#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
EPHA2	1969	hgsc.bcm.edu	37	1	16464471	16464471	+	Missense_Mutation	SNP	C	C	T			TCGA-5R-AAAM-01A-12D-A40R-10	TCGA-5R-AAAM-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9aba9aa4-9f40-456e-8aa4-fb9d20c57d93	bbe62607-8229-46d6-997d-47d1a49b89b0	g.chr1:16464471C>T	ENST00000358432.5	-	5	1343	c.1189G>A	c.(1189-1191)Gtg>Atg	p.V397M		NM_004431.3	NP_004422.2	P29317	EPHA2_HUMAN	EPH receptor A2	397	Fibronectin type-III 1. {ECO:0000255|PROSITE-ProRule:PRU00316}.				activation of Rac GTPase activity (GO:0032863)|angiogenesis (GO:0001525)|axial mesoderm formation (GO:0048320)|bone remodeling (GO:0046849)|branching involved in mammary gland duct morphogenesis (GO:0060444)|cell adhesion (GO:0007155)|cell chemotaxis (GO:0060326)|cell migration (GO:0016477)|ephrin receptor signaling pathway (GO:0048013)|intrinsic apoptotic signaling pathway in response to DNA damage (GO:0008630)|keratinocyte differentiation (GO:0030216)|lens fiber cell morphogenesis (GO:0070309)|mammary gland epithelial cell proliferation (GO:0033598)|multicellular organismal development (GO:0007275)|negative regulation of protein kinase B signaling (GO:0051898)|neural tube development (GO:0021915)|neuron differentiation (GO:0030182)|notochord cell development (GO:0060035)|notochord formation (GO:0014028)|osteoblast differentiation (GO:0001649)|osteoclast differentiation (GO:0030316)|peptidyl-tyrosine phosphorylation (GO:0018108)|positive regulation of establishment of protein localization to plasma membrane (GO:0090004)|post-anal tail morphogenesis (GO:0036342)|protein kinase B signaling (GO:0043491)|regulation of angiogenesis (GO:0045765)|regulation of blood vessel endothelial cell migration (GO:0043535)|regulation of cell adhesion mediated by integrin (GO:0033628)|regulation of ERK1 and ERK2 cascade (GO:0070372)|regulation of lamellipodium assembly (GO:0010591)|response to growth factor (GO:0070848)|skeletal system development (GO:0001501)|vasculogenesis (GO:0001570)|viral process (GO:0016032)	cell projection (GO:0042995)|cell surface (GO:0009986)|focal adhesion (GO:0005925)|integral component of plasma membrane (GO:0005887)|leading edge membrane (GO:0031256)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|ephrin receptor activity (GO:0005003)|transmembrane receptor protein tyrosine kinase activity (GO:0004714)			NS(1)|biliary_tract(1)|breast(3)|central_nervous_system(3)|cervix(2)|endometrium(1)|kidney(1)|large_intestine(6)|lung(12)|ovary(2)|pancreas(1)|prostate(3)|stomach(2)|upper_aerodigestive_tract(3)|urinary_tract(1)	42		Colorectal(325;3.46e-05)|Breast(348;0.000278)|Lung NSC(340;0.000419)|Renal(390;0.000518)|all_lung(284;0.000567)|Ovarian(437;0.0221)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0181)|Colorectal(212;3.63e-07)|COAD - Colon adenocarcinoma(227;2.25e-05)|BRCA - Breast invasive adenocarcinoma(304;9.58e-05)|Kidney(64;0.000175)|KIRC - Kidney renal clear cell carcinoma(64;0.00261)|STAD - Stomach adenocarcinoma(313;0.00669)|READ - Rectum adenocarcinoma(331;0.0649)	Dasatinib(DB01254)|Regorafenib(DB08896)	CTCACTGTCACACTGGTGCGG	0.647																																					p.V397M		Atlas-SNP	.											.	EPHA2	102	.	0			c.G1189A						.						64.0	60.0	61.0					1																	16464471		2203	4300	6503	SO:0001583	missense	1969	exon5			CTGTCACACTGGT	BC037166	CCDS169.1	1p36	2013-02-11	2004-10-28		ENSG00000142627	ENSG00000142627	2.7.10.1	"""EPH receptors"", ""Sterile alpha motif (SAM) domain containing"", ""Fibronectin type III domain containing"""	3386	protein-coding gene	gene with protein product		176946	"""EphA2"""	ECK		9119409	Standard	NM_004431		Approved		uc001aya.2	P29317	OTTHUMG00000009527	ENST00000358432.5:c.1189G>A	chr1.hg19:g.16464471C>T	ENSP00000351209:p.Val397Met	81.0	0.0		52.0	7.0	NM_004431	B5A968|Q8N3Z2	Missense_Mutation	SNP	ENST00000358432.5	hg19	CCDS169.1	.	.	.	.	.	.	.	.	.	.	C	15.83	2.949706	0.53186	.	.	ENSG00000142627	ENST00000358432	T	0.60424	0.19	4.97	3.04	0.35103	Fibronectin, type III (4);Immunoglobulin-like fold (1);	0.434432	0.19393	N	0.115344	T	0.71953	0.3401	M	0.86097	2.795	0.53005	D	0.999967	D;P	0.61697	0.99;0.482	P;B	0.60286	0.872;0.22	T	0.72408	-0.4303	10	0.87932	D	0	.	8.0626	0.30642	0.0:0.3706:0.5279:0.1016	.	397;397	B5A968;P29317	.;EPHA2_HUMAN	M	397	ENSP00000351209:V397M	ENSP00000351209:V397M	V	-	1	0	EPHA2	16337058	0.920000	0.31207	0.965000	0.40720	0.542000	0.35054	2.129000	0.42055	0.593000	0.29745	0.561000	0.74099	GTG	.	.		0.647	EPHA2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000026322.1	NM_004431	
NBL1	4681	hgsc.bcm.edu	37	1	19972500	19972500	+	Intron	SNP	T	T	G			TCGA-5R-AAAM-01A-12D-A40R-10	TCGA-5R-AAAM-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9aba9aa4-9f40-456e-8aa4-fb9d20c57d93	bbe62607-8229-46d6-997d-47d1a49b89b0	g.chr1:19972500T>G	ENST00000375136.3	+	1	284				NBL1_ENST00000289749.2_Intron|MINOS1-NBL1_ENST00000602662.1_Intron|NBL1_ENST00000548815.1_Intron	NM_001204085.1|NM_001204089.1|NM_001278164.1|NM_001278166.1	NP_001191014.1|NP_001191018.1|NP_001265093.1|NP_001265095.1	P41271	NBL1_HUMAN	neuroblastoma 1, DAN family BMP antagonist						determination of dorsal identity (GO:0048263)|negative regulation of BMP signaling pathway (GO:0030514)|negative regulation of monocyte chemotaxis (GO:0090027)|nervous system development (GO:0007399)|neuron projection morphogenesis (GO:0048812)|positive regulation of neuron differentiation (GO:0045666)|sequestering of BMP from receptor via BMP binding (GO:0038098)|sequestering of BMP in extracellular matrix (GO:0035582)	extracellular space (GO:0005615)	BMP binding (GO:0036122)|morphogen activity (GO:0016015)|protein homodimerization activity (GO:0042803)			lung(2)|ovary(2)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)	8		Colorectal(325;3.46e-05)|Renal(390;0.000147)|all_lung(284;0.000321)|Lung NSC(340;0.000398)|Breast(348;0.00043)|Ovarian(437;0.00373)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.00462)|BRCA - Breast invasive adenocarcinoma(304;5.9e-05)|Kidney(64;0.000173)|GBM - Glioblastoma multiforme(114;0.0012)|KIRC - Kidney renal clear cell carcinoma(64;0.0026)|STAD - Stomach adenocarcinoma(196;0.00644)|READ - Rectum adenocarcinoma(331;0.0649)		TGGAGACTGTTTTTCGTTTGC	0.597																																					p.F19C		Atlas-SNP	.											.	NBL1	21	.	0			c.T56G						.																																			SO:0001627	intron_variant	4681	exon1			GACTGTTTTTCGT		CCDS196.1, CCDS41278.1, CCDS196.2, CCDS72720.1	1p36.3-p36.2	2013-02-26	2013-02-26		ENSG00000158747	ENSG00000158747			7650	protein-coding gene	gene with protein product	"""neuroblastoma candidate region, suppression of tumorigenicity 1"", ""neuroblastoma suppressor of tumorigenicity 1"", ""differential screening-selected gene aberrant in neuroblastoma"""	600613	"""neuroblastoma, suppression of tumorigenicity 1"""			7633401	Standard	NM_182744		Approved	D1S1733E, NB, DAN, NO3, DAND1	uc001bcj.2	P41271	OTTHUMG00000002700	ENST00000375136.3:c.-20+1560T>G	chr1.hg19:g.19972500T>G		94.0	0.0		77.0	8.0	NM_001204086	A3KFI7|Q5TGZ2|Q5U0N4|Q96L68	Missense_Mutation	SNP	ENST00000375136.3	hg19	CCDS196.2	.	.	.	.	.	.	.	.	.	.	t	10.30	1.311632	0.23821	.	.	ENSG00000158747	ENST00000439278	T	0.51817	0.69	3.83	3.83	0.44106	.	.	.	.	.	T	0.48714	0.1515	.	.	.	0.36281	D	0.85575	.	.	.	.	.	.	T	0.55186	-0.8180	5	.	.	.	.	9.2608	0.37612	0.0:0.0:0.0:1.0	.	.	.	.	C	19	ENSP00000391858:F19C	.	F	+	2	0	NBL1	19845087	0.990000	0.36364	0.020000	0.16555	0.727000	0.41649	3.132000	0.50523	1.737000	0.51674	0.450000	0.29827	TTT	.	.		0.597	NBL1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000007681.4	NM_005380	
INADL	10207	hgsc.bcm.edu	37	1	62232108	62232108	+	Missense_Mutation	SNP	A	A	G			TCGA-5R-AAAM-01A-12D-A40R-10	TCGA-5R-AAAM-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9aba9aa4-9f40-456e-8aa4-fb9d20c57d93	bbe62607-8229-46d6-997d-47d1a49b89b0	g.chr1:62232108A>G	ENST00000371158.2	+	4	461	c.347A>G	c.(346-348)aAt>aGt	p.N116S	INADL_ENST00000316485.6_Missense_Mutation_p.N116S	NM_176877.2	NP_795352	Q8NI35	INADL_HUMAN	InaD-like (Drosophila)	116					cell junction assembly (GO:0034329)|cell-cell junction organization (GO:0045216)|intracellular signal transduction (GO:0035556)|tight junction assembly (GO:0070830)	apical part of cell (GO:0045177)|extracellular vesicular exosome (GO:0070062)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|protein complex (GO:0043234)|tight junction (GO:0005923)				breast(3)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(11)|large_intestine(8)|liver(1)|lung(51)|ovary(3)|pancreas(1)|prostate(7)|skin(5)|stomach(1)|upper_aerodigestive_tract(3)	103						AAGTTGGGAAATGAAGACTTT	0.398																																					p.N116S		Atlas-SNP	.											.	INADL	179	.	0			c.A347G						.						101.0	98.0	99.0					1																	62232108		2203	4300	6503	SO:0001583	missense	10207	exon4			TGGGAAATGAAGA	AB044807	CCDS617.2	1p31	2008-02-05			ENSG00000132849	ENSG00000132849			28881	protein-coding gene	gene with protein product		603199				9280290, 11374908	Standard	NM_176877		Approved	Cipp, PATJ	uc001dab.3	Q8NI35	OTTHUMG00000008560	ENST00000371158.2:c.347A>G	chr1.hg19:g.62232108A>G	ENSP00000360200:p.Asn116Ser	78.0	0.0		73.0	22.0	NM_176877	O15249|O43742|O60833|Q5VUA5|Q5VUA6|Q5VUA7|Q5VUA8|Q5VUA9|Q5VUB0|Q8WU78|Q9H3N9	Missense_Mutation	SNP	ENST00000371158.2	hg19	CCDS617.2	.	.	.	.	.	.	.	.	.	.	A	3.841	-0.033772	0.07543	.	.	ENSG00000132849	ENST00000371158;ENST00000316485;ENST00000371156;ENST00000395513;ENST00000255202	T;T	0.11604	2.89;2.76	6.08	3.72	0.42706	.	0.397923	0.26173	N	0.025908	T	0.06962	0.0177	L	0.36672	1.1	0.80722	D	1	B;B;B	0.15473	0.01;0.006;0.013	B;B;B	0.14023	0.01;0.003;0.003	T	0.22347	-1.0219	10	0.07325	T	0.83	.	5.8951	0.18935	0.7139:0.0:0.1368:0.1493	.	116;116;116	F8W8T2;Q8NI35;Q8NI35-4	.;INADL_HUMAN;.	S	116	ENSP00000360200:N116S;ENSP00000326199:N116S	ENSP00000255202:N116S	N	+	2	0	INADL	62004696	1.000000	0.71417	0.999000	0.59377	0.716000	0.41182	1.692000	0.37731	0.512000	0.28257	0.482000	0.46254	AAT	.	.		0.398	INADL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000023639.2	NM_170605	
CHIA	27159	hgsc.bcm.edu	37	1	111854972	111854972	+	Missense_Mutation	SNP	T	T	G			TCGA-5R-AAAM-01A-12D-A40R-10	TCGA-5R-AAAM-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9aba9aa4-9f40-456e-8aa4-fb9d20c57d93	bbe62607-8229-46d6-997d-47d1a49b89b0	g.chr1:111854972T>G	ENST00000369740.1	+	4	319	c.216T>G	c.(214-216)aaT>aaG	p.N72K	CHIA_ENST00000353665.6_Intron|CHIA_ENST00000451398.2_Intron|CHIA_ENST00000343320.6_Missense_Mutation_p.N72K|CHIA_ENST00000430615.1_Intron|CHIA_ENST00000483391.1_Intron	NM_001258001.1|NM_201653.3	NP_001244930.1|NP_970615.2	Q9BZP6	CHIA_HUMAN	chitinase, acidic	72					apoptotic process (GO:0006915)|cell wall chitin metabolic process (GO:0006037)|chitin catabolic process (GO:0006032)|chitin metabolic process (GO:0006030)|digestion (GO:0007586)|immune response (GO:0006955)|polysaccharide catabolic process (GO:0000272)|positive regulation of chemokine secretion (GO:0090197)|production of molecular mediator involved in inflammatory response (GO:0002532)|response to fungus (GO:0009620)	cytoplasm (GO:0005737)|extracellular space (GO:0005615)	carbohydrate binding (GO:0030246)|chitin binding (GO:0008061)|chitinase activity (GO:0004568)|kinase binding (GO:0019900)|lysozyme activity (GO:0003796)			central_nervous_system(1)|endometrium(5)|kidney(3)|large_intestine(3)|lung(9)|ovary(1)|skin(1)	23		all_cancers(81;3.23e-05)|all_epithelial(167;1.2e-05)|all_lung(203;0.000154)|Lung NSC(277;0.000304)		Colorectal(144;0.0115)|Lung(183;0.0292)|COAD - Colon adenocarcinoma(174;0.0314)|all cancers(265;0.0477)|Epithelial(280;0.0918)|LUSC - Lung squamous cell carcinoma(189;0.154)		TCGAATGGAATGATGTGACTC	0.468																																					p.N72K		Atlas-SNP	.											.	CHIA	115	.	0			c.T216G						.						121.0	116.0	118.0					1																	111854972		1987	4156	6143	SO:0001583	missense	27159	exon4			ATGGAATGATGTG	AF290004	CCDS832.1, CCDS41368.1, CCDS58017.1	1p13.2	2008-05-14			ENSG00000134216	ENSG00000134216			17432	protein-coding gene	gene with protein product		606080				11085997	Standard	NM_021797		Approved	AMCase, TSA1902, CHIT2	uc001eas.4	Q9BZP6	OTTHUMG00000011165	ENST00000369740.1:c.216T>G	chr1.hg19:g.111854972T>G	ENSP00000358755:p.Asn72Lys	94.0	0.0		105.0	16.0	NM_201653	Q32W79|Q32W80|Q3B866|Q5U5Z5|Q5VUV4|Q86UD8|Q9ULY3|Q9ULY4	Missense_Mutation	SNP	ENST00000369740.1	hg19	CCDS41368.1	.	.	.	.	.	.	.	.	.	.	T	14.96	2.692421	0.48202	.	.	ENSG00000134216	ENST00000369740;ENST00000343320	T;T	0.05319	3.46;3.46	4.93	0.785	0.18584	Chitinase II (1);Glycoside hydrolase, family 18, catalytic domain (1);Glycoside hydrolase, subgroup, catalytic domain (1);Glycoside hydrolase, superfamily (1);	0.163676	0.37577	U	0.002031	T	0.05502	0.0145	M	0.76938	2.355	0.80722	D	1	B	0.33135	0.399	P	0.44897	0.463	T	0.13495	-1.0507	10	0.51188	T	0.08	-2.086	3.7062	0.08401	0.1626:0.2275:0.0:0.6098	.	72	Q9BZP6	CHIA_HUMAN	K	72	ENSP00000358755:N72K;ENSP00000341828:N72K	ENSP00000341828:N72K	N	+	3	2	CHIA	111656495	0.183000	0.23186	0.946000	0.38457	0.689000	0.40095	-0.524000	0.06222	0.280000	0.22209	-0.274000	0.10170	AAT	.	.		0.468	CHIA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000030710.1		
ZNF687	57592	hgsc.bcm.edu	37	1	151258832	151258832	+	Missense_Mutation	SNP	A	A	G			TCGA-5R-AAAM-01A-12D-A40R-10	TCGA-5R-AAAM-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9aba9aa4-9f40-456e-8aa4-fb9d20c57d93	bbe62607-8229-46d6-997d-47d1a49b89b0	g.chr1:151258832A>G	ENST00000368879.2	+	2	163	c.65A>G	c.(64-66)gAt>gGt	p.D22G		NM_020832.1	NP_065883.1	Q8N1G0	ZN687_HUMAN	zinc finger protein 687	22					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleolus (GO:0005730)|nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			breast(2)|central_nervous_system(3)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(5)|lung(11)|ovary(1)|upper_aerodigestive_tract(2)	32	Lung SC(34;0.00471)|Ovarian(49;0.0147)|Hepatocellular(266;0.0997)|all_hematologic(923;0.127)|Melanoma(130;0.185)		UCEC - Uterine corpus endometrioid carcinoma (35;0.112)|LUSC - Lung squamous cell carcinoma(543;0.181)			CCTGACATTGATGCGAATGAA	0.512																																					p.D22G		Atlas-SNP	.											.	ZNF687	94	.	0			c.A65G						.						101.0	104.0	103.0					1																	151258832		2203	4300	6503	SO:0001583	missense	57592	exon2			ACATTGATGCGAA		CCDS992.1	1q21.2	2008-05-02			ENSG00000143373	ENSG00000143373			29277	protein-coding gene	gene with protein product		610568				10718198	Standard	NM_020832		Approved	KIAA1441	uc001exq.3	Q8N1G0	OTTHUMG00000012347	ENST00000368879.2:c.65A>G	chr1.hg19:g.151258832A>G	ENSP00000357874:p.Asp22Gly	89.0	0.0		85.0	13.0	NM_020832	D3DV17|Q68DQ8|Q9H937|Q9P2A7	Missense_Mutation	SNP	ENST00000368879.2	hg19		.	.	.	.	.	.	.	.	.	.	A	16.38	3.107408	0.56291	.	.	ENSG00000143373	ENST00000443959;ENST00000336715;ENST00000324048;ENST00000368879	T;T;T	0.01998	4.51;4.51;4.8	4.43	3.28	0.37604	.	0.000000	0.36555	N	0.002538	T	0.05318	0.0141	M	0.74881	2.28	0.44985	D	0.998	D;D;D	0.71674	0.998;0.993;0.996	D;D;D	0.81914	0.995;0.984;0.993	T	0.06698	-1.0812	10	0.87932	D	0	.	9.4423	0.38677	0.8407:0.0:0.0:0.1593	.	22;22;22	Q8N1G0-2;Q8N1G0;F8WCX2	.;ZN687_HUMAN;.	G	31;22;22;22	ENSP00000336620:D22G;ENSP00000319829:D22G;ENSP00000357874:D22G	ENSP00000319829:D22G	D	+	2	0	ZNF687	149525456	1.000000	0.71417	1.000000	0.80357	0.883000	0.51084	5.787000	0.69013	0.725000	0.32318	0.260000	0.18958	GAT	.	.		0.512	ZNF687-201	KNOWN	basic	protein_coding	protein_coding		NM_020832	
CD1B	910	hgsc.bcm.edu	37	1	158299379	158299379	+	Missense_Mutation	SNP	C	C	T			TCGA-5R-AAAM-01A-12D-A40R-10	TCGA-5R-AAAM-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9aba9aa4-9f40-456e-8aa4-fb9d20c57d93	bbe62607-8229-46d6-997d-47d1a49b89b0	g.chr1:158299379C>T	ENST00000368168.3	-	4	774	c.667G>A	c.(667-669)Gtg>Atg	p.V223M		NM_001764.2	NP_001755.1	P29016	CD1B_HUMAN	CD1b molecule	223	Ig-like.				antigen processing and presentation (GO:0019882)|immune response (GO:0006955)	cell surface (GO:0009986)|endosome (GO:0005768)|integral component of membrane (GO:0016021)|lysosome (GO:0005764)|plasma membrane (GO:0005886)				breast(2)|large_intestine(2)|lung(17)|ovary(2)|prostate(5)|skin(1)|upper_aerodigestive_tract(1)	30	all_hematologic(112;0.0378)					ACATGGCACACAAGCTGCAGA	0.572																																					p.V223M		Atlas-SNP	.											.	CD1B	78	.	0			c.G667A						.						75.0	73.0	74.0					1																	158299379		2203	4300	6503	SO:0001583	missense	910	exon4			GGCACACAAGCTG	M28826	CCDS1176.1	1q23.1	2014-01-14	2006-03-28		ENSG00000158485	ENSG00000158485		"""CD molecules"", ""Immunoglobulin superfamily / C1-set domain containing"""	1635	protein-coding gene	gene with protein product		188360	"""CD1B antigen, b polypeptide"", ""CD1b antigen"""	CD1		2447586	Standard	NM_001764		Approved		uc001frx.3	P29016	OTTHUMG00000017513	ENST00000368168.3:c.667G>A	chr1.hg19:g.158299379C>T	ENSP00000357150:p.Val223Met	157.0	0.0		141.0	7.0	NM_001764	Q5TDK9|Q5TDL0|Q9UMM2	Missense_Mutation	SNP	ENST00000368168.3	hg19	CCDS1176.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	17.06|17.06	3.292699|3.292699	0.59976|0.59976	.|.	.|.	ENSG00000158485|ENSG00000158485	ENST00000451207|ENST00000368168	.|T	.|0.03413	.|3.94	4.26|4.26	2.13|2.13	0.27403|0.27403	.|Immunoglobulin-like (1);MHC class I-like antigen recognition (1);Immunoglobulin C1-set (2);	.|0.202721	.|0.24698	.|N	.|0.036334	T|T	0.11110|0.11110	0.0271|0.0271	M|M	0.89601|0.89601	3.045|3.045	0.30264|0.30264	N|N	0.792917|0.792917	.|D;D	.|0.89917	.|1.0;1.0	.|D;D	.|0.83275	.|0.996;0.987	T|T	0.01182|0.01182	-1.1426|-1.1426	5|10	.|0.72032	.|D	.|0.01	-22.564|-22.564	9.9076|9.9076	0.41386|0.41386	0.0:0.5921:0.4079:0.0|0.0:0.5921:0.4079:0.0	.|.	.|223;223	.|P29016;P29016-2	.|CD1B_HUMAN;.	Y|M	190|223	.|ENSP00000357150:V223M	.|ENSP00000357150:V223M	C|V	-|-	2|1	0|0	CD1B|CD1B	156566003|156566003	0.722000|0.722000	0.28017|0.28017	0.999000|0.999000	0.59377|0.59377	0.968000|0.968000	0.65278|0.65278	0.581000|0.581000	0.23819|0.23819	1.078000|1.078000	0.41014|0.41014	0.655000|0.655000	0.94253|0.94253	TGT|GTG	.	.		0.572	CD1B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000046350.2	NM_001764	
SPTA1	6708	hgsc.bcm.edu	37	1	158585118	158585118	+	Missense_Mutation	SNP	C	C	T			TCGA-5R-AAAM-01A-12D-A40R-10	TCGA-5R-AAAM-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9aba9aa4-9f40-456e-8aa4-fb9d20c57d93	bbe62607-8229-46d6-997d-47d1a49b89b0	g.chr1:158585118C>T	ENST00000368147.4	-	48	6856	c.6676G>A	c.(6676-6678)Gct>Act	p.A2226T		NM_003126.2	NP_003117.2	P02549	SPTA1_HUMAN	spectrin, alpha, erythrocytic 1	2226					actin filament capping (GO:0051693)|actin filament organization (GO:0007015)|axon guidance (GO:0007411)|hemopoiesis (GO:0030097)|lymphocyte homeostasis (GO:0002260)|plasma membrane organization (GO:0007009)|porphyrin-containing compound biosynthetic process (GO:0006779)|positive regulation of protein binding (GO:0032092)|positive regulation of T cell proliferation (GO:0042102)|regulation of cell shape (GO:0008360)	actin cytoskeleton (GO:0015629)|cuticular plate (GO:0032437)|cytosol (GO:0005829)|intrinsic component of the cytoplasmic side of the plasma membrane (GO:0031235)|spectrin (GO:0008091)|spectrin-associated cytoskeleton (GO:0014731)	actin filament binding (GO:0051015)|calcium ion binding (GO:0005509)|structural constituent of cytoskeleton (GO:0005200)			NS(3)|breast(7)|cervix(1)|endometrium(22)|kidney(9)|large_intestine(29)|liver(2)|lung(183)|ovary(5)|prostate(18)|skin(11)|soft_tissue(1)|stomach(1)|upper_aerodigestive_tract(9)|urinary_tract(6)	307	all_hematologic(112;0.0378)					AGGATCAGAGCGTCTTCCAAG	0.498																																					p.A2226T		Atlas-SNP	.											SPTA1,caecum,carcinoma,0,2	SPTA1	720	.	0			c.G6676A						.						188.0	190.0	189.0					1																	158585118		2014	4196	6210	SO:0001583	missense	6708	exon48			TCAGAGCGTCTTC	M61877	CCDS41423.1	1q21	2014-06-23	2014-06-23		ENSG00000163554	ENSG00000163554		"""EF-hand domain containing"""	11272	protein-coding gene	gene with protein product	"""elliptocytosis 2"""	182860	"""spectrin, alpha, erythrocytic 1 (elliptocytosis 2)"""				Standard	NM_003126		Approved	EL2	uc001fst.1	P02549	OTTHUMG00000019636	ENST00000368147.4:c.6676G>A	chr1.hg19:g.158585118C>T	ENSP00000357129:p.Ala2226Thr	111.0	0.0		122.0	16.0	NM_003126	Q15514|Q5VYL1|Q5VYL2|Q6LDY5	Missense_Mutation	SNP	ENST00000368147.4	hg19	CCDS41423.1	.	.	.	.	.	.	.	.	.	.	C	21.5	4.157605	0.78114	.	.	ENSG00000163554	ENST00000368148;ENST00000368147	T;T	0.52526	0.66;0.66	5.54	5.54	0.83059	.	0.000000	0.32120	N	0.006555	T	0.46833	0.1413	M	0.67953	2.075	0.52099	D	0.999943	P	0.51537	0.946	P	0.51777	0.679	T	0.28299	-1.0048	10	0.15066	T	0.55	.	18.234	0.89944	0.0:1.0:0.0:0.0	.	2226	P02549	SPTA1_HUMAN	T	2226;2223	ENSP00000357130:A2226T;ENSP00000357129:A2223T	ENSP00000357129:A2223T	A	-	1	0	SPTA1	156851742	1.000000	0.71417	1.000000	0.80357	0.358000	0.29455	7.104000	0.77024	2.884000	0.98904	0.655000	0.94253	GCT	.	.		0.498	SPTA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051851.3	NM_003126	
ATP1A4	480	hgsc.bcm.edu	37	1	160128807	160128807	+	Silent	SNP	C	C	A			TCGA-5R-AAAM-01A-12D-A40R-10	TCGA-5R-AAAM-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9aba9aa4-9f40-456e-8aa4-fb9d20c57d93	bbe62607-8229-46d6-997d-47d1a49b89b0	g.chr1:160128807C>A	ENST00000368081.4	+	5	1012	c.541C>A	c.(541-543)Cga>Aga	p.R181R		NM_144699.3	NP_653300.2	Q13733	AT1A4_HUMAN	ATPase, Na+/K+ transporting, alpha 4 polypeptide	181					ATP biosynthetic process (GO:0006754)|ATP hydrolysis coupled proton transport (GO:0015991)|fertilization (GO:0009566)|ion transmembrane transport (GO:0034220)|potassium ion transport (GO:0006813)|regulation of cellular pH (GO:0030641)|regulation of membrane potential (GO:0042391)|sodium ion transmembrane transport (GO:0035725)|sodium ion transport (GO:0006814)|sperm motility (GO:0030317)|spermatogenesis (GO:0007283)|transmembrane transport (GO:0055085)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|sodium:potassium-exchanging ATPase complex (GO:0005890)	ATP binding (GO:0005524)|metal ion binding (GO:0046872)|sodium:potassium-exchanging ATPase activity (GO:0005391)			breast(3)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(16)|lung(34)|ovary(2)|prostate(4)|skin(5)|upper_aerodigestive_tract(1)|urinary_tract(2)	75	all_cancers(52;2.56e-18)|all_hematologic(112;0.093)		BRCA - Breast invasive adenocarcinoma(70;0.111)			TCTGGTAATTCGAGGAGGAGA	0.468																																					p.R181R		Atlas-SNP	.											.	ATP1A4	167	.	0			c.C541A						.						94.0	84.0	87.0					1																	160128807		2203	4300	6503	SO:0001819	synonymous_variant	480	exon5			GTAATTCGAGGAG	BC028297	CCDS1197.1, CCDS44255.1	1q23.2	2012-10-22	2002-02-25		ENSG00000132681	ENSG00000132681		"""ATPases / P-type"""	14073	protein-coding gene	gene with protein product	"""sodium/potassium-transporting ATPase subunit alpha-4"", ""sodium pump subunit alpha-4"", ""sodium-potassium ATPase catalytic subunit alpha-4"""	607321	"""ATPase, Na+/K+ transporting, alpha polypeptide-like 2"""	ATP1AL2		1981991, 3035563	Standard	NM_144699		Approved		uc001fve.4	Q13733	OTTHUMG00000031609	ENST00000368081.4:c.541C>A	chr1.hg19:g.160128807C>A		133.0	0.0		125.0	48.0	NM_144699	Q504T2|Q7Z4I9|Q8TBN8|Q8WXA7|Q8WXH7|Q8WY13	Silent	SNP	ENST00000368081.4	hg19	CCDS1197.1																																																																																			.	.		0.468	ATP1A4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000077415.1	NM_144699	
CCDC181	57821	hgsc.bcm.edu	37	1	169391306	169391306	+	Missense_Mutation	SNP	C	C	G			TCGA-5R-AAAM-01A-12D-A40R-10	TCGA-5R-AAAM-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9aba9aa4-9f40-456e-8aa4-fb9d20c57d93	bbe62607-8229-46d6-997d-47d1a49b89b0	g.chr1:169391306C>G	ENST00000367806.3	-	3	515	c.363G>C	c.(361-363)gaG>gaC	p.E121D	CCDC181_ENST00000545005.1_Missense_Mutation_p.E121D|CCDC181_ENST00000367805.3_Missense_Mutation_p.E121D|CCDC181_ENST00000491570.1_5'UTR	NM_021179.1	NP_067002.1	Q5TID7	CC181_HUMAN	coiled-coil domain containing 181	121	Poly-Glu.					nucleus (GO:0005634)											TCCTTACTTCCTCATCCTCTT	0.383																																					p.E121D		Atlas-SNP	.											.	C1orf114	67	.	0			c.G363C						.						79.0	81.0	80.0					1																	169391306		2203	4300	6503	SO:0001583	missense	57821	exon3			TACTTCCTCATCC	AL049687	CCDS1279.1, CCDS72979.1	1q24	2013-03-14	2013-03-14	2013-03-14	ENSG00000117477	ENSG00000117477			28051	protein-coding gene	gene with protein product			"""chromosome 1 open reading frame 114"""	C1orf114			Standard	XM_005245381		Approved	FLJ25846	uc001gfz.1	Q5TID7	OTTHUMG00000035448	ENST00000367806.3:c.363G>C	chr1.hg19:g.169391306C>G	ENSP00000356780:p.Glu121Asp	97.0	0.0		98.0	9.0	NM_021179	O60780|Q53FD5|Q5TID9|Q8TC48	Missense_Mutation	SNP	ENST00000367806.3	hg19		.	.	.	.	.	.	.	.	.	.	C	13.41	2.228427	0.39399	.	.	ENSG00000117477	ENST00000367805;ENST00000367806;ENST00000545005;ENST00000456107	T;T;T;T	0.55930	1.24;1.24;1.24;0.49	5.34	2.48	0.30137	.	0.000000	0.85682	D	0.000000	T	0.48484	0.1502	L	0.56769	1.78	0.34676	D	0.724226	D;D;D	0.89917	0.968;1.0;1.0	P;D;D	0.83275	0.708;0.996;0.996	T	0.46456	-0.9190	9	0.27082	T	0.32	-17.1823	7.3304	0.26580	0.0:0.5185:0.0:0.4815	.	121;121;121	Q5TID7-2;Q5TID7;Q5TID7-3	.;CA114_HUMAN;.	D	121	ENSP00000356779:E121D;ENSP00000356780:E121D;ENSP00000442297:E121D;ENSP00000411000:E121D	ENSP00000356779:E121D	E	-	3	2	C1orf114	167657930	1.000000	0.71417	1.000000	0.80357	0.977000	0.68977	0.670000	0.25157	0.258000	0.21686	0.563000	0.77884	GAG	.	.		0.383	CCDC181-002	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000086099.1	NM_021179	
NR5A2	2494	hgsc.bcm.edu	37	1	200008803	200008803	+	Nonsense_Mutation	SNP	C	C	T	rs537463980		TCGA-5R-AAAM-01A-12D-A40R-10	TCGA-5R-AAAM-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9aba9aa4-9f40-456e-8aa4-fb9d20c57d93	bbe62607-8229-46d6-997d-47d1a49b89b0	g.chr1:200008803C>T	ENST00000367362.3	+	2	328	c.82C>T	c.(82-84)Cga>Tga	p.R28*	NR5A2_ENST00000544748.1_5'Flank|NR5A2_ENST00000236914.3_Intron	NM_001276464.1|NM_205860.1	NP_001263393.1|NP_995582.1	O00482	NR5A2_HUMAN	nuclear receptor subfamily 5, group A, member 2	28					bile acid metabolic process (GO:0008206)|cholesterol homeostasis (GO:0042632)|embryo development (GO:0009790)|endocrine pancreas development (GO:0031018)|gene expression (GO:0010467)|homeostatic process (GO:0042592)|intracellular receptor signaling pathway (GO:0030522)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of viral genome replication (GO:0045070)|regulation of cell proliferation (GO:0042127)|regulation of transcription, DNA-templated (GO:0006355)|transcription initiation from RNA polymerase II promoter (GO:0006367)	cytoplasm (GO:0005737)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	DNA binding (GO:0003677)|ligand-activated sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0004879)|phospholipid binding (GO:0005543)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|RNA polymerase II distal enhancer sequence-specific DNA binding transcription factor activity (GO:0003705)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|steroid hormone receptor activity (GO:0003707)|transcription regulatory region DNA binding (GO:0044212)|zinc ion binding (GO:0008270)			cervix(1)|endometrium(1)|kidney(3)|large_intestine(6)|lung(15)|ovary(1)|prostate(1)|skin(2)|urinary_tract(1)	31	Prostate(682;0.19)					GCTTCCGGACCGACACGGATC	0.652																																					p.C28C	Melanoma(179;1138 2773 15678 26136)	Atlas-SNP	.											.	NR5A2	83	.	0			c.T82T						.						52.0	60.0	57.0					1																	200008803		2203	4300	6503	SO:0001587	stop_gained	2494	exon2			CCGGACCGACACG	U93553	CCDS1400.1, CCDS1401.1, CCDS60383.1	1q32.11	2013-01-16			ENSG00000116833	ENSG00000116833		"""Nuclear hormone receptors"""	7984	protein-coding gene	gene with protein product	"""liver receptor homolog-1"""	604453		FTF		9858833, 7680097	Standard	NM_205860		Approved	FTZ-F1beta, hB1F, LRH-1, FTZ-F1, hB1F-2, B1F2	uc001gvb.4	O00482	OTTHUMG00000035635	ENST00000367362.3:c.82C>T	chr1.hg19:g.200008803C>T	ENSP00000356331:p.Arg28*	169.0	0.0		191.0	51.0	NM_205860	B4E2P3|O95642|Q147U3	Silent	SNP	ENST00000367362.3	hg19	CCDS1401.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	11.43|11.43	1.636687|1.636687	0.29068|0.29068	.|.	.|.	ENSG00000116833|ENSG00000116833	ENST00000447034|ENST00000367362;ENST00000542116	.|.	.|.	.|.	5.02|5.02	-1.91|-1.91	0.07641|0.07641	.|.	.|0.569224	.|0.14329	.|N	.|0.326478	T|.	0.42966|.	0.1226|.	.|.	.|.	.|.	0.80722|0.80722	D|D	1|1	.|.	.|.	.|.	.|.	.|.	.|.	T|.	0.28038|.	-1.0056|.	4|.	.|.	.|.	.|.	.|.	4.0574|4.0574	0.09823|0.09823	0.1795:0.4258:0.3028:0.0919|0.1795:0.4258:0.3028:0.0919	.|.	.|.	.|.	.|.	L|X	40|28;52	.|.	.|.	P|R	+|+	2|1	0|2	NR5A2|NR5A2	198275426|198275426	0.020000|0.020000	0.18652|0.18652	0.396000|0.396000	0.26296|0.26296	0.173000|0.173000	0.22820|0.22820	0.061000|0.061000	0.14366|0.14366	-0.384000|-0.384000	0.07845|0.07845	-0.142000|-0.142000	0.14014|0.14014	CCG|CGA	.	.		0.652	NR5A2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000086497.2		
USH2A	7399	hgsc.bcm.edu	37	1	215848027	215848027	+	Missense_Mutation	SNP	G	G	A			TCGA-5R-AAAM-01A-12D-A40R-10	TCGA-5R-AAAM-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9aba9aa4-9f40-456e-8aa4-fb9d20c57d93	bbe62607-8229-46d6-997d-47d1a49b89b0	g.chr1:215848027G>A	ENST00000307340.3	-	63	13612	c.13226C>T	c.(13225-13227)tCc>tTc	p.S4409F	USH2A_ENST00000366943.2_Missense_Mutation_p.S4409F	NM_206933.2	NP_996816	O75445	USH2A_HUMAN	Usher syndrome 2A (autosomal recessive, mild)	4409	Fibronectin type-III 29. {ECO:0000255|PROSITE-ProRule:PRU00316}.				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)		CTGCAGGTGGGAAACCAGCAG	0.483										HNSCC(13;0.011)																											p.S4409F		Atlas-SNP	.											USH2A,NS,malignant_melanoma,0,1	USH2A	1168	.	0			c.C13226T						.						71.0	73.0	72.0					1																	215848027		2203	4300	6503	SO:0001583	missense	7399	exon63			AGGTGGGAAACCA	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.13226C>T	chr1.hg19:g.215848027G>A	ENSP00000305941:p.Ser4409Phe	61.0	0.0		94.0	29.0	NM_206933	Q5VVM9|Q6S362|Q9NS27	Missense_Mutation	SNP	ENST00000307340.3	hg19	CCDS31025.1	.	.	.	.	.	.	.	.	.	.	G	15.70	2.911594	0.52439	.	.	ENSG00000042781	ENST00000307340;ENST00000366943	T;T	0.58940	0.3;0.3	4.82	4.82	0.62117	Fibronectin, type III (4);Immunoglobulin-like fold (1);	0.000000	0.41938	U	0.000793	T	0.73125	0.3547	M	0.86651	2.83	0.23023	N	0.998418	D	0.54772	0.968	P	0.55999	0.789	T	0.68985	-0.5265	10	0.56958	D	0.05	.	12.7065	0.57063	0.0798:0.0:0.9202:0.0	.	4409	O75445	USH2A_HUMAN	F	4409	ENSP00000305941:S4409F;ENSP00000355910:S4409F	ENSP00000305941:S4409F	S	-	2	0	USH2A	213914650	0.985000	0.35326	0.012000	0.15200	0.873000	0.50193	3.689000	0.54706	2.384000	0.81235	0.467000	0.42956	TCC	.	.		0.483	USH2A-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000128138.1	NM_007123	
BIRC6	57448	hgsc.bcm.edu	37	2	32750591	32750591	+	Missense_Mutation	SNP	G	G	A	rs553403645		TCGA-5R-AAAM-01A-12D-A40R-10	TCGA-5R-AAAM-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9aba9aa4-9f40-456e-8aa4-fb9d20c57d93	bbe62607-8229-46d6-997d-47d1a49b89b0	g.chr2:32750591G>A	ENST00000421745.2	+	59	11950	c.11816G>A	c.(11815-11817)aGg>aAg	p.R3939K		NM_016252.3	NP_057336	Q9NR09	BIRC6_HUMAN	baculoviral IAP repeat containing 6	3939					apoptotic process (GO:0006915)|labyrinthine layer development (GO:0060711)|mitotic nuclear division (GO:0007067)|negative regulation of apoptotic process (GO:0043066)|negative regulation of endopeptidase activity (GO:0010951)|negative regulation of extrinsic apoptotic signaling pathway (GO:2001237)|positive regulation of cell proliferation (GO:0008284)|protein phosphorylation (GO:0006468)|protein ubiquitination (GO:0016567)|regulation of cell proliferation (GO:0042127)|regulation of cytokinesis (GO:0032465)|spongiotrophoblast layer development (GO:0060712)	endosome (GO:0005768)|membrane (GO:0016020)|microtubule organizing center (GO:0005815)|midbody (GO:0030496)|spindle pole (GO:0000922)|trans-Golgi network (GO:0005802)	acid-amino acid ligase activity (GO:0016881)|cysteine-type endopeptidase inhibitor activity (GO:0004869)|ubiquitin-protein transferase activity (GO:0004842)			NS(4)|breast(8)|central_nervous_system(3)|endometrium(21)|haematopoietic_and_lymphoid_tissue(1)|kidney(15)|large_intestine(31)|lung(65)|ovary(7)|pancreas(1)|prostate(5)|skin(5)|stomach(1)|urinary_tract(5)	172	Acute lymphoblastic leukemia(172;0.155)					CCATCCAGGAGGGGGAGGACA	0.448																																					p.R3939K	Pancreas(94;175 1509 16028 18060 45422)	Atlas-SNP	.											.	BIRC6	838	.	0			c.G11816A						.						94.0	91.0	92.0					2																	32750591		2203	4300	6503	SO:0001583	missense	57448	exon59			CCAGGAGGGGGAG	AF265555	CCDS33175.2	2p22.3	2011-01-25	2011-01-25		ENSG00000115760	ENSG00000115760		"""Baculoviral IAP repeat containing"", ""Ubiquitin-conjugating enzymes E2"""	13516	protein-coding gene	gene with protein product	"""apollon"""	605638	"""baculoviral IAP repeat-containing 6"""			10544019	Standard	NM_016252		Approved	BRUCE	uc010ezu.3	Q9NR09	OTTHUMG00000150528	ENST00000421745.2:c.11816G>A	chr2.hg19:g.32750591G>A	ENSP00000393596:p.Arg3939Lys	158.0	0.0		165.0	9.0	NM_016252	Q9ULD1	Missense_Mutation	SNP	ENST00000421745.2	hg19	CCDS33175.2	.	.	.	.	.	.	.	.	.	.	G	16.58	3.163074	0.57476	.	.	ENSG00000115760	ENST00000421745	T	0.73152	-0.72	5.62	4.73	0.59995	.	0.111765	0.64402	D	0.000018	T	0.57242	0.2040	L	0.27053	0.805	0.58432	D	0.999993	P	0.46656	0.882	B	0.41236	0.351	T	0.55347	-0.8155	10	0.09843	T	0.71	.	16.4961	0.84246	0.0:0.1312:0.8688:0.0	.	3939	Q9NR09	BIRC6_HUMAN	K	3939	ENSP00000393596:R3939K	ENSP00000393596:R3939K	R	+	2	0	BIRC6	32604095	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	9.160000	0.94734	1.362000	0.46000	0.561000	0.74099	AGG	.	.		0.448	BIRC6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318769.3	NM_016252	
FER1L5	90342	hgsc.bcm.edu	37	2	97357320	97357320	+	RNA	SNP	G	G	A			TCGA-5R-AAAM-01A-12D-A40R-10	TCGA-5R-AAAM-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9aba9aa4-9f40-456e-8aa4-fb9d20c57d93	bbe62607-8229-46d6-997d-47d1a49b89b0	g.chr2:97357320G>A	ENST00000457909.1	+	0	1505							A0AVI2	FR1L5_HUMAN	fer-1-like family member 5							integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				NS(1)|autonomic_ganglia(1)|breast(4)|cervix(1)|endometrium(9)|large_intestine(9)|lung(6)|ovary(2)|prostate(2)|skin(1)|urinary_tract(2)	38						CAAGGGCATCGCGCCCATATT	0.667																																					p.A1009T		Atlas-SNP	.											FER1L5,caecum,carcinoma,0,1	FER1L5	113	.	0			c.G3025A						.						33.0	40.0	38.0					2																	97357320		692	1591	2283			90342	exon28			GGCATCGCGCCCA	BC126368		2q11.2	2014-06-27	2014-06-27		ENSG00000249715	ENSG00000249715			19044	protein-coding gene	gene with protein product			"""fer-1-like 5 (C. elegans)"""				Standard	XM_006712826		Approved	DKFZp434I0121	uc010fia.3	A0AVI2	OTTHUMG00000154929		chr2.hg19:g.97357320G>A		186.0	0.0		165.0	21.0	NM_001113382	Q17RH2|Q6ZU24	Missense_Mutation	SNP	ENST00000457909.1	hg19		.	.	.	.	.	.	.	.	.	.	G	3.278	-0.147649	0.06627	.	.	ENSG00000214272	ENST00000414152;ENST00000436930	.	.	.	5.41	4.45	0.53987	.	.	.	.	.	T	0.64450	0.2599	M	0.68952	2.095	.	.	.	D	0.67145	0.996	P	0.50314	0.637	T	0.76870	-0.2799	7	0.87932	D	0	-10.5851	14.0812	0.64922	0.0:0.0:0.8392:0.1608	.	1009	A0AVI2	FR1L5_HUMAN	T	1009;1001	.	ENSP00000444148:A1009T	A	+	1	0	FER1L5	96721047	0.988000	0.35896	0.033000	0.17914	0.005000	0.04900	2.830000	0.48136	2.543000	0.85770	0.655000	0.94253	GCG	.	.		0.667	FER1L5-001	KNOWN	basic|exp_conf	retained_intron	pseudogene	OTTHUMT00000339030.1	NM_001077400	
LRP1B	53353	hgsc.bcm.edu	37	2	141473604	141473604	+	Silent	SNP	A	A	G			TCGA-5R-AAAM-01A-12D-A40R-10	TCGA-5R-AAAM-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9aba9aa4-9f40-456e-8aa4-fb9d20c57d93	bbe62607-8229-46d6-997d-47d1a49b89b0	g.chr2:141473604A>G	ENST00000389484.3	-	37	6932	c.5961T>C	c.(5959-5961)cgT>cgC	p.R1987R		NM_018557.2	NP_061027.2	Q9NZR2	LRP1B_HUMAN	low density lipoprotein receptor-related protein 1B	1987					protein transport (GO:0015031)|receptor-mediated endocytosis (GO:0006898)	integral component of membrane (GO:0016021)|receptor complex (GO:0043235)	calcium ion binding (GO:0005509)|low-density lipoprotein receptor activity (GO:0005041)			NS(5)|autonomic_ganglia(1)|biliary_tract(1)|breast(3)|central_nervous_system(7)|endometrium(25)|haematopoietic_and_lymphoid_tissue(10)|kidney(27)|large_intestine(98)|liver(4)|lung(337)|ovary(15)|pancreas(6)|prostate(11)|skin(30)|stomach(2)|upper_aerodigestive_tract(19)|urinary_tract(5)	606		all_cancers(3;1.1e-60)|all_epithelial(3;1.94e-59)|all_lung(3;1.09e-24)|Lung NSC(3;5.65e-24)|Esophageal squamous(3;5.41e-13)|Renal(3;0.000147)|Breast(3;0.000527)|Hepatocellular(3;0.011)|all_neural(3;0.014)|Colorectal(150;0.101)		UCEC - Uterine corpus endometrioid carcinoma (2;0.00139)|Epithelial(1;1.25e-24)|all cancers(1;8.86e-24)|OV - Ovarian serous cystadenocarcinoma(1;2.45e-12)|LUSC - Lung squamous cell carcinoma(1;2.97e-10)|Lung(1;6.05e-09)|BRCA - Breast invasive adenocarcinoma(221;0.0103)		TAATTACATAACGGAAAGAAC	0.348										TSP Lung(27;0.18)																											p.R1987R	Colon(99;50 2074 2507 20106)	Atlas-SNP	.											LRP1B,colon,carcinoma,-2,2	LRP1B	1315	.	0			c.T5961C						.						114.0	120.0	118.0					2																	141473604		2203	4300	6503	SO:0001819	synonymous_variant	53353	exon37			TACATAACGGAAA	AF176832	CCDS2182.1	2q21.2	2013-05-29	2010-01-26		ENSG00000168702	ENSG00000168702		"""Low density lipoprotein receptors"""	6693	protein-coding gene	gene with protein product	"""LRP-deleted in tumors"""	608766				10766186	Standard	NM_018557		Approved	LRP-DIT, LRPDIT	uc002tvj.1	Q9NZR2	OTTHUMG00000131799	ENST00000389484.3:c.5961T>C	chr2.hg19:g.141473604A>G		226.0	1.0		253.0	11.0	NM_018557	Q8WY29|Q8WY30|Q8WY31	Silent	SNP	ENST00000389484.3	hg19	CCDS2182.1																																																																																			.	.		0.348	LRP1B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254736.2	NM_018557	
NFE2L2	4780	hgsc.bcm.edu	37	2	178098806	178098806	+	Missense_Mutation	SNP	G	G	A			TCGA-5R-AAAM-01A-12D-A40R-10	TCGA-5R-AAAM-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9aba9aa4-9f40-456e-8aa4-fb9d20c57d93	bbe62607-8229-46d6-997d-47d1a49b89b0	g.chr2:178098806G>A	ENST00000397062.3	-	2	793	c.239C>T	c.(238-240)aCa>aTa	p.T80I	NFE2L2_ENST00000423513.1_Missense_Mutation_p.T64I|NFE2L2_ENST00000446151.2_Missense_Mutation_p.T64I|NFE2L2_ENST00000464747.1_Missense_Mutation_p.T64I|NFE2L2_ENST00000397063.4_Missense_Mutation_p.T64I	NM_006164.4	NP_006155.2	Q16236	NF2L2_HUMAN	nuclear factor, erythroid 2-like 2	80					cellular response to hydrogen peroxide (GO:0070301)|cellular response to laminar fluid shear stress (GO:0071499)|cellular response to tumor necrosis factor (GO:0071356)|endoplasmic reticulum unfolded protein response (GO:0030968)|negative regulation of endothelial cell apoptotic process (GO:2000352)|negative regulation of oxidative stress-induced intrinsic apoptotic signaling pathway (GO:1902176)|positive regulation of blood coagulation (GO:0030194)|positive regulation of reactive oxygen species metabolic process (GO:2000379)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription from RNA polymerase II promoter in response to stress (GO:0036003)|proteasomal ubiquitin-independent protein catabolic process (GO:0010499)|proteasome-mediated ubiquitin-dependent protein catabolic process (GO:0043161)|protein ubiquitination (GO:0016567)|regulation of embryonic development (GO:0045995)|regulation of removal of superoxide radicals (GO:2000121)|transcription from RNA polymerase II promoter (GO:0006366)	centrosome (GO:0005813)|chromatin (GO:0000785)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	DNA binding (GO:0003677)|protein domain specific binding (GO:0019904)|RNA polymerase II activating transcription factor binding (GO:0001102)|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)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.T80K(3)|p.T80R(2)|p.T80I(1)		central_nervous_system(1)|cervix(4)|endometrium(14)|kidney(5)|large_intestine(4)|liver(13)|lung(71)|oesophagus(29)|skin(2)|upper_aerodigestive_tract(11)|urinary_tract(4)	158			Epithelial(96;0.00442)|OV - Ovarian serous cystadenocarcinoma(117;0.00739)|all cancers(119;0.0195)|LUSC - Lung squamous cell carcinoma(2;0.036)|Lung(16;0.0935)			AAATTCACCTGTCTCTTCATC	0.443			Mis		"""NSCLC, HNSCC"""					HNSCC(56;0.16)																											p.T80I		Atlas-SNP	.		Dom	yes		2	2q31	4780	nuclear factor (erythroid-derived 2)-like 2 (NRF2)		E	NFE2L2,NS,carcinoma,0,8	NFE2L2	225	.	6	Substitution - Missense(6)	lung(2)|oesophagus(2)|upper_aerodigestive_tract(1)|endometrium(1)	c.C239T						.						146.0	145.0	145.0					2																	178098806		1901	4109	6010	SO:0001583	missense	4780	exon2			TCACCTGTCTCTT		CCDS42782.1, CCDS46457.1, CCDS46458.1	2q31	2013-08-23	2013-08-23		ENSG00000116044	ENSG00000116044		"""basic leucine zipper proteins"""	7782	protein-coding gene	gene with protein product	"""NF-E2-related factor 2"""	600492	"""nuclear factor (erythroid-derived 2)-like 2"""			7937919	Standard	NM_006164		Approved	NRF2	uc002ulh.5	Q16236	OTTHUMG00000133620	ENST00000397062.3:c.239C>T	chr2.hg19:g.178098806G>A	ENSP00000380252:p.Thr80Ile	58.0	0.0		76.0	24.0	NM_006164	B2RBU2|B4E338|E9PGJ7|Q53RW6|Q59HH2|Q96F71	Missense_Mutation	SNP	ENST00000397062.3	hg19	CCDS42782.1	.	.	.	.	.	.	.	.	.	.	G	19.08	3.758048	0.69648	.	.	ENSG00000116044	ENST00000397063;ENST00000397062;ENST00000446151;ENST00000449627;ENST00000448782;ENST00000421929;ENST00000423513	T;T;T;T;T;T;T	0.34275	1.37;1.37;1.37;1.37;1.37;1.37;1.37	5.78	5.78	0.91487	.	0.000000	0.85682	D	0.000000	T	0.68109	0.2965	M	0.87180	2.865	0.80722	D	1	D;D;D;D	0.89917	1.0;0.999;1.0;1.0	D;D;D;D	0.91635	0.997;0.996;0.999;0.997	T	0.72623	-0.4237	10	0.87932	D	0	.	19.9976	0.97389	0.0:0.0:1.0:0.0	.	64;64;64;80	E9PGJ7;B4DNB0;C9JFL6;Q16236	.;.;.;NF2L2_HUMAN	I	64;80;64;64;64;64;64	ENSP00000380253:T64I;ENSP00000380252:T80I;ENSP00000411575:T64I;ENSP00000391590:T64I;ENSP00000400073:T64I;ENSP00000412191:T64I;ENSP00000410015:T64I	ENSP00000380252:T80I	T	-	2	0	NFE2L2	177807052	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	9.229000	0.95273	2.737000	0.93849	0.563000	0.77884	ACA	.	.		0.443	NFE2L2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000257752.4	NM_006164	
TTN	7273	hgsc.bcm.edu	37	2	179436587	179436587	+	Nonsense_Mutation	SNP	G	G	A			TCGA-5R-AAAM-01A-12D-A40R-10	TCGA-5R-AAAM-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9aba9aa4-9f40-456e-8aa4-fb9d20c57d93	bbe62607-8229-46d6-997d-47d1a49b89b0	g.chr2:179436587G>A	ENST00000591111.1	-	276	69573	c.69349C>T	c.(69349-69351)Cag>Tag	p.Q23117*	TTN-AS1_ENST00000585451.1_RNA|TTN-AS1_ENST00000591332.1_RNA|TTN-AS1_ENST00000592630.1_RNA|TTN-AS1_ENST00000590807.1_RNA|TTN-AS1_ENST00000592689.1_RNA|TTN_ENST00000342175.6_Nonsense_Mutation_p.Q15885*|TTN-AS1_ENST00000419746.1_RNA|TTN_ENST00000589042.1_Nonsense_Mutation_p.Q24758*|TTN-AS1_ENST00000586831.1_RNA|TTN-AS1_ENST00000590932.1_RNA|TTN-AS1_ENST00000586707.1_RNA|TTN-AS1_ENST00000438095.1_RNA|TTN_ENST00000460472.2_Nonsense_Mutation_p.Q15693*|TTN-AS1_ENST00000586452.1_RNA|TTN-AS1_ENST00000592600.1_RNA|TTN-AS1_ENST00000456053.1_RNA|TTN_ENST00000342992.6_Nonsense_Mutation_p.Q22190*|TTN-AS1_ENST00000592750.1_RNA|TTN_ENST00000359218.5_Nonsense_Mutation_p.Q15818*			Q8WZ42	TITIN_HUMAN	titin	23117	Ig-like 118.				adult heart development (GO:0007512)|blood coagulation (GO:0007596)|cardiac muscle contraction (GO:0060048)|cardiac muscle fiber development (GO:0048739)|cardiac muscle hypertrophy (GO:0003300)|cardiac muscle tissue morphogenesis (GO:0055008)|cardiac myofibril assembly (GO:0055003)|detection of muscle stretch (GO:0035995)|forward locomotion (GO:0043056)|in utero embryonic development (GO:0001701)|mitotic chromosome condensation (GO:0007076)|muscle contraction (GO:0006936)|muscle filament sliding (GO:0030049)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|regulation of catalytic activity (GO:0050790)|regulation of protein kinase activity (GO:0045859)|regulation of relaxation of cardiac muscle (GO:1901897)|response to calcium ion (GO:0051592)|sarcomere organization (GO:0045214)|sarcomerogenesis (GO:0048769)|skeletal muscle myosin thick filament assembly (GO:0030241)|skeletal muscle thin filament assembly (GO:0030240)|somitogenesis (GO:0001756)|striated muscle contraction (GO:0006941)	condensed nuclear chromosome (GO:0000794)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|I band (GO:0031674)|M band (GO:0031430)|nucleus (GO:0005634)|striated muscle thin filament (GO:0005865)|Z disc (GO:0030018)	actin filament binding (GO:0051015)|actinin binding (GO:0042805)|ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|calmodulin binding (GO:0005516)|enzyme binding (GO:0019899)|identical protein binding (GO:0042802)|muscle alpha-actinin binding (GO:0051371)|protease binding (GO:0002020)|protein kinase binding (GO:0019901)|protein self-association (GO:0043621)|protein serine/threonine kinase activity (GO:0004674)|structural constituent of muscle (GO:0008307)|structural molecule activity conferring elasticity (GO:0097493)|telethonin binding (GO:0031433)			NS(24)|autonomic_ganglia(1)|breast(64)|central_nervous_system(14)|cervix(14)|endometrium(96)|haematopoietic_and_lymphoid_tissue(16)|kidney(91)|large_intestine(303)|liver(1)|lung(595)|ovary(58)|pancreas(17)|prostate(38)|skin(60)|stomach(29)|upper_aerodigestive_tract(1)|urinary_tract(26)	1448			OV - Ovarian serous cystadenocarcinoma(117;0.023)|Epithelial(96;0.0454)|all cancers(119;0.134)			CTAGTTGTCTGCTTCAGTGGT	0.438																																					p.Q24758X		Atlas-SNP	.											.	TTN	18412	.	0			c.C74272T						.						91.0	96.0	94.0					2																	179436587		1926	4136	6062	SO:0001587	stop_gained	7273	exon326			TTGTCTGCTTCAG	X90568	CCDS54421.1, CCDS54422.1, CCDS54423.1, CCDS54424.1, CCDS33337.1, CCDS59435.1, CCDS74610.1	2q31	2014-09-17	2004-02-13		ENSG00000155657	ENSG00000155657		"""Immunoglobulin superfamily / I-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"", ""Fibronectin type III domain containing"""	12403	protein-coding gene	gene with protein product		188840	"""cardiomyopathy, dilated 1G (autosomal dominant)"""	CMD1G		2129545, 10051295	Standard	NM_003319		Approved	CMPD4, FLJ32040, TMD, CMH9, LGMD2J, MYLK5	uc031rqd.1	Q8WZ42	OTTHUMG00000154448	ENST00000591111.1:c.69349C>T	chr2.hg19:g.179436587G>A	ENSP00000465570:p.Gln23117*	131.0	0.0		124.0	39.0	NM_001267550	A6NKB1|E7EQE6|E7ET18|K7ENY1|Q10465|Q10466|Q15598|Q2XUS3|Q32Q60|Q4U1Z6|Q4ZG20|Q6NSG0|Q6PDB1|Q6PJP0|Q7KYM2|Q7KYN4|Q7KYN5|Q7LDM3|Q7Z2X3|Q8TCG8|Q8WZ42|Q8WZ51|Q8WZ52|Q8WZ53|Q8WZB3|Q92761|Q92762|Q9UD97|Q9UP84|Q9Y6L9	Nonsense_Mutation	SNP	ENST00000591111.1	hg19		.	.	.	.	.	.	.	.	.	.	G	63	73.990175	0.99992	.	.	ENSG00000155657	ENST00000342992;ENST00000460472;ENST00000342175;ENST00000359218;ENST00000356127	.	.	.	6.07	5.18	0.71444	.	.	.	.	.	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.87932	D	0	.	16.9885	0.86347	0.0:0.0:0.8717:0.1283	.	.	.	.	X	22190;15693;15885;15818;15691	.	ENSP00000340554:Q15885X	Q	-	1	0	TTN	179144833	1.000000	0.71417	0.996000	0.52242	0.981000	0.71138	6.054000	0.71096	1.556000	0.49512	0.650000	0.86243	CAG	.	.		0.438	TTN-019	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000460310.1	NM_133378	
PAX3	5077	hgsc.bcm.edu	37	2	223086027	223086027	+	Missense_Mutation	SNP	G	G	T			TCGA-5R-AAAM-01A-12D-A40R-10	TCGA-5R-AAAM-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9aba9aa4-9f40-456e-8aa4-fb9d20c57d93	bbe62607-8229-46d6-997d-47d1a49b89b0	g.chr2:223086027G>T	ENST00000350526.4	-	6	1008	c.872C>A	c.(871-873)cCc>cAc	p.P291H	PAX3_ENST00000336840.6_Missense_Mutation_p.P291H|PAX3_ENST00000409551.3_Missense_Mutation_p.P290H|PAX3_ENST00000464706.1_5'UTR|PAX3_ENST00000392069.2_Missense_Mutation_p.P291H|PAX3_ENST00000392070.2_Missense_Mutation_p.P291H|PAX3_ENST00000344493.4_Missense_Mutation_p.P291H	NM_181457.3	NP_852122.1	P23760	PAX3_HUMAN	paired box 3	291					apoptotic process (GO:0006915)|cell proliferation (GO:0008283)|developmental pigmentation (GO:0048066)|heart development (GO:0007507)|mammary gland specification (GO:0060594)|muscle organ development (GO:0007517)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|neural crest cell migration (GO:0001755)|neural tube closure (GO:0001843)|neuron fate commitment (GO:0048663)|organ morphogenesis (GO:0009887)|positive regulation of cell proliferation (GO:0008284)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of somitogenesis (GO:0014807)|sensory perception of sound (GO:0007605)|spinal cord association neuron differentiation (GO:0021527)|transcription from RNA polymerase II promoter (GO:0006366)	nucleus (GO:0005634)	chromatin binding (GO:0003682)|RNA polymerase II distal enhancer sequence-specific DNA binding transcription factor activity (GO:0003705)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)		PAX3/NCOA2(4)|PAX3/NCOA1(8)|PAX3/FOXO1(749)	NS(1)|endometrium(3)|kidney(1)|large_intestine(12)|lung(13)|ovary(4)|pancreas(1)|skin(2)|upper_aerodigestive_tract(1)	38		Renal(207;0.0183)		Epithelial(121;4.13e-10)|all cancers(144;1.85e-07)|LUSC - Lung squamous cell carcinoma(224;0.008)|Lung(261;0.00942)		GAACCCCCCGGGAATGAGATG	0.522			T	"""FOXO1A, NCOA1"""	alveolar rhabdomyosarcoma		Waardenburg syndrome; craniofacial-deafness-hand syndrome																														p.P291H		Atlas-SNP	.		Dom	yes		2	2q35	5077	paired box gene 3	yes	M	.	PAX3	106	.	0			c.C872A						.						155.0	164.0	161.0					2																	223086027		2203	4300	6503	SO:0001583	missense	5077	exon6			CCCCCGGGAATGA		CCDS2449.1, CCDS2450.1, CCDS2451.1, CCDS42825.1, CCDS2448.1, CCDS42826.1, CCDS46522.1, CCDS46523.1	2q36.1	2011-06-20	2007-07-12		ENSG00000135903	ENSG00000135903		"""Paired boxes"", ""Homeoboxes / PRD class"""	8617	protein-coding gene	gene with protein product		606597	"""Waardenburg syndrome 1"", ""paired box gene 3 (Waardenburg syndrome 1)"""	WS1		1347149	Standard	NM_181461		Approved	HUP2	uc002vmt.2	P23760	OTTHUMG00000133157	ENST00000350526.4:c.872C>A	chr2.hg19:g.223086027G>T	ENSP00000343052:p.Pro291His	142.0	0.0		161.0	26.0	NM_181457	G5E9C1|Q16448|Q494Z3|Q494Z4|Q53T90|Q6GSJ9|Q86UQ2|Q86UQ3	Missense_Mutation	SNP	ENST00000350526.4	hg19	CCDS42826.1	.	.	.	.	.	.	.	.	.	.	G	32	5.132879	0.94517	.	.	ENSG00000135903	ENST00000392069;ENST00000344493;ENST00000350526;ENST00000392070;ENST00000336840;ENST00000409551;ENST00000464706;ENST00000555548	D;D;D;D;D;D	0.95103	-3.6;-3.6;-3.59;-3.58;-3.61;-3.59	6.06	6.06	0.98353	.	0.000000	0.85682	D	0.000000	D	0.96728	0.8932	L	0.60455	1.87	0.80722	D	1	D;D;D;D;D	0.89917	0.998;0.994;1.0;0.999;0.999	D;P;D;D;D	0.72625	0.928;0.707;0.961;0.978;0.912	D	0.96034	0.9019	10	0.52906	T	0.07	.	20.6208	0.99490	0.0:0.0:1.0:0.0	.	291;290;291;291;291	P23760;Q494Z4;P23760-4;P23760-5;G5E9C1	PAX3_HUMAN;.;.;.;.	H	291;291;291;291;291;290;8;8	ENSP00000375921:P291H;ENSP00000342092:P291H;ENSP00000343052:P291H;ENSP00000375922:P291H;ENSP00000338767:P291H;ENSP00000386750:P290H	ENSP00000338767:P291H	P	-	2	0	PAX3	222794271	1.000000	0.71417	1.000000	0.80357	0.987000	0.75469	9.414000	0.97362	2.882000	0.98803	0.655000	0.94253	CCC	.	.		0.522	PAX3-006	KNOWN	not_organism_supported|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000328670.1		
ATG16L1	55054	hgsc.bcm.edu	37	2	234173607	234173607	+	Silent	SNP	T	T	C			TCGA-5R-AAAM-01A-12D-A40R-10	TCGA-5R-AAAM-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9aba9aa4-9f40-456e-8aa4-fb9d20c57d93	bbe62607-8229-46d6-997d-47d1a49b89b0	g.chr2:234173607T>C	ENST00000392017.4	+	5	716	c.459T>C	c.(457-459)tgT>tgC	p.C153C	ATG16L1_ENST00000347464.5_Intron|ATG16L1_ENST00000392020.4_Silent_p.C153C|ATG16L1_ENST00000392018.1_Silent_p.C153C|ATG16L1_ENST00000373525.5_Intron	NM_001190266.1|NM_001190267.1|NM_030803.6	NP_001177195.1|NP_001177196.1|NP_110430.5	Q676U5	A16L1_HUMAN	autophagy related 16-like 1 (S. cerevisiae)	153					autophagic vacuole assembly (GO:0000045)|negative stranded viral RNA replication (GO:0039689)|protein homooligomerization (GO:0051260)|protein transport (GO:0015031)	autophagic vacuole (GO:0005776)|autophagic vacuole membrane (GO:0000421)|axoneme (GO:0005930)	identical protein binding (GO:0042802)			breast(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(3)|kidney(2)|large_intestine(5)|lung(7)|prostate(3)|skin(1)	25		Breast(86;0.0013)|Renal(207;0.00339)|all_hematologic(139;0.0116)|all_lung(227;0.0179)|Acute lymphoblastic leukemia(138;0.0327)|Lung NSC(271;0.0539)		Epithelial(121;1.53e-17)|BRCA - Breast invasive adenocarcinoma(100;0.000379)|LUSC - Lung squamous cell carcinoma(224;0.00619)|Lung(119;0.00732)|GBM - Glioblastoma multiforme(43;0.11)		CTAAGCTTTGTGACCTTGAAA	0.473																																					p.C153C		Atlas-SNP	.											.	ATG16L1	83	.	0			c.T459C						.						128.0	118.0	121.0					2																	234173607		2203	4300	6503	SO:0001819	synonymous_variant	55054	exon5			GCTTTGTGACCTT	AK000897	CCDS2502.2, CCDS2503.2, CCDS54438.1	2q37.1	2014-02-12	2012-06-06	2005-09-13	ENSG00000085978	ENSG00000085978		"""WD repeat domain containing"""	21498	protein-coding gene	gene with protein product		610767	"""APG16 autophagy 16-like (S. cerevisiae)"", ""ATG16 autophagy related 16-like (S. cerevisiae)"", ""ATG16 autophagy related 16-like 1 (S. cerevisiae)"""	APG16L, ATG16L			Standard	NM_017974		Approved	WDR30, FLJ10035, ATG16A	uc002vty.3	Q676U5	OTTHUMG00000133619	ENST00000392017.4:c.459T>C	chr2.hg19:g.234173607T>C		137.0	0.0		128.0	17.0	NM_017974	A3EXK9|A3EXL0|B6ZDH0|Q6IPN1|Q6UXW4|Q6ZVZ5|Q8NCY2|Q96JV5|Q9H619	Silent	SNP	ENST00000392017.4	hg19	CCDS2503.2																																																																																			.	.		0.473	ATG16L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257069.2	NM_017974	
GRM7	2917	hgsc.bcm.edu	37	3	6903173	6903173	+	Missense_Mutation	SNP	G	G	A			TCGA-5R-AAAM-01A-12D-A40R-10	TCGA-5R-AAAM-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9aba9aa4-9f40-456e-8aa4-fb9d20c57d93	bbe62607-8229-46d6-997d-47d1a49b89b0	g.chr3:6903173G>A	ENST00000357716.4	+	1	372	c.98G>A	c.(97-99)cGc>cAc	p.R33H	GRM7_ENST00000403881.1_Missense_Mutation_p.R33H|GRM7_ENST00000486284.1_Missense_Mutation_p.R33H|GRM7_ENST00000389336.4_Missense_Mutation_p.R33H|GRM7_ENST00000402647.2_Missense_Mutation_p.R33H	NM_000844.3	NP_000835.1	Q14831	GRM7_HUMAN	glutamate receptor, metabotropic 7	33					adenylate cyclase-inhibiting G-protein coupled glutamate receptor signaling pathway (GO:0007196)|adult behavior (GO:0030534)|conditioned taste aversion (GO:0001661)|multicellular organismal response to stress (GO:0033555)|negative regulation of adenylate cyclase activity (GO:0007194)|negative regulation of cAMP biosynthetic process (GO:0030818)|negative regulation of glutamate secretion (GO:0014050)|regulation of cyclase activity (GO:0031279)|regulation of synaptic transmission, glutamatergic (GO:0051966)|sensory perception of smell (GO:0007608)|sensory perception of sound (GO:0007605)|short-term memory (GO:0007614)|synaptic transmission (GO:0007268)|transmission of nerve impulse (GO:0019226)	asymmetric synapse (GO:0032279)|axon (GO:0030424)|cell cortex (GO:0005938)|dendrite (GO:0030425)|dendritic shaft (GO:0043198)|integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)|presynaptic active zone (GO:0048786)|presynaptic membrane (GO:0042734)|receptor complex (GO:0043235)	adenylate cyclase inhibitor activity (GO:0010855)|calcium channel regulator activity (GO:0005246)|calcium ion binding (GO:0005509)|glutamate binding (GO:0016595)|glutamate receptor activity (GO:0008066)|group III metabotropic glutamate receptor activity (GO:0001642)|PDZ domain binding (GO:0030165)|serine binding (GO:0070905)|voltage-gated calcium channel activity (GO:0005245)	p.R33H(1)		breast(2)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(14)|lung(35)|ovary(4)|prostate(2)|skin(6)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(2)	76						GCGGCGGCGCGCGGCCAGGAG	0.692																																					p.R33H		Atlas-SNP	.											GRM7,NS,carcinoma,0,1	GRM7	223	.	1	Substitution - Missense(1)	lung(1)	c.G98A						.						9.0	9.0	9.0					3																	6903173		2118	4167	6285	SO:0001583	missense	2917	exon1			CGGCGCGCGGCCA	U92458	CCDS43042.1	3p26-p25	2014-06-12			ENSG00000196277	ENSG00000196277		"""GPCR / Class C : Glutamate receptors, metabotropic"", ""Glutamate receptors"""	4599	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 87"""	604101				8288585, 8840028	Standard	NM_000844		Approved	GLUR7, GPRC1G, mGlu7, MGLUR7, PPP1R87	uc003bql.2	Q14831	OTTHUMG00000125549	ENST00000357716.4:c.98G>A	chr3.hg19:g.6903173G>A	ENSP00000350348:p.Arg33His	118.0	0.0		114.0	12.0	NM_000844	Q8NFS2|Q8NFS3|Q8NFS4	Missense_Mutation	SNP	ENST00000357716.4	hg19	CCDS43042.1	.	.	.	.	.	.	.	.	.	.	G	3.232	-0.157146	0.06544	.	.	ENSG00000196277	ENST00000357716;ENST00000486284;ENST00000389336;ENST00000403881;ENST00000525747;ENST00000402647;ENST00000413492	D;D;D;D;D	0.89415	-2.47;-2.51;-2.51;-2.51;-2.51	5.23	1.98	0.26296	.	0.420263	0.21050	N	0.081012	T	0.70404	0.3220	N	0.01352	-0.895	0.28094	N	0.931708	B;B;D	0.64830	0.001;0.0;0.994	B;B;P	0.51415	0.0;0.0;0.669	T	0.66300	-0.5958	10	0.16420	T	0.52	.	1.0944	0.01670	0.2192:0.3258:0.2877:0.1673	.	33;33;33	Q14831-5;Q14831;Q14831-2	.;GRM7_HUMAN;.	H	33	ENSP00000350348:R33H;ENSP00000417536:R33H;ENSP00000373987:R33H;ENSP00000385664:R33H;ENSP00000384585:R33H	ENSP00000350348:R33H	R	+	2	0	GRM7	6878173	0.709000	0.27886	1.000000	0.80357	0.239000	0.25481	0.784000	0.26816	0.575000	0.29434	-0.312000	0.09012	CGC	.	.		0.692	GRM7-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000246895.3	NM_000844	
TOPAZ1	375337	hgsc.bcm.edu	37	3	44362676	44362676	+	Silent	SNP	T	T	C			TCGA-5R-AAAM-01A-12D-A40R-10	TCGA-5R-AAAM-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9aba9aa4-9f40-456e-8aa4-fb9d20c57d93	bbe62607-8229-46d6-997d-47d1a49b89b0	g.chr3:44362676T>C	ENST00000309765.4	+	17	4632	c.4464T>C	c.(4462-4464)aaT>aaC	p.N1488N		NM_001145030.1	NP_001138502.1	Q8N9V7	TOPZ1_HUMAN	testis and ovary specific PAZ domain containing 1	1488						cytoplasm (GO:0005737)	metal ion binding (GO:0046872)										GTTTTCAAAATTCCCAAGGTA	0.323																																					p.N1488N		Atlas-SNP	.											.	.	.	.	0			c.T4464C						.						86.0	73.0	77.0					3																	44362676		692	1591	2283	SO:0001819	synonymous_variant	375337	exon17			TCAAAATTCCCAA	AK093476	CCDS46809.1	3p21.33	2012-10-08	2012-10-08	2012-10-08	ENSG00000173769	ENSG00000173769			24746	protein-coding gene	gene with protein product		614412	"""chromosome 3 open reading frame 77"""	C3orf77		22069478	Standard	NM_001145030		Approved	FLJ36157	uc003cna.4	Q8N9V7	OTTHUMG00000156172	ENST00000309765.4:c.4464T>C	chr3.hg19:g.44362676T>C		98.0	0.0		92.0	26.0	NM_001145030		Silent	SNP	ENST00000309765.4	hg19	CCDS46809.1																																																																																			.	.		0.323	TOPAZ1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000343247.1	NM_001145030	
CNBP	7555	hgsc.bcm.edu	37	3	128889414	128889414	+	Splice_Site	SNP	C	C	T			TCGA-5R-AAAM-01A-12D-A40R-10	TCGA-5R-AAAM-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9aba9aa4-9f40-456e-8aa4-fb9d20c57d93	bbe62607-8229-46d6-997d-47d1a49b89b0	g.chr3:128889414C>T	ENST00000422453.2	-	5	577		c.e5-1		CNBP_ENST00000504813.1_Splice_Site|CNBP_ENST00000500450.2_Splice_Site|CNBP_ENST00000446936.2_Splice_Site|CNBP_ENST00000451728.2_Splice_Site|CNBP_ENST00000502976.1_Splice_Site|CNBP_ENST00000441626.2_Splice_Site	NM_001127192.1|NM_001127193.1|NM_003418.4	NP_001120664.1|NP_001120665.1|NP_003409.1	P62633	CNBP_HUMAN	CCHC-type zinc finger, nucleic acid binding protein						cholesterol biosynthetic process (GO:0006695)|positive regulation of cell proliferation (GO:0008284)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)|sequence-specific DNA binding transcription factor activity (GO:0003700)|single-stranded DNA binding (GO:0003697)|single-stranded RNA binding (GO:0003727)|zinc ion binding (GO:0008270)			biliary_tract(1)|endometrium(1)|kidney(1)|lung(2)	5						TTCACCACACCTAAAAAAGAA	0.443																																					.		Atlas-SNP	.											.	CNBP	12	.	0			c.417-1G>A						.						121.0	117.0	118.0					3																	128889414		2203	4300	6503	SO:0001630	splice_region_variant	7555	exon6			CCACACCTAAAAA	U19765	CCDS3056.1, CCDS46906.1, CCDS46907.1, CCDS46908.1, CCDS54637.1	3q21	2013-01-09	2006-06-29	2006-06-29				"""RING-type (C3HC4) zinc fingers"", ""Zinc fingers, CCHC domain containing"""	13164	protein-coding gene	gene with protein product		116955	"""zinc finger protein 9 (a cellular retroviral nucleic acid binding protein)"", ""zinc finger protein 9"""	DM2, ZNF9		2249857, 11486088	Standard	NM_003418		Approved	RNF163, ZCCHC22, CNBP1	uc021xdw.1	P62633		ENST00000422453.2:c.417-1G>A	chr3.hg19:g.128889414C>T		118.0	0.0		107.0	12.0	NM_003418	A8K7V4|B2RAV9|B4DP17|D3DNB9|D3DNC0|D3DNC1|E9PDR7|P20694|Q4JGY0|Q4JGY1|Q5QJR0|Q5U0E9|Q6PJI7|Q96NV3	Splice_Site	SNP	ENST00000422453.2	hg19	CCDS3056.1	.	.	.	.	.	.	.	.	.	.	C	14.89	2.668973	0.47677	.	.	ENSG00000169714	ENST00000502976;ENST00000422453;ENST00000451728;ENST00000446936;ENST00000500450;ENST00000504813;ENST00000441626	.	.	.	5.92	4.13	0.48395	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	11.278	0.49178	0.1429:0.7197:0.1374:0.0	.	.	.	.	.	-1	.	.	.	-	.	.	CNBP	130372104	1.000000	0.71417	0.928000	0.36995	0.940000	0.58332	7.373000	0.79623	0.848000	0.35191	0.467000	0.42956	.	.	.		0.443	CNBP-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000358419.1	NM_003418	Intron
C3orf79	152118	hgsc.bcm.edu	37	3	153220256	153220256	+	Silent	SNP	T	T	C			TCGA-5R-AAAM-01A-12D-A40R-10	TCGA-5R-AAAM-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9aba9aa4-9f40-456e-8aa4-fb9d20c57d93	bbe62607-8229-46d6-997d-47d1a49b89b0	g.chr3:153220256T>C	ENST00000446603.2	+	3	350	c.288T>C	c.(286-288)gaT>gaC	p.D96D	RP11-23D24.2_ENST00000493214.2_RNA	NM_001101337.1	NP_001094807.1	P0CE67	CC079_HUMAN	chromosome 3 open reading frame 79	96										endometrium(1)|large_intestine(3)	4						ATCAAACAGATGCCAGTCACT	0.393																																					p.D96D		Atlas-SNP	.											.	C3orf79	13	.	0			c.T288C						.						103.0	101.0	102.0					3																	153220256		1865	4100	5965	SO:0001819	synonymous_variant	152118	exon3			AACAGATGCCAGT	AF086445	CCDS46937.1	3q25.2	2009-09-30			ENSG00000237787	ENSG00000237787			37259	protein-coding gene	gene with protein product							Standard	NM_001101337		Approved		uc003ezt.3	P0CE67	OTTHUMG00000159629	ENST00000446603.2:c.288T>C	chr3.hg19:g.153220256T>C		82.0	0.0		102.0	13.0	NM_001101337		Silent	SNP	ENST00000446603.2	hg19	CCDS46937.1																																																																																			.	.		0.393	C3orf79-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000356570.1	NM_001101337	
ACAP2	23527	hgsc.bcm.edu	37	3	195029516	195029516	+	Splice_Site	SNP	T	T	A			TCGA-5R-AAAM-01A-12D-A40R-10	TCGA-5R-AAAM-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9aba9aa4-9f40-456e-8aa4-fb9d20c57d93	bbe62607-8229-46d6-997d-47d1a49b89b0	g.chr3:195029516T>A	ENST00000326793.6	-	11	1138	c.908A>T	c.(907-909)aAg>aTg	p.K303M		NM_012287.5	NP_036419.3	Q15057	ACAP2_HUMAN	ArfGAP with coiled-coil, ankyrin repeat and PH domains 2	303	PH. {ECO:0000255|PROSITE- ProRule:PRU00145}.				cellular response to nerve growth factor stimulus (GO:1990090)|protein localization to endosome (GO:0036010)|regulation of ARF GTPase activity (GO:0032312)	endosome membrane (GO:0010008)|membrane (GO:0016020)	ARF GTPase activator activity (GO:0008060)|zinc ion binding (GO:0008270)			cervix(2)|endometrium(2)|kidney(4)|large_intestine(5)|lung(10)|ovary(1)|pancreas(1)|upper_aerodigestive_tract(2)	27						AACACCTACCTTAAATTTTTT	0.289																																					p.K303M		Atlas-SNP	.											.	ACAP2	72	.	0			c.A908T						.						53.0	55.0	54.0					3																	195029516		2200	4290	6490	SO:0001630	splice_region_variant	23527	exon11			CCTACCTTAAATT		CCDS33924.1	3q29	2013-01-10	2008-09-22	2008-09-22	ENSG00000114331	ENSG00000114331		"""ADP-ribosylation factor GTPase activating proteins"", ""Pleckstrin homology (PH) domain containing"", ""Ankyrin repeat domain containing"""	16469	protein-coding gene	gene with protein product		607766	"""centaurin, beta 2"""	CENTB2		11050434, 11062263	Standard	NM_012287		Approved	KIAA0041, CNT-B2	uc003fun.4	Q15057	OTTHUMG00000155885	ENST00000326793.6:c.909+1A>T	chr3.hg19:g.195029516T>A		119.0	0.0		98.0	8.0	NM_012287	A8K2V4|Q8N5Z8|Q9UQR3	Missense_Mutation	SNP	ENST00000326793.6	hg19	CCDS33924.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	20.3|20.3	3.968611|3.968611	0.74131|0.74131	.|.	.|.	ENSG00000114331|ENSG00000114331	ENST00000326793|ENST00000439758	T|.	0.78246|.	-1.16|.	5.76|5.76	5.76|5.76	0.90799|0.90799	Pleckstrin homology-type (1);Pleckstrin homology domain (3);|.	0.000000|.	0.85682|.	D|.	0.000000|.	T|.	0.70666|.	0.3250|.	M|M	0.64170|0.64170	1.965|1.965	0.80722|0.80722	D|D	1|1	D|.	0.89917|.	1.0|.	D|.	0.80764|.	0.994|.	T|.	0.70011|.	-0.4989|.	10|.	0.51188|.	T|.	0.08|.	.|.	13.8133|13.8133	0.63276|0.63276	0.0:0.0:0.0:1.0|0.0:0.0:0.0:1.0	.|.	303|.	Q15057|.	ACAP2_HUMAN|.	M|Y	303|177	ENSP00000324287:K303M|.	ENSP00000324287:K303M|.	K|X	-|-	2|3	0|2	ACAP2|ACAP2	196510805|196510805	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.980000|0.980000	0.70556|0.70556	5.869000|5.869000	0.69613|0.69613	2.189000|2.189000	0.69895|0.69895	0.528000|0.528000	0.53228|0.53228	AAG|TAA	.	.		0.289	ACAP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000342126.2	NM_012287	Missense_Mutation
WDR19	57728	hgsc.bcm.edu	37	4	39229946	39229946	+	Silent	SNP	C	C	T	rs539697450		TCGA-5R-AAAM-01A-12D-A40R-10	TCGA-5R-AAAM-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9aba9aa4-9f40-456e-8aa4-fb9d20c57d93	bbe62607-8229-46d6-997d-47d1a49b89b0	g.chr4:39229946C>T	ENST00000399820.3	+	16	1900	c.1746C>T	c.(1744-1746)taC>taT	p.Y582Y	WDR19_ENST00000288634.7_Silent_p.Y422Y	NM_025132.3	NP_079408.3	Q8NEZ3	WDR19_HUMAN	WD repeat domain 19	582					ciliary receptor clustering involved in smoothened signaling pathway (GO:0060830)|cilium assembly (GO:0042384)|digestive system development (GO:0055123)|ear morphogenesis (GO:0042471)|embryonic camera-type eye development (GO:0031076)|embryonic cranial skeleton morphogenesis (GO:0048701)|embryonic limb morphogenesis (GO:0030326)|in utero embryonic development (GO:0001701)|intraciliary retrograde transport (GO:0035721)|myotome development (GO:0061055)|neurological system process (GO:0050877)|smoothened signaling pathway involved in dorsal/ventral neural tube patterning (GO:0060831)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|intraciliary transport particle A (GO:0030991)|motile cilium (GO:0031514)|nonmotile primary cilium (GO:0031513)|photoreceptor connecting cilium (GO:0032391)				large_intestine(1)	1						ATAAGGTGTACACTTATGTCT	0.348													C|||	1	0.000199681	0.0	0.0	5008	,	,		21314	0.0		0.0	False		,,,				2504	0.001				p.Y582Y		Atlas-SNP	.											.	WDR19	96	.	0			c.C1746T						.						87.0	82.0	84.0					4																	39229946		1866	4108	5974	SO:0001819	synonymous_variant	57728	exon16			GGTGTACACTTAT	AB046858, AY029257	CCDS47042.1	4p14	2014-02-21			ENSG00000157796	ENSG00000157796		"""WD repeat domain containing"", ""Intraflagellar transport homologs"""	18340	protein-coding gene	gene with protein product	"""intraflagellar transport 144 homolog (Chlamydomonas)"""	608151				12906858, 22019273	Standard	XM_005262658		Approved	Pwdmp, KIAA1638, FLJ23127, ORF26, DYF-2, Oseg6, IFT144, NPHP13	uc003gtv.3	Q8NEZ3	OTTHUMG00000160466	ENST00000399820.3:c.1746C>T	chr4.hg19:g.39229946C>T		118.0	0.0		119.0	14.0	NM_025132	B5MEF2|Q8N5B4|Q9H5S0|Q9HCD4	Silent	SNP	ENST00000399820.3	hg19	CCDS47042.1																																																																																			.	.		0.348	WDR19-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000360689.1		
ODAM	54959	hgsc.bcm.edu	37	4	71063815	71063815	+	Missense_Mutation	SNP	G	G	T			TCGA-5R-AAAM-01A-12D-A40R-10	TCGA-5R-AAAM-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9aba9aa4-9f40-456e-8aa4-fb9d20c57d93	bbe62607-8229-46d6-997d-47d1a49b89b0	g.chr4:71063815G>T	ENST00000396094.2	+	4	364	c.316G>T	c.(316-318)Ggc>Tgc	p.G106C		NM_017855.3	NP_060325.3	A1E959	ODAM_HUMAN	odontogenic, ameloblast asssociated	106	Gln-rich.				biomineral tissue development (GO:0031214)|odontogenesis of dentin-containing tooth (GO:0042475)	cytoplasm (GO:0005737)|extracellular region (GO:0005576)|fibril (GO:0043205)|nucleus (GO:0005634)				NS(1)|breast(2)|endometrium(2)|large_intestine(2)|lung(8)|ovary(3)|skin(2)	20						AGCCCAGGCAGGCCAAGTTGA	0.517																																					p.G106C		Atlas-SNP	.											.	ODAM	38	.	0			c.G316T						.						135.0	140.0	138.0					4																	71063815		1940	4133	6073	SO:0001583	missense	54959	exon4			CAGGCAGGCCAAG	AK000520	CCDS3536.2	4q13.3	2010-11-23			ENSG00000109205	ENSG00000109205			26043	protein-coding gene	gene with protein product		614843				14647039	Standard	NM_017855		Approved	APin, FLJ20513	uc003hfc.3	A1E959	OTTHUMG00000129406	ENST00000396094.2:c.316G>T	chr4.hg19:g.71063815G>T	ENSP00000379401:p.Gly106Cys	105.0	0.0		102.0	9.0	NM_017855	Q8WWE5|Q9NWZ9	Missense_Mutation	SNP	ENST00000396094.2	hg19	CCDS3536.2	.	.	.	.	.	.	.	.	.	.	G	10.10	1.257197	0.22965	.	.	ENSG00000109205	ENST00000396094;ENST00000510709;ENST00000514097	T;T	0.46819	0.86;0.86	4.79	2.15	0.27550	.	.	.	.	.	T	0.54791	0.1880	L	0.50333	1.59	0.09310	N	1	D	0.69078	0.997	D	0.63192	0.912	T	0.39014	-0.9634	9	0.46703	T	0.11	3.1135	6.7114	0.23280	0.2947:0.0:0.7053:0.0	.	106	A1E959	ODAM_HUMAN	C	106;92;59	ENSP00000379401:G106C;ENSP00000426106:G59C	ENSP00000379401:G106C	G	+	1	0	ODAM	71098404	0.000000	0.05858	0.000000	0.03702	0.247000	0.25773	0.208000	0.17415	0.253000	0.21552	0.561000	0.74099	GGC	.	.		0.517	ODAM-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251562.1	NM_017855	
SEC24D	9871	hgsc.bcm.edu	37	4	119653989	119653989	+	Missense_Mutation	SNP	G	G	C			TCGA-5R-AAAM-01A-12D-A40R-10	TCGA-5R-AAAM-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9aba9aa4-9f40-456e-8aa4-fb9d20c57d93	bbe62607-8229-46d6-997d-47d1a49b89b0	g.chr4:119653989G>C	ENST00000280551.6	-	20	2813	c.2575C>G	c.(2575-2577)Cca>Gca	p.P859A	SEC24D_ENST00000429811.2_3'UTR|SEC24D_ENST00000379735.5_Missense_Mutation_p.P860A|SEC24D_ENST00000511481.1_Missense_Mutation_p.P490A|SEC24D_ENST00000505134.1_5'UTR			O94855	SC24D_HUMAN	SEC24 family member D	859					antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|antigen processing and presentation of peptide antigen via MHC class I (GO:0002474)|cellular protein metabolic process (GO:0044267)|COPII vesicle coating (GO:0048208)|ER to Golgi vesicle-mediated transport (GO:0006888)|in utero embryonic development (GO:0001701)|intracellular protein transport (GO:0006886)|membrane organization (GO:0061024)|post-translational protein modification (GO:0043687)|protein N-linked glycosylation via asparagine (GO:0018279)|small molecule metabolic process (GO:0044281)	COPII vesicle coat (GO:0030127)|cytosol (GO:0005829)|endoplasmic reticulum membrane (GO:0005789)|ER to Golgi transport vesicle membrane (GO:0012507)|Golgi membrane (GO:0000139)	zinc ion binding (GO:0008270)			breast(3)|cervix(1)|endometrium(5)|kidney(1)|large_intestine(10)|lung(13)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	37						GAGATCTCTGGTCTGCTGAGT	0.423																																					p.P859A		Atlas-SNP	.											.	SEC24D	96	.	0			c.C2575G						.						195.0	163.0	174.0					4																	119653989		2203	4300	6503	SO:0001583	missense	9871	exon20			TCTCTGGTCTGCT	AB018298	CCDS3710.1	4q26	2013-10-21	2013-10-21		ENSG00000150961	ENSG00000150961			10706	protein-coding gene	gene with protein product		607186	"""SEC24 (S. cerevisiae) related gene family, member D"", ""SEC24 family, member D (S. cerevisiae)"""			9872452, 10075675	Standard	NM_014822		Approved	KIAA0755	uc003ici.4	O94855	OTTHUMG00000132957	ENST00000280551.6:c.2575C>G	chr4.hg19:g.119653989G>C	ENSP00000280551:p.Pro859Ala	142.0	0.0		135.0	43.0	NM_014822	Q8IYI7	Missense_Mutation	SNP	ENST00000280551.6	hg19	CCDS3710.1	.	.	.	.	.	.	.	.	.	.	G	1.842	-0.467082	0.04476	.	.	ENSG00000150961	ENST00000280551;ENST00000379735;ENST00000511481	D;D;D	0.88431	-2.38;-2.38;-2.38	5.62	4.77	0.60923	Sec23/Sec24, helical domain (2);	0.214881	0.49305	D	0.000152	T	0.78991	0.4371	L	0.27053	0.805	0.80722	D	1	B;B;B	0.02656	0.0;0.0;0.0	B;B;B	0.04013	0.001;0.0;0.0	T	0.69595	-0.5103	10	0.07175	T	0.84	-4.9602	10.5038	0.44821	0.071:0.1327:0.7962:0.0	.	21;860;859	Q9NWP5;O94855-2;O94855	.;.;SC24D_HUMAN	A	859;860;490	ENSP00000280551:P859A;ENSP00000369059:P860A;ENSP00000425491:P490A	ENSP00000280551:P859A	P	-	1	0	SEC24D	119873437	1.000000	0.71417	0.845000	0.33349	0.990000	0.78478	2.122000	0.41987	1.340000	0.45581	0.591000	0.81541	CCA	.	.		0.423	SEC24D-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000256514.4		
SLC25A31	83447	hgsc.bcm.edu	37	4	128651788	128651788	+	Missense_Mutation	SNP	G	G	A			TCGA-5R-AAAM-01A-12D-A40R-10	TCGA-5R-AAAM-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9aba9aa4-9f40-456e-8aa4-fb9d20c57d93	bbe62607-8229-46d6-997d-47d1a49b89b0	g.chr4:128651788G>A	ENST00000281154.4	+	1	256	c.88G>A	c.(88-90)Gcg>Acg	p.A30T		NM_031291.2	NP_112581.1	Q9H0C2	ADT4_HUMAN	solute carrier family 25 (mitochondrial carrier; adenine nucleotide translocator), member 31	30					transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|mitochondrial inner membrane (GO:0005743)|mitochondrion (GO:0005739)|motile cilium (GO:0031514)|nucleus (GO:0005634)	transporter activity (GO:0005215)			NS(1)|breast(1)|large_intestine(10)|lung(8)|skin(2)	22						CGGCGGAGTCGCGGCAGCTGT	0.622																																					p.A30T		Atlas-SNP	.											.	SLC25A31	42	.	0			c.G88A						.						50.0	48.0	49.0					4																	128651788		2203	4300	6503	SO:0001583	missense	83447	exon1			GGAGTCGCGGCAG	AL136857	CCDS3733.1	4q28	2013-05-22			ENSG00000151475	ENSG00000151475		"""Solute carriers"""	25319	protein-coding gene	gene with protein product		610796				15670820	Standard	NM_031291		Approved	DKFZP434N1235, ANT4	uc003ifl.3	Q9H0C2	OTTHUMG00000133300	ENST00000281154.4:c.88G>A	chr4.hg19:g.128651788G>A	ENSP00000281154:p.Ala30Thr	213.0	0.0		226.0	46.0	NM_031291		Missense_Mutation	SNP	ENST00000281154.4	hg19	CCDS3733.1	.	.	.	.	.	.	.	.	.	.	G	17.44	3.389167	0.61956	.	.	ENSG00000151475	ENST00000281154	D	0.87103	-2.21	4.96	4.96	0.65561	Mitochondrial carrier domain (2);	0.140508	0.32901	N	0.005508	D	0.91181	0.7222	M	0.90814	3.15	0.43814	D	0.996373	D	0.67145	0.996	P	0.47864	0.559	D	0.93160	0.6557	10	0.87932	D	0	-0.5605	15.2429	0.73485	0.0:0.0:1.0:0.0	.	30	Q9H0C2	ADT4_HUMAN	T	30	ENSP00000281154:A30T	ENSP00000281154:A30T	A	+	1	0	SLC25A31	128871238	1.000000	0.71417	0.125000	0.21846	0.007000	0.05969	4.772000	0.62324	2.575000	0.86900	0.655000	0.94253	GCG	.	.		0.622	SLC25A31-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257094.2	NM_031291	
MAML3	55534	hgsc.bcm.edu	37	4	140811125	140811125	+	Missense_Mutation	SNP	G	G	T	rs62344940		TCGA-5R-AAAM-01A-12D-A40R-10	TCGA-5R-AAAM-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9aba9aa4-9f40-456e-8aa4-fb9d20c57d93	bbe62607-8229-46d6-997d-47d1a49b89b0	g.chr4:140811125G>T	ENST00000509479.2	-	2	2321	c.1465C>A	c.(1465-1467)Caa>Aaa	p.Q489K	MAML3_ENST00000327122.5_Missense_Mutation_p.Q333K|MAML3_ENST00000398940.1_Missense_Mutation_p.Q28K	NM_018717.4	NP_061187			mastermind-like 3 (Drosophila)											breast(1)|endometrium(7)|kidney(2)|large_intestine(1)|lung(9)|ovary(1)|prostate(2)|urinary_tract(2)	25	all_hematologic(180;0.162)					tgctgctgttgctgttgctgt	0.552																																					p.Q489K		Atlas-SNP	.											.	MAML3	192	.	0			c.C1465A						.						17.0	20.0	19.0					4																	140811125		2194	4294	6488	SO:0001583	missense	55534	exon2			GCTGTTGCTGTTG	AB058719	CCDS54805.1	4q31.1	2014-08-12	2003-09-24		ENSG00000196782	ENSG00000196782			16272	protein-coding gene	gene with protein product	"""mastermind (drosophila)-like 3"""	608991	"""trinucleotide repeat containing 3"""	TNRC3		12370315, 12386158	Standard	NM_018717		Approved	KIAA1816, MAM2, CAGH3, GDN	uc021xsg.1	Q96JK9	OTTHUMG00000161441	ENST00000509479.2:c.1465C>A	chr4.hg19:g.140811125G>T	ENSP00000421180:p.Gln489Lys	55.0	0.0		59.0	8.0	NM_018717		Missense_Mutation	SNP	ENST00000509479.2	hg19	CCDS54805.1	.	.	.	.	.	.	.	.	.	.	G	3.000	-0.206260	0.06180	.	.	ENSG00000196782	ENST00000509479;ENST00000327122;ENST00000398940	T;T	0.76448	0.83;-1.02	2.61	2.61	0.31194	.	0.000000	0.64402	D	0.000001	T	0.66607	0.2806	N	0.08118	0	0.31344	N	0.683255	P	0.43392	0.805	P	0.59424	0.857	T	0.64106	-0.6485	10	0.05436	T	0.98	.	8.8799	0.35367	0.0:0.0:1.0:0.0	rs62344940	489	Q96JK9	MAML3_HUMAN	K	489;333;28	ENSP00000421180:Q489K;ENSP00000313316:Q333K	ENSP00000313316:Q333K	Q	-	1	0	MAML3	141030575	1.000000	0.71417	1.000000	0.80357	0.631000	0.37964	3.291000	0.51764	1.788000	0.52465	0.484000	0.47621	CAA	.	.		0.552	MAML3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000364934.2		
FGB	2244	hgsc.bcm.edu	37	4	155487708	155487708	+	Missense_Mutation	SNP	A	A	G			TCGA-5R-AAAM-01A-12D-A40R-10	TCGA-5R-AAAM-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9aba9aa4-9f40-456e-8aa4-fb9d20c57d93	bbe62607-8229-46d6-997d-47d1a49b89b0	g.chr4:155487708A>G	ENST00000302068.4	+	3	437	c.374A>G	c.(373-375)aAt>aGt	p.N125S	FGB_ENST00000509493.1_Intron|FGB_ENST00000502545.1_3'UTR	NM_005141.4	NP_005132.2	P02675	FIBB_HUMAN	fibrinogen beta chain	125					blood coagulation (GO:0007596)|cell-matrix adhesion (GO:0007160)|cellular protein complex assembly (GO:0043623)|cellular response to interleukin-1 (GO:0071347)|cellular response to leptin stimulus (GO:0044320)|extracellular matrix organization (GO:0030198)|negative regulation of endothelial cell apoptotic process (GO:2000352)|negative regulation of extrinsic apoptotic signaling pathway via death domain receptors (GO:1902042)|platelet activation (GO:0030168)|platelet aggregation (GO:0070527)|platelet degranulation (GO:0002576)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of exocytosis (GO:0045921)|positive regulation of heterotypic cell-cell adhesion (GO:0034116)|positive regulation of peptide hormone secretion (GO:0090277)|positive regulation of protein secretion (GO:0050714)|positive regulation of substrate adhesion-dependent cell spreading (GO:1900026)|positive regulation of vasoconstriction (GO:0045907)|protein polymerization (GO:0051258)|response to calcium ion (GO:0051592)|signal transduction (GO:0007165)	blood microparticle (GO:0072562)|cell cortex (GO:0005938)|cell surface (GO:0009986)|external side of plasma membrane (GO:0009897)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|fibrinogen complex (GO:0005577)|plasma membrane (GO:0005886)|platelet alpha granule (GO:0031091)|platelet alpha granule lumen (GO:0031093)|vesicle (GO:0031982)	chaperone binding (GO:0051087)|structural molecule activity (GO:0005198)			endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(2)|liver(2)|lung(22)|ovary(3)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	34	all_hematologic(180;0.215)	Renal(120;0.0458)			Sucralfate(DB00364)	CCAATCAGAAATAGTGTTGAT	0.418																																					p.N125S	NSCLC(106;1133 1613 21870 46110 52656)	Atlas-SNP	.											.	FGB	71	.	0			c.A374G						.						159.0	149.0	152.0					4																	155487708		2203	4300	6503	SO:0001583	missense	2244	exon3			TCAGAAATAGTGT		CCDS3786.1	4q28	2014-09-17			ENSG00000171564	ENSG00000171564		"""Fibrinogen C domain containing"", ""Endogenous ligands"""	3662	protein-coding gene	gene with protein product		134830	"""fibrinogen, B beta polypeptide"""				Standard	NM_005141		Approved		uc003ioa.4	P02675	OTTHUMG00000150331	ENST00000302068.4:c.374A>G	chr4.hg19:g.155487708A>G	ENSP00000306099:p.Asn125Ser	137.0	0.0		135.0	22.0	NM_005141	A0JLR9|B2R7G3|Q32Q65|Q3KPF2	Missense_Mutation	SNP	ENST00000302068.4	hg19	CCDS3786.1	.	.	.	.	.	.	.	.	.	.	A	0.052	-1.246284	0.01481	.	.	ENSG00000171564	ENST00000302068;ENST00000537843	D	0.81659	-1.52	5.27	0.923	0.19413	Fibrinogen, alpha/beta/gamma chain, coiled coil domain (2);	0.674999	0.15593	N	0.254288	T	0.56108	0.1963	N	0.08118	0	0.09310	N	0.999992	B;B	0.02656	0.0;0.0	B;B	0.04013	0.001;0.0	T	0.37865	-0.9687	10	0.13853	T	0.58	.	6.3655	0.21453	0.6481:0.181:0.1709:0.0	.	108;125	B4E1D3;P02675	.;FIBB_HUMAN	S	125;108	ENSP00000306099:N125S	ENSP00000306099:N125S	N	+	2	0	FGB	155707158	0.000000	0.05858	0.002000	0.10522	0.001000	0.01503	0.382000	0.20635	0.055000	0.16094	-1.162000	0.01777	AAT	.	.		0.418	FGB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000317595.1	NM_005141	
PAPD7	11044	hgsc.bcm.edu	37	5	6753104	6753104	+	Missense_Mutation	SNP	C	C	A			TCGA-5R-AAAM-01A-12D-A40R-10	TCGA-5R-AAAM-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9aba9aa4-9f40-456e-8aa4-fb9d20c57d93	bbe62607-8229-46d6-997d-47d1a49b89b0	g.chr5:6753104C>A	ENST00000230859.6	+	12	1517	c.1388C>A	c.(1387-1389)cCc>cAc	p.P463H		NM_001171805.1|NM_001171806.1|NM_006999.4	NP_001165276.1|NP_001165277.1|NP_008930.1	Q5XG87	PAPD7_HUMAN	PAP associated domain containing 7	693	PAP-associated.				double-strand break repair (GO:0006302)|mitotic chromosome condensation (GO:0007076)|response to drug (GO:0042493)|sister chromatid cohesion (GO:0007062)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	DNA binding (GO:0003677)|DNA-directed DNA polymerase activity (GO:0003887)|metal ion binding (GO:0046872)|polynucleotide adenylyltransferase activity (GO:0004652)|SMC family protein binding (GO:0043221)			cervix(1)|endometrium(2)|large_intestine(8)|lung(10)|ovary(2)|pancreas(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	27						CCGGCCATTCCCTCAGCGTCC	0.562																																					p.P463H	NSCLC(7;212 333 5667 23379 46547)	Atlas-SNP	.											.	PAPD7	69	.	0			c.C1388A						.						154.0	142.0	146.0					5																	6753104		2203	4300	6503	SO:0001583	missense	11044	exon12			CCATTCCCTCAGC	AF089896	CCDS3871.1	5p15	2010-11-18	2010-01-19	2010-01-19	ENSG00000112941	ENSG00000112941			16705	protein-coding gene	gene with protein product	"""topoisomerase-related function protein 4-1"", ""polymerase (DNA-directed) sigma"", ""DNA polymerase kappa"", ""TUTase5"""	605198	"""polymerase (DNA directed) sigma"""	POLS		10066793, 10926539	Standard	NM_006999		Approved	POLK, TRF4, LAK-1, TRF4-1	uc003jdx.1	Q5XG87	OTTHUMG00000090457	ENST00000230859.6:c.1388C>A	chr5.hg19:g.6753104C>A	ENSP00000230859:p.Pro463His	118.0	0.0		122.0	7.0	NM_001171805	A8K1E2|M1JCE6|O43289|Q17RZ1|Q9Y6C1	Missense_Mutation	SNP	ENST00000230859.6	hg19	CCDS3871.1	.	.	.	.	.	.	.	.	.	.	C	14.13	2.444058	0.43429	.	.	ENSG00000112941	ENST00000230859	T	0.33654	1.4	5.24	5.24	0.73138	.	0.190471	0.45867	D	0.000330	T	0.39911	0.1096	L	0.27053	0.805	0.42241	D	0.991937	D;D	0.67145	0.996;0.996	P;P	0.54372	0.75;0.75	T	0.24440	-1.0160	10	0.49607	T	0.09	1.0E-4	15.5482	0.76126	0.0:1.0:0.0:0.0	.	463;463	B7ZLL4;Q5XG87	.;PAPD7_HUMAN	H	463	ENSP00000230859:P463H	ENSP00000230859:P463H	P	+	2	0	PAPD7	6806104	0.855000	0.29742	0.111000	0.21465	0.405000	0.30901	2.935000	0.48963	2.438000	0.82558	0.655000	0.94253	CCC	.	.		0.562	PAPD7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206904.1	NM_006999	
CARD6	84674	hgsc.bcm.edu	37	5	40852639	40852639	+	Missense_Mutation	SNP	A	A	C			TCGA-5R-AAAM-01A-12D-A40R-10	TCGA-5R-AAAM-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9aba9aa4-9f40-456e-8aa4-fb9d20c57d93	bbe62607-8229-46d6-997d-47d1a49b89b0	g.chr5:40852639A>C	ENST00000254691.5	+	3	1404	c.1205A>C	c.(1204-1206)cAg>cCg	p.Q402P	CARD6_ENST00000381677.3_Intron	NM_032587.3	NP_115976.2	Q9BX69	CARD6_HUMAN	caspase recruitment domain family, member 6	402					apoptotic process (GO:0006915)|regulation of apoptotic process (GO:0042981)					NS(1)|breast(2)|central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(10)|liver(2)|lung(29)|ovary(2)|pancreas(1)|prostate(2)|skin(3)|urinary_tract(1)	62						TATCAGTGCCAGTTTGCTCTT	0.453																																					p.Q402P		Atlas-SNP	.											.	CARD6	141	.	0			c.A1205C						.						73.0	70.0	71.0					5																	40852639		2203	4300	6503	SO:0001583	missense	84674	exon3			AGTGCCAGTTTGC	AF356193	CCDS3935.1	5p13.1	2008-05-23			ENSG00000132357	ENSG00000132357			16394	protein-coding gene	gene with protein product		609986				12775719	Standard	NM_032587		Approved	CINCIN1	uc003jmg.3	Q9BX69	OTTHUMG00000094775	ENST00000254691.5:c.1205A>C	chr5.hg19:g.40852639A>C	ENSP00000254691:p.Gln402Pro	98.0	0.0		98.0	30.0	NM_032587	Q52LR2	Missense_Mutation	SNP	ENST00000254691.5	hg19	CCDS3935.1	.	.	.	.	.	.	.	.	.	.	A	15.56	2.869137	0.51588	.	.	ENSG00000132357	ENST00000254691;ENST00000509771	T	0.58210	0.35	5.49	-1.45	0.08828	.	1.203030	0.05872	N	0.624793	T	0.49355	0.1552	M	0.72894	2.215	0.80722	D	1	B	0.25048	0.117	B	0.20184	0.028	T	0.44802	-0.9304	10	0.87932	D	0	0.3299	5.9549	0.19267	0.5768:0.129:0.2941:0.0	.	402	Q9BX69	CARD6_HUMAN	P	402	ENSP00000254691:Q402P	ENSP00000254691:Q402P	Q	+	2	0	CARD6	40888396	1.000000	0.71417	0.860000	0.33809	0.997000	0.91878	1.242000	0.32755	-0.356000	0.08187	0.533000	0.62120	CAG	.	.		0.453	CARD6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000211584.3		
C5orf51	285636	hgsc.bcm.edu	37	5	41912232	41912232	+	Nonsense_Mutation	SNP	T	T	G			TCGA-5R-AAAM-01A-12D-A40R-10	TCGA-5R-AAAM-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9aba9aa4-9f40-456e-8aa4-fb9d20c57d93	bbe62607-8229-46d6-997d-47d1a49b89b0	g.chr5:41912232T>G	ENST00000381647.2	+	5	567	c.548T>G	c.(547-549)tTa>tGa	p.L183*		NM_175921.4	NP_787117.3	A6NDU8	CE051_HUMAN	chromosome 5 open reading frame 51	183										endometrium(1)|large_intestine(5)|lung(2)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	11						CCTATCCAGTTAAATGAAGGA	0.323																																					p.L183X		Atlas-SNP	.											.	C5orf51	28	.	0			c.T548G						.						165.0	168.0	167.0					5																	41912232		2203	4298	6501	SO:0001587	stop_gained	285636	exon5			TCCAGTTAAATGA	AL833916, AK094002	CCDS34151.1	5p13.1	2008-07-18			ENSG00000205765	ENSG00000205765			27750	protein-coding gene	gene with protein product						14702039	Standard	NM_175921		Approved	LOC285636	uc003jmo.3	A6NDU8	OTTHUMG00000162084	ENST00000381647.2:c.548T>G	chr5.hg19:g.41912232T>G	ENSP00000371061:p.Leu183*	59.0	0.0		56.0	6.0	NM_175921	A2RRM9	Nonsense_Mutation	SNP	ENST00000381647.2	hg19	CCDS34151.1	.	.	.	.	.	.	.	.	.	.	T	25.8	4.679979	0.88542	.	.	ENSG00000205765	ENST00000381647	.	.	.	5.84	5.84	0.93424	.	0.000000	0.64402	D	0.000002	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-38.0925	9.9804	0.41811	0.0:0.0755:0.0:0.9245	.	.	.	.	X	183	.	ENSP00000371061:L183X	L	+	2	0	C5orf51	41947989	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	4.641000	0.61375	2.233000	0.73108	0.454000	0.30748	TTA	.	.		0.323	C5orf51-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000367144.1	NM_175921	
PDE8B	8622	hgsc.bcm.edu	37	5	76722294	76722294	+	Missense_Mutation	SNP	T	T	A			TCGA-5R-AAAM-01A-12D-A40R-10	TCGA-5R-AAAM-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9aba9aa4-9f40-456e-8aa4-fb9d20c57d93	bbe62607-8229-46d6-997d-47d1a49b89b0	g.chr5:76722294T>A	ENST00000264917.5	+	22	2618	c.2573T>A	c.(2572-2574)aTg>aAg	p.M858K	WDR41_ENST00000512033.1_5'Flank|PDE8B_ENST00000346042.3_Missense_Mutation_p.M761K|PDE8B_ENST00000340978.3_Missense_Mutation_p.M811K|PDE8B_ENST00000342343.4_Missense_Mutation_p.M838K|PDE8B_ENST00000505283.1_Missense_Mutation_p.M323K|PDE8B_ENST00000333194.4_Missense_Mutation_p.M803K	NM_003719.3	NP_003710.1	O95263	PDE8B_HUMAN	phosphodiesterase 8B	858	Catalytic. {ECO:0000250}.				cAMP catabolic process (GO:0006198)|cyclic nucleotide metabolic process (GO:0009187)|negative regulation of insulin secretion (GO:0046676)|negative regulation of steroid hormone biosynthetic process (GO:0090032)|phosphorelay signal transduction system (GO:0000160)	cytosol (GO:0005829)	3',5'-cyclic-AMP phosphodiesterase activity (GO:0004115)|3',5'-cyclic-nucleotide phosphodiesterase activity (GO:0004114)|metal ion binding (GO:0046872)|signal transducer activity (GO:0004871)		GMDS/PDE8B(2)	NS(1)|autonomic_ganglia(2)|breast(1)|central_nervous_system(1)|endometrium(4)|large_intestine(10)|lung(15)|ovary(1)|prostate(2)|skin(3)	40		all_lung(232;0.00043)|Lung NSC(167;0.00114)|Ovarian(174;0.0107)|Prostate(461;0.0605)		OV - Ovarian serous cystadenocarcinoma(54;2.21e-49)|Epithelial(54;5.82e-43)|all cancers(79;4.06e-38)	Caffeine(DB00201)|Ketotifen(DB00920)	CCAGCCCTGATGCAACATTTG	0.468																																					p.M858K		Atlas-SNP	.											.	PDE8B	103	.	0			c.T2573A						.						87.0	77.0	80.0					5																	76722294		2203	4300	6503	SO:0001583	missense	8622	exon22			CCCTGATGCAACA	AF079529	CCDS4037.1, CCDS34190.1, CCDS34191.1, CCDS34192.1, CCDS34193.1	5q14.1	2008-05-15			ENSG00000113231	ENSG00000113231	3.1.4.17	"""Phosphodiesterases"""	8794	protein-coding gene	gene with protein product		603390				9784418	Standard	NM_003719		Approved		uc003kfa.3	O95263	OTTHUMG00000102170	ENST00000264917.5:c.2573T>A	chr5.hg19:g.76722294T>A	ENSP00000264917:p.Met858Lys	171.0	0.0		199.0	8.0	NM_003719	Q5J7V7|Q86XK8|Q8IUJ7|Q8IUJ8|Q8IUJ9|Q8IUK0|Q8N3T2	Missense_Mutation	SNP	ENST00000264917.5	hg19	CCDS4037.1	.	.	.	.	.	.	.	.	.	.	T	29.7	5.030352	0.93575	.	.	ENSG00000113231	ENST00000340978;ENST00000346042;ENST00000264917;ENST00000342343;ENST00000333194;ENST00000505283	T;T;T;T;T;T	0.76448	-1.02;-1.02;-1.02;-1.02;-1.02;-1.02	5.63	5.63	0.86233	5&apos (1);-cyclic nucleotide phosphodiesterase, catalytic domain (1);3&apos (1);	0.036230	0.85682	D	0.000000	D	0.87577	0.6212	M	0.80183	2.485	0.80722	D	1	P;D;D;D;D	0.60160	0.818;0.984;0.984;0.984;0.987	P;P;P;P;D	0.63283	0.635;0.858;0.858;0.858;0.913	D	0.89308	0.3631	10	0.87932	D	0	.	16.1413	0.81528	0.0:0.0:0.0:1.0	.	761;811;803;838;858	O95263-2;O95263-6;O95263-3;O95263-4;O95263	.;.;.;.;PDE8B_HUMAN	K	811;761;858;838;803;323	ENSP00000345446:M811K;ENSP00000330428:M761K;ENSP00000264917:M858K;ENSP00000345646:M838K;ENSP00000331336:M803K;ENSP00000423461:M323K	ENSP00000264917:M858K	M	+	2	0	PDE8B	76758050	1.000000	0.71417	1.000000	0.80357	0.991000	0.79684	7.997000	0.88414	2.270000	0.75569	0.482000	0.46254	ATG	.	.		0.468	PDE8B-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000220015.3	NM_003719	
PCDHB6	56130	hgsc.bcm.edu	37	5	140532159	140532159	+	Missense_Mutation	SNP	C	C	T			TCGA-5R-AAAM-01A-12D-A40R-10	TCGA-5R-AAAM-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9aba9aa4-9f40-456e-8aa4-fb9d20c57d93	bbe62607-8229-46d6-997d-47d1a49b89b0	g.chr5:140532159C>T	ENST00000231136.1	+	1	2321	c.2321C>T	c.(2320-2322)cCt>cTt	p.P774L	PCDHB6_ENST00000543635.1_Missense_Mutation_p.P638L	NM_018939.2	NP_061762.1	Q9Y5E3	PCDB6_HUMAN	protocadherin beta 6	774					calcium-dependent cell-cell adhesion (GO:0016339)|cell adhesion (GO:0007155)|homophilic cell adhesion (GO:0007156)|nervous system development (GO:0007399)|synapse assembly (GO:0007416)|synaptic transmission (GO:0007268)	integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)	calcium ion binding (GO:0005509)			cervix(1)|endometrium(14)|kidney(6)|large_intestine(16)|liver(1)|lung(33)|ovary(1)|pancreas(2)|prostate(1)|skin(6)|upper_aerodigestive_tract(2)|urinary_tract(1)	84			KIRC - Kidney renal clear cell carcinoma(527;0.00185)|Kidney(363;0.00339)			AACTTCCCTCCTCAGGGCACT	0.473																																					p.P774L		Atlas-SNP	.											.	PCDHB6	161	.	0			c.C2321T						.						109.0	118.0	115.0					5																	140532159		2202	4300	6502	SO:0001583	missense	56130	exon1			TCCCTCCTCAGGG	AF152499	CCDS4248.1	5q31	2010-01-26			ENSG00000113211	ENSG00000113211		"""Cadherins / Protocadherins : Clustered"""	8691	other	protocadherin		606332				10380929	Standard	NM_018939		Approved	PCDH-BETA6	uc003lir.3	Q9Y5E3	OTTHUMG00000129623	ENST00000231136.1:c.2321C>T	chr5.hg19:g.140532159C>T	ENSP00000231136:p.Pro774Leu	191.0	0.0		216.0	27.0	NM_018939	B2R8R9	Missense_Mutation	SNP	ENST00000231136.1	hg19	CCDS4248.1	.	.	.	.	.	.	.	.	.	.	C	8.963	0.971165	0.18659	.	.	ENSG00000113211	ENST00000543635;ENST00000231136	T;T	0.13307	2.6;2.6	4.51	-0.855	0.10700	.	.	.	.	.	T	0.06416	0.0165	N	0.17631	0.505	0.09310	N	1	B	0.02656	0.0	B	0.04013	0.001	T	0.41822	-0.9487	9	0.21014	T	0.42	.	1.8217	0.03112	0.1317:0.4228:0.1292:0.3163	.	774	Q9Y5E3	PCDB6_HUMAN	L	638;774	ENSP00000438466:P638L;ENSP00000231136:P774L	ENSP00000231136:P774L	P	+	2	0	PCDHB6	140512343	0.000000	0.05858	0.000000	0.03702	0.025000	0.11179	-1.023000	0.03607	-0.147000	0.11254	-0.314000	0.08810	CCT	.	.		0.473	PCDHB6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251818.2	NM_018939	
PCDHGB1	56104	hgsc.bcm.edu	37	5	140731361	140731361	+	Missense_Mutation	SNP	G	G	A			TCGA-5R-AAAM-01A-12D-A40R-10	TCGA-5R-AAAM-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9aba9aa4-9f40-456e-8aa4-fb9d20c57d93	bbe62607-8229-46d6-997d-47d1a49b89b0	g.chr5:140731361G>A	ENST00000523390.1	+	1	1534	c.1534G>A	c.(1534-1536)Gcg>Acg	p.A512T	PCDHGA2_ENST00000394576.2_Intron|PCDHGA1_ENST00000517417.1_Intron|PCDHGA3_ENST00000253812.6_Intron	NM_018922.2|NM_032095.1	NP_061745.1|NP_115266.1	Q9Y5G3	PCDGD_HUMAN	protocadherin gamma subfamily B, 1	512	Cadherin 5. {ECO:0000255|PROSITE- ProRule:PRU00043}.				homophilic cell adhesion (GO:0007156)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			central_nervous_system(2)|endometrium(1)|kidney(1)|large_intestine(6)|lung(3)|ovary(2)|prostate(1)	16			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			GGTGGTGTTCGCGCAGCGCGC	0.682																																					p.A512T		Atlas-SNP	.											PCDHGB1_ENST00000523390,NS,carcinoma,0,2	PCDHGB1	198	.	0			c.G1534A						.						38.0	44.0	42.0					5																	140731361		2012	4186	6198	SO:0001583	missense	56104	exon1			GTGTTCGCGCAGC	AF152517	CCDS54923.1, CCDS75330.1	5q31	2010-01-26				ENSG00000254221		"""Cadherins / Protocadherins : Clustered"""	8708	other	protocadherin	"""protocadherin gamma subfamily B, 1, isoform 2"""	606299				10380929	Standard	NM_018922		Approved	PCDH-GAMMA-B1		Q9Y5G3		ENST00000523390.1:c.1534G>A	chr5.hg19:g.140731361G>A	ENSP00000429273:p.Ala512Thr	100.0	0.0		68.0	5.0	NM_018922	Q3SY75|Q9Y5C8	Missense_Mutation	SNP	ENST00000523390.1	hg19	CCDS54923.1	.	.	.	.	.	.	.	.	.	.	.	21.7	4.181064	0.78677	.	.	ENSG00000254221	ENST00000523390	T	0.42513	0.97	5.49	5.49	0.81192	Cadherin (5);Cadherin-like (1);	.	.	.	.	T	0.54240	0.1846	L	0.31926	0.97	0.33144	D	0.544792	D;D	0.89917	1.0;0.996	D;D	0.76575	0.988;0.917	T	0.63545	-0.6613	9	0.87932	D	0	.	15.0291	0.71694	0.0:0.0:0.8571:0.1429	.	512;512	Q9Y5G3-2;Q9Y5G3	.;PCDGD_HUMAN	T	512	ENSP00000429273:A512T	ENSP00000429273:A512T	A	+	1	0	PCDHGB1	140711545	0.050000	0.20438	1.000000	0.80357	0.985000	0.73830	1.472000	0.35376	2.740000	0.93945	0.563000	0.77884	GCG	.	.		0.682	PCDHGB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000374740.1	NM_018922	
CYFIP2	26999	hgsc.bcm.edu	37	5	156819926	156819926	+	Missense_Mutation	SNP	C	C	A			TCGA-5R-AAAM-01A-12D-A40R-10	TCGA-5R-AAAM-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9aba9aa4-9f40-456e-8aa4-fb9d20c57d93	bbe62607-8229-46d6-997d-47d1a49b89b0	g.chr5:156819926C>A	ENST00000521420.1	+	30	3693	c.3602C>A	c.(3601-3603)tCc>tAc	p.S1201Y	CYFIP2_ENST00000377576.3_Missense_Mutation_p.S1227Y|CYFIP2_ENST00000318218.6_Missense_Mutation_p.S1252Y|CYFIP2_ENST00000442283.2_3'UTR|CYFIP2_ENST00000347377.6_Missense_Mutation_p.S1227Y|CYFIP2_ENST00000541131.1_Missense_Mutation_p.S1152Y|CYFIP2_ENST00000522463.1_Missense_Mutation_p.S1031Y|CYFIP2_ENST00000435847.2_Missense_Mutation_p.S926Y					cytoplasmic FMR1 interacting protein 2											breast(1)|endometrium(12)|kidney(2)|lung(23)	38	Renal(175;0.00212)	Medulloblastoma(196;0.0306)|all_neural(177;0.0897)	Kidney(164;0.000171)|KIRC - Kidney renal clear cell carcinoma(164;0.000785)			TACATGAAGTCCGTGGAGACA	0.522																																					p.S1227Y		Atlas-SNP	.											.	CYFIP2	354	.	0			c.C3680A						.						90.0	97.0	95.0					5																	156819926		2151	4274	6425	SO:0001583	missense	26999	exon31			TGAAGTCCGTGGA	AF160973	CCDS75364.1	5q34	2008-07-18				ENSG00000055163			13760	protein-coding gene	gene with protein product	"""p53 inducible protein"""	606323				11438699	Standard	NM_001037333		Approved	PIR121	uc021ygm.1	Q96F07		ENST00000521420.1:c.3602C>A	chr5.hg19:g.156819926C>A	ENSP00000430904:p.Ser1201Tyr	86.0	0.0		78.0	14.0	NM_001037332		Missense_Mutation	SNP	ENST00000521420.1	hg19		.	.	.	.	.	.	.	.	.	.	C	28.4	4.917065	0.92249	.	.	ENSG00000055163	ENST00000318218;ENST00000522463;ENST00000521420;ENST00000347377;ENST00000377576;ENST00000541131;ENST00000435847	T;T;T;T;T;T;T	0.25749	2.11;2.11;2.11;2.11;2.11;2.11;1.78	5.38	5.38	0.77491	.	0.166812	0.53938	D	0.000048	T	0.39708	0.1088	L	0.27053	0.805	0.80722	D	1	P;P;P;D;P;P	0.89917	0.923;0.763;0.608;1.0;0.732;0.894	P;P;B;D;P;B	0.71184	0.655;0.563;0.157;0.972;0.459;0.202	T	0.10636	-1.0621	10	0.40728	T	0.16	-19.7475	19.5107	0.95140	0.0:1.0:0.0:0.0	.	1091;1031;1201;1227;1227;1252	A8MUM2;E7EW33;E7EVJ5;E7EVF4;Q96F07-2;Q96F07	.;.;.;.;.;CYFP2_HUMAN	Y	1252;1031;1201;1227;1227;1152;926	ENSP00000325817:S1252Y;ENSP00000428009:S1031Y;ENSP00000430904:S1201Y;ENSP00000313567:S1227Y;ENSP00000366799:S1227Y;ENSP00000444645:S1152Y;ENSP00000403793:S926Y	ENSP00000325817:S1252Y	S	+	2	0	CYFIP2	156752504	1.000000	0.71417	0.970000	0.41538	0.848000	0.48234	7.776000	0.85560	2.679000	0.91253	0.655000	0.94253	TCC	.	.		0.522	CYFIP2-001	NOVEL	basic	protein_coding	protein_coding	OTTHUMT00000373710.1	NM_001037332	
HIST1H3J	8356	hgsc.bcm.edu	37	6	27858205	27858205	+	Silent	SNP	A	A	C			TCGA-5R-AAAM-01A-12D-A40R-10	TCGA-5R-AAAM-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9aba9aa4-9f40-456e-8aa4-fb9d20c57d93	bbe62607-8229-46d6-997d-47d1a49b89b0	g.chr6:27858205A>C	ENST00000359303.2	-	1	365	c.366T>G	c.(364-366)ccT>ccG	p.P122P	HIST1H2BO_ENST00000303806.4_5'Flank|HIST1H3J_ENST00000479986.1_5'Flank	NM_003535.2	NP_003526.1	P68431	H31_HUMAN	histone cluster 1, H3j	122				P -> L (in Ref. 13; AAH66884). {ECO:0000305}.	blood coagulation (GO:0007596)|chromatin organization (GO:0006325)|DNA replication-dependent nucleosome assembly (GO:0006335)|regulation of gene silencing (GO:0060968)	extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|nuclear chromosome (GO:0000228)|nucleoplasm (GO:0005654)|nucleosome (GO:0000786)|nucleus (GO:0005634)|protein complex (GO:0043234)	DNA binding (GO:0003677)			central_nervous_system(1)|endometrium(1)|kidney(1)|lung(3)|ovary(1)|prostate(1)	8						GGATGTCCTTAGGCATAATAG	0.527																																					p.P122P		Atlas-SNP	.											.	HIST1H3J	16	.	0			c.T366G						.						65.0	65.0	65.0					6																	27858205		2203	4300	6503	SO:0001819	synonymous_variant	8356	exon1			GTCCTTAGGCATA	Z83737	CCDS4638.1	6p22.1	2011-01-27	2006-10-11	2003-02-14	ENSG00000197153	ENSG00000197153		"""Histones / Replication-dependent"""	4774	protein-coding gene	gene with protein product		602817	"""H3 histone family, member J"", ""histone 1, H3j"""	H3FJ		9439656, 12408966	Standard	NM_003535		Approved	H3/j	uc003nka.3	P68431	OTTHUMG00000016185	ENST00000359303.2:c.366T>G	chr6.hg19:g.27858205A>C		108.0	0.0		109.0	38.0	NM_003535	A0PJT7|A5PLR1|P02295|P02296|P16106|Q6ISV8|Q6NWP8|Q6NWP9|Q6NXU4|Q71DJ3|Q93081	Silent	SNP	ENST00000359303.2	hg19	CCDS4638.1																																																																																			.	.		0.527	HIST1H3J-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000043453.2	NM_003535	
PKHD1	5314	hgsc.bcm.edu	37	6	51491853	51491853	+	Missense_Mutation	SNP	G	G	C			TCGA-5R-AAAM-01A-12D-A40R-10	TCGA-5R-AAAM-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9aba9aa4-9f40-456e-8aa4-fb9d20c57d93	bbe62607-8229-46d6-997d-47d1a49b89b0	g.chr6:51491853G>C	ENST00000371117.3	-	66	12002	c.11727C>G	c.(11725-11727)atC>atG	p.I3909M		NM_138694.3	NP_619639.3	P08F94	PKHD1_HUMAN	polycystic kidney and hepatic disease 1 (autosomal recessive)	3909					cellular calcium ion homeostasis (GO:0006874)|cilium assembly (GO:0042384)|homeostatic process (GO:0042592)|kidney development (GO:0001822)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cellular component movement (GO:0051271)|negative regulation of NF-kappaB transcription factor activity (GO:0032088)|negative regulation of protein kinase B signaling (GO:0051898)|positive regulation of cell proliferation (GO:0008284)|regulation of centrosome duplication (GO:0010824)|regulation of ERK1 and ERK2 cascade (GO:0070372)|regulation of TOR signaling (GO:0032006)|single organismal cell-cell adhesion (GO:0016337)	anchored component of external side of plasma membrane (GO:0031362)|apical plasma membrane (GO:0016324)|centrosome (GO:0005813)|ciliary basal body (GO:0036064)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|mitotic spindle (GO:0072686)|perinuclear region of cytoplasm (GO:0048471)|primary cilium (GO:0072372)	receptor activity (GO:0004872)			NS(1)|autonomic_ganglia(1)|breast(8)|central_nervous_system(5)|cervix(1)|endometrium(16)|haematopoietic_and_lymphoid_tissue(4)|kidney(11)|large_intestine(59)|lung(139)|ovary(16)|prostate(8)|skin(20)|soft_tissue(1)|stomach(2)|upper_aerodigestive_tract(7)|urinary_tract(5)	304	Lung NSC(77;0.0605)					GTTTGGATGAGATGTGGATAT	0.418																																					p.I3909M		Atlas-SNP	.											.	PKHD1	927	.	0			c.C11727G						.						291.0	281.0	284.0					6																	51491853		2203	4300	6503	SO:0001583	missense	5314	exon66			GGATGAGATGTGG	AF480064	CCDS4935.1, CCDS4936.1	6p21.2-p12	2012-11-26	2003-04-16		ENSG00000170927	ENSG00000170927			9016	protein-coding gene	gene with protein product	"""tigmin"", ""polyductin"", ""fibrocystin"""	606702	"""TIG multiple domains 1"""	TIGM1		9503014	Standard	NM_138694		Approved	ARPKD, FCYT	uc003pah.1	P08F94	OTTHUMG00000014841	ENST00000371117.3:c.11727C>G	chr6.hg19:g.51491853G>C	ENSP00000360158:p.Ile3909Met	130.0	0.0		89.0	34.0	NM_138694	Q5VUA2|Q5VUA3|Q5VWV1|Q86Z26|Q8TCZ9	Missense_Mutation	SNP	ENST00000371117.3	hg19	CCDS4935.1	.	.	.	.	.	.	.	.	.	.	G	8.108	0.778177	0.16120	.	.	ENSG00000170927	ENST00000371117	D	0.86030	-2.06	4.44	1.6	0.23607	.	2.030180	0.02516	N	0.092055	T	0.49966	0.1588	N	0.03608	-0.345	0.09310	N	1	B	0.06786	0.001	B	0.06405	0.002	T	0.47724	-0.9095	10	0.46703	T	0.11	.	7.0109	0.24861	0.0951:0.3583:0.5466:0.0	.	3909	P08F94	PKHD1_HUMAN	M	3909	ENSP00000360158:I3909M	ENSP00000360158:I3909M	I	-	3	3	PKHD1	51599812	0.003000	0.15002	0.016000	0.15963	0.023000	0.10783	0.017000	0.13399	0.347000	0.23924	0.655000	0.94253	ATC	.	.		0.418	PKHD1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000040893.1	NM_138694	
EPHA7	2045	hgsc.bcm.edu	37	6	93967865	93967865	+	Nonsense_Mutation	SNP	G	G	A			TCGA-5R-AAAM-01A-12D-A40R-10	TCGA-5R-AAAM-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9aba9aa4-9f40-456e-8aa4-fb9d20c57d93	bbe62607-8229-46d6-997d-47d1a49b89b0	g.chr6:93967865G>A	ENST00000369303.4	-	11	2246	c.2062C>T	c.(2062-2064)Cag>Tag	p.Q688*		NM_004440.3	NP_004431.1	Q15375	EPHA7_HUMAN	EPH receptor A7	688	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				brain development (GO:0007420)|branching morphogenesis of a nerve (GO:0048755)|ephrin receptor signaling pathway (GO:0048013)|negative chemotaxis (GO:0050919)|peptidyl-tyrosine phosphorylation (GO:0018108)|phosphorylation (GO:0016310)|positive regulation of neuron apoptotic process (GO:0043525)|regulation of cell-cell adhesion (GO:0022407)|regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043281)|regulation of ERK1 and ERK2 cascade (GO:0070372)|regulation of peptidyl-tyrosine phosphorylation (GO:0050730)|regulation of protein autophosphorylation (GO:0031952)|retinal ganglion cell axon guidance (GO:0031290)	dendrite (GO:0030425)|integral component of plasma membrane (GO:0005887)|neuromuscular junction (GO:0031594)|neuronal cell body (GO:0043025)|postsynaptic membrane (GO:0045211)	ATP binding (GO:0005524)|axon guidance receptor activity (GO:0008046)|chemorepellent activity (GO:0045499)|GPI-linked ephrin receptor activity (GO:0005004)|protein tyrosine kinase activity (GO:0004713)			NS(1)|breast(1)|central_nervous_system(7)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(16)|lung(43)|ovary(8)|pancreas(1)|prostate(1)|skin(8)|stomach(1)|upper_aerodigestive_tract(13)|urinary_tract(1)	112		all_cancers(76;7.47e-10)|Acute lymphoblastic leukemia(125;1.88e-09)|all_hematologic(75;1.75e-07)|all_epithelial(107;3.6e-05)|Lung NSC(302;0.0368)|all_lung(197;0.0509)|Colorectal(196;0.142)		BRCA - Breast invasive adenocarcinoma(108;0.0847)		TGGTCAAACTGCCCCATGATG	0.388																																					p.Q688X		Atlas-SNP	.											.	EPHA7	251	.	0			c.C2062T						.						126.0	125.0	125.0					6																	93967865		2203	4300	6503	SO:0001587	stop_gained	2045	exon11			CAAACTGCCCCAT	L36642	CCDS5031.1, CCDS75494.1	6q16.3	2013-02-11	2004-10-28		ENSG00000135333	ENSG00000135333		"""EPH receptors"", ""Sterile alpha motif (SAM) domain containing"", ""Fibronectin type III domain containing"""	3390	protein-coding gene	gene with protein product		602190	"""EphA7"""			9267020	Standard	NM_004440		Approved	Hek11	uc003poe.3	Q15375	OTTHUMG00000015228	ENST00000369303.4:c.2062C>T	chr6.hg19:g.93967865G>A	ENSP00000358309:p.Gln688*	64.0	0.0		46.0	17.0	NM_004440	A0AUX7|B2R8W1|B7ZLJ9|B7ZLK0|Q59G40|Q5VTU0|Q8N368|Q9H124	Nonsense_Mutation	SNP	ENST00000369303.4	hg19	CCDS5031.1	.	.	.	.	.	.	.	.	.	.	G	41	8.647399	0.98899	.	.	ENSG00000135333	ENST00000369303	.	.	.	6.08	6.08	0.98989	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.87932	D	0	.	20.6721	0.99693	0.0:0.0:1.0:0.0	.	.	.	.	X	688	.	ENSP00000358309:Q688X	Q	-	1	0	EPHA7	94024586	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	9.869000	0.99810	2.894000	0.99253	0.591000	0.81541	CAG	.	.		0.388	EPHA7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041545.1		
TRDN	10345	hgsc.bcm.edu	37	6	123658784	123658784	+	Missense_Mutation	SNP	G	G	A			TCGA-5R-AAAM-01A-12D-A40R-10	TCGA-5R-AAAM-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9aba9aa4-9f40-456e-8aa4-fb9d20c57d93	bbe62607-8229-46d6-997d-47d1a49b89b0	g.chr6:123658784G>A	ENST00000398178.3	-	22	1421	c.1400C>T	c.(1399-1401)tCt>tTt	p.S467F	TRDN_ENST00000334268.4_Missense_Mutation_p.S467F	NM_006073.3	NP_006064.2	Q13061	TRDN_HUMAN	triadin	467					cellular calcium ion homeostasis (GO:0006874)|cytoplasmic microtubule organization (GO:0031122)|endoplasmic reticulum membrane organization (GO:0090158)|heart contraction (GO:0060047)|ion transmembrane transport (GO:0034220)|muscle contraction (GO:0006936)|myotube differentiation (GO:0014902)|negative regulation of ryanodine-sensitive calcium-release channel activity (GO:0060315)|positive regulation of cell communication by electrical coupling involved in cardiac conduction (GO:1901846)|positive regulation of ryanodine-sensitive calcium-release channel activity (GO:0060316)|regulation of cardiac muscle cell membrane potential (GO:0086036)|regulation of cell communication by electrical coupling (GO:0010649)|regulation of release of sequestered calcium ion into cytosol (GO:0051279)|regulation of release of sequestered calcium ion into cytosol by sarcoplasmic reticulum (GO:0010880)|release of sequestered calcium ion into cytosol by sarcoplasmic reticulum (GO:0014808)|response to organic cyclic compound (GO:0014070)|transmembrane transport (GO:0055085)	calcium channel complex (GO:0034704)|cytoplasm (GO:0005737)|endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|junctional membrane complex (GO:0030314)|junctional sarcoplasmic reticulum membrane (GO:0014701)|plasma membrane (GO:0005886)|sarcoplasmic reticulum (GO:0016529)|sarcoplasmic reticulum lumen (GO:0033018)|sarcoplasmic reticulum membrane (GO:0033017)	ion channel binding (GO:0044325)|protein binding, bridging (GO:0030674)|protein homodimerization activity (GO:0042803)			NS(1)|endometrium(1)|kidney(1)|large_intestine(8)|liver(1)|lung(22)|ovary(2)|skin(1)|stomach(2)|upper_aerodigestive_tract(2)	41				GBM - Glioblastoma multiforme(226;0.184)		CAGAATTGAAGAAGTCTTCCC	0.289																																					p.S467F		Atlas-SNP	.											.	TRDN	88	.	0			c.C1400T						.						24.0	22.0	23.0					6																	123658784		1163	2539	3702	SO:0001583	missense	10345	exon22			ATTGAAGAAGTCT	U18985	CCDS59035.1, CCDS75511.1	6q22.31	2008-05-15			ENSG00000186439	ENSG00000186439			12261	protein-coding gene	gene with protein product		603283				7588753	Standard	NM_001251987		Approved		uc003pzj.2	Q13061	OTTHUMG00000015497	ENST00000398178.3:c.1400C>T	chr6.hg19:g.123658784G>A	ENSP00000381240:p.Ser467Phe	205.0	0.0		178.0	30.0	NM_006073	A5D6W5|F5H2W7|Q6NSB8	Missense_Mutation	SNP	ENST00000398178.3	hg19	CCDS55053.1	.	.	.	.	.	.	.	.	.	.	G	12.06	1.824110	0.32237	.	.	ENSG00000186439	ENST00000398178;ENST00000398161;ENST00000334268	T;T	0.20069	2.1;2.11	4.68	4.68	0.58851	.	0.000000	0.41605	D	0.000860	T	0.20536	0.0494	N	0.24115	0.695	0.80722	D	1	D	0.69078	0.997	D	0.66196	0.942	T	0.01762	-1.1279	10	0.62326	D	0.03	-6.0861	13.2958	0.60296	0.0:0.0:1.0:0.0	.	467	Q13061	TRDN_HUMAN	F	467;469;467	ENSP00000381240:S467F;ENSP00000333984:S467F	ENSP00000333984:S467F	S	-	2	0	TRDN	123700483	1.000000	0.71417	0.980000	0.43619	0.037000	0.13140	4.759000	0.62227	2.608000	0.88229	0.650000	0.86243	TCT	.	.		0.289	TRDN-201	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding			
VWDE	221806	hgsc.bcm.edu	37	7	12409710	12409710	+	Missense_Mutation	SNP	T	T	C			TCGA-5R-AAAM-01A-12D-A40R-10	TCGA-5R-AAAM-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9aba9aa4-9f40-456e-8aa4-fb9d20c57d93	bbe62607-8229-46d6-997d-47d1a49b89b0	g.chr7:12409710T>C	ENST00000275358.3	-	12	2410	c.2222A>G	c.(2221-2223)gAa>gGa	p.E741G		NM_001135924.1	NP_001129396.1	Q8N2E2	VWDE_HUMAN	von Willebrand factor D and EGF domains	741						extracellular region (GO:0005576)				breast(4)|endometrium(2)|kidney(1)|skin(1)	8						GTACCTCATTTCTTGGCTGTG	0.418																																					p.E741G		Atlas-SNP	.											.	VWDE	123	.	0			c.A2222G						.						203.0	168.0	179.0					7																	12409710		692	1591	2283	SO:0001583	missense	221806	exon12			CTCATTTCTTGGC		CCDS47544.1	7p21.3	2008-09-23			ENSG00000146530	ENSG00000146530			21897	protein-coding gene	gene with protein product						14702039, 16303743	Standard	NM_001135924		Approved	FLJ14712	uc003ssj.2	Q8N2E2	OTTHUMG00000152315	ENST00000275358.3:c.2222A>G	chr7.hg19:g.12409710T>C	ENSP00000275358:p.Glu741Gly	109.0	0.0		110.0	29.0	NM_001135924	B7ZM77|Q96SQ3	Missense_Mutation	SNP	ENST00000275358.3	hg19	CCDS47544.1	.	.	.	.	.	.	.	.	.	.	T	3.996	-0.003550	0.07773	.	.	ENSG00000146530	ENST00000275358;ENST00000536307	D	0.83250	-1.7	4.75	4.75	0.60458	.	.	.	.	.	T	0.75474	0.3854	L	0.36672	1.1	0.09310	N	1	B	0.06786	0.001	B	0.08055	0.003	T	0.64483	-0.6397	9	0.42905	T	0.14	.	10.511	0.44862	0.0:0.079:0.0:0.921	.	741	Q8N2E2	VWDE_HUMAN	G	741;195	ENSP00000275358:E741G	ENSP00000275358:E741G	E	-	2	0	VWDE	12376235	0.014000	0.17966	0.003000	0.11579	0.003000	0.03518	1.710000	0.37920	2.003000	0.58678	0.533000	0.62120	GAA	.	.		0.418	VWDE-001	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000325870.3	XM_371878	
SUGCT	79783	hgsc.bcm.edu	37	7	40174633	40174633	+	Missense_Mutation	SNP	T	T	A			TCGA-5R-AAAM-01A-12D-A40R-10	TCGA-5R-AAAM-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9aba9aa4-9f40-456e-8aa4-fb9d20c57d93	bbe62607-8229-46d6-997d-47d1a49b89b0	g.chr7:40174633T>A	ENST00000335693.4	+	1	58	c.35T>A	c.(34-36)cTg>cAg	p.L12Q	MPLKIP_ENST00000306984.6_5'Flank|C7orf10_ENST00000540834.1_Missense_Mutation_p.L5Q|C7orf10_ENST00000309930.5_Missense_Mutation_p.L12Q|C7orf10_ENST00000401647.2_Missense_Mutation_p.L12Q	NM_001193313.1	NP_001180242.1	Q9HAC7	SUCHY_HUMAN		12					metabolic process (GO:0008152)	mitochondrion (GO:0005739)	succinate-hydroxymethylglutarate CoA-transferase activity (GO:0047369)			endometrium(3)|kidney(1)|large_intestine(2)|lung(10)|ovary(2)	18						CTGGCGACGCTGGCGAGGGTG	0.736																																					p.L12Q		Atlas-SNP	.											.	C7orf10	99	.	0			c.T35A						.						6.0	9.0	8.0					7																	40174633		1955	4073	6028	SO:0001583	missense	79783	exon1			CGACGCTGGCGAG																												ENST00000335693.4:c.35T>A	chr7.hg19:g.40174633T>A	ENSP00000338475:p.Leu12Gln	176.0	0.0		165.0	25.0	NM_001193313	A4D1W5|B4DR73|Q4KMW4|Q4KMW8|Q4KMZ0|Q8TE00|Q8TEY1	Missense_Mutation	SNP	ENST00000335693.4	hg19	CCDS55105.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	8.765|8.765	0.924496|0.924496	0.18056|0.18056	.|.	.|.	ENSG00000175600|ENSG00000175600	ENST00000309930;ENST00000401647;ENST00000335693;ENST00000540834|ENST00000413931;ENST00000416370	T;T;T;T|.	0.73575|.	0.87;0.84;0.87;-0.76|.	3.38|3.38	2.2|2.2	0.27929|0.27929	.|.	2.083540|.	0.03763|.	U|.	0.258475|.	T|T	0.16342|0.16342	0.0393|0.0393	N|N	0.08118|0.08118	0|0	0.09310|0.09310	N|N	1|1	P;P;P|.	0.48503|.	0.61;0.61;0.911|.	B;B;P|.	0.49421|.	0.193;0.193;0.61|.	T|T	0.24799|0.24799	-1.0150|-1.0150	10|5	0.62326|.	D|.	0.03|.	0.0534|0.0534	5.4743|5.4743	0.16688|0.16688	0.0:0.1337:0.0:0.8663|0.0:0.1337:0.0:0.8663	.|.	12;12;12|.	Q4KMW8;Q9HAC7;Q9HAC7-2|.	.;CG010_HUMAN;.|.	Q|R	12;12;12;5|7	ENSP00000312054:L12Q;ENSP00000385222:L12Q;ENSP00000338475:L12Q;ENSP00000445521:L5Q|.	ENSP00000312054:L12Q|.	L|W	+|+	2|1	0|0	C7orf10|C7orf10	40141158|40141158	0.003000|0.003000	0.15002|0.15002	0.015000|0.015000	0.15790|0.15790	0.025000|0.025000	0.11179|0.11179	-0.364000|-0.364000	0.07583|0.07583	0.487000|0.487000	0.27698|0.27698	0.450000|0.450000	0.29827|0.29827	CTG|TGG	.	.		0.736	C7orf10-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000338388.1		
C7orf25	79020	hgsc.bcm.edu	37	7	42949520	42949520	+	Missense_Mutation	SNP	G	G	A			TCGA-5R-AAAM-01A-12D-A40R-10	TCGA-5R-AAAM-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9aba9aa4-9f40-456e-8aa4-fb9d20c57d93	bbe62607-8229-46d6-997d-47d1a49b89b0	g.chr7:42949520G>A	ENST00000350427.4	-	2	1255	c.980C>T	c.(979-981)gCc>gTc	p.A327V	C7orf25_ENST00000447342.1_Missense_Mutation_p.A327V|PSMA2_ENST00000442788.1_3'UTR|C7orf25_ENST00000438029.1_Missense_Mutation_p.A327V|C7orf25_ENST00000431882.2_Missense_Mutation_p.A385V			Q9BPX7	CG025_HUMAN	chromosome 7 open reading frame 25	327										endometrium(6)|kidney(1)|large_intestine(7)|lung(2)|skin(1)	17						TAACACAGTGGCCCTCTCTCT	0.448																																					p.A385V		Atlas-SNP	.											.	C7orf25	36	.	0			c.C1154T						.						89.0	84.0	86.0					7																	42949520		2203	4300	6503	SO:0001583	missense	79020	exon2			ACAGTGGCCCTCT	BC001845	CCDS5466.1, CCDS47576.1	7p14.1	2011-11-24			ENSG00000136197	ENSG00000136197			21703	protein-coding gene	gene with protein product							Standard	NM_024054		Approved	MGC2821	uc003thx.4	Q9BPX7	OTTHUMG00000128869	ENST00000350427.4:c.980C>T	chr7.hg19:g.42949520G>A	ENSP00000343364:p.Ala327Val	190.0	0.0		173.0	15.0	NM_001099858	A4D1V2|J3KR36|Q9H779	Missense_Mutation	SNP	ENST00000350427.4	hg19	CCDS5466.1	.	.	.	.	.	.	.	.	.	.	G	23.0	4.363477	0.82353	.	.	ENSG00000136197	ENST00000350427;ENST00000447342;ENST00000431882;ENST00000438029	T;T;T;T	0.52526	0.66;0.66;0.66;0.66	5.79	5.79	0.91817	.	0.000000	0.85682	D	0.000000	T	0.71117	0.3302	M	0.76727	2.345	0.80722	D	1	D;D	0.89917	1.0;0.996	D;D	0.91635	0.999;0.934	T	0.71649	-0.4529	10	0.59425	D	0.04	-5.28	20.0212	0.97504	0.0:0.0:1.0:0.0	.	385;327	B4DQM3;Q9BPX7	.;CG025_HUMAN	V	327;327;385;327	ENSP00000343364:A327V;ENSP00000413029:A327V;ENSP00000416290:A385V;ENSP00000396597:A327V	ENSP00000343364:A327V	A	-	2	0	C7orf25	42916045	1.000000	0.71417	0.967000	0.41034	0.902000	0.53008	9.434000	0.97515	2.735000	0.93741	0.561000	0.74099	GCC	.	.		0.448	C7orf25-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250814.2	NM_024054	
GIMAP1	170575	hgsc.bcm.edu	37	7	150417974	150417974	+	Missense_Mutation	SNP	G	G	T			TCGA-5R-AAAM-01A-12D-A40R-10	TCGA-5R-AAAM-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9aba9aa4-9f40-456e-8aa4-fb9d20c57d93	bbe62607-8229-46d6-997d-47d1a49b89b0	g.chr7:150417974G>T	ENST00000307194.5	+	3	1022	c.882G>T	c.(880-882)agG>agT	p.R294S		NM_130759.3	NP_570115.1	Q8WWP7	GIMA1_HUMAN	GTPase, IMAP family member 1	294					B cell differentiation (GO:0030183)|T cell differentiation (GO:0030217)	endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)	GTP binding (GO:0005525)			NS(1)|breast(1)|central_nervous_system(1)|endometrium(4)|large_intestine(3)|lung(14)|ovary(1)|skin(1)|upper_aerodigestive_tract(2)	28			OV - Ovarian serous cystadenocarcinoma(82;0.0145)	UCEC - Uterine corpus endometrioid carcinoma (81;0.168)		TGCTCCACAGGCGGTGGTCGG	0.652																																					p.R294S		Atlas-SNP	.											.	GIMAP1	61	.	0			c.G882T						.						13.0	13.0	13.0					7																	150417974		1894	3819	5713	SO:0001583	missense	170575	exon3			CCACAGGCGGTGG	AJ306287	CCDS5906.1	7q36.1	2014-04-04			ENSG00000213203	ENSG00000213203		"""GTPases, IMAP"""	23237	protein-coding gene	gene with protein product	"""immune-associated nucleotide-binding protein 2"""	608084				15474311, 18701445	Standard	NM_130759		Approved	HIMAP1, IMAP38, IMAP1, IAN2		Q8WWP7	OTTHUMG00000157489	ENST00000307194.5:c.882G>T	chr7.hg19:g.150417974G>T	ENSP00000302833:p.Arg294Ser	85.0	0.0		85.0	28.0	NM_130759	B2RCI3|Q8NAZ0	Missense_Mutation	SNP	ENST00000307194.5	hg19	CCDS5906.1	.	.	.	.	.	.	.	.	.	.	G	10.11	1.259425	0.23051	.	.	ENSG00000213203	ENST00000307194	T	0.06449	3.3	2.87	-3.77	0.04346	.	35.744600	0.01164	U	0.006710	T	0.04182	0.0116	L	0.29908	0.895	0.09310	N	1	P	0.43750	0.816	B	0.36719	0.231	T	0.23940	-1.0174	10	0.41790	T	0.15	.	1.2107	0.01904	0.454:0.1691:0.2222:0.1547	.	294	Q8WWP7	GIMA1_HUMAN	S	294	ENSP00000302833:R294S	ENSP00000302833:R294S	R	+	3	2	GIMAP1	150048907	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-0.856000	0.04290	-1.085000	0.03088	-0.142000	0.14014	AGG	.	.		0.652	GIMAP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000348951.2	NM_130759	
MYBL1	4603	hgsc.bcm.edu	37	8	67478976	67478976	+	Silent	SNP	A	A	G			TCGA-5R-AAAM-01A-12D-A40R-10	TCGA-5R-AAAM-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9aba9aa4-9f40-456e-8aa4-fb9d20c57d93	bbe62607-8229-46d6-997d-47d1a49b89b0	g.chr8:67478976A>G	ENST00000522677.3	-	14	2303	c.1893T>C	c.(1891-1893)aaT>aaC	p.N631N	MYBL1_ENST00000522419.1_5'UTR|MYBL1_ENST00000517885.1_Silent_p.N289N|MYBL1_ENST00000524176.2_Silent_p.N631N	NM_001080416.2|NM_001144755.1	NP_001073885.1|NP_001138227.1	P10243	MYBA_HUMAN	v-myb avian myeloblastosis viral oncogene homolog-like 1	631					positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)	nucleus (GO:0005634)	chromatin binding (GO:0003682)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)			breast(1)|endometrium(1)|kidney(3)|large_intestine(7)|lung(9)|ovary(2)|pancreas(1)|skin(1)	25			Epithelial(68;0.00211)|all cancers(69;0.00726)|OV - Ovarian serous cystadenocarcinoma(28;0.00989)|BRCA - Breast invasive adenocarcinoma(89;0.0938)			CTTTTTCCCAATTATCTAAGA	0.338																																					p.N631N		Atlas-SNP	.											.	MYBL1	73	.	0			c.T1893C						.						109.0	104.0	105.0					8																	67478976		1812	4077	5889	SO:0001819	synonymous_variant	4603	exon14			TTCCCAATTATCT	X13294	CCDS47867.1, CCDS55241.1	8q22	2013-07-09	2013-07-09		ENSG00000185697	ENSG00000185697			7547	protein-coding gene	gene with protein product		159405					Standard	XM_005251251		Approved	AMYB, A-myb	uc003xwj.3	P10243	OTTHUMG00000164559	ENST00000522677.3:c.1893T>C	chr8.hg19:g.67478976A>G		100.0	0.0		151.0	59.0	NM_001080416	E7EW29|Q495F9	Silent	SNP	ENST00000522677.3	hg19	CCDS47867.1																																																																																			.	.		0.338	MYBL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000379221.3	XM_034274	
SLCO5A1	81796	hgsc.bcm.edu	37	8	70674091	70674091	+	Silent	SNP	T	T	A			TCGA-5R-AAAM-01A-12D-A40R-10	TCGA-5R-AAAM-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9aba9aa4-9f40-456e-8aa4-fb9d20c57d93	bbe62607-8229-46d6-997d-47d1a49b89b0	g.chr8:70674091T>A	ENST00000260126.4	-	3	1633	c.927A>T	c.(925-927)ggA>ggT	p.G309G	SLCO5A1_ENST00000528658.1_5'UTR|SLCO5A1_ENST00000524945.1_Silent_p.G309G|SLCO5A1_ENST00000530307.1_Silent_p.G309G	NM_030958.2	NP_112220.2	Q9H2Y9	SO5A1_HUMAN	solute carrier organic anion transporter family, member 5A1	309						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	transporter activity (GO:0005215)			NS(1)|breast(2)|central_nervous_system(1)|endometrium(1)|kidney(2)|large_intestine(11)|lung(24)|ovary(3)|prostate(2)|skin(2)|upper_aerodigestive_tract(3)|urinary_tract(1)	53	Breast(64;0.0654)		Epithelial(68;0.0141)|OV - Ovarian serous cystadenocarcinoma(28;0.0315)|all cancers(69;0.0594)			GGCCAAGTGCTCCCATGACAT	0.423																																					p.G309G		Atlas-SNP	.											.	SLCO5A1	142	.	0			c.A927T						.						89.0	85.0	86.0					8																	70674091		2203	4300	6503	SO:0001819	synonymous_variant	81796	exon3			AAGTGCTCCCATG	AF205075	CCDS6205.1, CCDS55242.1, CCDS55243.1	8q13.1	2013-05-22	2003-11-25	2003-11-26	ENSG00000137571	ENSG00000137571		"""Solute carriers"""	19046	protein-coding gene	gene with protein product		613543	"""solute carrier family 21 (organic anion transporter), member 15"""	SLC21A15		12507753	Standard	NM_030958		Approved	OATPRP4, OATP-J, OATP5A1	uc003xyl.3	Q9H2Y9	OTTHUMG00000165121	ENST00000260126.4:c.927A>T	chr8.hg19:g.70674091T>A		69.0	0.0		101.0	22.0	NM_030958	A4QPC2|B2RPF7|B3KMU7|E9PKK5|G3V1C0	Silent	SNP	ENST00000260126.4	hg19	CCDS6205.1																																																																																			.	.		0.423	SLCO5A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000381990.3	NM_030958	
VPS13B	157680	hgsc.bcm.edu	37	8	100287443	100287443	+	Missense_Mutation	SNP	A	A	G			TCGA-5R-AAAM-01A-12D-A40R-10	TCGA-5R-AAAM-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9aba9aa4-9f40-456e-8aa4-fb9d20c57d93	bbe62607-8229-46d6-997d-47d1a49b89b0	g.chr8:100287443A>G	ENST00000358544.2	+	19	2896	c.2785A>G	c.(2785-2787)Atc>Gtc	p.I929V	VPS13B_ENST00000395996.1_Missense_Mutation_p.I929V|VPS13B_ENST00000357162.2_Missense_Mutation_p.I929V	NM_017890.4	NP_060360.3	Q7Z7G8	VP13B_HUMAN	vacuolar protein sorting 13 homolog B (yeast)	929					protein transport (GO:0015031)					NS(1)|autonomic_ganglia(1)|breast(6)|central_nervous_system(4)|cervix(3)|endometrium(11)|haematopoietic_and_lymphoid_tissue(4)|kidney(10)|large_intestine(37)|lung(78)|ovary(8)|pancreas(3)|prostate(5)|skin(9)|upper_aerodigestive_tract(4)|urinary_tract(9)	193	Breast(36;3.73e-07)		OV - Ovarian serous cystadenocarcinoma(57;0.00636)			GGCCTTCACAATCCAAGTTCC	0.393																																					p.I929V	Colon(161;2205 2542 7338 31318)	Atlas-SNP	.											.	VPS13B	811	.	0			c.A2785G						.						148.0	150.0	149.0					8																	100287443		2203	4300	6503	SO:0001583	missense	157680	exon19			TTCACAATCCAAG	AJ608772	CCDS6280.1, CCDS6281.1, CCDS6283.1, CCDS47903.1	8q22-q23	2014-09-17	2006-12-19	2005-04-08	ENSG00000132549	ENSG00000132549			2183	protein-coding gene	gene with protein product		607817	"""Cohen syndrome 1"""	CHS1, COH1		7920642, 15498460	Standard	NM_181661		Approved		uc003yiv.4	Q7Z7G8	OTTHUMG00000140383	ENST00000358544.2:c.2785A>G	chr8.hg19:g.100287443A>G	ENSP00000351346:p.Ile929Val	96.0	0.0		122.0	11.0	NM_152564	C9JD30|Q709C6|Q709C7|Q7Z7G4|Q7Z7G5|Q7Z7G6|Q7Z7G7|Q8NB77|Q9NWV1|Q9Y4E7	Missense_Mutation	SNP	ENST00000358544.2	hg19	CCDS6280.1	.	.	.	.	.	.	.	.	.	.	A	7.506	0.653672	0.14580	.	.	ENSG00000132549	ENST00000357162;ENST00000358544;ENST00000395996	T;T;T	0.68479	-0.33;-0.33;-0.04	5.43	3.04	0.35103	.	0.255369	0.32736	N	0.005702	T	0.41026	0.1141	N	0.12182	0.205	0.33665	D	0.610241	B;B;B;B	0.02656	0.0;0.0;0.0;0.0	B;B;B;B	0.01281	0.0;0.0;0.0;0.0	T	0.39722	-0.9600	10	0.13108	T	0.6	.	7.2037	0.25895	0.5697:0.0:0.4303:0.0	.	929;929;929;929	Q7Z7G8-6;Q7Z7G8-2;Q7Z7G8;Q7Z7G8-3	.;.;VP13B_HUMAN;.	V	929	ENSP00000349685:I929V;ENSP00000351346:I929V;ENSP00000379318:I929V	ENSP00000349685:I929V	I	+	1	0	VPS13B	100356619	0.989000	0.36119	0.975000	0.42487	0.992000	0.81027	0.280000	0.18790	1.098000	0.41479	0.482000	0.46254	ATC	.	.		0.393	VPS13B-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000277138.1	NM_184042	
ROR2	4920	hgsc.bcm.edu	37	9	94493238	94493238	+	Silent	SNP	C	C	T			TCGA-5R-AAAM-01A-12D-A40R-10	TCGA-5R-AAAM-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9aba9aa4-9f40-456e-8aa4-fb9d20c57d93	bbe62607-8229-46d6-997d-47d1a49b89b0	g.chr9:94493238C>T	ENST00000375708.3	-	7	1335	c.1137G>A	c.(1135-1137)acG>acA	p.T379T	ROR2_ENST00000375715.1_Silent_p.T239T|ROR2_ENST00000550066.1_5'UTR	NM_004560.3	NP_004551.2	Q01974	ROR2_HUMAN	receptor tyrosine kinase-like orphan receptor 2	379	Kringle. {ECO:0000255|PROSITE- ProRule:PRU00121}.				cartilage condensation (GO:0001502)|cell differentiation (GO:0030154)|embryonic genitalia morphogenesis (GO:0030538)|inner ear morphogenesis (GO:0042472)|JNK cascade (GO:0007254)|multicellular organismal development (GO:0007275)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of cell proliferation (GO:0008285)|peptidyl-tyrosine phosphorylation (GO:0018108)|positive regulation of canonical Wnt signaling pathway (GO:0090263)|positive regulation of cell migration (GO:0030335)|positive regulation of transcription, DNA-templated (GO:0045893)|signal transduction (GO:0007165)|somitogenesis (GO:0001756)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)|Wnt signaling pathway, calcium modulating pathway (GO:0007223)|Wnt signaling pathway, planar cell polarity pathway (GO:0060071)	clathrin-coated endocytic vesicle membrane (GO:0030669)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|transmembrane receptor protein tyrosine kinase activity (GO:0004714)|Wnt-protein binding (GO:0017147)			autonomic_ganglia(1)|breast(1)|central_nervous_system(5)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(12)|lung(31)|ovary(3)|prostate(6)|skin(4)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	71						TTTTATTCTGCGTAAAGCACC	0.527																																					p.T379T		Atlas-SNP	.											.	ROR2	167	.	0			c.G1137A						.						86.0	78.0	81.0					9																	94493238		2203	4300	6503	SO:0001819	synonymous_variant	4920	exon7			ATTCTGCGTAAAG	M97639	CCDS6691.1	9q22	2013-01-11			ENSG00000169071	ENSG00000169071		"""Immunoglobulin superfamily / I-set domain containing"""	10257	protein-coding gene	gene with protein product		602337		NTRKR2, BDB, BDB1		1334494, 10700182	Standard	NM_004560		Approved		uc004arj.2	Q01974	OTTHUMG00000020211	ENST00000375708.3:c.1137G>A	chr9.hg19:g.94493238C>T		132.0	0.0		99.0	23.0	NM_004560	Q59GF5|Q5SPI5|Q9HAY7|Q9HB61	Silent	SNP	ENST00000375708.3	hg19	CCDS6691.1																																																																																			.	.		0.527	ROR2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053040.1		
TNC	3371	hgsc.bcm.edu	37	9	117853261	117853261	+	Missense_Mutation	SNP	G	G	T			TCGA-5R-AAAM-01A-12D-A40R-10	TCGA-5R-AAAM-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9aba9aa4-9f40-456e-8aa4-fb9d20c57d93	bbe62607-8229-46d6-997d-47d1a49b89b0	g.chr9:117853261G>T	ENST00000350763.4	-	2	448	c.37C>A	c.(37-39)Ctt>Att	p.L13I	TNC_ENST00000537320.1_Missense_Mutation_p.L13I|TNC_ENST00000341037.4_Missense_Mutation_p.L13I|TNC_ENST00000535648.1_Missense_Mutation_p.L13I|TNC_ENST00000345230.3_Missense_Mutation_p.L13I|TNC_ENST00000423613.2_Missense_Mutation_p.L13I|TNC_ENST00000346706.3_Missense_Mutation_p.L13I|TNC_ENST00000542877.1_Missense_Mutation_p.L13I|TNC_ENST00000340094.3_Missense_Mutation_p.L13I	NM_002160.3	NP_002151.2	P24821	TENA_HUMAN	tenascin C	13					bud outgrowth involved in lung branching (GO:0060447)|cell adhesion (GO:0007155)|cellular response to prostaglandin D stimulus (GO:0071799)|cellular response to retinoic acid (GO:0071300)|cellular response to vitamin D (GO:0071305)|extracellular matrix organization (GO:0030198)|mesenchymal-epithelial cell signaling involved in prostate gland development (GO:0060739)|negative regulation of cell adhesion (GO:0007162)|neuromuscular junction development (GO:0007528)|odontogenesis of dentin-containing tooth (GO:0042475)|osteoblast differentiation (GO:0001649)|peripheral nervous system axon regeneration (GO:0014012)|positive regulation of cell proliferation (GO:0008284)|positive regulation of gene expression (GO:0010628)|prostate gland epithelium morphogenesis (GO:0060740)|response to ethanol (GO:0045471)|response to fibroblast growth factor (GO:0071774)|response to mechanical stimulus (GO:0009612)|response to wounding (GO:0009611)|wound healing (GO:0042060)	basement membrane (GO:0005604)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|focal adhesion (GO:0005925)|interstitial matrix (GO:0005614)|membrane (GO:0016020)	syndecan binding (GO:0045545)			NS(3)|breast(5)|central_nervous_system(4)|endometrium(8)|kidney(6)|large_intestine(32)|liver(1)|lung(39)|ovary(1)|pancreas(2)|prostate(5)|skin(5)|stomach(5)|upper_aerodigestive_tract(2)|urinary_tract(2)	120						AGGAAAGCAAGAAAGACACCT	0.587																																					p.L13I		Atlas-SNP	.											.	TNC	282	.	0			c.C37A						.						42.0	42.0	42.0					9																	117853261		2203	4300	6503	SO:0001583	missense	3371	exon2			AAGCAAGAAAGAC		CCDS6811.1	9q33.1	2014-01-28	2008-07-31	2002-06-07	ENSG00000041982	ENSG00000041982		"""Fibrinogen C domain containing"", ""Fibronectin type III domain containing"""	5318	protein-coding gene	gene with protein product	"""hexabrachion (tenascin)"""	187380	"""hexabrachion (tenascin C, cytotactin)"", ""deafness, autosomal dominant 56"""	HXB, DFNA56		1704365, 1707164, 23936043	Standard	NM_002160		Approved	TN, MGC167029	uc004bjj.4	P24821	OTTHUMG00000021010	ENST00000350763.4:c.37C>A	chr9.hg19:g.117853261G>T	ENSP00000265131:p.Leu13Ile	33.0	0.0		49.0	10.0	NM_002160	C9IYT7|C9J575|C9J6D9|C9J848|Q14583|Q15567|Q5T7S3	Missense_Mutation	SNP	ENST00000350763.4	hg19	CCDS6811.1	.	.	.	.	.	.	.	.	.	.	G	11.44	1.640089	0.29157	.	.	ENSG00000041982	ENST00000340094;ENST00000535648;ENST00000346706;ENST00000345230;ENST00000350763;ENST00000442945;ENST00000341037;ENST00000423613;ENST00000537320;ENST00000542877;ENST00000534839	T;T;T;T;T;T;T;T;T;T	0.34667	1.35;1.35;1.35;1.35;1.35;1.35;1.35;1.35;1.35;1.35	5.58	2.17	0.27698	.	0.758451	0.12410	N	0.471341	T	0.23611	0.0571	L	0.31065	0.9	0.09310	N	1	B;B	0.27791	0.189;0.004	B;B	0.25987	0.065;0.009	T	0.18871	-1.0323	10	0.48119	T	0.1	.	5.0289	0.14400	0.0759:0.2084:0.4899:0.2258	.	13;13	E9PC84;P24821	.;TENA_HUMAN	I	13	ENSP00000344400:L13I;ENSP00000438152:L13I;ENSP00000344555:L13I;ENSP00000345861:L13I;ENSP00000265131:L13I;ENSP00000339553:L13I;ENSP00000411406:L13I;ENSP00000443478:L13I;ENSP00000442242:L13I;ENSP00000443469:L13I	ENSP00000344400:L13I	L	-	1	0	TNC	116893082	0.079000	0.21365	0.111000	0.21465	0.051000	0.14879	0.120000	0.15647	0.661000	0.30985	0.462000	0.41574	CTT	.	.		0.587	TNC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055418.2	NM_002160	
SLC2A6	11182	hgsc.bcm.edu	37	9	136340120	136340120	+	Missense_Mutation	SNP	T	T	C			TCGA-5R-AAAM-01A-12D-A40R-10	TCGA-5R-AAAM-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9aba9aa4-9f40-456e-8aa4-fb9d20c57d93	bbe62607-8229-46d6-997d-47d1a49b89b0	g.chr9:136340120T>C	ENST00000371899.4	-	6	967	c.890A>G	c.(889-891)tAc>tGc	p.Y297C	SLC2A6_ENST00000371897.4_Missense_Mutation_p.Y297C|SLC2A6_ENST00000485978.1_5'UTR	NM_017585.3	NP_060055.2	Q9UGQ3	GTR6_HUMAN	solute carrier family 2 (facilitated glucose transporter), member 6	297					glucose transport (GO:0015758)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)	glucose transmembrane transporter activity (GO:0005355)			cervix(1)|endometrium(1)|large_intestine(1)|lung(3)|prostate(3)|skin(1)	10				OV - Ovarian serous cystadenocarcinoma(145;8.47e-08)|Epithelial(140;9.37e-07)|all cancers(34;1.03e-05)		GGACTGCAGGTAGACCAGGAT	0.711																																					p.Y297C		Atlas-SNP	.											.	SLC2A6	31	.	0			c.A890G						.						28.0	21.0	23.0					9																	136340120		2188	4294	6482	SO:0001583	missense	11182	exon6			TGCAGGTAGACCA	AJ011372	CCDS6975.1, CCDS48052.1	9q34	2013-05-22			ENSG00000160326	ENSG00000160326		"""Solute carriers"""	11011	protein-coding gene	gene with protein product		606813				10970791	Standard	NM_001145099		Approved	GLUT9, GLUT6, HSA011372	uc004cee.3	Q9UGQ3	OTTHUMG00000020874	ENST00000371899.4:c.890A>G	chr9.hg19:g.136340120T>C	ENSP00000360966:p.Tyr297Cys	127.0	0.0		89.0	4.0	NM_017585	A6NNU6|Q5SXD7|Q8NCC2	Missense_Mutation	SNP	ENST00000371899.4	hg19	CCDS6975.1	.	.	.	.	.	.	.	.	.	.	T	18.96	3.734260	0.69189	.	.	ENSG00000160326	ENST00000371897;ENST00000371899	D;D	0.84070	-1.8;-1.8	5.31	4.15	0.48705	Major facilitator superfamily domain, general substrate transporter (1);Major facilitator superfamily domain (1);	0.000000	0.85682	D	0.000000	D	0.93177	0.7827	H	0.97103	3.94	0.51767	D	0.999937	D;D	0.89917	1.0;1.0	D;D	0.97110	0.999;1.0	D	0.92916	0.6351	10	0.87932	D	0	.	9.2422	0.37504	0.2877:0.0:0.0:0.7123	.	297;297	Q9UGQ3-2;Q9UGQ3	.;GTR6_HUMAN	C	297	ENSP00000360964:Y297C;ENSP00000360966:Y297C	ENSP00000360964:Y297C	Y	-	2	0	SLC2A6	135329941	1.000000	0.71417	1.000000	0.80357	0.977000	0.68977	4.495000	0.60353	0.829000	0.34733	0.459000	0.35465	TAC	.	.		0.711	SLC2A6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054909.1	NM_017585	
ARMC4	55130	hgsc.bcm.edu	37	10	28228827	28228827	+	Splice_Site	SNP	T	T	C			TCGA-5R-AAAM-01A-12D-A40R-10	TCGA-5R-AAAM-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9aba9aa4-9f40-456e-8aa4-fb9d20c57d93	bbe62607-8229-46d6-997d-47d1a49b89b0	g.chr10:28228827T>C	ENST00000305242.5	-	14	2188	c.2096A>G	c.(2095-2097)cAg>cGg	p.Q699R	ARMC4_ENST00000545014.1_Splice_Site_p.Q224R|ARMC4_ENST00000537576.1_Splice_Site_p.Q391R	NM_018076.2	NP_060546.2	Q5T2S8	ARMC4_HUMAN	armadillo repeat containing 4	699					cell projection organization (GO:0030030)|cilium movement (GO:0003341)|left/right axis specification (GO:0070986)|outer dynein arm assembly (GO:0036158)|ventricular system development (GO:0021591)	axoneme (GO:0005930)|ciliary base (GO:0097546)|cytoskeleton (GO:0005856)|nucleus (GO:0005634)				NS(2)|breast(2)|central_nervous_system(1)|cervix(1)|endometrium(7)|kidney(6)|large_intestine(17)|liver(1)|lung(17)|ovary(5)|prostate(3)|skin(8)|stomach(2)|urinary_tract(3)	75						TCACTGCACCTGGTAAATGGC	0.473																																					p.Q699R		Atlas-SNP	.											.	ARMC4	177	.	0			c.A2096G						.						87.0	75.0	79.0					10																	28228827		2203	4300	6503	SO:0001630	splice_region_variant	55130	exon14			TGCACCTGGTAAA	AL136859	CCDS7157.1	10p12.1-p11.23	2014-02-03			ENSG00000169126	ENSG00000169126		"""Armadillo repeat containing"""	25583	protein-coding gene	gene with protein product		615408				11230166	Standard	XM_005252485		Approved	FLJ10817, FLJ10376, DKFZP434P1735, CILD23	uc001itz.3	Q5T2S8	OTTHUMG00000017867	ENST00000305242.5:c.2097+1A>G	chr10.hg19:g.28228827T>C		77.0	0.0		72.0	13.0	NM_018076	A8K906|B7Z7I1|Q9H0C0	Missense_Mutation	SNP	ENST00000305242.5	hg19	CCDS7157.1	.	.	.	.	.	.	.	.	.	.	T	14.71	2.617874	0.46736	.	.	ENSG00000169126	ENST00000537576;ENST00000305242;ENST00000545014	D;D;D	0.93763	-3.28;-3.28;-3.28	5.62	5.62	0.85841	Armadillo-like helical (1);Armadillo-type fold (1);	0.100059	0.64402	D	0.000001	D	0.86619	0.5976	N	0.08118	0	0.80722	D	1	B;B	0.18310	0.004;0.027	B;B	0.25759	0.005;0.063	T	0.83007	-0.0174	10	0.48119	T	0.1	-24.6254	14.94	0.70986	0.0:0.0:0.0:1.0	.	224;699	B7Z7I1;Q5T2S8	.;ARMC4_HUMAN	R	391;699;224	ENSP00000443208:Q391R;ENSP00000306410:Q699R;ENSP00000441076:Q224R	ENSP00000306410:Q699R	Q	-	2	0	ARMC4	28268833	1.000000	0.71417	1.000000	0.80357	0.584000	0.36387	6.444000	0.73452	2.266000	0.75297	0.533000	0.62120	CAG	.	.		0.473	ARMC4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047339.1	NM_018076	Missense_Mutation
VTI1A	143187	hgsc.bcm.edu	37	10	114298012	114298012	+	Missense_Mutation	SNP	A	A	T			TCGA-5R-AAAM-01A-12D-A40R-10	TCGA-5R-AAAM-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9aba9aa4-9f40-456e-8aa4-fb9d20c57d93	bbe62607-8229-46d6-997d-47d1a49b89b0	g.chr10:114298012A>T	ENST00000393077.2	+	5	466	c.350A>T	c.(349-351)cAt>cTt	p.H117L	VTI1A_ENST00000432306.1_Missense_Mutation_p.H117L	NM_145206.2	NP_660207.2	Q96AJ9	VTI1A_HUMAN	vesicle transport through interaction with t-SNAREs 1A	117					intracellular protein transport (GO:0006886)|retrograde transport, endosome to Golgi (GO:0042147)	clathrin-coated vesicle (GO:0030136)|endosome (GO:0005768)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|neuron projection terminus (GO:0044306)|neuronal cell body (GO:0043025)|perinuclear region of cytoplasm (GO:0048471)|SNARE complex (GO:0031201)|synaptic vesicle (GO:0008021)	SNAP receptor activity (GO:0005484)		VTI1A/TCF7L2(8)	breast(1)|large_intestine(1)|lung(2)|ovary(1)|skin(1)	6		Colorectal(252;0.0314)|Breast(234;0.183)		Epithelial(162;0.0126)|all cancers(201;0.0487)		CAGAGGGCACATCTGCTCGAT	0.428			T	TCF7L2	colorectal																																p.H117L		Atlas-SNP	.		Dom	yes		10	10q25.2	143187	vesicle transport through interaction with t-SNAREs homolog 1A		E	.	VTI1A	15	.	0			c.A350T						.						64.0	70.0	68.0					10																	114298012		2203	4300	6503	SO:0001583	missense	143187	exon5			GGGCACATCTGCT	BC017052	CCDS7575.2	10q25.2	2012-12-10	2012-12-10		ENSG00000151532	ENSG00000151532			17792	protein-coding gene	gene with protein product		614316	"""vesicle transport through interaction with t-SNAREs homolog 1A (yeast)"""			9446565	Standard	NM_145206		Approved	MVti1, Vti1a, Vti1-rp2	uc001kzz.3	Q96AJ9	OTTHUMG00000019063	ENST00000393077.2:c.350A>T	chr10.hg19:g.114298012A>T	ENSP00000376792:p.His117Leu	485.0	0.0		350.0	53.0	NM_145206	A2A307|B4E137|Q5W0D7	Missense_Mutation	SNP	ENST00000393077.2	hg19	CCDS7575.2	.	.	.	.	.	.	.	.	.	.	A	14.79	2.641967	0.47153	.	.	ENSG00000151532	ENST00000393077;ENST00000432306	.	.	.	5.86	5.86	0.93980	Target SNARE coiled-coil domain (1);	0.000000	0.85682	D	0.000000	T	0.40222	0.1108	N	0.08118	0	0.58432	D	0.999999	B;B	0.09022	0.002;0.001	B;B	0.14578	0.011;0.008	T	0.21075	-1.0256	9	0.34782	T	0.22	-17.2828	16.5602	0.84551	1.0:0.0:0.0:0.0	.	117;117	Q5W0D7;Q96AJ9	.;VTI1A_HUMAN	L	117	.	ENSP00000376792:H117L	H	+	2	0	VTI1A	114288002	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	8.611000	0.90905	2.367000	0.80283	0.528000	0.53228	CAT	.	.		0.428	VTI1A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050397.2		
OR5F1	338674	hgsc.bcm.edu	37	11	55761610	55761610	+	Missense_Mutation	SNP	G	G	T			TCGA-5R-AAAM-01A-12D-A40R-10	TCGA-5R-AAAM-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9aba9aa4-9f40-456e-8aa4-fb9d20c57d93	bbe62607-8229-46d6-997d-47d1a49b89b0	g.chr11:55761610G>T	ENST00000278409.1	-	1	491	c.492C>A	c.(490-492)agC>agA	p.S164R		NM_003697.1	NP_003688.1	O95221	OR5F1_HUMAN	olfactory receptor, family 5, subfamily F, member 1	164					detection of chemical stimulus involved in sensory perception of smell (GO:0050911)|sensory perception of smell (GO:0007608)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			endometrium(6)|kidney(1)|large_intestine(11)|liver(1)|lung(33)|ovary(2)|pancreas(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	58	Esophageal squamous(21;0.00448)					ATGACAAGCTGCTGACATGGC	0.473																																					p.S164R		Atlas-SNP	.											.	OR5F1	116	.	0			c.C492A						.						75.0	71.0	72.0					11																	55761610		2201	4296	6497	SO:0001583	missense	338674	exon1			CAAGCTGCTGACA	AF065863	CCDS31515.1	11q11	2012-08-09			ENSG00000149133	ENSG00000149133		"""GPCR / Class A : Olfactory receptors"""	8343	protein-coding gene	gene with protein product		608492				9787077	Standard	NM_003697		Approved	OR11-10	uc010riv.2	O95221	OTTHUMG00000166825	ENST00000278409.1:c.492C>A	chr11.hg19:g.55761610G>T	ENSP00000278409:p.Ser164Arg	142.0	0.0		144.0	38.0	NM_003697	Q495D1|Q6IFB9	Missense_Mutation	SNP	ENST00000278409.1	hg19	CCDS31515.1	.	.	.	.	.	.	.	.	.	.	G	7.753	0.703698	0.15172	.	.	ENSG00000149133	ENST00000278409	T	0.00164	8.64	3.03	1.97	0.26223	GPCR, rhodopsin-like superfamily (1);	.	.	.	.	T	0.00412	0.0013	M	0.87456	2.885	0.09310	N	1	D	0.89917	1.0	D	0.79108	0.992	T	0.47959	-0.9076	9	0.87932	D	0	.	2.372	0.04333	0.2559:0.0:0.4899:0.2542	.	164	O95221	OR5F1_HUMAN	R	164	ENSP00000278409:S164R	ENSP00000278409:S164R	S	-	3	2	OR5F1	55518186	0.000000	0.05858	0.082000	0.20525	0.016000	0.09150	0.040000	0.13905	1.422000	0.47177	0.297000	0.19635	AGC	.	.		0.473	OR5F1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391532.1	NM_003697	
TMPRSS13	84000	hgsc.bcm.edu	37	11	117789435	117789435	+	Missense_Mutation	SNP	G	G	T			TCGA-5R-AAAM-01A-12D-A40R-10	TCGA-5R-AAAM-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9aba9aa4-9f40-456e-8aa4-fb9d20c57d93	bbe62607-8229-46d6-997d-47d1a49b89b0	g.chr11:117789435G>T	ENST00000430170.2	-	2	227	c.140C>A	c.(139-141)gCt>gAt	p.A47D	TMPRSS13_ENST00000524993.1_Missense_Mutation_p.A47D|TMPRSS13_ENST00000445164.2_Missense_Mutation_p.A47D|TMPRSS13_ENST00000526090.1_Missense_Mutation_p.A47D|TMPRSS13_ENST00000528626.1_Missense_Mutation_p.A47D	NM_001244995.1	NP_001231924.1	Q9BYE2	TMPSD_HUMAN	transmembrane protease, serine 13	47	13 X 5 AA repeats of A-S-P-A-[GLQR].|4 X 5 AA repeats of T-P-P-G-R.|Ala-rich.					blood microparticle (GO:0072562)|integral component of membrane (GO:0016021)	scavenger receptor activity (GO:0005044)|serine-type endopeptidase activity (GO:0004252)			endometrium(1)|kidney(3)|large_intestine(6)|lung(7)|pancreas(1)|prostate(1)|urinary_tract(1)	20	all_hematologic(175;0.0487)	Medulloblastoma(222;0.0425)|all_hematologic(192;0.196)|all_neural(223;0.234)		BRCA - Breast invasive adenocarcinoma(274;1.78e-05)|Epithelial(105;0.00106)		AGGTGTCCCAGCTGGAGATGC	0.672																																					p.A47D		Atlas-SNP	.											.	TMPRSS13	75	.	0			c.C140A						.						40.0	47.0	45.0					11																	117789435		1886	4105	5991	SO:0001583	missense	84000	exon2			GTCCCAGCTGGAG	AB048796	CCDS41721.1, CCDS55788.1, CCDS55789.1, CCDS58185.1	11q23	2010-04-13	2005-03-11	2005-03-12	ENSG00000137747	ENSG00000137747		"""Serine peptidases / Transmembrane"""	29808	protein-coding gene	gene with protein product		610050	"""transmembrane protease, serine 11"""	TMPRSS11		11267681	Standard	NM_001077263		Approved	MSPL	uc001prs.2	Q9BYE2	OTTHUMG00000166992	ENST00000430170.2:c.140C>A	chr11.hg19:g.117789435G>T	ENSP00000387702:p.Ala47Asp	69.0	0.0		95.0	4.0	NM_001206790	B4DTM9|E9PIJ5|F8WAJ3|Q86YM4|Q96JY8|Q9BYE1	Missense_Mutation	SNP	ENST00000430170.2	hg19	CCDS58185.1	.	.	.	.	.	.	.	.	.	.	G	12.96	2.093951	0.36952	.	.	ENSG00000137747	ENST00000528626;ENST00000336500;ENST00000524993;ENST00000430170;ENST00000445164;ENST00000526090	D;D;D;D;D	0.89050	-2.46;-2.44;-2.44;-2.45;-2.36	2.19	0.0442	0.14224	.	.	.	.	.	T	0.78457	0.4286	L	0.27053	0.805	0.09310	N	1	B;B	0.15141	0.003;0.012	B;B	0.11329	0.006;0.004	T	0.62849	-0.6767	9	0.33940	T	0.23	.	4.476	0.11739	0.1482:0.4707:0.3811:0.0	.	47;47	Q9BYE2-4;E9PRA0	.;.	D	47	ENSP00000435813:A47D;ENSP00000434279:A47D;ENSP00000387702:A47D;ENSP00000394114:A47D;ENSP00000436502:A47D	ENSP00000337113:A47D	A	-	2	0	TMPRSS13	117294645	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-0.354000	0.07681	0.031000	0.15407	-0.122000	0.15005	GCT	.	.		0.672	TMPRSS13-006	PUTATIVE	basic|appris_candidate|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000392318.1	NM_032046	
HSPA8	3312	hgsc.bcm.edu	37	11	122929825	122929825	+	Missense_Mutation	SNP	G	G	T			TCGA-5R-AAAM-01A-12D-A40R-10	TCGA-5R-AAAM-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9aba9aa4-9f40-456e-8aa4-fb9d20c57d93	bbe62607-8229-46d6-997d-47d1a49b89b0	g.chr11:122929825G>T	ENST00000532636.1	-	6	1384	c.1265C>A	c.(1264-1266)aCc>aAc	p.T422N	HSPA8_ENST00000453788.2_Missense_Mutation_p.T422N|SNORD14E_ENST00000364009.1_RNA|HSPA8_ENST00000526862.1_5'Flank|SNORD14C_ENST00000365382.1_RNA|HSPA8_ENST00000526110.1_Missense_Mutation_p.T403N|HSPA8_ENST00000533540.1_Missense_Mutation_p.T276N|HSPA8_ENST00000534319.1_Missense_Mutation_p.T186N|HSPA8_ENST00000227378.3_Missense_Mutation_p.T422N|HSPA8_ENST00000534624.1_Missense_Mutation_p.T422N|SNORD14D_ENST00000384390.1_RNA			P11142	HSP7C_HUMAN	heat shock 70kDa protein 8	422					ATP catabolic process (GO:0006200)|axon guidance (GO:0007411)|chaperone mediated protein folding requiring cofactor (GO:0051085)|clathrin coat disassembly (GO:0072318)|gene expression (GO:0010467)|membrane organization (GO:0061024)|mRNA metabolic process (GO:0016071)|mRNA processing (GO:0006397)|negative regulation of fibril organization (GO:1902904)|negative regulation of transcription, DNA-templated (GO:0045892)|neurotransmitter secretion (GO:0007269)|post-Golgi vesicle-mediated transport (GO:0006892)|protein folding (GO:0006457)|protein refolding (GO:0042026)|regulation of cell cycle (GO:0051726)|response to unfolded protein (GO:0006986)|RNA metabolic process (GO:0016070)|RNA splicing (GO:0008380)|synaptic transmission (GO:0007268)|transcription, DNA-templated (GO:0006351)|viral process (GO:0016032)	blood microparticle (GO:0072562)|clathrin-sculpted gamma-aminobutyric acid transport vesicle membrane (GO:0061202)|cytosol (GO:0005829)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|intracellular (GO:0005622)|membrane (GO:0016020)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|Prp19 complex (GO:0000974)|ribonucleoprotein complex (GO:0030529)|spliceosomal complex (GO:0005681)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|ATPase activity, coupled (GO:0042623)|enzyme binding (GO:0019899)|G-protein coupled receptor binding (GO:0001664)|heat shock protein binding (GO:0031072)|MHC class II protein complex binding (GO:0023026)|poly(A) RNA binding (GO:0044822)|ubiquitin protein ligase binding (GO:0031625)|unfolded protein binding (GO:0051082)			breast(1)|central_nervous_system(7)|endometrium(1)|kidney(9)|large_intestine(4)|lung(13)|upper_aerodigestive_tract(1)	36		Breast(109;0.00249)|Lung NSC(97;0.0177)|all_lung(97;0.0179)|Medulloblastoma(222;0.0425)|all_neural(223;0.112)		BRCA - Breast invasive adenocarcinoma(274;4.88e-06)|OV - Ovarian serous cystadenocarcinoma(99;0.0279)		TGTCTGCTTGGTAGGAATGGT	0.448																																					p.T422N	Colon(21;486 594 5900 6733 14272)	Atlas-SNP	.											.	HSPA8	168	.	0			c.C1265A						.						140.0	124.0	129.0					11																	122929825		2202	4299	6501	SO:0001583	missense	3312	exon6			TGCTTGGTAGGAA	Y00371	CCDS8440.1, CCDS44754.1	11q24.1	2011-09-02	2002-08-29		ENSG00000109971	ENSG00000109971		"""Heat shock proteins / HSP70"""	5241	protein-coding gene	gene with protein product		600816	"""heat shock 70kD protein 8"""	HSPA10		8530083, 3037489	Standard	NM_006597		Approved	HSC71, HSC70, HSP73	uc001pyo.3	P11142	OTTHUMG00000166030	ENST00000532636.1:c.1265C>A	chr11.hg19:g.122929825G>T	ENSP00000437125:p.Thr422Asn	165.0	0.0		150.0	46.0	NM_006597	Q9H3R6	Missense_Mutation	SNP	ENST00000532636.1	hg19	CCDS8440.1	.	.	.	.	.	.	.	.	.	.	G	20.1	3.934284	0.73442	.	.	ENSG00000109971	ENST00000532636;ENST00000533540;ENST00000534624;ENST00000453788;ENST00000227378;ENST00000534319;ENST00000526110;ENST00000524552	T;T;T;T;T;T;T;T	0.04917	3.53;3.53;3.53;3.53;3.53;3.53;3.53;3.53	4.85	4.85	0.62838	.	0.000000	0.85682	D	0.000000	T	0.23886	0.0578	H	0.97415	4	0.80722	D	1	B;B;B	0.25105	0.022;0.118;0.022	B;B;B	0.24974	0.057;0.044;0.057	T	0.39014	-0.9634	10	0.87932	D	0	-14.5597	18.3089	0.90192	0.0:0.0:1.0:0.0	.	422;422;422	Q53GZ6;P11142-2;P11142	.;.;HSP7C_HUMAN	N	422;276;422;422;422;186;403;13	ENSP00000437125:T422N;ENSP00000437189:T276N;ENSP00000432083:T422N;ENSP00000404372:T422N;ENSP00000227378:T422N;ENSP00000433316:T186N;ENSP00000433584:T403N;ENSP00000435908:T13N	ENSP00000227378:T422N	T	-	2	0	HSPA8	122435035	1.000000	0.71417	1.000000	0.80357	0.881000	0.50899	9.583000	0.98217	2.390000	0.81377	0.561000	0.74099	ACC	.	.		0.448	HSPA8-004	PUTATIVE	alternative_5_UTR|basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000387515.1		
LMNTD1	160492	hgsc.bcm.edu	37	12	25679068	25679068	+	Missense_Mutation	SNP	C	C	G			TCGA-5R-AAAM-01A-12D-A40R-10	TCGA-5R-AAAM-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9aba9aa4-9f40-456e-8aa4-fb9d20c57d93	bbe62607-8229-46d6-997d-47d1a49b89b0	g.chr12:25679068C>G	ENST00000282881.6	-	5	849	c.700G>C	c.(700-702)Gat>Cat	p.D234H	IFLTD1_ENST00000458174.2_Missense_Mutation_p.D255H|IFLTD1_ENST00000539744.1_Missense_Mutation_p.D137H|IFLTD1_ENST00000445693.1_Missense_Mutation_p.D171H|IFLTD1_ENST00000413632.2_Intron	NM_152590.3	NP_689803.2	Q8N9Z9	LMTD1_HUMAN		234	LTD.				cell proliferation (GO:0008283)	cytoplasm (GO:0005737)|intermediate filament (GO:0005882)|nuclear envelope (GO:0005635)	structural molecule activity (GO:0005198)			breast(1)|central_nervous_system(1)|endometrium(2)|large_intestine(6)|lung(7)|ovary(2)|skin(1)|upper_aerodigestive_tract(2)	22	all_lung(3;2.75e-22)|Lung NSC(3;1.77e-21)|all_hematologic(7;0.00656)|Colorectal(261;0.0847)					GTTATACAATCAGGACTTGCT	0.363																																					p.D255H		Atlas-SNP	.											.	IFLTD1	121	.	0			c.G763C						.						115.0	107.0	110.0					12																	25679068		2203	4300	6503	SO:0001583	missense	160492	exon6			TACAATCAGGACT																												ENST00000282881.6:c.700G>C	chr12.hg19:g.25679068C>G	ENSP00000282881:p.Asp234His	66.0	0.0		99.0	32.0	NM_001145728	B4DL27|B4DY70|Q8IY38	Missense_Mutation	SNP	ENST00000282881.6	hg19	CCDS8704.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	11.50|11.50	1.657786|1.657786	0.29425|0.29425	.|.	.|.	ENSG00000152936|ENSG00000152936	ENST00000282881;ENST00000539744;ENST00000458174;ENST00000445693;ENST00000545543|ENST00000543629	D;D;D;D;D|.	0.98633|.	-5.04;-5.04;-5.04;-5.04;-5.04|.	5.81|5.81	1.44|1.44	0.22558|0.22558	Intermediate filament, C-terminal (1);|.	.|.	.|.	.|.	.|.	T|.	0.33411|.	0.0862|.	L|L	0.38838|0.38838	1.175|1.175	0.09310|0.09310	N|N	0.999999|0.999999	D;D;D|.	0.60575|.	0.967;0.967;0.988|.	P;P;D|.	0.64237|.	0.562;0.773;0.923|.	T|.	0.24083|.	-1.0170|.	9|.	0.72032|.	D|.	0.01|.	-1.0338|-1.0338	6.7724|6.7724	0.23601|0.23601	0.0:0.5079:0.0:0.4921|0.0:0.5079:0.0:0.4921	.|.	171;255;234|.	Q8N9Z9-3;Q8N9Z9-5;Q8N9Z9|.	.;.;ILFT1_HUMAN|.	H|S	234;137;255;171;64|8	ENSP00000282881:D234H;ENSP00000443132:D137H;ENSP00000407353:D255H;ENSP00000407043:D171H;ENSP00000443596:D64H|.	ENSP00000282881:D234H|.	D|X	-|-	1|2	0|2	IFLTD1|IFLTD1	25570335|25570335	0.002000|0.002000	0.14202|0.14202	0.003000|0.003000	0.11579|0.11579	0.227000|0.227000	0.25037|0.25037	0.582000|0.582000	0.23834|0.23834	0.252000|0.252000	0.21531|0.21531	0.655000|0.655000	0.94253|0.94253	GAT|TGA	.	.		0.363	IFLTD1-008	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000402279.1		
ANO6	196527	hgsc.bcm.edu	37	12	45814873	45814873	+	Missense_Mutation	SNP	C	C	T			TCGA-5R-AAAM-01A-12D-A40R-10	TCGA-5R-AAAM-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9aba9aa4-9f40-456e-8aa4-fb9d20c57d93	bbe62607-8229-46d6-997d-47d1a49b89b0	g.chr12:45814873C>T	ENST00000320560.8	+	18	2439	c.2237C>T	c.(2236-2238)aCg>aTg	p.T746M	ANO6_ENST00000435642.1_Missense_Mutation_p.T746M|ANO6_ENST00000441606.2_Missense_Mutation_p.T728M|ANO6_ENST00000423947.3_Missense_Mutation_p.T767M|ANO6_ENST00000426898.2_3'UTR|ANO6_ENST00000425752.2_Missense_Mutation_p.T746M	NM_001025356.2	NP_001020527.2	Q4KMQ2	ANO6_HUMAN	anoctamin 6	746					activation of blood coagulation via clotting cascade (GO:0002543)|blood coagulation (GO:0007596)|bone mineralization involved in bone maturation (GO:0035630)|calcium activated galactosylceramide scrambling (GO:0061591)|calcium activated phosphatidylcholine scrambling (GO:0061590)|calcium activated phosphatidylserine scrambling (GO:0061589)|cation transmembrane transport (GO:0098655)|cation transport (GO:0006812)|chloride transmembrane transport (GO:1902476)|chloride transport (GO:0006821)|dendritic cell chemotaxis (GO:0002407)|ion transmembrane transport (GO:0034220)|phosphatidylserine exposure on blood platelet (GO:0097045)|phospholipid scrambling (GO:0017121)|positive regulation of endothelial cell apoptotic process (GO:2000353)|regulation of anion transport (GO:0044070)|transmembrane transport (GO:0055085)	cell surface (GO:0009986)|chloride channel complex (GO:0034707)|extracellular vesicular exosome (GO:0070062)|intracellular (GO:0005622)|membrane (GO:0016020)|plasma membrane (GO:0005886)	calcium activated cation channel activity (GO:0005227)|intracellular calcium activated chloride channel activity (GO:0005229)|phospholipid scramblase activity (GO:0017128)|voltage-gated chloride channel activity (GO:0005247)|voltage-gated ion channel activity (GO:0005244)			central_nervous_system(1)|endometrium(3)|kidney(3)|large_intestine(8)|lung(23)|ovary(2)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	46						ATAGCTTTCACGTCGGACATG	0.488																																					p.T767M		Atlas-SNP	.											.	ANO6	163	.	0			c.C2300T						.						176.0	153.0	161.0					12																	45814873		2203	4300	6503	SO:0001583	missense	196527	exon19			CTTTCACGTCGGA	AL832340	CCDS31782.1, CCDS44865.1, CCDS44866.1, CCDS55819.1	12q12-q13.11	2014-09-17	2008-08-28	2008-08-28				"""Ion channels / Chloride channels : Calcium activated : Anoctamins"""	25240	protein-coding gene	gene with protein product		608663	"""transmembrane protein 16F"""	TMEM16F		15067359, 24692353	Standard	NM_001025356		Approved	DKFZp313M0720	uc010slf.2	Q4KMQ2	OTTHUMG00000169564	ENST00000320560.8:c.2237C>T	chr12.hg19:g.45814873C>T	ENSP00000320087:p.Thr746Met	146.0	0.0		143.0	34.0	NM_001204803	A6NNM6|B9EGG0|E7ENK4|E9PB30|E9PCT2|Q8N3Q2	Missense_Mutation	SNP	ENST00000320560.8	hg19	CCDS31782.1	.	.	.	.	.	.	.	.	.	.	C	28.6	4.937115	0.92458	.	.	ENSG00000177119	ENST00000425752;ENST00000423947;ENST00000435642;ENST00000320560;ENST00000441606	T;T;T;T;T	0.66280	-0.2;-0.2;-0.2;-0.2;-0.2	5.05	5.05	0.67936	.	0.000000	0.85682	D	0.000000	D	0.85513	0.5714	H	0.95004	3.61	0.80722	D	1	D;D;D;D	0.89917	1.0;1.0;1.0;1.0	D;D;D;D	0.83275	0.992;0.986;0.979;0.996	D	0.89344	0.3656	10	0.87932	D	0	.	19.2834	0.94061	0.0:1.0:0.0:0.0	.	728;767;746;746	E9PB30;B9EGG0;E9PCT2;Q4KMQ2	.;.;.;ANO6_HUMAN	M	746;767;746;746;728	ENSP00000391417:T746M;ENSP00000409126:T767M;ENSP00000413840:T746M;ENSP00000320087:T746M;ENSP00000413137:T728M	ENSP00000320087:T746M	T	+	2	0	ANO6	44101140	1.000000	0.71417	0.966000	0.40874	0.994000	0.84299	5.983000	0.70540	2.717000	0.92951	0.650000	0.86243	ACG	.	.		0.488	ANO6-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000404822.1	XM_113743	
RPL21	6144	hgsc.bcm.edu	37	13	27830355	27830355	+	Missense_Mutation	SNP	A	A	C			TCGA-5R-AAAM-01A-12D-A40R-10	TCGA-5R-AAAM-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9aba9aa4-9f40-456e-8aa4-fb9d20c57d93	bbe62607-8229-46d6-997d-47d1a49b89b0	g.chr13:27830355A>C	ENST00000311549.6	+	5	566	c.277A>C	c.(277-279)Att>Ctt	p.I93L	RPL21_ENST00000272274.4_Missense_Mutation_p.I93L|SNORD102_ENST00000384769.1_RNA|SNORA27_ENST00000384323.1_RNA|RPL21_ENST00000326092.4_Missense_Mutation_p.I93L|RPL21_ENST00000319826.4_Missense_Mutation_p.I93L	NM_000982.3	NP_000973.2	P46778	RL21_HUMAN	ribosomal protein L21	93					cellular protein metabolic process (GO:0044267)|gene expression (GO:0010467)|mRNA metabolic process (GO:0016071)|nuclear-transcribed mRNA catabolic process, nonsense-mediated decay (GO:0000184)|RNA metabolic process (GO:0016070)|SRP-dependent cotranslational protein targeting to membrane (GO:0006614)|translation (GO:0006412)|translational elongation (GO:0006414)|translational initiation (GO:0006413)|translational termination (GO:0006415)|viral life cycle (GO:0019058)|viral process (GO:0016032)|viral transcription (GO:0019083)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|cytosolic large ribosomal subunit (GO:0022625)|membrane (GO:0016020)|nucleolus (GO:0005730)	poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)|structural constituent of ribosome (GO:0003735)			large_intestine(1)|lung(1)	2		Lung SC(185;0.0156)	Colorectal(13;0.00042)|READ - Rectum adenocarcinoma(15;0.105)	all cancers(112;0.0287)|OV - Ovarian serous cystadenocarcinoma(117;0.118)|Epithelial(112;0.139)|GBM - Glioblastoma multiforme(144;0.21)		TAATGTGCGTATTGAGCACAT	0.378																																					p.I93L		Atlas-SNP	.											.	RPL21	12	.	0			c.A277C						.						21.0	24.0	23.0					13																	27830355		2203	4297	6500	SO:0001583	missense	6144	exon5			GTGCGTATTGAGC	AB007176	CCDS9320.1	13q12.2	2008-07-18			ENSG00000122026	ENSG00000122026		"""L ribosomal proteins"""	10313	protein-coding gene	gene with protein product	"""60S ribosomal protein L21"""	603636				3459254, 7772601	Standard	NM_000982		Approved	L21, FLJ27458, MGC71252, MGC104274, MGC104275, DKFZp686C06101	uc001ura.3	P46778	OTTHUMG00000016630	ENST00000311549.6:c.277A>C	chr13.hg19:g.27830355A>C	ENSP00000346027:p.Ile93Leu	196.0	0.0		170.0	32.0	NM_000982	Q16699	Missense_Mutation	SNP	ENST00000311549.6	hg19	CCDS9320.1	.	.	.	.	.	.	.	.	.	.	A	15.21	2.766037	0.49574	.	.	ENSG00000122026	ENST00000311549;ENST00000272274;ENST00000319826;ENST00000326092	T;T;T;T	0.64260	-0.09;-0.09;-0.09;-0.09	4.83	2.37	0.29283	Translation protein SH3-like (1);	0.059658	0.64402	U	0.000003	T	0.64159	0.2573	M	0.84433	2.695	0.52501	D	0.99995	B;B	0.10296	0.003;0.003	B;B	0.26416	0.069;0.069	T	0.61821	-0.6984	10	0.87932	D	0	.	7.8007	0.29172	0.7662:0.0:0.2338:0.0	.	93;93	P46778;Q6IAX2	RL21_HUMAN;.	L	93	ENSP00000346027:I93L;ENSP00000351021:I93L;ENSP00000370574:I93L;ENSP00000370569:I93L	ENSP00000351021:I93L	I	+	1	0	RPL21	26728355	0.998000	0.40836	0.897000	0.35233	0.843000	0.47879	3.627000	0.54252	0.298000	0.22638	0.459000	0.35465	ATT	.	.		0.378	RPL21-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044270.1	NM_000982	
FOXO1	2308	hgsc.bcm.edu	37	13	41240285	41240285	+	Missense_Mutation	SNP	G	G	C			TCGA-5R-AAAM-01A-12D-A40R-10	TCGA-5R-AAAM-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9aba9aa4-9f40-456e-8aa4-fb9d20c57d93	bbe62607-8229-46d6-997d-47d1a49b89b0	g.chr13:41240285G>C	ENST00000379561.5	-	1	449	c.65C>G	c.(64-66)tCg>tGg	p.S22W		NM_002015.3	NP_002006.2	Q12778	FOXO1_HUMAN	forkhead box O1	22					apoptotic process (GO:0006915)|autophagy (GO:0006914)|blood vessel development (GO:0001568)|cellular glucose homeostasis (GO:0001678)|cellular response to cold (GO:0070417)|cellular response to DNA damage stimulus (GO:0006974)|cellular response to hyperoxia (GO:0071455)|cellular response to insulin stimulus (GO:0032869)|cellular response to nitric oxide (GO:0071732)|cellular response to oxidative stress (GO:0034599)|cellular response to starvation (GO:0009267)|endocrine pancreas development (GO:0031018)|epidermal growth factor receptor signaling pathway (GO:0007173)|fat cell differentiation (GO:0045444)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|innate immune response (GO:0045087)|insulin receptor signaling pathway (GO:0008286)|negative regulation of apoptotic process (GO:0043066)|negative regulation of fat cell differentiation (GO:0045599)|negative regulation of stress-activated MAPK cascade (GO:0032873)|negative regulation of transcription, DNA-templated (GO:0045892)|neurotrophin TRK receptor signaling pathway (GO:0048011)|phosphatidylinositol-mediated signaling (GO:0048015)|positive regulation of apoptotic process (GO:0043065)|positive regulation of autophagy (GO:0010508)|positive regulation of gluconeogenesis (GO:0045722)|positive regulation of protein catabolic process (GO:0045732)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|protein acetylation (GO:0006473)|regulation of cell proliferation (GO:0042127)|regulation of energy homeostasis (GO:2000505)|regulation of gluconeogenesis by regulation of transcription from RNA polymerase II promoter (GO:0035947)|temperature homeostasis (GO:0001659)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|mitochondrion (GO:0005739)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	chromatin binding (GO:0003682)|protein phosphatase 2A binding (GO:0051721)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in negative regulation of transcription (GO:0001078)|sequence-specific DNA binding (GO:0043565)|transcription factor binding transcription factor activity (GO:0000989)|ubiquitin protein ligase binding (GO:0031625)		PAX7/FOXO1(197)|PAX3/FOXO1(749)	central_nervous_system(1)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(7)|kidney(1)|large_intestine(2)|lung(2)|upper_aerodigestive_tract(1)	20		Lung NSC(96;1.18e-05)|Breast(139;0.00394)|Prostate(109;0.0181)|Lung SC(185;0.0262)|Hepatocellular(188;0.194)		all cancers(112;7.32e-09)|Epithelial(112;2.87e-06)|OV - Ovarian serous cystadenocarcinoma(117;6.98e-05)|GBM - Glioblastoma multiforme(144;0.00394)|BRCA - Breast invasive adenocarcinoma(63;0.0815)		CCAGGTGCACGAGCGCGGCCG	0.761																																					p.S22W		Atlas-SNP	.											.	FOXO1	110	.	0			c.C65G						.						1.0	2.0	1.0					13																	41240285		1143	2568	3711	SO:0001583	missense	2308	exon1			GTGCACGAGCGCG		CCDS9371.1	13q14.1	2011-08-01	2007-05-02	2007-05-02	ENSG00000150907	ENSG00000150907		"""Forkhead boxes"""	3819	protein-coding gene	gene with protein product		136533	"""forkhead homolog in rhabdomyosarcoma"""	FKHR, FOXO1A		8275086, 15057823	Standard	NM_002015		Approved	FKH1	uc001uxl.4	Q12778	OTTHUMG00000016775	ENST00000379561.5:c.65C>G	chr13.hg19:g.41240285G>C	ENSP00000368880:p.Ser22Trp	36.0	0.0		27.0	8.0	NM_002015	O43523|Q5VYC7|Q6NSK6	Missense_Mutation	SNP	ENST00000379561.5	hg19	CCDS9371.1	.	.	.	.	.	.	.	.	.	.	G	16.32	3.088994	0.55968	.	.	ENSG00000150907	ENST00000379561	D	0.97831	-4.56	4.0	4.0	0.46444	.	0.000000	0.64402	U	0.000006	D	0.98438	0.9480	M	0.80982	2.52	0.80722	D	1	D	0.71674	0.998	D	0.68039	0.955	D	0.99482	1.0948	10	0.87932	D	0	-7.8406	14.673	0.68958	0.0:0.0:1.0:0.0	.	22	Q12778	FOXO1_HUMAN	W	22	ENSP00000368880:S22W	ENSP00000368880:S22W	S	-	2	0	FOXO1	40138285	1.000000	0.71417	0.979000	0.43373	0.044000	0.14063	6.832000	0.75329	1.768000	0.52137	0.514000	0.50259	TCG	.	.		0.761	FOXO1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044634.3	NM_002015	
RNASE6	6039	hgsc.bcm.edu	37	14	21250306	21250306	+	Missense_Mutation	SNP	C	C	G			TCGA-5R-AAAM-01A-12D-A40R-10	TCGA-5R-AAAM-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9aba9aa4-9f40-456e-8aa4-fb9d20c57d93	bbe62607-8229-46d6-997d-47d1a49b89b0	g.chr14:21250306C>G	ENST00000304677.2	+	2	741	c.448C>G	c.(448-450)Ctc>Gtc	p.L150V	RP11-219E7.1_ENST00000556624.1_RNA	NM_005615.4	NP_005606.1	Q93091	RNAS6_HUMAN	ribonuclease, RNase A family, k6	150					defense response (GO:0006952)|RNA catabolic process (GO:0006401)|RNA phosphodiester bond hydrolysis (GO:0090501)	extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)	endonuclease activity (GO:0004519)|nucleic acid binding (GO:0003676)|ribonuclease activity (GO:0004540)			large_intestine(1)	1	all_cancers(95;0.00406)		Epithelial(56;9.21e-07)|all cancers(55;2.9e-06)	GBM - Glioblastoma multiforme(265;0.0126)		AGATAGTATTCTCTAAGGCAT	0.423																																					p.L150V		Atlas-SNP	.											.	RNASE6	7	.	0			c.C448G						.						74.0	75.0	75.0					14																	21250306		2203	4300	6503	SO:0001583	missense	6039	exon2			AGTATTCTCTAAG	U64998	CCDS9558.1	14q11	2008-07-09			ENSG00000169413	ENSG00000169413		"""Ribonucleases, RNase A"""	10048	protein-coding gene	gene with protein product	"""RNase k6"""	601981		RNS6		8836175, 9647635	Standard	NM_005615		Approved		uc001vye.4	Q93091	OTTHUMG00000029585	ENST00000304677.2:c.448C>G	chr14.hg19:g.21250306C>G	ENSP00000302046:p.Leu150Val	107.0	0.0		107.0	31.0	NM_005615		Missense_Mutation	SNP	ENST00000304677.2	hg19	CCDS9558.1	.	.	.	.	.	.	.	.	.	.	C	0.018	-1.484530	0.01027	.	.	ENSG00000169413	ENST00000304677	T	0.78126	-1.15	4.94	-1.42	0.08913	Ribonuclease A, domain (2);	1.303180	0.05300	N	0.522833	T	0.49098	0.1537	N	0.08118	0	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.43426	-0.9392	10	0.02654	T	1	.	1.3783	0.02225	0.238:0.2673:0.3584:0.1363	.	150	Q93091	RNAS6_HUMAN	V	150	ENSP00000302046:L150V	ENSP00000302046:L150V	L	+	1	0	RNASE6	20320146	0.001000	0.12720	0.008000	0.14137	0.104000	0.19210	-0.888000	0.04148	-0.373000	0.07979	-1.148000	0.01847	CTC	.	.		0.423	RNASE6-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000073750.2		
MKRN3	7681	hgsc.bcm.edu	37	15	23811290	23811290	+	Missense_Mutation	SNP	C	C	G			TCGA-5R-AAAM-01A-12D-A40R-10	TCGA-5R-AAAM-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9aba9aa4-9f40-456e-8aa4-fb9d20c57d93	bbe62607-8229-46d6-997d-47d1a49b89b0	g.chr15:23811290C>G	ENST00000314520.3	+	1	837	c.361C>G	c.(361-363)Ctt>Gtt	p.L121V	RP11-73C9.1_ENST00000563044.1_RNA|MKRN3_ENST00000568252.1_Intron|MKRN3_ENST00000564592.1_Intron	NM_005664.3	NP_005655.1	Q13064	MKRN3_HUMAN	makorin ring finger protein 3	121					protein ubiquitination (GO:0016567)	ribonucleoprotein complex (GO:0030529)	ligase activity (GO:0016874)|zinc ion binding (GO:0008270)			breast(2)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(7)|lung(33)|ovary(2)|prostate(3)|skin(3)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	61		all_cancers(20;8.44e-25)|all_epithelial(15;3.69e-22)|Lung NSC(15;2.96e-18)|all_lung(15;2.8e-17)|Breast(32;0.000353)|Colorectal(260;0.14)		all cancers(64;3.02e-06)|Epithelial(43;1.94e-05)|BRCA - Breast invasive adenocarcinoma(123;0.0012)		TTCGCACGACCTTTCTGGTCG	0.602																																					p.L121V		Atlas-SNP	.											.	MKRN3	155	.	0			c.C361G						.						56.0	58.0	57.0					15																	23811290		2203	4300	6503	SO:0001583	missense	7681	exon1			CACGACCTTTCTG	U19107	CCDS10013.1	15q11-q13	2013-01-09	2008-08-13		ENSG00000179455	ENSG00000179455		"""RING-type (C3HC4) zinc fingers"""	7114	protein-coding gene	gene with protein product	"""zinc finger protein 127"""	603856		ZNF127, D15S9		10196367	Standard	NM_005664		Approved	RNF63, ZFP127, MGC88288	uc001ywh.4	Q13064	OTTHUMG00000129160	ENST00000314520.3:c.361C>G	chr15.hg19:g.23811290C>G	ENSP00000313881:p.Leu121Val	83.0	0.0		106.0	11.0	NM_005664		Missense_Mutation	SNP	ENST00000314520.3	hg19	CCDS10013.1	.	.	.	.	.	.	.	.	.	.	C	19.86	3.904712	0.72868	.	.	ENSG00000179455	ENST00000314520	T	0.34667	1.35	3.94	2.05	0.26809	Zinc finger, CCCH-type (2);	0.280449	0.29451	N	0.012115	T	0.24084	0.0583	L	0.47016	1.485	0.48341	D	0.999631	P	0.37061	0.58	B	0.31245	0.126	T	0.04294	-1.0962	10	0.51188	T	0.08	.	4.7645	0.13125	0.2134:0.6766:0.0:0.1099	.	121	Q13064	MKRN3_HUMAN	V	121	ENSP00000313881:L121V	ENSP00000313881:L121V	L	+	1	0	MKRN3	21362383	0.221000	0.23642	0.010000	0.14722	0.327000	0.28475	1.320000	0.33666	0.631000	0.30412	0.563000	0.77884	CTT	.	.		0.602	MKRN3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251225.1	NM_005664	
MYO5A	4644	hgsc.bcm.edu	37	15	52635319	52635319	+	Silent	SNP	G	G	A			TCGA-5R-AAAM-01A-12D-A40R-10	TCGA-5R-AAAM-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9aba9aa4-9f40-456e-8aa4-fb9d20c57d93	bbe62607-8229-46d6-997d-47d1a49b89b0	g.chr15:52635319G>A	ENST00000399231.3	-	31	4278	c.4035C>T	c.(4033-4035)gcC>gcT	p.A1345A	MYO5A_ENST00000356338.6_Intron|MYO5A_ENST00000553916.1_Intron|MYO5A_ENST00000399233.2_Silent_p.A1342A|MYO5A_ENST00000358212.6_Silent_p.A1345A	NM_000259.3	NP_000250	Q9Y4I1	MYO5A_HUMAN	myosin VA (heavy chain 12, myoxin)	1345					actin filament-based movement (GO:0030048)|anagen (GO:0042640)|cellular protein metabolic process (GO:0044267)|cellular response to insulin stimulus (GO:0032869)|endoplasmic reticulum localization (GO:0051643)|exocytosis (GO:0006887)|insulin secretion (GO:0030073)|locomotion involved in locomotory behavior (GO:0031987)|long-chain fatty acid biosynthetic process (GO:0042759)|melanin biosynthetic process (GO:0042438)|melanocyte differentiation (GO:0030318)|melanosome transport (GO:0032402)|membrane organization (GO:0061024)|myelination (GO:0042552)|odontogenesis (GO:0042476)|post-Golgi vesicle-mediated transport (GO:0006892)|protein localization to plasma membrane (GO:0072659)|protein transport (GO:0015031)|regulation of inositol 1,4,5-trisphosphate-sensitive calcium-release channel activity (GO:0031585)|secretory granule localization (GO:0032252)|synapse organization (GO:0050808)|synaptic transmission (GO:0007268)|transport (GO:0006810)|vesicle transport along actin filament (GO:0030050)|vesicle-mediated transport (GO:0016192)|visual perception (GO:0007601)	actomyosin (GO:0042641)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|filopodium tip (GO:0032433)|Golgi apparatus (GO:0005794)|growth cone (GO:0030426)|insulin-responsive compartment (GO:0032593)|intermediate filament (GO:0005882)|melanosome (GO:0042470)|membrane (GO:0016020)|microtubule plus-end (GO:0035371)|myosin complex (GO:0016459)|neuron projection (GO:0043005)|neuronal cell body (GO:0043025)|photoreceptor outer segment (GO:0001750)|ruffle (GO:0001726)	ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|microfilament motor activity (GO:0000146)|poly(A) RNA binding (GO:0044822)|Rab GTPase binding (GO:0017137)			breast(4)|central_nervous_system(1)|cervix(2)|endometrium(5)|kidney(7)|large_intestine(12)|lung(19)|ovary(3)|skin(3)|stomach(1)	57				all cancers(107;0.0085)|Colorectal(133;0.077)|READ - Rectum adenocarcinoma(133;0.196)		ATAACCTGTTGGCTTGTTTTA	0.388																																					p.A1345A		Atlas-SNP	.											.	MYO5A	145	.	0			c.C4035T						.						98.0	94.0	95.0					15																	52635319		1858	4092	5950	SO:0001819	synonymous_variant	4644	exon31			CCTGTTGGCTTGT		CCDS42037.1, CCDS45262.1	15q21	2014-09-17	2006-09-29		ENSG00000197535	ENSG00000197535		"""Myosins / Myosin superfamily : Class V"""	7602	protein-coding gene	gene with protein product	"""myosin, heavy polypeptide kinase"", ""myosin heavy chain 12"", ""myoxin"", ""myosin V"""	160777	"""myosin VA (heavy polypeptide 12, myoxin)"""	MYH12		8188282, 8022818	Standard	NM_000259		Approved	MYO5, GS1, MYR12	uc002aby.2	Q9Y4I1	OTTHUMG00000137383	ENST00000399231.3:c.4035C>T	chr15.hg19:g.52635319G>A		74.0	0.0		90.0	12.0	NM_000259	A8MZC5|O60653|Q07902|Q16249|Q9UE30|Q9UE31	Silent	SNP	ENST00000399231.3	hg19	CCDS42037.1																																																																																			.	.		0.388	MYO5A-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000268102.1	NM_000259	
USP10	9100	hgsc.bcm.edu	37	16	84778402	84778402	+	Silent	SNP	T	T	C			TCGA-5R-AAAM-01A-12D-A40R-10	TCGA-5R-AAAM-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9aba9aa4-9f40-456e-8aa4-fb9d20c57d93	bbe62607-8229-46d6-997d-47d1a49b89b0	g.chr16:84778402T>C	ENST00000219473.7	+	4	428	c.315T>C	c.(313-315)acT>acC	p.T105T	USP10_ENST00000570191.1_Silent_p.T109T|USP10_ENST00000562743.1_3'UTR	NM_001272075.1|NM_005153.2	NP_001259004.1|NP_005144.2	Q14694	UBP10_HUMAN	ubiquitin specific peptidase 10	105					autophagy (GO:0006914)|DNA damage response, signal transduction by p53 class mediator (GO:0030330)|DNA repair (GO:0006281)|protein deubiquitination (GO:0016579)|regulation of autophagy (GO:0010506)|ubiquitin-dependent protein catabolic process (GO:0006511)	cytoplasm (GO:0005737)|early endosome (GO:0005769)|intermediate filament cytoskeleton (GO:0045111)|nucleus (GO:0005634)	cysteine-type endopeptidase activity (GO:0004197)|ion channel binding (GO:0044325)|p53 binding (GO:0002039)|poly(A) RNA binding (GO:0044822)|ubiquitin thiolesterase activity (GO:0004221)|ubiquitin-specific protease activity (GO:0004843)			endometrium(3)|kidney(1)|large_intestine(7)|lung(3)|prostate(1)|stomach(1)|urinary_tract(1)	17						ATGGTATCACTAAAGAAGCAA	0.488																																					p.T109T		Atlas-SNP	.											.	USP10	51	.	0			c.T327C						.						75.0	73.0	74.0					16																	84778402		1846	4086	5932	SO:0001819	synonymous_variant	9100	exon5			TATCACTAAAGAA	D80012	CCDS45537.1, CCDS62004.1	16q	2008-03-25	2005-08-08			ENSG00000103194		"""Ubiquitin-specific peptidases"""	12608	protein-coding gene	gene with protein product		609818	"""ubiquitin specific protease 10"""			12838346	Standard	NM_005153		Approved	UBPO, KIAA0190	uc002fii.3	Q14694		ENST00000219473.7:c.315T>C	chr16.hg19:g.84778402T>C		142.0	0.0		95.0	29.0	NM_001272075	B2RDJ8|B4DS84|Q9BWG7|Q9NSL7	Silent	SNP	ENST00000219473.7	hg19	CCDS45537.1																																																																																			.	.		0.488	USP10-001	KNOWN	upstream_ATG|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000433660.1		
CCT6B	10693	hgsc.bcm.edu	37	17	33267596	33267596	+	Silent	SNP	T	T	G			TCGA-5R-AAAM-01A-12D-A40R-10	TCGA-5R-AAAM-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9aba9aa4-9f40-456e-8aa4-fb9d20c57d93	bbe62607-8229-46d6-997d-47d1a49b89b0	g.chr17:33267596T>G	ENST00000314144.5	-	8	1045	c.930A>C	c.(928-930)atA>atC	p.I310I	CCT6B_ENST00000421975.3_Silent_p.I273I|CCT6B_ENST00000436961.3_Silent_p.I265I	NM_006584.3	NP_006575.2	Q92526	TCPW_HUMAN	chaperonin containing TCP1, subunit 6B (zeta 2)	310					chaperone-mediated protein complex assembly (GO:0051131)|protein folding (GO:0006457)|protein transport (GO:0015031)|spermatogenesis (GO:0007283)	chaperonin-containing T-complex (GO:0005832)	ATP binding (GO:0005524)|protein transporter activity (GO:0008565)|unfolded protein binding (GO:0051082)			NS(1)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(3)|lung(7)|ovary(1)|pancreas(1)	20		Ovarian(249;0.17)				GAAGAGCTACTATTCCATGTT	0.294																																					p.I310I		Atlas-SNP	.											.	CCT6B	63	.	0			c.A930C						.						68.0	72.0	71.0					17																	33267596		2203	4290	6493	SO:0001819	synonymous_variant	10693	exon8			AGCTACTATTCCA	D78333	CCDS32617.1, CCDS54105.1, CCDS54106.1	17q	2011-09-02			ENSG00000132141	ENSG00000132141		"""Heat Shock Proteins / Chaperonins"""	1621	protein-coding gene	gene with protein product		610730				8812458, 9013858	Standard	NM_006584		Approved	Cctz2, TSA303	uc002hig.3	Q92526		ENST00000314144.5:c.930A>C	chr17.hg19:g.33267596T>G		173.0	0.0		164.0	11.0	NM_006584	B4DX20|B4DYB0|Q8TC34	Silent	SNP	ENST00000314144.5	hg19	CCDS32617.1																																																																																			.	.		0.294	CCT6B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000448014.1	NM_006584	
HEATR9	256957	hgsc.bcm.edu	37	17	34182344	34182344	+	Missense_Mutation	SNP	A	A	G			TCGA-5R-AAAM-01A-12D-A40R-10	TCGA-5R-AAAM-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9aba9aa4-9f40-456e-8aa4-fb9d20c57d93	bbe62607-8229-46d6-997d-47d1a49b89b0	g.chr17:34182344A>G	ENST00000311880.2	-	15	1584	c.1436T>C	c.(1435-1437)cTc>cCc	p.L479P	C17orf66_ENST00000592980.1_Missense_Mutation_p.L439P	NM_152781.2	NP_689994.2	A2RTY3	HEAT9_HUMAN		479					hematopoietic progenitor cell differentiation (GO:0002244)			p.L479H(1)		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)		ATATACAGAGAGAACCTTGTT	0.438																																					p.L479P		Atlas-SNP	.											C17orf66,NS,carcinoma,0,1	C17orf66	57	.	1	Substitution - Missense(1)	kidney(1)	c.T1436C						.						91.0	88.0	89.0					17																	34182344		2203	4300	6503	SO:0001583	missense	256957	exon15			ACAGAGAGAACCT																												ENST00000311880.2:c.1436T>C	chr17.hg19:g.34182344A>G	ENSP00000309560:p.Leu479Pro	95.0	1.0		96.0	25.0	NM_152781	B4DX21|B4DXA4|B4DXF0|Q8N4R4|Q96M46	Missense_Mutation	SNP	ENST00000311880.2	hg19	CCDS11299.1	.	.	.	.	.	.	.	.	.	.	A	12.76	2.034273	0.35893	.	.	ENSG00000172653	ENST00000311880	T	0.55930	0.49	4.08	3.0	0.34707	.	0.960417	0.08546	N	0.929817	T	0.44008	0.1273	N	0.24115	0.695	0.09310	N	0.999998	D;P	0.54207	0.965;0.94	P;B	0.47981	0.563;0.36	T	0.27088	-1.0084	10	0.62326	D	0.03	.	6.2039	0.20591	0.8831:0.0:0.1169:0.0	.	439;479	A2RTY3-3;A2RTY3	.;CQ066_HUMAN	P	479	ENSP00000309560:L479P	ENSP00000309560:L479P	L	-	2	0	C17orf66	31206457	0.360000	0.24964	0.006000	0.13384	0.035000	0.12851	3.807000	0.55591	0.726000	0.32339	0.460000	0.39030	CTC	.	.		0.438	C17orf66-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256487.1		
MTCL1	23255	hgsc.bcm.edu	37	18	8796353	8796353	+	Missense_Mutation	SNP	C	C	T	rs369991737		TCGA-5R-AAAM-01A-12D-A40R-10	TCGA-5R-AAAM-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9aba9aa4-9f40-456e-8aa4-fb9d20c57d93	bbe62607-8229-46d6-997d-47d1a49b89b0	g.chr18:8796353C>T	ENST00000306329.11	+	7	3091	c.3091C>T	c.(3091-3093)Cgg>Tgg	p.R1031W	SOGA2_ENST00000517570.1_Missense_Mutation_p.R671W|SOGA2_ENST00000359865.3_Missense_Mutation_p.R712W|SOGA2_ENST00000306285.7_Missense_Mutation_p.R27W|SOGA2_ENST00000400050.3_Missense_Mutation_p.R671W|SOGA2_ENST00000518815.1_Missense_Mutation_p.R27W																							GCAGGAGCTCCGGTCCTTGAA	0.517																																					p.R712W		Atlas-SNP	.											.	.	.	.	0			c.C2134T						.	C	TRP/ARG	1,4405	2.1+/-5.4	0,1,2202	126.0	118.0	120.0		2134	-0.6	0.0	18		120	0,8600		0,0,4300	no	missense	CCDC165	NM_015210.3	101	0,1,6502	TT,TC,CC		0.0,0.0227,0.0077	probably-damaging	712/1587	8796353	1,13005	2203	4300	6503	SO:0001583	missense	23255	exon9			GAGCTCCGGTCCT																												ENST00000306329.11:c.3091C>T	chr18.hg19:g.8796353C>T	ENSP00000305027:p.Arg1031Trp	150.0	0.0		138.0	7.0	NM_015210		Missense_Mutation	SNP	ENST00000306329.11	hg19		.	.	.	.	.	.	.	.	.	.	C	17.28	3.350425	0.61183	2.27E-4	0.0	ENSG00000168502	ENST00000306329;ENST00000517570;ENST00000359865;ENST00000400050;ENST00000306285	T;T;T;T	0.54279	0.58;0.58;0.58;0.58	5.91	-0.648	0.11464	.	0.299057	0.24640	N	0.036810	T	0.59046	0.2165	M	0.63843	1.955	0.09310	N	0.999995	D;D	0.89917	0.999;1.0	P;D	0.74023	0.893;0.982	T	0.50197	-0.8856	10	0.87932	D	0	-12.7546	2.3471	0.04274	0.4628:0.2188:0.1851:0.1333	.	1022;712	Q9Y4B5;Q9Y4B5-3	CC165_HUMAN;.	W	733;671;712;671;27	ENSP00000429556:R671W;ENSP00000352927:R712W;ENSP00000382924:R671W;ENSP00000303670:R27W	ENSP00000303670:R27W	R	+	1	2	CCDC165	8786353	0.113000	0.22115	0.030000	0.17652	0.985000	0.73830	-0.144000	0.10280	-0.117000	0.11872	-0.182000	0.12963	CGG	.	.		0.517	SOGA2-015	PUTATIVE	basic|appris_candidate_longest|exp_conf	protein_coding	protein_coding	OTTHUMT00000444141.1		
INSR	3643	hgsc.bcm.edu	37	19	7119538	7119538	+	Missense_Mutation	SNP	C	C	T			TCGA-5R-AAAM-01A-12D-A40R-10	TCGA-5R-AAAM-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9aba9aa4-9f40-456e-8aa4-fb9d20c57d93	bbe62607-8229-46d6-997d-47d1a49b89b0	g.chr19:7119538C>T	ENST00000302850.5	-	21	3858	c.3716G>A	c.(3715-3717)gGc>gAc	p.G1239D	INSR_ENST00000341500.5_Missense_Mutation_p.G1227D	NM_000208.2	NP_000199.2	P06213	INSR_HUMAN	insulin receptor	1239	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				activation of MAPK activity (GO:0000187)|activation of protein kinase activity (GO:0032147)|activation of protein kinase B activity (GO:0032148)|carbohydrate metabolic process (GO:0005975)|cellular response to growth factor stimulus (GO:0071363)|cellular response to insulin stimulus (GO:0032869)|epidermis development (GO:0008544)|exocrine pancreas development (GO:0031017)|G-protein coupled receptor signaling pathway (GO:0007186)|glucose homeostasis (GO:0042593)|heart morphogenesis (GO:0003007)|insulin receptor signaling pathway (GO:0008286)|male sex determination (GO:0030238)|peptidyl-tyrosine autophosphorylation (GO:0038083)|peptidyl-tyrosine phosphorylation (GO:0018108)|positive regulation of cell migration (GO:0030335)|positive regulation of cell proliferation (GO:0008284)|positive regulation of developmental growth (GO:0048639)|positive regulation of DNA replication (GO:0045740)|positive regulation of glucose import (GO:0046326)|positive regulation of glycogen biosynthetic process (GO:0045725)|positive regulation of glycolytic process (GO:0045821)|positive regulation of MAPK cascade (GO:0043410)|positive regulation of mitosis (GO:0045840)|positive regulation of nitric oxide biosynthetic process (GO:0045429)|positive regulation of protein kinase B signaling (GO:0051897)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of respiratory burst (GO:0060267)|protein autophosphorylation (GO:0046777)|protein heterotetramerization (GO:0051290)|regulation of embryonic development (GO:0045995)|regulation of transcription, DNA-templated (GO:0006355)|signal transduction by phosphorylation (GO:0023014)|transformation of host cell by virus (GO:0019087)	caveola (GO:0005901)|endosome membrane (GO:0010008)|extracellular vesicular exosome (GO:0070062)|insulin receptor complex (GO:0005899)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	ATP binding (GO:0005524)|GTP binding (GO:0005525)|insulin binding (GO:0043559)|insulin receptor substrate binding (GO:0043560)|insulin-activated receptor activity (GO:0005009)|insulin-like growth factor I binding (GO:0031994)|insulin-like growth factor II binding (GO:0031995)|insulin-like growth factor receptor binding (GO:0005159)|phosphatidylinositol 3-kinase binding (GO:0043548)|protein tyrosine kinase activity (GO:0004713)|PTB domain binding (GO:0051425)|receptor signaling protein tyrosine kinase activity (GO:0004716)			breast(1)|central_nervous_system(4)|endometrium(6)|kidney(2)|large_intestine(13)|lung(25)|ovary(4)|prostate(4)|skin(3)|stomach(2)|urinary_tract(2)	66					"""""""Insulin(DB00071)|""""Insulin(DB08914)|Insulin Aspart(DB01306)|Insulin Detemir(DB01307)|Insulin Glargine(DB00047)|Insulin Glulisine(DB01309)|Insulin Lispro(DB00046)|Insulin Regular(DB00030)|Mecasermin(DB01277)"""	ATTAGACAGGCCTTGGTAAGG	0.463																																					p.G1239D		Atlas-SNP	.											.	INSR	265	.	0			c.G3716A						.						168.0	138.0	148.0					19																	7119538		2203	4300	6503	SO:0001583	missense	3643	exon21			GACAGGCCTTGGT	M10051	CCDS12176.1, CCDS42487.1	19p13.3-p13.2	2013-02-11				ENSG00000171105		"""CD molecules"", ""Fibronectin type III domain containing"""	6091	protein-coding gene	gene with protein product		147670				2983222	Standard	NM_000208		Approved	CD220	uc002mgd.1	P06213		ENST00000302850.5:c.3716G>A	chr19.hg19:g.7119538C>T	ENSP00000303830:p.Gly1239Asp	131.0	0.0		116.0	17.0	NM_000208	Q17RW0|Q59H98|Q9UCB7|Q9UCB8|Q9UCB9	Missense_Mutation	SNP	ENST00000302850.5	hg19	CCDS12176.1	.	.	.	.	.	.	.	.	.	.	C	29.0	4.972756	0.92919	.	.	ENSG00000171105	ENST00000302850;ENST00000341500	D;D	0.90133	-2.62;-2.62	5.0	5.0	0.66597	Serine-threonine/tyrosine-protein kinase (2);Protein kinase-like domain (1);Tyrosine-protein kinase, catalytic domain (1);Protein kinase, catalytic domain (1);	0.000000	0.46758	D	0.000265	D	0.92374	0.7580	L	0.33137	0.985	0.80722	D	1	D;D	0.76494	0.999;0.999	D;D	0.79108	0.986;0.992	D	0.93378	0.6741	10	0.72032	D	0.01	.	15.8435	0.78868	0.0:1.0:0.0:0.0	.	1227;1239	P06213-2;P06213	.;INSR_HUMAN	D	1239;1227	ENSP00000303830:G1239D;ENSP00000342838:G1227D	ENSP00000303830:G1239D	G	-	2	0	INSR	7070538	1.000000	0.71417	1.000000	0.80357	0.990000	0.78478	7.485000	0.81204	2.322000	0.78497	0.449000	0.29647	GGC	.	.		0.463	INSR-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000458544.1		
KMT2B	9757	hgsc.bcm.edu	37	19	36222961	36222961	+	Nonsense_Mutation	SNP	C	C	T			TCGA-5R-AAAM-01A-12D-A40R-10	TCGA-5R-AAAM-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9aba9aa4-9f40-456e-8aa4-fb9d20c57d93	bbe62607-8229-46d6-997d-47d1a49b89b0	g.chr19:36222961C>T	ENST00000222270.7	+	27	5590	c.5590C>T	c.(5590-5592)Cga>Tga	p.R1864*	KMT2B_ENST00000420124.1_Nonsense_Mutation_p.R1864*|KMT2B_ENST00000607650.1_RNA	NM_014727.1	NP_055542.1	Q9UMN6	KMT2B_HUMAN	lysine (K)-specific methyltransferase 2B	1864					chromatin-mediated maintenance of transcription (GO:0048096)|gene silencing (GO:0016458)|histone H3-K4 methylation (GO:0051568)|histone H3-K4 trimethylation (GO:0080182)|oocyte differentiation (GO:0009994)|ovarian follicle development (GO:0001541)|ovulation (GO:0030728)|regulation of histone H3-K4 methylation (GO:0051569)|transcription, DNA-templated (GO:0006351)	histone methyltransferase complex (GO:0035097)|nucleus (GO:0005634)	DNA binding (GO:0003677)|histone methyltransferase activity (H3-K4 specific) (GO:0042800)|sequence-specific DNA binding transcription factor activity (GO:0003700)|zinc ion binding (GO:0008270)										TTCGGGGGCTCGAATCAAAGT	0.662																																					p.R1864X		Atlas-SNP	.											MLL4,colon,carcinoma,0,3	MLL4	229	.	0			c.C5590T						.						20.0	22.0	21.0					19																	36222961		1889	4099	5988	SO:0001587	stop_gained	8085	exon27			GGGGCTCGAATCA	AJ007041	CCDS46055.1	19q13.1	2014-02-18			ENSG00000105663	ENSG00000272333		"""Chromatin-modifying enzymes / K-methyltransferases"""	15840	protein-coding gene	gene with protein product	"""myeloid/lymphoid or mixed-lineage leukemia (trithorax homolog, Drosophila) 4"""	606834				10409430, 10637508	Standard	XM_006723513		Approved	KIAA0304, MLL2, TRX2, HRX2, WBP7, MLL1B, MLL4		Q9UMN6	OTTHUMG00000048119	ENST00000222270.7:c.5590C>T	chr19.hg19:g.36222961C>T	ENSP00000222270:p.Arg1864*	69.0	0.0		68.0	17.0	NM_014727	O15022|O95836|Q96GP2|Q96IP3|Q9UK25|Q9Y668|Q9Y669	Nonsense_Mutation	SNP	ENST00000222270.7	hg19	CCDS46055.1	.	.	.	.	.	.	.	.	.	.	C	44	10.759291	0.99462	.	.	ENSG00000105663	ENST00000222270;ENST00000420124	.	.	.	5.33	4.24	0.50183	.	0.000000	0.36665	N	0.002463	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	14.8877	0.70582	0.1434:0.8566:0.0:0.0	.	.	.	.	X	1864	.	ENSP00000222270:R1864X	R	+	1	2	AD000671.1	40914801	0.998000	0.40836	1.000000	0.80357	0.962000	0.63368	2.373000	0.44266	2.659000	0.90383	0.655000	0.94253	CGA	.	.		0.662	KMT2B-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_014727	
FBXO17	115290	hgsc.bcm.edu	37	19	39435635	39435635	+	Nonsense_Mutation	SNP	G	G	A			TCGA-5R-AAAM-01A-12D-A40R-10	TCGA-5R-AAAM-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9aba9aa4-9f40-456e-8aa4-fb9d20c57d93	bbe62607-8229-46d6-997d-47d1a49b89b0	g.chr19:39435635G>A	ENST00000292852.4	-	5	1008	c.667C>T	c.(667-669)Cag>Tag	p.Q223*	FBXO17_ENST00000595329.1_Nonsense_Mutation_p.Q223*|SARS2_ENST00000448145.2_Nonsense_Mutation_p.Q58*|CTC-360G5.8_ENST00000599996.1_Missense_Mutation_p.S127L	NM_024907.5	NP_079183.4	Q96EF6	FBX17_HUMAN	F-box protein 17	223	FBA. {ECO:0000255|PROSITE- ProRule:PRU00482}.					SCF ubiquitin ligase complex (GO:0019005)	glycoprotein binding (GO:0001948)			breast(1)|endometrium(1)|large_intestine(1)|lung(3)|prostate(1)	7	all_cancers(60;8.37e-07)|all_lung(34;3.71e-07)|Lung NSC(34;4.17e-07)|all_epithelial(25;1.13e-06)|Ovarian(47;0.0454)		Lung(45;0.000419)|LUSC - Lung squamous cell carcinoma(53;0.000554)			TCAGTCCACTGAAGGACCGGG	0.612																																					p.Q232X		Atlas-SNP	.											.	FBXO17	42	.	0			c.C694T						.						74.0	68.0	70.0					19																	39435635		2203	4300	6503	SO:0001587	stop_gained	115290	exon5			TCCACTGAAGGAC	AF386743	CCDS12526.1	19q13.2	2010-07-02	2004-06-15	2004-06-16		ENSG00000269190		"""F-boxes /  ""other"""""	18754	protein-coding gene	gene with protein product	"""F-box only protein 26"""	609094	"""F-box only protein 17"""	FBXO26			Standard	NM_148169		Approved	FBG4, FLJ25205, MGC9379, FLJ11798, Fbx17		Q96EF6		ENST00000292852.4:c.667C>T	chr19.hg19:g.39435635G>A	ENSP00000292852:p.Gln223*	106.0	0.0		103.0	10.0	NM_148169	Q96LQ4	Nonsense_Mutation	SNP	ENST00000292852.4	hg19	CCDS12526.1	.	.	.	.	.	.	.	.	.	.	G	20.5	4.005405	0.74932	.	.	ENSG00000104835	ENST00000448145;ENST00000392076;ENST00000292852	.	.	.	5.45	4.34	0.51931	.	0.000000	0.53938	D	0.000046	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	0.30854	T	0.27	.	10.9866	0.47526	0.0:0.0:0.814:0.186	.	.	.	.	X	58;232;223	.	ENSP00000292852:Q223X	Q	-	1	0	FBXO17	44127475	1.000000	0.71417	1.000000	0.80357	0.140000	0.21249	3.425000	0.52771	2.716000	0.92895	0.467000	0.42956	CAG	.	.		0.612	FBXO17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000463273.1	NM_024907	
PSG9	5678	hgsc.bcm.edu	37	19	43766112	43766112	+	Nonsense_Mutation	SNP	A	A	T	rs139948336		TCGA-5R-AAAM-01A-12D-A40R-10	TCGA-5R-AAAM-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9aba9aa4-9f40-456e-8aa4-fb9d20c57d93	bbe62607-8229-46d6-997d-47d1a49b89b0	g.chr19:43766112A>T	ENST00000270077.3	-	3	705	c.609T>A	c.(607-609)taT>taA	p.Y203*	PSG9_ENST00000593948.1_Nonsense_Mutation_p.Y203*|PSG9_ENST00000443718.3_Intron|PSG9_ENST00000596730.1_Intron|PSG9_ENST00000291752.5_Intron|PSG9_ENST00000244293.7_Nonsense_Mutation_p.Y203*|PSG9_ENST00000418820.2_Intron	NM_002784.3	NP_002775.3	Q00887	PSG9_HUMAN	pregnancy specific beta-1-glycoprotein 9	203	Ig-like C2-type 1.			Y -> C (in Ref. 1; CAA35612). {ECO:0000305}.	female pregnancy (GO:0007565)	extracellular region (GO:0005576)				central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(9)|lung(15)|ovary(1)|prostate(2)|skin(4)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	41		Prostate(69;0.00682)				CACCAAATAGATAGAGGGTCC	0.507																																					p.Y203X		Atlas-SNP	.											.	PSG9	77	.	0			c.T609A						.						207.0	208.0	208.0					19																	43766112		2203	4298	6501	SO:0001587	stop_gained	5678	exon3			AAATAGATAGAGG	M34481	CCDS12618.1	19q13.2	2013-01-29			ENSG00000183668	ENSG00000183668		"""Immunoglobulin superfamily / V-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	9526	protein-coding gene	gene with protein product		176398		PSG11		7806221	Standard	XM_005259076		Approved	PSGII	uc002owd.4	Q00887	OTTHUMG00000182826	ENST00000270077.3:c.609T>A	chr19.hg19:g.43766112A>T	ENSP00000270077:p.Tyr203*	89.0	0.0		102.0	23.0	NM_002784	B2R869|Q15227|Q15236|Q15237|Q8WW78|Q9UQ73	Nonsense_Mutation	SNP	ENST00000270077.3	hg19	CCDS12618.1	.	.	.	.	.	.	.	.	.	.	N	15.14	2.744589	0.49151	.	.	ENSG00000183668	ENST00000270077;ENST00000435220;ENST00000244293	.	.	.	2.12	2.12	0.27331	.	.	.	.	.	.	.	.	.	.	.	0.19300	N	0.999977	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	6.2622	0.20907	1.0:0.0:0.0:0.0	.	.	.	.	X	203;164;203	.	ENSP00000244293:Y203X	Y	-	3	2	PSG9	48457952	0.000000	0.05858	0.001000	0.08648	0.002000	0.02628	-0.773000	0.04689	0.715000	0.32103	0.163000	0.16589	TAT	.	A|0.999;G|0.001		0.507	PSG9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000323065.1	NM_002784	
IRGQ	126298	hgsc.bcm.edu	37	19	44096253	44096253	+	Silent	SNP	G	G	A			TCGA-5R-AAAM-01A-12D-A40R-10	TCGA-5R-AAAM-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9aba9aa4-9f40-456e-8aa4-fb9d20c57d93	bbe62607-8229-46d6-997d-47d1a49b89b0	g.chr19:44096253G>A	ENST00000602269.1	-	2	1982	c.1797C>T	c.(1795-1797)ggC>ggT	p.G599G	L34079.2_ENST00000594374.1_Intron|IRGQ_ENST00000601520.1_Intron|IRGQ_ENST00000422989.1_Silent_p.G599G			Q8WZA9	IRGQ_HUMAN	immunity-related GTPase family, Q	599	Ala-rich.									endometrium(2)|large_intestine(4)|lung(6)|ovary(2)|pancreas(1)|prostate(3)	18		Prostate(69;0.0199)				GCAGCAGGACGCCGTGAGCCG	0.701																																					p.G599G		Atlas-SNP	.											.	IRGQ	40	.	0			c.C1797T						.						33.0	40.0	38.0					19																	44096253		2192	4277	6469	SO:0001819	synonymous_variant	126298	exon3			CAGGACGCCGTGA	AF322648	CCDS33040.1	19q13.31	2013-07-03	2005-10-31	2005-10-31		ENSG00000167378			24868	protein-coding gene	gene with protein product			"""immunity-related GTPase family, Q1"""	IRGQ1		16277747	Standard	NM_001007561		Approved	FKSG27	uc010eiv.2	Q8WZA9		ENST00000602269.1:c.1797C>T	chr19.hg19:g.44096253G>A		146.0	0.0		93.0	9.0	NM_001007561	B2RNP3	Silent	SNP	ENST00000602269.1	hg19	CCDS33040.1																																																																																			.	.		0.701	IRGQ-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000463205.1	NM_001007561	
LILRA6	79168	hgsc.bcm.edu	37	19	54744224	54744224	+	Missense_Mutation	SNP	C	C	A			TCGA-5R-AAAM-01A-12D-A40R-10	TCGA-5R-AAAM-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9aba9aa4-9f40-456e-8aa4-fb9d20c57d93	bbe62607-8229-46d6-997d-47d1a49b89b0	g.chr19:54744224C>A	ENST00000396365.2	-	6	1223	c.1184G>T	c.(1183-1185)aGg>aTg	p.R395M	LILRA6_ENST00000270464.5_Intron|LILRA6_ENST00000440558.2_Intron|LILRA6_ENST00000245621.5_Missense_Mutation_p.R395M|LILRA6_ENST00000391735.3_3'UTR|LILRB3_ENST00000407860.2_Intron|LILRA6_ENST00000419410.2_Missense_Mutation_p.R395M	NM_024318.2	NP_077294	Q6PI73	LIRA6_HUMAN	leukocyte immunoglobulin-like receptor, subfamily A (with TM domain), member 6	395	Ig-like C2-type 2.				immune system process (GO:0002376)	integral component of membrane (GO:0016021)				central_nervous_system(1)|endometrium(3)|kidney(3)|large_intestine(4)|lung(20)|ovary(3)|skin(2)|urinary_tract(2)	38	all_cancers(19;0.00723)|all_epithelial(19;0.00389)|all_lung(19;0.0175)|Lung NSC(19;0.0325)|Ovarian(34;0.19)			GBM - Glioblastoma multiforme(193;0.105)		GCCGTAGCACCTGTAGGTCCC	0.602																																					p.R395M		Atlas-SNP	.											.	LILRA6	75	.	0			c.G1184T						.						75.0	104.0	94.0					19																	54744224		2203	4300	6503	SO:0001583	missense	79168	exon6			TAGCACCTGTAGG	AF041262	CCDS42610.1	19q13.4	2013-01-11	2005-05-17	2005-05-17	ENSG00000244482	ENSG00000244482		"""Leukocyte immunoglobulin-like receptors"", ""CD molecules"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	15495	protein-coding gene	gene with protein product			"""leukocyte immunoglobulin-like receptor, subfamily B (with TM and ITIM domains), member 6"""	LILRB6		10941842	Standard	NM_024318		Approved	ILT8, CD85b		Q6PI73	OTTHUMG00000066635	ENST00000396365.2:c.1184G>T	chr19.hg19:g.54744224C>A	ENSP00000379651:p.Arg395Met	239.0	0.0		238.0	18.0	NM_024318		Missense_Mutation	SNP	ENST00000396365.2	hg19	CCDS42610.1	.	.	.	.	.	.	.	.	.	.	C	15.35	2.808881	0.50421	.	.	ENSG00000244482	ENST00000419410;ENST00000421123;ENST00000396365;ENST00000245621	T;T;T	0.03301	3.98;3.98;3.98	2.39	1.33	0.21861	Immunoglobulin subtype (1);Immunoglobulin (1);Immunoglobulin-like fold (1);	0.408932	0.18095	N	0.151861	T	0.28532	0.0706	H	0.99668	4.69	0.80722	D	1	D;B;D	0.89917	1.0;0.148;1.0	D;B;D	0.91635	0.998;0.015;0.999	T	0.10337	-1.0634	10	0.87932	D	0	.	4.3828	0.11302	0.0:0.7999:0.0:0.2001	.	395;395;395	C9JFH3;Q6PI73;D3YTC4	.;LIRA6_HUMAN;.	M	395	ENSP00000411227:R395M;ENSP00000379651:R395M;ENSP00000245621:R395M	ENSP00000245621:R395M	R	-	2	0	LILRA6	59436036	0.004000	0.15560	0.999000	0.59377	0.235000	0.25334	1.259000	0.32956	1.360000	0.45960	0.195000	0.17529	AGG	.	.		0.602	LILRA6-003	NOVEL	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000313725.1	NM_024318	
TTLL9	164395	hgsc.bcm.edu	37	20	30510825	30510825	+	Silent	SNP	G	G	A			TCGA-5R-AAAM-01A-12D-A40R-10	TCGA-5R-AAAM-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9aba9aa4-9f40-456e-8aa4-fb9d20c57d93	bbe62607-8229-46d6-997d-47d1a49b89b0	g.chr20:30510825G>A	ENST00000375938.4	+	8	886	c.633G>A	c.(631-633)caG>caA	p.Q211Q	TTLL9_ENST00000310998.4_Silent_p.Q161Q|TTLL9_ENST00000375934.4_Silent_p.Q193Q|TTLL9_ENST00000535842.1_Silent_p.Q211Q|TTLL9_ENST00000375921.2_Silent_p.Q138Q|TTLL9_ENST00000375922.4_Silent_p.Q138Q			Q3SXZ7	TTLL9_HUMAN	tubulin tyrosine ligase-like family, member 9	211	TTL. {ECO:0000255|PROSITE- ProRule:PRU00568}.				cellular protein modification process (GO:0006464)	cilium (GO:0005929)|cytoplasm (GO:0005737)|microtubule (GO:0005874)	ligase activity (GO:0016874)			breast(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(8)|lung(8)|ovary(2)|prostate(1)|upper_aerodigestive_tract(1)	26			Colorectal(19;0.00306)|COAD - Colon adenocarcinoma(19;0.0347)			ATGTGGCTCAGCGTTACATTG	0.403																																					p.Q211Q		Atlas-SNP	.											.	TTLL9	95	.	0			c.G633A						.						150.0	152.0	151.0					20																	30510825		2027	4194	6221	SO:0001819	synonymous_variant	164395	exon8			GGCTCAGCGTTAC	AL031658	CCDS42863.1	20q11	2013-02-14	2005-07-28	2005-07-28		ENSG00000131044		"""Tubulin tyrosine ligase-like family"""	16118	protein-coding gene	gene with protein product			"""chromosome 20 open reading frame 125"""	C20orf125		15890843	Standard	NM_001008409		Approved	dJ310O13.1	uc010gdx.1	Q3SXZ7		ENST00000375938.4:c.633G>A	chr20.hg19:g.30510825G>A		81.0	0.0		103.0	7.0	NM_001008409	A6NH06|A6NIS5|B3KSG8|Q3SXZ8|Q5JYS3|Q5JYS4	Silent	SNP	ENST00000375938.4	hg19	CCDS42863.1																																																																																			.	.		0.403	TTLL9-205	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_001008409	
EDN3	1908	hgsc.bcm.edu	37	20	57876550	57876550	+	Silent	SNP	T	T	C			TCGA-5R-AAAM-01A-12D-A40R-10	TCGA-5R-AAAM-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9aba9aa4-9f40-456e-8aa4-fb9d20c57d93	bbe62607-8229-46d6-997d-47d1a49b89b0	g.chr20:57876550T>C	ENST00000337938.2	+	2	524	c.138T>C	c.(136-138)tgT>tgC	p.C46C	EDN3_ENST00000371028.2_Silent_p.C46C|EDN3_ENST00000395654.3_Silent_p.C46C|EDN3_ENST00000371025.3_Silent_p.C46C|EDN3_ENST00000311585.7_Silent_p.C46C	NM_207034.1	NP_996917.1	P14138	EDN3_HUMAN	endothelin 3	46					blood circulation (GO:0008015)|cell surface receptor signaling pathway (GO:0007166)|cell-cell signaling (GO:0007267)|inositol phosphate-mediated signaling (GO:0048016)|melanocyte differentiation (GO:0030318)|multicellular organismal development (GO:0007275)|neural crest cell migration (GO:0001755)|neuron differentiation (GO:0030182)|neutrophil chemotaxis (GO:0030593)|peptide hormone secretion (GO:0030072)|positive regulation of cell proliferation (GO:0008284)|positive regulation of heart rate (GO:0010460)|positive regulation of hormone secretion (GO:0046887)|positive regulation of leukocyte chemotaxis (GO:0002690)|positive regulation of MAP kinase activity (GO:0043406)|positive regulation of mitosis (GO:0045840)|regulation of developmental pigmentation (GO:0048070)|regulation of systemic arterial blood pressure by endothelin (GO:0003100)|regulation of vasoconstriction (GO:0019229)|signal transduction (GO:0007165)|vasoconstriction (GO:0042310)|vein smooth muscle contraction (GO:0014826)	extracellular region (GO:0005576)|extracellular space (GO:0005615)	hormone activity (GO:0005179)|receptor binding (GO:0005102)			endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(2)|liver(1)|lung(9)|skin(2)|upper_aerodigestive_tract(2)	19	all_lung(29;0.0115)					AGGGGGACTGTGAAGAGACTG	0.672																																					p.C46C		Atlas-SNP	.											.	EDN3	83	.	0			c.T138C						.						28.0	32.0	31.0					20																	57876550		2203	4300	6503	SO:0001819	synonymous_variant	1908	exon2			GGACTGTGAAGAG	X52001	CCDS13477.1, CCDS13478.1, CCDS13479.1	20q13.2-q13.3	2013-02-26			ENSG00000124205	ENSG00000124205		"""Endogenous ligands"""	3178	protein-coding gene	gene with protein product		131242					Standard	NM_000114		Approved	ET3	uc002yaq.3	P14138	OTTHUMG00000032867	ENST00000337938.2:c.138T>C	chr20.hg19:g.57876550T>C		109.0	0.0		111.0	14.0	NM_207034	E1P5I5|Q03229|Q7Z6D2|Q9UGT7	Silent	SNP	ENST00000337938.2	hg19	CCDS13477.1																																																																																			.	.		0.672	EDN3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000079919.2	NM_000114	
TOP3B	8940	hgsc.bcm.edu	37	22	22314746	22314746	+	Missense_Mutation	SNP	C	C	T			TCGA-5R-AAAM-01A-12D-A40R-10	TCGA-5R-AAAM-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9aba9aa4-9f40-456e-8aa4-fb9d20c57d93	bbe62607-8229-46d6-997d-47d1a49b89b0	g.chr22:22314746C>T	ENST00000398793.2	-	14	2035	c.1601G>A	c.(1600-1602)cGg>cAg	p.R534Q	TOP3B_ENST00000357179.5_Missense_Mutation_p.R534Q|TOP3B_ENST00000413067.2_3'UTR	NM_003935.3	NP_003926.1	O95985	TOP3B_HUMAN	topoisomerase (DNA) III beta	534					chromosome segregation (GO:0007059)|DNA topological change (GO:0006265)	condensed chromosome (GO:0000793)|nucleus (GO:0005634)	DNA binding (GO:0003677)|DNA topoisomerase activity (GO:0003916)|DNA topoisomerase type I activity (GO:0003917)|poly(A) RNA binding (GO:0044822)			breast(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(4)|lung(9)|ovary(1)	26	Colorectal(54;0.105)			READ - Rectum adenocarcinoma(21;0.145)		GGGCTTGAGCCGGCGCCCGCT	0.612																																					p.R534Q		Atlas-SNP	.											.	TOP3B	107	.	0			c.G1601A						.						96.0	77.0	84.0					22																	22314746		2203	4300	6503	SO:0001583	missense	8940	exon14			TTGAGCCGGCGCC	AF017146	CCDS13797.1	22q11.22	2011-05-24			ENSG00000100038	ENSG00000100038			11993	protein-coding gene	gene with protein product		603582				9786842, 9074928	Standard	XM_005261811		Approved		uc002zvs.3	O95985	OTTHUMG00000167438	ENST00000398793.2:c.1601G>A	chr22.hg19:g.22314746C>T	ENSP00000381773:p.Arg534Gln	71.0	0.0		70.0	11.0	NM_003935	A0M8Q3|Q9BUP5	Missense_Mutation	SNP	ENST00000398793.2	hg19	CCDS13797.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	22.8|22.8	4.334934|4.334934	0.81801|0.81801	.|.	.|.	ENSG00000100038|ENSG00000100038	ENST00000457270|ENST00000357179;ENST00000398793	.|T;T	.|0.21734	.|1.99;1.99	5.69|5.69	5.69|5.69	0.88448|0.88448	.|DNA topoisomerase, type IA, core domain (1);DNA topoisomerase, type IA, central (1);DNA topoisomerase, type IA, DNA-binding (1);DNA topoisomerase, type IA, central region, subdomain 1 (1);	.|0.151961	.|0.64402	.|D	.|0.000020	T|T	0.31263|0.31263	0.0791|0.0791	L|L	0.58583|0.58583	1.82|1.82	0.80722|0.80722	D|D	1|1	.|P;P;P	.|0.43231	.|0.801;0.801;0.763	.|B;B;B	.|0.43658	.|0.426;0.426;0.3	T|T	0.02713|0.02713	-1.1120|-1.1120	5|10	.|0.62326	.|D	.|0.03	.|.	19.8208|19.8208	0.96592|0.96592	0.0:1.0:0.0:0.0|0.0:1.0:0.0:0.0	.|.	.|79;534;534	.|B3KU89;O95985;O95985-2	.|.;TOP3B_HUMAN;.	S|Q	329|534	.|ENSP00000349705:R534Q;ENSP00000381773:R534Q	.|ENSP00000349705:R534Q	G|R	-|-	1|2	0|0	TOP3B|TOP3B	20644746|20644746	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.895000|0.895000	0.52256|0.52256	3.291000|3.291000	0.51764|0.51764	2.688000|2.688000	0.91661|0.91661	0.563000|0.563000	0.77884|0.77884	GGC|CGG	.	.		0.612	TOP3B-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000320251.1	NM_003935	
TCF20	6942	hgsc.bcm.edu	37	22	42610966	42610967	+	Nonsense_Mutation	DNP	GC	GC	AA			TCGA-5R-AAAM-01A-12D-A40R-10	TCGA-5R-AAAM-10A-01D-A40U-10	G|C	G|C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9aba9aa4-9f40-456e-8aa4-fb9d20c57d93	bbe62607-8229-46d6-997d-47d1a49b89b0	g.chr22:42610966_42610967GC>AA	ENST00000359486.3	-	1	481_482	c.345_346GC>TT	c.(343-348)gtGCag>gtTTag	p.Q116*	TCF20_ENST00000335626.4_Nonsense_Mutation_p.Q116*	NM_005650.1	NP_005641.1	Q9UGU0	TCF20_HUMAN	transcription factor 20 (AR1)	116					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|poly(A) RNA binding (GO:0044822)|transcription coactivator activity (GO:0003713)|zinc ion binding (GO:0008270)			breast(1)|central_nervous_system(1)|cervix(1)|endometrium(5)|kidney(7)|large_intestine(13)|lung(22)|ovary(5)|prostate(1)|skin(2)|soft_tissue(1)|upper_aerodigestive_tract(2)|urinary_tract(5)	66						CCATAGCTCTGCACAGGCCCAG	0.574																																					p.Q116X|p.V115V		Atlas-SNP	.											.	TCF20	164	.	0			c.C346T|c.G345T						.																																			SO:0001587	stop_gained	6942	exon1			AGCTCTGCACAGG|GCTCTGCACAGGC	U19345	CCDS14032.1, CCDS14033.1	22q13.3	2011-02-08			ENSG00000100207	ENSG00000100207			11631	protein-coding gene	gene with protein product	"""stromelysin-1 platelet-derived growth factor-responsive element binding protein"""	603107				9730594, 10995766	Standard	NM_005650		Approved	AR1, SPBP	uc003bcj.1	Q9UGU0	OTTHUMG00000150920	ENST00000359486.3:c.345_346delinsAA	chr22.hg19:g.42610966_42610967delinsAA	ENSP00000352463:p.Gln116*	89.0	0.0		96.0|97.0	40.0	NM_181492	A9JX12|O14528|Q13078|Q4V353|Q9H4M0	Nonsense_Mutation|Silent	SNP	ENST00000359486.3	hg19	CCDS14033.1																																																																																			.	.		0.574	TCF20-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000320531.1	NM_181492	
NHS	4810	hgsc.bcm.edu	37	X	17743756	17743756	+	Silent	SNP	A	A	G			TCGA-5R-AAAM-01A-12D-A40R-10	TCGA-5R-AAAM-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9aba9aa4-9f40-456e-8aa4-fb9d20c57d93	bbe62607-8229-46d6-997d-47d1a49b89b0	g.chrX:17743756A>G	ENST00000380060.3	+	6	1805	c.1467A>G	c.(1465-1467)gaA>gaG	p.E489E	NHS_ENST00000398097.3_Silent_p.E333E	NM_198270.2	NP_938011.1	Q6T4R5	NHS_HUMAN	Nance-Horan syndrome (congenital cataracts and dental anomalies)	510					cell differentiation (GO:0030154)|lens development in camera-type eye (GO:0002088)	cell projection (GO:0042995)|cytoplasm (GO:0005737)|plasma membrane (GO:0005886)|tight junction (GO:0005923)				breast(5)|central_nervous_system(2)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(17)|liver(1)|lung(26)|ovary(2)|prostate(1)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)	71	Hepatocellular(33;0.183)					TTCCCCGGGAAGGTAATAGAG	0.522																																					p.E489E		Atlas-SNP	.											.	NHS	302	.	0			c.A1467G						.						86.0	81.0	82.0					X																	17743756		2203	4300	6503	SO:0001819	synonymous_variant	4810	exon6			CCGGGAAGGTAAT		CCDS14181.1, CCDS48087.1	Xp22.3-p21.1	2014-06-18			ENSG00000188158	ENSG00000188158			7820	protein-coding gene	gene with protein product		300457					Standard	NM_001136024		Approved		uc004cxx.3	Q6T4R5	OTTHUMG00000022799	ENST00000380060.3:c.1467A>G	chrX.hg19:g.17743756A>G		133.0	0.0		129.0	13.0	NM_198270	B7ZVX8|E2DH69|Q5J7Q0|Q5J7Q1|Q68DR5	Silent	SNP	ENST00000380060.3	hg19	CCDS14181.1																																																																																			.	.		0.522	NHS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000059120.1	NM_198270	
CACNA1F	778	hgsc.bcm.edu	37	X	49065046	49065046	+	Silent	SNP	G	G	A			TCGA-5R-AAAM-01A-12D-A40R-10	TCGA-5R-AAAM-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9aba9aa4-9f40-456e-8aa4-fb9d20c57d93	bbe62607-8229-46d6-997d-47d1a49b89b0	g.chrX:49065046G>A	ENST00000376265.2	-	43	5146	c.5085C>T	c.(5083-5085)ccC>ccT	p.P1695P	CACNA1F_ENST00000376251.1_Silent_p.P1630P|CACNA1F_ENST00000323022.5_Silent_p.P1684P	NM_005183.2	NP_005174.2	O60840	CAC1F_HUMAN	calcium channel, voltage-dependent, L type, alpha 1F subunit	1695					axonogenesis (GO:0007409)|calcium ion import (GO:0070509)|cellular calcium ion homeostasis (GO:0006874)|dendrite morphogenesis (GO:0048813)|detection of light stimulus involved in visual perception (GO:0050908)|membrane depolarization during action potential (GO:0086010)|retina development in camera-type eye (GO:0060041)|visual perception (GO:0007601)	integral component of membrane (GO:0016021)|perikaryon (GO:0043204)|photoreceptor outer segment (GO:0001750)|voltage-gated calcium channel complex (GO:0005891)	high voltage-gated calcium channel activity (GO:0008331)|metal ion binding (GO:0046872)|voltage-gated calcium channel activity (GO:0005245)			autonomic_ganglia(1)|breast(8)|central_nervous_system(3)|endometrium(14)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(17)|lung(24)|ovary(5)|prostate(3)|skin(4)|urinary_tract(1)	85					Cinnarizine(DB00568)|Clevidipine(DB04920)|Dronedarone(DB04855)|Nimodipine(DB00393)|Spironolactone(DB00421)|Verapamil(DB00661)	CATCATCACTGGGCCCAAAGG	0.587																																					p.P1695P		Atlas-SNP	.											.	CACNA1F	218	.	0			c.C5085T						.						67.0	57.0	60.0					X																	49065046		2203	4300	6503	SO:0001819	synonymous_variant	778	exon43			ATCACTGGGCCCA	AA019975	CCDS35253.1, CCDS59166.1, CCDS59167.1	Xp11.23	2013-01-23	2007-02-16		ENSG00000102001	ENSG00000102001		"""Calcium channel subunits"", ""Voltage-gated ion channels / Calcium channels"""	1393	protein-coding gene	gene with protein product		300110	"""Aland island eye disease (Forsius-Eriksson ocular albinism, ocular albinism type 2)"""	CSNB2, AIED		9344658, 9662400, 16382099, 12111638, 17525176	Standard	NM_005183		Approved	Cav1.4, JM8, JMC8, CSNBX2, CORDX3, CSNB2A, OA2	uc010nip.3	O60840	OTTHUMG00000022703	ENST00000376265.2:c.5085C>T	chrX.hg19:g.49065046G>A		160.0	0.0		135.0	18.0	NM_005183	A6NI29|F5CIQ9|O43901|O95226|Q9UHB1	Silent	SNP	ENST00000376265.2	hg19	CCDS35253.1																																																																																			.	.		0.587	CACNA1F-007	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000358157.1	NM_005183	
PPP1R3F	89801	hgsc.bcm.edu	37	X	49126707	49126707	+	Silent	SNP	G	G	T			TCGA-5R-AAAM-01A-12D-A40R-10	TCGA-5R-AAAM-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9aba9aa4-9f40-456e-8aa4-fb9d20c57d93	bbe62607-8229-46d6-997d-47d1a49b89b0	g.chrX:49126707G>T	ENST00000055335.6	+	1	391	c.375G>T	c.(373-375)ccG>ccT	p.P125P	LL0XNC01-7P3.1_ENST00000602455.1_lincRNA|PPP1R3F_ENST00000495799.1_Intron|PPP1R3F_ENST00000466508.1_Intron|PPP1R3F_ENST00000438316.1_Intron	NM_033215.4	NP_149992.3	Q6ZSY5	PPR3F_HUMAN	protein phosphatase 1, regulatory subunit 3F	125					regulation of glycogen (starch) synthase activity (GO:2000465)|regulation of glycogen biosynthetic process (GO:0005979)	integral component of membrane (GO:0016021)|membrane (GO:0016020)	glycogen binding (GO:2001069)|protein phosphatase binding (GO:0019903)			endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(8)|lung(8)|ovary(2)|skin(4)	27	Ovarian(276;0.236)					CGCCCGCGCCGGGCCGTCTGG	0.746																																					p.P125P		Atlas-SNP	.											.	PPP1R3F	56	.	0			c.G375T						.						3.0	4.0	3.0					X																	49126707		1668	3402	5070	SO:0001819	synonymous_variant	89801	exon1			CGCGCCGGGCCGT		CCDS35254.1, CCDS55415.1	Xp11.23	2012-04-17	2011-10-04		ENSG00000049769	ENSG00000049769		"""Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"""	14944	protein-coding gene	gene with protein product			"""protein phosphatase 1, regulatory (inhibitor) subunit 3F"""			11948623	Standard	NM_033215		Approved	Hb2E	uc004dnh.2	Q6ZSY5	OTTHUMG00000024139	ENST00000055335.6:c.375G>T	chrX.hg19:g.49126707G>T		81.0	0.0		97.0	4.0	NM_033215	A2VDJ8|B3KPW2|E9PCM3	Silent	SNP	ENST00000055335.6	hg19	CCDS35254.1																																																																																			.	.		0.746	PPP1R3F-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000060819.2	NM_033215	
BRWD3	254065	hgsc.bcm.edu	37	X	79971674	79971674	+	Silent	SNP	T	T	C			TCGA-5R-AAAM-01A-12D-A40R-10	TCGA-5R-AAAM-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9aba9aa4-9f40-456e-8aa4-fb9d20c57d93	bbe62607-8229-46d6-997d-47d1a49b89b0	g.chrX:79971674T>C	ENST00000373275.4	-	20	2523	c.2307A>G	c.(2305-2307)ccA>ccG	p.P769P	BRWD3_ENST00000473691.1_5'UTR	NM_153252.4	NP_694984	Q6RI45	BRWD3_HUMAN	bromodomain and WD repeat domain containing 3	769					cytoskeleton organization (GO:0007010)|regulation of cell shape (GO:0008360)					breast(4)|cervix(1)|endometrium(12)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(18)|lung(39)|ovary(4)|prostate(2)|skin(3)	87						TAGTGTAAGATGGCTTTTTCT	0.353																																					p.P769P		Atlas-SNP	.											.	BRWD3	251	.	0			c.A2307G						.						176.0	152.0	160.0					X																	79971674		2201	4298	6499	SO:0001819	synonymous_variant	254065	exon20			GTAAGATGGCTTT		CCDS14447.1	Xq21.1	2013-01-09			ENSG00000165288	ENSG00000165288		"""WD repeat domain containing"""	17342	protein-coding gene	gene with protein product		300553				15543602, 16094372	Standard	NM_153252		Approved	FLJ38568, MRX93	uc004edt.3	Q6RI45	OTTHUMG00000021908	ENST00000373275.4:c.2307A>G	chrX.hg19:g.79971674T>C		105.0	0.0		84.0	8.0	NM_153252	C9IZ39|C9J3F3|Q2T9J6|Q5JRN1|Q6RI37|Q6RI42|Q6RI44|Q8N916	Silent	SNP	ENST00000373275.4	hg19	CCDS14447.1																																																																																			.	.		0.353	BRWD3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057344.1	NM_153252	
TEX13A	56157	hgsc.bcm.edu	37	X	104464278	104464278	+	Splice_Site	SNP	A	A	C	rs371523271		TCGA-5R-AAAM-01A-12D-A40R-10	TCGA-5R-AAAM-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9aba9aa4-9f40-456e-8aa4-fb9d20c57d93	bbe62607-8229-46d6-997d-47d1a49b89b0	g.chrX:104464278A>C	ENST00000413579.1	-	4	710	c.599T>G	c.(598-600)gTt>gGt	p.V200G	TEX13A_ENST00000372575.1_Missense_Mutation_p.C200W|IL1RAPL2_ENST00000372582.1_Intron|IL1RAPL2_ENST00000344799.4_Intron|TEX13A_ENST00000372578.3_Missense_Mutation_p.C200W			Q9BXU3	TX13A_HUMAN	testis expressed 13A	200							zinc ion binding (GO:0008270)			large_intestine(5)|ovary(2)|upper_aerodigestive_tract(1)	8						ACAACCTCCAACATCCCCTCT	0.652																																					.		Atlas-SNP	.											.	TEX13A	55	.	0			c.598+1T>G						.						16.0	19.0	18.0					X																	104464278		2040	4059	6099	SO:0001630	splice_region_variant	56157	exon5			CCTCCAACATCCC	AF285597	CCDS76005.1	Xq28	2012-04-20	2007-03-13		ENSG00000133149	ENSG00000268629			11735	protein-coding gene	gene with protein product		300312	"""testis expressed sequence 13A"""			11279525	Standard	NM_031274		Approved		uc004ema.3	Q9BXU3	OTTHUMG00000022133	ENST00000413579.1:c.600+1T>G	chrX.hg19:g.104464278A>C		0.0	0.0		6.0	4.0	NM_031274	B1B1G8|Q32NB6	Splice_Site	SNP	ENST00000413579.1	hg19		.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	6.024|6.024	0.372734|0.372734	0.11409|0.11409	.|.	.|.	ENSG00000133149|ENSG00000133149	ENST00000372578;ENST00000372575|ENST00000413579	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	0.22898|0.22898	0.0553|0.0553	.|.	.|.	.|.	0.09310|0.09310	N|N	1|1	.|.	.|.	.|.	.|.	.|.	.|.	T|T	0.28964|0.28964	-1.0027|-1.0027	3|3	0.72032|0.23302	D|T	0.01|0.38	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	W|G	200|200	.|.	ENSP00000361656:C200W|ENSP00000399753:V200G	C|V	-|-	3|2	2|0	TEX13A|TEX13A	104350934|104350934	0.000000|0.000000	0.05858|0.05858	0.000000|0.000000	0.03702|0.03702	0.099000|0.099000	0.18886|0.18886	-0.302000|-0.302000	0.08221|0.08221	0.000000|0.000000	0.14550|0.14550	0.000000|0.000000	0.15137|0.15137	TGT|GTT	.	.		0.652	TEX13A-201	KNOWN	basic|appris_principal	protein_coding	protein_coding		NM_031274	Missense_Mutation
LRCH2	57631	hgsc.bcm.edu	37	X	114357372	114357372	+	Missense_Mutation	SNP	T	T	C			TCGA-5R-AAAM-01A-12D-A40R-10	TCGA-5R-AAAM-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9aba9aa4-9f40-456e-8aa4-fb9d20c57d93	bbe62607-8229-46d6-997d-47d1a49b89b0	g.chrX:114357372T>C	ENST00000317135.8	-	19	2081	c.2051A>G	c.(2050-2052)cAt>cGt	p.H684R	LRCH2_ENST00000538422.1_Missense_Mutation_p.H667R	NM_020871.3	NP_065922.3	Q5VUJ6	LRCH2_HUMAN	leucine-rich repeats and calponin homology (CH) domain containing 2	684	CH. {ECO:0000255|PROSITE- ProRule:PRU00044}.									breast(1)|endometrium(4)|kidney(3)|large_intestine(3)|lung(6)|ovary(1)|prostate(1)	19						TGGCCTTATATGATTGGCTAA	0.373																																					p.H684R		Atlas-SNP	.											.	LRCH2	138	.	0			c.A2051G						.						113.0	103.0	106.0					X																	114357372		1975	4152	6127	SO:0001583	missense	57631	exon19			CTTATATGATTGG	AB040928	CCDS48155.1, CCDS59175.1	Xq24	2008-02-05			ENSG00000130224	ENSG00000130224			29292	protein-coding gene	gene with protein product						10819331	Standard	NM_020871		Approved	KIAA1495	uc010nqe.3	Q5VUJ6	OTTHUMG00000022233	ENST00000317135.8:c.2051A>G	chrX.hg19:g.114357372T>C	ENSP00000325091:p.His684Arg	237.0	0.0		246.0	28.0	NM_020871	F5H2T1|Q08AD5|Q9HA88|Q9P233	Missense_Mutation	SNP	ENST00000317135.8	hg19	CCDS48155.1	.	.	.	.	.	.	.	.	.	.	T	15.06	2.720323	0.48728	.	.	ENSG00000130224	ENST00000317135;ENST00000536655;ENST00000538422	D;D	0.94687	-3.49;-3.49	5.39	5.39	0.77823	Calponin homology domain (5);	0.176916	0.48286	D	0.000183	D	0.95796	0.8632	L	0.60957	1.885	0.58432	D	0.999997	D;B	0.61697	0.99;0.361	P;B	0.62491	0.903;0.217	D	0.96106	0.9073	10	0.87932	D	0	-15.544	13.1876	0.59691	0.0:0.0:0.0:1.0	.	684;667	Q5VUJ6;F5H2T1	LRCH2_HUMAN;.	R	684;163;667	ENSP00000325091:H684R;ENSP00000439366:H667R	ENSP00000325091:H684R	H	-	2	0	LRCH2	114263628	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	7.525000	0.81892	1.995000	0.58328	0.345000	0.21793	CAT	.	.		0.373	LRCH2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000057971.2	NM_020871	
TENM1	10178	hgsc.bcm.edu	37	X	123514879	123514879	+	Missense_Mutation	SNP	T	T	C			TCGA-5R-AAAM-01A-12D-A40R-10	TCGA-5R-AAAM-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9aba9aa4-9f40-456e-8aa4-fb9d20c57d93	bbe62607-8229-46d6-997d-47d1a49b89b0	g.chrX:123514879T>C	ENST00000371130.3	-	31	7748	c.7685A>G	c.(7684-7686)aAc>aGc	p.N2562S	STAG2_ENST00000469481.1_Intron|TENM1_ENST00000422452.2_Missense_Mutation_p.N2569S	NM_014253.3	NP_055068.2	Q9UKZ4	TEN1_HUMAN	teneurin transmembrane protein 1	2562					immune response (GO:0006955)|negative regulation of cell proliferation (GO:0008285)|nervous system development (GO:0007399)|neuropeptide signaling pathway (GO:0007218)|positive regulation of actin filament polymerization (GO:0030838)|positive regulation of filopodium assembly (GO:0051491)|positive regulation of intracellular protein transport (GO:0090316)|positive regulation of MAP kinase activity (GO:0043406)|positive regulation of peptidyl-serine phosphorylation (GO:0033138)|regulation of transcription from RNA polymerase III promoter (GO:0006359)|response to stress (GO:0006950)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|endoplasmic reticulum (GO:0005783)|extracellular region (GO:0005576)|Golgi apparatus (GO:0005794)|integral component of plasma membrane (GO:0005887)|nuclear matrix (GO:0016363)|nuclear speck (GO:0016607)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)	heparin binding (GO:0008201)|protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)										AAAATGTAGGTTTTCCAGGTA	0.493																																					p.N2569S		Atlas-SNP	.											.	.	.	.	0			c.A7706G						.						92.0	80.0	84.0					X																	123514879		2203	4300	6503	SO:0001583	missense	10178	exon32			TGTAGGTTTTCCA	AF100772	CCDS14609.1, CCDS55488.1	Xq25	2012-10-02	2012-10-02	2012-10-02	ENSG00000009694	ENSG00000009694			8117	protein-coding gene	gene with protein product		300588	"""tenascin M"", ""odz, odd Oz/ten-m homolog 1 (Drosophila)"""	ODZ3, TNM, ODZ1		10331952, 10341219	Standard	NM_001163278		Approved	TEN-M1	uc010nqy.3	Q9UKZ4	OTTHUMG00000022721	ENST00000371130.3:c.7685A>G	chrX.hg19:g.123514879T>C	ENSP00000360171:p.Asn2562Ser	154.0	0.0		207.0	13.0	NM_001163278	B2RTR5|Q5JZ17	Missense_Mutation	SNP	ENST00000371130.3	hg19	CCDS14609.1	.	.	.	.	.	.	.	.	.	.	T	9.967	1.224370	0.22457	.	.	ENSG00000009694	ENST00000371130;ENST00000422452	D;D	0.85484	-1.99;-1.95	5.83	5.83	0.93111	.	0.091536	0.85682	D	0.000000	T	0.81113	0.4755	L	0.46157	1.445	0.37779	D	0.926945	B;B;B	0.24483	0.104;0.049;0.059	B;B;B	0.19148	0.024;0.024;0.021	T	0.78833	-0.2048	10	0.33940	T	0.23	.	15.1686	0.72850	0.0:0.0:0.0:1.0	.	2568;2569;2562	B7ZMH4;B2RTR5;Q9UKZ4	.;.;TEN1_HUMAN	S	2562;2569	ENSP00000360171:N2562S;ENSP00000403954:N2569S	ENSP00000360171:N2562S	N	-	2	0	ODZ1	123342560	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	3.021000	0.49651	1.965000	0.57142	0.486000	0.48141	AAC	.	.		0.493	TENM1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000058985.1	NM_014253	
PLXNA3	55558	hgsc.bcm.edu	37	X	153689565	153689565	+	Silent	SNP	C	C	T			TCGA-5R-AAAM-01A-12D-A40R-10	TCGA-5R-AAAM-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9aba9aa4-9f40-456e-8aa4-fb9d20c57d93	bbe62607-8229-46d6-997d-47d1a49b89b0	g.chrX:153689565C>T	ENST00000369682.3	+	3	896	c.721C>T	c.(721-723)Ctg>Ttg	p.L241L		NM_017514.3	NP_059984.3	P51805	PLXA3_HUMAN	plexin A3	241	Sema. {ECO:0000255|PROSITE- ProRule:PRU00352}.				axon guidance (GO:0007411)|branchiomotor neuron axon guidance (GO:0021785)|facial nerve structural organization (GO:0021612)|hippocampus development (GO:0021766)|multicellular organismal development (GO:0007275)|negative chemotaxis (GO:0050919)|negative regulation of axon extension involved in axon guidance (GO:0048843)|positive regulation of cytoskeleton organization (GO:0051495)|pyramidal neuron development (GO:0021860)|semaphorin-plexin signaling pathway (GO:0071526)|semaphorin-plexin signaling pathway involved in axon guidance (GO:1902287)|trigeminal nerve structural organization (GO:0021637)	integral component of membrane (GO:0016021)|intracellular (GO:0005622)|membrane (GO:0016020)|plasma membrane (GO:0005886)|semaphorin receptor complex (GO:0002116)	semaphorin receptor activity (GO:0017154)|transmembrane signaling receptor activity (GO:0004888)			breast(2)|central_nervous_system(2)|cervix(2)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(2)|lung(26)|ovary(2)|prostate(1)|upper_aerodigestive_tract(4)|urinary_tract(1)	48	all_cancers(53;5.05e-16)|all_epithelial(53;1.87e-10)|all_lung(58;1.84e-07)|Lung NSC(58;5.84e-07)|all_hematologic(71;2.45e-06)|Acute lymphoblastic leukemia(192;6.56e-05)|Breast(217;0.176)					CTTCCTGACGCTGCAGCTGGA	0.557																																					p.L241L		Atlas-SNP	.											.	PLXNA3	156	.	0			c.C721T						.						115.0	90.0	98.0					X																	153689565		2203	4300	6503	SO:0001819	synonymous_variant	55558	exon3			CTGACGCTGCAGC	X74609	CCDS14752.1	Xq28	2008-02-05			ENSG00000130827	ENSG00000130827		"""Plexins"""	9101	protein-coding gene	gene with protein product		300022		PLXN4		8248200, 8733135	Standard	NM_017514		Approved	SEX, XAP-6, 6.3, Plxn3	uc004flm.3	P51805	OTTHUMG00000033290	ENST00000369682.3:c.721C>T	chrX.hg19:g.153689565C>T		131.0	0.0		107.0	14.0	NM_017514	Q5HY36	Silent	SNP	ENST00000369682.3	hg19	CCDS14752.1																																																																																			.	.		0.557	PLXNA3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000081634.1	NM_017514	
MT-ND5	4540	hgsc.bcm.edu	37	M	12806	12806	+	Silent	SNP	G	G	A			TCGA-5R-AAAM-01A-12D-A40R-10	TCGA-5R-AAAM-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9aba9aa4-9f40-456e-8aa4-fb9d20c57d93	bbe62607-8229-46d6-997d-47d1a49b89b0	g.chrM:12806G>A	ENST00000361567.2	+	1	470	c.470G>A	c.(469-471)tGa>tAa	p.*157*	MT-TE_ENST00000387459.1_RNA|MT-TR_ENST00000387439.1_RNA|MT-TH_ENST00000387441.1_RNA|MT-CYB_ENST00000361789.2_5'Flank|MT-TS2_ENST00000387449.1_RNA|MT-TL2_ENST00000387456.1_RNA|MT-TG_ENST00000387429.1_RNA			P03915	NU5M_HUMAN	mitochondrially encoded NADH dehydrogenase 5	157					cellular metabolic process (GO:0044237)|mitochondrial electron transport, NADH to ubiquinone (GO:0006120)|respiratory electron transport chain (GO:0022904)|small molecule metabolic process (GO:0044281)	integral component of membrane (GO:0016021)|mitochondrial inner membrane (GO:0005743)|mitochondrial respiratory chain complex I (GO:0005747)	NADH dehydrogenase (ubiquinone) activity (GO:0008137)			breast(4)|endometrium(29)|kidney(33)|pancreas(1)|prostate(7)	74						GCTCATCAGTTGATGATACGC	0.443																																					p.W157X		Atlas-SNP	.											.	.	.	.	0			c.G470A						.																																			SO:0001819	synonymous_variant	0	exon1			TCAGTTGATGATA			mitochondria	2011-07-04	2005-02-15	2005-02-16	ENSG00000198786	ENSG00000198786	1.6.5.3	"""Mitochondrial respiratory chain complex / Complex I"""	7461	protein-coding gene	gene with protein product	"""complex I ND5 subunit"", ""NADH-ubiquinone oxidoreductase chain 5"""	516005	"""NADH dehydrogenase 5"""	MTND5			Standard			Approved	ND5, NAD5		P03915		ENST00000361567.2:c.470G>A	chrM.hg19:g.12806G>A		40.0	0.0		58.0	5.0	ENST00000361567	Q34773|Q8WCY3	Nonsense_Mutation	SNP	ENST00000361567.2	hg19																																																																																				.	.		0.443	MT-ND5-201	KNOWN	basic|appris_principal	protein_coding	protein_coding		YP_003024036	
MT-ND5	4540	hgsc.bcm.edu	37	M	13787	13787	+	Missense_Mutation	SNP	T	T	C			TCGA-5R-AAAM-01A-12D-A40R-10	TCGA-5R-AAAM-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9aba9aa4-9f40-456e-8aa4-fb9d20c57d93	bbe62607-8229-46d6-997d-47d1a49b89b0	g.chrM:13787T>C	ENST00000361567.2	+	1	1451	c.1451T>C	c.(1450-1452)cTc>cCc	p.L484P	MT-TE_ENST00000387459.1_RNA|MT-TT_ENST00000387460.2_RNA|MT-TP_ENST00000387461.2_RNA|MT-TH_ENST00000387441.1_RNA|MT-CYB_ENST00000361789.2_5'Flank|MT-TS2_ENST00000387449.1_RNA|MT-TL2_ENST00000387456.1_RNA			P03915	NU5M_HUMAN	mitochondrially encoded NADH dehydrogenase 5	484					cellular metabolic process (GO:0044237)|mitochondrial electron transport, NADH to ubiquinone (GO:0006120)|respiratory electron transport chain (GO:0022904)|small molecule metabolic process (GO:0044281)	integral component of membrane (GO:0016021)|mitochondrial inner membrane (GO:0005743)|mitochondrial respiratory chain complex I (GO:0005747)	NADH dehydrogenase (ubiquinone) activity (GO:0008137)			breast(4)|endometrium(29)|kidney(33)|pancreas(1)|prostate(7)	74						AACAATCCCCCTCTACCTAAA	0.468																																					p.L484P		Atlas-SNP	.											.	.	.	.	0			c.T1451C						.																																			SO:0001583	missense	0	exon1			TCCCCCTCTACCT			mitochondria	2011-07-04	2005-02-15	2005-02-16	ENSG00000198786	ENSG00000198786	1.6.5.3	"""Mitochondrial respiratory chain complex / Complex I"""	7461	protein-coding gene	gene with protein product	"""complex I ND5 subunit"", ""NADH-ubiquinone oxidoreductase chain 5"""	516005	"""NADH dehydrogenase 5"""	MTND5			Standard			Approved	ND5, NAD5		P03915		ENST00000361567.2:c.1451T>C	chrM.hg19:g.13787T>C	ENSP00000354813:p.Leu484Pro	35.0	0.0		63.0	10.0	ENST00000361567	Q34773|Q8WCY3	Missense_Mutation	SNP	ENST00000361567.2	hg19																																																																																				.	.		0.468	MT-ND5-201	KNOWN	basic|appris_principal	protein_coding	protein_coding		YP_003024036	
CDC42BPA	8476	hgsc.bcm.edu	37	1	227222368	227222369	+	Frame_Shift_Ins	INS	-	-	C			TCGA-5R-AAAM-01A-12D-A40R-10	TCGA-5R-AAAM-10A-01D-A40U-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9aba9aa4-9f40-456e-8aa4-fb9d20c57d93	bbe62607-8229-46d6-997d-47d1a49b89b0	g.chr1:227222368_227222369insC	ENST00000366769.3	-	25	4649_4650	c.3358_3359insG	c.(3358-3360)gtgfs	p.V1120fs	CDC42BPA_ENST00000366766.2_Frame_Shift_Ins_p.V1155fs|CDC42BPA_ENST00000334218.5_Frame_Shift_Ins_p.V1120fs|CDC42BPA_ENST00000366767.3_Frame_Shift_Ins_p.V1039fs|CDC42BPA_ENST00000366764.2_Frame_Shift_Ins_p.V1092fs|CDC42BPA_ENST00000366765.3_Frame_Shift_Ins_p.V1133fs|CDC42BPA_ENST00000535525.1_Frame_Shift_Ins_p.V1100fs	NM_003607.3	NP_003598.2			CDC42 binding protein kinase alpha (DMPK-like)											NS(1)|breast(4)|cervix(1)|endometrium(8)|kidney(8)|large_intestine(12)|lung(32)|ovary(2)|pancreas(1)|prostate(1)|skin(2)|stomach(3)|urinary_tract(2)	77		all_cancers(173;0.156)|Prostate(94;0.0792)				CATGTCAATCACTTGACTAATG	0.371																																					p.V1120fs		Atlas-Indel,Pindel	.											.	CDC42BPA	528	.	0			c.3359_3360insG						.																																			SO:0001589	frameshift_variant	8476	exon25			.	U59305	CCDS1558.1, CCDS1559.1	1q42.11	2011-11-23	2001-11-28		ENSG00000143776	ENSG00000143776			1737	protein-coding gene	gene with protein product	"""myotonic dystrophy kinase-related Cdc42-binding kinase"""	603412	"""CDC42-binding protein kinase alpha (DMPK-like)"""				Standard	NM_003607		Approved	MRCKA, PK428, FLJ23347, KIAA0451, MRCK	uc001hqr.3	Q5VT25	OTTHUMG00000037618	ENST00000366769.3:c.3359dupG	chr1.hg19:g.227222369_227222369dupC	ENSP00000355731:p.Val1120fs	52.0	0.0		54.0	15.0	NM_003607		Frame_Shift_Ins	INS	ENST00000366769.3	hg19	CCDS1558.1																																																																																			.	.		0.371	CDC42BPA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000091696.1	NM_014826	
NAV2	89797	hgsc.bcm.edu	37	11	20136228	20136228	+	Frame_Shift_Del	DEL	C	C	-			TCGA-5R-AAAM-01A-12D-A40R-10	TCGA-5R-AAAM-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9aba9aa4-9f40-456e-8aa4-fb9d20c57d93	bbe62607-8229-46d6-997d-47d1a49b89b0	g.chr11:20136228delC	ENST00000396087.3	+	40	7327	c.7228delC	c.(7228-7230)cctfs	p.P2411fs	NAV2_ENST00000360655.4_Frame_Shift_Del_p.P2288fs|NAV2_ENST00000349880.4_Frame_Shift_Del_p.P2352fs|NAV2_ENST00000311043.8_Frame_Shift_Del_p.P1416fs|NAV2_ENST00000533917.1_Frame_Shift_Del_p.P1416fs|NAV2_ENST00000396085.1_Frame_Shift_Del_p.P2355fs|NAV2_ENST00000540292.1_Frame_Shift_Del_p.P2342fs|NAV2_ENST00000527559.2_Frame_Shift_Del_p.P2340fs	NM_001244963.1	NP_001231892.1	Q8IVL1	NAV2_HUMAN	neuron navigator 2	2411					glossopharyngeal nerve development (GO:0021563)|locomotory behavior (GO:0007626)|optic nerve development (GO:0021554)|regulation of systemic arterial blood pressure by baroreceptor feedback (GO:0003025)|sensory perception of smell (GO:0007608)|sensory perception of sound (GO:0007605)|vagus nerve development (GO:0021564)	interstitial matrix (GO:0005614)|nucleus (GO:0005634)	ATP binding (GO:0005524)|helicase activity (GO:0004386)|heparin binding (GO:0008201)			NS(1)|breast(2)|central_nervous_system(5)|endometrium(15)|haematopoietic_and_lymphoid_tissue(2)|kidney(7)|large_intestine(26)|lung(38)|ovary(3)|pancreas(1)|prostate(7)|skin(5)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	116						GCACGAGTGGCCTCCCCTGCT	0.612																																					p.W2409fs		Atlas-INDEL	.											.	NAV2	255	.	0			c.7227delG						.						78.0	60.0	66.0					11																	20136228		2203	4300	6503	SO:0001589	frameshift_variant	89797	exon39			.	AB037840	CCDS7850.1, CCDS7851.2, CCDS44552.1, CCDS53612.1, CCDS58126.1	11p15.1	2008-07-18			ENSG00000166833	ENSG00000166833	3.6.1.1		15997	protein-coding gene	gene with protein product	"""pore membrane and/or filament interacting like protein 2"", ""retinoic acid inducible gene in neuroblastoma 1"", ""helicase, APC down-regulated 1"""	607026				12079279, 12062803	Standard	NM_145117		Approved	FLJ10633, FLJ11030, HELAD1, KIAA1419, POMFIL2, RAINB1, FLJ23707	uc010rdm.2	Q8IVL1	OTTHUMG00000151837	ENST00000396087.3:c.7228delC	chr11.hg19:g.20136228delC	ENSP00000379396:p.Pro2411fs	66.0	0.0		101.0	11.0	NM_001244963	A6NEC1|Q8IVK3|Q8IVK4|Q8IVK5|Q8IVK6|Q8IVK7|Q8IVK8|Q8NHC9|Q8NHD0|Q8TDE9|Q8TDF0|Q8TEB3|Q96B30|Q9NUZ6|Q9NVM7|Q9P2C8	Frame_Shift_Del	DEL	ENST00000396087.3	hg19	CCDS58126.1																																																																																			.	.		0.612	NAV2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000324112.1	NM_145117	
FAM47E-STBD1	100631383	hgsc.bcm.edu	37	4	77231109	77231148	+	Frame_Shift_Del	DEL	GGCCATGAGGATAAAGTGGTTCACGCATGGTGGGGGATTC	GGCCATGAGGATAAAGTGGTTCACGCATGGTGGGGGATTC	-	rs199743271|rs527950885|rs561957942|rs144679126|rs148507767	byFrequency	TCGA-5R-AAAM-01A-12D-A40R-10	TCGA-5R-AAAM-10A-01D-A40U-10	GGCCATGAGGATAAAGTGGTTCACGCATGGTGGGGGATTC	GGCCATGAGGATAAAGTGGTTCACGCATGGTGGGGGATTC	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9aba9aa4-9f40-456e-8aa4-fb9d20c57d93	bbe62607-8229-46d6-997d-47d1a49b89b0	g.chr4:77231109_77231148delGGCCATGAGGATAAAGTGGTTCACGCATGGTGGGGGATTC	ENST00000237642.6	+	2	1777_1816	c.1033_1072delGGCCATGAGGATAAAGTGGTTCACGCATGGTGGGGGATTC	c.(1033-1074)ggccatgaggataaagtggttcacgcatggtgggggattcacfs	p.GHEDKVVHAWWGIH345fs	FAM47E_ENST00000515604.1_3'UTR|FAM47E-STBD1_ENST00000539752.1_Frame_Shift_Del_p.GHEDKVVHAWWGIH196fs	NM_003943.4	NP_003934.1			FAM47E-STBD1 readthrough									p.W355L(1)									CCTAGAAACTGGCCATGAGGATAAAGTGGTTCACGCATGGTGGGGGATTCACTGATTCAG	0.463																																					p.344_357del		Pindel	.											.	STBD1	22	.	1	Substitution - Missense(1)	lung(1)	c.1032_1071del						.																																			SO:0001589	frameshift_variant	8987	exon2			.		CCDS58908.1	4q21.1	2013-04-23			ENSG00000118804	ENSG00000118804			44667	other	readthrough							Standard	NM_001242939		Approved				OTTHUMG00000160966	ENST00000237642.6:c.1033_1072delGGCCATGAGGATAAAGTGGTTCACGCATGGTGGGGGATTC	chr4.hg19:g.77231109_77231148delGGCCATGAGGATAAAGTGGTTCACGCATGGTGGGGGATTC	ENSP00000237642:p.Gly345fs	32.0	0.0		23.0	10.0	NM_003943		Frame_Shift_Del	DEL	ENST00000237642.6	hg19	CCDS3578.1																																																																																			.	.		0.463	FAM47E-STBD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252415.2		
PAPLN	89932	hgsc.bcm.edu	37	14	73729359	73729404	+	Frame_Shift_Del	DEL	AAAGCCCTGGCCTTCTGGTGGTCTCTGGCGGCAAGACCAACAGCCT	AAAGCCCTGGCCTTCTGGTGGTCTCTGGCGGCAAGACCAACAGCCT	-	rs371499346|rs201201042|rs200348311|rs563152502|rs577625666		TCGA-5R-AAAM-01A-12D-A40R-10	TCGA-5R-AAAM-10A-01D-A40U-10	AAAGCCCTGGCCTTCTGGTGGTCTCTGGCGGCAAGACCAACAGCCT	AAAGCCCTGGCCTTCTGGTGGTCTCTGGCGGCAAGACCAACAGCCT	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9aba9aa4-9f40-456e-8aa4-fb9d20c57d93	bbe62607-8229-46d6-997d-47d1a49b89b0	g.chr14:73729359_73729404delAAAGCCCTGGCCTTCTGGTGGTCTCTGGCGGCAAGACCAACAGCCT	ENST00000554301.1	+	18	2710_2755	c.2547_2592delAAAGCCCTGGCCTTCTGGTGGTCTCTGGCGGCAAGACCAACAGCCT	c.(2545-2592)agaaagccctggccttctggtggtctctggcggcaagaccaacagcctfs	p.RKPWPSGGLWRQDQQP849fs	PAPLN_ENST00000340738.5_Frame_Shift_Del_p.RKPWPSGGLWRQDQQP822fs|PAPLN_ENST00000381166.3_Frame_Shift_Del_p.RKPWPSGGLWRQDQQP849fs|PAPLN_ENST00000555445.1_Frame_Shift_Del_p.RKPWPSGGLWRQDQQP833fs|PAPLN_ENST00000427855.1_Frame_Shift_Del_p.RKPWPSGGLWRQDQQP849fs|PAPLN_ENST00000554314.1_3'UTR			O95428	PPN_HUMAN	papilin, proteoglycan-like sulfated glycoprotein	849						basement membrane (GO:0005604)	metalloendopeptidase activity (GO:0004222)|serine-type endopeptidase inhibitor activity (GO:0004867)|zinc ion binding (GO:0008270)			NS(2)|central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(4)|lung(11)|ovary(3)|pancreas(3)|prostate(5)|skin(3)|upper_aerodigestive_tract(3)	42				BRCA - Breast invasive adenocarcinoma(234;0.00394)|OV - Ovarian serous cystadenocarcinoma(108;0.0468)		CGGTGCAGAGAAAGCCCTGGCCTTCTGGTGGTCTCTGGCGGCAAGACCAACAGCCTGGGCCAGGGG	0.679																																					p.822_837del		Pindel	.											.	PAPLN	180	.	0			c.2465_2510del						.																																			SO:0001589	frameshift_variant	89932	exon18			.	BC042057	CCDS32114.1	14q24.2	2013-01-11				ENSG00000100767		"""Immunoglobulin superfamily / I-set domain containing"""	19262	protein-coding gene	gene with protein product						11076767, 19734141	Standard	NM_173462		Approved	MGC50452	uc001xnw.4	O95428		ENST00000554301.1:c.2547_2592delAAAGCCCTGGCCTTCTGGTGGTCTCTGGCGGCAAGACCAACAGCCT	chr14.hg19:g.73729359_73729404delAAAGCCCTGGCCTTCTGGTGGTCTCTGGCGGCAAGACCAACAGCCT	ENSP00000451803:p.Arg849fs	128.0	0.0		126.0	18.0	NM_173462	B4DES8|B4DGE6|Q659F2|Q6UXJ4|Q6ZNM1|Q6ZUJ0|Q7Z681|Q8IVU0	Frame_Shift_Del	DEL	ENST00000554301.1	hg19																																																																																				.	.		0.679	PAPLN-002	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000413182.1	NM_173462	
