#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_ACHILLES_Lineage_Results_Top_Genes	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_n_overlapping_mutations	i_COSMIC_overlapping_mutation_descriptions	i_COSMIC_overlapping_primary_sites	i_ClinVar_ASSEMBLY	i_ClinVar_HGMD_ID	i_ClinVar_SYM	i_ClinVar_TYPE	i_ClinVar_rs	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_Familial_Cancer_Genes_Reference	i_Familial_Cancer_Genes_Synonym	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_ORegAnno_bin	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_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	i_t_alt_count_full	i_t_ref_count_full	t_alt_count	t_ref_count
ANKK1	255239	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	11	113267965	113267965	+	Silent	SNP	C	C	T			TCGA-HT-7857-01A-11D-2395-08	TCGA-HT-7857-10A-01D-2396-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	58282498-c68f-4b15-89bb-68f49431393c	370dc8dd-90cf-4a60-be75-ccc17f9310fb	g.chr11:113267965C>T	ENST00000303941.3	+	6	952	c.858C>T	c.(856-858)gaC>gaT	p.D286D		NM_178510.1	NP_848605.1	Q8NFD2	ANKK1_HUMAN	ankyrin repeat and kinase domain containing 1	286	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.						ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)			NS(1)|breast(1)|central_nervous_system(1)|cervix(1)|endometrium(2)|kidney(2)|large_intestine(3)|liver(2)|lung(14)|ovary(1)|stomach(1)	29		all_cancers(61;1.53e-11)|all_epithelial(67;3e-06)|Melanoma(852;4.04e-05)|all_hematologic(158;0.000315)|Acute lymphoblastic leukemia(157;0.000966)|Breast(348;0.0461)|Medulloblastoma(222;0.0523)|all_neural(223;0.0663)|Prostate(24;0.194)		BRCA - Breast invasive adenocarcinoma(274;4.82e-06)|Epithelial(105;5.41e-05)|all cancers(92;0.000442)|OV - Ovarian serous cystadenocarcinoma(223;0.238)		TCGAGACAGACATACTGCTGT	0.582																																																0													58.0	62.0	61.0					11																	113267965		2131	4233	6364	SO:0001819	synonymous_variant	255239			AJ541797	CCDS44734.1	11q23.2	2013-01-10			ENSG00000170209	ENSG00000170209		"""Ankyrin repeat domain containing"""	21027	protein-coding gene	gene with protein product		608774				15146457	Standard	NM_178510		Approved	X-kinase	uc001pny.3	Q8NFD2	OTTHUMG00000167715	ENST00000303941.3:c.858C>T	11.37:g.113267965C>T				Silent	SNP	ENST00000303941.3	37	CCDS44734.1																																																																																				0.582	ANKK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000395830.1	NM_178510		10	42	10	42
FMNL3	91010	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	12	50043069	50043069	+	Silent	SNP	A	A	G			TCGA-HT-7857-01A-11D-2395-08	TCGA-HT-7857-10A-01D-2396-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	58282498-c68f-4b15-89bb-68f49431393c	370dc8dd-90cf-4a60-be75-ccc17f9310fb	g.chr12:50043069A>G	ENST00000293590.5	-	20	2591	c.2358T>C	c.(2356-2358)taT>taC	p.Y786Y	FMNL3_ENST00000352151.5_Silent_p.Y735Y|FMNL3_ENST00000335154.5_Silent_p.Y786Y|FMNL3_ENST00000550488.1_Silent_p.Y786Y			Q8IVF7	FMNL3_HUMAN	formin-like 3	786	FH2. {ECO:0000255|PROSITE- ProRule:PRU00774}.				actin cytoskeleton organization (GO:0030036)|cell migration (GO:0016477)|cytoskeleton organization (GO:0007010)|regulation of cell shape (GO:0008360)	cytoplasm (GO:0005737)	GTPase activating protein binding (GO:0032794)			breast(4)|endometrium(7)|kidney(2)|large_intestine(6)|lung(11)|ovary(2)|pancreas(2)|prostate(2)|skin(2)|stomach(1)	39						GCTTGAAGCCATACACAGCTC	0.572																																																0													80.0	86.0	84.0					12																	50043069		2124	4257	6381	SO:0001819	synonymous_variant	91010			AK128195	CCDS41780.1, CCDS44874.1	12q13.12	2006-04-10							23698	protein-coding gene	gene with protein product						12684686	Standard	NM_198900		Approved	DKFZp762B245, MGC45819, WBP3	uc001ruv.1	Q8IVF7	OTTHUMG00000169651	ENST00000293590.5:c.2358T>C	12.37:g.50043069A>G			B0JZA7|Q6ZRJ1	Silent	SNP	ENST00000293590.5	37																																																																																					0.572	FMNL3-201	KNOWN	basic	protein_coding	protein_coding		NM_175736		18	99	18	99
PTPN11	5781	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	12	112888197	112888197	+	Missense_Mutation	SNP	T	T	A			TCGA-HT-7857-01A-11D-2395-08	TCGA-HT-7857-10A-01D-2396-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	58282498-c68f-4b15-89bb-68f49431393c	370dc8dd-90cf-4a60-be75-ccc17f9310fb	g.chr12:112888197T>A	ENST00000351677.2	+	3	411	c.213T>A	c.(211-213)ttT>ttA	p.F71L	PTPN11_ENST00000392597.1_Missense_Mutation_p.F71L	NM_002834.3	NP_002825.3	Q06124	PTN11_HUMAN	protein tyrosine phosphatase, non-receptor type 11	71	SH2 1. {ECO:0000255|PROSITE- ProRule:PRU00191}.		F -> K (in acute myeloid leukemia; requires 2 nucleotide substitutions). {ECO:0000269|PubMed:12717436}.|F -> L (in myelodysplastic syndrome). {ECO:0000269|PubMed:12634870, ECO:0000269|PubMed:12717436}.		abortive mitotic cell cycle (GO:0033277)|activation of MAPK activity (GO:0000187)|atrioventricular canal development (GO:0036302)|axon guidance (GO:0007411)|blood coagulation (GO:0007596)|brain development (GO:0007420)|cytokine-mediated signaling pathway (GO:0019221)|DNA damage checkpoint (GO:0000077)|ephrin receptor signaling pathway (GO:0048013)|epidermal growth factor receptor signaling pathway (GO:0007173)|ERBB signaling pathway (GO:0038127)|face morphogenesis (GO:0060325)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|genitalia development (GO:0048806)|glucose homeostasis (GO:0042593)|heart development (GO:0007507)|hormone metabolic process (GO:0042445)|hormone-mediated signaling pathway (GO:0009755)|innate immune response (GO:0045087)|inner ear development (GO:0048839)|insulin receptor signaling pathway (GO:0008286)|integrin-mediated signaling pathway (GO:0007229)|interferon-gamma-mediated signaling pathway (GO:0060333)|leukocyte migration (GO:0050900)|megakaryocyte development (GO:0035855)|multicellular organismal reproductive process (GO:0048609)|negative regulation of cell adhesion mediated by integrin (GO:0033629)|negative regulation of cortisol secretion (GO:0051463)|negative regulation of growth hormone secretion (GO:0060125)|negative regulation of insulin secretion (GO:0046676)|neurotrophin TRK receptor signaling pathway (GO:0048011)|organ growth (GO:0035265)|peptidyl-tyrosine dephosphorylation (GO:0035335)|phosphatidylinositol-mediated signaling (GO:0048015)|platelet formation (GO:0030220)|positive regulation of glucose import in response to insulin stimulus (GO:2001275)|positive regulation of hormone secretion (GO:0046887)|regulation of cell adhesion mediated by integrin (GO:0033628)|regulation of interferon-gamma-mediated signaling pathway (GO:0060334)|regulation of multicellular organism growth (GO:0040014)|regulation of protein export from nucleus (GO:0046825)|regulation of type I interferon-mediated signaling pathway (GO:0060338)|T cell costimulation (GO:0031295)|triglyceride metabolic process (GO:0006641)|type I interferon signaling pathway (GO:0060337)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|mitochondrion (GO:0005739)|nucleus (GO:0005634)|protein complex (GO:0043234)	insulin receptor binding (GO:0005158)|non-membrane spanning protein tyrosine phosphatase activity (GO:0004726)|phosphoprotein phosphatase activity (GO:0004721)|protein tyrosine phosphatase activity (GO:0004725)|SH3/SH2 adaptor activity (GO:0005070)	p.F71L(5)|p.F71K(1)		NS(1)|autonomic_ganglia(2)|breast(1)|central_nervous_system(2)|endometrium(7)|haematopoietic_and_lymphoid_tissue(406)|kidney(2)|large_intestine(6)|lung(16)|ovary(1)|skin(1)|soft_tissue(3)|stomach(3)	451						GGGAGAAATTTGCCACTTTGG	0.418			Mis		"""JMML, AML, MDS"""		Noonan Syndrome		Noonan syndrome																														Dom	yes		12	12q24.1	5781	"""protein tyrosine phosphatase, non-receptor type 11"""	yes	L	6	Substitution - Missense(6)	haematopoietic_and_lymphoid_tissue(6)											154.0	142.0	146.0					12																	112888197		2203	4300	6503	SO:0001583	missense	5781	Familial Cancer Database	Male Turner syndrome, Pterygium Colli syndrome, incl. Noonan-like/Multiple Giant Cell Lesion syndrome; Noonan s. with multiple lentigines/LEOPARD syndrome	D13540	CCDS9163.1, CCDS58280.1	12q24.1	2014-09-17	2008-07-31		ENSG00000179295	ENSG00000179295		"""Protein tyrosine phosphatases / Class I Cys-based PTPs : Non-receptor"", ""SH2 domain containing"""	9644	protein-coding gene	gene with protein product		176876	"""Noonan syndrome 1"""	NS1		7894486, 1280823	Standard	NM_080601		Approved	BPTP3, SH-PTP2, SHP-2, PTP2C, SHP2	uc001ttx.3	Q06124	OTTHUMG00000134334	ENST00000351677.2:c.213T>A	12.37:g.112888197T>A	ENSP00000340944:p.Phe71Leu		A8K1D9|Q96HD7	Missense_Mutation	SNP	ENST00000351677.2	37	CCDS9163.1	.	.	.	.	.	.	.	.	.	.	T	24.9	4.577946	0.86645	.	.	ENSG00000179295	ENST00000392597;ENST00000351677;ENST00000392596	D;D	0.98313	-4.86;-4.86	5.9	3.57	0.40892	.	0.000000	0.85682	D	0.000000	D	0.99146	0.9705	H	0.96175	3.78	0.58432	D	0.999998	D;D	0.89917	0.998;1.0	P;D	0.77557	0.864;0.99	D	0.98808	1.0742	10	0.87932	D	0	.	10.0515	0.42219	0.0:0.1351:0.0:0.8649	.	71;71	Q06124-2;Q06124-3	.;.	L	71	ENSP00000376376:F71L;ENSP00000340944:F71L	ENSP00000340944:F71L	F	+	3	2	PTPN11	111372580	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	2.314000	0.43743	0.503000	0.28060	0.528000	0.53228	TTT		0.418	PTPN11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000259496.2			50	101	50	101
NPAP1	23742	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	15	24921605	24921605	+	Silent	SNP	C	C	T	rs371279086		TCGA-HT-7857-01A-11D-2395-08	TCGA-HT-7857-10A-01D-2396-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	58282498-c68f-4b15-89bb-68f49431393c	370dc8dd-90cf-4a60-be75-ccc17f9310fb	g.chr15:24921605C>T	ENST00000329468.2	+	1	1065	c.591C>T	c.(589-591)gaC>gaT	p.D197D		NM_018958.2	NP_061831.2	Q9NZP6	NPAP1_HUMAN	nuclear pore associated protein 1	197					cell differentiation (GO:0030154)|multicellular organismal development (GO:0007275)|spermatogenesis (GO:0007283)	extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|nucleus (GO:0005634)											CCCAGGGAGACGTGGCCTCCT	0.592													C|||	1	0.000199681	0.0	0.0	5008	,	,		18068	0.0		0.0	False		,,,				2504	0.001															0								C		0,4406		0,0,2203	44.0	38.0	40.0		591	-0.1	0.0	15		40	1,8599		0,1,4299	no	coding-synonymous	C15orf2	NM_018958.2		0,1,6502	TT,TC,CC		0.0116,0.0,0.0077		197/1157	24921605	1,13005	2203	4300	6503	SO:0001819	synonymous_variant	23742			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.591C>T	15.37:g.24921605C>T				Silent	SNP	ENST00000329468.2	37	CCDS10015.1																																																																																				0.592	NPAP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251253.1	NM_018958		6	47	6	47
VPS9D1	9605	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	16	89785502	89785502	+	Silent	SNP	G	G	A	rs375598205		TCGA-HT-7857-01A-11D-2395-08	TCGA-HT-7857-10A-01D-2396-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	58282498-c68f-4b15-89bb-68f49431393c	370dc8dd-90cf-4a60-be75-ccc17f9310fb	g.chr16:89785502G>A	ENST00000389386.3	-	2	232	c.108C>T	c.(106-108)taC>taT	p.Y36Y	ZNF276_ENST00000443381.2_5'Flank|ZNF276_ENST00000289816.5_5'Flank|VPS9D1-AS1_ENST00000562866.1_RNA|VPS9D1-AS1_ENST00000562298.1_RNA|ZNF276_ENST00000568064.1_5'Flank|VPS9D1_ENST00000561976.1_5'UTR|ZNF276_ENST00000446326.2_5'Flank	NM_004913.2	NP_004904.2	Q9Y2B5	VP9D1_HUMAN	VPS9 domain containing 1	36					ATP synthesis coupled proton transport (GO:0015986)		GTPase activator activity (GO:0005096)|transporter activity (GO:0005215)										GGTATTCCGTGTATGCCTCCT	0.552																																																0								G		1,3883		0,1,1941	114.0	118.0	116.0		108	-3.5	0.0	16		116	0,8264		0,0,4132	no	coding-synonymous	C16orf7	NM_004913.2		0,1,6073	AA,AG,GG		0.0,0.0257,0.0082		36/632	89785502	1,12147	1942	4132	6074	SO:0001819	synonymous_variant	9605			AB018551	CCDS42220.1	16q24.3	2012-10-09	2012-10-09	2012-10-09	ENSG00000075399	ENSG00000075399			13526	protein-coding gene	gene with protein product			"""chromosome 16 open reading frame 7"""	C16orf7		10231027	Standard	NM_004913		Approved	ATP-BL	uc002fom.1	Q9Y2B5	OTTHUMG00000173219	ENST00000389386.3:c.108C>T	16.37:g.89785502G>A				Silent	SNP	ENST00000389386.3	37	CCDS42220.1																																																																																				0.552	VPS9D1-002	KNOWN	non_canonical_conserved|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000422508.1	NM_004913		19	114	19	114
NF1	4763	hgsc.bcm.edu;broad.mit.edu	37	17	29576001	29576001	+	Splice_Site	SNP	G	G	A			TCGA-HT-7857-01A-11D-2395-08	TCGA-HT-7857-10A-01D-2396-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	58282498-c68f-4b15-89bb-68f49431393c	370dc8dd-90cf-4a60-be75-ccc17f9310fb	g.chr17:29576001G>A	ENST00000358273.4	+	30	4357		c.e30-1		NF1_ENST00000356175.3_Splice_Site	NM_001042492.2	NP_001035957.1	P21359	NF1_HUMAN	neurofibromin 1						actin cytoskeleton organization (GO:0030036)|adrenal gland development (GO:0030325)|artery morphogenesis (GO:0048844)|brain development (GO:0007420)|camera-type eye morphogenesis (GO:0048593)|cell communication (GO:0007154)|cerebral cortex development (GO:0021987)|cognition (GO:0050890)|collagen fibril organization (GO:0030199)|extracellular matrix organization (GO:0030198)|extrinsic apoptotic signaling pathway via death domain receptors (GO:0008625)|forebrain astrocyte development (GO:0021897)|forebrain morphogenesis (GO:0048853)|heart development (GO:0007507)|liver development (GO:0001889)|MAPK cascade (GO:0000165)|metanephros development (GO:0001656)|myelination in peripheral nervous system (GO:0022011)|negative regulation of angiogenesis (GO:0016525)|negative regulation of astrocyte differentiation (GO:0048712)|negative regulation of cell migration (GO:0030336)|negative regulation of cell-matrix adhesion (GO:0001953)|negative regulation of endothelial cell proliferation (GO:0001937)|negative regulation of fibroblast proliferation (GO:0048147)|negative regulation of MAP kinase activity (GO:0043407)|negative regulation of MAPK cascade (GO:0043409)|negative regulation of neuroblast proliferation (GO:0007406)|negative regulation of neurotransmitter secretion (GO:0046929)|negative regulation of oligodendrocyte differentiation (GO:0048715)|negative regulation of osteoclast differentiation (GO:0045671)|negative regulation of protein kinase activity (GO:0006469)|negative regulation of Rac protein signal transduction (GO:0035021)|negative regulation of Ras protein signal transduction (GO:0046580)|negative regulation of transcription factor import into nucleus (GO:0042992)|neural tube development (GO:0021915)|osteoblast differentiation (GO:0001649)|peripheral nervous system development (GO:0007422)|phosphatidylinositol 3-kinase signaling (GO:0014065)|pigmentation (GO:0043473)|positive regulation of adenylate cyclase activity (GO:0045762)|positive regulation of apoptotic process (GO:0043065)|positive regulation of endothelial cell proliferation (GO:0001938)|positive regulation of extrinsic apoptotic signaling pathway in absence of ligand (GO:2001241)|positive regulation of extrinsic apoptotic signaling pathway via death domain receptors (GO:1902043)|positive regulation of neuron apoptotic process (GO:0043525)|positive regulation of Ras GTPase activity (GO:0032320)|Ras protein signal transduction (GO:0007265)|regulation of angiogenesis (GO:0045765)|regulation of blood vessel endothelial cell migration (GO:0043535)|regulation of bone resorption (GO:0045124)|regulation of cell-matrix adhesion (GO:0001952)|regulation of glial cell differentiation (GO:0045685)|regulation of long-term neuronal synaptic plasticity (GO:0048169)|regulation of Ras GTPase activity (GO:0032318)|regulation of synaptic transmission, GABAergic (GO:0032228)|response to hypoxia (GO:0001666)|Schwann cell development (GO:0014044)|skeletal muscle tissue development (GO:0007519)|smooth muscle tissue development (GO:0048745)|spinal cord development (GO:0021510)|sympathetic nervous system development (GO:0048485)|visual learning (GO:0008542)|wound healing (GO:0042060)	axon (GO:0030424)|cytoplasm (GO:0005737)|dendrite (GO:0030425)|intrinsic component of the cytoplasmic side of the plasma membrane (GO:0031235)|membrane (GO:0016020)|nucleus (GO:0005634)	phosphatidylcholine binding (GO:0031210)|phosphatidylethanolamine binding (GO:0008429)|Ras GTPase activator activity (GO:0005099)	p.0?(8)|p.?(4)	NF1/ACCN1(2)	autonomic_ganglia(12)|breast(11)|central_nervous_system(72)|cervix(6)|endometrium(12)|haematopoietic_and_lymphoid_tissue(59)|kidney(9)|large_intestine(39)|liver(1)|lung(80)|ovary(20)|pancreas(2)|prostate(2)|skin(8)|soft_tissue(249)|stomach(2)|thyroid(1)|upper_aerodigestive_tract(5)|urinary_tract(9)	599		all_cancers(10;1.29e-12)|all_epithelial(10;0.00347)|all_hematologic(16;0.00556)|Acute lymphoblastic leukemia(14;0.00593)|Breast(31;0.014)|Myeloproliferative disorder(56;0.0255)|all_lung(9;0.0321)|Lung NSC(157;0.0659)		UCEC - Uterine corpus endometrioid carcinoma (4;4.38e-05)|all cancers(4;1.64e-26)|Epithelial(4;9.15e-23)|OV - Ovarian serous cystadenocarcinoma(4;3.58e-21)|GBM - Glioblastoma multiforme(4;0.00146)		TTTTTTTGTAGGTTAGAACCA	0.368			"""D, Mis, N, F, S, O"""		"""neurofibroma, glioma"""	"""neurofibroma, glioma"""			Neurofibromatosis, type 1	TCGA GBM(6;<1E-08)|TSP Lung(7;0.0071)|TCGA Ovarian(3;0.0088)																												yes	Rec	yes	Neurofibromatosis type 1	17	17q12	4763	neurofibromatosis type 1 gene		O	12	Whole gene deletion(8)|Unknown(4)	soft_tissue(7)|autonomic_ganglia(2)|central_nervous_system(2)|lung(1)											73.0	71.0	72.0					17																	29576001		2203	4300	6503	SO:0001630	splice_region_variant	4763	Familial Cancer Database	NF1, von Recklinghausen disease, incl.: Hereditary Spinal Neurofibromatosis, Neurofibromatosis-Noonan syndrome		CCDS11264.1, CCDS42292.1, CCDS45645.1	17q11.2	2014-09-17	2008-07-31		ENSG00000196712	ENSG00000196712			7765	protein-coding gene	gene with protein product	"""neurofibromatosis"", ""von Recklinghausen disease"", ""Watson disease"""	613113				1715669	Standard	NM_000267		Approved		uc002hgg.3	P21359	OTTHUMG00000132871	ENST00000358273.4:c.3975-1G>A	17.37:g.29576001G>A			O00662|Q14284|Q14930|Q14931|Q9UMK3	Splice_Site	SNP	ENST00000358273.4	37	CCDS42292.1	.	.	.	.	.	.	.	.	.	.	G	15.99	2.994304	0.54041	.	.	ENSG00000196712	ENST00000358273;ENST00000356175;ENST00000456735	.	.	.	5.74	5.74	0.90152	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	20.2982	0.98569	0.0:0.0:1.0:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	NF1	26600127	1.000000	0.71417	0.429000	0.26710	0.370000	0.29829	9.378000	0.97191	2.873000	0.98535	0.563000	0.77884	.		0.368	NF1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000256351.2	NM_000267	Intron	48	38	48	38
DMRTC2	63946	hgsc.bcm.edu;ucsc.edu	37	19	42354645	42354645	+	Silent	SNP	C	C	T			TCGA-HT-7857-01A-11D-2395-08	TCGA-HT-7857-10A-01D-2396-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	58282498-c68f-4b15-89bb-68f49431393c	370dc8dd-90cf-4a60-be75-ccc17f9310fb	g.chr19:42354645C>T	ENST00000269945.3	+	8	919	c.868C>T	c.(868-870)Ctg>Ttg	p.L290L	DMRTC2_ENST00000596827.1_Silent_p.L341L	NM_001040283.1	NP_001035373.1	Q8IXT2	DMRTD_HUMAN	DMRT-like family C2	290	Pro-rich.				male meiosis I (GO:0007141)|positive regulation of histone H3-K9 dimethylation (GO:1900111)|positive regulation of histone H3-K9 trimethylation (GO:1900114)|sex differentiation (GO:0007548)|spermatid nucleus elongation (GO:0007290)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)|XY body (GO:0001741)	metal ion binding (GO:0046872)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)			endometrium(1)|large_intestine(2)|lung(5)|prostate(1)|skin(1)	10						AGAGTGGCAGCTGCAGCAAGA	0.637																																																0													40.0	46.0	44.0					19																	42354645		2203	4299	6502	SO:0001819	synonymous_variant	63946			AJ291669	CCDS33034.1	19q13.2	2008-07-16				ENSG00000142025			13911	protein-coding gene	gene with protein product		614806				11863363	Standard	NM_001040283		Approved		uc002ors.3	Q8IXT2		ENST00000269945.3:c.868C>T	19.37:g.42354645C>T			Q8N6Q2|Q96M39|Q96SD4	Silent	SNP	ENST00000269945.3	37	CCDS33034.1																																																																																				0.637	DMRTC2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000463045.1	NM_001040283		28	50	28	50
ABCA4	24	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	1	94528252	94528252	+	Silent	SNP	G	G	T	rs377164833		TCGA-HT-7857-01A-11D-2395-08	TCGA-HT-7857-10A-01D-2396-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	58282498-c68f-4b15-89bb-68f49431393c	370dc8dd-90cf-4a60-be75-ccc17f9310fb	g.chr1:94528252G>T	ENST00000370225.3	-	13	1904	c.1818C>A	c.(1816-1818)ggC>ggA	p.G606G	ABCA4_ENST00000535735.1_Silent_p.G606G	NM_000350.2	NP_000341.2	P78363	ABCA4_HUMAN	ATP-binding cassette, sub-family A (ABC1), member 4	606					phospholipid transfer to membrane (GO:0006649)|photoreceptor cell maintenance (GO:0045494)|phototransduction, visible light (GO:0007603)|retinoid metabolic process (GO:0001523)|transmembrane transport (GO:0055085)|transport (GO:0006810)|visual perception (GO:0007601)	integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|photoreceptor disc membrane (GO:0097381)	ATP binding (GO:0005524)|ATPase activity, coupled to transmembrane movement of substances (GO:0042626)|phospholipid-translocating ATPase activity (GO:0004012)|transporter activity (GO:0005215)			NS(2)|breast(6)|central_nervous_system(5)|endometrium(9)|haematopoietic_and_lymphoid_tissue(5)|kidney(10)|large_intestine(25)|lung(57)|ovary(4)|pancreas(1)|prostate(4)|skin(10)|stomach(4)|upper_aerodigestive_tract(3)|urinary_tract(2)	147		all_lung(203;0.000757)|Lung NSC(277;0.00335)		all cancers(265;0.00432)|GBM - Glioblastoma multiforme(16;0.00715)|Epithelial(280;0.171)		AGGCAAACCCGCCCCAGATGT	0.562																																																0													65.0	64.0	65.0					1																	94528252		2203	4300	6503	SO:0001819	synonymous_variant	24			U88667	CCDS747.1	1p22	2013-01-23			ENSG00000198691	ENSG00000198691		"""ATP binding cassette transporters / subfamily A"""	34	protein-coding gene	gene with protein product	"""Stargardt disease"""	601691	"""ATP-binding cassette transporter, retinal-specific"""	STGD1, ABCR, RP19, STGD		9490294	Standard	NM_000350		Approved	FFM, ARMD2, CORD3	uc001dqh.3	P78363	OTTHUMG00000010622	ENST00000370225.3:c.1818C>A	1.37:g.94528252G>T			O15112|O60438|O60915|Q0QD48|Q4LE31	Silent	SNP	ENST00000370225.3	37	CCDS747.1																																																																																				0.562	ABCA4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000029320.1	NM_000350		10	38	10	38
TET2	54790	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	4	106155166	106155166	+	Missense_Mutation	SNP	C	C	T			TCGA-HT-7857-01A-11D-2395-08	TCGA-HT-7857-10A-01D-2396-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	58282498-c68f-4b15-89bb-68f49431393c	370dc8dd-90cf-4a60-be75-ccc17f9310fb	g.chr4:106155166C>T	ENST00000540549.1	+	3	927	c.67C>T	c.(67-69)Ccc>Tcc	p.P23S	TET2_ENST00000513237.1_Missense_Mutation_p.P44S|TET2_ENST00000413648.2_Missense_Mutation_p.P23S|TET2_ENST00000380013.4_Missense_Mutation_p.P23S|TET2_ENST00000394764.1_Missense_Mutation_p.P23S|TET2_ENST00000305737.2_Missense_Mutation_p.P23S|TET2_ENST00000545826.1_Missense_Mutation_p.P23S			Q6N021	TET2_HUMAN	tet methylcytosine dioxygenase 2	23					5-methylcytosine catabolic process (GO:0006211)|cell cycle (GO:0007049)|DNA demethylation (GO:0080111)|histone H3-K4 trimethylation (GO:0080182)|kidney development (GO:0001822)|myeloid cell differentiation (GO:0030099)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|post-embryonic development (GO:0009791)|protein O-linked glycosylation (GO:0006493)		DNA binding (GO:0003677)|ferrous iron binding (GO:0008198)|methylcytosine dioxygenase activity (GO:0070579)|zinc ion binding (GO:0008270)			NS(1)|breast(2)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1272)|kidney(3)|large_intestine(11)|lung(10)|ovary(1)|pancreas(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	1314		Myeloproliferative disorder(5;0.0393)		OV - Ovarian serous cystadenocarcinoma(123;7.18e-08)		ACCATCACCTCCCATTTGCCA	0.527			"""Mis N, F"""		MDS																																		Rec	yes		4	4q24	54790	tet oncogene family member 2		L	0													76.0	65.0	68.0					4																	106155166		2203	4300	6503	SO:0001583	missense	54790			AB046766	CCDS3666.1, CCDS47120.1	4q24	2014-09-17	2011-09-30	2008-03-12	ENSG00000168769	ENSG00000168769			25941	protein-coding gene	gene with protein product		612839	"""KIAA1546"", ""tet oncogene family member 2"""	KIAA1546		10997877, 12646957	Standard	NM_017628		Approved	FLJ20032	uc003hxk.3	Q6N021	OTTHUMG00000131213	ENST00000540549.1:c.67C>T	4.37:g.106155166C>T	ENSP00000442788:p.Pro23Ser		B5MDU0|Q2TB88|Q3LIB8|Q96JX5|Q9HCM6|Q9NXW0	Missense_Mutation	SNP	ENST00000540549.1	37	CCDS47120.1	.	.	.	.	.	.	.	.	.	.	C	10.87	1.473141	0.26423	.	.	ENSG00000168769	ENST00000305737;ENST00000540549;ENST00000545826;ENST00000513237;ENST00000380013;ENST00000394764;ENST00000413648;ENST00000535110;ENST00000514870	T;T;T;T;T;T;T;T	0.28454	3.91;4.57;3.91;4.57;4.57;3.91;3.92;1.61	5.4	3.65	0.41850	.	0.675928	0.12153	U	0.494685	T	0.20088	0.0483	N	0.19112	0.55	0.24770	N	0.992871	B;B;B	0.18610	0.01;0.01;0.029	B;B;B	0.18561	0.01;0.01;0.022	T	0.22382	-1.0218	10	0.31617	T	0.26	.	9.2917	0.37791	0.0:0.5779:0.3454:0.0767	.	44;23;23	E7EQS8;Q6N021;Q6N021-2	.;TET2_HUMAN;.	S	23;23;23;44;23;23;23;23;23	ENSP00000306705:P23S;ENSP00000442788:P23S;ENSP00000442867:P23S;ENSP00000425443:P44S;ENSP00000369351:P23S;ENSP00000378245:P23S;ENSP00000391448:P23S;ENSP00000426885:P23S	ENSP00000265149:P23S	P	+	1	0	TET2	106374615	0.996000	0.38824	0.699000	0.30290	0.980000	0.70556	1.624000	0.37018	0.613000	0.30089	0.591000	0.81541	CCC		0.527	TET2-202	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000253952.2	NM_017628		11	43	11	43
NAA15	80155	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	4	140262069	140262069	+	Nonsense_Mutation	SNP	G	G	A			TCGA-HT-7857-01A-11D-2395-08	TCGA-HT-7857-10A-01D-2396-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	58282498-c68f-4b15-89bb-68f49431393c	370dc8dd-90cf-4a60-be75-ccc17f9310fb	g.chr4:140262069G>A	ENST00000296543.5	+	4	571	c.248G>A	c.(247-249)tGg>tAg	p.W83*	NAA15_ENST00000398947.1_Nonsense_Mutation_p.W83*|NAA15_ENST00000480277.2_3'UTR	NM_057175.3	NP_476516.1	Q9BXJ9	NAA15_HUMAN	N(alpha)-acetyltransferase 15, NatA auxiliary subunit	83					angiogenesis (GO:0001525)|cell differentiation (GO:0030154)|N-terminal protein amino acid acetylation (GO:0006474)|negative regulation of apoptotic process (GO:0043066)|positive regulation of transcription, DNA-templated (GO:0045893)|protein stabilization (GO:0050821)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|membrane (GO:0016020)|NatA complex (GO:0031415)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	N-acetyltransferase activity (GO:0008080)|poly(A) RNA binding (GO:0044822)|ribosome binding (GO:0043022)			NS(1)|endometrium(3)|large_intestine(7)|liver(2)|lung(8)|ovary(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	29						TCTTTAGGTTGGCACGTTTAT	0.363																																																0													68.0	62.0	64.0					4																	140262069		1828	4089	5917	SO:0001587	stop_gained	80155			AY039242	CCDS43270.1	4q31.1	2010-01-14	2010-01-14	2010-01-14	ENSG00000164134	ENSG00000164134		"""N(alpha)-acetyltransferase subunits"""	30782	protein-coding gene	gene with protein product		608000	"""NMDA receptor regulated 1"""	NARG1		12140756, 11478804, 19660095	Standard	XM_005263236		Approved	TBDN100, NATH, FLJ13340	uc003ihu.1	Q9BXJ9	OTTHUMG00000137363	ENST00000296543.5:c.248G>A	4.37:g.140262069G>A	ENSP00000296543:p.Trp83*		D3DNY6|Q52LG9|Q8IWH4|Q8NEV2|Q9H8P6	Nonsense_Mutation	SNP	ENST00000296543.5	37	CCDS43270.1	.	.	.	.	.	.	.	.	.	.	G	38	6.666260	0.97747	.	.	ENSG00000164134	ENST00000296543;ENST00000398947	.	.	.	5.62	5.62	0.85841	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-6.0146	19.6544	0.95831	0.0:0.0:1.0:0.0	.	.	.	.	X	83	.	ENSP00000296543:W83X	W	+	2	0	NAA15	140481519	1.000000	0.71417	1.000000	0.80357	0.910000	0.53928	9.378000	0.97191	2.647000	0.89833	0.467000	0.42956	TGG		0.363	NAA15-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000267839.2	NM_057175		26	53	26	53
DUSP22	56940	hgsc.bcm.edu;broad.mit.edu	37	6	348272	348272	+	Nonsense_Mutation	SNP	C	C	T			TCGA-HT-7857-01A-11D-2395-08	TCGA-HT-7857-10A-01D-2396-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	58282498-c68f-4b15-89bb-68f49431393c	370dc8dd-90cf-4a60-be75-ccc17f9310fb	g.chr6:348272C>T	ENST00000344450.5	+	6	876	c.433C>T	c.(433-435)Cag>Tag	p.Q145*	DUSP22_ENST00000603453.1_Nonsense_Mutation_p.Q42*|DUSP22_ENST00000419235.2_Nonsense_Mutation_p.Q145*|DUSP22_ENST00000604971.1_Nonsense_Mutation_p.Q42*|DUSP22_ENST00000605315.1_Nonsense_Mutation_p.Q42*|DUSP22_ENST00000605863.1_Nonsense_Mutation_p.Q42*|DUSP22_ENST00000605035.1_Nonsense_Mutation_p.Q42*	NM_020185.3	NP_064570.1	Q9NRW4	DUS22_HUMAN	dual specificity phosphatase 22	145					apoptotic process (GO:0006915)|cell proliferation (GO:0008283)|inactivation of MAPK activity (GO:0000188)|multicellular organismal development (GO:0007275)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of JNK cascade (GO:0046330)|protein dephosphorylation (GO:0006470)|regulation of cell proliferation (GO:0042127)|transforming growth factor beta receptor signaling pathway (GO:0007179)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	protein tyrosine phosphatase activity (GO:0004725)|protein tyrosine/serine/threonine phosphatase activity (GO:0008138)			central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(4)|lung(16)|ovary(1)|skin(2)	26	all_hematologic(77;0.228)	Breast(5;0.0249)|all_hematologic(90;0.0489)		OV - Ovarian serous cystadenocarcinoma(45;0.0277)|BRCA - Breast invasive adenocarcinoma(62;0.0669)		TGAGGTCCATCAGGTAAGCAG	0.577																																																0													93.0	84.0	87.0					6																	348272		2203	4300	6503	SO:0001587	stop_gained	56940			AF165519	CCDS4468.1, CCDS69035.1	6p25.3	2013-09-19			ENSG00000112679	ENSG00000112679		"""Protein tyrosine phosphatases / Class I Cys-based PTPs : Atypical dual specificity phosphatases"""	16077	protein-coding gene	gene with protein product						9205128, 11717427	Standard	NM_001286555		Approved	MKPX, JSP1, JKAP, VHX	uc003msx.3	Q9NRW4	OTTHUMG00000014113	ENST00000344450.5:c.433C>T	6.37:g.348272C>T	ENSP00000345281:p.Gln145*		B4DK56|Q59GW2|Q5VWR2|Q96AR1	Nonsense_Mutation	SNP	ENST00000344450.5	37	CCDS4468.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	28.9|28.9	4.964370|4.964370	0.92791|0.92791	.|.	.|.	ENSG00000112679|ENSG00000112679	ENST00000344450|ENST00000419235	.|.	.|.	.|.	5.82|5.82	4.94|4.94	0.65067|0.65067	.|.	0.146075|.	0.48767|.	D|.	0.000169|.	.|T	.|0.62258	.|0.2413	.|.	.|.	.|.	0.80722|0.80722	A|A	1|1	.|.	.|.	.|.	.|.	.|.	.|.	.|T	.|0.64398	.|-0.6417	.|3	0.09843|.	T|.	0.71|.	.|.	15.9672|15.9672	0.79984|0.79984	0.0:0.7454:0.2546:0.0|0.0:0.7454:0.2546:0.0	.|.	.|.	.|.	.|.	X|L	145|82	.|.	ENSP00000345281:Q145X|.	Q|S	+|+	1|2	0|0	DUSP22|DUSP22	293272|293272	0.956000|0.956000	0.32656|0.32656	0.898000|0.898000	0.35279|0.35279	0.857000|0.857000	0.48899|0.48899	2.170000|2.170000	0.42443|0.42443	1.434000|1.434000	0.47414|0.47414	0.655000|0.655000	0.94253|0.94253	CAG|TCA		0.577	DUSP22-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000039621.1	NM_020185		15	140	15	140
DNAH8	1769	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	6	38810444	38810444	+	Missense_Mutation	SNP	G	G	A	rs375507271		TCGA-HT-7857-01A-11D-2395-08	TCGA-HT-7857-10A-01D-2396-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	58282498-c68f-4b15-89bb-68f49431393c	370dc8dd-90cf-4a60-be75-ccc17f9310fb	g.chr6:38810444G>A	ENST00000359357.3	+	33	4213	c.3959G>A	c.(3958-3960)cGt>cAt	p.R1320H	DNAH8_ENST00000441566.1_Missense_Mutation_p.R1320H|DNAH8_ENST00000449981.2_Missense_Mutation_p.R1537H			Q96JB1	DYH8_HUMAN	dynein, axonemal, heavy chain 8	1320					cilium or flagellum-dependent cell motility (GO:0001539)|metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)	axonemal dynein complex (GO:0005858)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)			NS(7)|breast(9)|central_nervous_system(4)|cervix(1)|endometrium(12)|haematopoietic_and_lymphoid_tissue(3)|kidney(16)|large_intestine(44)|liver(4)|lung(101)|ovary(7)|pancreas(2)|prostate(8)|skin(28)|stomach(4)|upper_aerodigestive_tract(6)|urinary_tract(4)	260						GAAAGATGTCGTAAACTTCCA	0.323																																																0								G	HIS/ARG	0,4402		0,0,2201	53.0	59.0	57.0		4610	4.6	1.0	6		57	2,8598	1.2+/-3.3	0,2,4298	no	missense	DNAH8	NM_001206927.1	29	0,2,6499	AA,AG,GG		0.0233,0.0,0.0154	probably-damaging	1537/4708	38810444	2,13000	2201	4300	6501	SO:0001583	missense	1769			Z83806	CCDS75447.1	6p21.2	2012-04-19	2006-09-04		ENSG00000124721	ENSG00000124721		"""Axonemal dyneins"""	2952	protein-coding gene	gene with protein product		603337	"""dynein, axonemal, heavy polypeptide 8"""			9373155	Standard	NM_001206927		Approved	hdhc9	uc021yzh.1	Q96JB1	OTTHUMG00000016253	ENST00000359357.3:c.3959G>A	6.37:g.38810444G>A	ENSP00000352312:p.Arg1320His		O00438|Q5JYI2|Q5T2M3|Q5T2M4|Q5TG00|Q9UEM4	Missense_Mutation	SNP	ENST00000359357.3	37		.	.	.	.	.	.	.	.	.	.	G	23.4	4.407189	0.83230	0.0	2.33E-4	ENSG00000124721	ENST00000449981;ENST00000327475;ENST00000359357;ENST00000441566	T;T;T	0.61859	0.07;0.07;0.07	5.46	4.59	0.56863	Dynein heavy chain, domain-2 (1);	0.055231	0.64402	D	0.000001	T	0.55337	0.1914	M	0.75777	2.31	0.80722	D	1	D	0.56968	0.978	P	0.48982	0.597	T	0.62124	-0.6920	10	0.49607	T	0.09	.	14.8197	0.70062	0.0698:0.0:0.9302:0.0	.	1320	Q96JB1	DYH8_HUMAN	H	1525;1525;1320;1320	ENSP00000333363:R1525H;ENSP00000352312:R1320H;ENSP00000402294:R1320H	ENSP00000333363:R1525H	R	+	2	0	DNAH8	38918422	1.000000	0.71417	1.000000	0.80357	0.959000	0.62525	5.747000	0.68689	1.433000	0.47394	0.650000	0.86243	CGT		0.323	DNAH8-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000043574.1	NM_001206927		25	68	25	68
EXOC4	60412	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	7	133749244	133749244	+	Missense_Mutation	SNP	A	A	G			TCGA-HT-7857-01A-11D-2395-08	TCGA-HT-7857-10A-01D-2396-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	58282498-c68f-4b15-89bb-68f49431393c	370dc8dd-90cf-4a60-be75-ccc17f9310fb	g.chr7:133749244A>G	ENST00000253861.4	+	18	2917	c.2888A>G	c.(2887-2889)aAg>aGg	p.K963R	EXOC4_ENST00000539845.1_Missense_Mutation_p.K862R|EXOC4_ENST00000541309.1_Missense_Mutation_p.K251R|EXOC4_ENST00000545148.1_Missense_Mutation_p.K573R	NM_021807.3	NP_068579.3	Q96A65	EXOC4_HUMAN	exocyst complex component 4	963					cellular protein metabolic process (GO:0044267)|membrane organization (GO:0061024)|protein transport (GO:0015031)|vesicle docking involved in exocytosis (GO:0006904)	cytoplasm (GO:0005737)|exocyst (GO:0000145)|growth cone membrane (GO:0032584)|membrane (GO:0016020)|myelin sheath abaxonal region (GO:0035748)|plasma membrane (GO:0005886)	protein N-terminus binding (GO:0047485)			NS(1)|breast(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(10)|lung(16)|ovary(4)|prostate(1)|skin(5)|upper_aerodigestive_tract(2)	50		Esophageal squamous(399;0.129)				GCTGCCATCAAGCAAGCCACC	0.572																																																0													89.0	79.0	82.0					7																	133749244		2203	4300	6503	SO:0001583	missense	60412			AL831989	CCDS5829.1, CCDS43648.1	7q31	2013-01-22	2005-11-01	2005-11-01	ENSG00000131558	ENSG00000131558			30389	protein-coding gene	gene with protein product		608185	"""SEC8-like 1 (S. cerevisiae)"""	SEC8L1		11214970, 12687004	Standard	XM_005250523		Approved	KIAA1699, MGC27170, SEC8, Sec8p	uc003vrk.3	Q96A65	OTTHUMG00000155259	ENST00000253861.4:c.2888A>G	7.37:g.133749244A>G	ENSP00000253861:p.Lys963Arg		E9PED2|Q541U8|Q9C0G4|Q9H9K0|Q9P102	Missense_Mutation	SNP	ENST00000253861.4	37	CCDS5829.1	.	.	.	.	.	.	.	.	.	.	A	31	5.076827	0.94000	.	.	ENSG00000131558	ENST00000253861;ENST00000546185;ENST00000539845;ENST00000545148;ENST00000541309	.	.	.	5.11	5.11	0.69529	.	0.000000	0.85682	D	0.000000	T	0.59404	0.2191	N	0.14661	0.345	0.54753	D	0.999983	D;D;P	0.71674	0.974;0.998;0.956	D;D;D	0.78314	0.969;0.991;0.931	T	0.59408	-0.7460	9	0.27785	T	0.31	.	15.0802	0.72108	1.0:0.0:0.0:0.0	.	495;573;963	B7Z689;F5GZT1;Q96A65	.;.;EXOC4_HUMAN	R	963;582;862;573;251	.	ENSP00000253861:K963R	K	+	2	0	EXOC4	133399784	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	8.719000	0.91436	2.135000	0.66039	0.528000	0.53228	AAG		0.572	EXOC4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000339182.1	NM_021807		21	80	21	80
UBR5	51366	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	8	103266680	103266680	+	Silent	SNP	G	G	A			TCGA-HT-7857-01A-11D-2395-08	TCGA-HT-7857-10A-01D-2396-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	58282498-c68f-4b15-89bb-68f49431393c	370dc8dd-90cf-4a60-be75-ccc17f9310fb	g.chr8:103266680G>A	ENST00000520539.1	-	59	8856	c.8250C>T	c.(8248-8250)ccC>ccT	p.P2750P	UBR5_ENST00000521922.1_Silent_p.P2743P|KB-431C1.5_ENST00000606361.1_RNA|KB-431C1.4_ENST00000499653.1_RNA|UBR5_ENST00000518205.1_Silent_p.P478P|UBR5_ENST00000220959.4_Silent_p.P2749P|KB-431C1.4_ENST00000520820.1_RNA	NM_001282873.1|NM_015902.5	NP_001269802.1|NP_056986.2	O95071	UBR5_HUMAN	ubiquitin protein ligase E3 component n-recognin 5	2750	HECT. {ECO:0000255|PROSITE- ProRule:PRU00104}.|Pro-rich.				cell proliferation (GO:0008283)|cellular response to DNA damage stimulus (GO:0006974)|DNA repair (GO:0006281)|negative regulation of double-strand break repair (GO:2000780)|negative regulation of histone H2A K63-linked ubiquitination (GO:1901315)|positive regulation of canonical Wnt signaling pathway (GO:0090263)|positive regulation of catenin import into nucleus (GO:0035413)|positive regulation of protein import into nucleus, translocation (GO:0033160)|progesterone receptor signaling pathway (GO:0050847)|protein polyubiquitination (GO:0000209)|protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:0042787)|ubiquitin-dependent protein catabolic process (GO:0006511)	cytoplasm (GO:0005737)|membrane (GO:0016020)|nucleus (GO:0005634)	ligase activity (GO:0016874)|RNA binding (GO:0003723)|ubiquitin-protein transferase activity (GO:0004842)|ubiquitin-ubiquitin ligase activity (GO:0034450)|zinc ion binding (GO:0008270)			NS(1)|breast(13)|central_nervous_system(1)|cervix(1)|endometrium(7)|kidney(8)|large_intestine(19)|liver(1)|lung(51)|ovary(6)|pancreas(1)|prostate(5)|skin(6)|upper_aerodigestive_tract(2)|urinary_tract(2)	124	all_cancers(14;8e-07)|all_epithelial(15;2.18e-08)|Lung NSC(17;2.55e-05)|all_lung(17;8.85e-05)		OV - Ovarian serous cystadenocarcinoma(57;0.000442)			TTGTGATTGAGGGCATAGGCT	0.408																																					Ovarian(131;96 1741 5634 7352 27489)											0													191.0	172.0	178.0					8																	103266680		2203	4300	6503	SO:0001819	synonymous_variant	51366			AF006010	CCDS34933.1, CCDS64946.1	8q22	2008-06-23	2007-06-19	2007-06-19	ENSG00000104517	ENSG00000104517		"""Ubiquitin protein ligase E3 component n-recognins"""	16806	protein-coding gene	gene with protein product		608413	"""E3 ubiquitin protein ligase, HECT domain containing, 1"""	EDD1		10030672, 16055722	Standard	NM_015902		Approved	DD5, HYD, EDD, KIAA0896	uc003ykr.2	O95071	OTTHUMG00000164755	ENST00000520539.1:c.8250C>T	8.37:g.103266680G>A			B2RP24|J3KMW7|O94970|Q9NPL3	Silent	SNP	ENST00000520539.1	37	CCDS34933.1																																																																																				0.408	UBR5-001	KNOWN	NAGNAG_splice_site|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000380075.2	NM_015902		11	77	11	77
KLHL25	64410	broad.mit.edu;ucsc.edu	37	15	86311637	86311637	+	Missense_Mutation	SNP	C	C	T			TCGA-HT-7857-01A-11D-2395-08	TCGA-HT-7857-10A-01D-2396-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	58282498-c68f-4b15-89bb-68f49431393c	370dc8dd-90cf-4a60-be75-ccc17f9310fb	g.chr15:86311637C>T	ENST00000337975.5	-	2	1679	c.1405G>A	c.(1405-1407)Gag>Aag	p.E469K	KLHL25_ENST00000559131.1_Intron|MIR1276_ENST00000408707.1_RNA|KLHL25_ENST00000536947.1_Missense_Mutation_p.E469K	NM_022480.3	NP_071925.2	Q9H0H3	KLH25_HUMAN	kelch-like family member 25	469					protein ubiquitination (GO:0016567)|protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:0042787)|regulation of translational initiation (GO:0006446)	Cul3-RING ubiquitin ligase complex (GO:0031463)|cytoplasm (GO:0005737)				breast(1)|central_nervous_system(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(4)|lung(7)|ovary(2)|prostate(1)|skin(1)|upper_aerodigestive_tract(2)	25						CACCTGTTCTCCGAGGGGTCA	0.602																																																0													94.0	83.0	87.0					15																	86311637		2202	4299	6501	SO:0001583	missense	64410				CCDS10339.1	15q25.3	2013-02-22	2013-02-22		ENSG00000183655	ENSG00000183655		"""Kelch-like"", ""BTB/POZ domain containing"""	25732	protein-coding gene	gene with protein product	"""ectodermal-neural cortex 2"""		"""kelch-like 25 (Drosophila)"""				Standard	XM_006720635		Approved	FLJ12587, ENC2, ENC-2	uc002bly.3	Q9H0H3	OTTHUMG00000148672	ENST00000337975.5:c.1405G>A	15.37:g.86311637C>T	ENSP00000336800:p.Glu469Lys		B2RDH2|B3KRT7	Missense_Mutation	SNP	ENST00000337975.5	37	CCDS10339.1	.	.	.	.	.	.	.	.	.	.	C	12.39	1.922708	0.33908	.	.	ENSG00000183655	ENST00000337975;ENST00000538153;ENST00000536947	T;T	0.77877	-1.13;-1.13	5.56	4.59	0.56863	Kelch-type beta propeller (1);	0.346209	0.29233	N	0.012755	T	0.67636	0.2914	L	0.27944	0.81	0.48185	D	0.999601	B	0.14805	0.011	B	0.25759	0.063	T	0.62163	-0.6912	10	0.29301	T	0.29	.	14.9943	0.71418	0.0:0.8572:0.1428:0.0	.	469	Q9H0H3	ENC2_HUMAN	K	469;438;469	ENSP00000336800:E469K;ENSP00000444739:E469K	ENSP00000336800:E469K	E	-	1	0	KLHL25	84112641	0.991000	0.36638	0.951000	0.38953	0.457000	0.32468	3.204000	0.51082	2.619000	0.88677	0.462000	0.41574	GAG		0.602	KLHL25-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000309023.1	NM_022480		17	140	17	140
OR10C1	442194	broad.mit.edu;ucsc.edu	37	6	29407957	29407957	+	Missense_Mutation	SNP	G	G	T			TCGA-HT-7857-01A-11D-2395-08	TCGA-HT-7857-10A-01D-2396-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	58282498-c68f-4b15-89bb-68f49431393c	370dc8dd-90cf-4a60-be75-ccc17f9310fb	g.chr6:29407957G>T	ENST00000444197.2	+	1	875	c.165G>T	c.(163-165)caG>caT	p.Q55H	OR11A1_ENST00000377149.1_Intron	NM_013941.3	NP_039229.3	Q96KK4	O10C1_HUMAN	olfactory receptor, family 10, subfamily C, member 1 (gene/pseudogene)	55						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			NS(1)|breast(2)|kidney(1)|large_intestine(3)|liver(2)|lung(14)|ovary(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	27						CTGCCCTCCAGTCCCCTATGT	0.567																																																0													193.0	164.0	174.0					6																	29407957		1510	2708	4218	SO:0001583	missense	442194				CCDS34364.1	6p22.2-p21.31	2013-10-10	2013-10-10		ENSG00000206474	ENSG00000206474		"""GPCR / Class A : Olfactory receptors"""	8165	protein-coding gene	gene with protein product			"""olfactory receptor, family 10, subfamily C, member 2"", ""olfactory receptor, family 10, subfamily C, member 1"""	OR10C2			Standard	NM_013941		Approved	hs6M1-17, OR10C1P	uc011dlp.2	Q96KK4	OTTHUMG00000031207	ENST00000444197.2:c.165G>T	6.37:g.29407957G>T	ENSP00000419119:p.Gln55His		Q5SUN7|Q96R18	Missense_Mutation	SNP	ENST00000444197.2	37	CCDS34364.1	.	.	.	.	.	.	.	.	.	.	G	1.598	-0.527357	0.04141	.	.	ENSG00000206474	ENST00000444197	T	0.00705	5.81	3.6	-1.63	0.08345	GPCR, rhodopsin-like superfamily (1);	0.227458	0.22242	U	0.062675	T	0.00073	0.0002	N	0.00385	-1.57	0.18873	N	0.999989	B	0.02656	0.0	B	0.04013	0.001	T	0.09640	-1.0665	10	0.02654	T	1	.	6.5302	0.22322	0.3368:0.4973:0.1659:0.0	.	55	Q96KK4	O10C1_HUMAN	H	55	ENSP00000419119:Q55H	ENSP00000419119:Q55H	Q	+	3	2	OR10C1	29515936	0.000000	0.05858	0.000000	0.03702	0.402000	0.30811	-0.330000	0.07925	-0.388000	0.07797	-0.450000	0.05554	CAG		0.567	OR10C1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076415.2			20	164	20	164
EMC10	284361	broad.mit.edu;ucsc.edu	37	19	50981247	50981247	+	Nonsense_Mutation	SNP	C	C	G			TCGA-HT-7857-01A-11D-2395-08	TCGA-HT-7857-10A-01D-2396-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	58282498-c68f-4b15-89bb-68f49431393c	370dc8dd-90cf-4a60-be75-ccc17f9310fb	g.chr19:50981247C>G	ENST00000334976.6	+	2	222	c.176C>G	c.(175-177)tCa>tGa	p.S59*	CTD-2545M3.2_ENST00000598194.1_RNA|EMC10_ENST00000376918.3_Nonsense_Mutation_p.S59*|EMC10_ENST00000598585.1_Nonsense_Mutation_p.S59*|FAM71E1_ENST00000595790.1_5'Flank|FAM71E1_ENST00000600100.1_5'Flank	NM_206538.2	NP_996261.1	Q5UCC4	EMC10_HUMAN	ER membrane protein complex subunit 10	59						ER membrane protein complex (GO:0072546)|extracellular region (GO:0005576)|integral component of membrane (GO:0016021)											CTGGAGCACTCATTTGAGATC	0.607																																																0													115.0	106.0	109.0					19																	50981247		2203	4300	6503	SO:0001587	stop_gained	284361			BC062607	CCDS12796.1, CCDS42594.1	19q13.33	2012-05-30	2012-05-30	2012-05-30	ENSG00000161671	ENSG00000161671			27609	protein-coding gene	gene with protein product	"""hematopoietic signal peptide-containing secreted 1"", ""hematopoietic signal peptide-containing membrane domain-containing 1"""	614545	"""chromosome 19 open reading frame 63"""	C19orf63		12975309, 22119785	Standard	NM_175063		Approved	INM02, HSS1, HSM1	uc002psl.3	Q5UCC4		ENST00000334976.6:c.176C>G	19.37:g.50981247C>G	ENSP00000334037:p.Ser59*		Q5UCC6|Q69YT5|Q6UWP3|Q86YL4|Q8N541	Nonsense_Mutation	SNP	ENST00000334976.6	37	CCDS12796.1	.	.	.	.	.	.	.	.	.	.	C	37	6.178158	0.97352	.	.	ENSG00000161671	ENST00000334976;ENST00000376918;ENST00000376920	.	.	.	4.4	4.4	0.53042	.	0.151315	0.45867	D	0.000336	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.72032	D	0.01	-27.0784	14.7052	0.69186	0.0:1.0:0.0:0.0	.	.	.	.	X	59	.	ENSP00000334037:S59X	S	+	2	0	C19orf63	55673059	0.997000	0.39634	0.975000	0.42487	0.988000	0.76386	4.573000	0.60893	2.359000	0.80004	0.491000	0.48974	TCA		0.607	EMC10-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000464760.2	NM_175063		3	33	3	33
PSME4	23198	broad.mit.edu;hgsc.bcm.edu	37	2	54148047	54148049	+	In_Frame_Del	DEL	AGG	AGG	-			TCGA-HT-7857-01A-11D-2395-08	TCGA-HT-7857-10A-01D-2396-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	58282498-c68f-4b15-89bb-68f49431393c	370dc8dd-90cf-4a60-be75-ccc17f9310fb	g.chr2:54148047_54148049delAGG	ENST00000404125.1	-	18	2294_2296	c.2239_2241delCCT	c.(2239-2241)cctdel	p.P747del	PSME4_ENST00000421748.2_Intron	NM_014614.2	NP_055429.2	Q14997	PSME4_HUMAN	proteasome (prosome, macropain) activator subunit 4	747					anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process (GO:0031145)|antigen processing and presentation of exogenous peptide antigen via MHC class I (GO:0042590)|antigen processing and presentation of exogenous peptide antigen via MHC class I, TAP-dependent (GO:0002479)|antigen processing and presentation of peptide antigen via MHC class I (GO:0002474)|apoptotic process (GO:0006915)|cellular nitrogen compound metabolic process (GO:0034641)|cellular response to DNA damage stimulus (GO:0006974)|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest (GO:0006977)|DNA repair (GO:0006281)|gene expression (GO:0010467)|mitotic cell cycle (GO:0000278)|mRNA metabolic process (GO:0016071)|multicellular organismal development (GO:0007275)|negative regulation of apoptotic process (GO:0043066)|positive regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051437)|proteasomal ubiquitin-independent protein catabolic process (GO:0010499)|protein polyubiquitination (GO:0000209)|regulation of apoptotic process (GO:0042981)|regulation of cellular amino acid metabolic process (GO:0006521)|regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051439)|RNA metabolic process (GO:0016070)|small molecule metabolic process (GO:0044281)|spermatogenesis, exchange of chromosomal proteins (GO:0035093)|viral process (GO:0016032)	cytosol (GO:0005829)|nucleus (GO:0005634)|spermatoproteasome complex (GO:1990111)	lysine-acetylated histone binding (GO:0070577)|peptidase activator activity (GO:0016504)			breast(5)|endometrium(8)|kidney(1)|large_intestine(11)|lung(26)|ovary(4)|pancreas(1)|prostate(1)|stomach(1)|urinary_tract(2)	60			Lung(47;0.125)|LUSC - Lung squamous cell carcinoma(58;0.181)			AGTATTCAGAAGGAGGCTTGTCA	0.374																																																0																																										SO:0001651	inframe_deletion	23198			D38521	CCDS33197.2	2p16.1	2003-04-14			ENSG00000068878	ENSG00000068878		"""Proteasome (prosome, macropain) subunits"""	20635	protein-coding gene	gene with protein product		607705				7584044, 12093752	Standard	NM_014614		Approved	PA200, KIAA0077	uc002rxp.2	Q14997	OTTHUMG00000151852	ENST00000404125.1:c.2239_2241delCCT	2.37:g.54148050_54148052delAGG	ENSP00000384211:p.Pro747del		Q1XBG4|Q1XBG5|Q1XBG6|Q2M1Z0|Q6IPR2|Q86XF8	In_Frame_Del	DEL	ENST00000404125.1	37	CCDS33197.2																																																																																				0.374	PSME4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000324163.1	XM_040158		22	75	22	75
PLA2G15	23659	broad.mit.edu;hgsc.bcm.edu	37	16	68293167	68293171	+	Frame_Shift_Del	DEL	CGTGC	CGTGC	-	rs200562766|rs142263893		TCGA-HT-7857-01A-11D-2395-08	TCGA-HT-7857-10A-01D-2396-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	58282498-c68f-4b15-89bb-68f49431393c	370dc8dd-90cf-4a60-be75-ccc17f9310fb	g.chr16:68293167_68293171delCGTGC	ENST00000219345.5	+	6	929_933	c.846_850delCGTGC	c.(844-852)ttcgtgcagfs	p.FVQ282fs	RP11-96D1.7_ENST00000563175.1_RNA|PLA2G15_ENST00000566188.1_3'UTR|RP11-96D1.7_ENST00000569843.1_RNA|PLA2G15_ENST00000413021.2_Frame_Shift_Del_p.FVQ188fs|PLA2G15_ENST00000444212.2_Frame_Shift_Del_p.FVQ82fs	NM_012320.3	NP_036452.1	Q8NCC3	PAG15_HUMAN	phospholipase A2, group XV	282					ceramide metabolic process (GO:0006672)|fatty acid catabolic process (GO:0009062)|phosphatidylcholine metabolic process (GO:0046470)	extracellular vesicular exosome (GO:0070062)|lysosome (GO:0005764)|mitochondrion (GO:0005739)	calcium-independent phospholipase A2 activity (GO:0047499)|lysophospholipase activity (GO:0004622)|O-acyltransferase activity (GO:0008374)|phospholipid binding (GO:0005543)			kidney(2)|large_intestine(2)|lung(2)|ovary(2)|prostate(3)|skin(1)	12						AGAAGGTGTTCGTGCAGACACCCAC	0.58																																																0																																										SO:0001589	frameshift_variant	23659			AB017494	CCDS10864.1	16q22.1	2008-09-19	2008-09-19	2008-09-19	ENSG00000103066	ENSG00000103066			17163	protein-coding gene	gene with protein product		609362	"""lysophospholipase 3 (lysosomal phospholipase A2)"""	LYPLA3		10092508, 16973413	Standard	XM_005255886		Approved	LLPL, GXVPLA2	uc002evr.3	Q8NCC3	OTTHUMG00000137554	ENST00000219345.5:c.846_850delCGTGC	16.37:g.68293167_68293171delCGTGC	ENSP00000219345:p.Phe282fs		B3KMF3|B4DUD1|Q53GZ1|Q9NPQ6|Q9UG04|Q9Y2B3	Frame_Shift_Del	DEL	ENST00000219345.5	37	CCDS10864.1																																																																																				0.580	PLA2G15-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000268888.2	NM_012320		16	67	16	67
ATRX	546	broad.mit.edu	37	X	76814303	76814306	+	Frame_Shift_Del	DEL	ATAA	ATAA	-			TCGA-HT-7857-01A-11D-2395-08	TCGA-HT-7857-10A-01D-2396-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	58282498-c68f-4b15-89bb-68f49431393c	370dc8dd-90cf-4a60-be75-ccc17f9310fb	g.chrX:76814303_76814306delATAA	ENST00000373344.5	-	29	6552_6555	c.6338_6341delTTAT	c.(6337-6342)tttatcfs	p.FI2113fs	ATRX_ENST00000395603.3_Frame_Shift_Del_p.FI2075fs|ATRX_ENST00000480283.1_5'UTR	NM_000489.3	NP_000480.3	P46100	ATRX_HUMAN	alpha thalassemia/mental retardation syndrome X-linked	2113	Helicase C-terminal. {ECO:0000255|PROSITE-ProRule:PRU00542}.|Interaction with MECP2.				ATP catabolic process (GO:0006200)|cellular response to hydroxyurea (GO:0072711)|chromatin remodeling (GO:0006338)|DNA damage response, signal transduction by p53 class mediator (GO:0030330)|DNA duplex unwinding (GO:0032508)|DNA methylation (GO:0006306)|DNA recombination (GO:0006310)|DNA repair (GO:0006281)|DNA replication-independent nucleosome assembly (GO:0006336)|forebrain development (GO:0030900)|negative regulation of telomeric RNA transcription from RNA pol II promoter (GO:1901581)|nucleosome assembly (GO:0006334)|positive regulation of nuclear cell cycle DNA replication (GO:0010571)|positive regulation of telomere maintenance (GO:0032206)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of transcription, DNA-templated (GO:0006355)|replication fork processing (GO:0031297)|seminiferous tubule development (GO:0072520)|Sertoli cell development (GO:0060009)|spermatogenesis (GO:0007283)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|mitochondrion (GO:0005739)|nuclear heterochromatin (GO:0005720)|nucleolus (GO:0005730)|nucleus (GO:0005634)|SWI/SNF superfamily-type complex (GO:0070603)|telomeric heterochromatin (GO:0031933)	ATP binding (GO:0005524)|chromatin binding (GO:0003682)|chromo shadow domain binding (GO:0070087)|DNA binding (GO:0003677)|DNA helicase activity (GO:0003678)|DNA translocase activity (GO:0015616)|helicase activity (GO:0004386)|histone binding (GO:0042393)|methylated histone binding (GO:0035064)|zinc ion binding (GO:0008270)	p.F2113fs*9(1)|p.?(1)		bone(1)|breast(6)|central_nervous_system(31)|cervix(2)|endometrium(7)|haematopoietic_and_lymphoid_tissue(15)|kidney(14)|large_intestine(1)|liver(1)|lung(40)|ovary(2)|pancreas(13)|prostate(5)|skin(2)|upper_aerodigestive_tract(3)|urinary_tract(2)	145						AGTAGAAATGATAAATAATCGTCC	0.289			"""Mis, F, N"""		"""Pancreatic neuroendocrine tumors, paediatric GBM"""		ATR-X (alpha thalassemia/mental retardation) syndrome																																Rec	yes		X	Xq21.1	546	alpha thalassemia/mental retardation syndrome X-linked	yes	E	2	Unknown(1)|Deletion - Frameshift(1)	bone(1)|pancreas(1)																																								SO:0001589	frameshift_variant	546			U72937	CCDS14434.1, CCDS14435.1	Xq21.1	2014-06-17	2010-06-24		ENSG00000085224	ENSG00000085224			886	protein-coding gene	gene with protein product	"""RAD54 homolog (S. cerevisiae)"""	300032	"""alpha thalassemia/mental retardation syndrome X-linked (RAD54 (S. cerevisiae) homolog)"", ""Juberg-Marsidi syndrome"""	RAD54, JMS		7874112, 1415255, 8503439, 8630485	Standard	NM_000489		Approved	XH2, XNP	uc004ecp.4	P46100	OTTHUMG00000022686	ENST00000373344.5:c.6338_6341delTTAT	X.37:g.76814307_76814310delATAA	ENSP00000362441:p.Phe2113fs		D3DTE2|P51068|Q15886|Q59FB5|Q59H31|Q5H9A2|Q5JWI4|Q7Z2J1|Q9H0Z1|Q9NTS3	Frame_Shift_Del	DEL	ENST00000373344.5	37	CCDS14434.1																																																																																				0.289	ATRX-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000058860.2	NM_000489		18	68	18	68
