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000046349.2	NM_001763	
OR10Z1	128368	hgsc.bcm.edu	37	1	158576910	158576910	+	Missense_Mutation	SNP	A	A	G			TCGA-WJ-A86L-01A-12D-A45V-10	TCGA-WJ-A86L-10A-01D-A38X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	80e4fac9-c066-47a9-9fc0-2a42eef954cd	cebd5a99-cbde-441d-b98a-b84cf1825d65	g.chr1:158576910A>G	ENST00000361284.1	+	1	682	c.682A>G	c.(682-684)Atc>Gtc	p.I228V		NM_001004478.1	NP_001004478.1	Q8NGY1	O10Z1_HUMAN	olfactory receptor, family 10, subfamily Z, member 1	228						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			endometrium(2)|large_intestine(6)|lung(21)|pancreas(1)|prostate(3)|skin(4)	37	all_hematologic(112;0.0378)					AATACTGAGGATCCCCTCTGC	0.502																																					p.I228V		Atlas-SNP	.											.	OR10Z1	99	.	0			c.A682G						.						157.0	154.0	155.0					1																	158576910		2203	4300	6503	SO:0001583	missense	128368	exon1			CTGAGGATCCCCT	AB065635	CCDS30901.1	1q23.1	2012-08-23			ENSG00000198967	ENSG00000198967		"""GPCR / Class A : Olfactory receptors"""	14996	protein-coding gene	gene with protein product							Standard	NM_001004478		Approved		uc010pio.2	Q8NGY1	OTTHUMG00000019637	ENST00000361284.1:c.682A>G	chr1.hg19:g.158576910A>G	ENSP00000354707:p.Ile228Val	56.0	0.0		112.0	36.0	NM_001004478	Q5VYL0|Q6IFR7	Missense_Mutation	SNP	ENST00000361284.1	hg19	CCDS30901.1	.	.	.	.	.	.	.	.	.	.	A	12.26	1.885767	0.33255	.	.	ENSG00000198967	ENST00000361284	T	0.00267	8.38	5.25	5.25	0.73442	GPCR, rhodopsin-like superfamily (1);	0.167587	0.28600	N	0.014761	T	0.00210	0.0006	L	0.58428	1.81	0.24946	N	0.991823	D	0.60575	0.988	P	0.61722	0.893	T	0.53865	-0.8378	10	0.51188	T	0.08	.	14.274	0.66167	1.0:0.0:0.0:0.0	.	228	Q8NGY1	O10Z1_HUMAN	V	228	ENSP00000354707:I228V	ENSP00000354707:I228V	I	+	1	0	OR10Z1	156843534	0.956000	0.32656	0.772000	0.31596	0.173000	0.22820	3.915000	0.56409	2.197000	0.70478	0.528000	0.53228	ATC	.	.		0.502	OR10Z1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051853.1	NM_001004478	
CACNA1E	777	hgsc.bcm.edu	37	1	181724436	181724436	+	Missense_Mutation	SNP	C	C	G			TCGA-WJ-A86L-01A-12D-A45V-10	TCGA-WJ-A86L-10A-01D-A38X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	80e4fac9-c066-47a9-9fc0-2a42eef954cd	cebd5a99-cbde-441d-b98a-b84cf1825d65	g.chr1:181724436C>G	ENST00000367573.2	+	28	3892	c.3892C>G	c.(3892-3894)Ctc>Gtc	p.L1298V	CACNA1E_ENST00000357570.5_Missense_Mutation_p.L1249V|CACNA1E_ENST00000358338.5_Missense_Mutation_p.L1230V|CACNA1E_ENST00000367570.1_Missense_Mutation_p.L1298V|CACNA1E_ENST00000360108.3_Missense_Mutation_p.L1279V|CACNA1E_ENST00000526775.1_Missense_Mutation_p.L1279V|CACNA1E_ENST00000367567.4_Missense_Mutation_p.L905V	NM_001205293.1	NP_001192222.1	Q15878	CAC1E_HUMAN	calcium channel, voltage-dependent, R type, alpha 1E subunit	1298					calcium ion import (GO:0070509)|energy reserve metabolic process (GO:0006112)|membrane depolarization (GO:0051899)|membrane depolarization during action potential (GO:0086010)|regulation of insulin secretion (GO:0050796)|small molecule metabolic process (GO:0044281)|synaptic transmission (GO:0007268)|transport (GO:0006810)	plasma membrane (GO:0005886)|voltage-gated calcium channel complex (GO:0005891)	calcium ion binding (GO:0005509)|high voltage-gated calcium channel activity (GO:0008331)|voltage-gated calcium channel activity (GO:0005245)			NS(2)|breast(9)|central_nervous_system(3)|cervix(1)|endometrium(22)|haematopoietic_and_lymphoid_tissue(6)|kidney(4)|large_intestine(34)|lung(99)|ovary(6)|pancreas(1)|prostate(9)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	204						TGTGTACAAGCTCTTCATGTT	0.473																																					p.L1298V		Atlas-SNP	.											.	CACNA1E	778	.	0			c.C3892G						.						219.0	210.0	213.0					1																	181724436		2039	4212	6251	SO:0001583	missense	777	exon28			TACAAGCTCTTCA	AK096563	CCDS53443.1, CCDS55664.1, CCDS55665.1	1q25.3	2013-01-10	2007-02-16		ENSG00000198216	ENSG00000198216		"""Calcium channel subunits"", ""Voltage-gated ion channels / Calcium channels"", ""EF-hand domain containing"""	1392	protein-coding gene	gene with protein product		601013		CACNL1A6		8388125, 16382099	Standard	NM_001205293		Approved	Cav2.3, BII, CACH6	uc009wxt.3	Q15878	OTTHUMG00000037301	ENST00000367573.2:c.3892C>G	chr1.hg19:g.181724436C>G	ENSP00000356545:p.Leu1298Val	54.0	0.0		111.0	33.0	NM_001205293	B1AM12|B1AM13|B1AM14|Q14580|Q14581	Missense_Mutation	SNP	ENST00000367573.2	hg19	CCDS55664.1	.	.	.	.	.	.	.	.	.	.	C	24.6	4.549492	0.86127	.	.	ENSG00000198216	ENST00000367570;ENST00000526775;ENST00000357570;ENST00000358338;ENST00000367567;ENST00000360108;ENST00000367573	D;D;D;D;D;D;D	0.98701	-5.08;-5.08;-5.08;-5.08;-5.08;-5.08;-5.08	5.29	4.38	0.52667	Ion transport (1);	0.060200	0.64402	D	0.000002	D	0.98957	0.9645	M	0.81802	2.56	0.80722	D	1	P;D;P	0.69078	0.939;0.997;0.827	P;D;B	0.72338	0.901;0.977;0.269	D	0.99593	1.0976	10	0.87932	D	0	.	13.1804	0.59651	0.0:0.9224:0.0:0.0776	.	1279;1298;1298	Q15878-2;Q15878;Q15878-3	.;CAC1E_HUMAN;.	V	1298;1279;1249;1230;905;1279;1298	ENSP00000356542:L1298V;ENSP00000434814:L1279V;ENSP00000350183:L1249V;ENSP00000351101:L1230V;ENSP00000356539:L905V;ENSP00000353222:L1279V;ENSP00000356545:L1298V	ENSP00000350183:L1249V	L	+	1	0	CACNA1E	179991059	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.676000	0.84012	1.227000	0.43598	0.650000	0.86243	CTC	.	.		0.473	CACNA1E-003	KNOWN	non_canonical_U12|basic|CCDS	protein_coding	protein_coding	OTTHUMT00000090793.2	NM_000721	
ELK4	2005	hgsc.bcm.edu	37	1	205589082	205589082	+	Intron	SNP	C	C	A			TCGA-WJ-A86L-01A-12D-A45V-10	TCGA-WJ-A86L-10A-01D-A38X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	80e4fac9-c066-47a9-9fc0-2a42eef954cd	cebd5a99-cbde-441d-b98a-b84cf1825d65	g.chr1:205589082C>A	ENST00000357992.4	-	3	1420				ELK4_ENST00000289703.4_Silent_p.S364S|ELK4_ENST00000468523.1_5'Flank	NM_001973.3	NP_001964.2	P28324	ELK4_HUMAN	ELK4, ETS-domain protein (SRF accessory protein 1)						cell differentiation (GO:0030154)|histone H3 deacetylation (GO:0070932)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|transcription from RNA polymerase II promoter (GO:0006366)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	chromatin binding (GO:0003682)|core promoter binding (GO:0001047)|DNA binding (GO:0003677)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0000981)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription cofactor activity (GO:0003712)	p.S364S(1)	SLC45A3/ELK4(18)	breast(1)|endometrium(1)|kidney(2)|large_intestine(1)|lung(6)|skin(1)	12	Breast(84;0.07)		BRCA - Breast invasive adenocarcinoma(75;0.0908)			CCATAAAGAGCGAGCAAGCTA	0.418			T	SLC45A3	prostate																																p.S364S		Atlas-SNP	.		Dom	yes		1	1q32	2005	"""ELK4, ETS-domain protein (SRF accessory protein 1)"""		E	ELK4_ENST00000289703,colon,carcinoma,0,1	ELK4	45	.	1	Substitution - coding silent(1)	large_intestine(1)	c.G1092T						.						77.0	79.0	78.0					1																	205589082		2203	4300	6503	SO:0001627	intron_variant	2005	exon3			AAAGAGCGAGCAA	M85165	CCDS1456.1, CCDS1457.1	1q32	2008-02-05			ENSG00000158711	ENSG00000158711			3326	protein-coding gene	gene with protein product		600246				7851904, 8575773	Standard	NM_001973		Approved	SAP1		P28324	OTTHUMG00000037221	ENST00000357992.4:c.1080+11G>T	chr1.hg19:g.205589082C>A		93.0	0.0		143.0	42.0	NM_021795	P28323|Q6GSJ2	Silent	SNP	ENST00000357992.4	hg19	CCDS1456.1																																																																																			.	.		0.418	ELK4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000090615.1	NM_021795	
SLC26A9	115019	hgsc.bcm.edu	37	1	205886474	205886474	+	Silent	SNP	C	C	A			TCGA-WJ-A86L-01A-12D-A45V-10	TCGA-WJ-A86L-10A-01D-A38X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	80e4fac9-c066-47a9-9fc0-2a42eef954cd	cebd5a99-cbde-441d-b98a-b84cf1825d65	g.chr1:205886474C>A	ENST00000367135.3	-	20	2378	c.2265G>T	c.(2263-2265)ggG>ggT	p.G755G	SLC26A9_ENST00000367134.2_Silent_p.G755G|SLC26A9_ENST00000340781.4_Silent_p.G755G	NM_052934.3	NP_443166.1	Q7LBE3	S26A9_HUMAN	solute carrier family 26 (anion exchanger), member 9	755					anion transport (GO:0006820)|bicarbonate transport (GO:0015701)|chloride transmembrane transport (GO:1902476)|chloride transport (GO:0006821)|ion transport (GO:0006811)|positive regulation of gene expression (GO:0010628)|regulation of pH (GO:0006885)|transmembrane transport (GO:0055085)	apical plasma membrane (GO:0016324)|cell surface (GO:0009986)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	anion:anion antiporter activity (GO:0015301)|ATPase binding (GO:0051117)|bicarbonate transmembrane transporter activity (GO:0015106)|chloride channel activity (GO:0005254)|secondary active sulfate transmembrane transporter activity (GO:0008271)			NS(1)|breast(3)|endometrium(11)|kidney(1)|large_intestine(6)|lung(17)|ovary(1)|skin(7)|urinary_tract(5)	52	Breast(84;0.201)		BRCA - Breast invasive adenocarcinoma(75;0.0458)			GCTCAGCATCCCCTGGAGCCT	0.587																																					p.G755G		Atlas-SNP	.											.	SLC26A9	176	.	0			c.G2265T						.						178.0	163.0	168.0					1																	205886474		2203	4300	6503	SO:0001819	synonymous_variant	115019	exon20			AGCATCCCCTGGA	AF331525	CCDS30989.1, CCDS30990.1	1q32.1	2013-07-18	2013-07-18		ENSG00000174502	ENSG00000174502		"""Solute carriers"""	14469	protein-coding gene	gene with protein product	"""anion transporter/exchanger-9"""	608481	"""solute carrier family 26, member 9"""			11834742	Standard	NM_134325		Approved		uc001hdp.3	Q7LBE3	OTTHUMG00000036001	ENST00000367135.3:c.2265G>T	chr1.hg19:g.205886474C>A		70.0	0.0		74.0	23.0	NM_134325	A7E2V6|B1AVM8|B1AVM9|B7ZKK2|Q96PK9|Q96RN0	Silent	SNP	ENST00000367135.3	hg19	CCDS30990.1																																																																																			.	.		0.587	SLC26A9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000087742.1	NM_052934	
PLXNA2	5362	hgsc.bcm.edu	37	1	208257756	208257756	+	Missense_Mutation	SNP	T	T	C			TCGA-WJ-A86L-01A-12D-A45V-10	TCGA-WJ-A86L-10A-01D-A38X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	80e4fac9-c066-47a9-9fc0-2a42eef954cd	cebd5a99-cbde-441d-b98a-b84cf1825d65	g.chr1:208257756T>C	ENST00000367033.3	-	10	3024	c.2267A>G	c.(2266-2268)aAc>aGc	p.N756S		NM_025179.3	NP_079455.3	O75051	PLXA2_HUMAN	plexin A2	756					axon guidance (GO:0007411)|centrosome localization (GO:0051642)|cerebellar granule cell precursor tangential migration (GO:0021935)|limb bud formation (GO:0060174)|neural tube development (GO:0021915)|pharyngeal system development (GO:0060037)|regulation of cell migration (GO:0030334)|semaphorin-plexin signaling pathway (GO:0071526)|somitogenesis (GO:0001756)	integral component of plasma membrane (GO:0005887)|intracellular (GO:0005622)|plasma membrane (GO:0005886)|semaphorin receptor complex (GO:0002116)	semaphorin receptor activity (GO:0017154)			NS(1)|breast(3)|central_nervous_system(5)|cervix(1)|endometrium(15)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(9)|liver(1)|lung(28)|ovary(3)|prostate(5)|skin(2)|upper_aerodigestive_tract(3)	80				OV - Ovarian serous cystadenocarcinoma(81;0.199)		GCTGGAGCTGTTGAAGCGCAG	0.617																																					p.N756S		Atlas-SNP	.											.	PLXNA2	178	.	0			c.A2267G						.						62.0	67.0	65.0					1																	208257756		2203	4300	6503	SO:0001583	missense	5362	exon10			GAGCTGTTGAAGC	X87831	CCDS31013.1	1q32.2	2008-07-18			ENSG00000076356	ENSG00000076356		"""Plexins"""	9100	protein-coding gene	gene with protein product	"""plexin 2"", ""plexin-A2"", ""semaphorin receptor OCT"", ""transmembrane protein OCT"""	601054		PLXN2		8570614	Standard	NM_025179		Approved	OCT, FLJ11751, FLJ30634, KIAA0463	uc001hgz.3	O75051	OTTHUMG00000036564	ENST00000367033.3:c.2267A>G	chr1.hg19:g.208257756T>C	ENSP00000356000:p.Asn756Ser	90.0	0.0		103.0	59.0	NM_025179	A2RTX9|B2RMX7|Q6UX61|Q96GN9|Q9BRL1|Q9UIW1	Missense_Mutation	SNP	ENST00000367033.3	hg19	CCDS31013.1	.	.	.	.	.	.	.	.	.	.	T	17.34	3.363753	0.61513	.	.	ENSG00000076356	ENST00000367033	T	0.00949	5.51	5.7	4.55	0.56014	.	0.041334	0.85682	D	0.000000	T	0.01905	0.0060	M	0.71206	2.165	0.80722	D	1	P	0.51057	0.941	P	0.45343	0.477	T	0.67757	-0.5588	10	0.16896	T	0.51	.	12.036	0.53425	0.1295:0.0:0.0:0.8705	.	756	O75051	PLXA2_HUMAN	S	756	ENSP00000356000:N756S	ENSP00000356000:N756S	N	-	2	0	PLXNA2	206324379	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	7.751000	0.85126	0.946000	0.37632	0.528000	0.53228	AAC	.	.		0.617	PLXNA2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000088932.6	NM_025179	
RPS6KC1	26750	hgsc.bcm.edu	37	1	213403855	213403855	+	Missense_Mutation	SNP	G	G	A			TCGA-WJ-A86L-01A-12D-A45V-10	TCGA-WJ-A86L-10A-01D-A38X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	80e4fac9-c066-47a9-9fc0-2a42eef954cd	cebd5a99-cbde-441d-b98a-b84cf1825d65	g.chr1:213403855G>A	ENST00000366960.3	+	9	1210	c.1060G>A	c.(1060-1062)Gac>Aac	p.D354N	RPS6KC1_ENST00000543470.1_Missense_Mutation_p.D142N|RPS6KC1_ENST00000366959.3_Missense_Mutation_p.D342N|RPS6KC1_ENST00000490299.1_3'UTR|RPS6KC1_ENST00000543354.1_Missense_Mutation_p.D57N	NM_012424.3	NP_036556.2	Q96S38	KS6C1_HUMAN	ribosomal protein S6 kinase, 52kDa, polypeptide 1	354	Protein kinase 1. {ECO:0000255|PROSITE- ProRule:PRU00159}.				signal transduction (GO:0007165)	cytoplasm (GO:0005737)|early endosome (GO:0005769)|intracellular membrane-bounded organelle (GO:0043231)|membrane (GO:0016020)	ATP binding (GO:0005524)|phosphatidylinositol binding (GO:0035091)|protein serine/threonine kinase activity (GO:0004674)			breast(1)|endometrium(6)|kidney(4)|large_intestine(8)|liver(2)|lung(15)|ovary(3)|prostate(1)|urinary_tract(3)	43				OV - Ovarian serous cystadenocarcinoma(81;0.00705)|all cancers(67;0.016)|GBM - Glioblastoma multiforme(131;0.0663)|Epithelial(68;0.145)		ACTTGTAATGGACACAAGGAC	0.353																																					p.D354N		Atlas-SNP	.											.	RPS6KC1	114	.	0			c.G1060A						.						63.0	65.0	65.0					1																	213403855		2202	4300	6502	SO:0001583	missense	26750	exon9			GTAATGGACACAA	AF037447	CCDS1513.1, CCDS44317.1, CCDS73028.1, CCDS73029.1, CCDS73030.1	1q41	2011-04-05	2002-08-29		ENSG00000136643	ENSG00000136643			10439	protein-coding gene	gene with protein product			"""ribosomal protein S6 kinase, 52kD, polypeptide 1"""			10552933	Standard	XM_005273095		Approved	humS6PKh1	uc010ptr.2	Q96S38	OTTHUMG00000036926	ENST00000366960.3:c.1060G>A	chr1.hg19:g.213403855G>A	ENSP00000355927:p.Asp354Asn	82.0	0.0		122.0	29.0	NM_012424	B1APS8|B3KVM4|D3DTA4|Q8TDD3|Q9NSF4|Q9UL66	Missense_Mutation	SNP	ENST00000366960.3	hg19	CCDS1513.1	.	.	.	.	.	.	.	.	.	.	G	32	5.140250	0.94560	.	.	ENSG00000136643	ENST00000543470;ENST00000366960;ENST00000366959;ENST00000543354	T;T;T;T	0.26223	1.75;1.75;1.75;1.75	5.45	5.45	0.79879	.	0.000000	0.85682	D	0.000000	T	0.50616	0.1626	L	0.56769	1.78	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.87578	0.998;0.987;0.987	T	0.48864	-0.8997	10	0.87932	D	0	-27.0026	19.6558	0.95837	0.0:0.0:1.0:0.0	.	142;354;342	F5H7T0;Q96S38;B1APS8	.;KS6C1_HUMAN;.	N	142;354;342;57	ENSP00000442306:D142N;ENSP00000355927:D354N;ENSP00000355926:D342N;ENSP00000439282:D57N	ENSP00000355926:D342N	D	+	1	0	RPS6KC1	211470478	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	8.409000	0.90223	2.719000	0.93026	0.655000	0.94253	GAC	.	.		0.353	RPS6KC1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000089690.3	NM_012424	
USH2A	7399	hgsc.bcm.edu	37	1	216420308	216420308	+	Missense_Mutation	SNP	C	C	A			TCGA-WJ-A86L-01A-12D-A45V-10	TCGA-WJ-A86L-10A-01D-A38X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	80e4fac9-c066-47a9-9fc0-2a42eef954cd	cebd5a99-cbde-441d-b98a-b84cf1825d65	g.chr1:216420308C>A	ENST00000307340.3	-	13	2814	c.2428G>T	c.(2428-2430)Gct>Tct	p.A810S	USH2A_ENST00000366942.3_Missense_Mutation_p.A810S|USH2A_ENST00000366943.2_Missense_Mutation_p.A810S	NM_206933.2	NP_996816	O75445	USH2A_HUMAN	Usher syndrome 2A (autosomal recessive, mild)	810	Laminin EGF-like 6. {ECO:0000255|PROSITE- ProRule:PRU00460}.				hair cell differentiation (GO:0035315)|inner ear receptor cell differentiation (GO:0060113)|maintenance of organ identity (GO:0048496)|photoreceptor cell maintenance (GO:0045494)|response to stimulus (GO:0050896)|sensory perception of light stimulus (GO:0050953)|sensory perception of sound (GO:0007605)|visual perception (GO:0007601)	apical plasma membrane (GO:0016324)|basement membrane (GO:0005604)|cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)|stereocilia ankle link complex (GO:0002142)|stereocilium bundle (GO:0032421)|stereocilium membrane (GO:0060171)	collagen binding (GO:0005518)|myosin binding (GO:0017022)			NS(7)|breast(20)|central_nervous_system(3)|cervix(2)|endometrium(32)|haematopoietic_and_lymphoid_tissue(4)|kidney(13)|large_intestine(71)|liver(2)|lung(282)|ovary(25)|pancreas(2)|prostate(12)|skin(22)|stomach(7)|upper_aerodigestive_tract(20)|urinary_tract(3)	527				OV - Ovarian serous cystadenocarcinoma(81;0.0547)|all cancers(67;0.0875)		CCTGTCTTAGCATTACAGACA	0.463										HNSCC(13;0.011)																											p.A810S		Atlas-SNP	.											.	USH2A	1168	.	0			c.G2428T						.						116.0	110.0	112.0					1																	216420308		2203	4300	6503	SO:0001583	missense	7399	exon13			TCTTAGCATTACA	AF055580	CCDS1516.1, CCDS31025.1	1q41	2013-02-11			ENSG00000042781	ENSG00000042781		"""Fibronectin type III domain containing"""	12601	protein-coding gene	gene with protein product	"""usherin"""	608400		USH2		9624053, 10729113	Standard	NM_007123		Approved	RP39	uc001hku.1	O75445	OTTHUMG00000037079	ENST00000307340.3:c.2428G>T	chr1.hg19:g.216420308C>A	ENSP00000305941:p.Ala810Ser	127.0	0.0		224.0	73.0	NM_007123	Q5VVM9|Q6S362|Q9NS27	Missense_Mutation	SNP	ENST00000307340.3	hg19	CCDS31025.1	.	.	.	.	.	.	.	.	.	.	C	9.229	1.035302	0.19590	.	.	ENSG00000042781	ENST00000307340;ENST00000366943;ENST00000366942	T;T;T	0.60424	0.19;0.19;0.19	5.65	0.136	0.14780	EGF-like, laminin (2);	0.327586	0.21579	N	0.072262	T	0.36690	0.0976	L	0.28400	0.85	0.09310	N	1	B;B	0.17038	0.011;0.02	B;B	0.17098	0.017;0.017	T	0.12915	-1.0529	10	0.27082	T	0.32	.	4.3236	0.11029	0.1225:0.4311:0.3186:0.1278	.	810;810	O75445-2;O75445	.;USH2A_HUMAN	S	810	ENSP00000305941:A810S;ENSP00000355910:A810S;ENSP00000355909:A810S	ENSP00000305941:A810S	A	-	1	0	USH2A	214486931	0.000000	0.05858	0.000000	0.03702	0.696000	0.40369	-0.836000	0.04382	-0.239000	0.09710	-0.165000	0.13383	GCT	.	.		0.463	USH2A-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000128138.1	NM_007123	
OR2T4	127074	hgsc.bcm.edu	37	1	248524962	248524962	+	Missense_Mutation	SNP	A	A	C			TCGA-WJ-A86L-01A-12D-A45V-10	TCGA-WJ-A86L-10A-01D-A38X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	80e4fac9-c066-47a9-9fc0-2a42eef954cd	cebd5a99-cbde-441d-b98a-b84cf1825d65	g.chr1:248524962A>C	ENST00000366475.1	+	1	80	c.80A>C	c.(79-81)cAt>cCt	p.H27P		NM_001004696.1	NP_001004696.1	Q8NH00	OR2T4_HUMAN	olfactory receptor, family 2, subfamily T, member 4	27						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			central_nervous_system(1)|endometrium(1)|kidney(2)|large_intestine(3)|liver(2)|lung(47)	56	all_cancers(71;0.000108)|all_epithelial(71;1.03e-05)|Breast(184;0.00909)|Ovarian(71;0.0377)|all_lung(81;0.127)|Lung NSC(105;0.136)		OV - Ovarian serous cystadenocarcinoma(106;0.0265)			CAATCCAAACATCCAATGGCC	0.493																																					p.H27P		Atlas-SNP	.											.	OR2T4	126	.	0			c.A80C						.						108.0	92.0	97.0					1																	248524962		2203	4299	6502	SO:0001583	missense	127074	exon1			CCAAACATCCAAT	BK004464	CCDS31113.1	1q44	2012-08-09			ENSG00000196944	ENSG00000196944		"""GPCR / Class A : Olfactory receptors"""	15016	protein-coding gene	gene with protein product							Standard	NM_001004696		Approved	OR2T4Q	uc001ieh.1	Q8NH00	OTTHUMG00000040453	ENST00000366475.1:c.80A>C	chr1.hg19:g.248524962A>C	ENSP00000355431:p.His27Pro	253.0	0.0		361.0	91.0	NM_001004696	Q6IEZ8	Missense_Mutation	SNP	ENST00000366475.1	hg19	CCDS31113.1	.	.	.	.	.	.	.	.	.	.	A	9.295	1.051596	0.19827	.	.	ENSG00000196944	ENST00000366475	T	0.01629	4.72	1.28	1.28	0.21552	.	.	.	.	.	T	0.01156	0.0038	N	0.08118	0	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.47636	-0.9102	9	0.40728	T	0.16	.	6.2492	0.20835	1.0:0.0:0.0:0.0	.	27	Q8NH00	OR2T4_HUMAN	P	27	ENSP00000355431:H27P	ENSP00000355431:H27P	H	+	2	0	OR2T4	246591585	0.518000	0.26234	0.516000	0.27786	0.274000	0.26718	0.000000	0.12993	0.505000	0.28104	0.352000	0.21897	CAT	.	.		0.493	OR2T4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000097349.2	NM_001004696	
KIAA1841	84542	hgsc.bcm.edu	37	2	61297534	61297534	+	Missense_Mutation	SNP	C	C	G			TCGA-WJ-A86L-01A-12D-A45V-10	TCGA-WJ-A86L-10A-01D-A38X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	80e4fac9-c066-47a9-9fc0-2a42eef954cd	cebd5a99-cbde-441d-b98a-b84cf1825d65	g.chr2:61297534C>G	ENST00000402291.1	+	3	290	c.49C>G	c.(49-51)Caa>Gaa	p.Q17E	KIAA1841_ENST00000356719.2_Missense_Mutation_p.Q17E|KIAA1841_ENST00000295031.5_Missense_Mutation_p.Q17E|KIAA1841_ENST00000453873.1_Missense_Mutation_p.Q17E|KIAA1841_ENST00000482513.1_3'UTR	NM_001129993.1	NP_001123465.1	Q6NSI8	K1841_HUMAN	KIAA1841	17										breast(3)|kidney(1)|large_intestine(4)|lung(12)|ovary(1)|skin(2)|stomach(1)|urinary_tract(1)	25			Epithelial(17;0.193)			CAATAATAACCAAATGGTATT	0.373																																					p.Q17E		Atlas-SNP	.											.	KIAA1841	95	.	0			c.C49G						.						115.0	113.0	113.0					2																	61297534		2203	4300	6503	SO:0001583	missense	84542	exon3			AATAACCAAATGG	BC070104	CCDS1867.1, CCDS46296.1	2p15	2010-06-22			ENSG00000162929	ENSG00000162929			29387	protein-coding gene	gene with protein product						11347906	Standard	NM_032506		Approved		uc002saw.4	Q6NSI8	OTTHUMG00000129421	ENST00000402291.1:c.49C>G	chr2.hg19:g.61297534C>G	ENSP00000385579:p.Gln17Glu	93.0	0.0		98.0	40.0	NM_032506	Q49AF0|Q6ZND0|Q96JI6	Missense_Mutation	SNP	ENST00000402291.1	hg19	CCDS46296.1	.	.	.	.	.	.	.	.	.	.	C	12.04	1.818084	0.32145	.	.	ENSG00000162929	ENST00000402291;ENST00000295031;ENST00000356719;ENST00000453873	.	.	.	5.95	5.95	0.96441	.	0.268713	0.39274	N	0.001401	T	0.44138	0.1279	L	0.29908	0.895	0.34599	D	0.716367	P;B;P	0.46859	0.729;0.435;0.885	B;B;B	0.40066	0.21;0.104;0.318	T	0.49224	-0.8962	9	0.22109	T	0.4	-16.1475	20.3932	0.98965	0.0:1.0:0.0:0.0	.	17;17;17	Q6NSI8-2;Q6NSI8;Q6NSI8-4	.;K1841_HUMAN;.	E	17	.	ENSP00000295031:Q17E	Q	+	1	0	KIAA1841	61151038	1.000000	0.71417	1.000000	0.80357	0.981000	0.71138	2.417000	0.44653	2.824000	0.97209	0.655000	0.94253	CAA	.	.		0.373	KIAA1841-003	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000325477.1	NM_032506	
APLF	200558	hgsc.bcm.edu	37	2	68753315	68753315	+	Missense_Mutation	SNP	C	C	A			TCGA-WJ-A86L-01A-12D-A45V-10	TCGA-WJ-A86L-10A-01D-A38X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	80e4fac9-c066-47a9-9fc0-2a42eef954cd	cebd5a99-cbde-441d-b98a-b84cf1825d65	g.chr2:68753315C>A	ENST00000303795.4	+	6	916	c.745C>A	c.(745-747)Caa>Aaa	p.Q249K		NM_173545.2	NP_775816.1	Q8IW19	APLF_HUMAN	aprataxin and PNKP like factor	249					cellular response to DNA damage stimulus (GO:0006974)|DNA catabolic process, endonucleolytic (GO:0000737)|double-strand break repair (GO:0006302)|nucleic acid phosphodiester bond hydrolysis (GO:0090305)|positive regulation of DNA ligation (GO:0051106)|regulation of isotype switching (GO:0045191)|single strand break repair (GO:0000012)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|site of double-strand break (GO:0035861)	3'-5' exonuclease activity (GO:0008408)|DNA-(apurinic or apyrimidinic site) lyase activity (GO:0003906)|endodeoxyribonuclease activity (GO:0004520)|metal ion binding (GO:0046872)|nucleotide binding (GO:0000166)			autonomic_ganglia(1)|breast(1)|endometrium(1)|kidney(1)|large_intestine(5)|liver(2)|lung(9)|ovary(3)|prostate(1)|skin(1)	25						ATCAGCAGAACAAGACACAGG	0.338																																					p.Q249K		Atlas-SNP	.											.	APLF	69	.	0			c.C745A						.						107.0	111.0	110.0					2																	68753315		2203	4300	6503	SO:0001583	missense	200558	exon6			GCAGAACAAGACA	BC030711	CCDS1888.1	2p14	2014-02-20	2008-10-01	2008-10-01	ENSG00000169621	ENSG00000169621			28724	protein-coding gene	gene with protein product	"""XRCC1-interacting protein 1"", ""zinc finger, CX5CX6HX5H motif containing 1"""	611035	"""chromosome 2 open reading frame 13"""	C2orf13		18474613, 18077224, 17353262	Standard	NM_173545		Approved	MGC47799, Xip1, ZCCHH1	uc002sep.3	Q8IW19	OTTHUMG00000129566	ENST00000303795.4:c.745C>A	chr2.hg19:g.68753315C>A	ENSP00000307004:p.Gln249Lys	250.0	0.0		273.0	137.0	NM_173545	A8K476|Q53P47|Q53PB9|Q53QU0	Missense_Mutation	SNP	ENST00000303795.4	hg19	CCDS1888.1	.	.	.	.	.	.	.	.	.	.	c	10.75	1.439547	0.25900	.	.	ENSG00000169621	ENST00000303795	T	0.23147	1.92	4.71	0.44	0.16572	.	1.022680	0.07738	N	0.946347	T	0.24699	0.0599	M	0.62723	1.935	0.09310	N	1	B;B	0.31318	0.037;0.319	B;B	0.27608	0.018;0.081	T	0.25641	-1.0126	10	0.27082	T	0.32	.	9.035	0.36282	0.1587:0.3777:0.4636:0.0	.	249;249	F8WET0;Q8IW19	.;APLF_HUMAN	K	249	ENSP00000307004:Q249K	ENSP00000307004:Q249K	Q	+	1	0	APLF	68606819	0.982000	0.34865	0.002000	0.10522	0.475000	0.33008	0.242000	0.18087	-0.019000	0.14055	0.585000	0.79938	CAA	.	.		0.338	APLF-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251759.1	NM_173545	
ITGA4	3676	hgsc.bcm.edu	37	2	182388920	182388920	+	Missense_Mutation	SNP	A	A	T			TCGA-WJ-A86L-01A-12D-A45V-10	TCGA-WJ-A86L-10A-01D-A38X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	80e4fac9-c066-47a9-9fc0-2a42eef954cd	cebd5a99-cbde-441d-b98a-b84cf1825d65	g.chr2:182388920A>T	ENST00000397033.2	+	20	2622	c.2192A>T	c.(2191-2193)gAt>gTt	p.D731V		NM_000885.4	NP_000876.3	P13612	ITA4_HUMAN	integrin, alpha 4 (antigen CD49D, alpha 4 subunit of VLA-4 receptor)	731					B cell differentiation (GO:0030183)|blood coagulation (GO:0007596)|blood vessel remodeling (GO:0001974)|cell-matrix adhesion (GO:0007160)|cell-matrix adhesion involved in ameboidal cell migration (GO:0003366)|chorio-allantoic fusion (GO:0060710)|endodermal cell differentiation (GO:0035987)|extracellular matrix organization (GO:0030198)|face development (GO:0060324)|heart development (GO:0007507)|heterophilic cell-cell adhesion (GO:0007157)|heterotypic cell-cell adhesion (GO:0034113)|integrin-mediated signaling pathway (GO:0007229)|leukocyte cell-cell adhesion (GO:0007159)|leukocyte migration (GO:0050900)|leukocyte tethering or rolling (GO:0050901)|negative regulation of protein homodimerization activity (GO:0090074)|receptor clustering (GO:0043113)|regulation of immune response (GO:0050776)|substrate adhesion-dependent cell spreading (GO:0034446)|T cell migration (GO:0072678)	cell surface (GO:0009986)|cell-cell junction (GO:0005911)|external side of plasma membrane (GO:0009897)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|integrin alpha4-beta7 complex (GO:0034669)|membrane (GO:0016020)|plasma membrane (GO:0005886)	cell adhesion molecule binding (GO:0050839)|metal ion binding (GO:0046872)			breast(3)|central_nervous_system(2)|cervix(1)|endometrium(4)|kidney(3)|large_intestine(9)|lung(27)|ovary(3)|pancreas(1)|prostate(1)|upper_aerodigestive_tract(1)|urinary_tract(3)	58			OV - Ovarian serous cystadenocarcinoma(117;0.0593)		Natalizumab(DB00108)|Tinzaparin(DB06822)	TTTCTCCTGGATGTGAGCTCA	0.338																																					p.D731V		Atlas-SNP	.											.	ITGA4	142	.	0			c.A2192T						.						71.0	66.0	67.0					2																	182388920		1831	4076	5907	SO:0001583	missense	3676	exon20			TCCTGGATGTGAG		CCDS42788.1	2q31-q32	2010-03-23			ENSG00000115232	ENSG00000115232		"""CD molecules"", ""Integrins"""	6140	protein-coding gene	gene with protein product		192975		CD49D		1537388	Standard	NM_000885		Approved	CD49d	uc002unu.3	P13612	OTTHUMG00000154212	ENST00000397033.2:c.2192A>T	chr2.hg19:g.182388920A>T	ENSP00000380227:p.Asp731Val	165.0	0.0		141.0	54.0	NM_000885	D3DPG4|Q7Z4L6	Missense_Mutation	SNP	ENST00000397033.2	hg19	CCDS42788.1	.	.	.	.	.	.	.	.	.	.	A	19.05	3.751738	0.69533	.	.	ENSG00000115232	ENST00000397033	T	0.52057	0.68	5.91	5.91	0.95273	Integrin alpha-2 (1);	0.000000	0.85682	D	0.000000	T	0.67988	0.2952	M	0.72118	2.19	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;1.0	T	0.66960	-0.5791	10	0.38643	T	0.18	.	16.3436	0.83110	1.0:0.0:0.0:0.0	.	553;731	Q59H74;P13612	.;ITA4_HUMAN	V	731	ENSP00000380227:D731V	ENSP00000380227:D731V	D	+	2	0	ITGA4	182097165	1.000000	0.71417	1.000000	0.80357	0.971000	0.66376	6.778000	0.75043	2.269000	0.75478	0.533000	0.62120	GAT	.	.		0.338	ITGA4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000334427.1		
FAM171B	165215	hgsc.bcm.edu	37	2	187626928	187626928	+	Nonsense_Mutation	SNP	G	G	A			TCGA-WJ-A86L-01A-12D-A45V-10	TCGA-WJ-A86L-10A-01D-A38X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	80e4fac9-c066-47a9-9fc0-2a42eef954cd	cebd5a99-cbde-441d-b98a-b84cf1825d65	g.chr2:187626928G>A	ENST00000304698.5	+	8	2062	c.1859G>A	c.(1858-1860)tGg>tAg	p.W620*		NM_177454.3	NP_803237.3	Q6P995	F171B_HUMAN	family with sequence similarity 171, member B	620						integral component of membrane (GO:0016021)	DNA binding (GO:0003677)			NS(1)|breast(6)|central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(10)|lung(22)|ovary(6)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	54						GCTTCAGATTGGAGCCGATAC	0.473																																					p.W620X		Atlas-SNP	.											.	FAM171B	146	.	0			c.G1859A						.						79.0	85.0	83.0					2																	187626928		2203	4300	6503	SO:0001587	stop_gained	165215	exon8			CAGATTGGAGCCG	AF361495	CCDS33347.1	2q32.2	2008-06-16	2008-06-16	2008-06-16	ENSG00000144369	ENSG00000144369			29412	protein-coding gene	gene with protein product			"""KIAA1946"""	KIAA1946		11853319	Standard	NM_177454		Approved	FLJ34104	uc002ups.3	Q6P995	OTTHUMG00000154278	ENST00000304698.5:c.1859G>A	chr2.hg19:g.187626928G>A	ENSP00000304108:p.Trp620*	86.0	0.0		93.0	35.0	NM_177454	Q53SK3|Q8N1Y4|Q8N3K1|Q8N970|Q8NB81|Q8TF55|Q8WYR8	Nonsense_Mutation	SNP	ENST00000304698.5	hg19	CCDS33347.1	.	.	.	.	.	.	.	.	.	.	G	39	7.364543	0.98238	.	.	ENSG00000144369	ENST00000304698	.	.	.	6.03	6.03	0.97812	.	0.056641	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-6.6	20.5666	0.99351	0.0:0.0:1.0:0.0	.	.	.	.	X	620	.	ENSP00000304108:W620X	W	+	2	0	FAM171B	187335173	1.000000	0.71417	1.000000	0.80357	0.986000	0.74619	9.194000	0.94962	2.854000	0.98071	0.655000	0.94253	TGG	.	.		0.473	FAM171B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000334679.1	NM_177454	
RAPH1	65059	hgsc.bcm.edu	37	2	204354655	204354655	+	Missense_Mutation	SNP	C	C	A			TCGA-WJ-A86L-01A-12D-A45V-10	TCGA-WJ-A86L-10A-01D-A38X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	80e4fac9-c066-47a9-9fc0-2a42eef954cd	cebd5a99-cbde-441d-b98a-b84cf1825d65	g.chr2:204354655C>A	ENST00000319170.5	-	4	683	c.384G>T	c.(382-384)ttG>ttT	p.L128F	RAPH1_ENST00000308091.4_Missense_Mutation_p.L128F|RAPH1_ENST00000419464.1_Missense_Mutation_p.L128F|RAPH1_ENST00000418114.1_Missense_Mutation_p.L128F|RAPH1_ENST00000374489.2_Missense_Mutation_p.L128F|RAPH1_ENST00000439222.1_Missense_Mutation_p.L128F|RAPH1_ENST00000374488.2_Missense_Mutation_p.L128F|RAPH1_ENST00000453034.1_Missense_Mutation_p.L128F|RAPH1_ENST00000374493.3_Missense_Mutation_p.L128F|RAPH1_ENST00000457812.1_Missense_Mutation_p.L128F|RAPH1_ENST00000423104.1_Missense_Mutation_p.L128F	NM_213589.1	NP_998754.1	Q70E73	RAPH1_HUMAN	Ras association (RalGDS/AF-6) and pleckstrin homology domains 1	128					axon extension (GO:0048675)|cell-matrix adhesion (GO:0007160)|signal transduction (GO:0007165)	cell leading edge (GO:0031252)|cell projection (GO:0042995)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|plasma membrane (GO:0005886)				breast(5)|central_nervous_system(2)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(4)|lung(7)|ovary(3)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	32						TGCCATGTTTCAATGTATGTC	0.443																																					p.L128F		Atlas-SNP	.											.	RAPH1	118	.	0			c.G384T						.						235.0	225.0	228.0					2																	204354655		2203	4300	6503	SO:0001583	missense	65059	exon4			ATGTTTCAATGTA	AJ584699	CCDS2359.1, CCDS2360.1	2q33	2013-01-10	2003-11-25	2003-11-26	ENSG00000173166	ENSG00000173166		"""Pleckstrin homology (PH) domain containing"""	14436	protein-coding gene	gene with protein product	"""amyotrophic lateral sclerosis 2 (juvenile) chromosome region, candidate 18"""	609035	"""amyotrophic lateral sclerosis 2 (juvenile) chromosome region, candidate 9"""	ALS2CR9, ALS2CR18			Standard	NM_203365		Approved	KIAA1681	uc002vad.3	Q70E73	OTTHUMG00000132876	ENST00000319170.5:c.384G>T	chr2.hg19:g.204354655C>A	ENSP00000316543:p.Leu128Phe	119.0	0.0		118.0	49.0	NM_213589	Q96Q37|Q9C0I2	Missense_Mutation	SNP	ENST00000319170.5	hg19	CCDS2359.1	.	.	.	.	.	.	.	.	.	.	C	8.392	0.839969	0.16891	.	.	ENSG00000173166	ENST00000457812;ENST00000319170;ENST00000374493;ENST00000374489;ENST00000374488;ENST00000308091;ENST00000439222;ENST00000419464;ENST00000423104;ENST00000453034;ENST00000432342;ENST00000418114;ENST00000413201;ENST00000428637	T;T;T;T;T;T;T;T;T;T;T	0.44881	0.94;0.94;0.93;0.91;0.91;0.93;0.91;0.94;0.91;0.93;0.94	5.51	1.78	0.24846	.	0.423925	0.17554	N	0.170057	T	0.23649	0.0572	N	0.22421	0.69	0.09310	N	0.999991	B;B;B	0.24882	0.113;0.006;0.031	B;B;B	0.25140	0.058;0.016;0.024	T	0.18555	-1.0333	10	0.59425	D	0.04	-8.5221	1.6917	0.02853	0.151:0.2113:0.4018:0.2358	.	128;128;128	Q70E73-6;C9K0J5;Q70E73	.;.;RAPH1_HUMAN	F	128	ENSP00000392854:L128F;ENSP00000316543:L128F;ENSP00000363617:L128F;ENSP00000363613:L128F;ENSP00000363612:L128F;ENSP00000311293:L128F;ENSP00000411138:L128F;ENSP00000390578:L128F;ENSP00000397751:L128F;ENSP00000406662:L128F;ENSP00000396711:L128F	ENSP00000311293:L128F	L	-	3	2	RAPH1	204062900	0.989000	0.36119	0.984000	0.44739	0.258000	0.26162	0.522000	0.22909	0.356000	0.24157	-0.312000	0.09012	TTG	.	.		0.443	RAPH1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000256363.2	NM_025252	
UGT1A9	54600	hgsc.bcm.edu	37	2	234580748	234580748	+	Silent	SNP	T	T	C			TCGA-WJ-A86L-01A-12D-A45V-10	TCGA-WJ-A86L-10A-01D-A38X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	80e4fac9-c066-47a9-9fc0-2a42eef954cd	cebd5a99-cbde-441d-b98a-b84cf1825d65	g.chr2:234580748T>C	ENST00000354728.4	+	1	250	c.168T>C	c.(166-168)gtT>gtC	p.V56V	UGT1A1_ENST00000609637.1_Silent_p.V56V|UGT1A1_ENST00000373450.4_Intron|UGT1A10_ENST00000344644.5_Intron|UGT1A10_ENST00000373445.1_Intron			O60656	UD19_HUMAN	UDP glucuronosyltransferase 1 family, polypeptide A9	56					cellular glucuronidation (GO:0052695)|cellular lipid metabolic process (GO:0044255)|drug metabolic process (GO:0017144)|flavone metabolic process (GO:0051552)|flavonoid glucuronidation (GO:0052696)|metabolic process (GO:0008152)|negative regulation of catalytic activity (GO:0043086)|negative regulation of cellular glucuronidation (GO:2001030)|negative regulation of fatty acid metabolic process (GO:0045922)|retinoic acid metabolic process (GO:0042573)|small molecule metabolic process (GO:0044281)|xenobiotic glucuronidation (GO:0052697)|xenobiotic metabolic process (GO:0006805)	endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)	enzyme binding (GO:0019899)|enzyme inhibitor activity (GO:0004857)|glucuronosyltransferase activity (GO:0015020)|protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)|retinoic acid binding (GO:0001972)	p.V56V(1)		breast(2)|endometrium(3)|kidney(3)|large_intestine(9)|lung(14)|ovary(3)|skin(2)|upper_aerodigestive_tract(1)	37		Breast(86;0.000766)|all_lung(227;0.00269)|Renal(207;0.00339)|all_hematologic(139;0.0116)|Acute lymphoblastic leukemia(138;0.0331)|Lung NSC(271;0.0459)|Lung SC(224;0.128)		Epithelial(121;1.26e-17)|BRCA - Breast invasive adenocarcinoma(100;0.000436)|Lung(119;0.00347)|LUSC - Lung squamous cell carcinoma(224;0.00757)	Acetaminophen(DB00316)|Buprenorphine(DB00921)|Canagliflozin(DB08907)|Dabigatran etexilate(DB06695)|Dapagliflozin(DB06292)|Entacapone(DB00494)|Etodolac(DB00749)|Ezogabine(DB04953)|Flurbiprofen(DB00712)|Haloperidol(DB00502)|Human Serum Albumin(DB00062)|Hydromorphone(DB00327)|Ibuprofen(DB01050)|Indomethacin(DB00328)|Irinotecan(DB00762)|Ketobemidone(DB06738)|Lumiracoxib(DB01283)|Mycophenolate mofetil(DB00688)|Mycophenolic acid(DB01024)|Nateglinide(DB00731)|Niflumic Acid(DB04552)|Oxazepam(DB00842)|Propofol(DB00818)|Regorafenib(DB08896)|Sorafenib(DB00398)|Sulfamethoxazole(DB01015)|Tapentadol(DB06204)|Valproic Acid(DB00313)|Zileuton(DB00744)	ATGAGGTGGTTGTAGTCATGC	0.532																																					p.V56V		Atlas-SNP	.											UGT1A9,NS,carcinoma,0,1	UGT1A9	79	.	1	Substitution - coding silent(1)	kidney(1)	c.T168C						.						100.0	85.0	90.0					2																	234580748		2203	4300	6503	SO:0001819	synonymous_variant	54600	exon1			GGTGGTTGTAGTC	AF056188	CCDS2505.1	2q37	2010-03-05	2005-07-20		ENSG00000241119	ENSG00000241119		"""UDP glucuronosyltransferases"""	12541	other	complex locus constituent		606434	"""UDP glycosyltransferase 1 family, polypeptide A9"""			9295054, 1910331	Standard	NM_021027		Approved	HLUGP4, LUGP4, UGT1AI		O60656	OTTHUMG00000059124	ENST00000354728.4:c.168T>C	chr2.hg19:g.234580748T>C		79.0	0.0		73.0	29.0	NM_021027	B8K285|P36509|Q9HAX0	Silent	SNP	ENST00000354728.4	hg19	CCDS2505.1																																																																																			.	.		0.532	UGT1A9-001	KNOWN	basic|appris_principal|readthrough_transcript|CCDS	protein_coding	protein_coding	OTTHUMT00000130995.1	NM_021027	
OXTR	5021	hgsc.bcm.edu	37	3	8794828	8794828	+	Silent	SNP	G	G	A			TCGA-WJ-A86L-01A-12D-A45V-10	TCGA-WJ-A86L-10A-01D-A38X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	80e4fac9-c066-47a9-9fc0-2a42eef954cd	cebd5a99-cbde-441d-b98a-b84cf1825d65	g.chr3:8794828G>A	ENST00000316793.3	-	4	1629	c.1005C>T	c.(1003-1005)caC>caT	p.H335H	CAV3_ENST00000472766.1_Intron	NM_000916.3	NP_000907.2	P30559	OXYR_HUMAN	oxytocin receptor	335					cell surface receptor signaling pathway (GO:0007166)|digestive tract development (GO:0048565)|eating behavior (GO:0042755)|ERK1 and ERK2 cascade (GO:0070371)|estrous cycle phase (GO:0060206)|female pregnancy (GO:0007565)|heart development (GO:0007507)|lactation (GO:0007595)|maternal behavior (GO:0042711)|maternal process involved in parturition (GO:0060137)|memory (GO:0007613)|muscle contraction (GO:0006936)|negative regulation of gastric acid secretion (GO:0060455)|positive regulation of blood pressure (GO:0045777)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|positive regulation of norepinephrine secretion (GO:0010701)|positive regulation of penile erection (GO:0060406)|positive regulation of synapse assembly (GO:0051965)|positive regulation of synaptic transmission, GABAergic (GO:0032230)|positive regulation of synaptic transmission, glutamatergic (GO:0051968)|positive regulation of uterine smooth muscle contraction (GO:0070474)|response to amphetamine (GO:0001975)|response to anoxia (GO:0034059)|response to cocaine (GO:0042220)|response to cytokine (GO:0034097)|response to drug (GO:0042493)|response to estradiol (GO:0032355)|response to peptide hormone (GO:0043434)|response to progesterone (GO:0032570)|sleep (GO:0030431)|social behavior (GO:0035176)|sperm ejaculation (GO:0042713)|suckling behavior (GO:0001967)|telencephalon development (GO:0021537)	apical plasma membrane (GO:0016324)|cell-cell adherens junction (GO:0005913)|integral component of plasma membrane (GO:0005887)|microvillus (GO:0005902)|plasma membrane (GO:0005886)	oxytocin receptor activity (GO:0004990)|peptide hormone binding (GO:0017046)|vasopressin receptor activity (GO:0005000)			NS(1)|endometrium(2)|large_intestine(4)|lung(5)|urinary_tract(1)	13				OV - Ovarian serous cystadenocarcinoma(96;0.15)	Carbetocin(DB01282)|Oxytocin(DB00107)	CGTGGAAGAGGTGGCCCGTGA	0.617																																					p.H335H		Atlas-SNP	.											.	OXTR	31	.	0			c.C1005T						.						73.0	65.0	67.0					3																	8794828		2203	4300	6503	SO:0001819	synonymous_variant	5021	exon4			GAAGAGGTGGCCC		CCDS2570.1	3p25	2012-08-08			ENSG00000180914	ENSG00000180914		"""GPCR / Class A : Vasopressin and oxytocin receptors"""	8529	protein-coding gene	gene with protein product		167055				1313946	Standard	NM_000916		Approved		uc003brc.3	P30559	OTTHUMG00000090537	ENST00000316793.3:c.1005C>T	chr3.hg19:g.8794828G>A		126.0	0.0		117.0	45.0	NM_000916	Q15071	Silent	SNP	ENST00000316793.3	hg19	CCDS2570.1																																																																																			.	.		0.617	OXTR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207061.2		
DLEC1	9940	hgsc.bcm.edu	37	3	38080872	38080872	+	Silent	SNP	T	T	A			TCGA-WJ-A86L-01A-12D-A45V-10	TCGA-WJ-A86L-10A-01D-A38X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	80e4fac9-c066-47a9-9fc0-2a42eef954cd	cebd5a99-cbde-441d-b98a-b84cf1825d65	g.chr3:38080872T>A	ENST00000308059.6	+	1	177	c.156T>A	c.(154-156)tcT>tcA	p.S52S	DLEC1_ENST00000346219.3_Silent_p.S52S|DLEC1_ENST00000452631.2_Silent_p.S52S					deleted in lung and esophageal cancer 1											NS(1)|breast(3)|central_nervous_system(3)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(9)|lung(14)|ovary(3)|pancreas(3)|prostate(1)|skin(5)|upper_aerodigestive_tract(2)	51				KIRC - Kidney renal clear cell carcinoma(284;0.0664)|Kidney(284;0.0827)		TCGCCTACTCTGAGGCCTTCC	0.687																																					p.S52S		Atlas-SNP	.											.	DLEC1	278	.	0			c.T156A						.						52.0	62.0	59.0					3																	38080872		2023	4195	6218	SO:0001819	synonymous_variant	9940	exon1			CTACTCTGAGGCC	AB020522	CCDS2672.2	3p21.3	2014-07-31			ENSG00000008226	ENSG00000008226			2899	protein-coding gene	gene with protein product	"""cilia and flagella associated protein 81"""	604050				10213508	Standard	XM_005265630		Approved	DLC1, CFAP81	uc003chp.1	Q9Y238	OTTHUMG00000131085	ENST00000308059.6:c.156T>A	chr3.hg19:g.38080872T>A		157.0	0.0		130.0	53.0	NM_007337		Silent	SNP	ENST00000308059.6	hg19	CCDS2672.2																																																																																			.	.		0.687	DLEC1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000253745.3	NM_007337	
RNF123	63891	hgsc.bcm.edu	37	3	49725184	49725184	+	5'Flank	SNP	G	G	A	rs191996618		TCGA-WJ-A86L-01A-12D-A45V-10	TCGA-WJ-A86L-10A-01D-A38X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	80e4fac9-c066-47a9-9fc0-2a42eef954cd	cebd5a99-cbde-441d-b98a-b84cf1825d65	g.chr3:49725184G>A	ENST00000327697.6	+	0	0				MST1_ENST00000449682.2_Splice_Site_p.R81W|MST1_ENST00000494828.2_Intron|MST1_ENST00000545762.1_Splice_Site_p.R67W|AC099668.5_ENST00000563780.1_RNA|RNF123_ENST00000432042.1_5'Flank|MST1_ENST00000383728.3_Intron	NM_022064.3	NP_071347.2	Q5XPI4	RN123_HUMAN	ring finger protein 123						protein ubiquitination (GO:0016567)	cytoplasm (GO:0005737)	ligase activity (GO:0016874)|zinc ion binding (GO:0008270)	p.R67W(1)		NS(1)|breast(4)|cervix(2)|endometrium(4)|kidney(4)|large_intestine(6)|lung(11)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	38				BRCA - Breast invasive adenocarcinoma(193;4.71e-05)|Kidney(197;0.00227)|KIRC - Kidney renal clear cell carcinoma(197;0.00255)		GCCACTCACCGGCAGTCCATT	0.617																																					p.R81W		Atlas-SNP	.											MST1,trunk,malignant_melanoma,0,1	MST1	84	.	1	Substitution - Missense(1)	skin(1)	c.C241T						.																																			SO:0001631	upstream_gene_variant	4485	exon2			CTCACCGGCAGTC	AK022627	CCDS33758.1	3p24.3	2008-02-05			ENSG00000164068	ENSG00000164068		"""RING-type (C3HC4) zinc fingers"""	21148	protein-coding gene	gene with protein product		614472					Standard	NM_022064		Approved	FLJ12565	uc003cxh.4	Q5XPI4	OTTHUMG00000156891		chr3.hg19:g.49725184G>A	Exception_encountered	93.0	2.0		73.0	5.0	NM_020998	A1L4Q3|A6NLS5|Q5I022|Q6PFW4|Q71RH0|Q8IW18|Q9H0M8|Q9H5L8|Q9H9T2	Missense_Mutation	SNP	ENST00000327697.6	hg19	CCDS33758.1	.	.	.	.	.	.	.	.	.	.	G	11.82	1.753661	0.31046	.	.	ENSG00000173531	ENST00000449682;ENST00000545762	T;T	0.71222	-0.55;-0.55	4.22	2.22	0.28083	.	0.177772	0.26836	N	0.022260	T	0.63908	0.2551	M	0.65498	2.005	0.39552	D	0.968993	B;P	0.35208	0.169;0.49	B;B	0.28784	0.049;0.094	T	0.65973	-0.6038	10	0.54805	T	0.06	.	11.5769	0.50866	0.0:0.0:0.4124:0.5876	.	67;81	B7Z538;G3XAK1	.;.	W	81;67	ENSP00000414287:R81W;ENSP00000437535:R67W	ENSP00000411117:R81W	R	-	1	2	MST1	49700188	1.000000	0.71417	0.998000	0.56505	0.537000	0.34900	1.595000	0.36708	0.595000	0.29777	-0.293000	0.09583	CGG	.	.		0.617	RNF123-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000346475.2	NM_022064	
EPHA3	2042	hgsc.bcm.edu	37	3	89480381	89480381	+	Missense_Mutation	SNP	A	A	T			TCGA-WJ-A86L-01A-12D-A45V-10	TCGA-WJ-A86L-10A-01D-A38X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	80e4fac9-c066-47a9-9fc0-2a42eef954cd	cebd5a99-cbde-441d-b98a-b84cf1825d65	g.chr3:89480381A>T	ENST00000336596.2	+	13	2443	c.2218A>T	c.(2218-2220)Atg>Ttg	p.M740L	EPHA3_ENST00000494014.1_Missense_Mutation_p.M740L	NM_005233.5	NP_005224.2	P29320	EPHA3_HUMAN	EPH receptor A3	740	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				cell adhesion (GO:0007155)|cell migration (GO:0016477)|cellular response to retinoic acid (GO:0071300)|ephrin receptor signaling pathway (GO:0048013)|fasciculation of motor neuron axon (GO:0097156)|fasciculation of sensory neuron axon (GO:0097155)|positive regulation of neuron projection development (GO:0010976)|regulation of actin cytoskeleton organization (GO:0032956)|regulation of epithelial to mesenchymal transition (GO:0010717)|regulation of focal adhesion assembly (GO:0051893)|regulation of microtubule cytoskeleton organization (GO:0070507)|regulation of Rho GTPase activity (GO:0032319)	early endosome (GO:0005769)|extracellular region (GO:0005576)|integral component of plasma membrane (GO:0005887)	ATP binding (GO:0005524)|GPI-linked ephrin receptor activity (GO:0005004)			NS(1)|breast(4)|central_nervous_system(4)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(26)|liver(3)|lung(67)|ovary(7)|pancreas(1)|prostate(4)|skin(8)|stomach(1)|upper_aerodigestive_tract(5)	139	all_cancers(8;0.0406)|Melanoma(1;0.00142)|all_epithelial(1;0.0612)	Lung NSC(201;0.0782)		LUSC - Lung squamous cell carcinoma(29;0.00344)|Lung(72;0.00942)		CCTGTCAGACATGGGCTATGT	0.488										TSP Lung(6;0.00050)																											p.M740L		Atlas-SNP	.											.	EPHA3	501	.	0			c.A2218T						.						168.0	144.0	152.0					3																	89480381		2203	4300	6503	SO:0001583	missense	2042	exon13			TCAGACATGGGCT	M83941	CCDS2922.1, CCDS46875.1	3p11.2	2013-02-11	2004-10-28		ENSG00000044524	ENSG00000044524	2.7.10.1	"""EPH receptors"", ""Sterile alpha motif (SAM) domain containing"", ""Fibronectin type III domain containing"""	3387	protein-coding gene	gene with protein product		179611	"""EphA3"""	ETK, ETK1, TYRO4		1737782, 1311845	Standard	NM_005233		Approved	HEK, HEK4	uc003dqy.3	P29320	OTTHUMG00000159040	ENST00000336596.2:c.2218A>T	chr3.hg19:g.89480381A>T	ENSP00000337451:p.Met740Leu	91.0	0.0		106.0	43.0	NM_005233	Q9H2V3|Q9H2V4	Missense_Mutation	SNP	ENST00000336596.2	hg19	CCDS2922.1	.	.	.	.	.	.	.	.	.	.	A	21.7	4.186290	0.78789	.	.	ENSG00000044524	ENST00000336596;ENST00000494014	D;D	0.82344	-1.6;-1.6	5.33	5.33	0.75918	Serine-threonine/tyrosine-protein kinase (2);Protein kinase-like domain (1);Tyrosine-protein kinase, catalytic domain (1);Protein kinase, catalytic domain (1);	0.000000	0.85682	D	0.000000	T	0.74076	0.3669	N	0.01668	-0.77	0.80722	D	1	P	0.44139	0.827	P	0.56278	0.795	T	0.76769	-0.2837	9	.	.	.	.	15.5821	0.76452	1.0:0.0:0.0:0.0	.	740	P29320	EPHA3_HUMAN	L	740	ENSP00000337451:M740L;ENSP00000419190:M740L	.	M	+	1	0	EPHA3	89563071	1.000000	0.71417	0.976000	0.42696	0.878000	0.50629	9.287000	0.95975	2.139000	0.66308	0.477000	0.44152	ATG	.	.		0.488	EPHA3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000352995.1	NM_005233	
FAM162A	26355	hgsc.bcm.edu	37	3	122126169	122126169	+	Missense_Mutation	SNP	A	A	C			TCGA-WJ-A86L-01A-12D-A45V-10	TCGA-WJ-A86L-10A-01D-A38X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	80e4fac9-c066-47a9-9fc0-2a42eef954cd	cebd5a99-cbde-441d-b98a-b84cf1825d65	g.chr3:122126169A>C	ENST00000477892.1	+	4	389	c.305A>C	c.(304-306)aAg>aCg	p.K102T	FAM162A_ENST00000469967.1_Missense_Mutation_p.K102T|FAM162A_ENST00000232125.5_Missense_Mutation_p.K92T	NM_014367.3	NP_055182.3	Q96A26	F162A_HUMAN	family with sequence similarity 162, member A	102	Required for proapoptotic activity.				activation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0006919)|cellular response to hypoxia (GO:0071456)|neuron apoptotic process (GO:0051402)|positive regulation of apoptotic process (GO:0043065)|positive regulation of release of cytochrome c from mitochondria (GO:0090200)|transformed cell apoptotic process (GO:0006927)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|mitochondrion (GO:0005739)|nucleus (GO:0005634)				breast(1)|kidney(1)|large_intestine(1)|lung(2)|ovary(1)	6						ATGCGAGTGAAGATCAGCTAT	0.413																																					p.K102T		Atlas-SNP	.											.	FAM162A	18	.	0			c.A305C						.						176.0	171.0	173.0					3																	122126169		1963	4169	6132	SO:0001583	missense	26355	exon4			GAGTGAAGATCAG	AF191020	CCDS43139.1	3q21.1	2008-06-05	2008-06-05	2008-06-05	ENSG00000114023	ENSG00000114023			17865	protein-coding gene	gene with protein product		608017	"""chromosome 3 open reading frame 28"""	C3orf28		11085516	Standard	NM_014367		Approved	E2IG5	uc003eez.3	Q96A26	OTTHUMG00000159494	ENST00000477892.1:c.305A>C	chr3.hg19:g.122126169A>C	ENSP00000419088:p.Lys102Thr	68.0	0.0		66.0	27.0	NM_014367	Q9NRN6|Q9UJX8	Missense_Mutation	SNP	ENST00000477892.1	hg19	CCDS43139.1	.	.	.	.	.	.	.	.	.	.	A	14.08	2.429549	0.43122	.	.	ENSG00000114023	ENST00000232125;ENST00000477892;ENST00000469967;ENST00000440333	T;T;T	0.40225	1.04;1.04;1.04	5.54	4.36	0.52297	.	0.087798	0.85682	D	0.000000	T	0.61173	0.2326	M	0.80847	2.515	0.36610	D	0.875176	D;D	0.76494	0.999;0.999	D;D	0.71656	0.974;0.934	T	0.69957	-0.5004	10	0.66056	D	0.02	.	8.2745	0.31864	0.9107:0.0:0.0893:0.0	.	102;102	E9PH05;Q96A26	.;F162A_HUMAN	T	92;102;102;101	ENSP00000232125:K92T;ENSP00000419088:K102T;ENSP00000419491:K102T	ENSP00000232125:K92T	K	+	2	0	FAM162A	123608859	1.000000	0.71417	0.998000	0.56505	0.009000	0.06853	4.484000	0.60271	2.323000	0.78572	0.528000	0.53228	AAG	.	.		0.413	FAM162A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000355766.1	NM_014367	
PLXNA1	5361	hgsc.bcm.edu	37	3	126726661	126726661	+	Missense_Mutation	SNP	G	G	T			TCGA-WJ-A86L-01A-12D-A45V-10	TCGA-WJ-A86L-10A-01D-A38X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	80e4fac9-c066-47a9-9fc0-2a42eef954cd	cebd5a99-cbde-441d-b98a-b84cf1825d65	g.chr3:126726661G>T	ENST00000393409.2	+	8	2017	c.2017G>T	c.(2017-2019)Ggc>Tgc	p.G673C	PLXNA1_ENST00000251772.4_Missense_Mutation_p.G650C	NM_032242.3	NP_115618.3	Q9UIW2	PLXA1_HUMAN	plexin A1	673					axon guidance (GO:0007411)|dichotomous subdivision of terminal units involved in salivary gland branching (GO:0060666)|multicellular organismal development (GO:0007275)|regulation of smooth muscle cell migration (GO:0014910)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|semaphorin receptor complex (GO:0002116)	receptor activity (GO:0004872)|semaphorin receptor activity (GO:0017154)			breast(3)|central_nervous_system(5)|endometrium(10)|kidney(5)|large_intestine(4)|lung(32)|ovary(2)|pancreas(1)|prostate(2)|skin(3)	67				GBM - Glioblastoma multiforme(114;0.155)		CTGTGTCAACGGCTCCTTTCC	0.617																																					p.G673C		Atlas-SNP	.											.	PLXNA1	185	.	0			c.G2017T						.						80.0	68.0	72.0					3																	126726661		2203	4300	6503	SO:0001583	missense	5361	exon8			GTCAACGGCTCCT	X87832	CCDS33847.1, CCDS33847.2	3q21.2	2006-12-19				ENSG00000114554		"""Plexins"""	9099	protein-coding gene	gene with protein product		601055		PLXN1		8570614	Standard	NM_032242		Approved	NOV	uc003ejg.3	Q9UIW2		ENST00000393409.2:c.2017G>T	chr3.hg19:g.126726661G>T	ENSP00000377061:p.Gly673Cys	42.0	0.0		27.0	20.0	NM_032242		Missense_Mutation	SNP	ENST00000393409.2	hg19	CCDS33847.2	.	.	.	.	.	.	.	.	.	.	G	18.33	3.600044	0.66332	.	.	ENSG00000114554	ENST00000393409;ENST00000251772	T;T	0.17213	2.29;2.29	3.63	3.63	0.41609	.	0.000000	0.64402	D	0.000016	T	0.33089	0.0851	L	0.41236	1.265	0.58432	D	0.99999	D	0.89917	1.0	D	0.85130	0.997	T	0.18493	-1.0335	10	0.87932	D	0	.	15.8357	0.78796	0.0:0.0:1.0:0.0	.	673	Q9UIW2	PLXA1_HUMAN	C	673;650	ENSP00000377061:G673C;ENSP00000251772:G650C	ENSP00000251772:G650C	G	+	1	0	PLXNA1	128209351	1.000000	0.71417	0.994000	0.49952	0.967000	0.64934	3.957000	0.56730	2.025000	0.59659	0.467000	0.42956	GGC	.	.		0.617	PLXNA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000356451.1	NM_032242	
TBC1D1	23216	hgsc.bcm.edu	37	4	38138875	38138875	+	Silent	SNP	G	G	A	rs375379532		TCGA-WJ-A86L-01A-12D-A45V-10	TCGA-WJ-A86L-10A-01D-A38X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	80e4fac9-c066-47a9-9fc0-2a42eef954cd	cebd5a99-cbde-441d-b98a-b84cf1825d65	g.chr4:38138875G>A	ENST00000261439.4	+	20	3781	c.3426G>A	c.(3424-3426)acG>acA	p.T1142T	TBC1D1_ENST00000407365.1_3'UTR|TBC1D1_ENST00000508802.1_Silent_p.T1133T	NM_001253914.1|NM_001253915.1|NM_015173.3	NP_001240843.1|NP_001240844.1|NP_055988.2	Q86TI0	TBCD1_HUMAN	TBC1 (tre-2/USP6, BUB2, cdc16) domain family, member 1	1142					membrane organization (GO:0061024)|regulation of protein localization (GO:0032880)	cytosol (GO:0005829)|nucleus (GO:0005634)	Rab GTPase activator activity (GO:0005097)			NS(1)|breast(3)|kidney(1)|large_intestine(5)|lung(19)|ovary(2)|prostate(2)|skin(2)|urinary_tract(1)	36						TGCTGCAGACGGTGGAGGAGC	0.642													G|||	1	0.000199681	0.0008	0.0	5008	,	,		15446	0.0		0.0	False		,,,				2504	0.0				p.T1142T		Atlas-SNP	.											.	TBC1D1	94	.	0			c.G3426A						.	G		1,4403	2.1+/-5.4	0,1,2201	31.0	36.0	34.0		3426	-2.6	0.0	4		34	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous	TBC1D1	NM_015173.2		0,2,6500	AA,AG,GG		0.0116,0.0227,0.0154		1142/1169	38138875	2,13002	2202	4300	6502	SO:0001819	synonymous_variant	23216	exon20			GCAGACGGTGGAG	AB029031	CCDS33972.1, CCDS58897.1	4p14	2013-07-09			ENSG00000065882	ENSG00000065882			11578	protein-coding gene	gene with protein product		609850				10965142, 18258599	Standard	NM_015173		Approved	TBC, TBC1, KIAA1108	uc003gtb.3	Q86TI0	OTTHUMG00000150302	ENST00000261439.4:c.3426G>A	chr4.hg19:g.38138875G>A		109.0	0.0		138.0	44.0	NM_015173	B7Z3D9|E9PGH8|Q96K82|Q9UPP4	Silent	SNP	ENST00000261439.4	hg19	CCDS33972.1	.	.	.	.	.	.	.	.	.	.	G	0.992	-0.693597	0.03303	2.27E-4	1.16E-4	ENSG00000065882	ENST00000510573	.	.	.	5.16	-2.62	0.06152	.	.	.	.	.	T	0.20577	0.0495	.	.	.	0.26265	N	0.978517	.	.	.	.	.	.	T	0.28332	-1.0047	4	.	.	.	-0.0394	3.4262	0.07412	0.2121:0.4531:0.1507:0.1841	.	.	.	.	S	830	.	.	G	+	1	0	TBC1D1	37815270	0.566000	0.26618	0.002000	0.10522	0.122000	0.20287	0.029000	0.13666	-0.434000	0.07275	-0.156000	0.13503	GGT	.	.		0.642	TBC1D1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000317443.2	NM_015173	
PHOX2B	8929	hgsc.bcm.edu	37	4	41748004	41748004	+	Silent	SNP	C	C	T	rs543135182|rs17879189	byFrequency	TCGA-WJ-A86L-01A-12D-A45V-10	TCGA-WJ-A86L-10A-01D-A38X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	80e4fac9-c066-47a9-9fc0-2a42eef954cd	cebd5a99-cbde-441d-b98a-b84cf1825d65	g.chr4:41748004C>T	ENST00000226382.2	-	3	1124	c.765G>A	c.(763-765)gcG>gcA	p.A255A	RP11-227F19.1_ENST00000508038.1_RNA	NM_003924.3	NP_003915.2	Q99453	PHX2B_HUMAN	paired-like homeobox 2b	255	Poly-Ala.		Missing. {ECO:0000269|PubMed:14566559}.		autonomic nervous system development (GO:0048483)|brainstem development (GO:0003360)|cell differentiation in hindbrain (GO:0021533)|cellular response to BMP stimulus (GO:0071773)|dopaminergic neuron differentiation (GO:0071542)|efferent axon development in a lateral line nerve (GO:0048894)|enteric nervous system development (GO:0048484)|glial cell differentiation (GO:0010001)|hindbrain tangential cell migration (GO:0021934)|inner ear development (GO:0048839)|medullary reticular formation development (GO:0021723)|negative regulation of cell cycle arrest (GO:0071157)|negative regulation of cell proliferation (GO:0008285)|negative regulation of neuron differentiation (GO:0045665)|neural crest cell migration involved in autonomic nervous system development (GO:1901166)|neuron migration (GO:0001764)|noradrenergic neuron development (GO:0003358)|noradrenergic neuron differentiation (GO:0003357)|parasympathetic nervous system development (GO:0048486)|positive regulation of G2/M transition of mitotic cell cycle (GO:0010971)|positive regulation of neuron differentiation (GO:0045666)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of gene expression (GO:0010468)|regulation of respiratory gaseous exchange by neurological system process (GO:0002087)|respiratory system development (GO:0060541)|retrotrapezoid nucleus neuron differentiation (GO:0061452)|skeletal muscle cell differentiation (GO:0035914)|sympathetic ganglion development (GO:0061549)|sympathetic nervous system development (GO:0048485)|transcription, DNA-templated (GO:0006351)	nuclear chromatin (GO:0000790)	RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II regulatory region sequence-specific DNA binding (GO:0000977)			autonomic_ganglia(7)|central_nervous_system(1)|endometrium(2)|large_intestine(5)|lung(11)|ovary(2)|skin(1)|urinary_tract(1)	30						ccgccgctgccgctgccgccg	0.821			"""Mis, F"""		neuroblastoma	neuroblastoma	congenital central hypoventilation syndrome		Neuroblastoma, Familial Clustering of;Congenital Central Hypoventilation Syndrome				C|||	2	0.000399361	0.0	0.0	5008	,	,		3548	0.0		0.001	False		,,,				2504	0.001				p.A255A		Atlas-SNP	.	yes	Rec	yes	familial neuroblastoma	4	4p12	8929	paired-like homeobox 2b	yes	O	.	PHOX2B	53	.	0			c.G765A						.						2.0	4.0	3.0					4																	41748004		698	1850	2548	SO:0001819	synonymous_variant	8929	exon3	Familial Cancer Database	Familial Neuroblastoma;CCHS, Ondine Curse, incl. Ondine-Hirschsprung Disease	CGCTGCCGCTGCC	D82344	CCDS3463.1	4p13	2014-09-17	2003-02-10	2003-02-14	ENSG00000109132	ENSG00000109132		"""Homeoboxes / PRD class"""	9143	protein-coding gene	gene with protein product		603851	"""paired mesoderm homeobox 2b"""	PMX2B		9039501, 10395798	Standard	NM_003924		Approved	Phox2b, NBPhox	uc003gwf.4	Q99453	OTTHUMG00000099379	ENST00000226382.2:c.765G>A	chr4.hg19:g.41748004C>T		99.0	0.0		141.0	69.0	NM_003924	Q6PJD9	Silent	SNP	ENST00000226382.2	hg19	CCDS3463.1																																																																																			.	.		0.821	PHOX2B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000216832.2		
FRAS1	80144	hgsc.bcm.edu	37	4	79350344	79350344	+	Silent	SNP	C	C	A			TCGA-WJ-A86L-01A-12D-A45V-10	TCGA-WJ-A86L-10A-01D-A38X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	80e4fac9-c066-47a9-9fc0-2a42eef954cd	cebd5a99-cbde-441d-b98a-b84cf1825d65	g.chr4:79350344C>A	ENST00000325942.6	+	36	5247	c.4807C>A	c.(4807-4809)Cgg>Agg	p.R1603R	FRAS1_ENST00000264895.6_Silent_p.R1603R	NM_001166133.1	NP_001159605.1	Q86XX4	FRAS1_HUMAN	Fraser extracellular matrix complex subunit 1	1603					cell communication (GO:0007154)|embryonic limb morphogenesis (GO:0030326)|metanephros morphogenesis (GO:0003338)|morphogenesis of an epithelium (GO:0002009)|palate development (GO:0060021)|protein transport (GO:0015031)|skin development (GO:0043588)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|sublamina densa (GO:0061618)	metal ion binding (GO:0046872)			breast(2)|central_nervous_system(2)|cervix(2)|endometrium(14)|haematopoietic_and_lymphoid_tissue(2)|kidney(9)|large_intestine(5)|lung(54)|prostate(7)|skin(2)|urinary_tract(4)	103						CACAGCTCCACGGCTGGCGGT	0.517																																					p.R1603R		Atlas-SNP	.											.	FRAS1	779	.	0			c.C4807A						.						46.0	49.0	48.0					4																	79350344		2054	4193	6247	SO:0001819	synonymous_variant	80144	exon36			GCTCCACGGCTGG	AB040933	CCDS54772.1	4q21.21	2014-06-25	2014-06-25		ENSG00000138759	ENSG00000138759			19185	protein-coding gene	gene with protein product		607830	"""Fraser syndrome 1"""			12766769, 3118036	Standard	NM_025074		Approved	FLJ22031, FLJ14927, KIAA1500	uc003hlb.2	Q86XX4	OTTHUMG00000160856	ENST00000325942.6:c.4807C>A	chr4.hg19:g.79350344C>A		50.0	0.0		53.0	22.0	NM_001166133	A2RRR8|Q86UZ4|Q8N3U9|Q8NAU7|Q96JW7|Q9H6N9|Q9P228	Silent	SNP	ENST00000325942.6	hg19	CCDS54772.1	.	.	.	.	.	.	.	.	.	.	C	0.033	-1.319831	0.01320	.	.	ENSG00000138759	ENST00000510944	.	.	.	5.61	-1.1	0.09872	.	.	.	.	.	T	0.19127	0.0459	.	.	.	0.09310	N	1	.	.	.	.	.	.	T	0.24190	-1.0167	4	.	.	.	.	1.4515	0.02376	0.2465:0.1524:0.3944:0.2067	.	.	.	.	K	52	.	.	T	+	2	0	FRAS1	79569368	0.001000	0.12720	0.002000	0.10522	0.000000	0.00434	-0.289000	0.08365	0.044000	0.15775	-0.122000	0.15005	ACG	.	.		0.517	FRAS1-001	NOVEL	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000362706.2		
FRAS1	80144	hgsc.bcm.edu	37	4	79432632	79432632	+	Missense_Mutation	SNP	G	G	A			TCGA-WJ-A86L-01A-12D-A45V-10	TCGA-WJ-A86L-10A-01D-A38X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	80e4fac9-c066-47a9-9fc0-2a42eef954cd	cebd5a99-cbde-441d-b98a-b84cf1825d65	g.chr4:79432632G>A	ENST00000264895.6	+	64	10425	c.9985G>A	c.(9985-9987)Gat>Aat	p.D3329N		NM_025074.6	NP_079350.5	Q86XX4	FRAS1_HUMAN	Fraser extracellular matrix complex subunit 1	3325					cell communication (GO:0007154)|embryonic limb morphogenesis (GO:0030326)|metanephros morphogenesis (GO:0003338)|morphogenesis of an epithelium (GO:0002009)|palate development (GO:0060021)|protein transport (GO:0015031)|skin development (GO:0043588)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|sublamina densa (GO:0061618)	metal ion binding (GO:0046872)	p.D3330Y(1)|p.D3329Y(1)		breast(2)|central_nervous_system(2)|cervix(2)|endometrium(14)|haematopoietic_and_lymphoid_tissue(2)|kidney(9)|large_intestine(5)|lung(54)|prostate(7)|skin(2)|urinary_tract(4)	103						GAAATACCTGGATGTCAAACA	0.512																																					p.D3329N		Atlas-SNP	.											FRAS1_ENST00000264895,NS,carcinoma,0,2	FRAS1	779	.	2	Substitution - Missense(2)	lung(2)	c.G9985A						.						49.0	48.0	48.0					4																	79432632		1969	4156	6125	SO:0001583	missense	80144	exon64			TACCTGGATGTCA	AB040933	CCDS54772.1	4q21.21	2014-06-25	2014-06-25		ENSG00000138759	ENSG00000138759			19185	protein-coding gene	gene with protein product		607830	"""Fraser syndrome 1"""			12766769, 3118036	Standard	NM_025074		Approved	FLJ22031, FLJ14927, KIAA1500	uc003hlb.2	Q86XX4	OTTHUMG00000160856	ENST00000264895.6:c.9985G>A	chr4.hg19:g.79432632G>A	ENSP00000264895:p.Asp3329Asn	107.0	0.0		118.0	51.0	NM_025074	A2RRR8|Q86UZ4|Q8N3U9|Q8NAU7|Q96JW7|Q9H6N9|Q9P228	Missense_Mutation	SNP	ENST00000264895.6	hg19	CCDS54771.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	32|32	5.175004|5.175004	0.94807|0.94807	.|.	.|.	ENSG00000138759|ENSG00000138759	ENST00000264895|ENST00000512123	T|.	0.12672|.	2.66|.	5.86|5.86	5.86|5.86	0.93980|0.93980	.|.	0.000000|.	0.85682|.	D|.	0.000000|.	T|T	0.70185|0.70185	0.3195|0.3195	L|L	0.46741|0.46741	1.465|1.465	0.80722|0.80722	D|D	1|1	D;D|.	0.89917|.	0.994;1.0|.	D;D|.	0.74023|.	0.911;0.982|.	T|T	0.64149|0.64149	-0.6475|-0.6475	10|5	0.44086|.	T|.	0.13|.	.|.	20.1882|20.1882	0.98224|0.98224	0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0	.|.	3328;3329|.	Q86XX4-2;E9PHH6|.	.;.|.	N|E	3329|1557	ENSP00000264895:D3329N|.	ENSP00000264895:D3329N|.	D|G	+|+	1|2	0|0	FRAS1|FRAS1	79651656|79651656	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.893000|0.893000	0.52053|0.52053	9.657000|9.657000	0.98554|0.98554	2.783000|2.783000	0.95769|0.95769	0.591000|0.591000	0.81541|0.81541	GAT|GGA	.	.		0.512	FRAS1-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding			
QRFPR	84109	hgsc.bcm.edu	37	4	122250606	122250606	+	Missense_Mutation	SNP	T	T	C			TCGA-WJ-A86L-01A-12D-A45V-10	TCGA-WJ-A86L-10A-01D-A38X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	80e4fac9-c066-47a9-9fc0-2a42eef954cd	cebd5a99-cbde-441d-b98a-b84cf1825d65	g.chr4:122250606T>C	ENST00000394427.2	-	6	1570	c.1159A>G	c.(1159-1161)Aaa>Gaa	p.K387E	Y_RNA_ENST00000384419.1_RNA|QRFPR_ENST00000334383.5_3'UTR	NM_198179.2	NP_937822.2	Q96P65	QRFPR_HUMAN	pyroglutamylated RFamide peptide receptor	387					G-protein coupled receptor signaling pathway (GO:0007186)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|neuropeptide Y receptor activity (GO:0004983)			endometrium(1)|kidney(2)|large_intestine(9)|lung(10)|prostate(2)|skin(3)|stomach(1)	28						GCTTCTCCTTTGGTTTCCTCC	0.418																																					p.K387E		Atlas-SNP	.											.	QRFPR	65	.	0			c.A1159G						.						238.0	235.0	236.0					4																	122250606		2203	4300	6503	SO:0001583	missense	84109	exon6			CTCCTTTGGTTTC	AF411117	CCDS3719.1	4q27	2012-08-10	2008-12-18	2008-12-18	ENSG00000186867	ENSG00000186867		"""GPCR / Class A : RF amide peptide receptors"""	15565	protein-coding gene	gene with protein product		606925	"""G protein-coupled receptor 103"""	GPR103		11574155	Standard	NM_198179		Approved		uc010inj.1	Q96P65	OTTHUMG00000133036	ENST00000394427.2:c.1159A>G	chr4.hg19:g.122250606T>C	ENSP00000377948:p.Lys387Glu	107.0	0.0		123.0	55.0	NM_198179		Missense_Mutation	SNP	ENST00000394427.2	hg19	CCDS3719.1	.	.	.	.	.	.	.	.	.	.	T	10.00	1.233287	0.22626	.	.	ENSG00000186867	ENST00000394427	T	0.72394	-0.65	5.16	2.74	0.32292	.	0.290888	0.36703	N	0.002447	T	0.49677	0.1571	L	0.27053	0.805	0.46028	D	0.998822	B	0.14805	0.011	B	0.10450	0.005	T	0.34650	-0.9820	10	0.06099	T	0.92	.	8.9893	0.36014	0.0:0.1523:0.0:0.8477	.	387	Q96P65	QRFPR_HUMAN	E	387	ENSP00000377948:K387E	ENSP00000377948:K387E	K	-	1	0	QRFPR	122470056	0.626000	0.27120	0.900000	0.35374	0.099000	0.18886	2.414000	0.44627	0.805000	0.34159	0.260000	0.18958	AAA	.	.		0.418	QRFPR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256641.2	NM_198179	
KIAA1109	84162	hgsc.bcm.edu	37	4	123179983	123179983	+	Silent	SNP	T	T	C			TCGA-WJ-A86L-01A-12D-A45V-10	TCGA-WJ-A86L-10A-01D-A38X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	80e4fac9-c066-47a9-9fc0-2a42eef954cd	cebd5a99-cbde-441d-b98a-b84cf1825d65	g.chr4:123179983T>C	ENST00000264501.4	+	42	7120	c.6747T>C	c.(6745-6747)tcT>tcC	p.S2249S	KIAA1109_ENST00000388738.3_Silent_p.S2249S|KIAA1109_ENST00000455637.1_Silent_p.S2249S			Q2LD37	K1109_HUMAN	KIAA1109	2249					regulation of cell growth (GO:0001558)|regulation of epithelial cell differentiation (GO:0030856)	integral component of membrane (GO:0016021)|membrane (GO:0016020)|nucleus (GO:0005634)				breast(7)|central_nervous_system(1)|cervix(1)|endometrium(16)|kidney(6)|large_intestine(33)|liver(4)|lung(74)|ovary(9)|pancreas(1)|prostate(5)|skin(6)|upper_aerodigestive_tract(6)|urinary_tract(3)	172						ATAGTGACTCTGCATTAAAAA	0.368																																					p.S2249S		Atlas-SNP	.											.	KIAA1109	424	.	0			c.T6747C						.						78.0	73.0	74.0					4																	123179983		1831	4087	5918	SO:0001819	synonymous_variant	84162	exon40			TGACTCTGCATTA	AL137384	CCDS43267.1	4q28.1	2012-07-09			ENSG00000138688	ENSG00000138688			26953	protein-coding gene	gene with protein product	"""fragile site-associated"""	611565				16386706	Standard	NM_015312		Approved	FLJ21404, FSA, KIAA1371, Tweek	uc003ieh.3	Q2LD37	OTTHUMG00000150116	ENST00000264501.4:c.6747T>C	chr4.hg19:g.123179983T>C		81.0	0.0		75.0	26.0	NM_015312	Q4W598|Q5CZA9|Q6ZS70|Q6ZV75|Q86XA5|Q8WVD8|Q9H742|Q9NT48|Q9NTC3|Q9NTI4|Q9P2H6|Q9UPP3	Silent	SNP	ENST00000264501.4	hg19	CCDS43267.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	9.156|9.156	1.017492|1.017492	0.19355|0.19355	.|.	.|.	ENSG00000138688|ENSG00000138688	ENST00000419325|ENST00000446180	.|.	.|.	.|.	5.96|5.96	3.39|3.39	0.38822|0.38822	.|.	.|.	.|.	.|.	.|.	T|T	0.59046|0.59046	0.2165|0.2165	.|.	.|.	.|.	0.80722|0.80722	D|D	1|1	.|.	.|.	.|.	.|.	.|.	.|.	T|T	0.55392|0.55392	-0.8148|-0.8148	4|4	.|.	.|.	.|.	.|.	9.4181|9.4181	0.38534|0.38534	0.1206:0.0:0.1267:0.7527|0.1206:0.0:0.1267:0.7527	.|.	.|.	.|.	.|.	R|P	207|822	.|.	.|.	C|L	+|+	1|2	0|0	KIAA1109|KIAA1109	123399433|123399433	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.997000|0.997000	0.91878|0.91878	2.559000|2.559000	0.45888|0.45888	1.060000|1.060000	0.40578|0.40578	0.477000|0.477000	0.44152|0.44152	TGC|CTG	.	.		0.368	KIAA1109-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000316415.1	NM_020797	
ADAMTS16	170690	hgsc.bcm.edu	37	5	5235288	5235288	+	Missense_Mutation	SNP	C	C	G			TCGA-WJ-A86L-01A-12D-A45V-10	TCGA-WJ-A86L-10A-01D-A38X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	80e4fac9-c066-47a9-9fc0-2a42eef954cd	cebd5a99-cbde-441d-b98a-b84cf1825d65	g.chr5:5235288C>G	ENST00000274181.7	+	13	2150	c.2012C>G	c.(2011-2013)aCt>aGt	p.T671S	ADAMTS16_ENST00000513709.1_3'UTR	NM_139056.2	NP_620687.2	Q8TE57	ATS16_HUMAN	ADAM metallopeptidase with thrombospondin type 1 motif, 16	671	Cys-rich.				branching involved in ureteric bud morphogenesis (GO:0001658)	proteinaceous extracellular matrix (GO:0005578)	metalloendopeptidase activity (GO:0004222)|zinc ion binding (GO:0008270)			breast(2)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(12)|lung(72)|ovary(4)|pancreas(1)|prostate(2)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	107						AAGCCTTACACTCAAGTAGAA	0.468																																					p.T671S		Atlas-SNP	.											.	ADAMTS16	543	.	0			c.C2012G						.						63.0	66.0	65.0					5																	5235288		1940	4138	6078	SO:0001583	missense	170690	exon13			CTTACACTCAAGT	AJ315734	CCDS43299.1	5p15	2008-07-18	2005-08-19		ENSG00000145536	ENSG00000145536		"""ADAM metallopeptidases with thrombospondin type 1 motif"""	17108	protein-coding gene	gene with protein product		607510	"""a disintegrin-like and metalloprotease (reprolysin type) with thrombospondin type 1 motif, 16"""			11867212	Standard	NM_139056		Approved	ADAMTS16s	uc003jdl.3	Q8TE57	OTTHUMG00000161663	ENST00000274181.7:c.2012C>G	chr5.hg19:g.5235288C>G	ENSP00000274181:p.Thr671Ser	111.0	0.0		108.0	52.0	NM_139056	C6G490|Q8IVE2	Missense_Mutation	SNP	ENST00000274181.7	hg19	CCDS43299.1	.	.	.	.	.	.	.	.	.	.	C	14.41	2.526794	0.44969	.	.	ENSG00000145536	ENST00000274181;ENST00000536857	T	0.03468	3.92	4.57	3.69	0.42338	.	0.058374	0.64402	D	0.000003	T	0.10551	0.0258	L	0.51853	1.615	0.53688	D	0.999979	D;D	0.89917	0.999;1.0	D;D	0.80764	0.991;0.994	T	0.28235	-1.0050	10	0.09084	T	0.74	.	13.1971	0.59745	0.1609:0.8391:0.0:0.0	.	671;671	Q8TE57;Q8TE57-2	ATS16_HUMAN;.	S	671	ENSP00000274181:T671S	ENSP00000274181:T671S	T	+	2	0	ADAMTS16	5288288	1.000000	0.71417	0.781000	0.31783	0.204000	0.24138	7.400000	0.79949	1.050000	0.40346	-0.169000	0.13324	ACT	.	.		0.468	ADAMTS16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000365657.1	NM_139056	
CDH10	1008	hgsc.bcm.edu	37	5	24537662	24537662	+	Missense_Mutation	SNP	T	T	A			TCGA-WJ-A86L-01A-12D-A45V-10	TCGA-WJ-A86L-10A-01D-A38X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	80e4fac9-c066-47a9-9fc0-2a42eef954cd	cebd5a99-cbde-441d-b98a-b84cf1825d65	g.chr5:24537662T>A	ENST00000264463.4	-	3	860	c.353A>T	c.(352-354)gAt>gTt	p.D118V		NM_006727.3	NP_006718.2	Q9Y6N8	CAD10_HUMAN	cadherin 10, type 2 (T2-cadherin)	118	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)|single organismal cell-cell adhesion (GO:0016337)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			NS(1)|breast(8)|central_nervous_system(2)|cervix(1)|endometrium(9)|kidney(2)|large_intestine(29)|lung(111)|ovary(6)|pancreas(6)|skin(4)|stomach(2)|upper_aerodigestive_tract(4)	185				STAD - Stomach adenocarcinoma(35;0.0556)		TTCCTCCCTATCAATTCGCCT	0.398										HNSCC(23;0.051)																											p.D118V		Atlas-SNP	.											.	CDH10	391	.	0			c.A353T						.						153.0	141.0	145.0					5																	24537662		2203	4300	6503	SO:0001583	missense	1008	exon3			TCCCTATCAATTC	AF039747	CCDS3892.1	5p14.2	2010-01-26			ENSG00000040731	ENSG00000040731		"""Cadherins / Major cadherins"""	1749	protein-coding gene	gene with protein product		604555				2059658	Standard	NM_006727		Approved		uc003jgr.2	Q9Y6N8	OTTHUMG00000090667	ENST00000264463.4:c.353A>T	chr5.hg19:g.24537662T>A	ENSP00000264463:p.Asp118Val	92.0	0.0		84.0	46.0	NM_006727	Q9ULB3	Missense_Mutation	SNP	ENST00000264463.4	hg19	CCDS3892.1	.	.	.	.	.	.	.	.	.	.	T	23.7	4.450592	0.84101	.	.	ENSG00000040731	ENST00000264463	T	0.65364	-0.15	5.82	5.82	0.92795	Cadherin (5);Cadherin-like (1);	0.000000	0.85682	D	0.000000	D	0.87354	0.6156	H	0.98295	4.195	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.92124	0.5706	10	0.87932	D	0	.	15.3558	0.74425	0.0:0.0:0.0:1.0	.	118	Q9Y6N8	CAD10_HUMAN	V	118	ENSP00000264463:D118V	ENSP00000264463:D118V	D	-	2	0	CDH10	24573419	1.000000	0.71417	1.000000	0.80357	0.957000	0.61999	7.698000	0.84413	2.225000	0.72522	0.455000	0.32223	GAT	.	.		0.398	CDH10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207345.2	NM_006727	
CMYA5	202333	hgsc.bcm.edu	37	5	79032250	79032250	+	Missense_Mutation	SNP	G	G	T			TCGA-WJ-A86L-01A-12D-A45V-10	TCGA-WJ-A86L-10A-01D-A38X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	80e4fac9-c066-47a9-9fc0-2a42eef954cd	cebd5a99-cbde-441d-b98a-b84cf1825d65	g.chr5:79032250G>T	ENST00000446378.2	+	2	7693	c.7662G>T	c.(7660-7662)caG>caT	p.Q2554H		NM_153610.3	NP_705838.3	Q8N3K9	CMYA5_HUMAN	cardiomyopathy associated 5	2554					negative regulation of calcineurin-NFAT signaling cascade (GO:0070885)|negative regulation of protein phosphatase type 2B activity (GO:0032513)|regulation of skeletal muscle adaptation (GO:0014733)	costamere (GO:0043034)				NS(2)|breast(4)|central_nervous_system(1)|cervix(2)|endometrium(7)|haematopoietic_and_lymphoid_tissue(4)|kidney(4)|large_intestine(37)|lung(34)|ovary(6)|pancreas(2)|prostate(5)|skin(5)|stomach(11)|upper_aerodigestive_tract(3)|urinary_tract(1)	128		Lung NSC(167;0.00296)|all_lung(232;0.00327)|Ovarian(174;0.0262)		OV - Ovarian serous cystadenocarcinoma(54;9.85e-46)|Epithelial(54;3.38e-40)|all cancers(79;3.43e-35)		GAAAGAAGCAGCAGGAACATC	0.368																																					p.Q2554H		Atlas-SNP	.											.	CMYA5	643	.	0			c.G7662T						.						69.0	66.0	67.0					5																	79032250		1893	4115	6008	SO:0001583	missense	202333	exon2			GAAGCAGCAGGAA	AW755254, AL831986	CCDS47238.1	5q14.1	2013-02-11			ENSG00000164309	ENSG00000164309		"""Tripartite motif containing / Tripartite motif containing"", ""A-kinase anchor proteins"", ""Fibronectin type III domain containing"""	14305	protein-coding gene	gene with protein product	"""genethonin-3"", ""tripartite motif-containing 76"""	612193	"""chromosome 5 open reading frame 10"""	C5orf10		14688250	Standard	NM_153610		Approved	myospryn, SPRYD2, DKFZp451G223, TRIM76	uc003kgc.3	Q8N3K9	OTTHUMG00000162548	ENST00000446378.2:c.7662G>T	chr5.hg19:g.79032250G>T	ENSP00000394770:p.Gln2554His	86.0	0.0		98.0	35.0	NM_153610	A0PJB7|Q05CT4|Q2NKX1|Q2T9G9|Q69YQ8|Q69YQ9|Q6P517|Q6P5U3|Q7Z4I1|Q86T34|Q86T49|Q8N3S4|Q8N3S7|Q8NAG8|Q9UK88	Missense_Mutation	SNP	ENST00000446378.2	hg19	CCDS47238.1	.	.	.	.	.	.	.	.	.	.	G	9.557	1.117480	0.20877	.	.	ENSG00000164309	ENST00000446378	T	0.21361	2.01	5.16	0.983	0.19767	.	1.661270	0.03317	N	0.191328	T	0.24736	0.0600	L	0.57536	1.79	0.09310	N	1	B	0.32693	0.38	B	0.37198	0.243	T	0.26985	-1.0087	10	0.51188	T	0.08	.	3.7823	0.08686	0.186:0.0:0.4559:0.3581	.	2554	Q8N3K9	CMYA5_HUMAN	H	2554	ENSP00000394770:Q2554H	ENSP00000394770:Q2554H	Q	+	3	2	CMYA5	79068006	0.851000	0.29673	0.457000	0.27056	0.331000	0.28603	0.180000	0.16860	0.331000	0.23511	0.462000	0.41574	CAG	.	.		0.368	CMYA5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000369497.1	NM_153610	
CTNNA1	1495	hgsc.bcm.edu	37	5	138260300	138260300	+	Missense_Mutation	SNP	G	G	T			TCGA-WJ-A86L-01A-12D-A45V-10	TCGA-WJ-A86L-10A-01D-A38X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	80e4fac9-c066-47a9-9fc0-2a42eef954cd	cebd5a99-cbde-441d-b98a-b84cf1825d65	g.chr5:138260300G>T	ENST00000302763.7	+	12	1738	c.1648G>T	c.(1648-1650)Gcc>Tcc	p.A550S	CTNNA1_ENST00000540387.1_Missense_Mutation_p.A180S|CTNNA1_ENST00000355078.5_Missense_Mutation_p.A447S|CTNNA1_ENST00000518825.1_Missense_Mutation_p.A550S	NM_001903.2	NP_001894.2	P35221	CTNA1_HUMAN	catenin (cadherin-associated protein), alpha 1, 102kDa	550					adherens junction organization (GO:0034332)|aging (GO:0007568)|apical junction assembly (GO:0043297)|axon regeneration (GO:0031103)|cell adhesion (GO:0007155)|cell junction assembly (GO:0034329)|cell-cell junction organization (GO:0045216)|cellular protein localization (GO:0034613)|cellular response to indole-3-methanol (GO:0071681)|epithelial cell-cell adhesion (GO:0090136)|establishment or maintenance of cell polarity (GO:0007163)|gap junction assembly (GO:0016264)|male gonad development (GO:0008584)|muscle cell differentiation (GO:0042692)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cell motility (GO:2000146)|negative regulation of extrinsic apoptotic signaling pathway in absence of ligand (GO:2001240)|negative regulation of integrin-mediated signaling pathway (GO:2001045)|negative regulation of neuroblast proliferation (GO:0007406)|odontogenesis of dentin-containing tooth (GO:0042475)|ovarian follicle development (GO:0001541)|positive regulation of extrinsic apoptotic signaling pathway in absence of ligand (GO:2001241)|positive regulation of muscle cell differentiation (GO:0051149)|positive regulation of smoothened signaling pathway (GO:0045880)|protein heterooligomerization (GO:0051291)|response to estrogen (GO:0043627)	acrosomal vesicle (GO:0001669)|actin cytoskeleton (GO:0015629)|catenin complex (GO:0016342)|cell-cell junction (GO:0005911)|cytosol (GO:0005829)|focal adhesion (GO:0005925)|intercalated disc (GO:0014704)|lamellipodium (GO:0030027)|plasma membrane (GO:0005886)|zonula adherens (GO:0005915)	beta-catenin binding (GO:0008013)|cadherin binding (GO:0045296)|gamma-catenin binding (GO:0045295)|poly(A) RNA binding (GO:0044822)|structural molecule activity (GO:0005198)|vinculin binding (GO:0017166)			NS(1)|breast(7)|cervix(2)|endometrium(4)|kidney(6)|large_intestine(16)|lung(9)|oesophagus(2)|ovary(3)|prostate(1)|upper_aerodigestive_tract(1)	52			KIRC - Kidney renal clear cell carcinoma(527;0.00185)|Kidney(363;0.00325)			AGGCCGGGCAGCCCGGGTCAT	0.522																																					p.A550S		Atlas-SNP	.											.	CTNNA1	114	.	0			c.G1648T						.						54.0	49.0	50.0					5																	138260300		2203	4300	6503	SO:0001583	missense	1495	exon12			CGGGCAGCCCGGG	D13866	CCDS34243.1, CCDS75315.1	5q31.2	2008-02-05	2002-08-29			ENSG00000044115			2509	protein-coding gene	gene with protein product		116805	"""catenin (cadherin-associated protein), alpha 1 (102kD)"""			1924379	Standard	XM_005271898		Approved	CAP102	uc003ldh.3	P35221		ENST00000302763.7:c.1648G>T	chr5.hg19:g.138260300G>T	ENSP00000304669:p.Ala550Ser	153.0	0.0		113.0	55.0	NM_001903	Q12795|Q8N1C0	Missense_Mutation	SNP	ENST00000302763.7	hg19	CCDS34243.1	.	.	.	.	.	.	.	.	.	.	G	20.1	3.934068	0.73442	.	.	ENSG00000044115	ENST00000355078;ENST00000302763;ENST00000537034;ENST00000541863;ENST00000518825;ENST00000540387	T;T;T;T	0.37411	1.2;1.2;1.2;1.2	5.51	5.51	0.81932	.	0.000000	0.85682	D	0.000000	T	0.33147	0.0853	L	0.41415	1.275	0.80722	D	1	B;B;B	0.14012	0.009;0.002;0.001	B;B;B	0.26770	0.073;0.027;0.054	T	0.13683	-1.0500	10	0.09338	T	0.73	-14.4517	19.3816	0.94540	0.0:0.0:1.0:0.0	.	550;427;550	G3XAM7;B4DKT9;P35221	.;.;CTNA1_HUMAN	S	447;550;550;535;550;180	ENSP00000347190:A447S;ENSP00000304669:A550S;ENSP00000427821:A550S;ENSP00000438476:A180S	ENSP00000304669:A550S	A	+	1	0	CTNNA1	138288199	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	9.869000	0.99810	2.756000	0.94617	0.655000	0.94253	GCC	.	.		0.522	CTNNA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000373868.1	NM_001903	
PCDHA6	56142	hgsc.bcm.edu	37	5	140208117	140208117	+	Silent	SNP	G	G	A			TCGA-WJ-A86L-01A-12D-A45V-10	TCGA-WJ-A86L-10A-01D-A38X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	80e4fac9-c066-47a9-9fc0-2a42eef954cd	cebd5a99-cbde-441d-b98a-b84cf1825d65	g.chr5:140208117G>A	ENST00000529310.1	+	1	555	c.441G>A	c.(439-441)ctG>ctA	p.L147L	PCDHA4_ENST00000512229.2_Intron|PCDHA5_ENST00000529619.1_Intron|PCDHA6_ENST00000527624.1_Silent_p.L147L|PCDHA1_ENST00000504120.2_Intron|PCDHA2_ENST00000526136.1_Intron|PCDHA5_ENST00000529859.1_Intron|PCDHA3_ENST00000522353.2_Intron|PCDHA1_ENST00000394633.3_Intron|PCDHA4_ENST00000530339.1_Intron	NM_018909.2|NM_031848.2|NM_031849.1	NP_061732.1|NP_114036.1|NP_114037.1	Q9UN73	PCDA6_HUMAN	protocadherin alpha 6	147					cell adhesion (GO:0007155)|homophilic cell adhesion (GO:0007156)|nervous system development (GO:0007399)	extracellular region (GO:0005576)|integral component of plasma membrane (GO:0005887)	calcium ion binding (GO:0005509)			NS(1)|breast(2)|cervix(1)|endometrium(10)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(11)|lung(42)|prostate(8)|skin(5)|upper_aerodigestive_tract(1)|urinary_tract(1)	89			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			AATCTAGGCTGCCAGATTCTG	0.498																																					p.L147L		Atlas-SNP	.											.	PCDHA6	442	.	0			c.G441A						.						88.0	93.0	91.0					5																	140208117		2203	4300	6503	SO:0001819	synonymous_variant	56142	exon1			TAGGCTGCCAGAT	AF152484	CCDS47281.1, CCDS47282.1	5q31	2010-11-26			ENSG00000081842	ENSG00000081842		"""Cadherins / Protocadherins : Clustered"""	8672	other	complex locus constituent	"""KIAA0345-like 8"""	606312		CNRS2		10380929, 10662547	Standard	NM_018909		Approved	CNR2, CRNR2, PCDH-ALPHA6		Q9UN73	OTTHUMG00000163353	ENST00000529310.1:c.441G>A	chr5.hg19:g.140208117G>A		148.0	0.0		129.0	63.0	NM_018909	O75283|Q9NRT8	Silent	SNP	ENST00000529310.1	hg19	CCDS47281.1																																																																																			.	.		0.498	PCDHA6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000372829.3	NM_018909	
GABRG2	2566	hgsc.bcm.edu	37	5	161576316	161576316	+	Missense_Mutation	SNP	C	C	G			TCGA-WJ-A86L-01A-12D-A45V-10	TCGA-WJ-A86L-10A-01D-A38X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	80e4fac9-c066-47a9-9fc0-2a42eef954cd	cebd5a99-cbde-441d-b98a-b84cf1825d65	g.chr5:161576316C>G	ENST00000361925.4	+	8	1345	c.1125C>G	c.(1123-1125)aaC>aaG	p.N375K	GABRG2_ENST00000393933.4_Missense_Mutation_p.N280K|GABRG2_ENST00000414552.2_Missense_Mutation_p.N415K|GABRG2_ENST00000356592.3_Missense_Mutation_p.N375K			P18507	GBRG2_HUMAN	gamma-aminobutyric acid (GABA) A receptor, gamma 2	375					adult behavior (GO:0030534)|cellular response to histamine (GO:0071420)|chloride transmembrane transport (GO:1902476)|gamma-aminobutyric acid signaling pathway (GO:0007214)|ion transmembrane transport (GO:0034220)|post-embryonic development (GO:0009791)|synaptic transmission (GO:0007268)|synaptic transmission, GABAergic (GO:0051932)|transmembrane transport (GO:0055085)|transport (GO:0006810)	axon (GO:0030424)|cell junction (GO:0030054)|chloride channel complex (GO:0034707)|cytoplasm (GO:0005737)|dendrite membrane (GO:0032590)|GABA-A receptor complex (GO:1902711)|inhibitory synapse (GO:0060077)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)	benzodiazepine receptor activity (GO:0008503)|chloride channel activity (GO:0005254)|extracellular ligand-gated ion channel activity (GO:0005230)|GABA-A receptor activity (GO:0004890)			NS(1)|breast(1)|cervix(1)|endometrium(6)|kidney(4)|large_intestine(15)|lung(24)|ovary(4)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)	62	Renal(175;0.000319)	Medulloblastoma(196;0.0208)|all_neural(177;0.0672)	Kidney(164;7.83e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000525)	all cancers(165;0.0734)|OV - Ovarian serous cystadenocarcinoma(192;0.135)|Epithelial(171;0.136)	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)|Ginkgo biloba(DB01381)|Glutethimide(DB01437)|Halazepam(DB00801)|Halothane(DB01159)|Isoflurane(DB00753)|Lorazepam(DB00186)|Meprobamate(DB00371)|Methoxyflurane(DB01028)|Methyprylon(DB01107)|Midazolam(DB00683)|Nitrazepam(DB01595)|Olanzapine(DB00334)|Oxazepam(DB00842)|Pentobarbital(DB00312)|Prazepam(DB01588)|Primidone(DB00794)|Propofol(DB00818)|Quazepam(DB01589)|Sevoflurane(DB01236)|Talbutal(DB00306)|Temazepam(DB00231)|Topiramate(DB00273)|Triazolam(DB00897)	AGAAGAAAAACCCTGTATGTA	0.393																																					p.N415K		Atlas-SNP	.											.	GABRG2	142	.	0			c.C1245G						.						93.0	80.0	84.0					5																	161576316		2203	4300	6503	SO:0001583	missense	2566	exon9			GAAAAACCCTGTA		CCDS4358.1, CCDS4359.1, CCDS47333.1	5q34	2012-06-22			ENSG00000113327	ENSG00000113327		"""GABA receptors"", ""Ligand-gated ion channels / GABA(A) receptors"""	4087	protein-coding gene	gene with protein product	"""GABA(A) receptor, gamma 2"""	137164					Standard	NM_198904		Approved		uc010jjc.3	P18507	OTTHUMG00000130350	ENST00000361925.4:c.1125C>G	chr5.hg19:g.161576316C>G	ENSP00000354651:p.Asn375Lys	52.0	0.0		72.0	28.0	NM_198903	F5HB82|Q6GRL6|Q6PCC3|Q9UDB3|Q9UN15	Missense_Mutation	SNP	ENST00000361925.4	hg19	CCDS4358.1	.	.	.	.	.	.	.	.	.	.	C	0.880	-0.729058	0.03135	.	.	ENSG00000113327	ENST00000356592;ENST00000414552;ENST00000361925;ENST00000393933	D;D;D;D	0.85088	-1.85;-1.85;-1.94;-1.94	5.61	-0.367	0.12541	Neurotransmitter-gated ion-channel transmembrane domain (2);	0.873625	0.09863	N	0.745948	T	0.72622	0.3483	N	0.25647	0.755	0.80722	D	1	B;B;B	0.16603	0.01;0.005;0.018	B;B;B	0.18263	0.008;0.021;0.012	T	0.57957	-0.7721	10	0.02654	T	1	.	12.4207	0.55518	0.0:0.5703:0.0:0.4297	.	415;375;375	F5HB82;P18507;P18507-2	.;GBRG2_HUMAN;.	K	375;415;375;280	ENSP00000349000:N375K;ENSP00000410732:N415K;ENSP00000354651:N375K;ENSP00000377510:N280K	ENSP00000349000:N375K	N	+	3	2	GABRG2	161508894	0.336000	0.24757	0.993000	0.49108	0.726000	0.41606	-0.392000	0.07314	-0.160000	0.11002	-0.961000	0.02630	AAC	.	.		0.393	GABRG2-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000252706.1		
RANBP17	64901	hgsc.bcm.edu	37	5	170319441	170319441	+	Missense_Mutation	SNP	G	G	T			TCGA-WJ-A86L-01A-12D-A45V-10	TCGA-WJ-A86L-10A-01D-A38X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	80e4fac9-c066-47a9-9fc0-2a42eef954cd	cebd5a99-cbde-441d-b98a-b84cf1825d65	g.chr5:170319441G>T	ENST00000523189.1	+	4	471	c.307G>T	c.(307-309)Gtc>Ttc	p.V103F		NM_022897.3	NP_075048.1	Q9H2T7	RBP17_HUMAN	RAN binding protein 17	103					mRNA transport (GO:0051028)|protein import into nucleus (GO:0006606)	cytoplasm (GO:0005737)|nuclear pore (GO:0005643)	GTP binding (GO:0005525)			breast(1)|central_nervous_system(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(8)|lung(25)|ovary(3)|prostate(3)|skin(3)|upper_aerodigestive_tract(1)	50	Renal(175;0.000159)|Lung NSC(126;0.00751)|all_lung(126;0.0123)	Medulloblastoma(196;0.0399)|all_neural(177;0.0966)	Kidney(164;7.24e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000516)			GGCTCCCTTTGTCATCCAAGC	0.403			T	TRD@	ALL																																p.V103F		Atlas-SNP	.		Dom	yes		5	5q34	64901	RAN binding protein 17		L	.	RANBP17	108	.	0			c.G307T						.						171.0	167.0	168.0					5																	170319441		2203	4300	6503	SO:0001583	missense	64901	exon4			CCCTTTGTCATCC	AF222747	CCDS34287.1	5q34	2009-01-12			ENSG00000204764	ENSG00000204764			14428	protein-coding gene	gene with protein product		606141				11024021	Standard	NM_022897		Approved		uc003mba.3	Q9H2T7	OTTHUMG00000163203	ENST00000523189.1:c.307G>T	chr5.hg19:g.170319441G>T	ENSP00000427975:p.Val103Phe	124.0	0.0		110.0	51.0	NM_022897	Q8IU74	Missense_Mutation	SNP	ENST00000523189.1	hg19	CCDS34287.1	.	.	.	.	.	.	.	.	.	.	G	33	5.270013	0.95429	.	.	ENSG00000204764	ENST00000523189;ENST00000545246;ENST00000519944	T	0.73152	-0.72	5.92	5.92	0.95590	Armadillo-type fold (1);	0.000000	0.56097	D	0.000024	D	0.88559	0.6469	M	0.92122	3.275	0.80722	D	1	D;D	0.89917	1.0;0.999	D;D	0.80764	0.994;0.994	D	0.90012	0.4122	10	0.66056	D	0.02	-14.9791	19.9157	0.97061	0.0:0.0:1.0:0.0	.	103;153	Q9H2T7;B4DQG2	RBP17_HUMAN;.	F	103;21;21	ENSP00000427975:V103F	ENSP00000373770:V103F	V	+	1	0	RANBP17	170252019	1.000000	0.71417	1.000000	0.80357	0.988000	0.76386	9.386000	0.97228	2.813000	0.96785	0.561000	0.74099	GTC	.	.		0.403	RANBP17-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000372036.1	NM_022897	
SCUBE3	222663	hgsc.bcm.edu	37	6	35211877	35211877	+	Missense_Mutation	SNP	G	G	A			TCGA-WJ-A86L-01A-12D-A45V-10	TCGA-WJ-A86L-10A-01D-A38X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	80e4fac9-c066-47a9-9fc0-2a42eef954cd	cebd5a99-cbde-441d-b98a-b84cf1825d65	g.chr6:35211877G>A	ENST00000274938.7	+	17	2209	c.2209G>A	c.(2209-2211)Gcc>Acc	p.A737T	SCUBE3_ENST00000394681.1_Missense_Mutation_p.A753T	NM_152753.2	NP_689966.2			signal peptide, CUB domain, EGF-like 3											breast(1)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(3)|kidney(1)|large_intestine(12)|lung(11)|ovary(1)|prostate(1)|skin(2)|urinary_tract(1)	37						GCATGAAGGGGCCATTTCCTT	0.567																																					p.A737T		Atlas-SNP	.											.	SCUBE3	99	.	0			c.G2209A						.						90.0	79.0	82.0					6																	35211877		2203	4299	6502	SO:0001583	missense	222663	exon17			GAAGGGGCCATTT	AF452494.1	CCDS4800.1	6p21.3	2008-02-05	2004-05-19	2004-05-21		ENSG00000146197			13655	protein-coding gene	gene with protein product		614708	"""CUB domain and EGF-like repeat containing 3"""	CEGF3		12270931	Standard	NM_152753		Approved	FLJ34743	uc003okf.1	Q8IX30		ENST00000274938.7:c.2209G>A	chr6.hg19:g.35211877G>A	ENSP00000274938:p.Ala737Thr	79.0	0.0		69.0	31.0	NM_152753		Missense_Mutation	SNP	ENST00000274938.7	hg19	CCDS4800.1	.	.	.	.	.	.	.	.	.	.	G	17.97	3.519592	0.64634	.	.	ENSG00000146197	ENST00000394681;ENST00000274938	T;T	0.21031	2.03;2.03	5.75	5.75	0.90469	Tyrosine-protein kinase ephrin type A/B receptor-like (1);Growth factor, receptor (1);	0.000000	0.85682	D	0.000000	T	0.30479	0.0766	L	0.42744	1.35	0.80722	D	1	D;D	0.76494	0.998;0.999	D;D	0.85130	0.995;0.997	T	0.00692	-1.1607	10	0.23891	T	0.37	.	19.9447	0.97177	0.0:0.0:1.0:0.0	.	753;737	Q8IX30-2;Q8IX30	.;SCUB3_HUMAN	T	753;737	ENSP00000378174:A753T;ENSP00000274938:A737T	ENSP00000274938:A737T	A	+	1	0	SCUBE3	35319855	1.000000	0.71417	0.999000	0.59377	0.983000	0.72400	3.594000	0.54008	2.719000	0.93026	0.655000	0.94253	GCC	.	.		0.567	SCUBE3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040275.1	NM_152753	
MOCS1	4337	hgsc.bcm.edu	37	6	39876849	39876849	+	Missense_Mutation	SNP	G	G	A	rs149586823		TCGA-WJ-A86L-01A-12D-A45V-10	TCGA-WJ-A86L-10A-01D-A38X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	80e4fac9-c066-47a9-9fc0-2a42eef954cd	cebd5a99-cbde-441d-b98a-b84cf1825d65	g.chr6:39876849G>A	ENST00000340692.5	-	10	1135	c.1132C>T	c.(1132-1134)Cgg>Tgg	p.R378W	MOCS1_ENST00000373186.4_Missense_Mutation_p.R378W|MOCS1_ENST00000308559.7_Intron|MOCS1_ENST00000373188.2_Missense_Mutation_p.R378W|MOCS1_ENST00000373175.4_Missense_Mutation_p.R349W|MOCS1_ENST00000432280.2_Missense_Mutation_p.R349W|MOCS1_ENST00000373195.3_Intron|MOCS1_ENST00000425303.2_Missense_Mutation_p.R378W			Q9NZB8	MOCS1_HUMAN	molybdenum cofactor synthesis 1	378	Molybdenum cofactor biosynthesis protein A.				Mo-molybdopterin cofactor biosynthetic process (GO:0006777)|molybdopterin cofactor biosynthetic process (GO:0032324)|small molecule metabolic process (GO:0044281)|vitamin metabolic process (GO:0006766)|water-soluble vitamin metabolic process (GO:0006767)	cytosol (GO:0005829)|molybdopterin synthase complex (GO:0019008)|nucleus (GO:0005634)	4 iron, 4 sulfur cluster binding (GO:0051539)|cyclic pyranopterin monophosphate synthase activity (GO:0061597)|GTP binding (GO:0005525)|metal ion binding (GO:0046872)	p.R378W(2)		central_nervous_system(1)|endometrium(5)|kidney(1)|large_intestine(1)|liver(2)|lung(6)|ovary(1)|pancreas(1)|prostate(1)|skin(2)	21	Ovarian(28;0.0355)|Colorectal(47;0.196)					ATCATGGGCCGGTTCTTCATC	0.597																																					p.R378W	NSCLC(84;861 1413 23785 24908 42279)|Melanoma(182;611 2047 9114 11847 26639)	Atlas-SNP	.											MOCS1_ENST00000340692,NS,carcinoma,0,2	MOCS1	87	.	2	Substitution - Missense(2)	endometrium(2)	c.C1132T						.						113.0	96.0	102.0					6																	39876849		2203	4300	6503	SO:0001583	missense	4337	exon9			TGGGCCGGTTCTT	AJ224328	CCDS4846.1, CCDS43460.1	6p21.2	2012-05-08			ENSG00000124615	ENSG00000124615			7190	protein-coding gene	gene with protein product		603707				9731530, 10053004	Standard	NM_001075098		Approved	MOCOD	uc003opb.3	Q9NZB8	OTTHUMG00000014656	ENST00000340692.5:c.1132C>T	chr6.hg19:g.39876849G>A	ENSP00000344794:p.Arg378Trp	74.0	0.0		63.0	36.0	NM_005943	B3KPT7|B4DTP1|O14940|O14941|O75710|Q5J7W0|Q5TCE1|Q5TCE2|Q5TCE6|Q5TCE9|Q5TCF0|Q5TCF1|Q8N418|Q9NZB7|Q9UEM1	Missense_Mutation	SNP	ENST00000340692.5	hg19		.	.	.	.	.	.	.	.	.	.	g	18.84	3.709600	0.68730	.	.	ENSG00000124615	ENST00000373186;ENST00000373175;ENST00000373188;ENST00000340692;ENST00000425303;ENST00000432280	T;T	0.48201	0.83;0.82	5.2	4.3	0.51218	.	0.062741	0.64402	D	0.000008	T	0.48677	0.1513	L	0.39898	1.24	0.45867	D	0.998724	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.97110	1.0;0.997;1.0	T	0.40403	-0.9565	9	.	.	.	-26.4702	13.4252	0.61022	0.0:0.0:0.7233:0.2767	.	378;378;378	Q9NZB8-5;Q9NZB8-8;Q9NZB8-6	.;.;.	W	378;349;378;378;378;349	ENSP00000344794:R378W;ENSP00000416478:R378W	.	R	-	1	2	MOCS1	39984827	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	2.041000	0.41213	2.409000	0.81822	0.645000	0.84053	CGG	.	G|1.000;C|0.000		0.597	MOCS1-005	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000040476.2	NM_005943	
PHIP	55023	hgsc.bcm.edu	37	6	79692616	79692616	+	Missense_Mutation	SNP	T	T	A			TCGA-WJ-A86L-01A-12D-A45V-10	TCGA-WJ-A86L-10A-01D-A38X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	80e4fac9-c066-47a9-9fc0-2a42eef954cd	cebd5a99-cbde-441d-b98a-b84cf1825d65	g.chr6:79692616T>A	ENST00000275034.4	-	23	2923	c.2756A>T	c.(2755-2757)gAa>gTa	p.E919V	PHIP_ENST00000479165.1_5'UTR	NM_017934.5	NP_060404	Q8WWQ0	PHIP_HUMAN	pleckstrin homology domain interacting protein	919	Lys-rich.				cytoskeleton organization (GO:0007010)|insulin receptor signaling pathway (GO:0008286)|negative regulation of apoptotic process (GO:0043066)|negative regulation of extrinsic apoptotic signaling pathway (GO:2001237)|positive regulation of cell proliferation (GO:0008284)|positive regulation of insulin-like growth factor receptor signaling pathway (GO:0043568)|positive regulation of mitosis (GO:0045840)|positive regulation of peptidyl-serine phosphorylation (GO:0033138)|positive regulation of peptidyl-threonine phosphorylation (GO:0010800)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|protein import into nucleus (GO:0006606)|regulation of cell morphogenesis (GO:0022604)|regulation of growth (GO:0040008)|regulation of protein phosphorylation (GO:0001932)	extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)	insulin receptor binding (GO:0005158)|lysine-acetylated histone binding (GO:0070577)			NS(1)|breast(1)|central_nervous_system(2)|endometrium(10)|kidney(4)|large_intestine(20)|lung(20)|ovary(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(3)	68		all_cancers(76;0.00125)|Acute lymphoblastic leukemia(125;1.1e-05)|all_hematologic(105;0.00117)|all_epithelial(107;0.219)		BRCA - Breast invasive adenocarcinoma(397;0.231)		ttgttttctttctttgggctt	0.294																																					p.E919V		Atlas-SNP	.											.	PHIP	177	.	0			c.A2756T						.						45.0	42.0	43.0					6																	79692616		2199	4293	6492	SO:0001583	missense	55023	exon23			TTTCTTTCTTTGG	AF310250	CCDS4987.1	6q14	2013-01-09			ENSG00000146247	ENSG00000146247		"""WD repeat domain containing"", ""DDB1 and CUL4 associated factors"""	15673	protein-coding gene	gene with protein product	"""DDB1 and CUL4 associated factor 14"""	612870		WDR11		11018022	Standard	NM_017934		Approved	ndrp, FLJ20705, DCAF14, BRWD2	uc003pir.3	Q8WWQ0	OTTHUMG00000015071	ENST00000275034.4:c.2756A>T	chr6.hg19:g.79692616T>A	ENSP00000275034:p.Glu919Val	19.0	0.0		18.0	10.0	NM_017934	A7J992|B2RPK4|Q05CQ9|Q5VVH4|Q66I29|Q69YV1|Q8NBZ5|Q96H52|Q96ME2|Q9H261	Missense_Mutation	SNP	ENST00000275034.4	hg19	CCDS4987.1	.	.	.	.	.	.	.	.	.	.	T	15.94	2.982290	0.53827	.	.	ENSG00000146247	ENST00000275034	T	0.43688	0.94	4.95	4.95	0.65309	.	0.000000	0.85682	D	0.000000	T	0.18593	0.0446	L	0.34521	1.04	0.52099	D	0.999948	P;P	0.38978	0.652;0.652	B;B	0.36464	0.225;0.225	T	0.03750	-1.1007	9	.	.	.	-6.8477	13.7982	0.63184	0.0:0.0:0.0:1.0	.	919;919	A7J992;Q8WWQ0	.;PHIP_HUMAN	V	919	ENSP00000275034:E919V	.	E	-	2	0	PHIP	79749335	1.000000	0.71417	1.000000	0.80357	0.979000	0.70002	7.662000	0.83803	1.856000	0.53863	0.377000	0.23210	GAA	.	.		0.294	PHIP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041297.2		
PHIP	55023	hgsc.bcm.edu	37	6	79727210	79727210	+	Missense_Mutation	SNP	T	T	A			TCGA-WJ-A86L-01A-12D-A45V-10	TCGA-WJ-A86L-10A-01D-A38X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	80e4fac9-c066-47a9-9fc0-2a42eef954cd	cebd5a99-cbde-441d-b98a-b84cf1825d65	g.chr6:79727210T>A	ENST00000275034.4	-	11	1252	c.1085A>T	c.(1084-1086)gAg>gTg	p.E362V		NM_017934.5	NP_060404	Q8WWQ0	PHIP_HUMAN	pleckstrin homology domain interacting protein	362					cytoskeleton organization (GO:0007010)|insulin receptor signaling pathway (GO:0008286)|negative regulation of apoptotic process (GO:0043066)|negative regulation of extrinsic apoptotic signaling pathway (GO:2001237)|positive regulation of cell proliferation (GO:0008284)|positive regulation of insulin-like growth factor receptor signaling pathway (GO:0043568)|positive regulation of mitosis (GO:0045840)|positive regulation of peptidyl-serine phosphorylation (GO:0033138)|positive regulation of peptidyl-threonine phosphorylation (GO:0010800)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|protein import into nucleus (GO:0006606)|regulation of cell morphogenesis (GO:0022604)|regulation of growth (GO:0040008)|regulation of protein phosphorylation (GO:0001932)	extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)	insulin receptor binding (GO:0005158)|lysine-acetylated histone binding (GO:0070577)			NS(1)|breast(1)|central_nervous_system(2)|endometrium(10)|kidney(4)|large_intestine(20)|lung(20)|ovary(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(3)	68		all_cancers(76;0.00125)|Acute lymphoblastic leukemia(125;1.1e-05)|all_hematologic(105;0.00117)|all_epithelial(107;0.219)		BRCA - Breast invasive adenocarcinoma(397;0.231)		AGTATGAAACTCCAATTCTGA	0.338																																					p.E362V		Atlas-SNP	.											.	PHIP	177	.	0			c.A1085T						.						41.0	42.0	42.0					6																	79727210		2203	4296	6499	SO:0001583	missense	55023	exon11			TGAAACTCCAATT	AF310250	CCDS4987.1	6q14	2013-01-09			ENSG00000146247	ENSG00000146247		"""WD repeat domain containing"", ""DDB1 and CUL4 associated factors"""	15673	protein-coding gene	gene with protein product	"""DDB1 and CUL4 associated factor 14"""	612870		WDR11		11018022	Standard	NM_017934		Approved	ndrp, FLJ20705, DCAF14, BRWD2	uc003pir.3	Q8WWQ0	OTTHUMG00000015071	ENST00000275034.4:c.1085A>T	chr6.hg19:g.79727210T>A	ENSP00000275034:p.Glu362Val	218.0	0.0		236.0	96.0	NM_017934	A7J992|B2RPK4|Q05CQ9|Q5VVH4|Q66I29|Q69YV1|Q8NBZ5|Q96H52|Q96ME2|Q9H261	Missense_Mutation	SNP	ENST00000275034.4	hg19	CCDS4987.1	.	.	.	.	.	.	.	.	.	.	T	23.2	4.385424	0.82792	.	.	ENSG00000146247	ENST00000275034	T	0.60920	0.15	5.28	5.28	0.74379	WD40/YVTN repeat-like-containing domain (1);Quinonprotein alcohol dehydrogenase-like (1);WD40-repeat-containing domain (1);	0.000000	0.64402	D	0.000001	T	0.57577	0.2063	L	0.37750	1.13	0.80722	D	1	D;D	0.76494	0.999;0.999	D;D	0.85130	0.997;0.997	T	0.58538	-0.7619	9	.	.	.	-14.2641	14.3848	0.66938	0.0:0.0:0.0:1.0	.	362;362	A7J992;Q8WWQ0	.;PHIP_HUMAN	V	362	ENSP00000275034:E362V	.	E	-	2	0	PHIP	79783929	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.698000	0.84413	1.987000	0.57996	0.454000	0.30748	GAG	.	.		0.338	PHIP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041297.2		
TWISTNB	221830	hgsc.bcm.edu	37	7	19748398	19748398	+	Missense_Mutation	SNP	C	C	T			TCGA-WJ-A86L-01A-12D-A45V-10	TCGA-WJ-A86L-10A-01D-A38X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	80e4fac9-c066-47a9-9fc0-2a42eef954cd	cebd5a99-cbde-441d-b98a-b84cf1825d65	g.chr7:19748398C>T	ENST00000222567.5	-	1	312	c.242G>A	c.(241-243)cGc>cAc	p.R81H		NM_001002926.1	NP_001002926.1	Q3B726	RPA43_HUMAN	TWIST neighbor	81					transcription from RNA polymerase I promoter (GO:0006360)	DNA-directed RNA polymerase I complex (GO:0005736)|microtubule cytoskeleton (GO:0015630)|nucleolus (GO:0005730)|nucleus (GO:0005634)	DNA-directed RNA polymerase activity (GO:0003899)			kidney(1)|large_intestine(3)|lung(13)|ovary(1)|prostate(2)	20						CTCAGAATAGCGAAGGAGCTC	0.572											OREG0017879	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.R81H		Atlas-SNP	.											.	TWISTNB	63	.	0			c.G242A						.						116.0	104.0	108.0					7																	19748398		2203	4300	6503	SO:0001583	missense	221830	exon1			GAATAGCGAAGGA	AK090846	CCDS34606.1	7p21.1	2010-08-05			ENSG00000105849	ENSG00000105849			18027	protein-coding gene	gene with protein product		608312				12438708	Standard	NM_001002926		Approved		uc003sup.1	Q3B726	OTTHUMG00000152497	ENST00000222567.5:c.242G>A	chr7.hg19:g.19748398C>T	ENSP00000222567:p.Arg81His	48.0	0.0	735	56.0	31.0	NM_001002926	A0PJ45|B7Z724	Missense_Mutation	SNP	ENST00000222567.5	hg19	CCDS34606.1	.	.	.	.	.	.	.	.	.	.	C	20.3	3.968558	0.74131	.	.	ENSG00000105849	ENST00000222567	.	.	.	4.06	4.06	0.47325	RNA polymerase Rpb7, N-terminal (1);	0.351936	0.26753	N	0.022674	T	0.69142	0.3078	M	0.63843	1.955	0.37807	D	0.927926	D	0.89917	1.0	D	0.70716	0.97	T	0.72297	-0.4335	9	0.46703	T	0.11	-11.8811	10.4566	0.44555	0.0:0.9085:0.0:0.0915	.	81	Q3B726	RPA43_HUMAN	H	81	.	ENSP00000222567:R81H	R	-	2	0	TWISTNB	19714923	1.000000	0.71417	1.000000	0.80357	0.854000	0.48673	3.602000	0.54066	2.246000	0.74042	0.655000	0.94253	CGC	.	.		0.572	TWISTNB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000326463.1		
ABCB5	340273	hgsc.bcm.edu	37	7	20698196	20698196	+	Missense_Mutation	SNP	T	T	G			TCGA-WJ-A86L-01A-12D-A45V-10	TCGA-WJ-A86L-10A-01D-A38X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	80e4fac9-c066-47a9-9fc0-2a42eef954cd	cebd5a99-cbde-441d-b98a-b84cf1825d65	g.chr7:20698196T>G	ENST00000404938.2	+	14	2256	c.1604T>G	c.(1603-1605)aTt>aGt	p.I535S	ABCB5_ENST00000258738.6_Missense_Mutation_p.I90S|ABCB5_ENST00000443026.2_Missense_Mutation_p.I90S|ABCB5_ENST00000406935.1_Missense_Mutation_p.I90S	NM_001163941.1	NP_001157413.1	Q2M3G0	ABCB5_HUMAN	ATP-binding cassette, sub-family B (MDR/TAP), member 5	535	ABC transporter 1. {ECO:0000255|PROSITE- ProRule:PRU00434}.				antigen processing and presentation of endogenous peptide antigen via MHC class I via ER pathway, TAP-dependent (GO:0002485)|antigen processing and presentation of endogenous peptide antigen via MHC class Ib via ER pathway, TAP-dependent (GO:0002489)|antigen processing and presentation of exogenous protein antigen via MHC class Ib, TAP-dependent (GO:0002481)|cell differentiation (GO:0030154)|compound eye corneal lens development (GO:0048058)|positive regulation of antigen processing and presentation of peptide antigen via MHC class I (GO:0002591)|regulation of membrane potential (GO:0042391)|transmembrane transport (GO:0055085)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|ATPase activity, coupled to transmembrane movement of substances (GO:0042626)|efflux transmembrane transporter activity (GO:0015562)	p.I90N(2)|p.I535N(1)		breast(2)|central_nervous_system(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(2)|kidney(4)|large_intestine(11)|liver(1)|lung(37)|ovary(1)|pancreas(1)|prostate(1)|skin(10)|upper_aerodigestive_tract(1)	77						AGGATCGCAATTGCTCGTGCC	0.438																																					p.I535S		Atlas-SNP	.											ABCB5_ENST00000443026,NS,carcinoma,0,3	ABCB5	357	.	3	Substitution - Missense(3)	lung(3)	c.T1604G						.						133.0	117.0	122.0					7																	20698196		2203	4300	6503	SO:0001583	missense	340273	exon14			TCGCAATTGCTCG	U66692	CCDS5371.1, CCDS55090.1, CCDS55091.1, CCDS55092.1	7p14	2012-03-14			ENSG00000004846	ENSG00000004846		"""ATP binding cassette transporters / subfamily B"""	46	protein-coding gene	gene with protein product	"""P-glycoprotein ABCB5"", ""ATP-binding cassette protein"""	611785				8894702, 12960149	Standard	NM_001163942		Approved	EST422562, ABCB5beta, ABCB5alpha	uc010kuh.3	Q2M3G0	OTTHUMG00000094789	ENST00000404938.2:c.1604T>G	chr7.hg19:g.20698196T>G	ENSP00000384881:p.Ile535Ser	66.0	0.0		67.0	30.0	NM_001163941	A4D131|A7BKA4|B5MD19|B7WPL1|F8QQP8|F8QQP9|J3KQ04|Q2M3I5|Q5I5Q7|Q5I5Q8|Q6KG50|Q6XFQ5|Q8IXA1	Missense_Mutation	SNP	ENST00000404938.2	hg19	CCDS55090.1	.	.	.	.	.	.	.	.	.	.	T	18.87	3.715060	0.68844	.	.	ENSG00000004846	ENST00000404938;ENST00000443026;ENST00000406935;ENST00000258738	D;D;D;D	0.96136	-3.92;-3.92;-3.92;-3.92	5.77	4.61	0.57282	ABC transporter, conserved site (1);ATPase, AAA+ type, core (1);ABC transporter-like (2);	0.086851	0.46442	D	0.000297	D	0.98563	0.9520	H	0.98883	4.36	0.51767	D	0.999934	D;D;D;D	0.89917	1.0;1.0;1.0;1.0	D;D;D;D	0.97110	1.0;0.999;0.998;1.0	D	0.98552	1.0637	10	0.87932	D	0	.	10.7801	0.46374	0.0:0.074:0.0:0.926	.	90;535;90;90	B5MD19;A7BKA4;Q2M3G0;Q2M3G0-2	.;.;ABCB5_HUMAN;.	S	535;90;90;90	ENSP00000384881:I535S;ENSP00000406730:I90S;ENSP00000383899:I90S;ENSP00000258738:I90S	ENSP00000258738:I90S	I	+	2	0	ABCB5	20664721	1.000000	0.71417	0.983000	0.44433	0.492000	0.33523	6.102000	0.71486	2.330000	0.79161	0.528000	0.53228	ATT	.	.		0.438	ABCB5-004	PUTATIVE	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000326736.2	NM_178559	
TBX20	57057	hgsc.bcm.edu	37	7	35242082	35242082	+	Missense_Mutation	SNP	C	C	T			TCGA-WJ-A86L-01A-12D-A45V-10	TCGA-WJ-A86L-10A-01D-A38X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	80e4fac9-c066-47a9-9fc0-2a42eef954cd	cebd5a99-cbde-441d-b98a-b84cf1825d65	g.chr7:35242082C>T	ENST00000408931.3	-	8	1830	c.1304G>A	c.(1303-1305)gGa>gAa	p.G435E		NM_001077653.2|NM_001166220.1	NP_001071121.1|NP_001159692.1	Q9UMR3	TBX20_HUMAN	T-box 20	435					aortic valve morphogenesis (GO:0003180)|atrial septum morphogenesis (GO:0060413)|blood circulation (GO:0008015)|cardiac chamber formation (GO:0003207)|cardiac muscle tissue morphogenesis (GO:0055008)|cardiac right ventricle morphogenesis (GO:0003215)|cardiac septum development (GO:0003279)|cell proliferation (GO:0008283)|dorsal/ventral pattern formation (GO:0009953)|embryonic heart tube elongation (GO:0036306)|embryonic heart tube morphogenesis (GO:0003143)|endocardial cushion formation (GO:0003272)|endocardial cushion morphogenesis (GO:0003203)|endoderm formation (GO:0001706)|foramen ovale closure (GO:0035922)|heart looping (GO:0001947)|lateral mesoderm formation (GO:0048370)|muscle contraction (GO:0006936)|negative regulation of SMAD protein complex assembly (GO:0010991)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|neuron migration (GO:0001764)|outflow tract septum morphogenesis (GO:0003148)|patterning of blood vessels (GO:0001569)|pericardium morphogenesis (GO:0003344)|positive regulation of cardiac muscle cell proliferation (GO:0060045)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|pulmonary valve formation (GO:0003193)|pulmonary vein morphogenesis (GO:0060577)|tricuspid valve development (GO:0003175)|visceral motor neuron differentiation (GO:0021524)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	RNA polymerase II activating transcription factor binding (GO:0001102)|RNA polymerase II regulatory region sequence-specific DNA binding (GO:0000977)|RNA polymerase II transcription coactivator activity (GO:0001105)|RNA polymerase II transcription factor binding (GO:0001085)|sequence-specific DNA binding transcription factor activity (GO:0003700)			central_nervous_system(1)|cervix(1)|endometrium(3)|large_intestine(1)|lung(9)|prostate(1)|skin(1)|stomach(1)	18						ATGGCGTAGTCCTTGAATGGC	0.488																																					p.G435E		Atlas-SNP	.											TBX20_ENST00000408931,colon,carcinoma,0,1	TBX20	96	.	0			c.G1304A						.						32.0	31.0	31.0					7																	35242082		1922	4129	6051	SO:0001583	missense	57057	exon8			CGTAGTCCTTGAA	AJ237589	CCDS43568.1	7p14.3	2014-09-17			ENSG00000164532	ENSG00000164532		"""T-boxes"""	11598	protein-coding gene	gene with protein product		606061				10936053	Standard	NM_001077653		Approved		uc011kas.2	Q9UMR3	OTTHUMG00000099411	ENST00000408931.3:c.1304G>A	chr7.hg19:g.35242082C>T	ENSP00000386170:p.Gly435Glu	123.0	1.0		160.0	53.0	NM_001077653	A4D1Y6|Q000T4|Q0IJ70|Q0VAS1|Q9Y2N5	Missense_Mutation	SNP	ENST00000408931.3	hg19	CCDS43568.1	.	.	.	.	.	.	.	.	.	.	C	27.2	4.805639	0.90623	.	.	ENSG00000164532	ENST00000408931	D	0.88509	-2.39	5.66	5.66	0.87406	.	0.696409	0.13852	N	0.358302	D	0.91033	0.7179	N	0.19112	0.55	0.80722	D	1	D	0.89917	1.0	D	0.83275	0.996	D	0.90044	0.4144	10	0.39692	T	0.17	.	19.7407	0.96230	0.0:1.0:0.0:0.0	.	435	Q9UMR3	TBX20_HUMAN	E	435	ENSP00000386170:G435E	ENSP00000386170:G435E	G	-	2	0	TBX20	35208607	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	7.487000	0.81328	2.654000	0.90174	0.609000	0.83330	GGA	.	.		0.488	TBX20-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000216870.2	NM_020417	
NACAD	23148	hgsc.bcm.edu	37	7	45122346	45122346	+	Missense_Mutation	SNP	T	T	C			TCGA-WJ-A86L-01A-12D-A45V-10	TCGA-WJ-A86L-10A-01D-A38X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	80e4fac9-c066-47a9-9fc0-2a42eef954cd	cebd5a99-cbde-441d-b98a-b84cf1825d65	g.chr7:45122346T>C	ENST00000490531.2	-	2	3452	c.3433A>G	c.(3433-3435)Aca>Gca	p.T1145A		NM_001146334.1	NP_001139806.1	O15069	NACAD_HUMAN	NAC alpha domain containing	1145					protein transport (GO:0015031)	cytoplasm (GO:0005737)|nucleus (GO:0005634)				breast(1)|endometrium(2)|skin(2)	5						CTGGCCTCTGTGGCCACAGCT	0.672																																					p.T1145A		Atlas-SNP	.											.	NACAD	44	.	0			c.A3433G						.						19.0	26.0	24.0					7																	45122346		692	1590	2282	SO:0001583	missense	23148	exon2			CCTCTGTGGCCAC	AB002361	CCDS47582.1	7p13	2010-07-14			ENSG00000136274	ENSG00000136274			22196	protein-coding gene	gene with protein product							Standard	NM_001146334		Approved	KIAA0363	uc003tmt.3	O15069	OTTHUMG00000159170	ENST00000490531.2:c.3433A>G	chr7.hg19:g.45122346T>C	ENSP00000420477:p.Thr1145Ala	82.0	0.0		82.0	28.0	NM_001146334		Missense_Mutation	SNP	ENST00000490531.2	hg19	CCDS47582.1	.	.	.	.	.	.	.	.	.	.	t	2.659	-0.280222	0.05642	.	.	ENSG00000136274	ENST00000490531	T	0.10668	2.85	2.87	-5.14	0.02875	.	.	.	.	.	T	0.04182	0.0116	N	0.14661	0.345	0.09310	N	1	B	0.10296	0.003	B	0.06405	0.002	T	0.41662	-0.9496	9	0.26408	T	0.33	-0.2802	1.3416	0.02155	0.1614:0.4239:0.1695:0.2451	.	1145	O15069	NACAD_HUMAN	A	1145	ENSP00000420477:T1145A	ENSP00000420477:T1145A	T	-	1	0	NACAD	45088871	0.000000	0.05858	0.000000	0.03702	0.708000	0.40852	-1.352000	0.02619	-0.965000	0.03591	0.241000	0.17934	ACA	.	.		0.672	NACAD-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000353652.2	NM_001146334	
ASL	435	hgsc.bcm.edu	37	7	65557597	65557597	+	Missense_Mutation	SNP	G	G	T			TCGA-WJ-A86L-01A-12D-A45V-10	TCGA-WJ-A86L-10A-01D-A38X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	80e4fac9-c066-47a9-9fc0-2a42eef954cd	cebd5a99-cbde-441d-b98a-b84cf1825d65	g.chr7:65557597G>T	ENST00000304874.9	+	16	1299	c.1197G>T	c.(1195-1197)gaG>gaT	p.E399D	ASL_ENST00000380839.4_Missense_Mutation_p.E373D|ASL_ENST00000395331.3_Missense_Mutation_p.E379D|AC068533.7_ENST00000450043.1_Missense_Mutation_p.D168Y|ASL_ENST00000464970.1_3'UTR|ASL_ENST00000395332.3_Missense_Mutation_p.E399D	NM_000048.3	NP_000039.2	P04424	ARLY_HUMAN	argininosuccinate lyase	399					arginine biosynthetic process via ornithine (GO:0042450)|arginine catabolic process (GO:0006527)|cellular nitrogen compound metabolic process (GO:0034641)|internal protein amino acid acetylation (GO:0006475)|small molecule metabolic process (GO:0044281)|urea cycle (GO:0000050)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)	argininosuccinate lyase activity (GO:0004056)			breast(3)|endometrium(3)|large_intestine(2)|lung(9)|upper_aerodigestive_tract(1)	18					L-Arginine(DB00125)	TCATGGCCGAGACCAAGGGGG	0.637																																					p.E399D		Atlas-SNP	.											.	ASL	39	.	0			c.G1197T						.						69.0	69.0	69.0					7																	65557597		2203	4300	6503	SO:0001583	missense	435	exon16			GGCCGAGACCAAG		CCDS5531.1, CCDS47597.1, CCDS47598.1	7q11.21	2012-10-02			ENSG00000126522	ENSG00000126522	4.3.2.1		746	protein-coding gene	gene with protein product		608310					Standard	NM_001024943		Approved		uc003tuo.3	P04424	OTTHUMG00000022876	ENST00000304874.9:c.1197G>T	chr7.hg19:g.65557597G>T	ENSP00000307188:p.Glu399Asp	59.0	0.0		54.0	25.0	NM_000048	E7EMI0|E9PE48|Q6LDS5|Q96HS2	Missense_Mutation	SNP	ENST00000304874.9	hg19	CCDS5531.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	g|g	19.99|19.99	3.928957|3.928957	0.73327|0.73327	.|.	.|.	ENSG00000249319|ENSG00000126522	ENST00000450043|ENST00000304874;ENST00000380839;ENST00000395332;ENST00000395331	.|D;D;D;D	.|0.91407	.|-2.84;-2.84;-2.84;-2.84	5.28|5.28	4.4|4.4	0.53042|0.53042	.|L-Aspartase-like (1);	.|0.000000	.|0.85682	.|D	.|0.000000	D|D	0.94699|0.94699	0.8290|0.8290	M|M	0.85099|0.85099	2.735|2.735	0.58432|0.58432	D|D	0.999998|0.999998	.|D;D;D	.|0.89917	.|1.0;0.995;0.991	.|D;D;D	.|0.91635	.|0.999;0.994;0.994	D|D	0.93749|0.93749	0.7057|0.7057	5|10	.|0.41790	.|T	.|0.15	.|.	9.4249|9.4249	0.38574|0.38574	0.1618:0.0:0.8382:0.0|0.1618:0.0:0.8382:0.0	.|.	.|373;379;399	.|E9PE48;E7EMI0;P04424	.|.;.;ARLY_HUMAN	Y|D	168|399;373;399;379	.|ENSP00000307188:E399D;ENSP00000370219:E373D;ENSP00000378741:E399D;ENSP00000378740:E379D	.|ENSP00000307188:E399D	D|E	+|+	1|3	0|2	AC068533.7|ASL	65195032|65195032	1.000000|1.000000	0.71417|0.71417	0.985000|0.985000	0.45067|0.45067	0.871000|0.871000	0.50021|0.50021	2.509000|2.509000	0.45459|0.45459	1.357000|1.357000	0.45904|0.45904	0.491000|0.491000	0.48974|0.48974	GAC|GAG	.	.		0.637	ASL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251695.2	NM_000048	
PODXL	5420	hgsc.bcm.edu	37	7	131241029	131241029	+	Silent	SNP	G	G	C	rs11277659|rs547816245|rs532078953|rs79759078|rs571821675	byFrequency	TCGA-WJ-A86L-01A-12D-A45V-10	TCGA-WJ-A86L-10A-01D-A38X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	80e4fac9-c066-47a9-9fc0-2a42eef954cd	cebd5a99-cbde-441d-b98a-b84cf1825d65	g.chr7:131241029G>C	ENST00000378555.3	-	1	337	c.90C>G	c.(88-90)ccC>ccG	p.P30P	PODXL_ENST00000537928.1_Silent_p.P30P|PODXL_ENST00000322985.9_Silent_p.P30P|PODXL_ENST00000465001.1_Intron|PODXL_ENST00000541194.1_Silent_p.P30P			O00592	PODXL_HUMAN	podocalyxin-like	30					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)					CATTCTGGGAGggcgacggcg	0.751																																					p.P30P		Atlas-SNP	.											.	PODXL	53	.	0			c.C90G						.						5.0	7.0	6.0					7																	131241029		1981	3946	5927	SO:0001819	synonymous_variant	5420	exon1			CTGGGAGGGCGAC		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.90C>G	chr7.hg19:g.131241029G>C		78.0	0.0		76.0	7.0	NM_001018111	A6NHX8|Q52LZ7|Q53ER6	Silent	SNP	ENST00000378555.3	hg19	CCDS34755.1																																																																																			.	.		0.751	PODXL-005	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000337627.2	NM_001018111	
KIAA1549	57670	hgsc.bcm.edu	37	7	138552730	138552730	+	Silent	SNP	G	G	A			TCGA-WJ-A86L-01A-12D-A45V-10	TCGA-WJ-A86L-10A-01D-A38X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	80e4fac9-c066-47a9-9fc0-2a42eef954cd	cebd5a99-cbde-441d-b98a-b84cf1825d65	g.chr7:138552730G>A	ENST00000422774.1	-	15	4968	c.4920C>T	c.(4918-4920)atC>atT	p.I1640I	KIAA1549_ENST00000242365.4_Silent_p.I1590I|KIAA1549_ENST00000440172.1_Silent_p.I1640I			Q9HCM3	K1549_HUMAN	KIAA1549	1640						integral component of membrane (GO:0016021)			KIAA1549/BRAF(703)	large_intestine(4)|pancreas(1)|upper_aerodigestive_tract(2)	7						CTGGGCATCCGATGTAGGCTG	0.627			O	BRAF	pilocytic astrocytoma																																p.I1640I	NSCLC(119;1534 1718 44213 46230 50068)	Atlas-SNP	.		Dom	yes		7	7q34	57670	KIAA1549		O	.	KIAA1549	314	.	0			c.C4920T						.						50.0	57.0	55.0					7																	138552730		2028	4162	6190	SO:0001819	synonymous_variant	57670	exon15			GCATCCGATGTAG		CCDS47723.1, CCDS47723.2, CCDS56513.1	7q34	2009-10-09			ENSG00000122778	ENSG00000122778			22219	protein-coding gene	gene with protein product		613344					Standard	NM_020910		Approved		uc011kql.2	Q9HCM3	OTTHUMG00000157214	ENST00000422774.1:c.4920C>T	chr7.hg19:g.138552730G>A		44.0	0.0		41.0	21.0	NM_020910	B6HY55|B6HY56|B6HY58|B6HY60|B6HY61|B6HY62|B6HY63|B6HY64|B6HY65|B6HY66|Q5BJD6|Q8IY15|Q9H0M3	Silent	SNP	ENST00000422774.1	hg19	CCDS56513.1																																																																																			.	.		0.627	KIAA1549-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000348092.1		
C7orf33	202865	hgsc.bcm.edu	37	7	148288121	148288121	+	Missense_Mutation	SNP	G	G	A	rs142396932		TCGA-WJ-A86L-01A-12D-A45V-10	TCGA-WJ-A86L-10A-01D-A38X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	80e4fac9-c066-47a9-9fc0-2a42eef954cd	cebd5a99-cbde-441d-b98a-b84cf1825d65	g.chr7:148288121G>A	ENST00000307003.2	+	1	465	c.104G>A	c.(103-105)cGg>cAg	p.R35Q		NM_145304.2	NP_660347.1	Q8WU49	CG033_HUMAN	chromosome 7 open reading frame 33	35										central_nervous_system(1)|large_intestine(4)|lung(7)|prostate(2)	14	Melanoma(164;0.15)		OV - Ovarian serous cystadenocarcinoma(82;0.00291)			GCAAGGCGCCGGATTGACCTT	0.567																																					p.R35Q		Atlas-SNP	.											.	C7orf33	28	.	0			c.G104A						.	G	GLN/ARG	0,4406		0,0,2203	83.0	71.0	75.0		104	-1.6	0.0	7	dbSNP_134	75	1,8599	1.2+/-3.3	0,1,4299	no	missense	C7orf33	NM_145304.2	43	0,1,6502	AA,AG,GG		0.0116,0.0,0.0077	benign	35/178	148288121	1,13005	2203	4300	6503	SO:0001583	missense	202865	exon1			GGCGCCGGATTGA	BC021251	CCDS5890.1	7q36.1	2011-11-24			ENSG00000170279	ENSG00000170279			21724	protein-coding gene	gene with protein product							Standard	NM_145304		Approved		uc003wew.3	Q8WU49	OTTHUMG00000152756	ENST00000307003.2:c.104G>A	chr7.hg19:g.148288121G>A	ENSP00000304071:p.Arg35Gln	114.0	0.0		91.0	35.0	NM_145304		Missense_Mutation	SNP	ENST00000307003.2	hg19	CCDS5890.1	.	.	.	.	.	.	.	.	.	.	G	9.336	1.061899	0.19987	0.0	1.16E-4	ENSG00000170279	ENST00000307003	.	.	.	2.59	-1.64	0.08318	.	.	.	.	.	T	0.15998	0.0385	N	0.08118	0	0.09310	N	1	B	0.14012	0.009	B	0.09377	0.004	T	0.18808	-1.0325	8	0.87932	D	0	.	3.8741	0.09048	0.2632:0.3981:0.3387:0.0	.	35	Q8WU49	CG033_HUMAN	Q	35	.	ENSP00000304071:R35Q	R	+	2	0	C7orf33	147919054	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-0.266000	0.08631	-0.427000	0.07350	-1.154000	0.01816	CGG	.	G|1.000;A|0.000		0.567	C7orf33-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000327684.1	NM_145304	
PREX2	80243	hgsc.bcm.edu	37	8	69032459	69032459	+	Missense_Mutation	SNP	G	G	C			TCGA-WJ-A86L-01A-12D-A45V-10	TCGA-WJ-A86L-10A-01D-A38X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	80e4fac9-c066-47a9-9fc0-2a42eef954cd	cebd5a99-cbde-441d-b98a-b84cf1825d65	g.chr8:69032459G>C	ENST00000288368.4	+	29	3810	c.3533G>C	c.(3532-3534)gGg>gCg	p.G1178A		NM_024870.2|NM_025170.4	NP_079146.2|NP_079446.3	Q70Z35	PREX2_HUMAN	phosphatidylinositol-3,4,5-trisphosphate-dependent Rac exchange factor 2	1178					adult locomotory behavior (GO:0008344)|dendrite morphogenesis (GO:0048813)|G-protein coupled receptor signaling pathway (GO:0007186)|intracellular signal transduction (GO:0035556)|positive regulation of Rac GTPase activity (GO:0032855)		Rac GTPase activator activity (GO:0030675)|Rac guanyl-nucleotide exchange factor activity (GO:0030676)			NS(6)|biliary_tract(1)|breast(4)|endometrium(11)|kidney(16)|large_intestine(25)|liver(4)|lung(57)|ovary(2)|pancreas(4)|prostate(3)|skin(42)|upper_aerodigestive_tract(1)|urinary_tract(2)	178						CTCCTAAAAGGGCAGGCTGTT	0.383																																					p.G1178A		Atlas-SNP	.											PREX2,NS,neuroblastoma,0,1	PREX2	614	.	0			c.G3533C						.						117.0	117.0	117.0					8																	69032459		2203	4300	6503	SO:0001583	missense	80243	exon29			TAAAAGGGCAGGC	AK024079	CCDS6201.1	8q13.1	2014-06-13	2008-09-15	2008-09-15	ENSG00000046889	ENSG00000046889		"""Rho guanine nucleotide exchange factors"""	22950	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 129"""	612139	"""DEP domain containing 2"""	DEPDC2		15304342, 15304343	Standard	NM_024870		Approved	DEP.2, FLJ12987, P-REX2, PPP1R129	uc003xxv.1	Q70Z35	OTTHUMG00000164402	ENST00000288368.4:c.3533G>C	chr8.hg19:g.69032459G>C	ENSP00000288368:p.Gly1178Ala	96.0	0.0		75.0	37.0	NM_024870	B4DFX0|Q32KL0|Q32KL1|Q6R7Q3|Q6R7Q4|Q9H805|Q9H961	Missense_Mutation	SNP	ENST00000288368.4	hg19	CCDS6201.1	.	.	.	.	.	.	.	.	.	.	G	32	5.176183	0.94846	.	.	ENSG00000046889	ENST00000288368	T	0.38560	1.13	5.29	5.29	0.74685	.	0.058678	0.64402	D	0.000002	T	0.60741	0.2292	M	0.68593	2.085	0.80722	D	1	D	0.57571	0.98	P	0.58721	0.844	T	0.61907	-0.6966	10	0.54805	T	0.06	.	19.3067	0.94165	0.0:0.0:1.0:0.0	.	1178	Q70Z35	PREX2_HUMAN	A	1178	ENSP00000288368:G1178A	ENSP00000288368:G1178A	G	+	2	0	PREX2	69195013	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	9.174000	0.94824	2.623000	0.88846	0.650000	0.86243	GGG	.	.		0.383	PREX2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000378620.1	NM_025170	
CNGB3	54714	hgsc.bcm.edu	37	8	87616352	87616352	+	Missense_Mutation	SNP	G	G	T			TCGA-WJ-A86L-01A-12D-A45V-10	TCGA-WJ-A86L-10A-01D-A38X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	80e4fac9-c066-47a9-9fc0-2a42eef954cd	cebd5a99-cbde-441d-b98a-b84cf1825d65	g.chr8:87616352G>T	ENST00000320005.5	-	15	1797	c.1750C>A	c.(1750-1752)Ctg>Atg	p.L584M		NM_019098.4	NP_061971.3	Q9NQW8	CNGB3_HUMAN	cyclic nucleotide gated channel beta 3	584					cation transport (GO:0006812)|phototransduction, visible light (GO:0007603)|potassium ion transmembrane transport (GO:0071805)|regulation of membrane potential (GO:0042391)|signal transduction (GO:0007165)|transport (GO:0006810)|visual perception (GO:0007601)	integral component of plasma membrane (GO:0005887)|photoreceptor outer segment (GO:0001750)|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)|voltage-gated potassium channel activity (GO:0005249)			NS(1)|breast(2)|endometrium(4)|kidney(6)|large_intestine(15)|lung(44)|ovary(2)|pancreas(1)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)	80						CCAGCTTTCAGAGTAACCAGA	0.368																																					p.L584M		Atlas-SNP	.											.	CNGB3	176	.	0			c.C1750A						.						79.0	78.0	79.0					8																	87616352		2203	4300	6503	SO:0001583	missense	54714	exon15			CTTTCAGAGTAAC	AF228520	CCDS6244.1	8q21.3	2013-01-23	2003-06-25		ENSG00000170289	ENSG00000170289		"""Voltage-gated ion channels / Cyclic nucleotide-regulated channels"""	2153	protein-coding gene	gene with protein product		605080	"""achromatopsia (rod monochromacy) 3"", ""achromatopsia (rod monochromacy) 1"""	ACHM3, ACHM1, RMCH		10888875, 10958649, 16382102	Standard	NM_019098		Approved		uc003ydx.3	Q9NQW8	OTTHUMG00000163738	ENST00000320005.5:c.1750C>A	chr8.hg19:g.87616352G>T	ENSP00000316605:p.Leu584Met	86.0	0.0		75.0	33.0	NM_019098	C9JA51|Q9NRE9	Missense_Mutation	SNP	ENST00000320005.5	hg19	CCDS6244.1	.	.	.	.	.	.	.	.	.	.	G	18.89	3.720129	0.68844	.	.	ENSG00000170289	ENST00000320005	D	0.97994	-4.65	5.97	5.09	0.68999	Cyclic nucleotide-binding-like (1);RmlC-like jelly roll fold (1);Cyclic nucleotide-binding domain (3);	0.087662	0.47455	D	0.000222	D	0.98548	0.9515	M	0.82193	2.58	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.91635	0.998;0.999	D	0.98537	1.0630	10	0.87932	D	0	.	12.6571	0.56793	0.13:0.0:0.87:0.0	.	584;584	Q9NQW8-2;Q9NQW8	.;CNGB3_HUMAN	M	584	ENSP00000316605:L584M	ENSP00000316605:L584M	L	-	1	2	CNGB3	87685468	0.997000	0.39634	1.000000	0.80357	0.929000	0.56500	2.207000	0.42788	2.837000	0.97791	0.655000	0.94253	CTG	.	.		0.368	CNGB3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000375107.1	NM_019098	
PKHD1L1	93035	hgsc.bcm.edu	37	8	110417293	110417294	+	Missense_Mutation	DNP	CC	CC	AA			TCGA-WJ-A86L-01A-12D-A45V-10	TCGA-WJ-A86L-10A-01D-A38X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	80e4fac9-c066-47a9-9fc0-2a42eef954cd	cebd5a99-cbde-441d-b98a-b84cf1825d65	g.chr8:110417293_110417294CC>AA	ENST00000378402.5	+	16	1707_1708	c.1603_1604CC>AA	c.(1603-1605)CCa>AAa	p.P535K		NM_177531.4	NP_803875.2	Q86WI1	PKHL1_HUMAN	polycystic kidney and hepatic disease 1 (autosomal recessive)-like 1	535					immune response (GO:0006955)	cytosol (GO:0005829)|extracellular space (GO:0005615)|integral component of membrane (GO:0016021)	receptor activity (GO:0004872)			NS(4)|breast(13)|central_nervous_system(6)|cervix(1)|endometrium(19)|kidney(17)|large_intestine(34)|lung(122)|ovary(11)|pancreas(3)|prostate(9)|skin(3)|stomach(4)|upper_aerodigestive_tract(13)|urinary_tract(4)	263			OV - Ovarian serous cystadenocarcinoma(57;9.88e-13)			GGTAACCAGCCCATGTGTGGAA	0.297										HNSCC(38;0.096)																											p.P535T|p.P535Q		Atlas-SNP	.											.|PKHD1L1,NS,carcinoma,0,1	PKHD1L1	522	.	0			c.C1603A|c.C1604A						.																																			SO:0001583	missense	93035	exon16			ACCAGCCCATGTG|CCAGCCCATGTGT	AY219181	CCDS47911.1	8q23	2003-03-28			ENSG00000205038	ENSG00000205038			20313	protein-coding gene	gene with protein product		607843				12620974	Standard	NM_177531		Approved		uc003yne.3	Q86WI1	OTTHUMG00000164934	Exception_encountered	chr8.hg19:g.110417293_110417294delinsAA	ENSP00000367655:p.Pro535Lys	203.0|204.0	0.0		134.0	37.0|38.0	NM_177531	Q567P2|Q9UF27	Missense_Mutation	SNP	ENST00000378402.5	hg19	CCDS47911.1																																																																																			.	.		0.297	PKHD1L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000381017.1	NM_177531	
AARD	441376	hgsc.bcm.edu	37	8	117954838	117954838	+	Missense_Mutation	SNP	A	A	C			TCGA-WJ-A86L-01A-12D-A45V-10	TCGA-WJ-A86L-10A-01D-A38X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	80e4fac9-c066-47a9-9fc0-2a42eef954cd	cebd5a99-cbde-441d-b98a-b84cf1825d65	g.chr8:117954838A>C	ENST00000378279.3	+	2	411	c.366A>C	c.(364-366)ttA>ttC	p.L122F	AARD_ENST00000523536.1_3'UTR	NM_001025357.2	NP_001020528.1	Q4LEZ3	AARD_HUMAN	alanine and arginine rich domain containing protein	122					lung development (GO:0030324)												CTAGAACTTTACTGGACCTAA	0.373																																					p.L122F		Atlas-SNP	.											.	.	.	.	0			c.A366C						.						61.0	58.0	59.0					8																	117954838		2203	4300	6503	SO:0001583	missense	441376	exon2			AACTTTACTGGAC	AB181519, BC140924	CCDS34935.1	8q24.11	2012-04-19	2012-04-19	2012-04-19	ENSG00000205002	ENSG00000205002			33842	protein-coding gene	gene with protein product	"""Alanine and arginine-rich domain-containing protein"""		"""chromosome 8 open reading frame 85"""	C8orf85			Standard	NM_001025357		Approved	LOC441376	uc003yof.3	Q4LEZ3	OTTHUMG00000164961	ENST00000378279.3:c.366A>C	chr8.hg19:g.117954838A>C	ENSP00000367528:p.Leu122Phe	95.0	0.0		54.0	33.0	NM_001025357	A5PKU8	Missense_Mutation	SNP	ENST00000378279.3	hg19	CCDS34935.1	.	.	.	.	.	.	.	.	.	.	A	14.80	2.643868	0.47258	.	.	ENSG00000205002	ENST00000378279	T	0.62639	0.01	5.38	-1.26	0.09376	.	0.276132	0.19444	N	0.114103	T	0.48840	0.1522	L	0.29908	0.895	0.24012	N	0.996175	P	0.50272	0.933	P	0.47786	0.557	T	0.46442	-0.9191	10	0.87932	D	0	-0.8538	5.4565	0.16594	0.3226:0.3046:0.3728:0.0	.	122	Q4LEZ3	AARD_HUMAN	F	122	ENSP00000367528:L122F	ENSP00000367528:L122F	L	+	3	2	C8orf85	118024019	0.018000	0.18449	0.871000	0.34182	0.649000	0.38597	-0.512000	0.06313	-0.095000	0.12351	-0.290000	0.09829	TTA	.	.		0.373	AARD-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000381195.1	NM_001025357	
DENND3	22898	hgsc.bcm.edu	37	8	142166010	142166010	+	Silent	SNP	G	G	T			TCGA-WJ-A86L-01A-12D-A45V-10	TCGA-WJ-A86L-10A-01D-A38X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	80e4fac9-c066-47a9-9fc0-2a42eef954cd	cebd5a99-cbde-441d-b98a-b84cf1825d65	g.chr8:142166010G>T	ENST00000262585.2	+	8	1175	c.897G>T	c.(895-897)acG>acT	p.T299T	DENND3_ENST00000424248.1_Silent_p.T299T|DENND3_ENST00000519811.1_Silent_p.T379T	NM_014957.2	NP_055772.2	A2RUS2	DEND3_HUMAN	DENN/MADD domain containing 3	299					cellular protein catabolic process (GO:0044257)|endosome to lysosome transport (GO:0008333)|positive regulation of Rab GTPase activity (GO:0032851)		Rab guanyl-nucleotide exchange factor activity (GO:0017112)			breast(2)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(12)|lung(19)|ovary(1)|prostate(3)|skin(4)|stomach(2)|urinary_tract(1)	55	all_cancers(97;7.36e-15)|all_epithelial(106;2.33e-13)|Lung NSC(106;1.23e-05)|all_lung(105;1.75e-05)|Ovarian(258;0.01)|Acute lymphoblastic leukemia(118;0.155)		BRCA - Breast invasive adenocarcinoma(115;0.105)			CCAAGTCCACGGACGATAACG	0.433																																					p.T299T		Atlas-SNP	.											.	DENND3	127	.	0			c.G897T						.						115.0	111.0	113.0					8																	142166010		2203	4300	6503	SO:0001819	synonymous_variant	22898	exon8			GTCCACGGACGAT	AB020677	CCDS34947.1	8q24.3	2013-01-10				ENSG00000105339		"""DENN/MADD domain containing"", ""WD repeat domain containing"""	29134	protein-coding gene	gene with protein product						10048485	Standard	NM_014957		Approved	KIAA0870	uc003yvy.3	A2RUS2		ENST00000262585.2:c.897G>T	chr8.hg19:g.142166010G>T		65.0	0.0		60.0	32.0	NM_014957	B7ZM28|O94947|Q2TAM7|Q6ZMS6|Q96DK3	Silent	SNP	ENST00000262585.2	hg19	CCDS34947.1	.	.	.	.	.	.	.	.	.	.	G	5.284	0.237884	0.10023	.	.	ENSG00000105339	ENST00000518668	.	.	.	5.06	-10.1	0.00402	.	.	.	.	.	.	.	.	.	.	.	0.09310	N	1	.	.	.	.	.	.	.	.	.	.	.	.	.	-0.7352	2.1436	0.03781	0.24:0.2567:0.0798:0.4236	.	.	.	.	X	356	.	.	G	+	1	0	DENND3	142235192	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-1.117000	0.03283	-2.854000	0.00330	-0.136000	0.14681	GGA	.	.		0.433	DENND3-201	KNOWN	basic|CCDS	protein_coding	protein_coding		NM_014957	
GRIN3A	116443	hgsc.bcm.edu	37	9	104449360	104449360	+	Nonsense_Mutation	SNP	C	C	T			TCGA-WJ-A86L-01A-12D-A45V-10	TCGA-WJ-A86L-10A-01D-A38X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	80e4fac9-c066-47a9-9fc0-2a42eef954cd	cebd5a99-cbde-441d-b98a-b84cf1825d65	g.chr9:104449360C>T	ENST00000361820.3	-	2	1422	c.822G>A	c.(820-822)tgG>tgA	p.W274*		NM_133445.2	NP_597702.2	Q8TCU5	NMD3A_HUMAN	glutamate receptor, ionotropic, N-methyl-D-aspartate 3A	274					calcium ion transport (GO:0006816)|dendrite development (GO:0016358)|ion transmembrane transport (GO:0034220)|ionotropic glutamate receptor signaling pathway (GO:0035235)|prepulse inhibition (GO:0060134)|response to ethanol (GO:0045471)|rhythmic process (GO:0048511)|synaptic transmission, glutamatergic (GO:0035249)	cell junction (GO:0030054)|dendrite (GO:0030425)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|N-methyl-D-aspartate selective glutamate receptor complex (GO:0017146)|neuron projection (GO:0043005)|neuronal cell body (GO:0043025)|postsynaptic membrane (GO:0045211)|synapse (GO:0045202)	calcium channel activity (GO:0005262)|extracellular-glutamate-gated ion channel activity (GO:0005234)|glycine binding (GO:0016594)|identical protein binding (GO:0042802)|N-methyl-D-aspartate selective glutamate receptor activity (GO:0004972)|neurotransmitter binding (GO:0042165)|protein phosphatase 2A binding (GO:0051721)			breast(2)|central_nervous_system(2)|endometrium(4)|kidney(3)|large_intestine(12)|lung(44)|ovary(4)|pancreas(1)|skin(7)|upper_aerodigestive_tract(1)	80		Acute lymphoblastic leukemia(62;0.0568)			Acamprosate(DB00659)|Acetylcysteine(DB06151)|Amantadine(DB00915)|Atomoxetine(DB00289)|Chloroprocaine(DB01161)|Dextromethorphan(DB00514)|Ethanol(DB00898)|Ethopropazine(DB00392)|Felbamate(DB00949)|Gabapentin(DB00996)|Halothane(DB01159)|Ketamine(DB01221)|Ketobemidone(DB06738)|Memantine(DB01043)|Methadone(DB00333)|Milnacipran(DB04896)|Orphenadrine(DB01173)|Pentobarbital(DB00312)|Phenobarbital(DB01174)|Procaine(DB00721)|Secobarbital(DB00418)|Tramadol(DB00193)	CGGTGATGTTCCAGTCTTCCT	0.453																																					p.W274X		Atlas-SNP	.											.	GRIN3A	186	.	0			c.G822A						.						138.0	125.0	129.0					9																	104449360		2203	4300	6503	SO:0001587	stop_gained	116443	exon2			GATGTTCCAGTCT		CCDS6758.1	9q31.1	2012-08-29			ENSG00000198785	ENSG00000198785		"""Ligand-gated ion channels / Glutamate receptors, ionotropic"", ""Glutamate receptors"""	16767	protein-coding gene	gene with protein product		606650					Standard	NM_133445		Approved	GluN3A	uc004bbp.2	Q8TCU5	OTTHUMG00000020387	ENST00000361820.3:c.822G>A	chr9.hg19:g.104449360C>T	ENSP00000355155:p.Trp274*	135.0	0.0		149.0	7.0	NM_133445	B3DLF9|Q5VTR3|Q8TF29|Q8WXI6	Nonsense_Mutation	SNP	ENST00000361820.3	hg19	CCDS6758.1	.	.	.	.	.	.	.	.	.	.	C	43	10.470887	0.99411	.	.	ENSG00000198785	ENST00000361820	.	.	.	5.82	5.82	0.92795	.	0.257045	0.39020	N	0.001492	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.33940	T	0.23	.	20.1178	0.97943	0.0:1.0:0.0:0.0	.	.	.	.	X	274	.	ENSP00000355155:W274X	W	-	3	0	GRIN3A	103489181	1.000000	0.71417	1.000000	0.80357	0.989000	0.77384	7.664000	0.83830	2.759000	0.94783	0.557000	0.71058	TGG	.	.		0.453	GRIN3A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053453.1		
CYLC2	1539	hgsc.bcm.edu	37	9	105767953	105767953	+	Missense_Mutation	SNP	G	G	A	rs373184793		TCGA-WJ-A86L-01A-12D-A45V-10	TCGA-WJ-A86L-10A-01D-A38X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	80e4fac9-c066-47a9-9fc0-2a42eef954cd	cebd5a99-cbde-441d-b98a-b84cf1825d65	g.chr9:105767953G>A	ENST00000374798.3	+	5	1110	c.1040G>A	c.(1039-1041)gGc>gAc	p.G347D	CYLC2_ENST00000487798.1_Missense_Mutation_p.G347D	NM_001340.3	NP_001331.1	Q14093	CYLC2_HUMAN	cylicin, basic protein of sperm head cytoskeleton 2	347	31 X 3 AA repeats of K-K-X.				cell differentiation (GO:0030154)|multicellular organismal development (GO:0007275)|spermatogenesis (GO:0007283)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|nucleus (GO:0005634)	structural constituent of cytoskeleton (GO:0005200)			NS(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(9)|lung(14)|ovary(1)|skin(5)|stomach(5)|upper_aerodigestive_tract(2)	41		all_hematologic(171;0.125)				aagaagaagggcaagtaggCC	0.358													G|||	1	0.000199681	0.0	0.0014	5008	,	,		17707	0.0		0.0	False		,,,				2504	0.0				p.G347D		Atlas-SNP	.											.	CYLC2	109	.	0			c.G1040A						.	G	ASP/GLY	0,4404		0,0,2202	53.0	57.0	55.0		1040	-2.8	0.0	9		55	1,8595	1.2+/-3.3	0,1,4297	no	missense	CYLC2	NM_001340.3	94	0,1,6499	AA,AG,GG		0.0116,0.0,0.0077	benign	347/349	105767953	1,12999	2202	4298	6500	SO:0001583	missense	1539	exon5			AGAAGGGCAAGTA	Z46788	CCDS35085.1	9q31.2	2008-07-21			ENSG00000155833	ENSG00000155833			2583	protein-coding gene	gene with protein product		604035				7737358	Standard	NM_001340		Approved		uc004bbs.2	Q14093	OTTHUMG00000020396	ENST00000374798.3:c.1040G>A	chr9.hg19:g.105767953G>A	ENSP00000420256:p.Gly347Asp	251.0	0.0		220.0	96.0	NM_001340	B2R8F4|Q5VVJ9	Missense_Mutation	SNP	ENST00000374798.3	hg19	CCDS35085.1	.	.	.	.	.	.	.	.	.	.	G	11.28	1.592247	0.28357	0.0	1.16E-4	ENSG00000155833	ENST00000374798;ENST00000487798	T;T	0.17528	2.27;2.27	4.39	-2.82	0.05787	.	.	.	.	.	T	0.07369	0.0186	N	0.08118	0	0.09310	N	1	B	0.30851	0.297	B	0.30179	0.112	T	0.37454	-0.9705	9	0.30078	T	0.28	4.4222	8.044	0.30538	0.1769:0.5598:0.2633:0.0	.	347	Q14093	CYLC2_HUMAN	D	347	ENSP00000420256:G347D;ENSP00000417674:G347D	ENSP00000420256:G347D	G	+	2	0	CYLC2	104807774	0.002000	0.14202	0.004000	0.12327	0.064000	0.16182	-0.386000	0.07370	-0.695000	0.05105	-0.291000	0.09656	GGC	.	.		0.358	CYLC2-001	KNOWN	alternative_3_UTR|NMD_exception|basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000053463.3	NM_001340	
GATA3	2625	hgsc.bcm.edu	37	10	8106075	8106075	+	Missense_Mutation	SNP	C	C	A			TCGA-WJ-A86L-01A-12D-A45V-10	TCGA-WJ-A86L-10A-01D-A38X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	80e4fac9-c066-47a9-9fc0-2a42eef954cd	cebd5a99-cbde-441d-b98a-b84cf1825d65	g.chr10:8106075C>A	ENST00000346208.3	+	4	1350	c.895C>A	c.(895-897)Ccc>Acc	p.P299T	GATA3_ENST00000379328.3_Missense_Mutation_p.P300T|GATA3_ENST00000461472.1_Intron			P23771	GATA3_HUMAN	GATA binding protein 3	299	Flexible linker.				anatomical structure formation involved in morphogenesis (GO:0048646)|anatomical structure morphogenesis (GO:0009653)|aortic valve morphogenesis (GO:0003180)|axon guidance (GO:0007411)|blood coagulation (GO:0007596)|canonical Wnt signaling pathway involved in metanephric kidney development (GO:0061290)|cardiac right ventricle morphogenesis (GO:0003215)|cell fate determination (GO:0001709)|cell maturation (GO:0048469)|cellular response to BMP stimulus (GO:0071773)|cellular response to interferon-alpha (GO:0035457)|cellular response to interleukin-4 (GO:0071353)|cellular response to tumor necrosis factor (GO:0071356)|defense response (GO:0006952)|developmental growth (GO:0048589)|ear development (GO:0043583)|embryonic hemopoiesis (GO:0035162)|erythrocyte differentiation (GO:0030218)|humoral immune response (GO:0006959)|in utero embryonic development (GO:0001701)|innate immune response (GO:0045087)|inner ear morphogenesis (GO:0042472)|interferon-gamma secretion (GO:0072643)|interleukin-4 secretion (GO:0072602)|kidney development (GO:0001822)|lens development in camera-type eye (GO:0002088)|lymphocyte migration (GO:0072676)|male gonad development (GO:0008584)|mast cell differentiation (GO:0060374)|mesenchymal to epithelial transition (GO:0060231)|mesonephros development (GO:0001823)|negative regulation of cell cycle (GO:0045786)|negative regulation of cell motility (GO:2000146)|negative regulation of cell proliferation (GO:0008285)|negative regulation of cell proliferation involved in mesonephros development (GO:2000607)|negative regulation of endothelial cell apoptotic process (GO:2000352)|negative regulation of fat cell differentiation (GO:0045599)|negative regulation of fibroblast growth factor receptor signaling pathway involved in ureteric bud formation (GO:2000703)|negative regulation of glial cell-derived neurotrophic factor receptor signaling pathway involved in ureteric bud formation (GO:2000734)|negative regulation of inflammatory response (GO:0050728)|negative regulation of interferon-gamma production (GO:0032689)|negative regulation of interleukin-2 production (GO:0032703)|negative regulation of mammary gland epithelial cell proliferation (GO:0033600)|negative regulation of transcription, DNA-templated (GO:0045892)|nephric duct formation (GO:0072179)|nephric duct morphogenesis (GO:0072178)|neuron migration (GO:0001764)|norepinephrine biosynthetic process (GO:0042421)|otic vesicle development (GO:0071599)|parathyroid gland development (GO:0060017)|parathyroid hormone secretion (GO:0035898)|pharyngeal system development (GO:0060037)|phosphatidylinositol 3-kinase signaling (GO:0014065)|positive regulation of endothelial cell migration (GO:0010595)|positive regulation of interleukin-13 production (GO:0032736)|positive regulation of interleukin-13 secretion (GO:2000667)|positive regulation of interleukin-4 production (GO:0032753)|positive regulation of interleukin-5 production (GO:0032754)|positive regulation of interleukin-5 secretion (GO:2000664)|positive regulation of protein kinase B signaling (GO:0051897)|positive regulation of signal transduction (GO:0009967)|positive regulation of T cell differentiation (GO:0045582)|positive regulation of thyroid hormone generation (GO:2000611)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription regulatory region DNA binding (GO:2000679)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of ureteric bud formation (GO:0072107)|post-embryonic development (GO:0009791)|pro-T cell differentiation (GO:0002572)|regulation of CD4-positive, alpha-beta T cell differentiation (GO:0043370)|regulation of cellular response to X-ray (GO:2000683)|regulation of cytokine biosynthetic process (GO:0042035)|regulation of establishment of cell polarity (GO:2000114)|regulation of histone H3-K27 methylation (GO:0061085)|regulation of histone H3-K4 methylation (GO:0051569)|regulation of nephron tubule epithelial cell differentiation (GO:0072182)|regulation of neuron apoptotic process (GO:0043523)|regulation of neuron projection development (GO:0010975)|response to drug (GO:0042493)|response to estrogen (GO:0043627)|response to ethanol (GO:0045471)|response to gamma radiation (GO:0010332)|response to virus (GO:0009615)|signal transduction (GO:0007165)|sympathetic nervous system development (GO:0048485)|T cell receptor signaling pathway (GO:0050852)|T-helper 2 cell differentiation (GO:0045064)|thymic T cell selection (GO:0045061)|thymus development (GO:0048538)|TOR signaling (GO:0031929)|transcription from RNA polymerase II promoter (GO:0006366)|type IV hypersensitivity (GO:0001806)|ureter maturation (GO:0035799)|ureteric bud formation (GO:0060676)|uterus development (GO:0060065)|ventricular septum development (GO:0003281)	nuclear chromatin (GO:0000790)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	core promoter proximal region sequence-specific DNA binding (GO:0000987)|core promoter sequence-specific DNA binding (GO:0001046)|DNA binding (GO:0003677)|E-box binding (GO:0070888)|enhancer sequence-specific DNA binding (GO:0001158)|HMG box domain binding (GO:0071837)|nucleic acid binding transcription factor activity (GO:0001071)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in negative regulation of transcription (GO:0001078)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|RNA polymerase II core promoter sequence-specific DNA binding (GO:0000979)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription coactivator activity (GO:0003713)|transcription factor binding (GO:0008134)|transcription regulatory region DNA binding (GO:0044212)|transcription regulatory region sequence-specific DNA binding (GO:0000976)|zinc ion binding (GO:0008270)			NS(1)|breast(44)|central_nervous_system(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(6)|lung(24)|ovary(3)|skin(2)	87						ACAGAACCGGCCCCTCATTAA	0.572			"""F, N, S"""		breast		"""HDR syndrome (HYPOPARATHYROIDISM, SENSORINEURAL DEAFNESS, AND RENAL DISEASE)"""																														p.P300T		Atlas-SNP	.		Rec	yes		10	10p15	2625	GATA binding protein 3	yes	E	.	GATA3	182	.	0			c.C898A						.						108.0	100.0	103.0					10																	8106075		2203	4300	6503	SO:0001583	missense	2625	exon4			AACCGGCCCCTCA	X55122	CCDS7083.1, CCDS31143.1	10p15	2013-01-25	2001-11-28		ENSG00000107485	ENSG00000107485		"""GATA zinc finger domain containing"""	4172	protein-coding gene	gene with protein product		131320	"""GATA-binding protein 3"""			2050118, 15087456	Standard	NM_002051		Approved	HDR	uc001ijz.3	P23771	OTTHUMG00000017640	ENST00000346208.3:c.895C>A	chr10.hg19:g.8106075C>A	ENSP00000341619:p.Pro299Thr	139.0	0.0		103.0	43.0	NM_001002295	Q5VWG7|Q5VWG8|Q96J16	Missense_Mutation	SNP	ENST00000346208.3	hg19	CCDS7083.1	.	.	.	.	.	.	.	.	.	.	C	28.8	4.953624	0.92660	.	.	ENSG00000107485	ENST00000379328;ENST00000346208	D;D	0.99745	-6.61;-6.61	5.29	5.29	0.74685	Zinc finger, NHR/GATA-type (1);Zinc finger, GATA-type (2);	0.000000	0.85682	D	0.000000	D	0.99851	0.9931	H	0.97516	4.02	0.80722	D	1	D;D	0.89917	1.0;0.989	D;D	0.97110	1.0;0.976	D	0.96664	0.9491	10	0.87932	D	0	-9.3523	18.9039	0.92453	0.0:1.0:0.0:0.0	.	299;300	P23771;P23771-2	GATA3_HUMAN;.	T	300;299	ENSP00000368632:P300T;ENSP00000341619:P299T	ENSP00000341619:P299T	P	+	1	0	GATA3	8146081	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	7.752000	0.85141	2.625000	0.88918	0.655000	0.94253	CCC	.	.		0.572	GATA3-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000046719.1	NM_001002295	
CHST3	9469	hgsc.bcm.edu	37	10	73767585	73767585	+	Missense_Mutation	SNP	C	C	G			TCGA-WJ-A86L-01A-12D-A45V-10	TCGA-WJ-A86L-10A-01D-A38X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	80e4fac9-c066-47a9-9fc0-2a42eef954cd	cebd5a99-cbde-441d-b98a-b84cf1825d65	g.chr10:73767585C>G	ENST00000373115.4	+	3	1233	c.796C>G	c.(796-798)Cgc>Ggc	p.R266G		NM_004273.4	NP_004264.2	Q7LGC8	CHST3_HUMAN	carbohydrate (chondroitin 6) sulfotransferase 3	266					carbohydrate metabolic process (GO:0005975)|chondroitin sulfate biosynthetic process (GO:0030206)|chondroitin sulfate metabolic process (GO:0030204)|glycosaminoglycan metabolic process (GO:0030203)|small molecule metabolic process (GO:0044281)|sulfur compound metabolic process (GO:0006790)|T cell homeostasis (GO:0043029)	Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)	chondroitin 6-sulfotransferase activity (GO:0008459)|proteoglycan sulfotransferase activity (GO:0050698)|sulfotransferase activity (GO:0008146)			endometrium(1)|lung(5)	6						GGCCTGCCGCCGCAAGGAGCA	0.677																																					p.R266G		Atlas-SNP	.											.	CHST3	36	.	0			c.C796G						.						11.0	12.0	11.0					10																	73767585		2000	3968	5968	SO:0001583	missense	9469	exon3			TGCCGCCGCAAGG	AB017915	CCDS7312.1	10q22.1	2007-03-14			ENSG00000122863	ENSG00000122863		"""Sulfotransferases, membrane-bound"""	1971	protein-coding gene	gene with protein product		603799				9883891, 9714738	Standard	NM_004273		Approved	C6ST, C6ST1	uc001jsn.3	Q7LGC8	OTTHUMG00000018431	ENST00000373115.4:c.796C>G	chr10.hg19:g.73767585C>G	ENSP00000362207:p.Arg266Gly	38.0	0.0		43.0	28.0	NM_004273	O75099|Q52M30	Missense_Mutation	SNP	ENST00000373115.4	hg19	CCDS7312.1	.	.	.	.	.	.	.	.	.	.	C	14.78	2.637042	0.47049	.	.	ENSG00000122863	ENST00000373115	D	0.82711	-1.64	5.8	5.8	0.92144	Sulfotransferase domain (1);	0.183504	0.50627	D	0.000114	T	0.78052	0.4223	L	0.39898	1.24	0.40911	D	0.984231	P	0.38992	0.653	B	0.39185	0.293	T	0.78718	-0.2095	10	0.44086	T	0.13	-29.025	13.9427	0.64066	0.1516:0.8484:0.0:0.0	.	266	Q7LGC8	CHST3_HUMAN	G	266	ENSP00000362207:R266G	ENSP00000362207:R266G	R	+	1	0	CHST3	73437591	0.906000	0.30813	1.000000	0.80357	0.997000	0.91878	1.100000	0.31025	2.758000	0.94735	0.561000	0.74099	CGC	.	.		0.677	CHST3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048563.1	NM_004273	
OPN4	94233	hgsc.bcm.edu	37	10	88417835	88417835	+	Missense_Mutation	SNP	G	G	A			TCGA-WJ-A86L-01A-12D-A45V-10	TCGA-WJ-A86L-10A-01D-A38X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	80e4fac9-c066-47a9-9fc0-2a42eef954cd	cebd5a99-cbde-441d-b98a-b84cf1825d65	g.chr10:88417835G>A	ENST00000241891.5	+	3	504	c.337G>A	c.(337-339)Gcg>Acg	p.A113T	OPN4_ENST00000372071.2_Missense_Mutation_p.A124T	NM_033282.3	NP_150598.1	Q9UHM6	OPN4_HUMAN	opsin 4	113					phototransduction (GO:0007602)|protein-chromophore linkage (GO:0018298)|regulation of circadian rhythm (GO:0042752)|rhodopsin mediated signaling pathway (GO:0016056)|rhythmic process (GO:0048511)|visual perception (GO:0007601)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	11-cis retinal binding (GO:0005502)|G-protein coupled photoreceptor activity (GO:0008020)			breast(1)|endometrium(3)|kidney(2)|large_intestine(2)|liver(2)|lung(5)|ovary(3)	18						TATCAACCTCGCGGTCAGCGA	0.562																																					p.A124T		Atlas-SNP	.											.	OPN4	61	.	0			c.G370A						.						117.0	113.0	114.0					10																	88417835		2203	4300	6503	SO:0001583	missense	94233	exon4			AACCTCGCGGTCA	AF147788	CCDS7376.1, CCDS31237.1	10q22	2012-08-08	2008-04-16		ENSG00000122375	ENSG00000122375		"""GPCR / Class A : Opsin receptors"""	14449	protein-coding gene	gene with protein product	"""melanopsin"""	606665	"""opsin 4 (melanopsin)"""			10632589	Standard	NM_001030015		Approved	MOP, melanopsin	uc001kdp.3	Q9UHM6	OTTHUMG00000018654	ENST00000241891.5:c.337G>A	chr10.hg19:g.88417835G>A	ENSP00000241891:p.Ala113Thr	63.0	0.0		70.0	33.0	NM_001030015	B7ZLB3|Q14D01|Q2PP22|Q8NGQ9	Missense_Mutation	SNP	ENST00000241891.5	hg19	CCDS7376.1	.	.	.	.	.	.	.	.	.	.	G	21.9	4.211457	0.79240	.	.	ENSG00000122375	ENST00000372071;ENST00000241891;ENST00000443292	T;T;T	0.56103	0.48;0.48;0.48	5.29	4.33	0.51752	GPCR, rhodopsin-like superfamily (1);	0.063064	0.64402	D	0.000011	T	0.76990	0.4065	M	0.91459	3.21	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.83275	0.996;0.996;0.984	T	0.82481	-0.0436	10	0.87932	D	0	.	13.7968	0.63175	0.0:0.0:0.8462:0.1537	.	124;113;124	C9JWU6;Q9UHM6;Q9UHM6-2	.;OPN4_HUMAN;.	T	124;113;124	ENSP00000361141:A124T;ENSP00000241891:A113T;ENSP00000393132:A124T	ENSP00000241891:A113T	A	+	1	0	OPN4	88407815	1.000000	0.71417	0.142000	0.22268	0.623000	0.37688	7.903000	0.87398	2.469000	0.83416	0.491000	0.48974	GCG	.	.		0.562	OPN4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049158.2	NM_033282	
LZTS2	84445	hgsc.bcm.edu	37	10	102770299	102770299	+	IGR	SNP	G	G	A			TCGA-WJ-A86L-01A-12D-A45V-10	TCGA-WJ-A86L-10A-01D-A38X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	80e4fac9-c066-47a9-9fc0-2a42eef954cd	cebd5a99-cbde-441d-b98a-b84cf1825d65	g.chr10:102770299G>A	ENST00000370220.1	+	0	5741									leucine zipper, putative tumor suppressor 2											breast(1)|large_intestine(6)|lung(7)|ovary(4)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	22				Epithelial(162;7.3e-09)|all cancers(201;3.72e-07)		CGgctgctgcggctgcggctg	0.697																																					p.R783C	Esophageal Squamous(8;38 437 13604 19902 37640)	Atlas-SNP	.											.	PDZD7	101	.	0			c.C2347T						.																																			SO:0001628	intergenic_variant	79955	exon15			TGCTGCGGCTGCG	AB058716	CCDS7507.1	10q24	2004-03-18			ENSG00000107816	ENSG00000107816			29381	protein-coding gene	gene with protein product		610454				11347906, 11709705	Standard	NM_032429		Approved	KIAA1813, LAPSER1	uc001ksj.3	Q9BRK4	OTTHUMG00000018914		chr10.hg19:g.102770299G>A		287.0	0.0		339.0	84.0	NM_001195263		Missense_Mutation	SNP	ENST00000370220.1	hg19	CCDS7507.1	.	.	.	.	.	.	.	.	.	.	G	3.825	-0.036948	0.07497	.	.	ENSG00000186862	ENST00000393462	.	.	.	0.593	0.593	0.17478	.	.	.	.	.	T	0.23094	0.0558	N	0.14661	0.345	0.21445	N	0.999681	.	.	.	.	.	.	T	0.26643	-1.0097	5	0.56958	D	0.05	.	.	.	.	.	.	.	.	C	783	.	ENSP00000377106:R783C	R	-	1	0	PDZD7	102760289	0.001000	0.12720	0.977000	0.42913	0.456000	0.32438	0.166000	0.16583	0.619000	0.30197	0.121000	0.15741	CGC	.	.		0.697	LZTS2-001	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049872.1	XM_046743	
JAKMIP3	282973	hgsc.bcm.edu	37	10	133930963	133930963	+	Missense_Mutation	SNP	C	C	T	rs371280434		TCGA-WJ-A86L-01A-12D-A45V-10	TCGA-WJ-A86L-10A-01D-A38X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	80e4fac9-c066-47a9-9fc0-2a42eef954cd	cebd5a99-cbde-441d-b98a-b84cf1825d65	g.chr10:133930963C>T	ENST00000298622.4	+	2	656	c.518C>T	c.(517-519)aCg>aTg	p.T173M		NM_001105521.2	NP_001098991.1	Q5VZ66	JKIP3_HUMAN	Janus kinase and microtubule interacting protein 3	173						Golgi apparatus (GO:0005794)				breast(1)|cervix(1)|endometrium(4)|kidney(3)|large_intestine(7)|lung(10)|ovary(2)|prostate(1)|upper_aerodigestive_tract(2)	31		all_cancers(35;5.63e-09)|all_epithelial(44;9.25e-07)|Lung NSC(174;0.0108)|all_lung(145;0.0173)|Colorectal(31;0.0721)|all_neural(114;0.0726)|Breast(234;0.0949)|Glioma(114;0.172)|Melanoma(40;0.175)		OV - Ovarian serous cystadenocarcinoma(35;0.000104)|Epithelial(32;0.000142)|all cancers(32;0.000185)|BRCA - Breast invasive adenocarcinoma(275;0.224)		GAGGCGCTGACGCTGGTGATC	0.607																																					p.T173M		Atlas-SNP	.											.	JAKMIP3	69	.	0			c.C518T						.	C	MET/THR	0,4328		0,0,2164	51.0	61.0	58.0		518	4.7	0.9	10		58	1,8533		0,1,4266	no	missense	JAKMIP3	NM_001105521.2	81	0,1,6430	TT,TC,CC		0.0117,0.0,0.0078	probably-damaging	173/845	133930963	1,12861	2164	4267	6431	SO:0001583	missense	282973	exon2			CGCTGACGCTGGT	AL832756	CCDS44494.1	10q26.3	2009-04-23	2009-04-23	2008-01-28	ENSG00000188385	ENSG00000188385			23523	protein-coding gene	gene with protein product	"""neuroendocrine long coiled-coil 2"""	611198	"""chromosome 10 open reading frame 39"", ""chromosome 10 open reading frame 14"""	C10orf39, C10orf14		15277531, 17572408	Standard	NM_001105521		Approved	FLJ37857, NECC2, KIAA4091, bA140A10.5	uc001lkx.4	Q5VZ66	OTTHUMG00000150167	ENST00000298622.4:c.518C>T	chr10.hg19:g.133930963C>T	ENSP00000298622:p.Thr173Met	88.0	0.0		101.0	53.0	NM_001105521	A6PW00|Q69YM6|Q6ZT29	Missense_Mutation	SNP	ENST00000298622.4	hg19	CCDS44494.1	.	.	.	.	.	.	.	.	.	.	C	17.15	3.315954	0.60524	0.0	1.17E-4	ENSG00000188385	ENST00000298622	T	0.08720	3.06	4.66	4.66	0.58398	.	0.054130	0.64402	D	0.000001	T	0.15652	0.0377	L	0.43152	1.355	0.28758	N	0.901076	D	0.76494	0.999	P	0.55667	0.781	T	0.01033	-1.1474	10	0.66056	D	0.02	-31.4226	12.8191	0.57683	0.1632:0.8368:0.0:0.0	.	173	Q5VZ66	JKIP3_HUMAN	M	173	ENSP00000298622:T173M	ENSP00000298622:T173M	T	+	2	0	JAKMIP3	133780953	0.855000	0.29742	0.941000	0.38009	0.963000	0.63663	1.395000	0.34520	2.419000	0.82065	0.591000	0.81541	ACG	.	.		0.607	JAKMIP3-001	KNOWN	NMD_exception|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051049.3	NM_194303	
INSC	387755	hgsc.bcm.edu	37	11	15243031	15243031	+	Silent	SNP	C	C	T			TCGA-WJ-A86L-01A-12D-A45V-10	TCGA-WJ-A86L-10A-01D-A38X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	80e4fac9-c066-47a9-9fc0-2a42eef954cd	cebd5a99-cbde-441d-b98a-b84cf1825d65	g.chr11:15243031C>T	ENST00000379554.3	+	8	1015	c.969C>T	c.(967-969)ggC>ggT	p.G323G	INSC_ENST00000447214.2_3'UTR|INSC_ENST00000528567.1_Silent_p.G276G|INSC_ENST00000530161.1_Silent_p.G276G|INSC_ENST00000379556.3_Silent_p.G276G|INSC_ENST00000525218.1_Silent_p.G234G|INSC_ENST00000424273.1_Silent_p.G234G	NM_001031853.3	NP_001027024.3	Q1MX18	INSC_HUMAN	inscuteable homolog (Drosophila)	323					establishment of mitotic spindle orientation (GO:0000132)|lung epithelial cell differentiation (GO:0060487)|nervous system development (GO:0007399)	apical part of cell (GO:0045177)|cytoplasm (GO:0005737)				NS(2)|breast(1)|central_nervous_system(2)|endometrium(6)|kidney(4)|large_intestine(3)|lung(24)|ovary(3)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	49						AGGTGGATGGCGTTCTGTGCT	0.612																																					p.G323G		Atlas-SNP	.											.	INSC	104	.	0			c.C969T						.						63.0	71.0	68.0					11																	15243031		2136	4244	6380	SO:0001819	synonymous_variant	387755	exon8			GGATGGCGTTCTG	AB231744	CCDS41621.1, CCDS41622.1, CCDS60735.1, CCDS60736.1	11p15.2	2014-02-05			ENSG00000188487	ENSG00000188487			33116	protein-coding gene	gene with protein product	"""inscuteable spindle orientation adaptor protein"""	610668				16458856	Standard	NM_001031853		Approved		uc001mly.4	Q1MX18	OTTHUMG00000165838	ENST00000379554.3:c.969C>T	chr11.hg19:g.15243031C>T		135.0	0.0		165.0	65.0	NM_001031853	A0PJX5|Q1MX19|Q3C1V6|Q4AC95|Q4AC96|Q4AC97|Q4AC98	Silent	SNP	ENST00000379554.3	hg19	CCDS41621.1																																																																																			.	.		0.612	INSC-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000386590.1	NM_001031853	
MS4A15	219995	hgsc.bcm.edu	37	11	60541328	60541328	+	Missense_Mutation	SNP	C	C	A			TCGA-WJ-A86L-01A-12D-A45V-10	TCGA-WJ-A86L-10A-01D-A38X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	80e4fac9-c066-47a9-9fc0-2a42eef954cd	cebd5a99-cbde-441d-b98a-b84cf1825d65	g.chr11:60541328C>A	ENST00000405633.3	+	6	596	c.517C>A	c.(517-519)Ctg>Atg	p.L173M	MS4A15_ENST00000337911.4_Missense_Mutation_p.L80M|MS4A15_ENST00000528170.1_Missense_Mutation_p.L132M	NM_001098835.1	NP_001092305.1	Q8N5U1	M4A15_HUMAN	membrane-spanning 4-domains, subfamily A, member 15	173						integral component of membrane (GO:0016021)				breast(1)|large_intestine(2)|lung(3)	6						CAGGGGCTATCTGGCCGTGCT	0.572																																					p.L173M		Atlas-SNP	.											.	MS4A15	37	.	0			c.C517A						.						245.0	190.0	209.0					11																	60541328		2203	4300	6503	SO:0001583	missense	219995	exon6			GGCTATCTGGCCG	AY584608	CCDS7991.1, CCDS44617.1, CCDS60802.1	11q12.2	2008-03-25							28573	protein-coding gene	gene with protein product							Standard	NM_001098835		Approved		uc009ynf.1	Q8N5U1		ENST00000405633.3:c.517C>A	chr11.hg19:g.60541328C>A	ENSP00000386022:p.Leu173Met	45.0	0.0		69.0	30.0	NM_001098835	A9UJY6|A9UJY7|F2Z2J5	Missense_Mutation	SNP	ENST00000405633.3	hg19	CCDS44617.1	.	.	.	.	.	.	.	.	.	.	C	8.805	0.933861	0.18206	.	.	ENSG00000166961	ENST00000528170;ENST00000337911;ENST00000405633	T;T;T	0.15017	2.46;2.46;2.82	4.83	1.93	0.25924	.	1.432310	0.04687	N	0.413446	T	0.36963	0.0986	M	0.63428	1.95	0.25018	N	0.991359	D;D	0.76494	0.979;0.999	P;D	0.83275	0.725;0.996	T	0.07986	-1.0744	10	0.34782	T	0.22	-15.1267	5.9902	0.19456	0.0:0.6787:0.0:0.3213	.	132;173	F2Z2J5;Q8N5U1	.;M4A15_HUMAN	M	132;80;173	ENSP00000434165:L132M;ENSP00000338692:L80M;ENSP00000386022:L173M	ENSP00000338692:L80M	L	+	1	2	MS4A15	60297904	0.396000	0.25262	0.924000	0.36721	0.062000	0.15995	0.521000	0.22893	0.474000	0.27392	0.555000	0.69702	CTG	.	.		0.572	MS4A15-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000395618.1		
CD6	923	hgsc.bcm.edu	37	11	60785356	60785356	+	Nonsense_Mutation	SNP	G	G	T			TCGA-WJ-A86L-01A-12D-A45V-10	TCGA-WJ-A86L-10A-01D-A38X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	80e4fac9-c066-47a9-9fc0-2a42eef954cd	cebd5a99-cbde-441d-b98a-b84cf1825d65	g.chr11:60785356G>T	ENST00000313421.7	+	11	1894	c.1708G>T	c.(1708-1710)Gag>Tag	p.E570*	CD6_ENST00000352009.5_Nonsense_Mutation_p.E538*|CD6_ENST00000452451.2_Nonsense_Mutation_p.E529*|CD6_ENST00000346437.4_Nonsense_Mutation_p.E497*|CD6_ENST00000344028.5_Nonsense_Mutation_p.E538*	NM_006725.4	NP_006716.3	P30203	CD6_HUMAN	CD6 molecule	570					cell adhesion (GO:0007155)	integral component of plasma membrane (GO:0005887)	scavenger receptor activity (GO:0005044)			endometrium(3)|kidney(1)|large_intestine(4)|lung(8)|pancreas(1)|prostate(1)	18						CTCTTCAGGGGAGGATTACTG	0.562																																					p.E570X	Pancreas(169;904 2017 4767 38890 42505)	Atlas-SNP	.											.	CD6	122	.	0			c.G1708T						.						79.0	80.0	79.0					11																	60785356		2203	4299	6502	SO:0001587	stop_gained	923	exon11			TCAGGGGAGGATT		CCDS7999.1, CCDS58137.1, CCDS58138.1	11q12.2	2006-03-28	2006-03-28		ENSG00000013725	ENSG00000013725		"""CD molecules"""	1691	protein-coding gene	gene with protein product		186720	"""CD6 antigen"""			9013954	Standard	NM_006725		Approved	Tp120	uc001nqq.3	P30203	OTTHUMG00000167823	ENST00000313421.7:c.1708G>T	chr11.hg19:g.60785356G>T	ENSP00000323280:p.Glu570*	113.0	0.0		112.0	57.0	NM_006725	A4KAD4|A4KAD5|Q9UMF2|Q9Y4K7|Q9Y4K8|Q9Y4K9|Q9Y4L0	Nonsense_Mutation	SNP	ENST00000313421.7	hg19	CCDS7999.1	.	.	.	.	.	.	.	.	.	.	G	34	5.365653	0.95900	.	.	ENSG00000013725	ENST00000344028;ENST00000346437;ENST00000313421;ENST00000452451;ENST00000352009	.	.	.	5.31	5.31	0.75309	.	1.075250	0.07326	N	0.878367	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.87932	D	0	.	14.4929	0.67665	0.0:0.0:1.0:0.0	.	.	.	.	X	538;497;570;529;538	.	ENSP00000323280:E570X	E	+	1	0	CD6	60541932	1.000000	0.71417	0.986000	0.45419	0.206000	0.24218	4.746000	0.62133	2.497000	0.84241	0.467000	0.42956	GAG	.	.		0.562	CD6-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000396449.1	NM_006725	
HEPHL1	341208	hgsc.bcm.edu	37	11	93839186	93839186	+	Missense_Mutation	SNP	C	C	G			TCGA-WJ-A86L-01A-12D-A45V-10	TCGA-WJ-A86L-10A-01D-A38X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	80e4fac9-c066-47a9-9fc0-2a42eef954cd	cebd5a99-cbde-441d-b98a-b84cf1825d65	g.chr11:93839186C>G	ENST00000315765.9	+	17	2943	c.2935C>G	c.(2935-2937)Cat>Gat	p.H979D		NM_001098672.1	NP_001092142.1	Q6MZM0	HPHL1_HUMAN	hephaestin-like 1	979	Plastocyanin-like 6.				copper ion transport (GO:0006825)|oxidation-reduction process (GO:0055114)	integral component of membrane (GO:0016021)	copper ion binding (GO:0005507)|ferroxidase activity (GO:0004322)			NS(2)|breast(4)|central_nervous_system(1)|endometrium(5)|kidney(2)|large_intestine(11)|lung(25)|ovary(3)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(3)	61		Acute lymphoblastic leukemia(157;2.34e-05)|all_hematologic(158;0.00824)				TGGGAATCTCCATGGCCTCAT	0.338																																					p.H979D		Atlas-SNP	.											.	HEPHL1	144	.	0			c.C2935G						.						97.0	93.0	94.0					11																	93839186		1854	4090	5944	SO:0001583	missense	341208	exon17			AATCTCCATGGCC	BX641008	CCDS44710.1	11q21	2008-02-05			ENSG00000181333	ENSG00000181333			30477	protein-coding gene	gene with protein product							Standard	NM_001098672		Approved	DKFZp686F22190	uc001pep.2	Q6MZM0	OTTHUMG00000167751	ENST00000315765.9:c.2935C>G	chr11.hg19:g.93839186C>G	ENSP00000313699:p.His979Asp	135.0	0.0		152.0	57.0	NM_001098672	Q3C1W7	Missense_Mutation	SNP	ENST00000315765.9	hg19	CCDS44710.1	.	.	.	.	.	.	.	.	.	.	C	12.47	1.947578	0.34377	.	.	ENSG00000181333	ENST00000315765	D	0.99737	-6.59	5.95	5.04	0.67666	Cupredoxin (2);Multicopper oxidase, type 2 (1);	0.387744	0.31601	N	0.007377	D	0.98229	0.9414	L	0.33753	1.03	0.27523	N	0.951331	B	0.10296	0.003	B	0.16289	0.015	D	0.94491	0.7701	10	0.13108	T	0.6	.	12.28	0.54759	0.0:0.8142:0.1204:0.0654	.	979	Q6MZM0	HPHL1_HUMAN	D	979	ENSP00000313699:H979D	ENSP00000313699:H979D	H	+	1	0	HEPHL1	93478834	0.740000	0.28207	0.964000	0.40570	0.991000	0.79684	2.877000	0.48506	1.511000	0.48818	0.655000	0.94253	CAT	.	.		0.338	HEPHL1-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000396103.2	XM_291947	
OR8B8	26493	hgsc.bcm.edu	37	11	124310418	124310418	+	Silent	SNP	A	A	G			TCGA-WJ-A86L-01A-12D-A45V-10	TCGA-WJ-A86L-10A-01D-A38X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	80e4fac9-c066-47a9-9fc0-2a42eef954cd	cebd5a99-cbde-441d-b98a-b84cf1825d65	g.chr11:124310418A>G	ENST00000328064.2	-	1	636	c.564T>C	c.(562-564)gcT>gcC	p.A188A		NM_012378.1	NP_036510.1	Q15620	OR8B8_HUMAN	olfactory receptor, family 8, subfamily B, member 8	188					detection of chemical stimulus involved in sensory perception of smell (GO:0050911)|sensory perception of smell (GO:0007608)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			cervix(1)|endometrium(4)|kidney(1)|large_intestine(5)|lung(15)|ovary(1)|skin(9)|upper_aerodigestive_tract(2)|urinary_tract(1)	39		Breast(109;0.0115)|Medulloblastoma(222;0.0523)|Lung NSC(97;0.118)|all_lung(97;0.126)|all_neural(223;0.224)		BRCA - Breast invasive adenocarcinoma(274;1.49e-06)|OV - Ovarian serous cystadenocarcinoma(99;0.0277)		TGCTGGTGCAAGCACACTCAA	0.493																																					p.A188A		Atlas-SNP	.											.	OR8B8	76	.	0			c.T564C						.						169.0	134.0	146.0					11																	124310418		2201	4299	6500	SO:0001819	synonymous_variant	26493	exon1			GGTGCAAGCACAC	AF238488	CCDS8446.1	11q24.2	2012-08-09			ENSG00000197125	ENSG00000197125		"""GPCR / Class A : Olfactory receptors"""	8477	protein-coding gene	gene with protein product						9119360	Standard	NM_012378		Approved	TPCR85	uc010sal.2	Q15620	OTTHUMG00000165917	ENST00000328064.2:c.564T>C	chr11.hg19:g.124310418A>G		134.0	0.0		137.0	66.0	NM_012378	A1L446|Q96RC8	Silent	SNP	ENST00000328064.2	hg19	CCDS8446.1																																																																																			.	.		0.493	OR8B8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000387056.1	NM_012378	
IGSF9B	22997	hgsc.bcm.edu	37	11	133801020	133801020	+	Missense_Mutation	SNP	G	G	T			TCGA-WJ-A86L-01A-12D-A45V-10	TCGA-WJ-A86L-10A-01D-A38X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	80e4fac9-c066-47a9-9fc0-2a42eef954cd	cebd5a99-cbde-441d-b98a-b84cf1825d65	g.chr11:133801020G>T	ENST00000321016.8	-	11	1608	c.1378C>A	c.(1378-1380)Ccc>Acc	p.P460T	IGSF9B_ENST00000533871.2_Missense_Mutation_p.P460T			Q9UPX0	TUTLB_HUMAN	immunoglobulin superfamily, member 9B	460	Ig-like 5.				homophilic cell adhesion (GO:0007156)|positive regulation of inhibitory postsynaptic membrane potential (GO:0097151)	dendrite (GO:0030425)|inhibitory synapse (GO:0060077)|integral component of membrane (GO:0016021)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)				breast(1)|endometrium(11)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(6)|lung(18)|ovary(1)|prostate(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	44	all_hematologic(175;0.127)	all_cancers(12;1.58e-21)|all_epithelial(12;5.17e-16)|all_lung(97;1.6e-05)|Lung NSC(97;3.86e-05)|Breast(109;0.000126)|Medulloblastoma(222;0.0245)|all_neural(223;0.0505)|Esophageal squamous(93;0.0559)		Epithelial(10;7.19e-10)|BRCA - Breast invasive adenocarcinoma(10;9.69e-09)|all cancers(11;1.23e-08)|OV - Ovarian serous cystadenocarcinoma(99;0.00328)|Lung(977;0.221)		CTTCTGCTGGGCTTCCCTACC	0.617																																					p.P460T		Atlas-SNP	.											.	IGSF9B	290	.	0			c.C1378A						.						71.0	81.0	77.0					11																	133801020		2159	4262	6421	SO:0001583	missense	22997	exon11			TGCTGGGCTTCCC	AK097578	CCDS61010.1	11q25	2013-02-11	2005-10-12	2005-11-20				"""Immunoglobulin superfamily / V-set domain containing"", ""Immunoglobulin superfamily / I-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"", ""Fibronectin type III domain containing"""	32326	protein-coding gene	gene with protein product		613773					Standard	NM_001277285		Approved	KIAA1030	uc031qfh.1	Q9UPX0		ENST00000321016.8:c.1378C>A	chr11.hg19:g.133801020G>T	ENSP00000317980:p.Pro460Thr	64.0	0.0		66.0	4.0	NM_014987	G5EA26	Missense_Mutation	SNP	ENST00000321016.8	hg19		.	.	.	.	.	.	.	.	.	.	G	15.00	2.704614	0.48412	.	.	ENSG00000080854	ENST00000321016;ENST00000533871;ENST00000527648	T;T;T	0.68025	-0.3;-0.3;-0.3	3.95	3.95	0.45737	Immunoglobulin I-set (1);Immunoglobulin subtype 2 (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	.	.	.	.	T	0.65037	0.2653	L	0.52823	1.66	0.49213	D	0.999764	B	0.32968	0.392	B	0.37304	0.246	T	0.65352	-0.6189	9	0.33141	T	0.24	.	16.1704	0.81808	0.0:0.0:1.0:0.0	.	460	Q9UPX0	TUTLB_HUMAN	T	460;302;460	ENSP00000317980:P460T;ENSP00000436552:P302T;ENSP00000436576:P460T	ENSP00000317980:P460T	P	-	1	0	IGSF9B	133306230	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	6.247000	0.72411	2.029000	0.59856	0.549000	0.68633	CCC	.	.		0.617	IGSF9B-201	KNOWN	basic|appris_candidate	protein_coding	protein_coding		XM_290502	
SLCO1C1	53919	hgsc.bcm.edu	37	12	20903660	20903660	+	Missense_Mutation	SNP	T	T	C			TCGA-WJ-A86L-01A-12D-A45V-10	TCGA-WJ-A86L-10A-01D-A38X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	80e4fac9-c066-47a9-9fc0-2a42eef954cd	cebd5a99-cbde-441d-b98a-b84cf1825d65	g.chr12:20903660T>C	ENST00000266509.2	+	14	2218	c.1850T>C	c.(1849-1851)cTc>cCc	p.L617P	SLCO1C1_ENST00000545102.1_Missense_Mutation_p.L499P|SLCO1C1_ENST00000381552.1_Missense_Mutation_p.L617P|SLCO1C1_ENST00000545604.1_Missense_Mutation_p.L617P|SLCO1C1_ENST00000540354.1_Missense_Mutation_p.L568P	NM_017435.4	NP_059131.1	Q9NYB5	SO1C1_HUMAN	solute carrier organic anion transporter family, member 1C1	617					sodium-independent organic anion transport (GO:0043252)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	transporter activity (GO:0005215)			NS(1)|cervix(1)|endometrium(4)|kidney(3)|large_intestine(9)|liver(1)|lung(28)|ovary(5)|pancreas(1)|prostate(2)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)	60	Esophageal squamous(101;0.149)				Conjugated Estrogens(DB00286)|Dextrothyroxine(DB00509)|Diclofenac(DB00586)|Digoxin(DB00390)|Dinoprostone(DB00917)|Estradiol(DB00783)|Levothyroxine(DB00451)|Liothyronine(DB00279)|Liotrix(DB01583)|Meclofenamic acid(DB00939)|Methotrexate(DB00563)|Ouabain(DB01092)|Phenytoin(DB00252)|Probenecid(DB01032)	ACTTCATGCCTCAAATGGGGA	0.363																																					p.L617P		Atlas-SNP	.											.	SLCO1C1	216	.	0			c.T1850C						.						118.0	112.0	114.0					12																	20903660		2203	4300	6503	SO:0001583	missense	53919	exon14			CATGCCTCAAATG	AF260704	CCDS8683.1, CCDS53757.1, CCDS53758.1, CCDS53759.1	12p12.2	2013-05-22	2003-11-25	2003-11-26	ENSG00000139155	ENSG00000139155		"""Solute carriers"""	13819	protein-coding gene	gene with protein product		613389	"""solute carrier family 21 (organic anion transporter), member 14"""	SLC21A14			Standard	NM_017435		Approved	OATP-F, OATP1C1, OATP1	uc010sii.2	Q9NYB5	OTTHUMG00000168966	ENST00000266509.2:c.1850T>C	chr12.hg19:g.20903660T>C	ENSP00000266509:p.Leu617Pro	149.0	0.0		144.0	72.0	NM_017435	B7Z251|B7Z3Q3|B7Z8P1|F5GZD6|Q5JPA4	Missense_Mutation	SNP	ENST00000266509.2	hg19	CCDS8683.1	.	.	.	.	.	.	.	.	.	.	T	21.8	4.207992	0.79240	.	.	ENSG00000139155	ENST00000545604;ENST00000540354;ENST00000266509;ENST00000381552;ENST00000545102	T;T;T;T;T	0.55930	0.49;0.49;0.49;0.49;0.49	5.32	5.32	0.75619	Major facilitator superfamily domain, general substrate transporter (1);Major facilitator superfamily domain (1);	0.000000	0.85682	D	0.000000	T	0.78861	0.4350	M	0.93720	3.45	0.80722	D	1	D;D;D;D	0.89917	1.0;1.0;1.0;1.0	D;D;D;D	0.97110	1.0;0.999;0.998;0.998	D	0.84469	0.0598	10	0.87932	D	0	.	13.6737	0.62440	0.0:0.0:0.0:1.0	.	499;568;617;617	F5GZD6;B7Z3Q3;Q5JPA4;Q9NYB5	.;.;.;SO1C1_HUMAN	P	617;568;617;617;499	ENSP00000444149:L617P;ENSP00000438665:L568P;ENSP00000266509:L617P;ENSP00000370964:L617P;ENSP00000444527:L499P	ENSP00000266509:L617P	L	+	2	0	SLCO1C1	20794927	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	6.638000	0.74309	2.229000	0.72834	0.533000	0.62120	CTC	.	.		0.363	SLCO1C1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000401765.1	NM_017435	
C2CD5	9847	hgsc.bcm.edu	37	12	22697019	22697019	+	Missense_Mutation	SNP	A	A	C			TCGA-WJ-A86L-01A-12D-A45V-10	TCGA-WJ-A86L-10A-01D-A38X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	80e4fac9-c066-47a9-9fc0-2a42eef954cd	cebd5a99-cbde-441d-b98a-b84cf1825d65	g.chr12:22697019A>C	ENST00000333957.4	-	2	321	c.66T>G	c.(64-66)agT>agG	p.S22R	C2CD5_ENST00000396028.2_Missense_Mutation_p.S22R|C2CD5_ENST00000545552.1_Missense_Mutation_p.S22R|C2CD5_ENST00000544930.1_5'UTR|C2CD5_ENST00000542676.1_Missense_Mutation_p.S22R|C2CD5_ENST00000446597.1_Missense_Mutation_p.S22R|C2CD5_ENST00000536386.1_Missense_Mutation_p.S22R	NM_014802.1	NP_055617.1	Q86YS7	C2CD5_HUMAN	C2 calcium-dependent domain containing 5	22	C2. {ECO:0000255|PROSITE- ProRule:PRU00041}.				cellular response to insulin stimulus (GO:0032869)|insulin receptor signaling pathway via phosphatidylinositol 3-kinase (GO:0038028)|intracellular protein transmembrane transport (GO:0065002)|positive regulation of glucose transport (GO:0010828)|positive regulation of protein targeting to membrane (GO:0090314)|positive regulation of vesicle fusion (GO:0031340)	cell cortex (GO:0005938)|cytoplasmic vesicle membrane (GO:0030659)|plasma membrane (GO:0005886)|ruffle membrane (GO:0032587)	calcium ion binding (GO:0005509)|calcium-dependent phospholipid binding (GO:0005544)										CAGTCAGGTCACTAGCACGGT	0.612																																					p.S22R		Atlas-SNP	.											.	.	.	.	0			c.T66G						.						175.0	130.0	145.0					12																	22697019		2203	4300	6503	SO:0001583	missense	9847	exon2			CAGGTCACTAGCA	AB011100	CCDS31758.1, CCDS66337.1, CCDS66338.1, CCDS66339.1, CCDS66340.1	12p12.1	2012-12-13	2012-12-13	2012-12-13	ENSG00000111731	ENSG00000111731			29062	protein-coding gene	gene with protein product	"""138 kDa C2 domain-containing phosphoprotein"""		"""KIAA0528"""	KIAA0528		21907143	Standard	XM_005253538		Approved	CDP138	uc001rfq.3	Q86YS7	OTTHUMG00000169100	ENST00000333957.4:c.66T>G	chr12.hg19:g.22697019A>C	ENSP00000334229:p.Ser22Arg	65.0	0.0		76.0	34.0	NM_014802	B4DJ03|B4DRN7|B7ZLL0|F5H2A1|F5H5R1|O60280|Q17RY7|Q7Z619|Q86SU3	Missense_Mutation	SNP	ENST00000333957.4	hg19	CCDS31758.1	.	.	.	.	.	.	.	.	.	.	A	20.2	3.946608	0.73672	.	.	ENSG00000111731	ENST00000333957;ENST00000446597;ENST00000536386;ENST00000396028;ENST00000542676;ENST00000545552	T;T;T;T;T;T	0.43294	0.95;0.95;0.95;0.95;0.95;0.95	4.28	1.93	0.25924	C2 membrane targeting protein (1);C2 calcium-dependent membrane targeting (2);C2 calcium/lipid-binding domain, CaLB (1);	0.000000	0.85682	D	0.000000	T	0.56171	0.1967	M	0.68728	2.09	0.80722	D	1	P;P;D;D;D	0.89917	0.925;0.939;0.999;1.0;0.999	P;P;D;D;D	0.85130	0.644;0.758;0.99;0.997;0.968	T	0.51942	-0.8641	10	0.51188	T	0.08	-18.0284	7.4334	0.27141	0.6409:0.0:0.3591:0.0	.	22;22;22;22;22	F5H2A1;B4DRN7;B7ZLL0;Q86YS7-2;Q86YS7	.;.;.;.;K0528_HUMAN	R	22	ENSP00000334229:S22R;ENSP00000388756:S22R;ENSP00000439392:S22R;ENSP00000379345:S22R;ENSP00000441951:S22R;ENSP00000443204:S22R	ENSP00000334229:S22R	S	-	3	2	KIAA0528	22588286	0.999000	0.42202	1.000000	0.80357	0.989000	0.77384	0.832000	0.27490	0.303000	0.22785	0.482000	0.46254	AGT	.	.		0.612	C2CD5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402257.1	NM_014802	
KRT6A	3853	hgsc.bcm.edu	37	12	52884732	52884732	+	Silent	SNP	C	C	T	rs368725695		TCGA-WJ-A86L-01A-12D-A45V-10	TCGA-WJ-A86L-10A-01D-A38X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	80e4fac9-c066-47a9-9fc0-2a42eef954cd	cebd5a99-cbde-441d-b98a-b84cf1825d65	g.chr12:52884732C>T	ENST00000330722.6	-	4	890	c.822G>A	c.(820-822)gtG>gtA	p.V274V		NM_005554.3	NP_005545.1	P02538	K2C6A_HUMAN	keratin 6A	274	Coil 1B.|Rod.				cell differentiation (GO:0030154)|positive regulation of cell proliferation (GO:0008284)	extracellular vesicular exosome (GO:0070062)|keratin filament (GO:0045095)|membrane (GO:0016020)|nucleus (GO:0005634)	structural constituent of cytoskeleton (GO:0005200)			breast(2)|central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(7)|liver(1)|lung(14)|ovary(4)|prostate(1)|skin(1)|stomach(1)|urinary_tract(1)	39				BRCA - Breast invasive adenocarcinoma(357;0.189)		AGGCAGCATCCACATCCTGGG	0.502																																					p.V274V		Atlas-SNP	.											.	KRT6A	89	.	0			c.G822A						.						69.0	65.0	67.0					12																	52884732		2203	4297	6500	SO:0001819	synonymous_variant	3853	exon4			AGCATCCACATCC	BC014152, L42593, L42610	CCDS41786.1	12q13.13	2013-01-16			ENSG00000205420	ENSG00000205420		"""-"", ""Intermediate filaments type II, keratins (basic)"""	6443	protein-coding gene	gene with protein product		148041	"""keratin 6C"", ""keratin 6D"""	KRT6C, KRT6D		1713141, 16831889	Standard	NM_005554		Approved	CK6C, K6C, CK6D, K6D	uc001sam.3	P02538	OTTHUMG00000169597	ENST00000330722.6:c.822G>A	chr12.hg19:g.52884732C>T		129.0	0.0		147.0	55.0	NM_005554	A4QPC1|P48667|Q08AR4|Q6NT67|Q96CL4	Silent	SNP	ENST00000330722.6	hg19	CCDS41786.1																																																																																			.	.		0.502	KRT6A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000404978.2	NM_005554	
KRT78	196374	hgsc.bcm.edu	37	12	53238491	53238491	+	Missense_Mutation	SNP	T	T	G			TCGA-WJ-A86L-01A-12D-A45V-10	TCGA-WJ-A86L-10A-01D-A38X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	80e4fac9-c066-47a9-9fc0-2a42eef954cd	cebd5a99-cbde-441d-b98a-b84cf1825d65	g.chr12:53238491T>G	ENST00000304620.4	-	5	836	c.773A>C	c.(772-774)cAg>cCg	p.Q258P	KRT78_ENST00000359499.4_Missense_Mutation_p.Q148P	NM_173352.2	NP_775487.2	Q8N1N4	K2C78_HUMAN	keratin 78	258	Coil 1B.|Rod.					extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|keratin filament (GO:0045095)	structural molecule activity (GO:0005198)			endometrium(1)|kidney(1)|large_intestine(6)|lung(5)|ovary(2)|prostate(1)|skin(1)|urinary_tract(1)	18						GGCCTGGGTCTGGAGCTGGCC	0.597																																					p.Q258P		Atlas-SNP	.											.	KRT78	41	.	0			c.A773C						.						69.0	58.0	61.0					12																	53238491		2203	4300	6503	SO:0001583	missense	196374	exon5			TGGGTCTGGAGCT	AK096419	CCDS8840.1, CCDS73473.1	12q13.13	2013-06-25			ENSG00000170423	ENSG00000170423		"""-"", ""Intermediate filaments type II, keratins (basic)"""	28926	protein-coding gene	gene with protein product		611159				16831889	Standard	XM_005268695		Approved	K5B	uc001sbc.1	Q8N1N4	OTTHUMG00000169880	ENST00000304620.4:c.773A>C	chr12.hg19:g.53238491T>G	ENSP00000306261:p.Gln258Pro	30.0	0.0		29.0	16.0	NM_173352	A8K4D6|Q5HYM7|Q7RTT2	Missense_Mutation	SNP	ENST00000304620.4	hg19	CCDS8840.1	.	.	.	.	.	.	.	.	.	.	T	16.88	3.243818	0.58995	.	.	ENSG00000170423	ENST00000359499;ENST00000304620;ENST00000539860;ENST00000547110	D;D;D	0.90069	-2.61;-2.61;-2.61	5.28	1.42	0.22433	Filament (1);	0.297821	0.18436	N	0.141294	D	0.95046	0.8396	H	0.96777	3.88	0.27207	N	0.960013	D	0.71674	0.998	D	0.65684	0.937	D	0.88319	0.2961	10	0.87932	D	0	.	7.0869	0.25261	0.0:0.0749:0.2797:0.6454	.	258	Q8N1N4	K2C78_HUMAN	P	148;258;29;29	ENSP00000352479:Q148P;ENSP00000306261:Q258P;ENSP00000447817:Q29P	ENSP00000306261:Q258P	Q	-	2	0	KRT78	51524758	1.000000	0.71417	0.005000	0.12908	0.009000	0.06853	5.074000	0.64401	0.052000	0.16007	0.460000	0.39030	CAG	.	.		0.597	KRT78-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000406380.1	NM_173352	
APAF1	317	hgsc.bcm.edu	37	12	99121087	99121087	+	Missense_Mutation	SNP	A	A	G			TCGA-WJ-A86L-01A-12D-A45V-10	TCGA-WJ-A86L-10A-01D-A38X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	80e4fac9-c066-47a9-9fc0-2a42eef954cd	cebd5a99-cbde-441d-b98a-b84cf1825d65	g.chr12:99121087A>G	ENST00000551964.1	+	26	4329	c.3593A>G	c.(3592-3594)tAt>tGt	p.Y1198C	APAF1_ENST00000552268.1_Intron|APAF1_ENST00000357310.1_Missense_Mutation_p.Y1155C|APAF1_ENST00000333991.1_Intron|APAF1_ENST00000549007.1_Missense_Mutation_p.Y1113C|APAF1_ENST00000339433.3_Missense_Mutation_p.Y1113C|APAF1_ENST00000547045.1_Missense_Mutation_p.Y1155C|APAF1_ENST00000359972.2_Missense_Mutation_p.Y1144C|APAF1_ENST00000550527.1_Missense_Mutation_p.Y1187C	NM_181861.1	NP_863651.1	O14727	APAF_HUMAN	apoptotic peptidase activating factor 1	1198					activation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0006919)|activation of cysteine-type endopeptidase activity involved in apoptotic process by cytochrome c (GO:0008635)|apoptotic process (GO:0006915)|forebrain development (GO:0030900)|intrinsic apoptotic signaling pathway (GO:0097193)|nervous system development (GO:0007399)|neural tube closure (GO:0001843)|neuron apoptotic process (GO:0051402)|positive regulation of apoptotic process (GO:0043065)|positive regulation of apoptotic signaling pathway (GO:2001235)|regulation of apoptotic DNA fragmentation (GO:1902510)|regulation of apoptotic process (GO:0042981)|response to G1 DNA damage checkpoint signaling (GO:0072432)	apoptosome (GO:0043293)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)	ADP binding (GO:0043531)|ATP binding (GO:0005524)|cysteine-type endopeptidase activator activity involved in apoptotic process (GO:0008656)|nucleotide binding (GO:0000166)			breast(1)|central_nervous_system(1)|endometrium(4)|kidney(2)|large_intestine(13)|liver(1)|lung(15)|ovary(2)|prostate(2)|skin(1)	42					Adenosine triphosphate(DB00171)	GCTGGAGGATATATTAAGGTA	0.428																																					p.Y1198C		Atlas-SNP	.											.	APAF1	111	.	0			c.A3593G						.						65.0	67.0	66.0					12																	99121087		2203	4300	6503	SO:0001583	missense	317	exon26			GAGGATATATTAA	AF013263	CCDS9069.1, CCDS9070.1, CCDS9071.1, CCDS55862.1, CCDS55863.1	12q23	2013-01-10	2006-10-23			ENSG00000120868		"""WD repeat domain containing"""	576	protein-coding gene	gene with protein product		602233	"""apoptotic protease activating factor"", ""apoptotic peptidase activating factor"""			9267021, 10702682	Standard	NM_181861		Approved	CED4, APAF-1	uc001tfz.3	O14727	OTTHUMG00000170214	ENST00000551964.1:c.3593A>G	chr12.hg19:g.99121087A>G	ENSP00000448165:p.Tyr1198Cys	46.0	0.0		31.0	14.0	NM_181861	B2RMX8|O43297|Q7Z438|Q9BXZ6|Q9UBZ5|Q9UGN8|Q9UGN9|Q9UGP0|Q9UJ58|Q9UJ59|Q9UJ60|Q9UJ61|Q9UJ62|Q9UJ63|Q9UJ64|Q9UJ65|Q9UJ66|Q9UJ67|Q9UNC9	Missense_Mutation	SNP	ENST00000551964.1	hg19	CCDS9069.1	.	.	.	.	.	.	.	.	.	.	A	13.35	2.210136	0.39003	.	.	ENSG00000120868	ENST00000551964;ENST00000359972;ENST00000357310;ENST00000339433;ENST00000550527;ENST00000547045;ENST00000549007	T;T;T;T;T;T;T	0.81163	-1.46;-1.46;2.23;1.06;-1.46;2.23;1.06	5.79	1.81	0.25067	WD40/YVTN repeat-like-containing domain (1);WD40 repeat-like-containing domain (1);WD40-repeat-containing domain (1);	0.255939	0.40554	N	0.001071	T	0.78698	0.4324	L	0.29908	0.895	0.34824	D	0.739014	P;P;P;D;D	0.71674	0.916;0.949;0.879;0.987;0.998	P;P;P;P;P	0.62298	0.841;0.866;0.669;0.9;0.896	T	0.79857	-0.1626	10	0.46703	T	0.11	-8.9857	7.613	0.28142	0.6265:0.1282:0.0:0.2453	.	1113;1155;1144;1198;1187	C9JLV4;O14727-4;O14727-3;O14727;O14727-2	.;.;.;APAF_HUMAN;.	C	1198;1144;1155;1113;1187;1155;1113	ENSP00000448165:Y1198C;ENSP00000353059:Y1144C;ENSP00000349862:Y1155C;ENSP00000341830:Y1113C;ENSP00000448449:Y1187C;ENSP00000449791:Y1155C;ENSP00000448161:Y1113C	ENSP00000341830:Y1113C	Y	+	2	0	APAF1	97645218	1.000000	0.71417	0.604000	0.28916	0.402000	0.30811	3.113000	0.50376	0.418000	0.25898	0.528000	0.53228	TAT	.	.		0.428	APAF1-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000408006.1	NM_181861.1	
HNF1A	6927	hgsc.bcm.edu	37	12	121437070	121437070	+	Splice_Site	SNP	G	G	A			TCGA-WJ-A86L-01A-12D-A45V-10	TCGA-WJ-A86L-10A-01D-A38X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	80e4fac9-c066-47a9-9fc0-2a42eef954cd	cebd5a99-cbde-441d-b98a-b84cf1825d65	g.chr12:121437070G>A	ENST00000257555.6	+	8	1727		c.e8-1		HNF1A_ENST00000541395.1_Splice_Site|RP11-216P16.2_ENST00000606238.1_RNA|HNF1A_ENST00000544413.1_Splice_Site			P20823	HNF1A_HUMAN	HNF1 homeobox A						glucose homeostasis (GO:0042593)|glucose import (GO:0046323)|insulin secretion (GO:0030073)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription initiation from RNA polymerase II promoter (GO:0060261)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|renal glucose absorption (GO:0035623)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|protein complex (GO:0043234)	DNA binding (GO:0003677)|protein dimerization activity (GO:0046983)|protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription regulatory region DNA binding (GO:0044212)			breast(3)|central_nervous_system(2)|cervix(1)|endometrium(8)|large_intestine(19)|liver(175)|lung(9)|ovary(2)|prostate(1)|urinary_tract(1)	221	all_neural(191;0.0684)|Medulloblastoma(191;0.0922)					CCTGCGGCCAGCCCTCTACAG	0.667									Hepatic Adenoma, Familial Clustering of																												.		Atlas-SNP	.											.	HNF1A	302	.	0			c.1502-1G>A						.						47.0	51.0	49.0					12																	121437070		2203	4300	6503	SO:0001630	splice_region_variant	6927	exon8	Familial Cancer Database	incl. Maturity-Onset Diabetes of the Young type 3, MODY3	CGGCCAGCCCTCT	M57732	CCDS9209.1	12q24.31	2014-09-17	2007-08-24	2007-08-24	ENSG00000135100	ENSG00000135100		"""Homeoboxes / HNF class"""	11621	protein-coding gene	gene with protein product		142410	"""transcription factor 1, hepatic; LF-B1, hepatic nuclear factor (HNF1), albumin proximal factor"""	MODY3, TCF1		1535333, 7795649	Standard	NM_000545		Approved	HNF1, LFB1	uc001tzg.3	P20823	OTTHUMG00000151015	ENST00000257555.6:c.1502-1G>A	chr12.hg19:g.121437070G>A		118.0	0.0		103.0	43.0	NM_000545	A5Z2R8|E0YMJ5|E0YMK0|E0YMK1|E2I9R4|E2I9R5|F5H5U3|Q2M3H2|Q99861	Splice_Site	SNP	ENST00000257555.6	hg19	CCDS9209.1	.	.	.	.	.	.	.	.	.	.	G	26.6	4.752217	0.89753	.	.	ENSG00000135100	ENST00000257555;ENST00000535125;ENST00000537424;ENST00000543027;ENST00000541395;ENST00000544413	.	.	.	5.52	5.52	0.82312	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	18.4622	0.90743	0.0:0.0:1.0:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	HNF1A	119921453	0.818000	0.29161	1.000000	0.80357	0.933000	0.57130	0.923000	0.28757	2.601000	0.87937	0.650000	0.86243	.	.	.		0.667	HNF1A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000320957.5	NM_000545	Intron
TRPC4	7223	hgsc.bcm.edu	37	13	38320590	38320590	+	Silent	SNP	C	C	T			TCGA-WJ-A86L-01A-12D-A45V-10	TCGA-WJ-A86L-10A-01D-A38X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	80e4fac9-c066-47a9-9fc0-2a42eef954cd	cebd5a99-cbde-441d-b98a-b84cf1825d65	g.chr13:38320590C>T	ENST00000379705.3	-	3	1238	c.381G>A	c.(379-381)gtG>gtA	p.V127V	TRPC4_ENST00000338947.5_Intron|TRPC4_ENST00000379679.1_Intron|TRPC4_ENST00000379673.2_Silent_p.V127V|TRPC4_ENST00000379681.3_Silent_p.V127V|TRPC4_ENST00000358477.2_Silent_p.V127V|TRPC4_ENST00000355779.2_Silent_p.V127V|TRPC4_ENST00000426868.2_Silent_p.V127V|TRPC4_ENST00000447043.1_Silent_p.V127V			Q9UBN4	TRPC4_HUMAN	transient receptor potential cation channel, subfamily C, member 4	127	Multimerization domain. {ECO:0000250}.				axon guidance (GO:0007411)|calcium ion import (GO:0070509)|calcium ion transmembrane transport (GO:0070588)|calcium ion transport (GO:0006816)|gamma-aminobutyric acid secretion (GO:0014051)|ion transmembrane transport (GO:0034220)|oligodendrocyte differentiation (GO:0048709)|transmembrane transport (GO:0055085)	basolateral plasma membrane (GO:0016323)|calcium channel complex (GO:0034704)|caveola (GO:0005901)|cell surface (GO:0009986)|cortical cytoskeleton (GO:0030863)|plasma membrane (GO:0005886)	beta-catenin binding (GO:0008013)|cadherin binding (GO:0045296)|inositol 1,4,5 trisphosphate binding (GO:0070679)|store-operated calcium channel activity (GO:0015279)			NS(2)|breast(4)|endometrium(3)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(26)|lung(30)|ovary(4)|prostate(1)|skin(4)|urinary_tract(2)	83				all cancers(112;1.92e-08)|Epithelial(112;5.04e-06)|OV - Ovarian serous cystadenocarcinoma(117;0.000677)|GBM - Glioblastoma multiforme(144;0.00623)|BRCA - Breast invasive adenocarcinoma(63;0.0126)		GTATAGGAGGCACCTAAAAAA	0.338																																					p.V127V		Atlas-SNP	.											.	TRPC4	389	.	0			c.G381A						.						56.0	68.0	64.0					13																	38320590		2159	4246	6405	SO:0001819	synonymous_variant	7223	exon3			AGGAGGCACCTAA	U40983	CCDS9365.1, CCDS45035.1, CCDS45036.1, CCDS45038.1, CCDS45039.1	13q13.3	2013-01-10			ENSG00000133107	ENSG00000133107		"""Voltage-gated ion channels / Transient receptor potential cation channels"", ""Ankyrin repeat domain containing"""	12336	protein-coding gene	gene with protein product		603651				8646775, 16382100	Standard	NM_016179		Approved	HTRP4, TRP4	uc010abx.3	Q9UBN4	OTTHUMG00000016752	ENST00000379705.3:c.381G>A	chr13.hg19:g.38320590C>T		49.0	0.0		37.0	26.0	NM_003306	B1ALE0|B1ALE1|B1ALE2|Q15721|Q3SWS6|Q96P03|Q96P04|Q96P05|Q9UIB0|Q9UIB1|Q9UIB2	Silent	SNP	ENST00000379705.3	hg19	CCDS9365.1																																																																																			.	.		0.338	TRPC4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044574.2	NM_003306	
TBC1D4	9882	hgsc.bcm.edu	37	13	76055872	76055872	+	Missense_Mutation	SNP	G	G	C			TCGA-WJ-A86L-01A-12D-A45V-10	TCGA-WJ-A86L-10A-01D-A38X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	80e4fac9-c066-47a9-9fc0-2a42eef954cd	cebd5a99-cbde-441d-b98a-b84cf1825d65	g.chr13:76055872G>C	ENST00000377636.3	-	1	378	c.32C>G	c.(31-33)cCg>cGg	p.P11R	TBC1D4_ENST00000431480.2_Missense_Mutation_p.P11R|TBC1D4_ENST00000377625.2_Missense_Mutation_p.P11R|TBC1D4_ENST00000425511.1_5'UTR	NM_014832.2	NP_055647.2	O60343	TBCD4_HUMAN	TBC1 domain family, member 4	11					cellular response to insulin stimulus (GO:0032869)|membrane organization (GO:0061024)|negative regulation of vesicle fusion (GO:0031339)|vesicle-mediated transport (GO:0016192)	cytoplasm (GO:0005737)|cytoplasmic vesicle membrane (GO:0030659)|extracellular vesicular exosome (GO:0070062)	Rab GTPase activator activity (GO:0005097)			breast(1)|central_nervous_system(1)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(3)|large_intestine(12)|lung(18)|ovary(4)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	50		Prostate(6;0.014)|Breast(118;0.0982)		GBM - Glioblastoma multiforme(99;0.0116)		GTGCGGGAACGGCTCATCCTG	0.726																																					p.P11R		Atlas-SNP	.											.	TBC1D4	142	.	0			c.C32G						.						9.0	11.0	11.0					13																	76055872		1797	3987	5784	SO:0001583	missense	9882	exon1			GGGAACGGCTCAT	AB011175	CCDS41901.1, CCDS66563.1, CCDS66564.1	13q22.2	2013-07-09			ENSG00000136111	ENSG00000136111			19165	protein-coding gene	gene with protein product	"""Akt substrate of 160 kDa"""	612465				11829485, 11994271, 15304337	Standard	XM_005266603		Approved	KIAA0603, AS160, DKFZp779C0666	uc001vjl.1	O60343	OTTHUMG00000017088	ENST00000377636.3:c.32C>G	chr13.hg19:g.76055872G>C	ENSP00000366863:p.Pro11Arg	96.0	0.0		58.0	49.0	NM_014832	A7E2X8|B4DU25|B4E235|B6ETN8|B6ETN9|Q5W0B9|Q68D14	Missense_Mutation	SNP	ENST00000377636.3	hg19	CCDS41901.1	.	.	.	.	.	.	.	.	.	.	G	17.58	3.425262	0.62733	.	.	ENSG00000136111	ENST00000377636;ENST00000431480;ENST00000377625	T;T;T	0.03951	3.8;3.78;3.75	3.87	3.02	0.34903	.	0.739627	0.11772	N	0.530988	T	0.13243	0.0321	L	0.40543	1.245	0.80722	D	1	D;D;D	0.76494	0.989;0.989;0.999	P;P;D	0.79784	0.865;0.865;0.993	T	0.03840	-1.0999	10	0.72032	D	0.01	-9.3355	9.7031	0.40198	0.0983:0.0:0.9017:0.0	.	11;11;11	O60343-2;O60343-3;O60343	.;.;TBCD4_HUMAN	R	11	ENSP00000366863:P11R;ENSP00000395986:P11R;ENSP00000366852:P11R	ENSP00000366852:P11R	P	-	2	0	TBC1D4	74953873	1.000000	0.71417	0.995000	0.50966	0.982000	0.71751	3.836000	0.55813	0.950000	0.37743	0.462000	0.41574	CCG	.	.		0.726	TBC1D4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045283.1	NM_014832	
GPC6	10082	hgsc.bcm.edu	37	13	95055461	95055461	+	Missense_Mutation	SNP	T	T	A			TCGA-WJ-A86L-01A-12D-A45V-10	TCGA-WJ-A86L-10A-01D-A38X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	80e4fac9-c066-47a9-9fc0-2a42eef954cd	cebd5a99-cbde-441d-b98a-b84cf1825d65	g.chr13:95055461T>A	ENST00000377047.4	+	9	2273	c.1658T>A	c.(1657-1659)cTg>cAg	p.L553Q		NM_005708.3	NP_005699.1	Q9Y625	GPC6_HUMAN	glypican 6	553					carbohydrate metabolic process (GO:0005975)|cell migration (GO:0016477)|chondroitin sulfate metabolic process (GO:0030204)|glycosaminoglycan biosynthetic process (GO:0006024)|glycosaminoglycan catabolic process (GO:0006027)|glycosaminoglycan metabolic process (GO:0030203)|phototransduction, visible light (GO:0007603)|retinoid metabolic process (GO:0001523)|small molecule metabolic process (GO:0044281)	anchored component of membrane (GO:0031225)|Golgi lumen (GO:0005796)|integral component of plasma membrane (GO:0005887)|lysosomal lumen (GO:0043202)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|proteinaceous extracellular matrix (GO:0005578)				NS(1)|breast(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(10)|lung(13)|skin(2)|stomach(1)|upper_aerodigestive_tract(4)|urinary_tract(1)	38	all_neural(89;0.0684)|Medulloblastoma(90;0.163)	all_cancers(2;5.48e-07)|all_epithelial(2;5.69e-08)|all_lung(2;2.19e-05)|Lung NSC(4;6.09e-05)|Breast(118;0.0395)|Renal(2;0.0568)|Hepatocellular(115;0.217)				CTGCAGAGACTGTGCAGATAA	0.517																																					p.L553Q		Atlas-SNP	.											.	GPC6	102	.	0			c.T1658A						.						55.0	47.0	49.0					13																	95055461		2203	4300	6503	SO:0001583	missense	10082	exon9			AGAGACTGTGCAG	AF111178	CCDS9469.1	13q32	2008-02-05			ENSG00000183098	ENSG00000183098		"""Proteoglycans / Cell Surface : Glypicans"""	4454	protein-coding gene	gene with protein product	"""glypican proteoglycan 6"""	604404				10329016	Standard	NM_005708		Approved		uc001vlt.3	Q9Y625	OTTHUMG00000017205	ENST00000377047.4:c.1658T>A	chr13.hg19:g.95055461T>A	ENSP00000366246:p.Leu553Gln	31.0	0.0		34.0	31.0	NM_005708	A8K279|Q96SG5|Q96SG8|Q9H1P4	Missense_Mutation	SNP	ENST00000377047.4	hg19	CCDS9469.1	.	.	.	.	.	.	.	.	.	.	T	6.784	0.513575	0.12944	.	.	ENSG00000183098	ENST00000377047	T	0.52057	0.68	5.77	4.54	0.55810	.	0.192672	0.34314	N	0.004079	T	0.35307	0.0927	L	0.47716	1.5	0.37437	D	0.914276	B	0.02656	0.0	B	0.04013	0.001	T	0.24404	-1.0161	10	0.11794	T	0.64	.	8.564	0.33527	0.3863:0.0:0.0:0.6137	.	553	Q9Y625	GPC6_HUMAN	Q	553	ENSP00000366246:L553Q	ENSP00000366246:L553Q	L	+	2	0	GPC6	93853462	1.000000	0.71417	1.000000	0.80357	0.433000	0.31745	4.347000	0.59373	2.203000	0.70933	0.454000	0.30748	CTG	.	.		0.517	GPC6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045460.4	NM_005708	
ARHGEF40	55701	hgsc.bcm.edu	37	14	21555482	21555482	+	Missense_Mutation	SNP	C	C	T			TCGA-WJ-A86L-01A-12D-A45V-10	TCGA-WJ-A86L-10A-01D-A38X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	80e4fac9-c066-47a9-9fc0-2a42eef954cd	cebd5a99-cbde-441d-b98a-b84cf1825d65	g.chr14:21555482C>T	ENST00000298694.4	+	21	4374	c.4247C>T	c.(4246-4248)gCc>gTc	p.A1416V	ARHGEF40_ENST00000298693.3_Intron			Q8TER5	ARH40_HUMAN	Rho guanine nucleotide exchange factor (GEF) 40	1416						cytoplasm (GO:0005737)	Rho guanyl-nucleotide exchange factor activity (GO:0005089)			large_intestine(4)|ovary(3)|upper_aerodigestive_tract(2)	9						TCTGCAGCCGCCCGCACCCGG	0.701																																					p.A1416V		Atlas-SNP	.											.	ARHGEF40	84	.	0			c.C4247T						.						31.0	41.0	38.0					14																	21555482		2193	4288	6481	SO:0001583	missense	55701	exon21			CAGCCGCCCGCAC		CCDS32041.1	14q11.2	2012-07-24			ENSG00000165801	ENSG00000165801		"""Rho guanine nucleotide exchange factors"""	25516	protein-coding gene	gene with protein product		610018				16143467	Standard	NM_001278529		Approved	solo, FLJ10357	uc001vzp.3	Q8TER5		ENST00000298694.4:c.4247C>T	chr14.hg19:g.21555482C>T	ENSP00000298694:p.Ala1416Val	44.0	0.0		72.0	26.0	NM_018071	A5PL07|Q9BWP5|Q9H7L6|Q9NTF9|Q9NW24	Missense_Mutation	SNP	ENST00000298694.4	hg19	CCDS32041.1	.	.	.	.	.	.	.	.	.	.	C	15.33	2.801172	0.50315	.	.	ENSG00000165801	ENST00000298694	T	0.02606	4.23	5.32	4.4	0.53042	.	0.000000	0.47093	D	0.000248	T	0.05135	0.0137	N	0.11427	0.14	0.80722	D	1	D	0.65815	0.995	D	0.68353	0.957	T	0.59156	-0.7507	10	0.37606	T	0.19	.	11.7417	0.51796	0.0:0.8219:0.1781:0.0	.	1416	Q8TER5	ARH40_HUMAN	V	1416	ENSP00000298694:A1416V	ENSP00000298694:A1416V	A	+	2	0	ARHGEF40	20625322	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	4.127000	0.57944	1.181000	0.42912	0.563000	0.77884	GCC	.	.		0.701	ARHGEF40-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000413122.1		
PRMT5	10419	hgsc.bcm.edu	37	14	23398484	23398484	+	Silent	SNP	T	T	A			TCGA-WJ-A86L-01A-12D-A45V-10	TCGA-WJ-A86L-10A-01D-A38X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	80e4fac9-c066-47a9-9fc0-2a42eef954cd	cebd5a99-cbde-441d-b98a-b84cf1825d65	g.chr14:23398484T>A	ENST00000324366.8	-	1	310	c.87A>T	c.(85-87)acA>acT	p.T29T	PRMT5_ENST00000553897.1_Silent_p.T29T|PRMT5_ENST00000553641.1_5'UTR|PRMT5_ENST00000397440.4_5'UTR|PRMT5_ENST00000216350.8_5'UTR|PRMT5-AS1_ENST00000590290.1_RNA|PRMT5-AS1_ENST00000587245.2_RNA|RP11-298I3.1_ENST00000548819.1_RNA|PRMT5-AS1_ENST00000595662.1_RNA|PRMT5-AS1_ENST00000599580.2_RNA|PRMT5_ENST00000538452.1_5'UTR|RP11-298I3.1_ENST00000548322.1_RNA|PRMT5_ENST00000397441.2_5'UTR	NM_006109.3	NP_006100.2	O14744	ANM5_HUMAN	protein arginine methyltransferase 5	29	TIM barrel. {ECO:0000269|PubMed:23071334}.				cell proliferation (GO:0008283)|circadian regulation of gene expression (GO:0032922)|endothelial cell activation (GO:0042118)|gene expression (GO:0010467)|histone H4-R3 methylation (GO:0043985)|ncRNA metabolic process (GO:0034660)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|peptidyl-arginine methylation (GO:0018216)|peptidyl-arginine methylation, to symmetrical-dimethyl arginine (GO:0019918)|peptidyl-arginine N-methylation (GO:0035246)|regulation of mitosis (GO:0007088)|regulation of transcription, DNA-templated (GO:0006355)|RNA metabolic process (GO:0016070)|spliceosomal snRNP assembly (GO:0000387)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|methylosome (GO:0034709)|nucleus (GO:0005634)	chromatin binding (GO:0003682)|core promoter sequence-specific DNA binding (GO:0001046)|histone-arginine N-methyltransferase activity (GO:0008469)|methyltransferase activity (GO:0008168)|protein-arginine omega-N symmetric methyltransferase activity (GO:0035243)|ribonucleoprotein complex binding (GO:0043021)|transcription corepressor activity (GO:0003714)			endometrium(4)|kidney(3)|large_intestine(3)|lung(9)|ovary(1)|prostate(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	25	all_cancers(95;2.76e-05)			GBM - Glioblastoma multiforme(265;0.0126)		CAGCCCCTAGTGTGTCAGCTA	0.672																																					p.T29T		Atlas-SNP	.											.	PRMT5	101	.	0			c.A87T						.						59.0	55.0	56.0					14																	23398484		2203	4300	6503	SO:0001819	synonymous_variant	10419	exon1			CCCTAGTGTGTCA	AF015913	CCDS9579.1, CCDS41922.1, CCDS61394.1, CCDS61395.1, CCDS61396.1	14q11.2	2014-06-12	2006-02-16	2006-02-16	ENSG00000100462	ENSG00000100462	2.1.1.125	"""Protein arginine methyltransferases"""	10894	protein-coding gene	gene with protein product		604045	"""skb1 (S. pombe) homolog"", ""SKB1 homolog (S. pombe)"""	HRMT1L5, SKB1		9843966	Standard	NM_001282955		Approved	SKB1Hs	uc001whm.1	O14744	OTTHUMG00000028709	ENST00000324366.8:c.87A>T	chr14.hg19:g.23398484T>A		36.0	0.0		45.0	19.0	NM_006109	A8MTP3|A8MZ91|B4DX49|B4DY30|B5BU10|D3DS33|E2QRE7|Q6IBR1|Q9UKH1	Silent	SNP	ENST00000324366.8	hg19	CCDS9579.1																																																																																			.	.		0.672	PRMT5-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000071674.3		
DCAF11	80344	hgsc.bcm.edu	37	14	24590150	24590150	+	Missense_Mutation	SNP	C	C	A			TCGA-WJ-A86L-01A-12D-A45V-10	TCGA-WJ-A86L-10A-01D-A38X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	80e4fac9-c066-47a9-9fc0-2a42eef954cd	cebd5a99-cbde-441d-b98a-b84cf1825d65	g.chr14:24590150C>A	ENST00000446197.3	+	12	1923	c.1196C>A	c.(1195-1197)gCt>gAt	p.A399D	DCAF11_ENST00000559115.1_Missense_Mutation_p.A399D|DCAF11_ENST00000396936.1_Missense_Mutation_p.A299D|DCAF11_ENST00000396941.4_Missense_Mutation_p.A373D|RP11-468E2.6_ENST00000558325.1_5'Flank	NM_025230.4	NP_079506.3	Q8TEB1	DCA11_HUMAN	DDB1 and CUL4 associated factor 11	399					protein ubiquitination (GO:0016567)	Cul4-RING E3 ubiquitin ligase complex (GO:0080008)											TCACGCCAGGCTGCCACACAG	0.542																																					p.A399D		Atlas-SNP	.											.	.	.	.	0			c.C1196A						.						75.0	74.0	74.0					14																	24590150		2203	4300	6503	SO:0001583	missense	80344	exon12			GCCAGGCTGCCAC	AF130070	CCDS9610.1, CCDS41929.1	14q11.2	2013-01-09	2009-07-17	2009-07-17	ENSG00000100897	ENSG00000100897		"""WD repeat domain containing"", ""DDB1 and CUL4 associated factors"""	20258	protein-coding gene	gene with protein product		613317	"""WD repeat domain 23"""	WDR23			Standard	NM_025230		Approved	PRO2389, GL014	uc001wlv.3	Q8TEB1	OTTHUMG00000028793	ENST00000446197.3:c.1196C>A	chr14.hg19:g.24590150C>A	ENSP00000415556:p.Ala399Asp	113.0	0.0		164.0	88.0	NM_025230	B3KQ83|D3DS56|Q5D039|Q86U00|Q86U39|Q8NDN2|Q9H2J0|Q9H3A3|Q9H5C9	Missense_Mutation	SNP	ENST00000446197.3	hg19	CCDS9610.1	.	.	.	.	.	.	.	.	.	.	c	26.7	4.762284	0.89932	.	.	ENSG00000100897	ENST00000326009;ENST00000446197;ENST00000396936;ENST00000396941	T;T	0.63255	0.64;-0.03	6.17	6.17	0.99709	WD40/YVTN repeat-like-containing domain (1);WD40 repeat-like-containing domain (1);WD40-repeat-containing domain (1);	0.000000	0.85682	D	0.000000	T	0.74658	0.3745	L	0.53249	1.67	0.80722	D	1	D;D;D;D;D	0.67145	0.995;0.996;0.981;0.992;0.994	P;D;P;P;P	0.66497	0.858;0.944;0.901;0.901;0.88	T	0.69405	-0.5154	10	0.33940	T	0.23	-14.5028	18.3732	0.90420	0.0:1.0:0.0:0.0	.	322;373;299;399;399	Q59GN6;Q8TEB1-2;Q8TEB1-3;A8K9T2;Q8TEB1	.;.;.;.;DCA11_HUMAN	D	399;373;299;373	ENSP00000380142:A299D;ENSP00000380146:A373D	ENSP00000323680:A399D	A	+	2	0	DCAF11	23659990	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	6.837000	0.75354	2.941000	0.99782	0.655000	0.94253	GCT	.	.		0.542	DCAF11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000071907.4		
RTN1	6252	hgsc.bcm.edu	37	14	60212828	60212828	+	Missense_Mutation	SNP	C	C	A			TCGA-WJ-A86L-01A-12D-A45V-10	TCGA-WJ-A86L-10A-01D-A38X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	80e4fac9-c066-47a9-9fc0-2a42eef954cd	cebd5a99-cbde-441d-b98a-b84cf1825d65	g.chr14:60212828C>A	ENST00000267484.5	-	2	948	c.613G>T	c.(613-615)Gtg>Ttg	p.V205L		NM_021136.2	NP_066959.1	Q16799	RTN1_HUMAN	reticulon 1	205					neuron differentiation (GO:0030182)	endoplasmic reticulum membrane (GO:0005789)|integral component of endoplasmic reticulum membrane (GO:0030176)				central_nervous_system(2)|kidney(2)|large_intestine(9)|lung(30)|ovary(2)|prostate(1)|skin(2)|urinary_tract(1)	49				OV - Ovarian serous cystadenocarcinoma(108;0.0968)		TGGTGCTTCACCTCCTCGGGT	0.458																																					p.V205L		Atlas-SNP	.											.	RTN1	139	.	0			c.G613T						.						261.0	254.0	257.0					14																	60212828		2203	4300	6503	SO:0001583	missense	6252	exon2			GCTTCACCTCCTC	L10333	CCDS9740.1, CCDS9741.1	14q21-q22	2008-08-29			ENSG00000139970	ENSG00000139970			10467	protein-coding gene	gene with protein product		600865	"""neuroendocrine-specific protein"""	NSP		8275708	Standard	NM_206852		Approved		uc001xen.1	Q16799	OTTHUMG00000028947	ENST00000267484.5:c.613G>T	chr14.hg19:g.60212828C>A	ENSP00000267484:p.Val205Leu	106.0	0.0		92.0	13.0	NM_021136	Q16800|Q16801|Q5BKZ4|Q9BQ59	Missense_Mutation	SNP	ENST00000267484.5	hg19	CCDS9740.1	.	.	.	.	.	.	.	.	.	.	C	5.891	0.348424	0.11126	.	.	ENSG00000139970	ENST00000267484;ENST00000433623	T	0.22336	1.96	5.7	-0.0625	0.13780	.	1.487350	0.03984	N	0.293816	T	0.19366	0.0465	L	0.51422	1.61	0.09310	N	1	B	0.17667	0.023	B	0.09377	0.004	T	0.25745	-1.0123	10	0.28530	T	0.3	.	5.839	0.18623	0.0:0.1995:0.5321:0.2684	.	205	Q16799	RTN1_HUMAN	L	205;131	ENSP00000267484:V205L	ENSP00000267484:V205L	V	-	1	0	RTN1	59282581	0.000000	0.05858	0.020000	0.16555	0.145000	0.21501	0.156000	0.16382	0.309000	0.22966	0.557000	0.71058	GTG	.	.		0.458	RTN1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000072278.2		
PCNX	22990	hgsc.bcm.edu	37	14	71524347	71524347	+	Silent	SNP	C	C	T			TCGA-WJ-A86L-01A-12D-A45V-10	TCGA-WJ-A86L-10A-01D-A38X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	80e4fac9-c066-47a9-9fc0-2a42eef954cd	cebd5a99-cbde-441d-b98a-b84cf1825d65	g.chr14:71524347C>T	ENST00000304743.2	+	26	5204	c.4758C>T	c.(4756-4758)ttC>ttT	p.F1586F	PCNX_ENST00000238570.5_Intron|PCNX_ENST00000439984.3_Silent_p.F1475F	NM_014982.2	NP_055797.2	Q96RV3	PCX1_HUMAN	pecanex homolog (Drosophila)	1586						integral component of membrane (GO:0016021)				NS(2)|biliary_tract(1)|breast(3)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(8)|large_intestine(14)|liver(2)|lung(40)|ovary(1)|prostate(7)|skin(2)|urinary_tract(1)	87			KIRC - Kidney renal clear cell carcinoma(12;0.206)	all cancers(60;0.00835)|BRCA - Breast invasive adenocarcinoma(234;0.00951)|OV - Ovarian serous cystadenocarcinoma(108;0.0417)		GGGACTGTTTCATCCTTGCCT	0.448																																					p.F1586F		Atlas-SNP	.											.	PCNX	198	.	0			c.C4758T						.						339.0	342.0	341.0					14																	71524347		2203	4300	6503	SO:0001819	synonymous_variant	22990	exon26			CTGTTTCATCCTT	AF233450, AB018348	CCDS9806.1	14q24.2	2014-07-03							19740	protein-coding gene	gene with protein product			"""pecanex-like 1 (Drosophila)"""	PCNXL1		9244429, 15777640	Standard	NM_014982		Approved	KIAA0995, KIAA0805, pecanex	uc001xmo.2	Q96RV3		ENST00000304743.2:c.4758C>T	chr14.hg19:g.71524347C>T		91.0	0.0		73.0	28.0	NM_014982	B2RTR6|O94897|Q96AI7|Q9Y2J9	Silent	SNP	ENST00000304743.2	hg19	CCDS9806.1																																																																																			.	.		0.448	PCNX-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000412479.1	NM_014982	
NEK9	91754	hgsc.bcm.edu	37	14	75593444	75593444	+	Missense_Mutation	SNP	C	C	A			TCGA-WJ-A86L-01A-12D-A45V-10	TCGA-WJ-A86L-10A-01D-A38X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	80e4fac9-c066-47a9-9fc0-2a42eef954cd	cebd5a99-cbde-441d-b98a-b84cf1825d65	g.chr14:75593444C>A	ENST00000238616.5	-	1	339	c.181G>T	c.(181-183)Ggc>Tgc	p.G61C	RP11-950C14.7_ENST00000556236.1_RNA	NM_033116.4	NP_149107.4	Q8TD19	NEK9_HUMAN	NIMA-related kinase 9	61	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				mitotic cell cycle (GO:0000278)|mitotic nuclear division (GO:0007067)|mitotic nuclear envelope disassembly (GO:0007077)	cytosol (GO:0005829)|nucleus (GO:0005634)	ATP binding (GO:0005524)|metal ion binding (GO:0046872)|protein kinase binding (GO:0019901)|protein serine/threonine kinase activity (GO:0004674)			endometrium(4)|kidney(2)|large_intestine(4)|lung(13)|ovary(1)|prostate(2)|skin(2)|stomach(2)|upper_aerodigestive_tract(1)	31				BRCA - Breast invasive adenocarcinoma(234;0.00718)		CCGAAGGCGCCGCGGCCCAGG	0.761																																					p.G61C		Atlas-SNP	.											.	NEK9	64	.	0			c.G181T						.						7.0	10.0	9.0					14																	75593444		2001	3888	5889	SO:0001583	missense	91754	exon1			AGGCGCCGCGGCC	AY048580	CCDS9839.1	14q24.2	2012-11-15	2012-11-15		ENSG00000119638	ENSG00000119638			18591	protein-coding gene	gene with protein product		609798	"""NIMA (never in mitosis gene a)- related kinase 9"""			11864968	Standard	NM_033116		Approved	Nek8, NERCC, DKFZp434D0935, MGC16714	uc001xrl.3	Q8TD19	OTTHUMG00000171768	ENST00000238616.5:c.181G>T	chr14.hg19:g.75593444C>A	ENSP00000238616:p.Gly61Cys	160.0	0.0		180.0	83.0	NM_033116	Q52LK6|Q8NCN0|Q8TCY4|Q9UPI4|Q9Y6S4|Q9Y6S5|Q9Y6S6	Missense_Mutation	SNP	ENST00000238616.5	hg19	CCDS9839.1	.	.	.	.	.	.	.	.	.	.	C	31	5.084849	0.94100	.	.	ENSG00000119638	ENST00000238616;ENST00000540227	D	0.85339	-1.97	4.01	3.12	0.35913	Serine/threonine-protein kinase-like domain (1);Serine/threonine-protein kinase, catalytic  domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.059310	0.64402	D	0.000002	D	0.95626	0.8578	H	0.99758	4.755	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.95902	0.8916	10	0.87932	D	0	.	11.8808	0.52574	0.0:0.9138:0.0:0.0862	.	61	Q8TD19	NEK9_HUMAN	C	61;43	ENSP00000238616:G61C	ENSP00000238616:G61C	G	-	1	0	NEK9	74663197	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	6.713000	0.74686	1.016000	0.39470	0.561000	0.74099	GGC	.	.		0.761	NEK9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000415021.1	NM_033116	
HSP90AA1	3320	hgsc.bcm.edu	37	14	102552710	102552710	+	Silent	SNP	A	A	T			TCGA-WJ-A86L-01A-12D-A45V-10	TCGA-WJ-A86L-10A-01D-A38X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	80e4fac9-c066-47a9-9fc0-2a42eef954cd	cebd5a99-cbde-441d-b98a-b84cf1825d65	g.chr14:102552710A>T	ENST00000216281.8	-	2	211	c.6T>A	c.(4-6)ccT>ccA	p.P2P	HSP90AA1_ENST00000441629.2_5'Flank|HSP90AA1_ENST00000334701.7_Silent_p.P124P	NM_005348.3	NP_005339.3	P07900	HS90A_HUMAN	heat shock protein 90kDa alpha (cytosolic), class A member 1	2					ATP catabolic process (GO:0006200)|axon guidance (GO:0007411)|chaperone-mediated protein complex assembly (GO:0051131)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|G2/M transition of mitotic cell cycle (GO:0000086)|innate immune response (GO:0045087)|mitochondrial transport (GO:0006839)|mitotic cell cycle (GO:0000278)|nitric oxide metabolic process (GO:0046209)|positive regulation of nitric oxide biosynthetic process (GO:0045429)|protein import into mitochondrial outer membrane (GO:0045040)|protein refolding (GO:0042026)|regulation of nitric-oxide synthase activity (GO:0050999)|response to unfolded protein (GO:0006986)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|endocytic vesicle lumen (GO:0071682)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|mitochondrion (GO:0005739)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|identical protein binding (GO:0042802)|MHC class II protein complex binding (GO:0023026)|nitric-oxide synthase regulator activity (GO:0030235)|nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)|protein homodimerization activity (GO:0042803)|TPR domain binding (GO:0030911)			breast(1)|central_nervous_system(2)|endometrium(2)|kidney(6)|large_intestine(3)|liver(1)|lung(10)|ovary(2)|prostate(1)	28					Nedocromil(DB00716)|Rifabutin(DB00615)	GGGTTTCCTCAGGCATCTGGA	0.488																																					p.P124P		Atlas-SNP	.											.	HSP90AA1	65	.	0			c.T372A						.						88.0	90.0	90.0					14																	102552710		2203	4300	6503	SO:0001819	synonymous_variant	3320	exon3			TTCCTCAGGCATC	M27024	CCDS9967.1, CCDS32160.1	14q32.33	2011-09-02	2006-02-24	2006-02-24	ENSG00000080824	ENSG00000080824		"""Heat shock proteins / HSPC"""	5253	protein-coding gene	gene with protein product		140571	"""heat shock 90kD protein 1, alpha"", ""heat shock 90kDa protein 1, alpha"""	HSPC1, HSPCA		2527334, 16269234	Standard	NM_001017963		Approved	Hsp89, Hsp90, FLJ31884, HSP90N	uc001ykv.4	P07900		ENST00000216281.8:c.6T>A	chr14.hg19:g.102552710A>T		124.0	0.0		95.0	32.0	NM_001017963	A8K500|B3KPJ9|Q2PP14|Q5CAQ6|Q5CAQ7|Q9BVQ5	Silent	SNP	ENST00000216281.8	hg19	CCDS9967.1																																																																																			.	.		0.488	HSP90AA1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000414952.2	NM_005348	
INF2	64423	hgsc.bcm.edu	37	14	105180840	105180840	+	Missense_Mutation	SNP	T	T	A			TCGA-WJ-A86L-01A-12D-A45V-10	TCGA-WJ-A86L-10A-01D-A38X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	80e4fac9-c066-47a9-9fc0-2a42eef954cd	cebd5a99-cbde-441d-b98a-b84cf1825d65	g.chr14:105180840T>A	ENST00000392634.4	+	21	3453	c.3341T>A	c.(3340-3342)cTc>cAc	p.L1114H	INF2_ENST00000330634.7_Missense_Mutation_p.L1114H	NM_022489.3	NP_071934.3	Q27J81	INF2_HUMAN	inverted formin, FH2 and WH2 domain containing	1114					actin cytoskeleton organization (GO:0030036)|cell death (GO:0008219)|regulation of cellular component size (GO:0032535)|regulation of mitochondrial fission (GO:0090140)	cytoplasm (GO:0005737)|endoplasmic reticulum (GO:0005783)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)				large_intestine(3)|lung(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	8		all_cancers(154;0.0896)|Melanoma(154;0.155)|all_epithelial(191;0.172)	all cancers(16;0.00188)|OV - Ovarian serous cystadenocarcinoma(23;0.0191)|Epithelial(46;0.047)|GBM - Glioblastoma multiforme(11;0.116)	Epithelial(152;0.176)		CTGAAGCCCCTCAAGTTCTCC	0.652																																					p.L1114H		Atlas-SNP	.											.	INF2	148	.	0			c.T3341A						.						34.0	41.0	39.0					14																	105180840		2020	4172	6192	SO:0001583	missense	64423	exon21			AGCCCCTCAAGTT	AK025709	CCDS9989.2, CCDS45173.1	14q32.33	2009-09-07	2007-11-29	2007-11-29	ENSG00000203485	ENSG00000203485			23791	protein-coding gene	gene with protein product	"""inverted formin 2"""	610982	"""chromosome 14 open reading frame 151"", ""chromosome 14 open reading frame 173"""	C14orf151, C14orf173		16818491	Standard	NM_001031714		Approved	MGC13251	uc001ypb.2	Q27J81	OTTHUMG00000029811	ENST00000392634.4:c.3341T>A	chr14.hg19:g.105180840T>A	ENSP00000376410:p.Leu1114His	50.0	0.0		75.0	32.0	NM_022489	Q27J83|Q69YL8|Q6P1X7|Q6PK22|Q86TR7|Q9BRM1|Q9H6N1	Missense_Mutation	SNP	ENST00000392634.4	hg19	CCDS9989.2	.	.	.	.	.	.	.	.	.	.	T	14.51	2.555781	0.45487	.	.	ENSG00000203485	ENST00000330634;ENST00000392634	D;D	0.82167	-1.57;-1.58	5.0	5.0	0.66597	.	0.599365	0.12676	U	0.448421	D	0.83427	0.5252	L	0.32530	0.975	0.24797	N	0.992729	D;D	0.61697	0.99;0.983	P;P	0.56474	0.799;0.635	T	0.74836	-0.3529	10	0.72032	D	0.01	.	11.0831	0.48072	0.0:0.0:0.0:1.0	.	1114;1114	Q27J81-2;Q27J81	.;INF2_HUMAN	H	1114	ENSP00000376406:L1114H;ENSP00000376410:L1114H	ENSP00000252527:L582H	L	+	2	0	INF2	104251885	0.577000	0.26708	0.066000	0.19879	0.948000	0.59901	2.211000	0.42825	1.871000	0.54225	0.482000	0.46254	CTC	.	.		0.652	INF2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000074371.4	NM_022489	
NIPA1	123606	hgsc.bcm.edu	37	15	23049159	23049159	+	Silent	SNP	G	G	A			TCGA-WJ-A86L-01A-12D-A45V-10	TCGA-WJ-A86L-10A-01D-A38X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	80e4fac9-c066-47a9-9fc0-2a42eef954cd	cebd5a99-cbde-441d-b98a-b84cf1825d65	g.chr15:23049159G>A	ENST00000337435.4	-	5	684	c.660C>T	c.(658-660)aaC>aaT	p.N220N	NIPA1_ENST00000437912.2_Silent_p.N145N|NIPA1_ENST00000538684.1_Silent_p.N50N|NIPA1_ENST00000561183.1_Silent_p.N145N	NM_001142275.1|NM_144599.4	NP_001135747.1|NP_653200.2	Q7RTP0	NIPA1_HUMAN	non imprinted in Prader-Willi/Angelman syndrome 1	220					cell death (GO:0008219)	early endosome (GO:0005769)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	magnesium ion transmembrane transporter activity (GO:0015095)			endometrium(2)|kidney(2)|large_intestine(1)|lung(9)|skin(1)	15		all_cancers(20;2.26e-25)|all_epithelial(15;2.1e-22)|Lung NSC(15;3.36e-17)|all_lung(15;1.04e-16)|Breast(32;0.000776)|Colorectal(260;0.0488)		all cancers(64;4.18e-06)|Epithelial(43;3.97e-05)|BRCA - Breast invasive adenocarcinoma(123;0.00165)		GACTGGACGGGTTGTTATGCA	0.582																																					p.N220N		Atlas-SNP	.											.	NIPA1	26	.	0			c.C660T						.						115.0	98.0	104.0					15																	23049159		2203	4300	6503	SO:0001819	synonymous_variant	123606	exon5			GGACGGGTTGTTA	BK001020	CCDS73691.1, CCDS73692.1	15q11.2	2006-10-06			ENSG00000170113	ENSG00000170113			17043	protein-coding gene	gene with protein product		608145	"""spastic paraplegia 6 (autosomal dominant)"""	SPG6		14508710	Standard	NM_144599		Approved	MGC35570	uc001yvc.3	Q7RTP0	OTTHUMG00000129099	ENST00000337435.4:c.660C>T	chr15.hg19:g.23049159G>A		95.0	0.0		73.0	30.0	NM_144599	B2RA76|Q5HYA9|Q7KZB0|Q86XW4	Silent	SNP	ENST00000337435.4	hg19	CCDS10011.1																																																																																			.	.		0.582	NIPA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251135.2	NM_144599	
AQR	9716	hgsc.bcm.edu	37	15	35196558	35196558	+	Silent	SNP	T	T	C			TCGA-WJ-A86L-01A-12D-A45V-10	TCGA-WJ-A86L-10A-01D-A38X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	80e4fac9-c066-47a9-9fc0-2a42eef954cd	cebd5a99-cbde-441d-b98a-b84cf1825d65	g.chr15:35196558T>C	ENST00000156471.5	-	19	2205	c.1980A>G	c.(1978-1980)aaA>aaG	p.K660K		NM_014691.2	NP_055506.1	O60306	AQR_HUMAN	aquarius intron-binding spliceosomal factor	660					mRNA splicing, via spliceosome (GO:0000398)	catalytic step 2 spliceosome (GO:0071013)|membrane (GO:0016020)|nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)			breast(1)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(10)|lung(18)|ovary(1)|prostate(6)|skin(4)|upper_aerodigestive_tract(2)	57		Lung NSC(122;8.7e-10)|all_lung(180;1.47e-08)		all cancers(64;4.34e-18)|GBM - Glioblastoma multiforme(113;4.59e-07)|BRCA - Breast invasive adenocarcinoma(123;0.0283)		TTTCCTTTGGTTTTCTCCTCA	0.289																																					p.K660K		Atlas-SNP	.											.	AQR	139	.	0			c.A1980G						.						82.0	76.0	78.0					15																	35196558		1788	4057	5845	SO:0001819	synonymous_variant	9716	exon19			CTTTGGTTTTCTC	AB011132	CCDS42013.1	15q13	2013-09-12	2013-09-12			ENSG00000021776			29513	protein-coding gene	gene with protein product	"""functional spliceosome-associated protein 164"""	610548	"""aquarius homolog (mouse)"""			9626505, 16949364	Standard	NM_014691		Approved	KIAA0560, fSAP164, IBP160	uc001ziv.3	O60306		ENST00000156471.5:c.1980A>G	chr15.hg19:g.35196558T>C		65.0	0.0		96.0	41.0	NM_014691	A0JP17|A5YKK3|Q2YDX9|Q6IRU8|Q6PIC8	Silent	SNP	ENST00000156471.5	hg19	CCDS42013.1																																																																																			.	.		0.289	AQR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000417526.2	NM_014691	
MYO1E	4643	hgsc.bcm.edu	37	15	59480390	59480390	+	Missense_Mutation	SNP	C	C	T			TCGA-WJ-A86L-01A-12D-A45V-10	TCGA-WJ-A86L-10A-01D-A38X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	80e4fac9-c066-47a9-9fc0-2a42eef954cd	cebd5a99-cbde-441d-b98a-b84cf1825d65	g.chr15:59480390C>T	ENST00000288235.4	-	18	2230	c.1831G>A	c.(1831-1833)Ggt>Agt	p.G611S		NM_004998.3	NP_004989.2	Q12965	MYO1E_HUMAN	myosin IE	611	Myosin motor.				actin filament-based movement (GO:0030048)|ATP catabolic process (GO:0006200)|endocytosis (GO:0006897)|glomerular basement membrane development (GO:0032836)|glomerular filtration (GO:0003094)|glomerular visceral epithelial cell development (GO:0072015)|in utero embryonic development (GO:0001701)|platelet-derived growth factor receptor signaling pathway (GO:0048008)|post-embryonic hemopoiesis (GO:0035166)|vasculogenesis (GO:0001570)	actin cytoskeleton (GO:0015629)|adherens junction (GO:0005912)|cell-cell junction (GO:0005911)|cytoplasm (GO:0005737)|cytoplasmic vesicle (GO:0031410)|cytoskeleton (GO:0005856)|extracellular vesicular exosome (GO:0070062)|myosin complex (GO:0016459)	actin filament binding (GO:0051015)|ATP binding (GO:0005524)|ATPase activity, coupled (GO:0042623)|calmodulin binding (GO:0005516)|microfilament motor activity (GO:0000146)|motor activity (GO:0003774)|phosphatidylinositol binding (GO:0035091)			breast(1)|central_nervous_system(3)|endometrium(5)|kidney(4)|large_intestine(6)|lung(10)|pancreas(2)|prostate(1)|urinary_tract(1)	33				all cancers(107;0.207)		TCTTTCAGACCCAAATATTCG	0.458																																					p.G611S		Atlas-SNP	.											.	MYO1E	99	.	0			c.G1831A						.						153.0	145.0	148.0					15																	59480390		2191	4291	6482	SO:0001583	missense	4643	exon18			TCAGACCCAAATA	U14391	CCDS32254.1	15q21-q22	2011-09-27				ENSG00000157483		"""Myosins / Myosin superfamily : Class I"""	7599	protein-coding gene	gene with protein product	"""myosin-IC"""	601479				8884266	Standard	NM_004998		Approved	MYO1C, HuncM-IC, MGC104638	uc002aga.4	Q12965		ENST00000288235.4:c.1831G>A	chr15.hg19:g.59480390C>T	ENSP00000288235:p.Gly611Ser	46.0	0.0		46.0	25.0	NM_004998	Q14778	Missense_Mutation	SNP	ENST00000288235.4	hg19	CCDS32254.1	.	.	.	.	.	.	.	.	.	.	C	35	5.418885	0.96092	.	.	ENSG00000157483	ENST00000288235	D	0.98666	-5.06	4.82	4.82	0.62117	Myosin head, motor domain (2);	0.000000	0.85682	D	0.000000	D	0.99296	0.9754	M	0.91510	3.215	0.80722	D	1	D	0.76494	0.999	D	0.77004	0.989	D	0.98977	1.0803	10	0.87932	D	0	.	17.7194	0.88347	0.0:1.0:0.0:0.0	.	611	Q12965	MYO1E_HUMAN	S	611	ENSP00000288235:G611S	ENSP00000288235:G611S	G	-	1	0	MYO1E	57267682	1.000000	0.71417	1.000000	0.80357	0.948000	0.59901	7.556000	0.82233	2.503000	0.84419	0.655000	0.94253	GGT	.	.		0.458	MYO1E-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000416024.1	NM_004998	
SEMA7A	8482	hgsc.bcm.edu	37	15	74704300	74704300	+	Missense_Mutation	SNP	C	C	T			TCGA-WJ-A86L-01A-12D-A45V-10	TCGA-WJ-A86L-10A-01D-A38X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	80e4fac9-c066-47a9-9fc0-2a42eef954cd	cebd5a99-cbde-441d-b98a-b84cf1825d65	g.chr15:74704300C>T	ENST00000261918.4	-	11	1896	c.1348G>A	c.(1348-1350)Gcc>Acc	p.A450T	SEMA7A_ENST00000543145.2_Missense_Mutation_p.A436T|SEMA7A_ENST00000542748.1_Missense_Mutation_p.A285T	NM_003612.3	NP_003603.1	O75326	SEM7A_HUMAN	semaphorin 7A, GPI membrane anchor (John Milton Hagen blood group)	450	Sema. {ECO:0000255|PROSITE- ProRule:PRU00352}.				axon extension (GO:0048675)|axon guidance (GO:0007411)|immune response (GO:0006955)|inflammatory response (GO:0006954)|integrin-mediated signaling pathway (GO:0007229)|olfactory lobe development (GO:0021988)|osteoblast differentiation (GO:0001649)|positive regulation of axon extension (GO:0045773)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of macrophage cytokine production (GO:0060907)|positive regulation of protein phosphorylation (GO:0001934)|regulation of inflammatory response (GO:0050727)	anchored component of membrane (GO:0031225)|external side of plasma membrane (GO:0009897)|membrane (GO:0016020)|plasma membrane (GO:0005886)	receptor activity (GO:0004872)			breast(3)|central_nervous_system(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(4)|large_intestine(3)|lung(12)|upper_aerodigestive_tract(1)	30						ATGTTGAAGGCGAAGCTGTGC	0.637																																					p.A450T		Atlas-SNP	.											.	SEMA7A	58	.	0			c.G1348A						.						120.0	83.0	95.0					15																	74704300		2197	4296	6493	SO:0001583	missense	8482	exon11			TGAAGGCGAAGCT	AF069493	CCDS10262.1, CCDS53958.1, CCDS53959.1	15q22.3-q23	2014-07-18	2006-02-23		ENSG00000138623	ENSG00000138623		"""Semaphorins"", ""CD molecules"", ""Blood group antigens"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	10741	protein-coding gene	gene with protein product	"""John Milton Hagen blood group"", ""H-Sema K1"""	607961	"""sema domain, immunoglobulin domain (Ig), and GPI membrane anchor, (semaphorin) 7A"", ""sema domain, immunoglobulin domain (Ig), and GPI membrane anchor, (semaphorin) 7A (JMH blood group)"""	SEMAL		9721204	Standard	NM_003612		Approved	H-Sema-L, CD108	uc002axv.3	O75326	OTTHUMG00000139000	ENST00000261918.4:c.1348G>A	chr15.hg19:g.74704300C>T	ENSP00000261918:p.Ala450Thr	56.0	0.0		77.0	15.0	NM_003612	B4DDP7|F5H1S0|Q1XE81|Q1XE82|Q1XE83|Q1XE84|Q3MIY5	Missense_Mutation	SNP	ENST00000261918.4	hg19	CCDS10262.1	.	.	.	.	.	.	.	.	.	.	C	3.830	-0.036002	0.07497	.	.	ENSG00000138623	ENST00000261918;ENST00000543145;ENST00000542748	T;T;T	0.10860	2.83;2.83;2.83	4.5	0.41	0.16387	WD40/YVTN repeat-like-containing domain (1);Semaphorin/CD100 antigen (4);	0.632817	0.15519	N	0.258152	T	0.07908	0.0198	L	0.38175	1.15	0.09310	N	1	B;B	0.33755	0.371;0.424	B;B	0.30782	0.073;0.12	T	0.29336	-1.0015	10	0.31617	T	0.26	-8.3131	9.3934	0.38388	0.0:0.6481:0.0:0.3519	.	436;450	F5H1S0;O75326	.;SEM7A_HUMAN	T	450;436;285	ENSP00000261918:A450T;ENSP00000438966:A436T;ENSP00000441493:A285T	ENSP00000261918:A450T	A	-	1	0	SEMA7A	72491353	0.016000	0.18221	0.002000	0.10522	0.000000	0.00434	0.818000	0.27295	-0.192000	0.10432	-1.579000	0.00862	GCC	.	.		0.637	SEMA7A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000272904.3	NM_003612	
ZNF774	342132	hgsc.bcm.edu	37	15	90903908	90903908	+	Missense_Mutation	SNP	A	A	G			TCGA-WJ-A86L-01A-12D-A45V-10	TCGA-WJ-A86L-10A-01D-A38X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	80e4fac9-c066-47a9-9fc0-2a42eef954cd	cebd5a99-cbde-441d-b98a-b84cf1825d65	g.chr15:90903908A>G	ENST00000354377.3	+	4	1031	c.845A>G	c.(844-846)cAg>cGg	p.Q282R	ZNF774_ENST00000379090.5_Intron	NM_001004309.2	NP_001004309.2	Q6NX45	ZN774_HUMAN	zinc finger protein 774	282					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			breast(1)|cervix(1)|endometrium(2)|large_intestine(4)|lung(4)|prostate(1)|stomach(1)	14	Melanoma(11;0.00551)|Lung NSC(78;0.0158)|all_lung(78;0.0331)		BRCA - Breast invasive adenocarcinoma(143;0.0224)|KIRC - Kidney renal clear cell carcinoma(17;0.138)|Kidney(142;0.194)			ATCACTCACCAGAGGACCCAC	0.512																																					p.Q282R		Atlas-SNP	.											.	ZNF774	35	.	0			c.A845G						.						57.0	60.0	59.0					15																	90903908		2199	4298	6497	SO:0001583	missense	342132	exon4			CTCACCAGAGGAC	BC067279	CCDS32330.1	15q26.1	2013-01-08				ENSG00000196391		"""Zinc fingers, C2H2-type"""	33108	protein-coding gene	gene with protein product							Standard	NM_001004309		Approved	MGC75360	uc002bpk.4	Q6NX45		ENST00000354377.3:c.845A>G	chr15.hg19:g.90903908A>G	ENSP00000346348:p.Gln282Arg	84.0	0.0		61.0	19.0	NM_001004309	A8K020	Missense_Mutation	SNP	ENST00000354377.3	hg19	CCDS32330.1	.	.	.	.	.	.	.	.	.	.	A	13.41	2.228331	0.39399	.	.	ENSG00000196391	ENST00000354377	T	0.21543	2.0	5.52	5.52	0.82312	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	0.000000	0.33834	N	0.004513	T	0.23133	0.0559	L	0.54908	1.71	0.80722	D	1	B	0.18013	0.025	B	0.20384	0.029	T	0.02220	-1.1193	10	0.40728	T	0.16	.	13.571	0.61847	1.0:0.0:0.0:0.0	.	282	Q6NX45	ZN774_HUMAN	R	282	ENSP00000346348:Q282R	ENSP00000346348:Q282R	Q	+	2	0	ZNF774	88704912	0.966000	0.33281	1.000000	0.80357	0.990000	0.78478	0.936000	0.28938	2.103000	0.63969	0.459000	0.35465	CAG	.	.		0.512	ZNF774-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000418048.1	NM_001004309	
SHISA9	729993	hgsc.bcm.edu	37	16	12996468	12996468	+	Missense_Mutation	SNP	A	A	T			TCGA-WJ-A86L-01A-12D-A45V-10	TCGA-WJ-A86L-10A-01D-A38X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	80e4fac9-c066-47a9-9fc0-2a42eef954cd	cebd5a99-cbde-441d-b98a-b84cf1825d65	g.chr16:12996468A>T	ENST00000424107.3	+	1	992	c.547A>T	c.(547-549)Agg>Tgg	p.R183W	SHISA9_ENST00000423335.2_Missense_Mutation_p.R183W|SHISA9_ENST00000558583.1_Missense_Mutation_p.R224W|SHISA9_ENST00000558318.1_Missense_Mutation_p.R224W			B4DS77	SHSA9_HUMAN	shisa family member 9	183					regulation of short-term neuronal synaptic plasticity (GO:0048172)	cell junction (GO:0030054)|dendritic spine membrane (GO:0032591)|ionotropic glutamate receptor complex (GO:0008328)|synapse (GO:0045202)				breast(1)|endometrium(2)|kidney(1)|lung(2)|prostate(1)|skin(2)	9						CCGGCCCCAAAGGGAGCACAT	0.657																																					p.R183W		Atlas-SNP	.											.	SHISA9	33	.	0			c.A547T						.						40.0	48.0	46.0					16																	12996468		692	1591	2283	SO:0001583	missense	729993	exon1			CCCCAAAGGGAGC		CCDS45417.1, CCDS45418.1, CCDS45417.2, CCDS45418.2	16p13.12	2013-07-31	2013-07-31		ENSG00000237515	ENSG00000237515		"""Shisa homologs"""	37231	protein-coding gene	gene with protein product		613346	"""shisa homolog 9 (Xenopus laevis)"""				Standard	NM_001145205		Approved		uc010uyy.2	B4DS77	OTTHUMG00000154258	ENST00000424107.3:c.547A>T	chr16.hg19:g.12996468A>T	ENSP00000407958:p.Arg183Trp	35.0	0.0		59.0	21.0	NM_001145204	C9J314|C9JCE9	Missense_Mutation	SNP	ENST00000424107.3	hg19	CCDS45417.2	.	.	.	.	.	.	.	.	.	.	A	17.42	3.385094	0.61956	.	.	ENSG00000237515	ENST00000424107;ENST00000423335	T	0.46451	0.87	2.81	1.54	0.23209	.	.	.	.	.	T	0.58323	0.2114	M	0.75615	2.305	0.45648	D	0.998575	D;D	0.89917	1.0;0.999	D;D	0.87578	0.998;0.977	T	0.60541	-0.7243	9	0.87932	D	0	.	7.0031	0.24821	0.7708:0.2292:0.0:0.0	.	183;183	B4DS77;B4DS77-3	SHSA9_HUMAN;.	W	224	ENSP00000407958:R224W	ENSP00000395245:R224W	R	+	1	2	SHISA9	12903969	1.000000	0.71417	0.999000	0.59377	0.961000	0.63080	1.952000	0.40343	1.277000	0.44412	0.379000	0.24179	AGG	.	.		0.657	SHISA9-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000334564.5	NM_001145204	
ABCC11	85320	hgsc.bcm.edu	37	16	48232119	48232119	+	Missense_Mutation	SNP	C	C	T			TCGA-WJ-A86L-01A-12D-A45V-10	TCGA-WJ-A86L-10A-01D-A38X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	80e4fac9-c066-47a9-9fc0-2a42eef954cd	cebd5a99-cbde-441d-b98a-b84cf1825d65	g.chr16:48232119C>T	ENST00000394747.1	-	15	2499	c.2150G>A	c.(2149-2151)aGt>aAt	p.S717N	ABCC11_ENST00000356608.2_Missense_Mutation_p.S717N|ABCC11_ENST00000394748.1_Missense_Mutation_p.S717N|ABCC11_ENST00000537808.1_Missense_Mutation_p.S717N|ABCC11_ENST00000353782.5_Missense_Mutation_p.S717N	NM_033151.3	NP_149163.2	Q96J66	ABCCB_HUMAN	ATP-binding cassette, sub-family C (CFTR/MRP), member 11	717	ABC transporter 1. {ECO:0000255|PROSITE- ProRule:PRU00434}.				organic anion transport (GO:0015711)|purine nucleotide transport (GO:0015865)|transmembrane transport (GO:0055085)	extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|ATPase activity, coupled to transmembrane movement of substances (GO:0042626)|organic anion transmembrane transporter activity (GO:0008514)|purine nucleotide transmembrane transporter activity (GO:0015216)			breast(3)|central_nervous_system(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(12)|lung(42)|ovary(3)|prostate(2)|skin(5)|urinary_tract(2)	83		all_cancers(37;0.127)|all_lung(18;0.132)|Breast(268;0.166)			Conjugated Estrogens(DB00286)|Folic Acid(DB00158)|Indomethacin(DB00328)|Methotrexate(DB00563)|Probenecid(DB01032)	CATTAACTCACTGTGAGTTCC	0.438																																					p.S717N		Atlas-SNP	.											.	ABCC11	177	.	0			c.G2150A						.						180.0	168.0	172.0					16																	48232119		2201	4300	6501	SO:0001583	missense	85320	exon15			AACTCACTGTGAG	AF367202	CCDS10732.1, CCDS10733.1	16q12	2012-03-14			ENSG00000121270	ENSG00000121270		"""ATP binding cassette transporters / subfamily C"""	14639	protein-coding gene	gene with protein product		607040				11483364, 11435397	Standard	NM_033151		Approved	MRP8	uc002efg.1	Q96J66	OTTHUMG00000133146	ENST00000394747.1:c.2150G>A	chr16.hg19:g.48232119C>T	ENSP00000378230:p.Ser717Asn	138.0	0.0		126.0	57.0	NM_033151	Q8TDJ0|Q96JA6|Q9BX80	Missense_Mutation	SNP	ENST00000394747.1	hg19	CCDS10732.1	.	.	.	.	.	.	.	.	.	.	C	6.018	0.371661	0.11409	.	.	ENSG00000121270	ENST00000353782;ENST00000356608;ENST00000394748;ENST00000394747;ENST00000537808	T;T;T;T;T	0.65364	-0.15;-0.15;-0.15;-0.15;-0.15	5.69	-2.73	0.05950	ABC transporter-like (1);	0.707775	0.14400	N	0.321945	T	0.36303	0.0962	N	0.13168	0.305	0.09310	N	1	B;B	0.09022	0.002;0.001	B;B	0.09377	0.004;0.003	T	0.12760	-1.0535	10	0.31617	T	0.26	-0.2843	6.5429	0.22390	0.126:0.2515:0.0:0.6225	.	717;717	Q96J66-2;Q96J66	.;ABCCB_HUMAN	N	717	ENSP00000311326:S717N;ENSP00000349017:S717N;ENSP00000378231:S717N;ENSP00000378230:S717N;ENSP00000438530:S717N	ENSP00000311326:S717N	S	-	2	0	ABCC11	46789620	0.000000	0.05858	0.182000	0.23118	0.193000	0.23685	-0.222000	0.09190	-0.464000	0.06963	0.561000	0.74099	AGT	.	.		0.438	ABCC11-004	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000429984.1	NM_032583	
NFAT5	10725	hgsc.bcm.edu	37	16	69727754	69727754	+	Silent	SNP	C	C	T			TCGA-WJ-A86L-01A-12D-A45V-10	TCGA-WJ-A86L-10A-01D-A38X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	80e4fac9-c066-47a9-9fc0-2a42eef954cd	cebd5a99-cbde-441d-b98a-b84cf1825d65	g.chr16:69727754C>T	ENST00000354436.2	+	12	4290	c.3972C>T	c.(3970-3972)ccC>ccT	p.P1324P	NFAT5_ENST00000432919.1_Silent_p.P1342P|NFAT5_ENST00000349945.1_Silent_p.P1248P|NFAT5_ENST00000566899.1_Silent_p.P1248P|NFAT5_ENST00000567239.1_Silent_p.P1341P|NFAT5_ENST00000393742.2_Silent_p.P1248P	NM_006599.3	NP_006590.1	O94916	NFAT5_HUMAN	nuclear factor of activated T-cells 5, tonicity-responsive	1324					cytokine production (GO:0001816)|excretion (GO:0007588)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of calcineurin-NFAT signaling cascade (GO:0070884)|signal transduction (GO:0007165)|transcription from RNA polymerase II promoter (GO:0006366)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	DNA binding (GO:0003677)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.P1342P(1)|p.P1248P(1)		NS(1)|breast(2)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(7)|lung(11)|prostate(3)|skin(3)|upper_aerodigestive_tract(1)	37						AGCAACAGCCCATGCAATTTC	0.463																																					p.P1342P		Atlas-SNP	.											NFAT5_ENST00000432919,NS,carcinoma,0,2	NFAT5	184	.	2	Substitution - coding silent(2)	cervix(2)	c.C4026T						.						94.0	89.0	91.0					16																	69727754		2198	4300	6498	SO:0001819	synonymous_variant	10725	exon13			ACAGCCCATGCAA	AF134870	CCDS10881.1, CCDS10882.1, CCDS45519.1	16q22.1	2009-11-24			ENSG00000102908	ENSG00000102908		"""Nuclear factor of activated T-cells"""	7774	protein-coding gene	gene with protein product		604708				10377394	Standard	NM_173214		Approved	TONEBP, KIAA0827, NFATL1, OREBP, NFATZ, NF-AT5	uc002exl.2	O94916	OTTHUMG00000137572	ENST00000354436.2:c.3972C>T	chr16.hg19:g.69727754C>T		127.0	0.0		71.0	57.0	NM_138713	A2RRB4|A6H8V5|E9PHR7|O95693|Q7LA65|Q969Q8|Q96QH3|Q9UN18	Silent	SNP	ENST00000354436.2	hg19	CCDS10881.1																																																																																			.	.		0.463	NFAT5-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000268952.2	NM_138714	
ZNF232	7775	hgsc.bcm.edu	37	17	5013065	5013065	+	Missense_Mutation	SNP	T	T	C			TCGA-WJ-A86L-01A-12D-A45V-10	TCGA-WJ-A86L-10A-01D-A38X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	80e4fac9-c066-47a9-9fc0-2a42eef954cd	cebd5a99-cbde-441d-b98a-b84cf1825d65	g.chr17:5013065T>C	ENST00000250076.3	-	3	776	c.122A>G	c.(121-123)cAg>cGg	p.Q41R	ZNF232_ENST00000575538.1_5'UTR|ZNF232_ENST00000416429.2_Missense_Mutation_p.Q14R|ZNF232_ENST00000575898.1_Missense_Mutation_p.Q41R|AC012146.7_ENST00000413077.1_RNA|AC012146.7_ENST00000571138.1_RNA	NM_014519.2	NP_055334.2	Q9UNY5	ZN232_HUMAN	zinc finger protein 232	14					transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			kidney(1)|large_intestine(2)|liver(1)|lung(4)|ovary(1)|prostate(2)	11						CTGTGTACCCTGAAGGGCCAG	0.517																																					p.Q41R		Atlas-SNP	.											.	ZNF232	42	.	0			c.A122G						.						151.0	142.0	145.0					17																	5013065		2203	4300	6503	SO:0001583	missense	7775	exon3			GTACCCTGAAGGG	AF080169	CCDS11068.1	17p13.2	2013-01-09			ENSG00000167840	ENSG00000167840		"""-"", ""Zinc fingers, C2H2-type"""	13026	protein-coding gene	gene with protein product						11311944	Standard	NM_014519		Approved	ZSCAN11	uc002gat.3	Q9UNY5	OTTHUMG00000099450	ENST00000250076.3:c.122A>G	chr17.hg19:g.5013065T>C	ENSP00000250076:p.Gln41Arg	73.0	0.0		42.0	31.0	NM_014519		Missense_Mutation	SNP	ENST00000250076.3	hg19	CCDS11068.1	.	.	.	.	.	.	.	.	.	.	T	0.825	-0.747437	0.03065	.	.	ENSG00000167840	ENST00000250076;ENST00000416429	T;T	0.08458	3.09;3.41	3.68	1.39	0.22231	.	0.000000	0.31031	N	0.008395	T	0.03651	0.0104	N	0.08118	0	0.09310	N	1	P;P;P;P	0.40476	0.596;0.596;0.596;0.718	B;B;B;B	0.41174	0.189;0.189;0.189;0.349	T	0.34775	-0.9815	10	0.30078	T	0.28	.	3.0022	0.06017	0.2124:0.1191:0.0:0.6685	.	41;14;14;14	B4DNA7;B4DP49;Q9UNY5;Q9UNY5-2	.;.;ZN232_HUMAN;.	R	41;14	ENSP00000250076:Q41R;ENSP00000416430:Q14R	ENSP00000250076:Q41R	Q	-	2	0	ZNF232	4953789	0.000000	0.05858	0.146000	0.22360	0.141000	0.21300	-0.031000	0.12287	0.138000	0.18790	0.459000	0.35465	CAG	.	.		0.517	ZNF232-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000216915.1	NM_014519	
TP53	7157	hgsc.bcm.edu	37	17	7578239	7578239	+	Nonsense_Mutation	SNP	C	C	A			TCGA-WJ-A86L-01A-12D-A45V-10	TCGA-WJ-A86L-10A-01D-A38X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	80e4fac9-c066-47a9-9fc0-2a42eef954cd	cebd5a99-cbde-441d-b98a-b84cf1825d65	g.chr17:7578239C>A	ENST00000269305.4	-	6	799	c.610G>T	c.(610-612)Gag>Tag	p.E204*	TP53_ENST00000455263.2_Nonsense_Mutation_p.E204*|TP53_ENST00000574684.1_Intron|TP53_ENST00000420246.2_Nonsense_Mutation_p.E204*|TP53_ENST00000445888.2_Nonsense_Mutation_p.E204*|TP53_ENST00000413465.2_Nonsense_Mutation_p.E204*|TP53_ENST00000359597.4_Nonsense_Mutation_p.E204*	NM_000546.5|NM_001126112.2|NM_001126118.1|NM_001276760.1|NM_001276761.1	NP_000537.3|NP_001119584.1|NP_001119590.1|NP_001263689.1|NP_001263690.1	P04637	P53_HUMAN	tumor protein p53	204	Interaction with AXIN1. {ECO:0000250}.|Interaction with HIPK1. {ECO:0000250}.|Required for interaction with FBXO42.|Required for interaction with ZNF385A.		E -> A (in sporadic cancers; somatic mutation).|E -> D (in sporadic cancers; somatic mutation).|E -> G (in sporadic cancers; somatic mutation).|E -> K (in sporadic cancers; somatic mutation).|E -> Q (in a sporadic cancer; somatic mutation).|E -> V (in a sporadic cancer; somatic mutation).|VE -> LV (in a sporadic cancer; somatic mutation).		apoptotic process (GO:0006915)|B cell lineage commitment (GO:0002326)|base-excision repair (GO:0006284)|blood coagulation (GO:0007596)|cell aging (GO:0007569)|cell cycle arrest (GO:0007050)|cell differentiation (GO:0030154)|cell proliferation (GO:0008283)|cellular protein localization (GO:0034613)|cellular response to DNA damage stimulus (GO:0006974)|cellular response to drug (GO:0035690)|cellular response to glucose starvation (GO:0042149)|cellular response to hypoxia (GO:0071456)|cellular response to ionizing radiation (GO:0071479)|cellular response to UV (GO:0034644)|cerebellum development (GO:0021549)|chromatin assembly (GO:0031497)|determination of adult lifespan (GO:0008340)|DNA damage response, signal transduction by p53 class mediator (GO:0030330)|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest (GO:0006977)|DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator (GO:0006978)|DNA strand renaturation (GO:0000733)|double-strand break repair (GO:0006302)|embryonic organ development (GO:0048568)|ER overload response (GO:0006983)|gastrulation (GO:0007369)|in utero embryonic development (GO:0001701)|intrinsic apoptotic signaling pathway (GO:0097193)|intrinsic apoptotic signaling pathway by p53 class mediator (GO:0072332)|intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator (GO:0042771)|mitotic cell cycle arrest (GO:0071850)|mitotic G1 DNA damage checkpoint (GO:0031571)|multicellular organism growth (GO:0035264)|multicellular organismal development (GO:0007275)|necroptotic process (GO:0070266)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cell growth (GO:0030308)|negative regulation of cell proliferation (GO:0008285)|negative regulation of DNA replication (GO:0008156)|negative regulation of fibroblast proliferation (GO:0048147)|negative regulation of helicase activity (GO:0051097)|negative regulation of macromitophagy (GO:1901525)|negative regulation of neuroblast proliferation (GO:0007406)|negative regulation of reactive oxygen species metabolic process (GO:2000378)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|negative regulation of transforming growth factor beta receptor signaling pathway (GO:0030512)|neuron apoptotic process (GO:0051402)|Notch signaling pathway (GO:0007219)|nucleotide-excision repair (GO:0006289)|oligodendrocyte apoptotic process (GO:0097252)|oxidative stress-induced premature senescence (GO:0090403)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cardiac muscle cell apoptotic process (GO:0010666)|positive regulation of cell aging (GO:0090343)|positive regulation of cell cycle arrest (GO:0071158)|positive regulation of histone deacetylation (GO:0031065)|positive regulation of intrinsic apoptotic signaling pathway (GO:2001244)|positive regulation of mitochondrial membrane permeability (GO:0035794)|positive regulation of neuron apoptotic process (GO:0043525)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|positive regulation of protein insertion into mitochondrial membrane involved in apoptotic signaling pathway (GO:1900740)|positive regulation of protein oligomerization (GO:0032461)|positive regulation of reactive oxygen species metabolic process (GO:2000379)|positive regulation of release of cytochrome c from mitochondria (GO:0090200)|positive regulation of thymocyte apoptotic process (GO:0070245)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|protein complex assembly (GO:0006461)|protein import into nucleus, translocation (GO:0000060)|protein localization (GO:0008104)|protein tetramerization (GO:0051262)|Ras protein signal transduction (GO:0007265)|regulation of apoptotic process (GO:0042981)|regulation of mitochondrial membrane permeability (GO:0046902)|regulation of mitochondrial membrane permeability involved in apoptotic process (GO:1902108)|regulation of tissue remodeling (GO:0034103)|regulation of transcription, DNA-templated (GO:0006355)|release of cytochrome c from mitochondria (GO:0001836)|replicative senescence (GO:0090399)|response to antibiotic (GO:0046677)|response to gamma radiation (GO:0010332)|response to ischemia (GO:0002931)|response to salt stress (GO:0009651)|response to X-ray (GO:0010165)|rRNA transcription (GO:0009303)|somitogenesis (GO:0001756)|T cell differentiation in thymus (GO:0033077)|T cell lineage commitment (GO:0002360)|T cell proliferation involved in immune response (GO:0002309)|transforming growth factor beta receptor signaling pathway (GO:0007179)|viral process (GO:0016032)	chromatin (GO:0000785)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)|nuclear chromatin (GO:0000790)|nuclear matrix (GO:0016363)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|PML body (GO:0016605)|protein complex (GO:0043234)|replication fork (GO:0005657)	ATP binding (GO:0005524)|chaperone binding (GO:0051087)|chromatin binding (GO:0003682)|copper ion binding (GO:0005507)|damaged DNA binding (GO:0003684)|DNA binding (GO:0003677)|enzyme binding (GO:0019899)|histone acetyltransferase binding (GO:0035035)|histone deacetylase regulator activity (GO:0035033)|identical protein binding (GO:0042802)|p53 binding (GO:0002039)|protease binding (GO:0002020)|protein heterodimerization activity (GO:0046982)|protein kinase binding (GO:0019901)|protein N-terminus binding (GO:0047485)|protein phosphatase 2A binding (GO:0051721)|protein phosphatase binding (GO:0019903)|receptor tyrosine kinase binding (GO:0030971)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|RNA polymerase II core promoter sequence-specific DNA binding (GO:0000979)|RNA polymerase II transcription factor binding (GO:0001085)|RNA polymerase II transcription regulatory region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001228)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription factor binding (GO:0008134)|transcription regulatory region DNA binding (GO:0044212)|ubiquitin protein ligase binding (GO:0031625)|zinc ion binding (GO:0008270)	p.E204*(33)|p.0?(8)|p.?(5)|p.E72*(3)|p.E111*(3)|p.E204K(2)|p.E204fs*43(2)|p.E204Q(1)|p.E204fs*4(1)|p.V203_E204>V*(1)|p.V203_E204>LV(1)|p.E204fs*39(1)|p.G199fs*42(1)|p.E204_N210delEYLDDRN(1)		NS(16)|adrenal_gland(37)|autonomic_ganglia(16)|biliary_tract(273)|bone(108)|breast(2530)|central_nervous_system(1264)|cervix(68)|endometrium(223)|eye(24)|fallopian_tube(1)|gastrointestinal_tract_(site_indeterminate)(1)|genital_tract(16)|haematopoietic_and_lymphoid_tissue(1301)|kidney(96)|large_intestine(5124)|liver(897)|lung(2388)|meninges(5)|oesophagus(1473)|ovary(1659)|pancreas(452)|penis(10)|peritoneum(33)|pituitary(4)|placenta(1)|pleura(3)|prostate(235)|salivary_gland(43)|skin(791)|small_intestine(14)|soft_tissue(220)|stomach(1158)|testis(11)|thymus(21)|thyroid(54)|upper_aerodigestive_tract(2271)|urinary_tract(1259)|vagina(6)|vulva(79)	24185		all_cancers(10;1.01e-06)|Myeloproliferative disorder(207;0.0122)|Prostate(122;0.081)		GBM - Glioblastoma multiforme(2;1.59e-06)|READ - Rectum adenocarcinoma(115;0.174)	Acetylsalicylic acid(DB00945)	TCCAAATACTCCACACGCAAA	0.542		111	"""Mis, N, F"""		"""breast, colorectal, lung, sarcoma, adrenocortical, glioma, multiple other tumour types"""	"""breast, sarcoma, adrenocortical carcinoma, glioma, multiple other tumour types"""		Other conserved DNA damage response genes	Osteosarcoma, Familial Clustering of;Li-Fraumeni syndrome;Hereditary Breast-Ovarian Cancer, non-BRCA1/2;Hereditary Adrenocortical Cancer;Endometrial Cancer, Familial Clustering of	HNSCC(1;<9.43e-08)|TCGA GBM(1;<1E-08)|TSP Lung(2;<1E-08)|TCGA Ovarian(1;<1.89e-07)|Multiple Myeloma(5;0.019)																											p.E204X	Pancreas(47;798 1329 9957 10801)	Atlas-SNP	.	yes	Rec	yes	Li-Fraumeni syndrome	17	17p13	7157	tumor protein p53		"""L, E, M, O"""	TP53_ENST00000545858,NS,carcinoma,+2,65	TP53	33396	.	63	Substitution - Nonsense(39)|Whole gene deletion(8)|Deletion - Frameshift(5)|Unknown(5)|Substitution - Missense(3)|Complex - compound substitution(2)|Deletion - In frame(1)	lung(15)|haematopoietic_and_lymphoid_tissue(7)|large_intestine(6)|upper_aerodigestive_tract(5)|biliary_tract(5)|NS(5)|breast(4)|bone(4)|oesophagus(3)|ovary(3)|central_nervous_system(2)|stomach(1)|liver(1)|urinary_tract(1)|pancreas(1)	c.G610T						.						133.0	118.0	123.0					17																	7578239		2203	4300	6503	SO:0001587	stop_gained	7157	exon6	Familial Cancer Database	Familial Osteogenic Sarcoma;LFS, SBLA syndrome (Sarcoma Breast Leukemia Adrenal cancer), incl.: Cancer with In Vitro Radioresistence, Familial, Li-Fraumeni-like s.;BRCAX;Familial Adrenocortical Carcinoma;	AATACTCCACACG	AF307851	CCDS11118.1, CCDS45605.1, CCDS45606.1, CCDS73963.1, CCDS73964.1, CCDS73965.1, CCDS73966.1, CCDS73967.1, CCDS73968.1, CCDS73969.1, CCDS73970.1, CCDS73971.1	17p13.1	2014-09-17	2008-01-16		ENSG00000141510	ENSG00000141510			11998	protein-coding gene	gene with protein product	"""Li-Fraumeni syndrome"""	191170				6396087, 3456488, 2047879	Standard	NM_001126115		Approved	p53, LFS1	uc002gij.3	P04637	OTTHUMG00000162125	ENST00000269305.4:c.610G>T	chr17.hg19:g.7578239C>A	ENSP00000269305:p.Glu204*	147.0	0.0		61.0	50.0	NM_000546	Q15086|Q15087|Q15088|Q16535|Q16807|Q16808|Q16809|Q16810|Q16811|Q16848|Q2XN98|Q3LRW1|Q3LRW2|Q3LRW3|Q3LRW4|Q3LRW5|Q86UG1|Q8J016|Q99659|Q9BTM4|Q9HAQ8|Q9NP68|Q9NPJ2|Q9NZD0|Q9UBI2|Q9UQ61	Nonsense_Mutation	SNP	ENST00000269305.4	hg19	CCDS11118.1	.	.	.	.	.	.	.	.	.	.	C	14.28	2.489037	0.44249	.	.	ENSG00000141510	ENST00000413465;ENST00000359597;ENST00000269305;ENST00000455263;ENST00000420246;ENST00000445888;ENST00000396473;ENST00000545858;ENST00000509690;ENST00000514944;ENST00000414315	.	.	.	5.41	-0.604	0.11626	.	0.445020	0.26082	N	0.026458	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.49607	T	0.09	-5.2849	1.4244	0.02320	0.133:0.2829:0.3261:0.258	.	.	.	.	X	204;204;204;204;204;204;193;111;72;111;72	.	ENSP00000269305:E204X	E	-	1	0	TP53	7518964	0.600000	0.26899	0.018000	0.16275	0.030000	0.12068	0.945000	0.29056	-0.004000	0.14419	0.655000	0.94253	GAG	.	.		0.542	TP53-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000367397.1	NM_000546	
HEATR9	256957	hgsc.bcm.edu	37	17	34183788	34183788	+	Nonsense_Mutation	SNP	G	G	A			TCGA-WJ-A86L-01A-12D-A45V-10	TCGA-WJ-A86L-10A-01D-A38X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	80e4fac9-c066-47a9-9fc0-2a42eef954cd	cebd5a99-cbde-441d-b98a-b84cf1825d65	g.chr17:34183788G>A	ENST00000311880.2	-	12	1322	c.1174C>T	c.(1174-1176)Caa>Taa	p.Q392*	C17orf66_ENST00000592980.1_Nonsense_Mutation_p.Q352*	NM_152781.2	NP_689994.2	A2RTY3	HEAT9_HUMAN		392					hematopoietic progenitor cell differentiation (GO:0002244)					breast(3)|central_nervous_system(1)|cervix(2)|endometrium(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(6)|large_intestine(6)|lung(11)|skin(2)|stomach(4)	38		Ovarian(249;0.17)		UCEC - Uterine corpus endometrioid carcinoma (308;0.0184)		TCCACAGTTTGAGCCACAGCC	0.527																																					p.Q392X		Atlas-SNP	.											.	C17orf66	57	.	0			c.C1174T						.						51.0	44.0	47.0					17																	34183788		2203	4300	6503	SO:0001587	stop_gained	256957	exon12			CAGTTTGAGCCAC																												ENST00000311880.2:c.1174C>T	chr17.hg19:g.34183788G>A	ENSP00000309560:p.Gln392*	30.0	0.0		40.0	15.0	NM_152781	B4DX21|B4DXA4|B4DXF0|Q8N4R4|Q96M46	Nonsense_Mutation	SNP	ENST00000311880.2	hg19	CCDS11299.1	.	.	.	.	.	.	.	.	.	.	G	16.99	3.274961	0.59649	.	.	ENSG00000172653	ENST00000311880	.	.	.	4.05	0.934	0.19477	.	0.552277	0.15382	N	0.265292	.	.	.	.	.	.	0.53005	D	0.999968	.	.	.	.	.	.	.	.	.	.	0.27082	T	0.32	.	4.2399	0.10643	0.0:0.5865:0.1962:0.2174	.	.	.	.	X	392	.	ENSP00000309560:Q392X	Q	-	1	0	C17orf66	31207901	0.985000	0.35326	0.728000	0.30774	0.386000	0.30323	0.131000	0.15870	0.133000	0.18654	-0.841000	0.03054	CAA	.	.		0.527	C17orf66-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256487.1		
PIGW	284098	hgsc.bcm.edu	37	17	34893593	34893593	+	Missense_Mutation	SNP	G	G	A			TCGA-WJ-A86L-01A-12D-A45V-10	TCGA-WJ-A86L-10A-01D-A38X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	80e4fac9-c066-47a9-9fc0-2a42eef954cd	cebd5a99-cbde-441d-b98a-b84cf1825d65	g.chr17:34893593G>A	ENST00000592983.1	+	2	1223	c.643G>A	c.(643-645)Gga>Aga	p.G215R	MYO19_ENST00000586007.1_5'Flank|MYO19_ENST00000590081.1_Intron|MYO19_ENST00000268852.9_5'Flank|PIGW_ENST00000328396.2_Missense_Mutation_p.G215R|MYO19_ENST00000544606.1_5'Flank|MYO19_ENST00000431794.3_5'Flank			Q7Z7B1	PIGW_HUMAN	phosphatidylinositol glycan anchor biosynthesis, class W	215					C-terminal protein lipidation (GO:0006501)|cellular protein metabolic process (GO:0044267)|post-translational protein modification (GO:0043687)|preassembly of GPI anchor in ER membrane (GO:0016254)	endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)	transferase activity, transferring acyl groups (GO:0016746)			breast(2)|endometrium(3)|kidney(1)|large_intestine(1)|lung(3)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	13		Breast(25;0.00957)|Ovarian(249;0.17)	Kidney(155;0.104)	UCEC - Uterine corpus endometrioid carcinoma (308;0.0182)		CCTAGGAATCGGACGATTAGC	0.358																																					p.G215R		Atlas-SNP	.											.	PIGW	50	.	0			c.G643A						.						100.0	104.0	103.0					17																	34893593		2203	4300	6503	SO:0001583	missense	284098	exon2			GGAATCGGACGAT	AB097818	CCDS11313.1	17q21.1	2014-05-06	2006-06-28		ENSG00000184886	ENSG00000277161		"""Phosphatidylinositol glycan anchor biosynthesis"""	23213	protein-coding gene	gene with protein product		610275	"""phosphatidylinositol glycan, class W"""			14517336, 12714589	Standard	XM_005257238		Approved	Gwt1, FLJ37433	uc002hmz.1	Q7Z7B1	OTTHUMG00000188438	ENST00000592983.1:c.643G>A	chr17.hg19:g.34893593G>A	ENSP00000468778:p.Gly215Arg	132.0	0.0		187.0	53.0	NM_178517	Q8N9G3	Missense_Mutation	SNP	ENST00000592983.1	hg19	CCDS11313.1	.	.	.	.	.	.	.	.	.	.	G	17.06	3.293729	0.60086	.	.	ENSG00000184886	ENST00000328396	.	.	.	5.59	5.59	0.84812	.	0.193818	0.43260	D	0.000596	D	0.83857	0.5345	M	0.84846	2.72	0.54753	D	0.999981	D	0.89917	1.0	D	0.73708	0.981	D	0.85025	0.0914	8	.	.	.	-9.1117	18.5841	0.91182	0.0:0.0:1.0:0.0	.	215	Q7Z7B1	PIGW_HUMAN	R	215	.	.	G	+	1	0	PIGW	31967706	1.000000	0.71417	0.952000	0.39060	0.920000	0.55202	6.034000	0.70933	2.631000	0.89168	0.561000	0.74099	GGA	.	.		0.358	PIGW-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000451318.1	NM_178517	
SYNRG	11276	hgsc.bcm.edu	37	17	35945538	35945538	+	Splice_Site	SNP	C	C	T			TCGA-WJ-A86L-01A-12D-A45V-10	TCGA-WJ-A86L-10A-01D-A38X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	80e4fac9-c066-47a9-9fc0-2a42eef954cd	cebd5a99-cbde-441d-b98a-b84cf1825d65	g.chr17:35945538C>T	ENST00000339208.6	-	5	512	c.372G>A	c.(370-372)caG>caA	p.Q124Q	SYNRG_ENST00000394378.2_Splice_Site_p.Q124Q|SYNRG_ENST00000345615.4_Splice_Site_p.Q124Q|SYNRG_ENST00000502449.2_Splice_Site_p.Q124Q|SYNRG_ENST00000346661.4_Splice_Site_p.Q124Q|SYNRG_ENST00000585472.1_Splice_Site_p.Q123Q|SYNRG_ENST00000591288.1_Splice_Site_p.Q124Q	NM_001163544.1|NM_001163545.1|NM_007247.4	NP_001157016.1|NP_001157017.1|NP_009178.3	Q9UMZ2	SYNRG_HUMAN	synergin, gamma	124					endocytosis (GO:0006897)|intracellular protein transport (GO:0006886)	AP-1 adaptor complex (GO:0030121)|cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)	calcium ion binding (GO:0005509)			breast(1)|endometrium(3)|kidney(3)|large_intestine(6)|lung(14)|ovary(2)|prostate(1)|skin(3)|upper_aerodigestive_tract(2)|urinary_tract(1)	36						CAAATCGTTTCCTGAAGGAAA	0.373																																					p.Q124Q		Atlas-SNP	.											.	SYNRG	101	.	0			c.G372A						.						97.0	100.0	99.0					17																	35945538		2203	4300	6503	SO:0001630	splice_region_variant	11276	exon5			TCGTTTCCTGAAG	AF169548	CCDS11321.1, CCDS11322.1, CCDS11322.2, CCDS54113.1, CCDS54114.1, CCDS59284.1, CCDS59285.1	17q12	2014-04-16	2009-07-20	2009-07-20	ENSG00000006114	ENSG00000275066			557	protein-coding gene	gene with protein product	"""gamma-synergin"", ""adaptor-related protein complex 1 gamma subunit-binding protein 1"""	607291	"""AP1 gamma subunit binding protein 1"""	AP1GBP1		10477754	Standard	XM_005256980		Approved	SYNG, MGC104959	uc010wdf.2	Q9UMZ2	OTTHUMG00000188473	ENST00000339208.6:c.372-1G>A	chr17.hg19:g.35945538C>T		31.0	0.0		42.0	14.0	NM_001163544	A8MWU4|B7ZKZ2|B7ZKZ3|Q17RI2|Q5BKU5|Q6ZT17	Silent	SNP	ENST00000339208.6	hg19	CCDS11321.1																																																																																			.	.		0.373	SYNRG-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000256811.2	NM_007247	Silent
ATP6V0A1	535	hgsc.bcm.edu	37	17	40620123	40620123	+	Missense_Mutation	SNP	G	G	A	rs370052932		TCGA-WJ-A86L-01A-12D-A45V-10	TCGA-WJ-A86L-10A-01D-A38X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	80e4fac9-c066-47a9-9fc0-2a42eef954cd	cebd5a99-cbde-441d-b98a-b84cf1825d65	g.chr17:40620123G>A	ENST00000343619.4	+	4	415	c.292G>A	c.(292-294)Gag>Aag	p.E98K	ATP6V0A1_ENST00000546249.1_Missense_Mutation_p.E98K|ATP6V0A1_ENST00000544137.1_Intron|ATP6V0A1_ENST00000585525.1_Missense_Mutation_p.E98K|ATP6V0A1_ENST00000264649.6_Missense_Mutation_p.E98K|ATP6V0A1_ENST00000537728.1_Missense_Mutation_p.E98K|ATP6V0A1_ENST00000393829.2_Missense_Mutation_p.E98K	NM_001130021.1	NP_001123493.1	Q93050	VPP1_HUMAN	ATPase, H+ transporting, lysosomal V0 subunit a1	98					ATP hydrolysis coupled proton transport (GO:0015991)|cellular iron ion homeostasis (GO:0006879)|insulin receptor signaling pathway (GO:0008286)|interaction with host (GO:0051701)|phagosome maturation (GO:0090382)|transferrin transport (GO:0033572)|transmembrane transport (GO:0055085)	cytoplasm (GO:0005737)|endosome membrane (GO:0010008)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|intracellular membrane-bounded organelle (GO:0043231)|nucleus (GO:0005634)|phagocytic vesicle membrane (GO:0030670)|plasma membrane (GO:0005886)|vacuolar proton-transporting V-type ATPase, V0 domain (GO:0000220)	ATPase binding (GO:0051117)|hydrogen ion transmembrane transporter activity (GO:0015078)			endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(4)|lung(8)|pancreas(1)|prostate(1)|urinary_tract(3)	26		all_cancers(22;1.18e-05)|Breast(137;0.000105)|all_epithelial(22;0.000254)		BRCA - Breast invasive adenocarcinoma(366;0.137)		GATTGACTTAGAGGTAAACAC	0.393													G|||	1	0.000199681	0.0	0.0	5008	,	,		14047	0.001		0.0	False		,,,				2504	0.0				p.E98K		Atlas-SNP	.											.	ATP6V0A1	67	.	0			c.G292A						.						59.0	58.0	58.0					17																	40620123		2203	4300	6503	SO:0001583	missense	535	exon4			GACTTAGAGGTAA	U73006	CCDS11426.1, CCDS45683.1, CCDS45684.1	17q21	2010-04-21	2006-01-20	2002-05-10	ENSG00000033627	ENSG00000033627		"""ATPases / V-type"""	865	protein-coding gene	gene with protein product		192130	"""ATPase, H+ transporting, lysosomal (vacuolar proton pump) non-catalytic accessory protein 1A (110/116kD)"", ""ATPase, H+ transporting, lysosomal V0 subunit a isoform 1"", ""ATPase, H+ transporting, lysosomal V0 subunit A1"""	VPP1, ATP6N1, ATP6N1A		7774924	Standard	NM_001130020		Approved	a1, Vph1, Stv1	uc002hzs.3	Q93050		ENST00000343619.4:c.292G>A	chr17.hg19:g.40620123G>A	ENSP00000342951:p.Glu98Lys	241.0	0.0		313.0	203.0	NM_001130020	B7Z3B7|Q8N5G7|Q9NSX0	Missense_Mutation	SNP	ENST00000343619.4	hg19	CCDS45684.1	.	.	.	.	.	.	.	.	.	.	G	37	6.103178	0.97286	.	.	ENSG00000033627	ENST00000343619;ENST00000546249;ENST00000393829;ENST00000264649;ENST00000537728	D;D;D;D;D	0.85702	-2.02;-2.02;-2.02;-2.02;-2.02	5.99	5.99	0.97316	.	0.092594	0.64402	N	0.000001	D	0.93151	0.7819	M	0.87758	2.905	0.80722	D	1	P;P;P;P;D;D	0.62365	0.811;0.934;0.871;0.933;0.991;0.982	P;P;P;P;P;P	0.61800	0.838;0.861;0.861;0.559;0.894;0.894	D	0.93373	0.6737	10	0.87932	D	0	-24.4696	20.4777	0.99188	0.0:0.0:1.0:0.0	.	98;98;98;98;98;98	B7Z641;B7Z2A9;B7Z3B7;Q93050;Q93050-1;F5H569	.;.;.;VPP1_HUMAN;.;.	K	98	ENSP00000342951:E98K;ENSP00000444676:E98K;ENSP00000377415:E98K;ENSP00000264649:E98K;ENSP00000443991:E98K	ENSP00000264649:E98K	E	+	1	0	ATP6V0A1	37873649	1.000000	0.71417	1.000000	0.80357	0.990000	0.78478	9.643000	0.98464	2.840000	0.97914	0.655000	0.94253	GAG	.	.		0.393	ATP6V0A1-006	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000450364.1	NM_001130020	
EFTUD2	9343	hgsc.bcm.edu	37	17	42937333	42937333	+	Silent	SNP	C	C	T			TCGA-WJ-A86L-01A-12D-A45V-10	TCGA-WJ-A86L-10A-01D-A38X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	80e4fac9-c066-47a9-9fc0-2a42eef954cd	cebd5a99-cbde-441d-b98a-b84cf1825d65	g.chr17:42937333C>T	ENST00000426333.2	-	18	2097	c.1800G>A	c.(1798-1800)ctG>ctA	p.L600L	EFTUD2_ENST00000591382.1_Silent_p.L600L|EFTUD2_ENST00000592576.1_Silent_p.L590L|EFTUD2_ENST00000402521.3_Silent_p.L565L	NM_001142605.1|NM_001258354.1|NM_004247.3	NP_001136077.1|NP_001245283.1|NP_004238.3	Q15029	U5S1_HUMAN	elongation factor Tu GTP binding domain containing 2	600					gene expression (GO:0010467)|GTP catabolic process (GO:0006184)|mRNA processing (GO:0006397)|mRNA splicing, via spliceosome (GO:0000398)|RNA splicing (GO:0008380)	Cajal body (GO:0015030)|catalytic step 2 spliceosome (GO:0071013)|cytoplasm (GO:0005737)|membrane (GO:0016020)|nuclear speck (GO:0016607)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|spliceosomal complex (GO:0005681)	GTP binding (GO:0005525)|GTPase activity (GO:0003924)|poly(A) RNA binding (GO:0044822)			breast(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(7)|lung(9)|ovary(1)|prostate(2)|skin(1)|urinary_tract(2)	32		Prostate(33;0.109)				GCATCTTGGGCAGCTCTGAGG	0.532																																					p.L600L	Ovarian(10;65 485 10258 29980 30707)	Atlas-SNP	.											.	EFTUD2	85	.	0			c.G1800A						.						142.0	125.0	130.0					17																	42937333		2203	4300	6503	SO:0001819	synonymous_variant	9343	exon18			CTTGGGCAGCTCT	D21163	CCDS11489.1, CCDS45707.1, CCDS59295.1	17q21.31	2014-08-12			ENSG00000108883	ENSG00000108883			30858	protein-coding gene	gene with protein product	"""U5 snRNP specific protein, 116 kD"""	603892				9233818	Standard	NM_004247		Approved	U5-116KD, Snrp116, Snu114, SNRNP116	uc002ihn.2	Q15029	OTTHUMG00000179865	ENST00000426333.2:c.1800G>A	chr17.hg19:g.42937333C>T		132.0	0.0		173.0	56.0	NM_004247	B4DK30|B4DMC0|D3DX58|K7EJ81|Q9BUR0	Silent	SNP	ENST00000426333.2	hg19	CCDS11489.1																																																																																			.	.		0.532	EFTUD2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000448672.1	NM_004247	
PNPO	55163	hgsc.bcm.edu	37	17	46023698	46023698	+	Missense_Mutation	SNP	A	A	C			TCGA-WJ-A86L-01A-12D-A45V-10	TCGA-WJ-A86L-10A-01D-A38X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	80e4fac9-c066-47a9-9fc0-2a42eef954cd	cebd5a99-cbde-441d-b98a-b84cf1825d65	g.chr17:46023698A>C	ENST00000225573.4	+	6	661	c.556A>C	c.(556-558)Aag>Cag	p.K186Q	PNPO_ENST00000434554.2_Missense_Mutation_p.K143Q|PNPO_ENST00000534893.1_Missense_Mutation_p.K91Q|RP11-6N17.6_ENST00000582142.1_RNA|RP11-6N17.6_ENST00000580372.1_RNA|RP11-6N17.9_ENST00000582262.1_RNA|PNPO_ENST00000544840.1_Missense_Mutation_p.K168Q	NM_018129.3	NP_060599.1	Q9NVS9	PNPO_HUMAN	pyridoxamine 5'-phosphate oxidase	186					pyridoxine biosynthetic process (GO:0008615)|small molecule metabolic process (GO:0044281)|vitamin B6 metabolic process (GO:0042816)|vitamin metabolic process (GO:0006766)|water-soluble vitamin metabolic process (GO:0006767)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)	FMN binding (GO:0010181)|pyridoxamine-phosphate oxidase activity (GO:0004733)			endometrium(2)|large_intestine(1)|lung(1)|urinary_tract(1)	5						GTATCTGAGAAAGAAAAATGA	0.498																																					p.K186Q		Atlas-SNP	.											.	PNPO	18	.	0			c.A556C						.						78.0	81.0	80.0					17																	46023698		2203	4300	6503	SO:0001583	missense	55163	exon6			CTGAGAAAGAAAA	AF468030	CCDS11522.1	17q21.32	2008-11-27	2006-07-12			ENSG00000108439	1.4.3.5		30260	protein-coding gene	gene with protein product		603287	"""pyridoxine 5'-phosphate oxidase"""			9601034, 15182361	Standard	NM_018129		Approved	PDXPO	uc002imo.3	Q9NVS9		ENST00000225573.4:c.556A>C	chr17.hg19:g.46023698A>C	ENSP00000225573:p.Lys186Gln	90.0	0.0		111.0	37.0	NM_018129	B4E0V0|B4E152|B4E1D7|D3DTT9	Missense_Mutation	SNP	ENST00000225573.4	hg19	CCDS11522.1	.	.	.	.	.	.	.	.	.	.	A	16.04	3.011247	0.54361	.	.	ENSG00000108439	ENST00000225573;ENST00000434554;ENST00000544840;ENST00000534893	T;T;T;T	0.76316	-1.01;-1.01;-1.01;-1.01	5.43	4.36	0.52297	FMN-binding split barrel-related (1);FMN-binding split barrel (1);	0.341357	0.35495	N	0.003174	T	0.48447	0.1500	N	0.05608	-0.01	0.33004	D	0.526586	P;B;B	0.36483	0.555;0.007;0.036	B;B;B	0.30316	0.114;0.001;0.006	T	0.57213	-0.7850	10	0.09338	T	0.73	-3.6318	6.1252	0.20176	0.7508:0.1648:0.0844:0.0	.	143;168;186	B4E152;B4E1D7;Q9NVS9	.;.;PNPO_HUMAN	Q	186;143;168;91	ENSP00000225573:K186Q;ENSP00000399960:K143Q;ENSP00000446182:K168Q;ENSP00000437480:K91Q	ENSP00000225573:K186Q	K	+	1	0	PNPO	43378697	1.000000	0.71417	1.000000	0.80357	0.990000	0.78478	2.794000	0.47853	2.064000	0.61679	0.459000	0.35465	AAG	.	.		0.498	PNPO-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000441407.1	NM_018129	
HOXB5	3215	hgsc.bcm.edu	37	17	46670490	46670490	+	Silent	SNP	G	G	A			TCGA-WJ-A86L-01A-12D-A45V-10	TCGA-WJ-A86L-10A-01D-A38X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	80e4fac9-c066-47a9-9fc0-2a42eef954cd	cebd5a99-cbde-441d-b98a-b84cf1825d65	g.chr17:46670490G>A	ENST00000239151.5	-	1	833	c.555C>T	c.(553-555)atC>atT	p.I185I	HOXB-AS3_ENST00000492897.3_RNA|HOXB-AS3_ENST00000480872.1_RNA|HOXB-AS3_ENST00000467155.2_RNA|HOXB3_ENST00000472863.1_5'Flank|HOXB-AS3_ENST00000487849.3_RNA|HOXB3_ENST00000552000.2_Intron|HOXB3_ENST00000498678.1_5'Flank|HOXB-AS3_ENST00000474040.1_RNA|HOXB-AS3_ENST00000474324.1_RNA|HOXB-AS3_ENST00000477144.1_RNA|HOXB-AS3_ENST00000429755.4_RNA|HOXB-AS3_ENST00000460041.1_RNA|HOXB3_ENST00000460160.1_5'Flank|HOXB-AS3_ENST00000481995.1_RNA|HOXB3_ENST00000476342.1_5'Flank|HOXB-AS3_ENST00000465846.2_RNA|HOXB-AS3_ENST00000476204.1_RNA	NM_002147.3	NP_002138.1	P09067	HXB5_HUMAN	homeobox B5	185					anatomical structure morphogenesis (GO:0009653)|anterior/posterior pattern specification (GO:0009952)|embryonic skeletal system morphogenesis (GO:0048704)|endothelial cell differentiation (GO:0045446)	nucleus (GO:0005634)	RNA polymerase II distal enhancer sequence-specific DNA binding (GO:0000980)|RNA polymerase II distal enhancer sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001205)			large_intestine(1)|lung(2)	3						TACCATGGCTGATGTGAAGCT	0.577																																					p.I185I		Atlas-SNP	.											.	HOXB5	20	.	0			c.C555T						.						40.0	44.0	42.0					17																	46670490		2202	4300	6502	SO:0001819	synonymous_variant	3215	exon1			ATGGCTGATGTGA		CCDS11530.1	17q21.32	2011-06-20	2005-12-22		ENSG00000120075	ENSG00000120075		"""Homeoboxes / ANTP class : HOXL subclass"""	5116	protein-coding gene	gene with protein product		142960	"""homeo box B5"""	HOX2, HOX2A		1973146, 1358459	Standard	NM_002147		Approved		uc002inr.3	P09067	OTTHUMG00000159913	ENST00000239151.5:c.555C>T	chr17.hg19:g.46670490G>A		45.0	0.0		117.0	74.0	NM_002147	B2RC69|P09069|Q17RP4	Silent	SNP	ENST00000239151.5	hg19	CCDS11530.1																																																																																			.	.		0.577	HOXB5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000358148.2		
ITGA3	3675	hgsc.bcm.edu	37	17	48148229	48148229	+	Missense_Mutation	SNP	G	G	A	rs140829923		TCGA-WJ-A86L-01A-12D-A45V-10	TCGA-WJ-A86L-10A-01D-A38X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	80e4fac9-c066-47a9-9fc0-2a42eef954cd	cebd5a99-cbde-441d-b98a-b84cf1825d65	g.chr17:48148229G>A	ENST00000320031.8	+	5	1016	c.686G>A	c.(685-687)cGc>cAc	p.R229H	ITGA3_ENST00000544892.1_Missense_Mutation_p.R4H|ITGA3_ENST00000007722.7_Missense_Mutation_p.R229H	NM_002204.2|NM_005501.2	NP_002195.1|NP_005492.1	P26006	ITA3_HUMAN	integrin, alpha 3 (antigen CD49C, alpha 3 subunit of VLA-3 receptor)	229					blood coagulation (GO:0007596)|cell-matrix adhesion (GO:0007160)|extracellular matrix organization (GO:0030198)|heart development (GO:0007507)|integrin-mediated signaling pathway (GO:0007229)|leukocyte migration (GO:0050900)|lung development (GO:0030324)|maternal process involved in female pregnancy (GO:0060135)|memory (GO:0007613)|mesodermal cell differentiation (GO:0048333)|negative regulation of cell projection organization (GO:0031345)|nephron development (GO:0072006)|neuron migration (GO:0001764)|positive regulation of cell-substrate adhesion (GO:0010811)|positive regulation of epithelial cell migration (GO:0010634)|positive regulation of establishment of protein localization to plasma membrane (GO:0090004)|positive regulation of gene expression (GO:0010628)|positive regulation of neuron projection development (GO:0010976)|regulation of BMP signaling pathway (GO:0030510)|regulation of transforming growth factor beta receptor signaling pathway (GO:0017015)|regulation of Wnt signaling pathway (GO:0030111)|renal filtration (GO:0097205)|response to drug (GO:0042493)|response to gonadotropin (GO:0034698)|skin development (GO:0043588)	basolateral plasma membrane (GO:0016323)|cell periphery (GO:0071944)|cell surface (GO:0009986)|external side of plasma membrane (GO:0009897)|extracellular vesicular exosome (GO:0070062)|filopodium membrane (GO:0031527)|focal adhesion (GO:0005925)|growth cone (GO:0030426)|integrin alpha3-beta1 complex (GO:0034667)|integrin complex (GO:0008305)|invadopodium membrane (GO:0071438)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)|synapse (GO:0045202)	glycoprotein binding (GO:0001948)|metal ion binding (GO:0046872)|protease binding (GO:0002020)|protein heterodimerization activity (GO:0046982)	p.R229H(1)		endometrium(3)|kidney(2)|large_intestine(7)|lung(11)|ovary(2)|pancreas(1)|prostate(1)|skin(2)|stomach(2)	31						ATGATTCAGCGCAAGGAGTGG	0.488																																					p.R229H		Atlas-SNP	.											ITGA3,colon,carcinoma,0,1	ITGA3	128	.	1	Substitution - Missense(1)	large_intestine(1)	c.G686A						.	G	HIS/ARG,HIS/ARG	0,4406		0,0,2203	193.0	200.0	197.0		686,686	5.7	1.0	17	dbSNP_134	197	1,8599	1.2+/-3.3	0,1,4299	no	missense,missense	ITGA3	NM_002204.2,NM_005501.2	29,29	0,1,6502	AA,AG,GG		0.0116,0.0,0.0077	possibly-damaging,possibly-damaging	229/1052,229/1067	48148229	1,13005	2203	4300	6503	SO:0001583	missense	3675	exon5			TTCAGCGCAAGGA	M59911	CCDS11557.1, CCDS11558.1	17q21.33	2010-03-23	2003-10-13		ENSG00000005884	ENSG00000005884		"""CD molecules"", ""Integrins"""	6139	protein-coding gene	gene with protein product		605025	"""antigen identified by monoclonal antibody J143"""	MSK18		1655803, 9704023	Standard	NM_005501		Approved	CD49c, VLA3a, VCA-2, GAP-B3	uc010dbm.3	P26006	OTTHUMG00000161890	ENST00000320031.8:c.686G>A	chr17.hg19:g.48148229G>A	ENSP00000315190:p.Arg229His	125.0	0.0		217.0	60.0	NM_005501	A7E246|B7ZM80|B9EGQ1|D3DTX4|D3DTX5	Missense_Mutation	SNP	ENST00000320031.8	hg19	CCDS11558.1	.	.	.	.	.	.	.	.	.	.	G	25.5	4.643051	0.87859	0.0	1.16E-4	ENSG00000005884	ENST00000544892;ENST00000007722;ENST00000538917;ENST00000320031	T;T;T	0.60040	0.22;0.22;0.22	5.69	5.69	0.88448	.	0.254993	0.34386	N	0.004011	T	0.68604	0.3019	L	0.52126	1.63	0.36301	D	0.857007	D;P	0.89917	1.0;0.476	D;B	0.64237	0.923;0.07	T	0.72478	-0.4281	10	0.42905	T	0.14	.	15.3058	0.73990	0.0:0.0:1.0:0.0	.	229;229	P26006-1;P26006	.;ITA3_HUMAN	H	4;229;215;229	ENSP00000446133:R4H;ENSP00000007722:R229H;ENSP00000315190:R229H	ENSP00000007722:R229H	R	+	2	0	ITGA3	45503228	1.000000	0.71417	1.000000	0.80357	0.960000	0.62799	5.342000	0.65970	2.682000	0.91365	0.655000	0.94253	CGC	.	G|1.000;A|0.000		0.488	ITGA3-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000366298.1	NM_005501	
CD300LB	124599	hgsc.bcm.edu	37	17	72518959	72518959	+	Missense_Mutation	SNP	G	G	A			TCGA-WJ-A86L-01A-12D-A45V-10	TCGA-WJ-A86L-10A-01D-A38X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	80e4fac9-c066-47a9-9fc0-2a42eef954cd	cebd5a99-cbde-441d-b98a-b84cf1825d65	g.chr17:72518959G>A	ENST00000392621.1	-	4	639	c.635C>T	c.(634-636)tCt>tTt	p.S212F		NM_174892.2	NP_777552	A8K4G0	CLM7_HUMAN	CD300 molecule-like family member b	175					cellular response to lipopolysaccharide (GO:0071222)|innate immune response (GO:0045087)|neutrophil mediated immunity (GO:0002446)|positive regulation of mast cell activation (GO:0033005)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				breast(1)|endometrium(2)|kidney(1)|large_intestine(3)|lung(10)|ovary(2)|prostate(1)|skin(1)	21						GACCCTCTGAGACCCCTTCAA	0.532																																					p.S212F		Atlas-SNP	.											.	CD300LB	38	.	0			c.C635T						.						129.0	112.0	118.0					17																	72518959		2203	4300	6503	SO:0001583	missense	124599	exon4			CTCTGAGACCCCT	AF427618	CCDS11700.1, CCDS11700.2	17q25.1	2013-01-11	2006-03-29		ENSG00000178789	ENSG00000178789		"""Immunoglobulin superfamily / V-set domain containing"""	30811	protein-coding gene	gene with protein product	"""triggering receptor expressed on myeloid cells 5"""	610705	"""CD300 antigen like family member B"""			12975309	Standard	NM_174892		Approved	TREM5, CLM7	uc002jkx.2	A8K4G0	OTTHUMG00000067606	ENST00000392621.1:c.635C>T	chr17.hg19:g.72518959G>A	ENSP00000376397:p.Ser212Phe	97.0	0.0		107.0	47.0	NM_174892	Q1EG73|Q8IX40|Q8N6D1	Missense_Mutation	SNP	ENST00000392621.1	hg19	CCDS11700.1	.	.	.	.	.	.	.	.	.	.	G	11.94	1.789374	0.31685	.	.	ENSG00000178789	ENST00000392621;ENST00000314401	.	.	.	4.39	-0.662	0.11413	.	1.430260	0.04706	N	0.416838	T	0.31104	0.0786	L	0.38175	1.15	0.09310	N	1	B	0.23058	0.079	B	0.18871	0.023	T	0.31998	-0.9923	9	0.62326	D	0.03	-8.2911	3.7213	0.08457	0.3843:0.1847:0.431:0.0	.	175	A8K4G0	CLM7_HUMAN	F	175;212	.	ENSP00000317337:S212F	S	-	2	0	CD300LB	70030554	0.000000	0.05858	0.000000	0.03702	0.430000	0.31655	0.213000	0.17521	0.038000	0.15604	-0.362000	0.07510	TCT	.	.		0.532	CD300LB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000145082.2	NM_174892	
SLC25A10	1468	hgsc.bcm.edu	37	17	79682599	79682599	+	Missense_Mutation	SNP	A	A	T			TCGA-WJ-A86L-01A-12D-A45V-10	TCGA-WJ-A86L-10A-01D-A38X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	80e4fac9-c066-47a9-9fc0-2a42eef954cd	cebd5a99-cbde-441d-b98a-b84cf1825d65	g.chr17:79682599A>T	ENST00000350690.5	+	3	391	c.305A>T	c.(304-306)aAg>aTg	p.K102M	SLC25A10_ENST00000541223.1_Missense_Mutation_p.K257M|SLC25A10_ENST00000571730.1_Missense_Mutation_p.K257M|SLC25A10_ENST00000545862.1_Missense_Mutation_p.K59M|SLC25A10_ENST00000331531.5_Missense_Mutation_p.K102M	NM_001270953.1|NM_012140.4	NP_001257882.1|NP_036272.2	Q9UBX3	DIC_HUMAN	solute carrier family 25 (mitochondrial carrier; dicarboxylate transporter), member 10	102					carbohydrate metabolic process (GO:0005975)|cellular nitrogen compound metabolic process (GO:0034641)|dicarboxylic acid transport (GO:0006835)|gluconeogenesis (GO:0006094)|glucose metabolic process (GO:0006006)|ion transport (GO:0006811)|mitochondrial transport (GO:0006839)|small molecule metabolic process (GO:0044281)|sulfide oxidation, using sulfide:quinone oxidoreductase (GO:0070221)|sulfur amino acid catabolic process (GO:0000098)|sulfur amino acid metabolic process (GO:0000096)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|mitochondrial inner membrane (GO:0005743)|nucleus (GO:0005634)	dicarboxylic acid transmembrane transporter activity (GO:0005310)			endometrium(1)|lung(9)|ovary(1)|prostate(1)|skin(2)	14	all_neural(118;0.0878)|Ovarian(332;0.12)|all_lung(278;0.23)		BRCA - Breast invasive adenocarcinoma(99;0.0117)|OV - Ovarian serous cystadenocarcinoma(97;0.0955)		Succinic acid(DB00139)	TTCCACGAGAAGGTGTTGCTG	0.692																																					p.K102M		Atlas-SNP	.											.	SLC25A10	24	.	0			c.A305T						.						100.0	105.0	103.0					17																	79682599		2203	4300	6503	SO:0001583	missense	1468	exon3			ACGAGAAGGTGTT		CCDS11786.1, CCDS59301.1, CCDS74176.1	17q25.3	2013-07-15			ENSG00000183048	ENSG00000183048		"""Solute carriers"""	10980	protein-coding gene	gene with protein product		606794		DIC		9733776, 10072589	Standard	NM_001270953		Approved		uc031rew.1	Q9UBX3	OTTHUMG00000178173	ENST00000350690.5:c.305A>T	chr17.hg19:g.79682599A>T	ENSP00000345580:p.Lys102Met	77.0	0.0		83.0	32.0	NM_001270888	Q542Z3|Q96BA1|Q96IP1	Missense_Mutation	SNP	ENST00000350690.5	hg19	CCDS11786.1	.	.	.	.	.	.	.	.	.	.	A	21.1	4.102274	0.76983	.	.	ENSG00000183048	ENST00000541223;ENST00000331531;ENST00000350690;ENST00000545862	T;T;T;T	0.79940	-1.32;-1.32;-1.32;-1.32	3.88	3.88	0.44766	Mitochondrial carrier domain (2);	0.000000	0.85682	D	0.000000	D	0.89798	0.6819	M	0.87547	2.89	0.80722	D	1	D;D;D	0.76494	0.999;0.999;0.999	D;D;D	0.77004	0.989;0.972;0.983	D	0.91115	0.4925	10	0.72032	D	0.01	-8.1945	12.3824	0.55313	1.0:0.0:0.0:0.0	.	257;102;102	B4DLN1;Q9UBX3-2;Q9UBX3	.;.;DIC_HUMAN	M	257;102;102;59	ENSP00000439565:K257M;ENSP00000328403:K102M;ENSP00000345580:K102M;ENSP00000446242:K59M	ENSP00000328403:K102M	K	+	2	0	SLC25A10	77293004	1.000000	0.71417	1.000000	0.80357	0.716000	0.41182	8.251000	0.89838	1.414000	0.47017	0.260000	0.18958	AAG	.	.		0.692	SLC25A10-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000440816.1		
DCXR	51181	hgsc.bcm.edu	37	17	79993869	79993869	+	Silent	SNP	A	A	C	rs552483270	byFrequency	TCGA-WJ-A86L-01A-12D-A45V-10	TCGA-WJ-A86L-10A-01D-A38X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	80e4fac9-c066-47a9-9fc0-2a42eef954cd	cebd5a99-cbde-441d-b98a-b84cf1825d65	g.chr17:79993869A>C	ENST00000306869.2	-	8	751	c.702T>G	c.(700-702)acT>acG	p.T234T	RP13-650J16.1_ENST00000584705.1_RNA|RP13-650J16.1_ENST00000582558.1_RNA|DCXR_ENST00000584318.1_5'Flank	NM_001195218.1|NM_016286.3	NP_001182147.1|NP_057370.1	Q7Z4W1	DCXR_HUMAN	dicarbonyl/L-xylulose reductase	234					D-xylose metabolic process (GO:0042732)|glucose metabolic process (GO:0006006)|NADP metabolic process (GO:0006739)|oxidation-reduction process (GO:0055114)|protein homotetramerization (GO:0051289)|xylulose metabolic process (GO:0005997)	brush border (GO:0005903)|cytoplasmic microtubule (GO:0005881)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|microvillus (GO:0005902)|nucleus (GO:0005634)	L-xylulose reductase (NADP+) activity (GO:0050038)|oxidoreductase activity, acting on NAD(P)H, quinone or similar compound as acceptor (GO:0016655)			kidney(1)|lung(3)	4	all_neural(118;0.0878)|Ovarian(332;0.227)|all_lung(278;0.246)		BRCA - Breast invasive adenocarcinoma(99;0.0114)|OV - Ovarian serous cystadenocarcinoma(97;0.0191)			CCACCGGCAAAGTGGAACCCG	0.612																																					p.T234T		Atlas-SNP	.											.	DCXR	10	.	0			c.T702G						.						63.0	54.0	57.0					17																	79993869		2203	4300	6503	SO:0001819	synonymous_variant	51181	exon8			CGGCAAAGTGGAA	AB013846	CCDS11799.1	17q25.3	2011-09-14				ENSG00000169738	1.1.1.10	"""Short chain dehydrogenase/reductase superfamily / Classical SDR fold cluster 1"""	18985	protein-coding gene	gene with protein product	"""short chain dehydrogenase/reductase family 20C, member 1"""	608347				11882650, 19027726	Standard	NM_016286		Approved	KIDCR, DCR, SDR20C1	uc002kdg.3	Q7Z4W1		ENST00000306869.2:c.702T>G	chr17.hg19:g.79993869A>C		59.0	0.0		64.0	34.0	NM_016286	Q9BTZ3|Q9UHY9	Silent	SNP	ENST00000306869.2	hg19	CCDS11799.1																																																																																			.	.		0.612	DCXR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000442153.2		
ZNF521	25925	hgsc.bcm.edu	37	18	22807356	22807356	+	Missense_Mutation	SNP	A	A	G			TCGA-WJ-A86L-01A-12D-A45V-10	TCGA-WJ-A86L-10A-01D-A38X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	80e4fac9-c066-47a9-9fc0-2a42eef954cd	cebd5a99-cbde-441d-b98a-b84cf1825d65	g.chr18:22807356A>G	ENST00000361524.3	-	4	674	c.526T>C	c.(526-528)Tgc>Cgc	p.C176R	ZNF521_ENST00000584787.1_5'UTR|ZNF521_ENST00000579111.1_5'Flank|ZNF521_ENST00000538137.2_Missense_Mutation_p.C176R	NM_015461.2	NP_056276.1	Q96K83	ZN521_HUMAN	zinc finger protein 521	176					cell differentiation (GO:0030154)|multicellular organismal development (GO:0007275)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|protein domain specific binding (GO:0019904)			NS(1)|breast(1)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(21)|lung(97)|ovary(5)|pancreas(1)|prostate(4)|skin(2)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(2)	149	all_cancers(21;0.0025)|all_epithelial(16;3.62e-05)|Ovarian(20;0.0991)					CATTCACTGCAGTGGTACTTC	0.478			T	PAX5	ALL																																p.C176R		Atlas-SNP	.		Dom	yes		18	18q11.2	25925	zinc finger protein 521		L	.	ZNF521	269	.	0			c.T526C						.						136.0	126.0	130.0					18																	22807356		2203	4300	6503	SO:0001583	missense	25925	exon4			CACTGCAGTGGTA	AK027354	CCDS32806.1	18q11.2	2013-01-08				ENSG00000198795		"""Zinc fingers, C2H2-type"""	24605	protein-coding gene	gene with protein product	"""early hematopoietic zinc finger"""	610974				11984006, 14630787	Standard	NM_015461		Approved	EHZF, Evi3	uc002kvk.2	Q96K83		ENST00000361524.3:c.526T>C	chr18.hg19:g.22807356A>G	ENSP00000354794:p.Cys176Arg	128.0	0.0		123.0	57.0	NM_015461	A3QVP7|B0YJB7|Q8IXI0|Q8TES6|Q9C065|Q9HAL5|Q9UFK4	Missense_Mutation	SNP	ENST00000361524.3	hg19	CCDS32806.1	.	.	.	.	.	.	.	.	.	.	A	10.53	1.376616	0.24857	.	.	ENSG00000198795	ENST00000361524;ENST00000538137;ENST00000399425	D;D	0.85258	-1.96;-1.96	5.98	5.98	0.97165	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	0.000000	0.85682	D	0.000000	D	0.95217	0.8449	H	0.96604	3.85	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.96705	0.9521	10	0.87932	D	0	-23.0284	16.4622	0.84064	1.0:0.0:0.0:0.0	.	176	Q96K83	ZN521_HUMAN	R	176;210;176	ENSP00000354794:C176R;ENSP00000382352:C176R	ENSP00000354794:C176R	C	-	1	0	ZNF521	21061354	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	8.962000	0.93254	2.289000	0.77006	0.533000	0.62120	TGC	.	.		0.478	ZNF521-001	KNOWN	overlapping_uORF|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000446781.2	NM_015461	
TAF4B	6875	hgsc.bcm.edu	37	18	23866000	23866000	+	Missense_Mutation	SNP	C	C	A			TCGA-WJ-A86L-01A-12D-A45V-10	TCGA-WJ-A86L-10A-01D-A38X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	80e4fac9-c066-47a9-9fc0-2a42eef954cd	cebd5a99-cbde-441d-b98a-b84cf1825d65	g.chr18:23866000C>A	ENST00000269142.5	+	7	2125	c.1127C>A	c.(1126-1128)tCt>tAt	p.S376Y	TAF4B_ENST00000578121.1_Missense_Mutation_p.S376Y|TAF4B_ENST00000400466.2_Missense_Mutation_p.S376Y	NM_005640.1	NP_005631.1	Q92750	TAF4B_HUMAN	TAF4b RNA polymerase II, TATA box binding protein (TBP)-associated factor, 105kDa	376					gene expression (GO:0010467)|transcription elongation from RNA polymerase II promoter (GO:0006368)|transcription from RNA polymerase II promoter (GO:0006366)|transcription initiation from RNA polymerase II promoter (GO:0006367)|viral process (GO:0016032)	cytoplasm (GO:0005737)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|transcription factor TFIID complex (GO:0005669)	DNA binding (GO:0003677)|NF-kappaB binding (GO:0051059)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(1)|central_nervous_system(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(7)|lung(13)|prostate(1)|skin(1)	29	all_cancers(21;0.00151)|Lung NSC(5;0.000401)|all_lung(6;0.00115)|Ovarian(20;0.124)		Epithelial(2;9.57e-07)|all cancers(3;5.15e-06)|OV - Ovarian serous cystadenocarcinoma(3;1.96e-05)|LUSC - Lung squamous cell carcinoma(2;0.00594)|Lung(2;0.0267)			TCAAGCCAGTCTGAAAAGTCA	0.458																																					p.S376Y		Atlas-SNP	.											.	TAF4B	71	.	0			c.C1127A						.						102.0	98.0	100.0					18																	23866000		1924	4150	6074	SO:0001583	missense	6875	exon7			GCCAGTCTGAAAA	Y09321	CCDS42421.1	18q11.1	2008-08-01	2002-08-29	2001-12-07		ENSG00000141384			11538	protein-coding gene	gene with protein product	"""TATA box binding protein (TBP)-associated factor 4B"""	601689	"""TATA box binding protein (TBP)-associated factor, RNA polymerase II, C2, 105kD"""	TAF2C2		8858156, 10849440	Standard	XM_005258339		Approved	TAFII105	uc002kvu.4	Q92750		ENST00000269142.5:c.1127C>A	chr18.hg19:g.23866000C>A	ENSP00000269142:p.Ser376Tyr	91.0	0.0		79.0	33.0	NM_005640	Q29YA4|Q29YA5	Missense_Mutation	SNP	ENST00000269142.5	hg19	CCDS42421.1	.	.	.	.	.	.	.	.	.	.	c	3.205	-0.162789	0.06502	.	.	ENSG00000141384	ENST00000418698;ENST00000269142;ENST00000400466	T;T;T	0.24908	1.83;1.85;1.83	5.35	4.44	0.53790	.	2.069230	0.01903	N	0.039345	T	0.25382	0.0617	L	0.27053	0.805	0.09310	N	0.999993	B;B	0.10296	0.003;0.003	B;B	0.06405	0.002;0.002	T	0.30327	-0.9982	10	0.87932	D	0	0.9424	11.3256	0.49446	0.1421:0.7206:0.1372:0.0	.	376;376	Q92750;A4PBF7	TAF4B_HUMAN;.	Y	376	ENSP00000389365:S376Y;ENSP00000269142:S376Y;ENSP00000383314:S376Y	ENSP00000269142:S376Y	S	+	2	0	TAF4B	22119998	0.720000	0.27996	0.645000	0.29479	0.162000	0.22319	1.527000	0.35975	1.190000	0.43042	0.558000	0.71614	TCT	.	.		0.458	TAF4B-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000446260.3	NM_005640	
LOXHD1	125336	hgsc.bcm.edu	37	18	44057756	44057756	+	Silent	SNP	C	C	T			TCGA-WJ-A86L-01A-12D-A45V-10	TCGA-WJ-A86L-10A-01D-A38X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	80e4fac9-c066-47a9-9fc0-2a42eef954cd	cebd5a99-cbde-441d-b98a-b84cf1825d65	g.chr18:44057756C>T	ENST00000398722.4	-	34	5666	c.5667G>A	c.(5665-5667)ggG>ggA	p.G1889G	LOXHD1_ENST00000582408.1_Silent_p.G994G|LOXHD1_ENST00000441893.2_Silent_p.G1038G|LOXHD1_ENST00000441551.2_Silent_p.G1961G|LOXHD1_ENST00000398705.2_Silent_p.G406G|LOXHD1_ENST00000398686.4_Silent_p.G406G|LOXHD1_ENST00000579038.1_Silent_p.G960G|LOXHD1_ENST00000536736.1_Silent_p.G2105G|LOXHD1_ENST00000300591.6_Silent_p.G1056G			Q8IVV2	LOXH1_HUMAN	lipoxygenase homology domains 1	1889	PLAT 14. {ECO:0000255|PROSITE- ProRule:PRU00152}.				calcium ion transmembrane transport (GO:0070588)|detection of mechanical stimulus (GO:0050982)|sensory perception of sound (GO:0007605)	membrane (GO:0016020)|stereocilium (GO:0032420)	calcium channel activity (GO:0005262)			NS(3)|autonomic_ganglia(1)|breast(4)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|lung(2)|pancreas(1)|prostate(4)|skin(4)|stomach(1)	36						CAGTGCCTGCCCCTGGCTCAT	0.567																																					p.G2105G		Atlas-SNP	.											.	LOXHD1	367	.	0			c.G6315A						.						124.0	114.0	117.0					18																	44057756		692	1591	2283	SO:0001819	synonymous_variant	125336	exon40			GCCTGCCCCTGGC	AK057232	CCDS45861.1, CCDS45862.1, CCDS54184.1	18q21.1	2009-09-11			ENSG00000167210	ENSG00000167210			26521	protein-coding gene	gene with protein product		613072	"""deafness, autosomal recessive 77"""	DFNB77		19732867	Standard	NM_144612		Approved	FLJ32670, LH2D1	uc010xcw.1	Q8IVV2	OTTHUMG00000132644	ENST00000398722.4:c.5667G>A	chr18.hg19:g.44057756C>T		72.0	0.0		52.0	23.0	NM_144612	B7WNN3|B7WNT1|B7WPI9|Q6ZRY7|Q86WW9|Q96DL7	Silent	SNP	ENST00000398722.4	hg19																																																																																				.	.		0.567	LOXHD1-201	KNOWN	basic	protein_coding	protein_coding		NM_144612	
ZNF407	55628	hgsc.bcm.edu	37	18	72346892	72346892	+	Missense_Mutation	SNP	A	A	T			TCGA-WJ-A86L-01A-12D-A45V-10	TCGA-WJ-A86L-10A-01D-A38X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	80e4fac9-c066-47a9-9fc0-2a42eef954cd	cebd5a99-cbde-441d-b98a-b84cf1825d65	g.chr18:72346892A>T	ENST00000299687.5	+	1	3917	c.3917A>T	c.(3916-3918)aAg>aTg	p.K1306M	ZNF407_ENST00000309902.6_Missense_Mutation_p.K1306M|ZNF407_ENST00000582337.1_Missense_Mutation_p.K1306M|ZNF407_ENST00000577538.1_Missense_Mutation_p.K1306M	NM_017757.2	NP_060227.2	Q9C0G0	ZN407_HUMAN	zinc finger protein 407	1306					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|zinc ion binding (GO:0008270)			central_nervous_system(1)|endometrium(6)|kidney(7)|large_intestine(21)|lung(23)|ovary(4)|prostate(3)|upper_aerodigestive_tract(2)	67		Esophageal squamous(42;0.131)|Prostate(75;0.173)		BRCA - Breast invasive adenocarcinoma(31;0.184)		CTGGGGAATAAGGAAATTCTG	0.448																																					p.K1306M		Atlas-SNP	.											.	ZNF407	231	.	0			c.A3917T						.						31.0	32.0	32.0					18																	72346892		1865	4106	5971	SO:0001583	missense	55628	exon1			GGAATAAGGAAAT	AB051490	CCDS45885.1, CCDS54191.1, CCDS58634.1	18q23	2013-01-08			ENSG00000215421	ENSG00000215421		"""Zinc fingers, C2H2-type"""	19904	protein-coding gene	gene with protein product		615894				11214970	Standard	NM_017757		Approved	FLJ20307, FLJ13839, KIAA1703	uc002llw.2	Q9C0G0		ENST00000299687.5:c.3917A>T	chr18.hg19:g.72346892A>T	ENSP00000299687:p.Lys1306Met	85.0	0.0		100.0	4.0	NM_001146190	B5MD54|Q96MY0|Q9H8A1|Q9NXD4|Q9NXD7	Missense_Mutation	SNP	ENST00000299687.5	hg19	CCDS45885.1	.	.	.	.	.	.	.	.	.	.	A	11.21	1.571474	0.28003	.	.	ENSG00000215421	ENST00000299687;ENST00000309902	T;T	0.12465	2.68;3.09	5.67	4.51	0.55191	.	0.202274	0.39985	N	0.001217	T	0.22820	0.0551	L	0.34521	1.04	0.22811	N	0.9987	D;D;D	0.89917	1.0;1.0;0.999	D;D;P	0.73380	0.98;0.964;0.862	T	0.02966	-1.1088	10	0.54805	T	0.06	.	8.5994	0.33736	0.8535:0.0:0.1465:0.0	.	1306;1306;1306	Q9C0G0-3;Q9C0G0-2;Q9C0G0	.;.;ZN407_HUMAN	M	1306	ENSP00000299687:K1306M;ENSP00000310359:K1306M	ENSP00000299687:K1306M	K	+	2	0	ZNF407	70475880	1.000000	0.71417	0.961000	0.40146	0.021000	0.10359	2.414000	0.44627	1.378000	0.46305	0.655000	0.94253	AAG	.	.		0.448	ZNF407-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000444903.1	NM_017757	
AP3D1	8943	hgsc.bcm.edu	37	19	2137788	2137788	+	Missense_Mutation	SNP	C	C	T			TCGA-WJ-A86L-01A-12D-A45V-10	TCGA-WJ-A86L-10A-01D-A38X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	80e4fac9-c066-47a9-9fc0-2a42eef954cd	cebd5a99-cbde-441d-b98a-b84cf1825d65	g.chr19:2137788C>T	ENST00000345016.5	-	3	442	c.211G>A	c.(211-213)Gac>Aac	p.D71N	AP3D1_ENST00000356926.4_Missense_Mutation_p.D71N|AP3D1_ENST00000350812.6_Missense_Mutation_p.D71N|AP3D1_ENST00000355272.6_Missense_Mutation_p.D71N	NM_003938.6	NP_003929.4	O14617	AP3D1_HUMAN	adaptor-related protein complex 3, delta 1 subunit	71					anterograde axon cargo transport (GO:0008089)|anterograde synaptic vesicle transport (GO:0048490)|antigen processing and presentation, exogenous lipid antigen via MHC class Ib (GO:0048007)|endosome to melanosome transport (GO:0035646)|eye pigment biosynthetic process (GO:0006726)|intracellular protein transport (GO:0006886)|melanosome organization (GO:0032438)|positive regulation of NK T cell differentiation (GO:0051138)|protein localization to membrane (GO:0072657)|protein localization to organelle (GO:0033365)|regulation of sequestering of zinc ion (GO:0061088)|synaptic vesicle membrane organization (GO:0048499)	endosome membrane (GO:0010008)|Golgi apparatus (GO:0005794)|lysosomal membrane (GO:0005765)|membrane (GO:0016020)|membrane coat (GO:0030117)|terminal bouton (GO:0043195)	protein transporter activity (GO:0008565)|transporter activity (GO:0005215)			breast(1)|endometrium(3)|kidney(1)|large_intestine(4)|lung(23)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	37		Hepatocellular(1079;0.137)		UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|OV - Ovarian serous cystadenocarcinoma(105;1.09e-113)|Epithelial(107;3.79e-112)|all cancers(105;1.67e-104)|BRCA - Breast invasive adenocarcinoma(158;0.00136)|STAD - Stomach adenocarcinoma(1328;0.18)		CAGCTGATGTCGTATCCCAAC	0.542																																					p.D71N		Atlas-SNP	.											.	AP3D1	81	.	0			c.G211A						.						153.0	152.0	152.0					19																	2137788		1995	4181	6176	SO:0001583	missense	8943	exon3			TGATGTCGTATCC	U91930	CCDS42459.1, CCDS58638.1	19p13.3	2014-09-04			ENSG00000065000	ENSG00000065000			568	protein-coding gene	gene with protein product		607246				9151686, 9303295	Standard	NM_003938		Approved	ADTD	uc002lva.4	O14617	OTTHUMG00000180354	ENST00000345016.5:c.211G>A	chr19.hg19:g.2137788C>T	ENSP00000344055:p.Asp71Asn	86.0	0.0		136.0	37.0	NM_001261826	O00202|O75262|Q59HF5|Q96G11|Q9H3C6	Missense_Mutation	SNP	ENST00000345016.5	hg19	CCDS42459.1	.	.	.	.	.	.	.	.	.	.	C	19.69	3.874782	0.72180	.	.	ENSG00000065000	ENST00000356926;ENST00000345016;ENST00000355272;ENST00000343722;ENST00000350812	T;T;T;T	0.16073	2.37;2.37;2.37;2.37	5.24	5.24	0.73138	Clathrin/coatomer adaptor, adaptin-like, N-terminal (1);Armadillo-like helical (1);Armadillo-type fold (1);	0.000000	0.85682	D	0.000000	T	0.54447	0.1859	M	0.93150	3.385	0.37522	D	0.917579	D;D;D	0.89917	1.0;0.998;1.0	D;D;D	0.87578	0.998;0.957;0.996	T	0.71321	-0.4628	10	0.87932	D	0	-54.9574	17.7918	0.88554	0.0:1.0:0.0:0.0	.	71;71;71	O14617-5;O14617;G5E988	.;AP3D1_HUMAN;.	N	71	ENSP00000349398:D71N;ENSP00000344055:D71N;ENSP00000347416:D71N;ENSP00000342321:D71N	ENSP00000341579:D71N	D	-	1	0	AP3D1	2088788	1.000000	0.71417	0.954000	0.39281	0.529000	0.34654	7.468000	0.80943	2.447000	0.82792	0.563000	0.77884	GAC	.	.		0.542	AP3D1-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000450912.1		
DPP9	91039	hgsc.bcm.edu	37	19	4704012	4704012	+	Missense_Mutation	SNP	C	C	G			TCGA-WJ-A86L-01A-12D-A45V-10	TCGA-WJ-A86L-10A-01D-A38X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	80e4fac9-c066-47a9-9fc0-2a42eef954cd	cebd5a99-cbde-441d-b98a-b84cf1825d65	g.chr19:4704012C>G	ENST00000598800.1	-	8	1073	c.568G>C	c.(568-570)Gac>Cac	p.D190H	DPP9_ENST00000597849.1_Missense_Mutation_p.D219H|DPP9_ENST00000262960.9_Missense_Mutation_p.D219H|DPP9_ENST00000594671.1_Missense_Mutation_p.D190H			Q86TI2	DPP9_HUMAN	dipeptidyl-peptidase 9	190						cytoplasm (GO:0005737)|membrane (GO:0016020)	aminopeptidase activity (GO:0004177)|identical protein binding (GO:0042802)|serine-type peptidase activity (GO:0008236)			cervix(2)|endometrium(3)|kidney(3)|large_intestine(2)|lung(6)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	20		Hepatocellular(1079;0.137)		UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|BRCA - Breast invasive adenocarcinoma(158;0.00884)		ATTTTGGGGTCCATCCGGGGC	0.627																																					p.D219H		Atlas-SNP	.											.	DPP9	59	.	0			c.G655C						.						50.0	55.0	53.0					19																	4704012		1943	4146	6089	SO:0001583	missense	91039	exon7			TGGGGTCCATCCG	AF452102	CCDS45928.1	19p13.3	2014-06-11	2006-01-12		ENSG00000142002	ENSG00000142002			18648	protein-coding gene	gene with protein product		608258	"""dipeptidylpeptidase 9"""				Standard	NM_139159		Approved		uc002mba.3	Q86TI2	OTTHUMG00000182040	ENST00000598800.1:c.568G>C	chr19.hg19:g.4704012C>G	ENSP00000469603:p.Asp190His	71.0	0.0		69.0	23.0	NM_139159	O75273|O75868|Q1ZZB8|Q6AI37|Q6UAL0|Q6ZMT2|Q6ZNJ5|Q8N2J7|Q8N3F5|Q8WXD8|Q96NT8|Q9BVR3	Missense_Mutation	SNP	ENST00000598800.1	hg19		.	.	.	.	.	.	.	.	.	.	C	24.3	4.516656	0.85495	.	.	ENSG00000142002	ENST00000357909;ENST00000381797;ENST00000262960	T	0.32515	1.45	4.64	4.64	0.57946	Peptidase S9B, dipeptidylpeptidase IV N-terminal (1);	0.000000	0.85682	D	0.000000	T	0.60366	0.2263	M	0.85041	2.73	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	0.998;1.0	T	0.66368	-0.5941	10	0.54805	T	0.06	-45.6084	16.6576	0.85232	0.0:1.0:0.0:0.0	.	190;219	Q86TI2;Q1ZZB8	DPP9_HUMAN;.	H	298;160;219	ENSP00000262960:D219H	ENSP00000262960:D219H	D	-	1	0	DPP9	4655012	1.000000	0.71417	1.000000	0.80357	0.942000	0.58702	7.559000	0.82265	2.424000	0.82194	0.561000	0.74099	GAC	.	.		0.627	DPP9-026	NOVEL	basic	protein_coding	protein_coding	OTTHUMT00000459343.2		
MUC16	94025	hgsc.bcm.edu	37	19	9064481	9064481	+	Missense_Mutation	SNP	C	C	A	rs546210055		TCGA-WJ-A86L-01A-12D-A45V-10	TCGA-WJ-A86L-10A-01D-A38X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	80e4fac9-c066-47a9-9fc0-2a42eef954cd	cebd5a99-cbde-441d-b98a-b84cf1825d65	g.chr19:9064481C>A	ENST00000397910.4	-	3	23168	c.22965G>T	c.(22963-22965)caG>caT	p.Q7655H		NM_024690.2	NP_078966.2	Q8WXI7	MUC16_HUMAN	mucin 16, cell surface associated	7657	Ser-rich.|Thr-rich.				cell adhesion (GO:0007155)|cellular protein metabolic process (GO:0044267)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	extracellular vesicular exosome (GO:0070062)|extrinsic component of membrane (GO:0019898)|Golgi lumen (GO:0005796)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|vesicle (GO:0031982)				NS(9)|autonomic_ganglia(1)|breast(26)|central_nervous_system(11)|cervix(1)|endometrium(46)|haematopoietic_and_lymphoid_tissue(5)|kidney(35)|large_intestine(91)|liver(1)|lung(278)|ovary(17)|pancreas(2)|prostate(17)|skin(18)|soft_tissue(1)|stomach(8)|upper_aerodigestive_tract(16)|urinary_tract(7)	590						GTGGAAATCCCTGAATTACTA	0.507																																					p.Q7655H		Atlas-SNP	.											.	MUC16	4315	.	0			c.G22965T						.						82.0	82.0	82.0					19																	9064481		1902	4103	6005	SO:0001583	missense	94025	exon3			AAATCCCTGAATT	AF414442	CCDS54212.1	19p13.2	2008-02-05	2006-03-14			ENSG00000181143		"""Mucins"""	15582	protein-coding gene	gene with protein product		606154				11369781	Standard	XM_006722941		Approved	CA125, FLJ14303	uc002mkp.3	Q8WXI7		ENST00000397910.4:c.22965G>T	chr19.hg19:g.9064481C>A	ENSP00000381008:p.Gln7655His	97.0	0.0		112.0	33.0	NM_024690	Q6ZQW5|Q96RK2	Missense_Mutation	SNP	ENST00000397910.4	hg19	CCDS54212.1	.	.	.	.	.	.	.	.	.	.	N	3.578	-0.086191	0.07097	.	.	ENSG00000181143	ENST00000397910	T	0.27104	1.69	2.19	-3.85	0.04243	.	.	.	.	.	T	0.12944	0.0314	N	0.24115	0.695	.	.	.	B	0.23540	0.087	B	0.26517	0.07	T	0.34527	-0.9825	8	0.87932	D	0	.	0.3705	0.00378	0.1994:0.3237:0.1967:0.2802	.	7655	B5ME49	.	H	7655	ENSP00000381008:Q7655H	ENSP00000381008:Q7655H	Q	-	3	2	MUC16	8925481	0.000000	0.05858	0.000000	0.03702	0.002000	0.02628	-1.464000	0.02359	-0.752000	0.04728	0.400000	0.26472	CAG	.	.		0.507	MUC16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402806.1	NM_024690	
NOTCH3	4854	hgsc.bcm.edu	37	19	15302777	15302777	+	Missense_Mutation	SNP	G	G	A			TCGA-WJ-A86L-01A-12D-A45V-10	TCGA-WJ-A86L-10A-01D-A38X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	80e4fac9-c066-47a9-9fc0-2a42eef954cd	cebd5a99-cbde-441d-b98a-b84cf1825d65	g.chr19:15302777G>A	ENST00000263388.2	-	4	748	c.673C>T	c.(673-675)Ctt>Ttt	p.L225F		NM_000435.2	NP_000426.2	Q9UM47	NOTC3_HUMAN	notch 3	225	EGF-like 5. {ECO:0000255|PROSITE- ProRule:PRU00076}.				forebrain development (GO:0030900)|gene expression (GO:0010467)|glomerular capillary formation (GO:0072104)|negative regulation of neuron differentiation (GO:0045665)|neuron fate commitment (GO:0048663)|Notch receptor processing (GO:0007220)|Notch signaling pathway (GO:0007219)|positive regulation of smooth muscle cell proliferation (GO:0048661)|regulation of transcription, DNA-templated (GO:0006355)|transcription initiation from RNA polymerase II promoter (GO:0006367)	actin cytoskeleton (GO:0015629)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|endoplasmic reticulum membrane (GO:0005789)|extracellular region (GO:0005576)|Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	calcium ion binding (GO:0005509)			breast(4)|central_nervous_system(3)|endometrium(10)|kidney(3)|large_intestine(16)|liver(1)|lung(31)|ovary(8)|prostate(3)|skin(7)|stomach(1)|upper_aerodigestive_tract(5)|urinary_tract(1)	93			OV - Ovarian serous cystadenocarcinoma(3;2.6e-20)|Epithelial(3;1.34e-16)|all cancers(3;5.13e-15)			TCACCAGGAAGACAGGCACAG	0.657																																					p.L225F		Atlas-SNP	.											.	NOTCH3	340	.	0			c.C673T						.						59.0	51.0	54.0					19																	15302777		2203	4300	6503	SO:0001583	missense	4854	exon4			CAGGAAGACAGGC	U97669	CCDS12326.1	19p13.2-p13.1	2013-01-10	2010-06-24			ENSG00000074181		"""Ankyrin repeat domain containing"""	7883	protein-coding gene	gene with protein product		600276	"""Notch (Drosophila) homolog 3"", ""Notch homolog 3 (Drosophila)"""	CADASIL		7835890	Standard	NM_000435		Approved	CASIL	uc002nan.3	Q9UM47		ENST00000263388.2:c.673C>T	chr19.hg19:g.15302777G>A	ENSP00000263388:p.Leu225Phe	43.0	0.0		54.0	27.0	NM_000435	Q9UEB3|Q9UPL3|Q9Y6L8	Missense_Mutation	SNP	ENST00000263388.2	hg19	CCDS12326.1	.	.	.	.	.	.	.	.	.	.	g	16.47	3.133634	0.56828	.	.	ENSG00000074181	ENST00000263388;ENST00000539383	D	0.99548	-6.14	5.35	4.31	0.51392	Epidermal growth factor-like (1);EGF-like region, conserved site (2);Epidermal growth factor-like, type 3 (1);	.	.	.	.	D	0.99223	0.9730	L	0.49126	1.545	0.49130	D	0.999756	D;D	0.89917	0.998;1.0	D;D	0.87578	0.985;0.998	D	0.98705	1.0702	9	0.38643	T	0.18	.	8.9869	0.35999	0.1706:0.0:0.8294:0.0	.	228;225	Q59FL3;Q9UM47	.;NOTC3_HUMAN	F	225;227	ENSP00000263388:L225F	ENSP00000263388:L225F	L	-	1	0	NOTCH3	15163777	1.000000	0.71417	1.000000	0.80357	0.709000	0.40893	2.410000	0.44592	1.258000	0.44101	0.558000	0.71614	CTT	.	.		0.657	NOTCH3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000465714.1	NM_000435	
DMKN	93099	hgsc.bcm.edu	37	19	36003635	36003635	+	Nonsense_Mutation	SNP	G	G	A	rs561680729		TCGA-WJ-A86L-01A-12D-A45V-10	TCGA-WJ-A86L-10A-01D-A38X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	80e4fac9-c066-47a9-9fc0-2a42eef954cd	cebd5a99-cbde-441d-b98a-b84cf1825d65	g.chr19:36003635G>A	ENST00000339686.3	-	2	660	c.484C>T	c.(484-486)Cag>Tag	p.Q162*	DMKN_ENST00000443640.1_5'Flank|DMKN_ENST00000451297.2_Nonsense_Mutation_p.Q162*|DMKN_ENST00000480502.1_5'Flank|DMKN_ENST00000424570.2_Nonsense_Mutation_p.Q162*|DMKN_ENST00000492341.2_5'Flank|DMKN_ENST00000414866.2_5'Flank|DMKN_ENST00000602781.1_5'Flank|DMKN_ENST00000429837.1_Nonsense_Mutation_p.Q162*|DMKN_ENST00000467637.1_5'Flank|DMKN_ENST00000488892.1_5'Flank|DMKN_ENST00000474928.1_5'Flank|DMKN_ENST00000392206.2_5'Flank|DMKN_ENST00000436012.1_5'Flank|DMKN_ENST00000462126.1_5'Flank|DMKN_ENST00000418261.1_Nonsense_Mutation_p.Q162*|DMKN_ENST00000402589.2_5'Flank|DMKN_ENST00000447113.2_Nonsense_Mutation_p.Q162*|DMKN_ENST00000458071.1_5'Flank|DMKN_ENST00000472252.2_5'Flank|DMKN_ENST00000461300.1_5'Flank|DMKN_ENST00000419602.1_Nonsense_Mutation_p.Q162*|DMKN_ENST00000440396.1_Nonsense_Mutation_p.Q162*	NM_033317.4	NP_201574	Q6E0U4	DMKN_HUMAN	dermokine	162	Gly-rich.					extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)				NS(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(8)|lung(7)|ovary(1)|prostate(1)|skin(2)	27	all_lung(56;1.89e-08)|Lung NSC(56;2.9e-08)|Esophageal squamous(110;0.162)		LUSC - Lung squamous cell carcinoma(66;0.0724)			GGATTGCCCTGGCCCTGGCCT	0.582													G|||	1	0.000199681	0.0	0.0	5008	,	,		18230	0.001		0.0	False		,,,				2504	0.0				p.Q162X		Atlas-SNP	.											.	DMKN	116	.	0			c.C484T						.						42.0	44.0	43.0					19																	36003635		2203	4300	6503	SO:0001587	stop_gained	93099	exon2			TGCCCTGGCCCTG	BC035311	CCDS12463.1, CCDS42549.1, CCDS46051.1, CCDS46052.1, CCDS46053.1, CCDS46054.1, CCDS46054.2, CCDS54250.1, CCDS54251.1, CCDS54252.1	19q13.12	2008-10-27			ENSG00000161249	ENSG00000161249			25063	protein-coding gene	gene with protein product						16374476	Standard	NM_001035516		Approved	ZD52F10	uc002nzm.4	Q6E0U4	OTTHUMG00000048101	ENST00000339686.3:c.484C>T	chr19.hg19:g.36003635G>A	ENSP00000342012:p.Gln162*	42.0	0.0		41.0	19.0	NM_001190347	A3EZ79|A3EZ80|A3EZ81|A3EZ82|A3EZ83|C9J4P6|C9J5N8|C9JAL3|Q32W58|Q32W62|Q32W63|Q32W64|Q32W65|Q32W66|Q32W67|Q6E0U5|Q6UXC7|Q96EW8|Q9BSY6	Nonsense_Mutation	SNP	ENST00000339686.3	hg19	CCDS12463.1	.	.	.	.	.	.	.	.	.	.	G	23.0	4.357609	0.82243	.	.	ENSG00000161249	ENST00000339686;ENST00000392207;ENST00000429837;ENST00000419602;ENST00000447113;ENST00000440396;ENST00000418261;ENST00000424570;ENST00000451297	.	.	.	4.66	3.6	0.41247	.	.	.	.	.	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.66056	D	0.02	0.0835	10.7739	0.46338	0.0:0.1912:0.8088:0.0	.	.	.	.	X	162	.	ENSP00000342012:Q162X	Q	-	1	0	DMKN	40695475	0.079000	0.21365	0.008000	0.14137	0.313000	0.28021	2.540000	0.45727	1.140000	0.42260	0.467000	0.42956	CAG	.	.		0.582	DMKN-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000109461.2	NM_033317	
RBM42	79171	hgsc.bcm.edu	37	19	36120568	36120568	+	Missense_Mutation	SNP	A	A	G			TCGA-WJ-A86L-01A-12D-A45V-10	TCGA-WJ-A86L-10A-01D-A38X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	80e4fac9-c066-47a9-9fc0-2a42eef954cd	cebd5a99-cbde-441d-b98a-b84cf1825d65	g.chr19:36120568A>G	ENST00000262633.4	+	2	380	c.275A>G	c.(274-276)tAc>tGc	p.Y92C	RBM42_ENST00000588161.1_Missense_Mutation_p.Y92C|RBM42_ENST00000586618.1_Missense_Mutation_p.Y92C|RBM42_ENST00000592202.1_Missense_Mutation_p.Y92C|RBM42_ENST00000589871.1_Missense_Mutation_p.Y92C|RBM42_ENST00000360475.4_Missense_Mutation_p.Y92C|RBM42_ENST00000589559.1_Missense_Mutation_p.Y92C	NM_024321.3	NP_077297.2	Q9BTD8	RBM42_HUMAN	RNA binding motif protein 42	92						cytoplasm (GO:0005737)|nucleus (GO:0005634)	nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)			breast(1)|endometrium(3)|large_intestine(7)|lung(9)|prostate(1)	21	all_lung(56;1.58e-07)|Lung NSC(56;2.43e-07)|Esophageal squamous(110;0.162)		LUSC - Lung squamous cell carcinoma(66;0.0724)			ACCAACACATACCAGCAGGTA	0.562																																					p.Y92C		Atlas-SNP	.											.	RBM42	40	.	0			c.A275G						.						72.0	65.0	67.0					19																	36120568		2203	4300	6503	SO:0001583	missense	79171	exon2			ACACATACCAGCA	BC004204	CCDS12468.1	19q13.12	2013-02-12				ENSG00000126254		"""RNA binding motif (RRM) containing"""	28117	protein-coding gene	gene with protein product		613232				12477932	Standard	NM_024321		Approved	MGC10433	uc002oan.3	Q9BTD8		ENST00000262633.4:c.275A>G	chr19.hg19:g.36120568A>G	ENSP00000262633:p.Tyr92Cys	61.0	0.0		51.0	25.0	NM_024321	O00320|Q8N5R7|Q9BU66	Missense_Mutation	SNP	ENST00000262633.4	hg19	CCDS12468.1	.	.	.	.	.	.	.	.	.	.	A	24.4	4.522841	0.85600	.	.	ENSG00000126254	ENST00000262633;ENST00000360475	T;T	0.32753	1.71;1.44	4.34	4.34	0.51931	.	0.000000	0.85682	D	0.000000	T	0.49558	0.1564	L	0.57536	1.79	0.58432	D	0.999996	D;D;D;D;D	0.89917	1.0;1.0;0.999;1.0;0.999	D;D;D;D;D	0.87578	0.998;0.996;0.993;0.996;0.99	T	0.51949	-0.8640	10	0.87932	D	0	-4.6272	11.5485	0.50706	1.0:0.0:0.0:0.0	.	92;92;92;92;92	B4DWT0;Q9BTD8-4;Q9BTD8-3;Q9BTD8-2;Q9BTD8	.;.;.;.;RBM42_HUMAN	C	92	ENSP00000262633:Y92C;ENSP00000353663:Y92C	ENSP00000262633:Y92C	Y	+	2	0	RBM42	40812408	1.000000	0.71417	0.998000	0.56505	0.974000	0.67602	8.269000	0.89878	1.827000	0.53221	0.459000	0.35465	TAC	.	.		0.562	RBM42-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000459057.2	NM_024321	
PLD3	23646	hgsc.bcm.edu	37	19	40882529	40882529	+	Missense_Mutation	SNP	A	A	G			TCGA-WJ-A86L-01A-12D-A45V-10	TCGA-WJ-A86L-10A-01D-A38X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	80e4fac9-c066-47a9-9fc0-2a42eef954cd	cebd5a99-cbde-441d-b98a-b84cf1825d65	g.chr19:40882529A>G	ENST00000409587.1	+	11	1430	c.1033A>G	c.(1033-1035)Att>Gtt	p.I345V	PLD3_ENST00000356508.5_Missense_Mutation_p.I345V|PLD3_ENST00000409419.1_Missense_Mutation_p.I345V|PLD3_ENST00000409281.1_Missense_Mutation_p.I345V|PLD3_ENST00000409735.4_Missense_Mutation_p.I345V			Q8IV08	PLD3_HUMAN	phospholipase D family, member 3	345					cell death (GO:0008219)|glycerophospholipid biosynthetic process (GO:0046474)|lipid catabolic process (GO:0016042)|phosphatidylglycerol biosynthetic process (GO:0006655)|phospholipid metabolic process (GO:0006644)|small molecule metabolic process (GO:0044281)	endoplasmic reticulum (GO:0005783)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)	N-acylphosphatidylethanolamine-specific phospholipase D activity (GO:0070290)|phospholipase D activity (GO:0004630)			breast(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(6)|liver(2)|lung(2)|ovary(1)|skin(2)|upper_aerodigestive_tract(1)	20			Lung(22;0.000636)|LUSC - Lung squamous cell carcinoma(20;0.00248)			CTGGCCTGCCATTGACGATGG	0.647																																					p.I345V		Atlas-SNP	.											.	PLD3	71	.	0			c.A1033G						.						76.0	77.0	77.0					19																	40882529		2203	4300	6503	SO:0001583	missense	23646	exon11			CCTGCCATTGACG	BC000553	CCDS33027.1	19q13.2	2014-03-14	2005-05-20		ENSG00000105223	ENSG00000105223			17158	protein-coding gene	gene with protein product		615698	"""phospholipase D3"""			9140189, 15794758	Standard	XM_005258704		Approved	HU-K4	uc002onj.4	Q8IV08	OTTHUMG00000152736	ENST00000409587.1:c.1033A>G	chr19.hg19:g.40882529A>G	ENSP00000387050:p.Ile345Val	24.0	0.0		26.0	9.0	NM_012268	Q92853|Q9BW87	Missense_Mutation	SNP	ENST00000409587.1	hg19	CCDS33027.1	.	.	.	.	.	.	.	.	.	.	A	12.81	2.048867	0.36181	.	.	ENSG00000105223	ENST00000409419;ENST00000409587;ENST00000356508;ENST00000536031;ENST00000409735;ENST00000409281	T;T;T;T;T	0.56611	0.45;0.45;0.45;0.45;0.45	4.29	3.25	0.37280	Phospholipase D/viral envelope (1);	0.107102	0.64402	D	0.000008	T	0.55545	0.1927	M	0.81682	2.555	0.52099	D	0.999945	B	0.18310	0.027	B	0.29785	0.107	T	0.56238	-0.8012	10	0.66056	D	0.02	-10.9258	9.0962	0.36640	0.9086:0.0:0.0914:0.0	.	345	Q8IV08	PLD3_HUMAN	V	345;345;345;326;345;345	ENSP00000386293:I345V;ENSP00000387050:I345V;ENSP00000348901:I345V;ENSP00000386938:I345V;ENSP00000387022:I345V	ENSP00000348901:I345V	I	+	1	0	PLD3	45574369	1.000000	0.71417	0.997000	0.53966	0.449000	0.32228	4.095000	0.57728	0.668000	0.31126	0.260000	0.18958	ATT	.	.		0.647	PLD3-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000327721.1	NM_012268	
NPAS1	4861	hgsc.bcm.edu	37	19	47548495	47548495	+	Missense_Mutation	SNP	C	C	A	rs147026903		TCGA-WJ-A86L-01A-12D-A45V-10	TCGA-WJ-A86L-10A-01D-A38X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	80e4fac9-c066-47a9-9fc0-2a42eef954cd	cebd5a99-cbde-441d-b98a-b84cf1825d65	g.chr19:47548495C>A	ENST00000602212.1	+	12	1579	c.1359C>A	c.(1357-1359)aaC>aaA	p.N453K	NPAS1_ENST00000602189.1_Missense_Mutation_p.N278K|NPAS1_ENST00000449844.2_Missense_Mutation_p.N453K|NPAS1_ENST00000439365.2_3'UTR			Q99742	NPAS1_HUMAN	neuronal PAS domain protein 1	453					central nervous system development (GO:0007417)|maternal behavior (GO:0042711)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|startle response (GO:0001964)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|sequence-specific DNA binding transcription factor activity (GO:0003700)|signal transducer activity (GO:0004871)			endometrium(2)|kidney(1)|large_intestine(2)|lung(1)	6		all_cancers(25;4.31e-08)|all_epithelial(76;2.96e-06)|all_lung(116;7.86e-06)|Lung NSC(112;2.31e-05)|all_neural(266;0.026)|Ovarian(192;0.0392)|Breast(70;0.102)		all cancers(93;6.02e-05)|OV - Ovarian serous cystadenocarcinoma(262;7.35e-05)|Epithelial(262;0.00389)|GBM - Glioblastoma multiforme(486;0.0252)		CAGCGGAGAACGAGGCCCCCC	0.662																																					p.N453K		Atlas-SNP	.											.	NPAS1	32	.	0			c.C1359A						.						38.0	43.0	41.0					19																	47548495		2199	4300	6499	SO:0001583	missense	4861	exon11			GGAGAACGAGGCC	U77968	CCDS12694.1	19q13.2-q13.3	2013-05-21				ENSG00000130751		"""Basic helix-loop-helix proteins"""	7894	protein-coding gene	gene with protein product	"""neuronal PAS1"", ""member of PAS superfamily 5"""	603346				9012850, 9079689	Standard	NM_002517		Approved	MOP5, PASD5, bHLHe11	uc002pfy.3	Q99742		ENST00000602212.1:c.1359C>A	chr19.hg19:g.47548495C>A	ENSP00000469142:p.Asn453Lys	131.0	0.0		150.0	32.0	NM_002517	B4DR69|Q99632|Q9BY83	Missense_Mutation	SNP	ENST00000602212.1	hg19	CCDS12694.1	.	.	.	.	.	.	.	.	.	.	C	0.338	-0.952149	0.02285	.	.	ENSG00000130751	ENST00000449844	T	0.40756	1.02	4.11	-3.78	0.04333	.	1.463600	0.04399	N	0.363777	T	0.14830	0.0358	N	0.02539	-0.55	0.19945	N	0.999947	B	0.15141	0.012	B	0.12837	0.008	T	0.16630	-1.0396	10	0.10111	T	0.7	.	4.8982	0.13760	0.0:0.3158:0.2757:0.4085	.	453	Q99742	NPAS1_HUMAN	K	453	ENSP00000405290:N453K	ENSP00000405290:N453K	N	+	3	2	NPAS1	52240335	0.000000	0.05858	0.049000	0.19019	0.167000	0.22549	-2.202000	0.01235	-0.608000	0.05731	-0.802000	0.03209	AAC	.	C|1.000;G|0.000		0.662	NPAS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466658.1	NM_002517	
DHX34	9704	hgsc.bcm.edu	37	19	47865878	47865878	+	Silent	SNP	G	G	T			TCGA-WJ-A86L-01A-12D-A45V-10	TCGA-WJ-A86L-10A-01D-A38X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	80e4fac9-c066-47a9-9fc0-2a42eef954cd	cebd5a99-cbde-441d-b98a-b84cf1825d65	g.chr19:47865878G>T	ENST00000328771.4	+	6	1870	c.1521G>T	c.(1519-1521)tcG>tcT	p.S507S	DHX34_ENST00000471451.1_Intron	NM_014681.5	NP_055496.2	Q14147	DHX34_HUMAN	DEAH (Asp-Glu-Ala-His) box polypeptide 34	507	Helicase C-terminal. {ECO:0000255|PROSITE-ProRule:PRU00542}.				negative regulation of nuclear-transcribed mRNA catabolic process, nonsense-mediated decay (GO:2000623)|nuclear-transcribed mRNA catabolic process (GO:0000956)	membrane (GO:0016020)	ATP binding (GO:0005524)|helicase activity (GO:0004386)|poly(A) RNA binding (GO:0044822)			breast(1)|central_nervous_system(1)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(2)|lung(8)|ovary(5)|prostate(5)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	36		all_cancers(25;1.65e-09)|all_epithelial(76;9.95e-08)|all_lung(116;7.27e-07)|Lung NSC(112;1.6e-06)|Ovarian(192;0.0139)|all_neural(266;0.026)|Breast(70;0.0503)		all cancers(93;7.16e-05)|OV - Ovarian serous cystadenocarcinoma(262;0.000489)|GBM - Glioblastoma multiforme(486;0.00413)|Epithelial(262;0.0132)		ATGCCGAATCGGACTATGATG	0.647																																					p.S507S		Atlas-SNP	.											.	DHX34	98	.	0			c.G1521T						.						26.0	27.0	27.0					19																	47865878		2203	4300	6503	SO:0001819	synonymous_variant	9704	exon6			CGAATCGGACTAT	D50924	CCDS12700.1	19q13.3	2003-06-13	2003-06-13	2003-06-13	ENSG00000134815	ENSG00000134815		"""DEAH-boxes"""	16719	protein-coding gene	gene with protein product		615475	"""DEAD/H (Asp-Glu-Ala-Asp/His) box polypeptide 34"""	DDX34		10708517, 8590280	Standard	NM_014681		Approved	KIAA0134	uc010xyn.2	Q14147	OTTHUMG00000149959	ENST00000328771.4:c.1521G>T	chr19.hg19:g.47865878G>T		108.0	0.0		110.0	53.0	NM_014681	B4DMY8	Silent	SNP	ENST00000328771.4	hg19	CCDS12700.1																																																																																			.	.		0.647	DHX34-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000314313.3	NM_014681	
ZIM3	114026	hgsc.bcm.edu	37	19	57646441	57646441	+	Missense_Mutation	SNP	T	T	C			TCGA-WJ-A86L-01A-12D-A45V-10	TCGA-WJ-A86L-10A-01D-A38X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	80e4fac9-c066-47a9-9fc0-2a42eef954cd	cebd5a99-cbde-441d-b98a-b84cf1825d65	g.chr19:57646441T>C	ENST00000269834.1	-	5	1649	c.1264A>G	c.(1264-1266)Agt>Ggt	p.S422G	U3_ENST00000516874.1_RNA	NM_052882.1	NP_443114.1	Q96PE6	ZIM3_HUMAN	zinc finger, imprinted 3	422					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(1)|endometrium(3)|kidney(2)|large_intestine(13)|lung(27)|pancreas(1)|prostate(3)|skin(1)|urinary_tract(1)	52		Colorectal(82;0.000256)|all_neural(62;0.0577)|Ovarian(87;0.243)		UCEC - Uterine corpus endometrioid carcinoma (67;0.168)|GBM - Glioblastoma multiforme(193;0.026)		CCACATTCACTACATCTATAG	0.388																																					p.S422G		Atlas-SNP	.											.	ZIM3	107	.	0			c.A1264G						.						163.0	165.0	165.0					19																	57646441		2203	4300	6503	SO:0001583	missense	114026	exon5			ATTCACTACATCT	AF365931	CCDS33125.1	19q13.4	2013-01-08				ENSG00000141946		"""Zinc fingers, C2H2-type"", ""-"""	16366	protein-coding gene	gene with protein product							Standard	NM_052882		Approved	ZNF657	uc002qnz.1	Q96PE6		ENST00000269834.1:c.1264A>G	chr19.hg19:g.57646441T>C	ENSP00000269834:p.Ser422Gly	89.0	0.0		78.0	40.0	NM_052882	Q14CA6	Missense_Mutation	SNP	ENST00000269834.1	hg19	CCDS33125.1	.	.	.	.	.	.	.	.	.	.	T	11.38	1.621654	0.28889	.	.	ENSG00000141946	ENST00000269834	T	0.07688	3.17	2.71	1.63	0.23807	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.07188	0.0182	L	0.43152	1.355	0.09310	N	1	P	0.36183	0.542	B	0.35971	0.215	T	0.32666	-0.9898	9	0.51188	T	0.08	.	3.3939	0.07299	0.2322:0.0:0.2387:0.5291	.	422	Q96PE6	ZIM3_HUMAN	G	422	ENSP00000269834:S422G	ENSP00000269834:S422G	S	-	1	0	ZIM3	62338253	0.000000	0.05858	0.004000	0.12327	0.028000	0.11728	-3.834000	0.00354	0.245000	0.21373	0.260000	0.18958	AGT	.	.		0.388	ZIM3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000465078.1		
SEL1L2	80343	hgsc.bcm.edu	37	20	13894546	13894546	+	Missense_Mutation	SNP	T	T	G			TCGA-WJ-A86L-01A-12D-A45V-10	TCGA-WJ-A86L-10A-01D-A38X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	80e4fac9-c066-47a9-9fc0-2a42eef954cd	cebd5a99-cbde-441d-b98a-b84cf1825d65	g.chr20:13894546T>G	ENST00000284951.5	-	5	505	c.431A>C	c.(430-432)aAa>aCa	p.K144T	SEL1L2_ENST00000378072.5_Missense_Mutation_p.K144T|SEL1L2_ENST00000486903.1_5'UTR			Q5TEA6	SE1L2_HUMAN	sel-1 suppressor of lin-12-like 2 (C. elegans)	144						integral component of membrane (GO:0016021)				cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(14)|lung(25)|ovary(2)|skin(3)|urinary_tract(1)	51						CTCCATAGCTTTCAAGTTTCC	0.363																																					p.K144T		Atlas-SNP	.											.	SEL1L2	103	.	0			c.A431C						.						74.0	68.0	70.0					20																	13894546		1813	4081	5894	SO:0001583	missense	80343	exon5			ATAGCTTTCAAGT	AL137678	CCDS59443.1	20p12.1	2011-03-31	2006-11-24	2006-11-24	ENSG00000101251	ENSG00000101251			15897	protein-coding gene	gene with protein product		614289	"""chromosome 20 open reading frame 50"""	C20orf50			Standard	NM_001271539		Approved	DKFZp434C1826	uc010zrl.3	Q5TEA6	OTTHUMG00000031910	ENST00000284951.5:c.431A>C	chr20.hg19:g.13894546T>G	ENSP00000284951:p.Lys144Thr	106.0	0.0		91.0	32.0	NM_001271539	B4DXX5	Missense_Mutation	SNP	ENST00000284951.5	hg19		.	.	.	.	.	.	.	.	.	.	T	20.5	4.005641	0.74932	.	.	ENSG00000101251	ENST00000378072;ENST00000284951;ENST00000473203	T;T;T	0.55234	0.72;0.72;0.53	5.87	5.87	0.94306	Tetratricopeptide-like helical (1);	0.108090	0.40640	N	0.001058	T	0.56031	0.1958	L	0.46157	1.445	0.43381	D	0.995488	D;P	0.57257	0.979;0.546	P;B	0.52957	0.714;0.115	T	0.52373	-0.8584	10	0.30078	T	0.28	-10.0748	12.9575	0.58438	0.0:0.0:0.0:1.0	.	144;144	B4DXX5;Q5TEA6	.;SE1L2_HUMAN	T	144;144;32	ENSP00000367312:K144T;ENSP00000284951:K144T;ENSP00000420372:K32T	ENSP00000284951:K144T	K	-	2	0	SEL1L2	13842546	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	1.875000	0.39578	2.371000	0.80710	0.533000	0.62120	AAA	.	.		0.363	SEL1L2-002	KNOWN	not_organism_supported|basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000078067.3	NM_025229	
OCSTAMP	128506	hgsc.bcm.edu	37	20	45170059	45170059	+	Missense_Mutation	SNP	C	C	T			TCGA-WJ-A86L-01A-12D-A45V-10	TCGA-WJ-A86L-10A-01D-A38X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	80e4fac9-c066-47a9-9fc0-2a42eef954cd	cebd5a99-cbde-441d-b98a-b84cf1825d65	g.chr20:45170059C>T	ENST00000279028.2	-	3	1568	c.1555G>A	c.(1555-1557)Gtg>Atg	p.V519M		NM_080721.1	NP_542452.1	Q9BR26	OCSTP_HUMAN	osteoclast stimulatory transmembrane protein	519					cellular response to estrogen stimulus (GO:0071391)|cellular response to tumor necrosis factor (GO:0071356)|multinuclear osteoclast differentiation (GO:0072674)|positive regulation of macrophage fusion (GO:0034241)|positive regulation of osteoclast differentiation (GO:0045672)|positive regulation of osteoclast proliferation (GO:0090290)	integral component of membrane (GO:0016021)				breast(1)|endometrium(1)	2						cccaaggtcacacagggaggc	0.517																																					p.V519M		Atlas-SNP	.											.	OCSTAMP	34	.	0			c.G1555A						.						183.0	169.0	173.0					20																	45170059		692	1591	2283	SO:0001583	missense	128506	exon3			AGGTCACACAGGG	AL034424	CCDS54468.1	20q13.12	2012-03-27	2012-03-27	2012-03-27	ENSG00000149635	ENSG00000149635			16116	protein-coding gene	gene with protein product			"""chromosome 20 open reading frame 123"""	C20orf123		18064667	Standard	NM_080721		Approved	dJ257E24.3	uc010zxu.2	Q9BR26	OTTHUMG00000032652	ENST00000279028.2:c.1555G>A	chr20.hg19:g.45170059C>T	ENSP00000279028:p.Val519Met	125.0	0.0		135.0	21.0	NM_080721		Missense_Mutation	SNP	ENST00000279028.2	hg19	CCDS54468.1	.	.	.	.	.	.	.	.	.	.	C	12.00	1.807766	0.31961	.	.	ENSG00000149635	ENST00000279028	T	0.54866	0.55	3.82	2.86	0.33363	.	.	.	.	.	T	0.27765	0.0683	N	0.08118	0	0.09310	N	1	P	0.38148	0.62	B	0.32211	0.142	T	0.11060	-1.0603	9	0.87932	D	0	.	6.6355	0.22881	0.0:0.8679:0.0:0.1321	.	519	Q9BR26	CT123_HUMAN	M	519	ENSP00000279028:V519M	ENSP00000279028:V519M	V	-	1	0	C20orf123	44603466	0.933000	0.31639	0.156000	0.22583	0.132000	0.20833	0.914000	0.28624	1.143000	0.42306	0.655000	0.94253	GTG	.	.		0.517	OCSTAMP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079573.2	XM_496476	
TRPM2	7226	hgsc.bcm.edu	37	21	45819301	45819301	+	Missense_Mutation	SNP	T	T	C			TCGA-WJ-A86L-01A-12D-A45V-10	TCGA-WJ-A86L-10A-01D-A38X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	80e4fac9-c066-47a9-9fc0-2a42eef954cd	cebd5a99-cbde-441d-b98a-b84cf1825d65	g.chr21:45819301T>C	ENST00000397928.1	+	14	2630	c.2185T>C	c.(2185-2187)Ttt>Ctt	p.F729L	TRPM2_ENST00000300481.9_Missense_Mutation_p.F709L|TRPM2_ENST00000498430.1_3'UTR|TRPM2_ENST00000397932.2_Missense_Mutation_p.F729L|TRPM2_ENST00000300482.5_Missense_Mutation_p.F729L	NM_003307.3	NP_003298	O94759	TRPM2_HUMAN	transient receptor potential cation channel, subfamily M, member 2	729					calcium ion transmembrane transport (GO:0070588)|calcium ion transport (GO:0006816)|ion transmembrane transport (GO:0034220)|response to hydroperoxide (GO:0033194)|transmembrane transport (GO:0055085)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	ADP-ribose diphosphatase activity (GO:0047631)|calcium channel activity (GO:0005262)|manganese ion transmembrane transporter activity (GO:0005384)|sodium channel activity (GO:0005272)			breast(3)|central_nervous_system(2)|endometrium(4)|kidney(3)|large_intestine(15)|lung(29)|ovary(3)|pancreas(1)|prostate(5)|skin(7)|upper_aerodigestive_tract(3)|urinary_tract(1)	76						GGACATGAAGTTTGTGTCTCA	0.632																																					p.F729L		Atlas-SNP	.											.	TRPM2	196	.	0			c.T2185C						.						62.0	55.0	57.0					21																	45819301		2203	4296	6499	SO:0001583	missense	7226	exon14			ATGAAGTTTGTGT	AB001535	CCDS13710.1	21q22.3	2011-12-14		2002-01-18	ENSG00000142185	ENSG00000142185		"""Voltage-gated ion channels / Transient receptor potential cation channels"", ""Nudix motif containing"""	12339	protein-coding gene	gene with protein product		603749		TRPC7		9806837, 11385575, 16382100	Standard	NR_038257		Approved	KNP3, LTRPC2, NUDT9L1, NUDT9H, EREG1	uc002zew.1	O94759	OTTHUMG00000040840	ENST00000397928.1:c.2185T>C	chr21.hg19:g.45819301T>C	ENSP00000381023:p.Phe729Leu	80.0	0.0		89.0	35.0	NM_003307	D3DSL6|Q5KTC2|Q6J3P5|Q96KN6|Q96Q93	Missense_Mutation	SNP	ENST00000397928.1	hg19	CCDS13710.1	.	.	.	.	.	.	.	.	.	.	T	33	5.230953	0.95207	.	.	ENSG00000142185	ENST00000300482;ENST00000397928;ENST00000300481;ENST00000397932	T;T;T;T	0.75938	-0.98;-0.98;-0.98;-0.98	5.08	5.08	0.68730	.	0.000000	0.85682	D	0.000000	D	0.85500	0.5711	M	0.76574	2.34	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.91635	0.997;0.999;0.997	D	0.87504	0.2435	10	0.87932	D	0	-22.3412	14.8441	0.70246	0.0:0.0:0.0:1.0	.	729;515;729	E9PGK7;Q5KTC1;O94759	.;.;TRPM2_HUMAN	L	729;729;709;729	ENSP00000300482:F729L;ENSP00000381023:F729L;ENSP00000300481:F709L;ENSP00000381026:F729L	ENSP00000300481:F709L	F	+	1	0	TRPM2	44643729	1.000000	0.71417	0.988000	0.46212	0.961000	0.63080	5.784000	0.68990	1.911000	0.55334	0.454000	0.30748	TTT	.	.		0.632	TRPM2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000098086.1	NM_003307	
THOC5	8563	hgsc.bcm.edu	37	22	29913322	29913322	+	Missense_Mutation	SNP	T	T	C			TCGA-WJ-A86L-01A-12D-A45V-10	TCGA-WJ-A86L-10A-01D-A38X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	80e4fac9-c066-47a9-9fc0-2a42eef954cd	cebd5a99-cbde-441d-b98a-b84cf1825d65	g.chr22:29913322T>C	ENST00000490103.1	-	16	1645	c.1523A>G	c.(1522-1524)cAg>cGg	p.Q508R	THOC5_ENST00000397871.1_Missense_Mutation_p.Q508R|CTA-256D12.11_ENST00000411969.1_RNA|THOC5_ENST00000397872.1_Missense_Mutation_p.Q508R|THOC5_ENST00000397873.2_Missense_Mutation_p.Q508R	NM_003678.4	NP_003669.4	Q13769	THOC5_HUMAN	THO complex 5	508					blastocyst development (GO:0001824)|cell morphogenesis (GO:0000902)|monocyte differentiation (GO:0030224)|mRNA export from nucleus (GO:0006406)|mRNA processing (GO:0006397)|negative regulation of DNA damage checkpoint (GO:2000002)|negative regulation of macrophage differentiation (GO:0045650)|positive regulation of DNA-templated transcription, elongation (GO:0032786)|primitive hemopoiesis (GO:0060215)|regulation of mRNA export from nucleus (GO:0010793)|regulation of stem cell division (GO:2000035)|RNA splicing (GO:0008380)|stem cell division (GO:0017145)|viral mRNA export from host cell nucleus (GO:0046784)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|THO complex (GO:0000347)|THO complex part of transcription export complex (GO:0000445)|transcription export complex (GO:0000346)	mRNA binding (GO:0003729)			NS(1)|breast(4)|cervix(1)|endometrium(2)|large_intestine(4)|lung(7)|upper_aerodigestive_tract(1)|urinary_tract(1)	21						GAAGAGGTACTGGCAATCACT	0.483																																					p.Q508R		Atlas-SNP	.											.	THOC5	58	.	0			c.A1523G						.						126.0	101.0	110.0					22																	29913322		2203	4300	6503	SO:0001583	missense	8563	exon17			AGGTACTGGCAAT	AB023200	CCDS13859.1	22q12	2013-02-11			ENSG00000100296	ENSG00000100296		"""THO complex subunits"""	19074	protein-coding gene	gene with protein product	"""functional spliceosome-associated protein 79"""	612733	"""chromosome 22 open reading frame 19"""	C22orf19		11979277, 8242058, 10231032, 19015024, 18373705	Standard	NM_003678		Approved	PK1.3, KIAA0983, Fmip, fSAP79	uc003afs.3	Q13769	OTTHUMG00000151291	ENST00000490103.1:c.1523A>G	chr22.hg19:g.29913322T>C	ENSP00000420306:p.Gln508Arg	125.0	0.0		102.0	49.0	NM_001002878	O60839|Q9UPZ5	Missense_Mutation	SNP	ENST00000490103.1	hg19	CCDS13859.1	.	.	.	.	.	.	.	.	.	.	T	17.57	3.421666	0.62622	.	.	ENSG00000100296	ENST00000490103;ENST00000397872;ENST00000397871;ENST00000397873	T;T;T;T	0.23552	1.9;1.9;1.9;1.9	5.81	5.81	0.92471	.	0.152728	0.64402	D	0.000015	T	0.26702	0.0653	M	0.62723	1.935	0.53688	D	0.999979	P	0.42827	0.791	B	0.37650	0.255	T	0.06807	-1.0806	10	0.15066	T	0.55	-26.8255	15.8194	0.78628	0.0:0.0:0.0:1.0	.	508	Q13769	THOC5_HUMAN	R	508	ENSP00000420306:Q508R;ENSP00000380970:Q508R;ENSP00000380969:Q508R;ENSP00000380971:Q508R	ENSP00000380969:Q508R	Q	-	2	0	THOC5	28243322	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	6.020000	0.70826	2.206000	0.71126	0.533000	0.62120	CAG	.	.		0.483	THOC5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000322097.1	NM_003678	
TTC38	55020	hgsc.bcm.edu	37	22	46685390	46685390	+	Missense_Mutation	SNP	G	G	T			TCGA-WJ-A86L-01A-12D-A45V-10	TCGA-WJ-A86L-10A-01D-A38X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	80e4fac9-c066-47a9-9fc0-2a42eef954cd	cebd5a99-cbde-441d-b98a-b84cf1825d65	g.chr22:46685390G>T	ENST00000381031.3	+	12	1250	c.1174G>T	c.(1174-1176)Gac>Tac	p.D392Y	TTC38_ENST00000445282.2_Missense_Mutation_p.D334Y	NM_017931.2	NP_060401	Q5R3I4	TTC38_HUMAN	tetratricopeptide repeat domain 38	392						extracellular vesicular exosome (GO:0070062)				endometrium(4)|large_intestine(3)|lung(4)|ovary(1)	12						CGGGAACCCTGACCGCGTCCT	0.697																																					p.D392Y		Atlas-SNP	.											.	TTC38	40	.	0			c.G1174T						.						26.0	33.0	31.0					22																	46685390		2079	4198	6277	SO:0001583	missense	55020	exon12			AACCCTGACCGCG		CCDS43030.1	22q13	2013-01-11			ENSG00000075234	ENSG00000075234		"""Tetratricopeptide (TTC) repeat domain containing"""	26082	protein-coding gene	gene with protein product							Standard	NM_017931		Approved	FLJ20699	uc003bhi.3	Q5R3I4	OTTHUMG00000150494	ENST00000381031.3:c.1174G>T	chr22.hg19:g.46685390G>T	ENSP00000370419:p.Asp392Tyr	72.0	0.0		59.0	29.0	NM_017931	Q8WV27|Q9NWP8	Missense_Mutation	SNP	ENST00000381031.3	hg19	CCDS43030.1	.	.	.	.	.	.	.	.	.	.	G	14.89	2.670675	0.47781	.	.	ENSG00000075234	ENST00000381031;ENST00000445282	T;T	0.47869	0.83;0.85	4.77	4.77	0.60923	.	0.230464	0.47455	D	0.000225	T	0.70544	0.3236	M	0.83953	2.67	0.52099	D	0.99994	D;D	0.89917	1.0;0.998	D;D	0.78314	0.991;0.969	T	0.75886	-0.3159	10	0.66056	D	0.02	-14.916	15.2969	0.73916	0.0:0.0:1.0:0.0	.	334;392	E7ES35;Q5R3I4	.;TTC38_HUMAN	Y	392;334	ENSP00000370419:D392Y;ENSP00000393960:D334Y	ENSP00000370419:D392Y	D	+	1	0	TTC38	45064054	1.000000	0.71417	0.872000	0.34217	0.064000	0.16182	5.079000	0.64431	2.212000	0.71576	0.655000	0.94253	GAC	.	.		0.697	TTC38-001	NOVEL	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000318469.1	NM_017931	
DCAF8L2	347442	hgsc.bcm.edu	37	X	27765423	27765423	+	Silent	SNP	G	G	A			TCGA-WJ-A86L-01A-12D-A45V-10	TCGA-WJ-A86L-10A-01D-A38X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	80e4fac9-c066-47a9-9fc0-2a42eef954cd	cebd5a99-cbde-441d-b98a-b84cf1825d65	g.chrX:27765423G>A	ENST00000451261.2	+	5	810	c.411G>A	c.(409-411)gaG>gaA	p.E137E		NM_001136533.1	NP_001130005.1	P0C7V8	DC8L2_HUMAN	DDB1 and CUL4 associated factor 8-like 2	137	Glu-rich.									central_nervous_system(1)|endometrium(9)|kidney(3)|lung(7)|pancreas(1)|skin(3)	24						aggaggaggaggaggaggagg	0.592																																					p.E137E		Atlas-SNP	.											.	DCAF8L2	79	.	0			c.G411A						.						13.0	13.0	13.0					X																	27765423		692	1584	2276	SO:0001819	synonymous_variant	347442	exon1			GGAGGAGGAGGAG		CCDS59162.1	Xp22.11	2013-01-09	2009-07-17	2009-07-17		ENSG00000189186		"""WD repeat domain containing"""	31811	protein-coding gene	gene with protein product			"""WD repeat domain 42C"""	WDR42C			Standard	NM_001136533		Approved		uc011mjy.2	P0C7V8		ENST00000451261.2:c.411G>A	chrX.hg19:g.27765423G>A		11.0	0.0		47.0	33.0	NM_001136533	B2RXH9|J3KT06	Silent	SNP	ENST00000451261.2	hg19	CCDS59162.1																																																																																			.	.		0.592	DCAF8L2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056143.4	XM_293354	
BMP15	9210	hgsc.bcm.edu	37	X	50658936	50658936	+	Missense_Mutation	SNP	G	G	T			TCGA-WJ-A86L-01A-12D-A45V-10	TCGA-WJ-A86L-10A-01D-A38X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	80e4fac9-c066-47a9-9fc0-2a42eef954cd	cebd5a99-cbde-441d-b98a-b84cf1825d65	g.chrX:50658936G>T	ENST00000252677.3	+	2	508	c.508G>T	c.(508-510)Gat>Tat	p.D170Y		NM_005448.2	NP_005439.2	O95972	BMP15_HUMAN	bone morphogenetic protein 15	170					female gamete generation (GO:0007292)|granulosa cell development (GO:0060016)|ovarian follicle development (GO:0001541)|positive regulation of transcription, DNA-templated (GO:0045893)	cytoplasm (GO:0005737)|extracellular space (GO:0005615)				NS(1)|breast(2)|endometrium(4)|kidney(1)|large_intestine(5)|lung(10)|ovary(2)|skin(1)	26	Ovarian(276;0.236)					CTCAGAAGGAGATTCCTCAAA	0.478																																					p.D170Y		Atlas-SNP	.											.	BMP15	62	.	0			c.G508T						.						110.0	86.0	94.0					X																	50658936		2203	4299	6502	SO:0001583	missense	9210	exon2			GAAGGAGATTCCT	AF082349	CCDS14334.1	Xp11.2	2013-02-06			ENSG00000130385	ENSG00000130385		"""Bone morphogenetic proteins"""	1068	protein-coding gene	gene with protein product		300247				9849956	Standard	NM_005448		Approved	GDF9B	uc011mnw.2	O95972	OTTHUMG00000021525	ENST00000252677.3:c.508G>T	chrX.hg19:g.50658936G>T	ENSP00000252677:p.Asp170Tyr	298.0	0.0		254.0	118.0	NM_005448	Q17RM6|Q5JST1|Q9UMS1	Missense_Mutation	SNP	ENST00000252677.3	hg19	CCDS14334.1	.	.	.	.	.	.	.	.	.	.	g	0.001	-2.882156	0.00061	.	.	ENSG00000130385	ENST00000252677	T	0.79454	-1.27	5.42	1.53	0.23141	.	1.054580	0.07219	N	0.860493	T	0.48978	0.1530	N	0.02011	-0.69	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.32824	-0.9892	10	0.15952	T	0.53	.	4.858	0.13570	0.2699:0.0:0.5831:0.147	.	170	O95972	BMP15_HUMAN	Y	170	ENSP00000252677:D170Y	ENSP00000252677:D170Y	D	+	1	0	BMP15	50675676	0.000000	0.05858	0.000000	0.03702	0.002000	0.02628	0.213000	0.17521	-0.134000	0.11516	0.556000	0.70494	GAT	.	.		0.478	BMP15-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056572.1	NM_005448	
FOXR2	139628	hgsc.bcm.edu	37	X	55650548	55650548	+	Missense_Mutation	SNP	C	C	T			TCGA-WJ-A86L-01A-12D-A45V-10	TCGA-WJ-A86L-10A-01D-A38X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	80e4fac9-c066-47a9-9fc0-2a42eef954cd	cebd5a99-cbde-441d-b98a-b84cf1825d65	g.chrX:55650548C>T	ENST00000339140.3	+	1	716	c.404C>T	c.(403-405)tCc>tTc	p.S135F		NM_198451.3	NP_940853.1	Q6PJQ5	FOXR2_HUMAN	forkhead box R2	135					transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)			biliary_tract(1)|central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(1)|liver(1)|lung(8)|prostate(1)|skin(1)|urinary_tract(1)	19						CCATCTTCCTCCAGTGAGCAG	0.517																																					p.S135F		Atlas-SNP	.											.	FOXR2	42	.	0			c.C404T						.						77.0	69.0	72.0					X																	55650548		2203	4300	6503	SO:0001583	missense	139628	exon1			CTTCCTCCAGTGA	BC012934	CCDS35308.1	Xp11	2006-12-15			ENSG00000189299	ENSG00000189299		"""Forkhead boxes"""	30469	protein-coding gene	gene with protein product						15202009, 15202027	Standard	NM_198451		Approved	MGC21658, FOXN6	uc004duo.3	Q6PJQ5	OTTHUMG00000021661	ENST00000339140.3:c.404C>T	chrX.hg19:g.55650548C>T	ENSP00000427329:p.Ser135Phe	134.0	0.0		134.0	72.0	NM_198451		Missense_Mutation	SNP	ENST00000339140.3	hg19	CCDS35308.1	.	.	.	.	.	.	.	.	.	.	C	1.498	-0.552799	0.03996	.	.	ENSG00000189299	ENST00000339140	D	0.94457	-3.43	3.63	1.55	0.23275	.	1.787790	0.03253	N	0.182135	D	0.91019	0.7175	L	0.58101	1.795	0.09310	N	1	B	0.31485	0.325	B	0.29267	0.1	T	0.76252	-0.3027	10	0.13470	T	0.59	.	3.4904	0.07636	0.3258:0.5363:0.0:0.1379	.	135	Q6PJQ5	FOXR2_HUMAN	F	135	ENSP00000427329:S135F	ENSP00000427329:S135F	S	+	2	0	FOXR2	55667273	0.004000	0.15560	0.000000	0.03702	0.071000	0.16799	0.350000	0.20079	0.231000	0.21079	0.600000	0.82982	TCC	.	.		0.517	FOXR2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056877.2	NM_198451	
DACH2	117154	hgsc.bcm.edu	37	X	86069740	86069740	+	Missense_Mutation	SNP	G	G	T			TCGA-WJ-A86L-01A-12D-A45V-10	TCGA-WJ-A86L-10A-01D-A38X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	80e4fac9-c066-47a9-9fc0-2a42eef954cd	cebd5a99-cbde-441d-b98a-b84cf1825d65	g.chrX:86069740G>T	ENST00000373125.4	+	10	1587	c.1587G>T	c.(1585-1587)ttG>ttT	p.L529F	DACH2_ENST00000508860.1_Missense_Mutation_p.L362F|DACH2_ENST00000373131.1_Missense_Mutation_p.L516F|DACH2_ENST00000510272.1_Missense_Mutation_p.L310F	NM_053281.3	NP_444511.1	Q96NX9	DACH2_HUMAN	dachshund family transcription factor 2	529	DACHbox-C.				development of primary female sexual characteristics (GO:0046545)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)			breast(2)|central_nervous_system(3)|cervix(1)|endometrium(7)|kidney(6)|large_intestine(14)|lung(28)|ovary(5)|pancreas(1)|skin(1)|upper_aerodigestive_tract(3)	71						AGAGAAAATTGCAGGAAGCCT	0.443																																					p.L529F		Atlas-SNP	.											.	DACH2	263	.	0			c.G1587T						.						62.0	57.0	59.0					X																	86069740		2203	4300	6503	SO:0001583	missense	117154	exon10			AAAATTGCAGGAA	AF428101	CCDS14455.1, CCDS48140.1, CCDS55457.1	Xq21.3	2014-02-03	2014-02-03		ENSG00000126733	ENSG00000126733			16814	protein-coding gene	gene with protein product		300608	"""dachshund homolog 2 (Drosophila)"""				Standard	NM_053281		Approved		uc004eew.2	Q96NX9	OTTHUMG00000021944	ENST00000373125.4:c.1587G>T	chrX.hg19:g.86069740G>T	ENSP00000362217:p.Leu529Phe	115.0	0.0		136.0	17.0	NM_053281	B1AJV3|B4DQG3|Q8NAY3|Q8ND17|Q96N55	Missense_Mutation	SNP	ENST00000373125.4	hg19	CCDS14455.1	.	.	.	.	.	.	.	.	.	.	G	15.21	2.766361	0.49574	.	.	ENSG00000126733	ENST00000344497;ENST00000373131;ENST00000373125;ENST00000508860;ENST00000510272;ENST00000400297;ENST00000484479	D;D	0.90788	-2.7;-2.73	4.76	2.86	0.33363	.	0.000000	0.51477	D	0.000098	D	0.93436	0.7906	M	0.72894	2.215	0.50467	D	0.999872	D;D;D;D	0.89917	1.0;1.0;1.0;0.999	D;D;D;D	0.87578	0.996;0.998;0.997;0.998	D	0.91433	0.5167	10	0.72032	D	0.01	.	7.7703	0.29004	0.0913:0.0:0.7436:0.165	.	395;529;516;529	Q1RMF5;A8K3I1;Q96NX9-2;Q96NX9	.;.;.;DACH2_HUMAN	F	529;516;529;362;310;362;194	ENSP00000362223:L516F;ENSP00000362217:L529F	ENSP00000345134:L529F	L	+	3	2	DACH2	85956396	1.000000	0.71417	0.999000	0.59377	0.622000	0.37654	0.726000	0.25984	0.212000	0.20703	0.415000	0.27848	TTG	.	.		0.443	DACH2-007	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000359266.1	NM_053281	
DLX5	1749	hgsc.bcm.edu	37	7	96653687	96653687	+	Frame_Shift_Del	DEL	G	G	-			TCGA-WJ-A86L-01A-12D-A45V-10	TCGA-WJ-A86L-10A-01D-A38X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	80e4fac9-c066-47a9-9fc0-2a42eef954cd	cebd5a99-cbde-441d-b98a-b84cf1825d65	g.chr7:96653687delG	ENST00000222598.4	-	1	722	c.249delC	c.(247-249)tccfs	p.S83fs	DLX5_ENST00000486603.2_Frame_Shift_Del_p.S83fs|DLX5_ENST00000493764.1_5'UTR	NM_005221.5	NP_005212.1	P56178	DLX5_HUMAN	distal-less homeobox 5	83					anatomical structure formation involved in morphogenesis (GO:0048646)|axon guidance (GO:0007411)|BMP signaling pathway (GO:0030509)|cell proliferation (GO:0008283)|cellular response to BMP stimulus (GO:0071773)|embryonic limb morphogenesis (GO:0030326)|endochondral ossification (GO:0001958)|epithelial cell differentiation (GO:0030855)|face morphogenesis (GO:0060325)|inner ear morphogenesis (GO:0042472)|nervous system development (GO:0007399)|olfactory pit development (GO:0060166)|osteoblast differentiation (GO:0001649)|palate development (GO:0060021)|positive regulation of canonical Wnt signaling pathway (GO:0090263)|positive regulation of epithelial cell proliferation (GO:0050679)|positive regulation of osteoblast differentiation (GO:0045669)|positive regulation of transcription from RNA polymerase II promoter involved in cellular response to chemical stimulus (GO:1901522)|positive regulation of transcription, DNA-templated (GO:0045893)|skeletal system development (GO:0001501)	cytoplasm (GO:0005737)|nuclear chromatin (GO:0000790)	RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|transcription regulatory region DNA binding (GO:0044212)			central_nervous_system(1)|endometrium(1)|large_intestine(7)|lung(9)|ovary(1)|prostate(1)	20	all_cancers(62;9.56e-09)|all_epithelial(64;7.38e-09)|Esophageal squamous(72;0.0125)|all_lung(186;0.0855)|Lung NSC(181;0.0858)					AGCTCCCGGCGGAGCCGTTCA	0.622																																					p.A84fs		Atlas-INDEL	.											.	DLX5	52	.	0			c.250delG						.						52.0	53.0	52.0					7																	96653687		2203	4300	6503	SO:0001589	frameshift_variant	1749	exon1			.		CCDS5647.1	7q21.3	2011-06-20	2005-12-22		ENSG00000105880	ENSG00000105880		"""Homeoboxes / ANTP class : NKL subclass"""	2918	protein-coding gene	gene with protein product		600028	"""distal-less homeo box 5"""			7907794	Standard	XM_005250185		Approved		uc003uon.3	P56178	OTTHUMG00000154200	ENST00000222598.4:c.249delC	chr7.hg19:g.96653687delG	ENSP00000222598:p.Ser83fs	95.0	0.0		112.0	50.0	NM_005221	B7Z4P3|Q9UPL1	Frame_Shift_Del	DEL	ENST00000222598.4	hg19	CCDS5647.1																																																																																			.	.		0.622	DLX5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000334371.2		
SLC9A1	6548	hgsc.bcm.edu	37	1	27429729	27429732	+	Frame_Shift_Del	DEL	TTCG	TTCG	-			TCGA-WJ-A86L-01A-12D-A45V-10	TCGA-WJ-A86L-10A-01D-A38X-10	TTCG	TTCG	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	80e4fac9-c066-47a9-9fc0-2a42eef954cd	cebd5a99-cbde-441d-b98a-b84cf1825d65	g.chr1:27429729_27429732delTTCG	ENST00000263980.3	-	6	2132_2135	c.1557_1560delCGAA	c.(1555-1560)aacgaafs	p.NE519fs	SLC9A1_ENST00000545949.1_Frame_Shift_Del_p.NE180fs	NM_003047.4	NP_003038.2	P19634	SL9A1_HUMAN	solute carrier family 9, subfamily A (NHE1, cation proton antiporter 1), member 1	519	Interaction with CHP2.				carbohydrate metabolic process (GO:0005975)|cardiac muscle cell differentiation (GO:0055007)|cell growth (GO:0016049)|cellular response to acidic pH (GO:0071468)|glycosaminoglycan metabolic process (GO:0030203)|hyaluronan catabolic process (GO:0030214)|hyaluronan metabolic process (GO:0030212)|hydrogen ion transmembrane transport (GO:1902600)|ion transport (GO:0006811)|negative regulation of apoptotic process (GO:0043066)|neuron death (GO:0070997)|positive regulation of action potential (GO:0045760)|positive regulation of cell growth (GO:0030307)|positive regulation of mitochondrial membrane permeability (GO:0035794)|protein oligomerization (GO:0051259)|regulation of intracellular pH (GO:0051453)|regulation of pH (GO:0006885)|regulation of sensory perception of pain (GO:0051930)|regulation of the force of heart contraction (GO:0002026)|response to acidic pH (GO:0010447)|response to drug (GO:0042493)|response to organic cyclic compound (GO:0014070)|small molecule metabolic process (GO:0044281)|sodium ion export (GO:0071436)|transmembrane transport (GO:0055085)	apical plasma membrane (GO:0016324)|basolateral plasma membrane (GO:0016323)|cytoplasm (GO:0005737)|endoplasmic reticulum (GO:0005783)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|integral component of membrane (GO:0016021)|membrane raft (GO:0045121)|mitochondrion (GO:0005739)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	calcium-dependent protein binding (GO:0048306)|sodium:proton antiporter activity (GO:0015385)|solute:proton antiporter activity (GO:0015299)			central_nervous_system(1)|cervix(3)|endometrium(3)|kidney(2)|large_intestine(4)|liver(1)|lung(7)|ovary(1)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)	27				UCEC - Uterine corpus endometrioid carcinoma (279;0.0178)|Epithelial(14;2.19e-50)|OV - Ovarian serous cystadenocarcinoma(117;1.8e-29)|Colorectal(126;7.61e-09)|COAD - Colon adenocarcinoma(152;9.32e-07)|BRCA - Breast invasive adenocarcinoma(304;0.000521)|KIRC - Kidney renal clear cell carcinoma(1967;0.00079)|STAD - Stomach adenocarcinoma(196;0.00125)|READ - Rectum adenocarcinoma(331;0.046)	Amiloride(DB00594)	TGTGGATCTCTTCGTTGATGGAGC	0.603											OREG0013277	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.520_521del		Atlas-INDEL	.											.	SLC9A1	68	.	0			c.1558_1561del						.																																			SO:0001589	frameshift_variant	6548	exon6			.	M81768	CCDS295.1	1p36.1-p35	2014-06-13	2012-03-22		ENSG00000090020	ENSG00000090020		"""Solute carriers"""	11071	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 143"""	107310	"""solute carrier family 9 (sodium/hydrogen exchanger), isoform 1 (antiporter, Na+/H+, amiloride sensitive)"", ""solute carrier family 9 (sodium/hydrogen exchanger), member 1"""	APNH, NHE1		8283968	Standard	NM_003047		Approved	PPP1R143	uc001bnm.4	P19634	OTTHUMG00000004271	ENST00000263980.3:c.1557_1560delCGAA	chr1.hg19:g.27429729_27429732delTTCG	ENSP00000263980:p.Asn519fs	74.0	0.0	794	61.0	20.0	NM_003047	B1ALD6|D3DPL4|Q96EM2	Frame_Shift_Del	DEL	ENST00000263980.3	hg19	CCDS295.1																																																																																			.	.		0.603	SLC9A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000012336.2	NM_003047	
DDX60L	91351	hgsc.bcm.edu	37	4	169327112	169327112	+	Frame_Shift_Del	DEL	G	G	-			TCGA-WJ-A86L-01A-12D-A45V-10	TCGA-WJ-A86L-10A-01D-A38X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	80e4fac9-c066-47a9-9fc0-2a42eef954cd	cebd5a99-cbde-441d-b98a-b84cf1825d65	g.chr4:169327112delG	ENST00000511577.1	-	24	3449	c.3202delC	c.(3202-3204)caafs	p.Q1068fs	DDX60L_ENST00000505890.1_Frame_Shift_Del_p.Q1068fs|DDX60L_ENST00000260184.7_Frame_Shift_Del_p.Q1068fs			Q5H9U9	DDX6L_HUMAN	DEAD (Asp-Glu-Ala-Asp) box polypeptide 60-like	1068							ATP binding (GO:0005524)|helicase activity (GO:0004386)|RNA binding (GO:0003723)			breast(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(7)|lung(23)|ovary(2)|prostate(1)|skin(1)|stomach(1)	43		Prostate(90;0.00876)|Renal(120;0.0183)|all_neural(102;0.0837)|Melanoma(52;0.132)		GBM - Glioblastoma multiforme(119;0.175)		TTCTTCACTTGGCCATTTTTA	0.274																																					p.Q1068fs		Atlas-INDEL	.											.	DDX60L	116	.	0			c.3203delA						.						110.0	98.0	101.0					4																	169327112		1837	4119	5956	SO:0001589	frameshift_variant	91351	exon24			.	AK092461	CCDS47161.1	4q32.3	2008-01-08				ENSG00000181381			26429	protein-coding gene	gene with protein product							Standard	XM_005263341		Approved	FLJ31033	uc003irq.4	Q5H9U9		ENST00000511577.1:c.3202delC	chr4.hg19:g.169327112delG	ENSP00000422423:p.Gln1068fs	99.0	0.0		81.0	32.0	NM_001012967	Q96ND6	Frame_Shift_Del	DEL	ENST00000511577.1	hg19																																																																																				.	.		0.274	DDX60L-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000364839.1	NM_001012967	
GNPNAT1	64841	hgsc.bcm.edu	37	14	53251349	53251349	+	Frame_Shift_Del	DEL	G	G	-			TCGA-WJ-A86L-01A-12D-A45V-10	TCGA-WJ-A86L-10A-01D-A38X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	80e4fac9-c066-47a9-9fc0-2a42eef954cd	cebd5a99-cbde-441d-b98a-b84cf1825d65	g.chr14:53251349delG	ENST00000216410.3	-	2	207	c.20delC	c.(19-21)cctfs	p.P7fs	RN7SL588P_ENST00000583393.1_RNA|GNPNAT1_ENST00000554230.1_Intron	NM_198066.3	NP_932332.1	Q96EK6	GNA1_HUMAN	glucosamine-phosphate N-acetyltransferase 1	7					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)					GTCAAACATAGGAGTTTCATC	0.348																																					p.P7fs		Atlas-INDEL	.											.	GNPNAT1	14	.	0			c.21delT						.						47.0	45.0	46.0					14																	53251349		2203	4300	6503	SO:0001589	frameshift_variant	64841	exon2			.	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.20delC	chr14.hg19:g.53251349delG	ENSP00000216410:p.Pro7fs	85.0	0.0		80.0	34.0	NM_198066		Frame_Shift_Del	DEL	ENST00000216410.3	hg19	CCDS9712.1																																																																																			.	.		0.348	GNPNAT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276898.1		
DCAF8L2	347442	hgsc.bcm.edu	37	X	27765410	27765410	+	Frame_Shift_Del	DEL	A	A	-			TCGA-WJ-A86L-01A-12D-A45V-10	TCGA-WJ-A86L-10A-01D-A38X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	80e4fac9-c066-47a9-9fc0-2a42eef954cd	cebd5a99-cbde-441d-b98a-b84cf1825d65	g.chrX:27765410delA	ENST00000451261.2	+	5	797	c.398delA	c.(397-399)gagfs	p.E147fs		NM_001136533.1	NP_001130005.1	P0C7V8	DC8L2_HUMAN	DDB1 and CUL4 associated factor 8-like 2	147	Glu-rich.			Missing (in Ref. 1; AAI57860). {ECO:0000305}.						central_nervous_system(1)|endometrium(9)|kidney(3)|lung(7)|pancreas(1)|skin(3)	24						gaggaggaggaggaggaggag	0.567																																					p.E133fs		Atlas-INDEL	.											.	DCAF8L2	79	.	0			c.397delG						.			40,2596		12,12,4,1144,296	17.0	15.0	16.0				0.0	X	dbSNP_126	16	48,4641		10,13,15,1764,1100	no	frameshift	DCAF8L2	NM_001136533.1		22,25,19,2908,1396	A1A1,A1R,A1,RR,R		1.0237,1.5175,1.2014			27765410	88,7237	692	1585	2277	SO:0001589	frameshift_variant	347442	exon1			.		CCDS59162.1	Xp22.11	2013-01-09	2009-07-17	2009-07-17		ENSG00000189186		"""WD repeat domain containing"""	31811	protein-coding gene	gene with protein product			"""WD repeat domain 42C"""	WDR42C			Standard	NM_001136533		Approved		uc011mjy.2	P0C7V8		ENST00000451261.2:c.398delA	chrX.hg19:g.27765410delA	ENSP00000462745:p.Glu147fs	60.0	0.0		52.0	10.0	NM_001136533	B2RXH9|J3KT06	Frame_Shift_Del	DEL	ENST00000451261.2	hg19	CCDS59162.1																																																																																			.	.		0.567	DCAF8L2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056143.4	XM_293354	
PTCH1	5727	hgsc.bcm.edu	37	9	98232184	98232184	+	Frame_Shift_Del	DEL	G	G	-			TCGA-WJ-A86L-01A-12D-A45V-10	TCGA-WJ-A86L-10A-01D-A38X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	80e4fac9-c066-47a9-9fc0-2a42eef954cd	cebd5a99-cbde-441d-b98a-b84cf1825d65	g.chr9:98232184delG	ENST00000331920.6	-	13	2057	c.1758delC	c.(1756-1758)gccfs	p.A586fs	PTCH1_ENST00000430669.2_Frame_Shift_Del_p.A520fs|PTCH1_ENST00000429896.2_Frame_Shift_Del_p.A435fs|PTCH1_ENST00000437951.1_Frame_Shift_Del_p.A520fs|PTCH1_ENST00000421141.1_Frame_Shift_Del_p.A435fs|PTCH1_ENST00000375274.2_Frame_Shift_Del_p.A585fs|PTCH1_ENST00000418258.1_Frame_Shift_Del_p.A435fs	NM_000264.3	NP_000255.2	Q13635	PTC1_HUMAN	patched 1	586	SSD. {ECO:0000255|PROSITE- ProRule:PRU00199}.				brain development (GO:0007420)|branching involved in ureteric bud morphogenesis (GO:0001658)|cell differentiation involved in kidney development (GO:0061005)|cell proliferation involved in metanephros development (GO:0072203)|cellular response to cholesterol (GO:0071397)|dorsal/ventral pattern formation (GO:0009953)|embryonic limb morphogenesis (GO:0030326)|embryonic organ development (GO:0048568)|epidermis development (GO:0008544)|glucose homeostasis (GO:0042593)|heart morphogenesis (GO:0003007)|hindlimb morphogenesis (GO:0035137)|in utero embryonic development (GO:0001701)|keratinocyte proliferation (GO:0043616)|limb morphogenesis (GO:0035108)|mammary gland duct morphogenesis (GO:0060603)|mammary gland epithelial cell differentiation (GO:0060644)|negative regulation of cell division (GO:0051782)|negative regulation of epithelial cell proliferation (GO:0050680)|negative regulation of multicellular organism growth (GO:0040015)|negative regulation of osteoblast differentiation (GO:0045668)|negative regulation of sequence-specific DNA binding transcription factor activity (GO:0043433)|negative regulation of smoothened signaling pathway (GO:0045879)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|neural plate axis specification (GO:0021997)|neural tube closure (GO:0001843)|neural tube patterning (GO:0021532)|organ morphogenesis (GO:0009887)|pharyngeal system development (GO:0060037)|positive regulation of cholesterol efflux (GO:0010875)|protein processing (GO:0016485)|protein targeting to plasma membrane (GO:0072661)|regulation of mitotic cell cycle (GO:0007346)|regulation of protein localization (GO:0032880)|regulation of smoothened signaling pathway (GO:0008589)|renal system development (GO:0072001)|response to chlorate (GO:0010157)|response to drug (GO:0042493)|response to estradiol (GO:0032355)|response to mechanical stimulus (GO:0009612)|response to retinoic acid (GO:0032526)|smoothened signaling pathway (GO:0007224)|smoothened signaling pathway involved in dorsal/ventral neural tube patterning (GO:0060831)|somite development (GO:0061053)|spinal cord motor neuron differentiation (GO:0021522)	axonal growth cone (GO:0044295)|caveola (GO:0005901)|dendritic growth cone (GO:0044294)|integral component of membrane (GO:0016021)|intracellular membrane-bounded organelle (GO:0043231)|midbody (GO:0030496)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|postsynaptic density (GO:0014069)|primary cilium (GO:0072372)	cholesterol binding (GO:0015485)|cyclin binding (GO:0030332)|hedgehog family protein binding (GO:0097108)|hedgehog receptor activity (GO:0008158)|heparin binding (GO:0008201)|smoothened binding (GO:0005119)			NS(8)|bone(33)|breast(10)|central_nervous_system(95)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(8)|kidney(2)|large_intestine(18)|lung(22)|meninges(1)|oesophagus(3)|ovary(6)|prostate(2)|skin(262)|upper_aerodigestive_tract(11)|urinary_tract(2)|vulva(1)	490		Medulloblastoma(1;7.87e-06)|all_neural(1;0.000555)|Acute lymphoblastic leukemia(62;0.136)				GCAGAACCATGGCAAAATTGA	0.438																																					p.M587fs		Atlas-INDEL	.											.	PTCH1	1850	.	0			c.1759delA						.						102.0	99.0	100.0					9																	98232184		2203	4300	6503	SO:0001589	frameshift_variant	5727	exon13			.	AI494442	CCDS6714.1, CCDS43851.1, CCDS47995.1, CCDS47996.1	9q22.1-q31	2014-09-17	2010-06-24	2006-09-26	ENSG00000185920	ENSG00000185920			9585	protein-coding gene	gene with protein product		601309	"""patched (Drosophila) homolog"", ""patched homolog (Drosophila)"", ""patched homolog 1 (Drosophila)"""	NBCCS, PTCH		8658145	Standard	NM_001083603		Approved	BCNS	uc004avk.4	Q13635	OTTHUMG00000020280	ENST00000331920.6:c.1758delC	chr9.hg19:g.98232184delG	ENSP00000332353:p.Ala586fs	90.0	0.0		79.0	32.0	NM_000264	A3KBI9|E9PEJ8|Q13463|Q5R1U7|Q5R1U9|Q5R1V0|Q5VZC0|Q5VZC2|Q86XG7	Frame_Shift_Del	DEL	ENST00000331920.6	hg19	CCDS6714.1																																																																																			.	.		0.438	PTCH1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053229.2	NM_000264	
PHOX2B	8929	hgsc.bcm.edu	37	4	41748009	41748009	+	Frame_Shift_Del	DEL	C	C	-	rs17879189		TCGA-WJ-A86L-01A-12D-A45V-10	TCGA-WJ-A86L-10A-01D-A38X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	80e4fac9-c066-47a9-9fc0-2a42eef954cd	cebd5a99-cbde-441d-b98a-b84cf1825d65	g.chr4:41748009delC	ENST00000226382.2	-	3	1119	c.760delG	c.(760-762)gcafs	p.A260fs	RP11-227F19.1_ENST00000508038.1_RNA	NM_003924.3	NP_003915.2	Q99453	PHX2B_HUMAN	paired-like homeobox 2b	260	Poly-Ala.				autonomic nervous system development (GO:0048483)|brainstem development (GO:0003360)|cell differentiation in hindbrain (GO:0021533)|cellular response to BMP stimulus (GO:0071773)|dopaminergic neuron differentiation (GO:0071542)|efferent axon development in a lateral line nerve (GO:0048894)|enteric nervous system development (GO:0048484)|glial cell differentiation (GO:0010001)|hindbrain tangential cell migration (GO:0021934)|inner ear development (GO:0048839)|medullary reticular formation development (GO:0021723)|negative regulation of cell cycle arrest (GO:0071157)|negative regulation of cell proliferation (GO:0008285)|negative regulation of neuron differentiation (GO:0045665)|neural crest cell migration involved in autonomic nervous system development (GO:1901166)|neuron migration (GO:0001764)|noradrenergic neuron development (GO:0003358)|noradrenergic neuron differentiation (GO:0003357)|parasympathetic nervous system development (GO:0048486)|positive regulation of G2/M transition of mitotic cell cycle (GO:0010971)|positive regulation of neuron differentiation (GO:0045666)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of gene expression (GO:0010468)|regulation of respiratory gaseous exchange by neurological system process (GO:0002087)|respiratory system development (GO:0060541)|retrotrapezoid nucleus neuron differentiation (GO:0061452)|skeletal muscle cell differentiation (GO:0035914)|sympathetic ganglion development (GO:0061549)|sympathetic nervous system development (GO:0048485)|transcription, DNA-templated (GO:0006351)	nuclear chromatin (GO:0000790)	RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II regulatory region sequence-specific DNA binding (GO:0000977)			autonomic_ganglia(7)|central_nervous_system(1)|endometrium(2)|large_intestine(5)|lung(11)|ovary(2)|skin(1)|urinary_tract(1)	30						gctgccgctgccgccgccgcc	0.821			"""Mis, F"""		neuroblastoma	neuroblastoma	congenital central hypoventilation syndrome		Neuroblastoma, Familial Clustering of;Congenital Central Hypoventilation Syndrome																												p.A254fs		Atlas-INDEL	.	yes	Rec	yes	familial neuroblastoma	4	4p12	8929	paired-like homeobox 2b	yes	O	.	PHOX2B	53	.	0			c.761delC						.						2.0	3.0	3.0					4																	41748009		528	1561	2089	SO:0001589	frameshift_variant	8929	exon3	Familial Cancer Database	Familial Neuroblastoma;CCHS, Ondine Curse, incl. Ondine-Hirschsprung Disease	.	D82344	CCDS3463.1	4p13	2014-09-17	2003-02-10	2003-02-14	ENSG00000109132	ENSG00000109132		"""Homeoboxes / PRD class"""	9143	protein-coding gene	gene with protein product		603851	"""paired mesoderm homeobox 2b"""	PMX2B		9039501, 10395798	Standard	NM_003924		Approved	Phox2b, NBPhox	uc003gwf.4	Q99453	OTTHUMG00000099379	ENST00000226382.2:c.760delG	chr4.hg19:g.41748009delC	ENSP00000226382:p.Ala260fs	78.0	0.0		128.0	49.0	NM_003924	Q6PJD9	Frame_Shift_Del	DEL	ENST00000226382.2	hg19	CCDS3463.1																																																																																			.	.		0.821	PHOX2B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000216832.2		
DDX31	64794	hgsc.bcm.edu	37	9	135505734	135505734	+	Frame_Shift_Del	DEL	C	C	-			TCGA-WJ-A86L-01A-12D-A45V-10	TCGA-WJ-A86L-10A-01D-A38X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	80e4fac9-c066-47a9-9fc0-2a42eef954cd	cebd5a99-cbde-441d-b98a-b84cf1825d65	g.chr9:135505734delC	ENST00000372159.3	-	16	2014	c.1863delG	c.(1861-1863)cggfs	p.R621fs	DDX31_ENST00000438527.3_Frame_Shift_Del_p.R492fs|DDX31_ENST00000372153.1_Frame_Shift_Del_p.G613fs	NM_022779.7	NP_073616.6	Q9H8H2	DDX31_HUMAN	DEAD (Asp-Glu-Ala-Asp) box polypeptide 31	621	Helicase C-terminal. {ECO:0000255|PROSITE-ProRule:PRU00542}.					nucleus (GO:0005634)	ATP binding (GO:0005524)|ATP-dependent helicase activity (GO:0008026)|poly(A) RNA binding (GO:0044822)			breast(1)|central_nervous_system(2)|endometrium(4)|kidney(3)|large_intestine(4)|lung(10)|prostate(1)|skin(1)|urinary_tract(1)	27				OV - Ovarian serous cystadenocarcinoma(145;2.67e-06)|Epithelial(140;7.61e-05)		GGCAGCCAATCCGGGCGGTTC	0.478																																					p.I622fs		Atlas-INDEL	.											.	DDX31	76	.	0			c.1864delA						.						103.0	109.0	107.0					9																	135505734		2203	4300	6503	SO:0001589	frameshift_variant	64794	exon16			.	AF427339	CCDS6951.1, CCDS6952.1	9q34.2	2012-04-17	2003-06-13		ENSG00000125485	ENSG00000125485		"""DEAD-boxes"", ""Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"""	16715	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 25"""		"""DEAD/H (Asp-Glu-Ala-Asp/His) box polypeptide 31"""				Standard	NM_022779		Approved	FLJ13633, FLJ23349, FLJ14578, PPP1R25	uc004cbq.1	Q9H8H2	OTTHUMG00000020843	ENST00000372159.3:c.1863delG	chr9.hg19:g.135505734delC	ENSP00000361232:p.Arg621fs	81.0	0.0		76.0	37.0	NM_022779	Q5K6N2|Q5K6N3|Q5K6N4|Q5VZJ4|Q5VZJ9|Q96E91|Q96NY2|Q96SX5|Q9H5K6	Frame_Shift_Del	DEL	ENST00000372159.3	hg19	CCDS6951.1																																																																																			.	.		0.478	DDX31-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000054794.1	NM_138620	
PUS7	54517	hgsc.bcm.edu	37	7	105098324	105098326	+	In_Frame_Del	DEL	AGT	AGT	-			TCGA-WJ-A86L-01A-12D-A45V-10	TCGA-WJ-A86L-10A-01D-A38X-10	AGT	AGT	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	80e4fac9-c066-47a9-9fc0-2a42eef954cd	cebd5a99-cbde-441d-b98a-b84cf1825d65	g.chr7:105098324_105098326delAGT	ENST00000356362.2	-	16	2111_2113	c.1897_1899delACT	c.(1897-1899)actdel	p.T633del	PUS7_ENST00000469408.1_In_Frame_Del_p.T633del	NM_019042.3	NP_061915.2	Q96PZ0	PUS7_HUMAN	pseudouridylate synthase 7 (putative)	633					pseudouridine synthesis (GO:0001522)|tRNA processing (GO:0008033)		enzyme binding (GO:0019899)|poly(A) RNA binding (GO:0044822)|pseudouridine synthase activity (GO:0009982)			breast(1)|endometrium(2)|kidney(1)|large_intestine(9)|lung(8)|pancreas(1)|skin(1)	23						TGGTGGCGTAAGTAGAAGGGGGT	0.468																																					p.633_634del	Colon(138;2387 3051 17860)	Atlas-INDEL	.											.	PUS7	59	.	0			c.1898_1900del						.																																			SO:0001651	inframe_deletion	54517	exon16			.	AK128629	CCDS34725.1	7q22.3	2014-02-14	2014-02-14		ENSG00000091127	ENSG00000091127			26033	protein-coding gene	gene with protein product			"""pseudouridylate synthase 7 homolog (S. cerevisiae)"""			11572484	Standard	NM_019042		Approved	FLJ20485	uc003vcx.3	Q96PZ0	OTTHUMG00000157399	ENST00000356362.2:c.1897_1899delACT	chr7.hg19:g.105098324_105098326delAGT	ENSP00000348722:p.Thr633del	78.0	0.0		89.0	34.0	NM_019042	Q75MG4|Q9NX19	In_Frame_Del	DEL	ENST00000356362.2	hg19	CCDS34725.1																																																																																			.	.		0.468	PUS7-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000348681.1	NM_019042	
SCOC	60592	hgsc.bcm.edu	37	4	141294733	141294742	+	Frame_Shift_Del	DEL	GGCTGGGACG	GGCTGGGACG	-			TCGA-WJ-A86L-01A-12D-A45V-10	TCGA-WJ-A86L-10A-01D-A38X-10	GGCTGGGACG	GGCTGGGACG	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	80e4fac9-c066-47a9-9fc0-2a42eef954cd	cebd5a99-cbde-441d-b98a-b84cf1825d65	g.chr4:141294733_141294742delGGCTGGGACG	ENST00000608372.1	+	1	70_79	c.43_52delGGCTGGGACG	c.(43-54)ggctgggacgggfs	p.GWDG15fs	SCOC_ENST00000394203.3_Intron|SCOC_ENST00000506597.1_Frame_Shift_Del_p.GWDG15fs|SCOC_ENST00000512749.1_Intron|SCOC_ENST00000510586.1_5'Flank|RP11-425I13.3_ENST00000512692.2_RNA|RP11-425I13.3_ENST00000609616.1_RNA|RP11-425I13.3_ENST00000608178.1_RNA|SCOC_ENST00000506322.1_Intron|SCOC_ENST00000394201.4_5'Flank|SCOC_ENST00000338517.4_Intron|SCOC_ENST00000394205.3_Intron|SCOC_ENST00000502535.1_5'Flank			Q9UIL1	SCOC_HUMAN	short coiled-coil protein	15					positive regulation of macroautophagy (GO:0016239)	Golgi apparatus (GO:0005794)|membrane (GO:0016020)				kidney(1)|large_intestine(1)|lung(2)|skin(1)	5	all_hematologic(180;0.162)					GCGGGCGAGCGGCTGGGACGGGATGGGATT	0.648																																					p.14_17del		Atlas-INDEL	.											.	SCOC	11	.	0			c.42_51del						.																																			SO:0001589	frameshift_variant	60592	exon1			.	AK027797	CCDS3750.1, CCDS54806.1, CCDS54807.1	4q28.3	2014-05-22	2003-03-19		ENSG00000153130	ENSG00000153130			20335	protein-coding gene	gene with protein product			"""short coiled coil protein"""			11303027	Standard	NM_032547		Approved	HRIHFB2072, SCOCO	uc011che.1	Q9UIL1	OTTHUMG00000133416	ENST00000608372.1:c.43_52delGGCTGGGACG	chr4.hg19:g.141294733_141294742delGGCTGGGACG	ENSP00000477352:p.Gly15fs	82.0	0.0		51.0	17.0	NM_001153552	B7WPH7|D3DNY7|E9PB65|Q6P5T9|Q7L2Y0|Q7Z4P2|Q96JY9|Q9BZB2	Frame_Shift_Del	DEL	ENST00000608372.1	hg19	CCDS54806.1																																																																																			.	.		0.648	SCOC-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000257274.2		
ZCCHC14	23174	hgsc.bcm.edu	37	16	87451264	87451264	+	Frame_Shift_Del	DEL	G	G	-			TCGA-WJ-A86L-01A-12D-A45V-10	TCGA-WJ-A86L-10A-01D-A38X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	80e4fac9-c066-47a9-9fc0-2a42eef954cd	cebd5a99-cbde-441d-b98a-b84cf1825d65	g.chr16:87451264delG	ENST00000268616.4	-	8	991	c.774delC	c.(772-774)cccfs	p.P258fs		NM_015144.2	NP_055959.1	Q8WYQ9	ZCH14_HUMAN	zinc finger, CCHC domain containing 14	258							nucleic acid binding (GO:0003676)|phosphatidylinositol binding (GO:0035091)|zinc ion binding (GO:0008270)			breast(2)|endometrium(6)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(5)|lung(10)|ovary(1)|prostate(2)|skin(3)|upper_aerodigestive_tract(2)|urinary_tract(2)	36				BRCA - Breast invasive adenocarcinoma(80;0.0285)		AGTGAGGCAAGGGGGCGGCGG	0.692																																					p.L259fs		Atlas-INDEL	.											.	ZCCHC14	87	.	0			c.775delT						.						55.0	66.0	62.0					16																	87451264		2198	4300	6498	SO:0001589	frameshift_variant	23174	exon8			.	AB011151	CCDS10961.1	16q24.2	2013-01-10			ENSG00000140948	ENSG00000140948		"""Zinc fingers, CCHC domain containing"", ""Sterile alpha motif (SAM) domain containing"""	24134	protein-coding gene	gene with protein product						9628581	Standard	XM_005255858		Approved	BDG29, MGC14139	uc002fjz.1	Q8WYQ9	OTTHUMG00000137655	ENST00000268616.4:c.774delC	chr16.hg19:g.87451264delG	ENSP00000268616:p.Pro258fs	68.0	0.0		75.0	26.0	NM_015144	D3DUN1|O60324|Q3MJD8|Q9UFP0	Frame_Shift_Del	DEL	ENST00000268616.4	hg19	CCDS10961.1																																																																																			.	.		0.692	ZCCHC14-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000269107.1	NM_015144	
CDH15	1013	hgsc.bcm.edu	37	16	89260206	89260206	+	Frame_Shift_Del	DEL	G	G	-			TCGA-WJ-A86L-01A-12D-A45V-10	TCGA-WJ-A86L-10A-01D-A38X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	80e4fac9-c066-47a9-9fc0-2a42eef954cd	cebd5a99-cbde-441d-b98a-b84cf1825d65	g.chr16:89260206delG	ENST00000289746.2	+	13	2101	c.2036delG	c.(2035-2037)agcfs	p.S679fs		NM_004933.2	NP_004924.1	P55291	CAD15_HUMAN	cadherin 15, type 1, M-cadherin (myotubule)	679					adherens junction organization (GO:0034332)|cell adhesion (GO:0007155)|cell junction assembly (GO:0034329)|cell-cell junction organization (GO:0045216)|homophilic cell adhesion (GO:0007156)|muscle cell differentiation (GO:0042692)|positive regulation of muscle cell differentiation (GO:0051149)	caveola (GO:0005901)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|neuromuscular junction (GO:0031594)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			central_nervous_system(1)|endometrium(2)|large_intestine(1)|lung(9)|ovary(1)|prostate(1)|skin(2)|urinary_tract(1)	18				BRCA - Breast invasive adenocarcinoma(80;0.0261)		ACAGCGCTGAGCCTGCCTCTG	0.711																																					p.S679fs		Atlas-INDEL	.											.	CDH15	54	.	0			c.2035delA						.						13.0	14.0	14.0					16																	89260206		2121	4242	6363	SO:0001589	frameshift_variant	1013	exon13			.	D83542	CCDS10976.1	16q24.3	2010-01-26	2008-10-30		ENSG00000129910	ENSG00000129910		"""Cadherins / Major cadherins"""	1754	protein-coding gene	gene with protein product		114019	"""cadherin 15, M-cadherin (myotubule)"""	CDH3, CDH14		1427864	Standard	NM_004933		Approved		uc002fmt.3	P55291	OTTHUMG00000138045	ENST00000289746.2:c.2036delG	chr16.hg19:g.89260206delG	ENSP00000289746:p.Ser679fs	56.0	0.0		41.0	30.0	NM_004933		Frame_Shift_Del	DEL	ENST00000289746.2	hg19	CCDS10976.1																																																																																			.	.		0.711	CDH15-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000269920.1	NM_004933	
