#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
WNT7A	7476	hgsc.bcm.edu	37	3	13921289	13921289	+	Missense_Mutation	SNP	G	G	C	rs145718587	byFrequency	TCGA-5R-AA1D-01A-11D-A382-10	TCGA-5R-AA1D-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1510db4c-4fd4-4758-b172-d85cc12cbf3f	0719e29a-6ab4-4c61-96ad-a9e3162b45fd	g.chr3:13921289G>C	ENST00000285018.4	-	1	329	c.25C>G	c.(25-27)Ctg>Gtg	p.L9V	WNT7A_ENST00000497808.1_5'Flank	NM_004625.3	NP_004616.2	O00755	WNT7A_HUMAN	wingless-type MMTV integration site family, member 7A	9					asymmetric protein localization (GO:0008105)|canonical Wnt signaling pathway (GO:0060070)|cartilage condensation (GO:0001502)|cell fate commitment (GO:0045165)|cell proliferation in forebrain (GO:0021846)|cellular response to transforming growth factor beta stimulus (GO:0071560)|central nervous system vasculogenesis (GO:0022009)|cerebellar granule cell differentiation (GO:0021707)|chondrocyte differentiation (GO:0002062)|dorsal/ventral pattern formation (GO:0009953)|embryonic axis specification (GO:0000578)|embryonic digit morphogenesis (GO:0042733)|embryonic forelimb morphogenesis (GO:0035115)|embryonic hindlimb morphogenesis (GO:0035116)|establishment of cell polarity (GO:0030010)|lens fiber cell development (GO:0070307)|negative regulation of apoptotic process (GO:0043066)|negative regulation of neurogenesis (GO:0050768)|neuron differentiation (GO:0030182)|neurotransmitter secretion (GO:0007269)|non-canonical Wnt signaling pathway (GO:0035567)|oviduct development (GO:0060066)|palate development (GO:0060021)|positive regulation of canonical Wnt signaling pathway (GO:0090263)|positive regulation of epithelial cell proliferation involved in wound healing (GO:0060054)|positive regulation of JNK cascade (GO:0046330)|positive regulation of synapse assembly (GO:0051965)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of axon diameter (GO:0031133)|response to estradiol (GO:0032355)|sex differentiation (GO:0007548)|skeletal muscle satellite cell activation (GO:0014719)|skeletal muscle satellite cell maintenance involved in skeletal muscle regeneration (GO:0014834)|somatic stem cell division (GO:0048103)|somatic stem cell maintenance (GO:0035019)|stem cell development (GO:0048864)|synapse organization (GO:0050808)|uterus morphogenesis (GO:0061038)|Wnt signaling pathway involved in wound healing, spreading of epidermal cells (GO:0035659)	cell surface (GO:0009986)|endoplasmic reticulum lumen (GO:0005788)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|Golgi lumen (GO:0005796)|plasma membrane (GO:0005886)|proteinaceous extracellular matrix (GO:0005578)	cytokine activity (GO:0005125)|frizzled binding (GO:0005109)|receptor agonist activity (GO:0048018)|receptor binding (GO:0005102)			NS(1)|breast(2)|endometrium(1)|kidney(1)|large_intestine(2)|lung(11)|ovary(3)|skin(2)|upper_aerodigestive_tract(1)	24						AGGTGGCCCAGGCAGCGCCGC	0.697																																					p.L9V		Atlas-SNP	.											.	WNT7A	70	.	0			c.C25G						.						45.0	45.0	45.0					3																	13921289		2203	4300	6503	SO:0001583	missense	7476	exon1			GGCCCAGGCAGCG	D83175	CCDS2616.1	3p25	2008-07-18			ENSG00000154764	ENSG00000154764		"""Wingless-type MMTV integration sites"""	12786	protein-coding gene	gene with protein product	"""proto-oncogene Wnt7a protein"""	601570				8893824, 9161407	Standard	NM_004625		Approved		uc003bye.1	O00755	OTTHUMG00000129803	ENST00000285018.4:c.25C>G	chr3.hg19:g.13921289G>C	ENSP00000285018:p.Leu9Val	232.0	0.0		223.0	37.0	NM_004625	Q96H90|Q9Y560	Missense_Mutation	SNP	ENST00000285018.4	hg19	CCDS2616.1	.	.	.	.	.	.	.	.	.	.	G	9.589	1.125520	0.20959	.	.	ENSG00000154764	ENST00000285018	T	0.75938	-0.98	3.71	0.473	0.16763	.	0.078049	0.51477	D	0.000093	T	0.47021	0.1423	N	0.08118	0	0.24291	N	0.995163	B	0.02656	0.0	B	0.04013	0.001	T	0.32771	-0.9894	10	0.51188	T	0.08	.	3.4506	0.07496	0.2418:0.0:0.4479:0.3102	.	9	O00755	WNT7A_HUMAN	V	9	ENSP00000285018:L9V	ENSP00000285018:L9V	L	-	1	2	WNT7A	13896290	1.000000	0.71417	1.000000	0.80357	0.163000	0.22366	2.565000	0.45939	0.254000	0.21573	-0.142000	0.14014	CTG	.	G|1.000;A|0.000		0.697	WNT7A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252031.2	NM_004625	
CDH9	1007	hgsc.bcm.edu	37	5	26885762	26885762	+	Missense_Mutation	SNP	C	C	T			TCGA-5R-AA1D-01A-11D-A382-10	TCGA-5R-AA1D-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1510db4c-4fd4-4758-b172-d85cc12cbf3f	0719e29a-6ab4-4c61-96ad-a9e3162b45fd	g.chr5:26885762C>T	ENST00000231021.4	-	11	2015	c.1843G>A	c.(1843-1845)Gct>Act	p.A615T		NM_016279.3	NP_057363.3	Q9ULB4	CADH9_HUMAN	cadherin 9, type 2 (T1-cadherin)	615					adherens junction organization (GO:0034332)|cell junction assembly (GO:0034329)|cell-cell junction organization (GO:0045216)|homophilic cell adhesion (GO:0007156)|single organismal cell-cell adhesion (GO:0016337)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			breast(6)|endometrium(7)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(25)|lung(80)|ovary(5)|prostate(4)|skin(5)|upper_aerodigestive_tract(2)|urinary_tract(1)	137						GCAACGAGAGCTCCCGTGCTC	0.507																																					p.A615T	Melanoma(8;187 585 15745 40864 52829)	Atlas-SNP	.											CDH9,right_upper_lobe,carcinoma,0,1	CDH9	305	.	0			c.G1843A						.						77.0	66.0	70.0					5																	26885762		2203	4300	6503	SO:0001583	missense	1007	exon11			CGAGAGCTCCCGT	AB035302	CCDS3893.1	5p14	2010-01-26			ENSG00000113100	ENSG00000113100		"""Cadherins / Major cadherins"""	1768	protein-coding gene	gene with protein product		609974				2059658	Standard	NM_016279		Approved		uc003jgs.1	Q9ULB4	OTTHUMG00000090671	ENST00000231021.4:c.1843G>A	chr5.hg19:g.26885762C>T	ENSP00000231021:p.Ala615Thr	162.0	0.0		160.0	29.0	NM_016279	Q3B7I5	Missense_Mutation	SNP	ENST00000231021.4	hg19	CCDS3893.1	.	.	.	.	.	.	.	.	.	.	C	34	5.327459	0.95733	.	.	ENSG00000113100	ENST00000231021	T	0.59638	0.25	5.89	5.89	0.94794	.	0.000000	0.85682	D	0.000000	D	0.83427	0.5252	H	0.94582	3.555	0.80722	D	1	D;D	0.89917	0.998;1.0	D;D	0.79108	0.979;0.992	D	0.87302	0.2306	9	.	.	.	.	18.82	0.92092	0.0:1.0:0.0:0.0	.	208;615	B4DFP0;Q9ULB4	.;CADH9_HUMAN	T	615	ENSP00000231021:A615T	.	A	-	1	0	CDH9	26921519	1.000000	0.71417	0.231000	0.23993	0.971000	0.66376	7.781000	0.85668	2.797000	0.96272	0.563000	0.77884	GCT	.	.		0.507	CDH9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207352.1	NM_016279	
PON2	5445	hgsc.bcm.edu	37	7	95040997	95040997	+	Missense_Mutation	SNP	A	A	C			TCGA-5R-AA1D-01A-11D-A382-10	TCGA-5R-AA1D-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1510db4c-4fd4-4758-b172-d85cc12cbf3f	0719e29a-6ab4-4c61-96ad-a9e3162b45fd	g.chr7:95040997A>C	ENST00000222572.3	-	5	708	c.462T>G	c.(460-462)caT>caG	p.H154Q	PON2_ENST00000433091.2_Missense_Mutation_p.H142Q|PON2_ENST00000536183.1_Missense_Mutation_p.H175Q|PON2_ENST00000483292.1_5'UTR			Q15165	PON2_HUMAN	paraoxonase 2	154					aromatic compound catabolic process (GO:0019439)|response to oxidative stress (GO:0006979)	extracellular region (GO:0005576)|lysosome (GO:0005764)|mitochondrion (GO:0005739)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	arylesterase activity (GO:0004064)|identical protein binding (GO:0042802)|metal ion binding (GO:0046872)			breast(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(2)|lung(3)|prostate(1)	9	all_cancers(62;9.35e-11)|all_epithelial(64;3.37e-09)		STAD - Stomach adenocarcinoma(171;0.0151)			CTGTTTTCAGATGCAACAGAG	0.363																																					p.H154Q	GBM(42;803 823 13649 23368 31463)	Atlas-SNP	.											.	PON2	32	.	0			c.T462G						.						76.0	78.0	78.0					7																	95040997		2203	4300	6503	SO:0001583	missense	5445	exon5			TTTCAGATGCAAC	M63012, AF001601	CCDS5640.1, CCDS47644.1	7q21.3	2014-03-14			ENSG00000105854	ENSG00000105854	3.1.1.2	"""Paraoxonases"""	9205	protein-coding gene	gene with protein product	"""paraoxonase nirs"", ""arylesterase 2"""	602447				8661009, 9714608	Standard	XM_005250453		Approved		uc003unv.3	Q15165	OTTHUMG00000153948	ENST00000222572.3:c.462T>G	chr7.hg19:g.95040997A>C	ENSP00000222572:p.His154Gln	168.0	0.0		149.0	27.0	NM_000305	A4D1H7|B2RCP9|B4DJD5|O15114|O15115|O75856|Q5FBX7|Q86YL0	Missense_Mutation	SNP	ENST00000222572.3	hg19	CCDS5640.1	.	.	.	.	.	.	.	.	.	.	A	13.15	2.152480	0.38021	.	.	ENSG00000105854	ENST00000536183;ENST00000355659;ENST00000433091;ENST00000222572	T;T;T	0.42513	2.32;0.97;2.32	4.94	-3.32	0.04973	Six-bladed beta-propeller, TolB-like (1);	0.093439	0.64402	D	0.000001	T	0.65344	0.2682	M	0.88241	2.94	0.51482	D	0.999924	D;D	0.89917	1.0;1.0	D;D	0.87578	0.998;0.998	T	0.73304	-0.4025	10	0.72032	D	0.01	-21.5209	15.3323	0.74223	0.3835:0.0:0.6165:0.0	.	154;154	A4D1H7;Q15165	.;PON2_HUMAN	Q	175;152;142;154	ENSP00000440282:H175Q;ENSP00000404622:H142Q;ENSP00000222572:H154Q	ENSP00000222572:H154Q	H	-	3	2	PON2	94878933	0.999000	0.42202	0.971000	0.41717	0.003000	0.03518	0.560000	0.23500	-0.448000	0.07128	0.528000	0.53228	CAT	.	.		0.363	PON2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000333142.1	NM_000305	
NLRP6	171389	hgsc.bcm.edu	37	11	281192	281192	+	Silent	SNP	G	G	T			TCGA-5R-AA1D-01A-11D-A382-10	TCGA-5R-AA1D-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1510db4c-4fd4-4758-b172-d85cc12cbf3f	0719e29a-6ab4-4c61-96ad-a9e3162b45fd	g.chr11:281192G>T	ENST00000312165.5	+	4	1458	c.1458G>T	c.(1456-1458)ccG>ccT	p.P486P	NLRP6_ENST00000534750.1_Silent_p.P486P	NM_138329.1	NP_612202.2	P59044	NALP6_HUMAN	NLR family, pyrin domain containing 6	486	NACHT. {ECO:0000255|PROSITE- ProRule:PRU00136}.				G-protein coupled receptor signaling pathway (GO:0007186)|negative regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043124)|negative regulation of immune response (GO:0050777)|negative regulation of MAPK cascade (GO:0043409)|negative regulation of toll-like receptor signaling pathway (GO:0034122)|regulation of inflammatory response (GO:0050727)|response to bacterium (GO:0009617)|wound healing (GO:0042060)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|vasopressin receptor activity (GO:0005000)			breast(1)|skin(1)|upper_aerodigestive_tract(2)	4		all_cancers(49;1.12e-06)|all_epithelial(84;0.000375)|Breast(177;0.00122)|Ovarian(85;0.0228)|Medulloblastoma(188;0.0321)|all_neural(188;0.0762)		all cancers(45;4.28e-28)|Epithelial(43;2.47e-27)|OV - Ovarian serous cystadenocarcinoma(40;4.66e-21)|BRCA - Breast invasive adenocarcinoma(625;3.57e-05)|Lung(200;0.0485)|LUSC - Lung squamous cell carcinoma(625;0.122)		AGGAGCTGCCGGGCGTGCTGG	0.612																																					p.P486P		Atlas-SNP	.											.	NLRP6	4	.	0			c.G1458T						.						79.0	79.0	79.0					11																	281192		2203	4300	6503	SO:0001819	synonymous_variant	171389	exon4			GCTGCCGGGCGTG	AF479748	CCDS7693.1, CCDS60680.1	11p15	2006-12-08	2006-12-08	2006-12-08	ENSG00000174885	ENSG00000174885		"""Nucleotide-binding domain and leucine rich repeat containing"""	22944	protein-coding gene	gene with protein product	"""nucleotide-binding oligomerization domain, leucine rich repeat and pyrin domain containing 6"""	609650	"""NACHT, leucine rich repeat and PYD containing 6"""	NALP6		12563287, 12019269	Standard	NM_138329		Approved	PYPAF5, PAN3, CLR11.4	uc010qvs.3	P59044	OTTHUMG00000119070	ENST00000312165.5:c.1458G>T	chr11.hg19:g.281192G>T		133.0	0.0		103.0	18.0	NM_138329	A8K9F3|E9PJZ8	Silent	SNP	ENST00000312165.5	hg19	CCDS7693.1																																																																																			.	.		0.612	NLRP6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000239283.1	NM_138329	
SAA4	6291	hgsc.bcm.edu	37	11	18254009	18254009	+	Missense_Mutation	SNP	A	A	T			TCGA-5R-AA1D-01A-11D-A382-10	TCGA-5R-AA1D-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1510db4c-4fd4-4758-b172-d85cc12cbf3f	0719e29a-6ab4-4c61-96ad-a9e3162b45fd	g.chr11:18254009A>T	ENST00000278222.4	-	3	343	c.163T>A	c.(163-165)Tat>Aat	p.Y55N	SAA2-SAA4_ENST00000524555.1_RNA	NM_006512.3	NP_006503.2	P35542	SAA4_HUMAN	serum amyloid A4, constitutive	55					acute-phase response (GO:0006953)	extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|high-density lipoprotein particle (GO:0034364)				haematopoietic_and_lymphoid_tissue(1)|large_intestine(3)|liver(1)|lung(6)|skin(1)|stomach(1)	13						CCCCGAGCATAGAGATATCTG	0.468																																					p.Y133N		Atlas-SNP	.											.	.	.	.	0			c.T397A						.						179.0	175.0	176.0					11																	18254009		2199	4293	6492	SO:0001583	missense	100528017	exon5			GAGCATAGAGATA	M81349	CCDS7832.1	11p15.1-p14	2008-07-21			ENSG00000148965	ENSG00000148965			10516	protein-coding gene	gene with protein product		104752				8325654	Standard	NM_006512		Approved	C-SAA, CSAA		P35542	OTTHUMG00000166483	ENST00000278222.4:c.163T>A	chr11.hg19:g.18254009A>T	ENSP00000278222:p.Tyr55Asn	131.0	0.0		103.0	18.0	NM_001199744	Q6FHJ4	Missense_Mutation	SNP	ENST00000278222.4	hg19	CCDS7832.1	.	.	.	.	.	.	.	.	.	.	A	10.76	1.440836	0.25900	.	.	ENSG00000148965	ENST00000278222	T	0.09817	2.94	3.26	0.932	0.19466	.	.	.	.	.	T	0.08891	0.0220	L	0.43152	1.355	0.33002	D	0.526322	P	0.43826	0.818	B	0.38985	0.287	T	0.24905	-1.0147	9	0.87932	D	0	-8.8289	5.6276	0.17490	0.3224:0.0:0.6776:0.0	.	55	P35542	SAA4_HUMAN	N	55	ENSP00000278222:Y55N	ENSP00000278222:Y55N	Y	-	1	0	SAA4	18210585	1.000000	0.71417	0.114000	0.21550	0.084000	0.17831	2.247000	0.43151	-0.129000	0.11620	-0.456000	0.05471	TAT	.	.		0.468	SAA4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000389988.1	NM_006512	
OTUB1	55611	hgsc.bcm.edu	37	11	63753947	63753947	+	Nonsense_Mutation	SNP	C	C	T			TCGA-5R-AA1D-01A-11D-A382-10	TCGA-5R-AA1D-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1510db4c-4fd4-4758-b172-d85cc12cbf3f	0719e29a-6ab4-4c61-96ad-a9e3162b45fd	g.chr11:63753947C>T	ENST00000538426.1	+	1	63	c.19C>T	c.(19-21)Cag>Tag	p.Q7*	OTUB1_ENST00000428192.2_Nonsense_Mutation_p.Q7*|AP000721.4_ENST00000535431.1_Missense_Mutation_p.S150L|OTUB1_ENST00000422031.2_Nonsense_Mutation_p.Q44*|OTUB1_ENST00000535715.1_Nonsense_Mutation_p.Q7*|OTUB1_ENST00000536443.1_3'UTR|OTUB1_ENST00000543004.1_Nonsense_Mutation_p.Q7*|OTUB1_ENST00000541478.1_Nonsense_Mutation_p.Q7*|OTUB1_ENST00000543988.1_5'Flank	NM_017670.2	NP_060140.2	Q96FW1	OTUB1_HUMAN	OTU deubiquitinase, ubiquitin aldehyde binding 1	7					cellular response to DNA damage stimulus (GO:0006974)|DNA repair (GO:0006281)|immune system process (GO:0002376)|negative regulation of double-strand break repair (GO:2000780)|negative regulation of histone H2A K63-linked ubiquitination (GO:1901315)|protein K48-linked deubiquitination (GO:0071108)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)	NEDD8-specific protease activity (GO:0019784)|omega peptidase activity (GO:0008242)|ubiquitin binding (GO:0043130)|ubiquitin protein ligase binding (GO:0031625)|ubiquitin-specific protease activity (GO:0004843)			breast(1)|endometrium(2)|kidney(1)|large_intestine(1)|lung(1)	6						GGAGGAACCTCAGCAGCAGAA	0.672																																					p.Q7X		Atlas-SNP	.											.	OTUB1	19	.	0			c.C19T						.						27.0	30.0	29.0					11																	63753947		2132	4179	6311	SO:0001587	stop_gained	55611	exon1			GAACCTCAGCAGC	AY177200	CCDS8055.1	11q13.1	2014-02-24	2014-02-24			ENSG00000167770		"""OTU domain containing"""	23077	protein-coding gene	gene with protein product		608337	"""OTU domain, ubiquitin aldehyde binding 1"""			12704427, 19383985	Standard	NM_017670		Approved	FLJ20113, FLJ40710	uc001nyf.1	Q96FW1		ENST00000538426.1:c.19C>T	chr11.hg19:g.63753947C>T	ENSP00000444357:p.Gln7*	159.0	0.0		124.0	15.0	NM_017670	Q32Q78|Q96II3|Q9NXQ4|Q9P0B8	Nonsense_Mutation	SNP	ENST00000538426.1	hg19	CCDS8055.1	.	.	.	.	.	.	.	.	.	.	c	35	5.521842	0.96416	.	.	ENSG00000167770	ENST00000541478;ENST00000535715;ENST00000428192;ENST00000422031;ENST00000538426;ENST00000543004	.	.	.	4.36	4.36	0.52297	.	.	.	.	.	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.38643	T	0.18	.	12.8577	0.57894	0.0:1.0:0.0:0.0	.	.	.	.	X	7;7;7;44;7;7	.	ENSP00000416973:Q44X	Q	+	1	0	OTUB1	63510523	1.000000	0.71417	1.000000	0.80357	0.695000	0.40330	1.417000	0.34770	2.155000	0.67459	0.552000	0.68991	CAG	.	.		0.672	OTUB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000396277.1	NM_017670	
ADAMTS20	80070	hgsc.bcm.edu	37	12	43748039	43748039	+	Silent	SNP	A	A	G			TCGA-5R-AA1D-01A-11D-A382-10	TCGA-5R-AA1D-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1510db4c-4fd4-4758-b172-d85cc12cbf3f	0719e29a-6ab4-4c61-96ad-a9e3162b45fd	g.chr12:43748039A>G	ENST00000389420.3	-	39	5705	c.5706T>C	c.(5704-5706)acT>acC	p.T1902T		NM_025003.3	NP_079279.3	P59510	ATS20_HUMAN	ADAM metallopeptidase with thrombospondin type 1 motif, 20	1902	GON. {ECO:0000255|PROSITE- ProRule:PRU00383}.				extracellular matrix organization (GO:0030198)|negative regulation of apoptotic process (GO:0043066)|positive regulation of melanocyte differentiation (GO:0045636)|positive regulation of signal transduction (GO:0009967)	extracellular space (GO:0005615)|proteinaceous extracellular matrix (GO:0005578)	metalloendopeptidase activity (GO:0004222)|zinc ion binding (GO:0008270)			breast(1)|central_nervous_system(6)|endometrium(3)|kidney(4)|large_intestine(11)|liver(1)|lung(43)|ovary(4)|pancreas(3)|prostate(5)|skin(12)|upper_aerodigestive_tract(1)|urinary_tract(1)	95	all_cancers(12;2.6e-05)|Lung SC(27;0.184)	Lung NSC(34;0.0569)|all_lung(34;0.129)		GBM - Glioblastoma multiforme(48;0.0473)		GGAGACCAGTAGTCATGTGAG	0.398																																					p.T1902T		Atlas-SNP	.											.	ADAMTS20	635	.	0			c.T5706C						.						67.0	59.0	61.0					12																	43748039		2202	4299	6501	SO:0001819	synonymous_variant	80070	exon39			ACCAGTAGTCATG	AF488804	CCDS31778.2	12q12	2005-08-19	2005-08-19			ENSG00000173157		"""ADAM metallopeptidases with thrombospondin type 1 motif"""	17178	protein-coding gene	gene with protein product		611681	"""a disintegrin-like and metalloprotease (reprolysin type) with thrombospondin type 1 motif, 20"""			12514189, 12562771	Standard	NM_025003		Approved	GON-1	uc010skx.2	P59510		ENST00000389420.3:c.5706T>C	chr12.hg19:g.43748039A>G		84.0	0.0		84.0	17.0	NM_025003	A6NNC9|J3QT00	Silent	SNP	ENST00000389420.3	hg19	CCDS31778.2																																																																																			.	.		0.398	ADAMTS20-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000403643.1	NM_025003	
APOF	319	hgsc.bcm.edu	37	12	56755172	56755172	+	Missense_Mutation	SNP	G	G	A			TCGA-5R-AA1D-01A-11D-A382-10	TCGA-5R-AA1D-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1510db4c-4fd4-4758-b172-d85cc12cbf3f	0719e29a-6ab4-4c61-96ad-a9e3162b45fd	g.chr12:56755172G>A	ENST00000398189.3	-	2	895	c.818C>T	c.(817-819)aCc>aTc	p.T273I	STAT2_ENST00000314128.4_5'Flank|STAT2_ENST00000418572.2_5'Flank|APOF_ENST00000541105.1_Missense_Mutation_p.T255I|STAT2_ENST00000557235.1_5'Flank	NM_001638.2	NP_001629.1	Q13790	APOF_HUMAN	apolipoprotein F	273					cholesterol efflux (GO:0033344)|cholesterol metabolic process (GO:0008203)|lipid metabolic process (GO:0006629)|lipid transport (GO:0006869)|triglyceride metabolic process (GO:0006641)	extracellular region (GO:0005576)|high-density lipoprotein particle (GO:0034364)|low-density lipoprotein particle (GO:0034362)	cholesterol binding (GO:0015485)|lipid transporter activity (GO:0005319)|receptor binding (GO:0005102)			breast(1)|lung(3)|prostate(1)|stomach(1)	6						CTCCTTGGTGGTCTCCGGCTG	0.473																																					p.T273I		Atlas-SNP	.											.	APOF	13	.	0			c.C818T						.						100.0	102.0	101.0					12																	56755172		1964	4152	6116	SO:0001583	missense	319	exon2			TTGGTGGTCTCCG	L27050	CCDS44923.1	12q13	2013-01-24				ENSG00000175336		"""Apolipoproteins"""	615	protein-coding gene	gene with protein product		107760				8093033	Standard	NM_001638		Approved		uc001sle.1	Q13790		ENST00000398189.3:c.818C>T	chr12.hg19:g.56755172G>A	ENSP00000381250:p.Thr273Ile	105.0	0.0		84.0	7.0	NM_001638	Q8TC13	Missense_Mutation	SNP	ENST00000398189.3	hg19	CCDS44923.1	.	.	.	.	.	.	.	.	.	.	G	11.12	1.546661	0.27652	.	.	ENSG00000175336	ENST00000398189;ENST00000541105	T;T	0.47869	0.83;0.84	5.12	-0.345	0.12624	.	1.274100	0.05849	N	0.620904	T	0.30978	0.0782	L	0.41236	1.265	0.09310	N	1	B	0.19583	0.037	B	0.17433	0.018	T	0.14615	-1.0466	10	0.09843	T	0.71	-0.4661	1.3687	0.02206	0.1962:0.3183:0.3226:0.1629	.	273	Q13790	APOF_HUMAN	I	273;255	ENSP00000381250:T273I;ENSP00000440997:T255I	ENSP00000381250:T273I	T	-	2	0	APOF	55041439	0.003000	0.15002	0.000000	0.03702	0.200000	0.23975	0.829000	0.27449	0.033000	0.15463	0.655000	0.94253	ACC	.	.		0.473	APOF-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000410076.1		
HHIPL1	84439	hgsc.bcm.edu	37	14	100135258	100135258	+	Intron	SNP	G	G	A			TCGA-5R-AA1D-01A-11D-A382-10	TCGA-5R-AA1D-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1510db4c-4fd4-4758-b172-d85cc12cbf3f	0719e29a-6ab4-4c61-96ad-a9e3162b45fd	g.chr14:100135258G>A	ENST00000330710.5	+	7	1828				HHIPL1_ENST00000357223.2_Nonsense_Mutation_p.W607*	NM_001127258.1	NP_001120730.1	Q96JK4	HIPL1_HUMAN	HHIP-like 1						carbohydrate metabolic process (GO:0005975)	extracellular region (GO:0005576)|membrane (GO:0016020)	oxidoreductase activity, acting on the CH-OH group of donors, quinone or similar compound as acceptor (GO:0016901)|quinone binding (GO:0048038)|scavenger receptor activity (GO:0005044)			breast(1)|endometrium(2)|large_intestine(2)|lung(8)|skin(2)	15		Melanoma(154;0.128)				ttacagtggtggaaatgagca	0.607																																					p.W607X		Atlas-SNP	.											.	HHIPL1	86	.	0			c.G1820A						.						61.0	55.0	57.0					14																	100135258		2203	4300	6503	SO:0001627	intron_variant	84439	exon8			AGTGGTGGAAATG	AB058725	CCDS9953.1, CCDS45162.1	14q32	2008-01-16	2008-01-16	2008-01-16		ENSG00000182218			19710	protein-coding gene	gene with protein product			"""KIAA1822"""	KIAA1822			Standard	NM_032425		Approved		uc010avs.3	Q96JK4		ENST00000330710.5:c.1730+618G>A	chr14.hg19:g.100135258G>A		56.0	0.0		45.0	12.0	NM_032425	A2RUF8|B2RN09|Q6UXX2	Nonsense_Mutation	SNP	ENST00000330710.5	hg19	CCDS45162.1	.	.	.	.	.	.	.	.	.	.	G	15.35	2.808904	0.50421	.	.	ENSG00000182218	ENST00000357223	.	.	.	1.49	0.549	0.17213	.	5.116030	0.00868	U	0.001997	.	.	.	.	.	.	0.09310	N	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	3.8652	0.09013	0.2445:0.0:0.7555:0.0	.	.	.	.	X	607	.	ENSP00000349757:W607X	W	+	2	0	HHIPL1	99205011	0.000000	0.05858	0.008000	0.14137	0.040000	0.13550	-0.511000	0.06321	0.172000	0.19760	0.462000	0.41574	TGG	.	.		0.607	HHIPL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000413811.1	XM_041566	
NPAP1	23742	hgsc.bcm.edu	37	15	24921813	24921813	+	Missense_Mutation	SNP	G	G	A			TCGA-5R-AA1D-01A-11D-A382-10	TCGA-5R-AA1D-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1510db4c-4fd4-4758-b172-d85cc12cbf3f	0719e29a-6ab4-4c61-96ad-a9e3162b45fd	g.chr15:24921813G>A	ENST00000329468.2	+	1	1273	c.799G>A	c.(799-801)Gtt>Att	p.V267I		NM_018958.2	NP_061831.2	Q9NZP6	NPAP1_HUMAN	nuclear pore associated protein 1	267					cell differentiation (GO:0030154)|multicellular organismal development (GO:0007275)|spermatogenesis (GO:0007283)	extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|nucleus (GO:0005634)											TGAGCCAGCCGTTGGCTGCTC	0.632																																					p.V267I		Atlas-SNP	.											C15orf2,NS,carcinoma,0,1	.	.	.	0			c.G799A						.						33.0	36.0	35.0					15																	24921813		2198	4293	6491	SO:0001583	missense	23742	exon1			CCAGCCGTTGGCT	AF179681	CCDS10015.1	15q11-q13	2012-07-19	2012-06-14	2012-06-14	ENSG00000185823	ENSG00000185823			1190	protein-coding gene	gene with protein product		610922	"""chromosome 15 open reading frame 2"""	C15orf2		10783265, 22694955	Standard	NM_018958		Approved		uc001ywo.3	Q9NZP6	OTTHUMG00000129179	ENST00000329468.2:c.799G>A	chr15.hg19:g.24921813G>A	ENSP00000333735:p.Val267Ile	87.0	0.0		80.0	7.0	NM_018958		Missense_Mutation	SNP	ENST00000329468.2	hg19	CCDS10015.1	.	.	.	.	.	.	.	.	.	.	.	6.795	0.515772	0.12944	.	.	ENSG00000185823	ENST00000329468	T	0.11821	2.74	1.39	0.392	0.16288	.	1.238710	0.06258	N	0.693365	T	0.06416	0.0165	N	0.08118	0	0.09310	N	1	B	0.30526	0.283	B	0.16289	0.015	T	0.34304	-0.9834	10	0.66056	D	0.02	.	5.3252	0.15903	0.0:0.6174:0.3826:0.0	.	267	Q9NZP6	CO002_HUMAN	I	267	ENSP00000333735:V267I	ENSP00000333735:V267I	V	+	1	0	C15orf2	22472906	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-1.832000	0.01696	0.143000	0.18926	-0.662000	0.03851	GTT	.	.		0.632	NPAP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251253.1	NM_018958	
OTUD7A	161725	hgsc.bcm.edu	37	15	31776670	31776670	+	Silent	SNP	G	G	A			TCGA-5R-AA1D-01A-11D-A382-10	TCGA-5R-AA1D-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1510db4c-4fd4-4758-b172-d85cc12cbf3f	0719e29a-6ab4-4c61-96ad-a9e3162b45fd	g.chr15:31776670G>A	ENST00000307050.4	-	11	1700	c.1608C>T	c.(1606-1608)ggC>ggT	p.G536G	OTUD7A_ENST00000382902.1_Silent_p.G543G	NM_130901.1	NP_570971.1	Q8TE49	OTU7A_HUMAN	OTU deubiquitinase 7A	536					protein K11-linked deubiquitination (GO:0035871)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	DNA binding (GO:0003677)|ubiquitin-specific protease activity (GO:0004843)|zinc ion binding (GO:0008270)			endometrium(7)|large_intestine(4)|lung(11)|pancreas(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(4)	30		all_lung(180;1.6e-09)		all cancers(64;2.44e-19)|Epithelial(43;6.82e-14)|GBM - Glioblastoma multiforme(186;1.49e-05)|BRCA - Breast invasive adenocarcinoma(123;0.00189)|Lung(196;0.208)		GCACCAGGCCGCCGAGGCCGC	0.647																																					p.G536G		Atlas-SNP	.											.	OTUD7A	89	.	0			c.C1608T						.						59.0	56.0	57.0					15																	31776670		2202	4300	6502	SO:0001819	synonymous_variant	161725	exon11			CAGGCCGCCGAGG	AJ430383	CCDS10026.1	15q13.1	2014-02-24	2014-02-24	2006-07-07	ENSG00000169918	ENSG00000169918		"""OTU domain containing"""	20718	protein-coding gene	gene with protein product		612024	"""chromosome 15 open reading frame 16"", ""OTU domain containing 7"", ""OTU domain containing 7A"""	C15orf16, OTUD7		23827681	Standard	NM_130901		Approved	CEZANNE2	uc001zfq.3	Q8TE49	OTTHUMG00000129275	ENST00000307050.4:c.1608C>T	chr15.hg19:g.31776670G>A		18.0	0.0		27.0	7.0	NM_130901	Q8IWK5	Silent	SNP	ENST00000307050.4	hg19	CCDS10026.1																																																																																			.	.		0.647	OTUD7A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251393.2	NM_130901	
HIRIP3	8479	hgsc.bcm.edu	37	16	30006907	30006907	+	Missense_Mutation	SNP	A	A	G			TCGA-5R-AA1D-01A-11D-A382-10	TCGA-5R-AA1D-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1510db4c-4fd4-4758-b172-d85cc12cbf3f	0719e29a-6ab4-4c61-96ad-a9e3162b45fd	g.chr16:30006907A>G	ENST00000279392.3	-	1	850	c.20T>C	c.(19-21)aTg>aCg	p.M7T	INO80E_ENST00000567705.1_5'Flank|INO80E_ENST00000563197.1_5'UTR|HIRIP3_ENST00000566471.1_5'UTR|HIRIP3_ENST00000564026.1_Missense_Mutation_p.M7T|INO80E_ENST00000304516.7_5'Flank|INO80E_ENST00000567254.1_5'Flank	NM_003609.4	NP_003600.2	Q9BW71	HIRP3_HUMAN	HIRA interacting protein 3	7					chromatin assembly or disassembly (GO:0006333)	nucleus (GO:0005634)				central_nervous_system(1)|endometrium(1)|kidney(2)|large_intestine(3)|liver(1)|lung(9)	17						GAACTCCTGCATCTCCTTCTC	0.652																																					p.M7T		Atlas-SNP	.											.	HIRIP3	45	.	0			c.T20C						.						77.0	73.0	74.0					16																	30006907		2197	4300	6497	SO:0001583	missense	8479	exon1			TCCTGCATCTCCT	AJ223351	CCDS10664.1, CCDS58449.1	16p12.1	2008-02-05	2001-11-29		ENSG00000149929	ENSG00000149929			4917	protein-coding gene	gene with protein product		603365	"""HIRA-interacting protein 3"""			9710638	Standard	NM_003609		Approved		uc002dve.3	Q9BW71	OTTHUMG00000132118	ENST00000279392.3:c.20T>C	chr16.hg19:g.30006907A>G	ENSP00000279392:p.Met7Thr	116.0	0.0		105.0	26.0	NM_001197323	H3BSR3|O75707|O75708	Missense_Mutation	SNP	ENST00000279392.3	hg19	CCDS10664.1	.	.	.	.	.	.	.	.	.	.	A	21.9	4.219737	0.79464	.	.	ENSG00000149929	ENST00000279392;ENST00000352552	T	0.38240	1.15	5.45	5.45	0.79879	.	0.109676	0.64402	D	0.000013	T	0.47600	0.1454	M	0.61703	1.905	0.80722	D	1	P;D	0.63880	0.952;0.993	P;P	0.52109	0.521;0.69	T	0.50591	-0.8810	10	0.66056	D	0.02	-15.9284	13.5297	0.61615	1.0:0.0:0.0:0.0	.	7;7	B2R6A9;Q9BW71	.;HIRP3_HUMAN	T	7	ENSP00000279392:M7T	ENSP00000279392:M7T	M	-	2	0	HIRIP3	29914408	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	2.992000	0.49417	2.288000	0.76882	0.528000	0.53228	ATG	.	.		0.652	HIRIP3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255160.2	NM_003609	
CLTC	1213	hgsc.bcm.edu	37	17	57761270	57761270	+	Missense_Mutation	SNP	G	G	A			TCGA-5R-AA1D-01A-11D-A382-10	TCGA-5R-AA1D-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1510db4c-4fd4-4758-b172-d85cc12cbf3f	0719e29a-6ab4-4c61-96ad-a9e3162b45fd	g.chr17:57761270G>A	ENST00000269122.3	+	28	4632	c.4358G>A	c.(4357-4359)cGt>cAt	p.R1453H	CLTC_ENST00000579456.1_Missense_Mutation_p.R390H|CLTC_ENST00000393043.1_Missense_Mutation_p.R1453H	NM_004859.3	NP_004850.1	Q00610	CLH1_HUMAN	clathrin, heavy chain (Hc)	1453	Heavy chain arm.|Involved in binding clathrin light chain. {ECO:0000250}.|Proximal segment.				antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|intracellular protein transport (GO:0006886)|membrane organization (GO:0061024)|mitotic nuclear division (GO:0007067)|negative regulation of hyaluronan biosynthetic process (GO:1900126)|negative regulation of protein localization to plasma membrane (GO:1903077)|osteoblast differentiation (GO:0001649)|post-Golgi vesicle-mediated transport (GO:0006892)|receptor internalization (GO:0031623)|receptor-mediated endocytosis (GO:0006898)|transferrin transport (GO:0033572)	clathrin coat (GO:0030118)|clathrin coat of coated pit (GO:0030132)|clathrin coat of trans-Golgi network vesicle (GO:0030130)|clathrin complex (GO:0071439)|clathrin-coated endocytic vesicle membrane (GO:0030669)|clathrin-coated vesicle (GO:0030136)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|membrane (GO:0016020)|mitochondrion (GO:0005739)|plasma membrane (GO:0005886)|protein complex (GO:0043234)|spindle (GO:0005819)|trans-Golgi network membrane (GO:0032588)|vesicle (GO:0031982)	clathrin light chain binding (GO:0032051)|double-stranded RNA binding (GO:0003725)|poly(A) RNA binding (GO:0044822)|protein kinase binding (GO:0019901)|structural molecule activity (GO:0005198)		CLTC/ALK(44)|CLTC/TFE3(2)	breast(2)|large_intestine(6)|ovary(1)	9	all_neural(34;0.0878)|Medulloblastoma(34;0.0922)					CCGTATTTGCGTTCAGTTCAG	0.328			T	"""ALK, TFE3"""	"""ALCL, renal """																																p.R1453H		Atlas-SNP	.		Dom	yes		17	17q11-qter	1213	"""clathrin, heavy polypeptide (Hc)"""		L	.	CLTC	124	.	0			c.G4358A						.						73.0	69.0	71.0					17																	57761270		2203	4300	6503	SO:0001583	missense	1213	exon28			ATTTGCGTTCAGT	X55878	CCDS32696.1, CCDS74115.1	17q23.1	2013-09-19	2006-09-29		ENSG00000141367	ENSG00000141367			2092	protein-coding gene	gene with protein product		118955	"""clathrin, heavy polypeptide (Hc)"", ""clathrin, heavy chain"", ""clathrin, heavy polypeptide-like 2"""	CLTCL2		1765375, 7584026	Standard	NM_004859		Approved	Hc	uc002ixq.1	Q00610	OTTHUMG00000134279	ENST00000269122.3:c.4358G>A	chr17.hg19:g.57761270G>A	ENSP00000269122:p.Arg1453His	194.0	0.0		195.0	8.0	NM_004859	D3DU00|Q6N0A0|Q86TF2	Missense_Mutation	SNP	ENST00000269122.3	hg19	CCDS32696.1	.	.	.	.	.	.	.	.	.	.	G	20.8	4.052072	0.75960	.	.	ENSG00000141367	ENST00000269122;ENST00000393043	T;T	0.20463	2.07;2.07	5.55	5.55	0.83447	Tetratricopeptide-like helical (1);Armadillo-type fold (1);	0.000000	0.85682	D	0.000000	T	0.53981	0.1830	M	0.87547	2.89	0.80722	D	1	D;B	0.71674	0.998;0.048	D;B	0.74023	0.982;0.046	T	0.55768	-0.8089	10	0.45353	T	0.12	.	19.8621	0.96787	0.0:0.0:1.0:0.0	.	1453;1453	Q00610;Q00610-2	CLH1_HUMAN;.	H	1453	ENSP00000269122:R1453H;ENSP00000376763:R1453H	ENSP00000269122:R1453H	R	+	2	0	CLTC	55116052	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	9.869000	0.99810	2.770000	0.95276	0.563000	0.77884	CGT	.	.		0.328	CLTC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000258859.1	NM_004859	
RALY	22913	hgsc.bcm.edu	37	20	32664865	32664865	+	Silent	SNP	C	C	T	rs57852506	byFrequency	TCGA-5R-AA1D-01A-11D-A382-10	TCGA-5R-AA1D-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1510db4c-4fd4-4758-b172-d85cc12cbf3f	0719e29a-6ab4-4c61-96ad-a9e3162b45fd	g.chr20:32664865C>T	ENST00000246194.3	+	8	1192	c.690C>T	c.(688-690)gcC>gcT	p.A230A	RALY_ENST00000375114.3_Silent_p.A214A	NM_016732.2	NP_057951.1	Q9UKM9	RALY_HUMAN	RALY heterogeneous nuclear ribonucleoprotein	230	Epitope (recognized by BKRF1 antibodies).|Poly-Gly.			A -> AS (in Ref. 2; AAC28898). {ECO:0000305}.	mRNA splicing, via spliceosome (GO:0000398)	catalytic step 2 spliceosome (GO:0071013)|nucleus (GO:0005634)	nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)			kidney(2)|large_intestine(3)|lung(2)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	12						GAggtggcgccggcggcggcg	0.662																																					p.A230A		Atlas-SNP	.											.,1	RALY	44	.	0			c.C690T						.						6.0	8.0	7.0					20																	32664865		2110	4142	6252	SO:0001819	synonymous_variant	22913	exon8			TGGCGCCGGCGGC	AF148457	CCDS13229.1, CCDS13230.1	20q11.21-q11.23	2013-08-06	2013-08-06		ENSG00000125970	ENSG00000125970		"""RNA binding motif (RRM) containing"""	15921	protein-coding gene	gene with protein product		614663	"""RNA-binding protein (autoantigenic, hnRNP-associated with lethal yellow)"", ""RNA binding protein, autoantigenic (hnRNP-associated with lethal yellow homolog (mouse))"""			10500250, 23614458	Standard	NM_016732		Approved	P542, HNRPCL2	uc002xab.3	Q9UKM9	OTTHUMG00000032283	ENST00000246194.3:c.690C>T	chr20.hg19:g.32664865C>T		126.0	0.0		112.0	0.0	NM_016732	Q14621|Q2M365|Q5QPL8|Q9BQX6|Q9UJE3	Silent	SNP	ENST00000246194.3	hg19	CCDS13230.1																																																																																			.	.		0.662	RALY-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000078753.1		
FAM3A	60343	hgsc.bcm.edu	37	X	153735650	153735650	+	Missense_Mutation	SNP	C	C	G			TCGA-5R-AA1D-01A-11D-A382-10	TCGA-5R-AA1D-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1510db4c-4fd4-4758-b172-d85cc12cbf3f	0719e29a-6ab4-4c61-96ad-a9e3162b45fd	g.chrX:153735650C>G	ENST00000447601.2	-	8	947	c.481G>C	c.(481-483)Gag>Cag	p.E161Q	FAM3A_ENST00000369643.1_Missense_Mutation_p.E161Q|FAM3A_ENST00000492763.1_5'Flank|FAM3A_ENST00000359889.5_Missense_Mutation_p.E161Q|FAM3A_ENST00000393572.1_Missense_Mutation_p.E123Q|FAM3A_ENST00000369641.3_Missense_Mutation_p.E168Q|FAM3A_ENST00000434658.2_Missense_Mutation_p.E144Q	NM_021806.2	NP_068578.2	P98173	FAM3A_HUMAN	family with sequence similarity 3, member A	161						extracellular region (GO:0005576)				kidney(2)|large_intestine(1)|lung(1)|upper_aerodigestive_tract(1)	5	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)					TTTCTGGTCTCTTCATTCATC	0.602																																					p.E161Q		Atlas-SNP	.											.	FAM3A	11	.	0			c.G481C						.						64.0	53.0	57.0					X																	153735650		2203	4300	6503	SO:0001583	missense	60343	exon9			TGGTCTCTTCATT	X74610	CCDS35453.1, CCDS55542.1, CCDS55543.1, CCDS76060.1	Xq28	2008-07-29			ENSG00000071889	ENSG00000071889			13749	protein-coding gene	gene with protein product		300492				8733135, 8281148	Standard	NM_021806		Approved	DXS560S, 2-19, XAP-7	uc004fls.2	P98173	OTTHUMG00000013418	ENST00000447601.2:c.481G>C	chrX.hg19:g.153735650C>G	ENSP00000416146:p.Glu161Gln	128.0	0.0		99.0	13.0	NM_001171132	A6QRH6|B2RBI7|B4DFI8|D3DWX4|Q5HY76|Q96H51	Missense_Mutation	SNP	ENST00000447601.2	hg19	CCDS35453.1	.	.	.	.	.	.	.	.	.	.	C	26.6	4.753475	0.89753	.	.	ENSG00000071889	ENST00000434658;ENST00000359889;ENST00000369643;ENST00000447601;ENST00000369641;ENST00000393572	T;T;T;T;T;T	0.23950	1.88;1.88;1.88;1.88;1.88;1.88	5.06	5.06	0.68205	.	0.050323	0.85682	D	0.000000	T	0.50069	0.1594	M	0.72894	2.215	0.58432	D	0.999999	D;D;D;D	0.76494	0.961;0.997;0.999;0.987	P;D;D;D	0.71184	0.756;0.972;0.972;0.913	T	0.51576	-0.8688	10	0.51188	T	0.08	-18.7323	16.2748	0.82638	0.0:1.0:0.0:0.0	.	144;168;175;161	B4DFI8;Q5HY75;D3DWX8;P98173	.;.;.;FAM3A_HUMAN	Q	144;161;161;161;168;123	ENSP00000396243:E144Q;ENSP00000352955:E161Q;ENSP00000358657:E161Q;ENSP00000416146:E161Q;ENSP00000358655:E168Q;ENSP00000377202:E123Q	ENSP00000352955:E161Q	E	-	1	0	FAM3A	153388844	1.000000	0.71417	0.990000	0.47175	0.990000	0.78478	5.610000	0.67668	2.094000	0.63399	0.529000	0.55759	GAG	.	.		0.602	FAM3A-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000037362.2		
RYR1	6261	hgsc.bcm.edu	37	19	38964339	38964340	+	Frame_Shift_Ins	INS	-	-	GGGGG			TCGA-5R-AA1D-01A-11D-A382-10	TCGA-5R-AA1D-10A-01D-A385-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1510db4c-4fd4-4758-b172-d85cc12cbf3f	0719e29a-6ab4-4c61-96ad-a9e3162b45fd	g.chr19:38964339_38964340insGGGGG	ENST00000359596.3	+	28	4088_4089	c.4088_4089insGGGGG	c.(4087-4092)gcggggfs	p.-1365fs	RYR1_ENST00000360985.3_Frame_Shift_Ins_p.-1365fs|RYR1_ENST00000355481.4_Frame_Shift_Ins_p.-1365fs			P21817	RYR1_HUMAN	ryanodine receptor 1 (skeletal)						calcium ion transport (GO:0006816)|cellular response to caffeine (GO:0071313)|cytosolic calcium ion homeostasis (GO:0051480)|ion transmembrane transport (GO:0034220)|muscle contraction (GO:0006936)|ossification involved in bone maturation (GO:0043931)|outflow tract morphogenesis (GO:0003151)|release of sequestered calcium ion into cytosol (GO:0051209)|release of sequestered calcium ion into cytosol by sarcoplasmic reticulum (GO:0014808)|response to caffeine (GO:0031000)|response to hypoxia (GO:0001666)|skeletal muscle fiber development (GO:0048741)|skin development (GO:0043588)|transmembrane transport (GO:0055085)	cell cortex (GO:0005938)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|I band (GO:0031674)|integral component of plasma membrane (GO:0005887)|junctional membrane complex (GO:0030314)|junctional sarcoplasmic reticulum membrane (GO:0014701)|plasma membrane (GO:0005886)|sarcoplasmic reticulum (GO:0016529)|sarcoplasmic reticulum membrane (GO:0033017)|smooth endoplasmic reticulum (GO:0005790)|T-tubule (GO:0030315)|terminal cisterna (GO:0014802)	calcium channel activity (GO:0005262)|calcium ion binding (GO:0005509)|calcium-release channel activity (GO:0015278)|calmodulin binding (GO:0005516)|ryanodine-sensitive calcium-release channel activity (GO:0005219)|voltage-gated calcium channel activity (GO:0005245)			NS(4)|autonomic_ganglia(2)|breast(3)|central_nervous_system(5)|endometrium(26)|haematopoietic_and_lymphoid_tissue(3)|kidney(34)|large_intestine(42)|liver(1)|lung(106)|ovary(11)|pancreas(5)|prostate(9)|skin(12)|stomach(11)|upper_aerodigestive_tract(4)|urinary_tract(7)	285	all_cancers(60;7.91e-06)		Lung(45;0.00172)|LUSC - Lung squamous cell carcinoma(53;0.00272)		Caffeine(DB00201)|Dantrolene(DB01219)|Suramin(DB04786)	ACCCCGCAGGCGGGGGGAGAGG	0.678																																					p.A1363fs		Atlas-INDEL	.											.	RYR1	708	.	0			c.4088_4089insGGGGG						.																																			SO:0001589	frameshift_variant	6261	exon28			.	J05200	CCDS33011.1, CCDS42563.1	19q13.1	2014-09-17				ENSG00000196218		"""Ion channels / Ryanodine receptors"""	10483	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 137"""	180901	"""central core disease of muscle"""	MHS, MHS1, CCO		1862346, 16621918	Standard	NM_000540		Approved	RYR, PPP1R137	uc002oit.3	P21817		ENST00000359596.3:c.4089_4093dupGGGGG	chr19.hg19:g.38964340_38964344dupGGGGG	ENSP00000352608:p.Gly1365fs	326.0	0.0		241.0	20.0	NM_001042723	Q16314|Q16368|Q9NPK1|Q9P1U4	Frame_Shift_Ins	INS	ENST00000359596.3	hg19	CCDS33011.1																																																																																			.	.		0.678	RYR1-010	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000462137.1		
