#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
PTEN	5728	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	10	89692835	89692835	+	Missense_Mutation	SNP	G	G	T	rs57374291		TCGA-DU-6402-01A-11D-1705-08	TCGA-DU-6402-10A-01D-1705-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	896ec7d7-5443-49bb-969b-7b483e9b518c	3bc825bc-5589-4e0b-b380-38fceee3231b	g.chr10:89692835G>T	ENST00000371953.3	+	5	1676	c.319G>T	c.(319-321)Gat>Tat	p.D107Y		NM_000314.4	NP_000305.3	P60484	PTEN_HUMAN	phosphatase and tensin homolog	107	Phosphatase tensin-type. {ECO:0000255|PROSITE-ProRule:PRU00590}.		D -> Y (in BRRS and glioblastoma; loss of phosphatase activity towards Ins(1,3,4,5)P4). {ECO:0000269|PubMed:9331071}.		activation of mitotic anaphase-promoting complex activity (GO:0007092)|aging (GO:0007568)|angiogenesis (GO:0001525)|apoptotic process (GO:0006915)|brain morphogenesis (GO:0048854)|canonical Wnt signaling pathway (GO:0060070)|cardiac muscle tissue development (GO:0048738)|cell migration (GO:0016477)|cell proliferation (GO:0008283)|central nervous system development (GO:0007417)|central nervous system myelin maintenance (GO:0032286)|central nervous system neuron axonogenesis (GO:0021955)|dendritic spine morphogenesis (GO:0060997)|dentate gyrus development (GO:0021542)|endothelial cell migration (GO:0043542)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|forebrain morphogenesis (GO:0048853)|heart development (GO:0007507)|innate immune response (GO:0045087)|inositol phosphate dephosphorylation (GO:0046855)|inositol phosphate metabolic process (GO:0043647)|learning or memory (GO:0007611)|locomotor rhythm (GO:0045475)|locomotory behavior (GO:0007626)|long term synaptic depression (GO:0060292)|long-term synaptic potentiation (GO:0060291)|male mating behavior (GO:0060179)|maternal behavior (GO:0042711)|memory (GO:0007613)|multicellular organismal response to stress (GO:0033555)|negative regulation of apoptotic process (GO:0043066)|negative regulation of axonogenesis (GO:0050771)|negative regulation of cell aging (GO:0090344)|negative regulation of cell migration (GO:0030336)|negative regulation of cell proliferation (GO:0008285)|negative regulation of cell size (GO:0045792)|negative regulation of cyclin-dependent protein serine/threonine kinase activity involved in G1/S transition of mitotic cell cycle (GO:0031658)|negative regulation of dendritic spine morphogenesis (GO:0061002)|negative regulation of epithelial cell proliferation (GO:0050680)|negative regulation of excitatory postsynaptic membrane potential (GO:0090394)|negative regulation of focal adhesion assembly (GO:0051895)|negative regulation of G1/S transition of mitotic cell cycle (GO:2000134)|negative regulation of myelination (GO:0031642)|negative regulation of organ growth (GO:0046621)|negative regulation of phagocytosis (GO:0050765)|negative regulation of phosphatidylinositol 3-kinase signaling (GO:0014067)|negative regulation of protein kinase B signaling (GO:0051898)|negative regulation of protein phosphorylation (GO:0001933)|negative regulation of ribosome biogenesis (GO:0090071)|negative regulation of synaptic vesicle clustering (GO:2000808)|neuron-neuron synaptic transmission (GO:0007270)|neurotrophin TRK receptor signaling pathway (GO:0048011)|peptidyl-tyrosine dephosphorylation (GO:0035335)|phosphatidylinositol biosynthetic process (GO:0006661)|phosphatidylinositol dephosphorylation (GO:0046856)|phosphatidylinositol-mediated signaling (GO:0048015)|phospholipid metabolic process (GO:0006644)|platelet-derived growth factor receptor signaling pathway (GO:0048008)|positive regulation of apoptotic process (GO:0043065)|positive regulation of apoptotic signaling pathway (GO:2001235)|positive regulation of cell proliferation (GO:0008284)|positive regulation of excitatory postsynaptic membrane potential (GO:2000463)|positive regulation of protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:2000060)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|postsynaptic density assembly (GO:0097107)|prepulse inhibition (GO:0060134)|presynaptic membrane assembly (GO:0097105)|prostate gland growth (GO:0060736)|protein dephosphorylation (GO:0006470)|protein kinase B signaling (GO:0043491)|protein stabilization (GO:0050821)|regulation of B cell apoptotic process (GO:0002902)|regulation of cellular component size (GO:0032535)|regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0000079)|regulation of myeloid cell apoptotic process (GO:0033032)|regulation of neuron projection development (GO:0010975)|regulation of protein stability (GO:0031647)|response to arsenic-containing substance (GO:0046685)|response to ATP (GO:0033198)|response to drug (GO:0042493)|response to estradiol (GO:0032355)|response to ethanol (GO:0045471)|response to glucose (GO:0009749)|response to nutrient (GO:0007584)|response to zinc ion (GO:0010043)|rhythmic synaptic transmission (GO:0060024)|small molecule metabolic process (GO:0044281)|social behavior (GO:0035176)|synapse assembly (GO:0007416)|synapse maturation (GO:0060074)|T cell receptor signaling pathway (GO:0050852)	cell projection (GO:0042995)|cytoplasm (GO:0005737)|cytoplasmic side of plasma membrane (GO:0009898)|cytosol (GO:0005829)|dendritic spine (GO:0043197)|extracellular region (GO:0005576)|mitochondrion (GO:0005739)|myelin sheath adaxonal region (GO:0035749)|neuron projection (GO:0043005)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)|Schmidt-Lanterman incisure (GO:0043220)	anaphase-promoting complex binding (GO:0010997)|enzyme binding (GO:0019899)|inositol-1,3,4,5-tetrakisphosphate 3-phosphatase activity (GO:0051717)|lipid binding (GO:0008289)|magnesium ion binding (GO:0000287)|PDZ domain binding (GO:0030165)|phosphatidylinositol-3,4,5-trisphosphate 3-phosphatase activity (GO:0016314)|phosphatidylinositol-3,4-bisphosphate 3-phosphatase activity (GO:0051800)|phosphatidylinositol-3-phosphatase activity (GO:0004438)|phosphoprotein phosphatase activity (GO:0004721)|protein serine/threonine phosphatase activity (GO:0004722)|protein tyrosine phosphatase activity (GO:0004725)|protein tyrosine/serine/threonine phosphatase activity (GO:0008138)	p.0?(37)|p.?(5)|p.R55fs*1(5)|p.D107Y(3)|p.Y27fs*1(2)|p.F56fs*2(1)|p.P103fs*3(1)|p.D107N(1)		NS(28)|autonomic_ganglia(2)|biliary_tract(6)|bone(5)|breast(92)|central_nervous_system(676)|cervix(26)|endometrium(1068)|eye(8)|haematopoietic_and_lymphoid_tissue(137)|kidney(24)|large_intestine(98)|liver(20)|lung(91)|meninges(2)|oesophagus(2)|ovary(82)|pancreas(6)|prostate(129)|salivary_gland(5)|skin(127)|soft_tissue(19)|stomach(30)|testis(1)|thyroid(29)|upper_aerodigestive_tract(29)|urinary_tract(12)|vulva(17)	2771		all_cancers(4;3.61e-31)|all_epithelial(4;3.96e-23)|Prostate(4;8.12e-23)|Breast(4;0.000111)|Melanoma(5;0.00146)|all_hematologic(4;0.00227)|Colorectal(252;0.00494)|all_neural(4;0.00513)|Acute lymphoblastic leukemia(4;0.0116)|Glioma(4;0.0274)|all_lung(38;0.132)	KIRC - Kidney renal clear cell carcinoma(1;0.214)	UCEC - Uterine corpus endometrioid carcinoma (6;0.000228)|all cancers(1;4.16e-84)|GBM - Glioblastoma multiforme(1;7.77e-49)|Epithelial(1;7.67e-41)|OV - Ovarian serous cystadenocarcinoma(1;6.22e-15)|BRCA - Breast invasive adenocarcinoma(1;1.1e-06)|Lung(2;3.18e-06)|Colorectal(12;4.88e-06)|LUSC - Lung squamous cell carcinoma(2;4.97e-06)|COAD - Colon adenocarcinoma(12;1.13e-05)|Kidney(1;0.000288)|KIRC - Kidney renal clear cell carcinoma(1;0.00037)|STAD - Stomach adenocarcinoma(243;0.218)		CTTTTGTGAAGATCTTGACCA	0.368		31	"""D, Mis, N, F, S"""		"""glioma,  prostate, endometrial"""	"""harmartoma, glioma,  prostate, endometrial"""			Proteus syndrome;Juvenile Polyposis;Hereditary Mixed Polyposis Syndrome type 1;Cowden syndrome;Bannayan-Riley-Ruvalcaba syndrome	HNSCC(9;0.0022)|TCGA GBM(2;<1E-08)|TSP Lung(26;0.18)																												yes	Rec	yes	"""Cowden Syndrome, Bannayan-Riley-Ruvalcaba syndrome"""	10	10q23.3	5728	phosphatase and tensin homolog gene		"""L, E, M, O"""	55	Whole gene deletion(37)|Deletion - Frameshift(9)|Unknown(5)|Substitution - Missense(4)	prostate(16)|central_nervous_system(12)|skin(6)|lung(5)|haematopoietic_and_lymphoid_tissue(4)|breast(4)|endometrium(3)|ovary(3)|soft_tissue(1)|urinary_tract(1)											118.0	109.0	112.0					10																	89692835		2203	4297	6500	SO:0001583	missense	5728	Familial Cancer Database	Incl.: Encephalocraniocutaneous Lipomatosis, ECCL, Proteus-like s.;incl.: Juvenile Polyposis of the Stomach;HMPS1, Colorectal Adenoma Carcinoma syndrome, CRAC, CRAC1;CS, Cowden disease, Multiple Hamartoma Syndrome, incl.: Lhermitte-Duclos; part of PTEN hamartoma tumour syndrome (PHTS) / PTEN-MATCHS, Cowden-like syndrome;subset of PTEN-Hamartoma Tumor Syndrome; incl.: Ruvalcaba-Myhre-Smith s.	U92436	CCDS31238.1	10q23	2014-09-17	2008-07-31		ENSG00000171862	ENSG00000171862		"""Protein tyrosine phosphatases / Class I Cys-based PTPs : PTENs"""	9588	protein-coding gene	gene with protein product	"""mutated in multiple advanced cancers 1"""	601728		BZS, MHAM		9090379	Standard	NM_000314		Approved	MMAC1, TEP1, PTEN1	uc001kfb.3	P60484	OTTHUMG00000018688	ENST00000371953.3:c.319G>T	10.37:g.89692835G>T	ENSP00000361021:p.Asp107Tyr		B2R904|F2YHV0|O00633|O02679|Q6ICT7	Missense_Mutation	SNP	ENST00000371953.3	37	CCDS31238.1	.	.	.	.	.	.	.	.	.	.	G	26.2	4.714715	0.89112	.	.	ENSG00000171862	ENST00000371953	D	0.86297	-2.1	5.07	5.07	0.68467	Phosphatase tensin type (1);Dual specificity phosphatase, catalytic domain (1);	0.000000	0.85682	D	0.000000	D	0.94810	0.8324	M	0.90309	3.105	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.95560	0.8628	9	.	.	.	-8.2539	18.4584	0.90729	0.0:0.0:1.0:0.0	.	107	P60484	PTEN_HUMAN	Y	107	ENSP00000361021:D107Y	.	D	+	1	0	PTEN	89682815	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	9.425000	0.97467	2.318000	0.78349	0.655000	0.94253	GAT		0.368	PTEN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049241.1	NM_000314		25	48	25	48
MS4A6E	245802	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	11	60107365	60107365	+	Silent	SNP	T	T	A			TCGA-DU-6402-01A-11D-1705-08	TCGA-DU-6402-10A-01D-1705-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	896ec7d7-5443-49bb-969b-7b483e9b518c	3bc825bc-5589-4e0b-b380-38fceee3231b	g.chr11:60107365T>A	ENST00000300182.4	+	3	446	c.381T>A	c.(379-381)tcT>tcA	p.S127S		NM_139249.2	NP_640342.1	Q96DS6	M4A6E_HUMAN	membrane-spanning 4-domains, subfamily A, member 6E	127						integral component of membrane (GO:0016021)				endometrium(2)|kidney(1)|lung(9)|stomach(1)	13						TGCTGGTTTCTACTGTGTTGG	0.493																																																0													263.0	247.0	252.0					11																	60107365		2203	4300	6503	SO:0001819	synonymous_variant	245802			AF354931	CCDS7984.1	11q12	2008-03-25				ENSG00000166926			14285	protein-coding gene	gene with protein product		608402				11486273	Standard	NM_139249		Approved		uc001npd.3	Q96DS6		ENST00000300182.4:c.381T>A	11.37:g.60107365T>A			Q3MIL2|Q8NE56|Q96PG4|Q96PG5	Silent	SNP	ENST00000300182.4	37	CCDS7984.1																																																																																				0.493	MS4A6E-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000394296.1			76	200	76	200
EXPH5	23086	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	11	108381685	108381685	+	Missense_Mutation	SNP	G	G	T			TCGA-DU-6402-01A-11D-1705-08	TCGA-DU-6402-10A-01D-1705-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	896ec7d7-5443-49bb-969b-7b483e9b518c	3bc825bc-5589-4e0b-b380-38fceee3231b	g.chr11:108381685G>T	ENST00000265843.4	-	6	4659	c.4549C>A	c.(4549-4551)Cta>Ata	p.L1517I	EXPH5_ENST00000524840.1_5'Flank|EXPH5_ENST00000428840.1_Missense_Mutation_p.L1441I|EXPH5_ENST00000443411.1_Missense_Mutation_p.L1329I|EXPH5_ENST00000525344.1_Missense_Mutation_p.L1510I	NM_015065.2	NP_055880	Q8NEV8	EXPH5_HUMAN	exophilin 5	1517					intracellular protein transport (GO:0006886)|keratinocyte development (GO:0003334)|multivesicular body sorting pathway (GO:0071985)|positive regulation of exocytosis (GO:0045921)|positive regulation of protein secretion (GO:0050714)	endosome (GO:0005768)	Rab GTPase binding (GO:0017137)			breast(3)|central_nervous_system(3)|endometrium(6)|haematopoietic_and_lymphoid_tissue(2)|kidney(7)|large_intestine(13)|liver(1)|lung(34)|ovary(3)|pancreas(2)|prostate(2)|skin(11)|stomach(3)|upper_aerodigestive_tract(1)	91		all_cancers(61;3.99e-08)|Acute lymphoblastic leukemia(157;3.97e-05)|Melanoma(852;4.04e-05)|all_epithelial(67;0.000116)|all_hematologic(158;0.000315)|Breast(348;0.104)|all_neural(303;0.16)		Epithelial(105;8.1e-06)|BRCA - Breast invasive adenocarcinoma(274;1.22e-05)|all cancers(92;0.000129)|OV - Ovarian serous cystadenocarcinoma(223;0.11)|Colorectal(284;0.184)		CCAAGCTGTAGTTTATGCAAT	0.433																																																0													72.0	65.0	67.0					11																	108381685		2201	4298	6499	SO:0001583	missense	23086				CCDS8341.1	11q22.3	2008-02-05			ENSG00000110723	ENSG00000110723			30578	protein-coding gene	gene with protein product	"""synaptotagmin-like homologue lacking C2 domains b"""	612878				9734811, 11773082	Standard	NM_015065		Approved	SLAC2-B	uc001pkk.3	Q8NEV8	OTTHUMG00000166536	ENST00000265843.4:c.4549C>A	11.37:g.108381685G>T	ENSP00000265843:p.Leu1517Ile		Q2KHM1|Q9Y4D6	Missense_Mutation	SNP	ENST00000265843.4	37	CCDS8341.1	.	.	.	.	.	.	.	.	.	.	G	12.19	1.862730	0.32884	.	.	ENSG00000110723	ENST00000265843;ENST00000428840;ENST00000443411;ENST00000525344;ENST00000526312	T;T;T;T;T	0.03801	4.02;3.94;3.8;4.02;3.85	5.43	3.55	0.40652	.	0.277670	0.25881	N	0.027686	T	0.12561	0.0305	M	0.67953	2.075	0.09310	N	1	D	0.89917	1.0	D	0.71870	0.975	T	0.15407	-1.0438	10	0.27785	T	0.31	-6.8204	3.2979	0.06973	0.2567:0.0:0.5496:0.1937	.	1517	Q8NEV8	EXPH5_HUMAN	I	1517;1441;1329;1510;1441	ENSP00000265843:L1517I;ENSP00000391966:L1441I;ENSP00000411390:L1329I;ENSP00000432546:L1510I;ENSP00000432683:L1441I	ENSP00000265843:L1517I	L	-	1	2	EXPH5	107886895	0.993000	0.37304	0.395000	0.26283	0.106000	0.19336	2.626000	0.46460	1.289000	0.44618	0.491000	0.48974	CTA		0.433	EXPH5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000390279.1	NM_015065		8	30	8	30
EXPH5	23086	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	11	108382533	108382533	+	Missense_Mutation	SNP	G	G	C			TCGA-DU-6402-01A-11D-1705-08	TCGA-DU-6402-10A-01D-1705-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	896ec7d7-5443-49bb-969b-7b483e9b518c	3bc825bc-5589-4e0b-b380-38fceee3231b	g.chr11:108382533G>C	ENST00000265843.4	-	6	3811	c.3701C>G	c.(3700-3702)aCg>aGg	p.T1234R	EXPH5_ENST00000524840.1_5'Flank|EXPH5_ENST00000428840.1_Missense_Mutation_p.T1158R|EXPH5_ENST00000443411.1_Missense_Mutation_p.T1046R|EXPH5_ENST00000525344.1_Missense_Mutation_p.T1227R	NM_015065.2	NP_055880	Q8NEV8	EXPH5_HUMAN	exophilin 5	1234					intracellular protein transport (GO:0006886)|keratinocyte development (GO:0003334)|multivesicular body sorting pathway (GO:0071985)|positive regulation of exocytosis (GO:0045921)|positive regulation of protein secretion (GO:0050714)	endosome (GO:0005768)	Rab GTPase binding (GO:0017137)			breast(3)|central_nervous_system(3)|endometrium(6)|haematopoietic_and_lymphoid_tissue(2)|kidney(7)|large_intestine(13)|liver(1)|lung(34)|ovary(3)|pancreas(2)|prostate(2)|skin(11)|stomach(3)|upper_aerodigestive_tract(1)	91		all_cancers(61;3.99e-08)|Acute lymphoblastic leukemia(157;3.97e-05)|Melanoma(852;4.04e-05)|all_epithelial(67;0.000116)|all_hematologic(158;0.000315)|Breast(348;0.104)|all_neural(303;0.16)		Epithelial(105;8.1e-06)|BRCA - Breast invasive adenocarcinoma(274;1.22e-05)|all cancers(92;0.000129)|OV - Ovarian serous cystadenocarcinoma(223;0.11)|Colorectal(284;0.184)		AACAGAAAACGTACTAGTCGT	0.373																																																0													87.0	88.0	88.0					11																	108382533		2201	4298	6499	SO:0001583	missense	23086				CCDS8341.1	11q22.3	2008-02-05			ENSG00000110723	ENSG00000110723			30578	protein-coding gene	gene with protein product	"""synaptotagmin-like homologue lacking C2 domains b"""	612878				9734811, 11773082	Standard	NM_015065		Approved	SLAC2-B	uc001pkk.3	Q8NEV8	OTTHUMG00000166536	ENST00000265843.4:c.3701C>G	11.37:g.108382533G>C	ENSP00000265843:p.Thr1234Arg		Q2KHM1|Q9Y4D6	Missense_Mutation	SNP	ENST00000265843.4	37	CCDS8341.1	.	.	.	.	.	.	.	.	.	.	G	11.71	1.718640	0.30503	.	.	ENSG00000110723	ENST00000265843;ENST00000428840;ENST00000443411;ENST00000525344;ENST00000526312;ENST00000533052	T;T;T;T;T;T	0.04862	4.1;4.03;3.88;4.1;3.94;3.54	5.85	-5.91	0.02269	.	1.082130	0.06980	N	0.819688	T	0.09949	0.0244	N	0.19112	0.55	0.09310	N	1	P	0.47545	0.897	P	0.53593	0.73	T	0.31024	-0.9958	10	0.59425	D	0.04	1.2068	18.5995	0.91242	0.1727:0.0:0.8273:0.0	.	1234	Q8NEV8	EXPH5_HUMAN	R	1234;1158;1046;1227;1158;1046	ENSP00000265843:T1234R;ENSP00000391966:T1158R;ENSP00000411390:T1046R;ENSP00000432546:T1227R;ENSP00000432683:T1158R;ENSP00000446434:T1046R	ENSP00000265843:T1234R	T	-	2	0	EXPH5	107887743	0.035000	0.19736	0.000000	0.03702	0.181000	0.23173	-0.017000	0.12590	-1.050000	0.03230	-0.290000	0.09829	ACG		0.373	EXPH5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000390279.1	NM_015065		24	99	24	99
FZD10	11211	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	12	130648631	130648631	+	Missense_Mutation	SNP	G	G	A			TCGA-DU-6402-01A-11D-1705-08	TCGA-DU-6402-10A-01D-1705-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	896ec7d7-5443-49bb-969b-7b483e9b518c	3bc825bc-5589-4e0b-b380-38fceee3231b	g.chr12:130648631G>A	ENST00000229030.4	+	1	1628	c.1144G>A	c.(1144-1146)Ggg>Agg	p.G382R	FZD10-AS1_ENST00000505807.2_RNA|FZD10_ENST00000539839.1_Missense_Mutation_p.R349Q			Q9ULW2	FZD10_HUMAN	frizzled class receptor 10	382					brain development (GO:0007420)|canonical Wnt signaling pathway (GO:0060070)|cellular response to retinoic acid (GO:0071300)|gonad development (GO:0008406)|negative regulation of Rho GTPase activity (GO:0034259)|neuron differentiation (GO:0030182)|non-canonical Wnt signaling pathway via JNK cascade (GO:0038031)|positive regulation of JUN kinase activity (GO:0043507)|positive regulation of Rac GTPase activity (GO:0032855)|regulation of actin cytoskeleton organization (GO:0032956)|vasculature development (GO:0001944)	cell projection (GO:0042995)|cell surface (GO:0009986)|cytoplasm (GO:0005737)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|PDZ domain binding (GO:0030165)|Wnt-activated receptor activity (GO:0042813)|Wnt-protein binding (GO:0017147)			breast(1)|central_nervous_system(1)|endometrium(3)|kidney(4)|large_intestine(7)|lung(14)|pancreas(1)|prostate(3)|urinary_tract(1)	35	all_neural(191;0.101)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;1.3e-06)|Epithelial(86;1.66e-05)|all cancers(50;5.18e-05)		CGAGCTCACCGGGGTCTGCTA	0.647																																																0													84.0	77.0	79.0					12																	130648631		2203	4300	6503	SO:0001583	missense	11211			AB027464	CCDS9267.1	12q24.33	2014-01-29	2014-01-29			ENSG00000111432		"""GPCR / Class F : Frizzled receptors"", ""CD molecules"""	4039	protein-coding gene	gene with protein product		606147	"""frizzled (Drosophila) homolog 10"", ""frizzled homolog 10 (Drosophila)"", ""frizzled 10, seven transmembrane spanning receptor"", ""frizzled family receptor 10"""			10448064	Standard	NM_007197		Approved	CD350	uc001uii.3	Q9ULW2		ENST00000229030.4:c.1144G>A	12.37:g.130648631G>A	ENSP00000229030:p.Gly382Arg			Missense_Mutation	SNP	ENST00000229030.4	37	CCDS9267.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	16.76|16.76	3.213050|3.213050	0.58452|0.58452	.|.	.|.	ENSG00000111432|ENSG00000111432	ENST00000229030|ENST00000539839	D|.	0.92299|.	-3.01|.	5.21|5.21	5.21|5.21	0.72293|0.72293	GPCR, family 2-like (1);|.	0.000000|.	0.85682|.	U|.	0.000000|.	D|D	0.88500|0.88500	0.6453|0.6453	H|H	0.96720|0.96720	3.87|3.87	0.80722|0.80722	D|D	1|1	D|.	0.89917|.	1.0|.	D|.	0.97110|.	1.0|.	D|D	0.92436|0.92436	0.5958|0.5958	10|6	0.87932|0.87932	D|D	0|0	.|.	18.7539|18.7539	0.91825|0.91825	0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0	.|.	382|.	Q9ULW2|.	FZD10_HUMAN|.	R|Q	382|349	ENSP00000229030:G382R|.	ENSP00000229030:G382R|ENSP00000438460:R349Q	G|R	+|+	1|2	0|0	FZD10|FZD10	129214584|129214584	1.000000|1.000000	0.71417|0.71417	0.976000|0.976000	0.42696|0.42696	0.981000|0.981000	0.71138|0.71138	9.643000|9.643000	0.98464|0.98464	2.432000|2.432000	0.82394|0.82394	0.561000|0.561000	0.74099|0.74099	GGG|CGG		0.647	FZD10-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding				18	43	18	43
TICRR	90381	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	15	90167424	90167424	+	Missense_Mutation	SNP	C	C	A			TCGA-DU-6402-01A-11D-1705-08	TCGA-DU-6402-10A-01D-1705-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	896ec7d7-5443-49bb-969b-7b483e9b518c	3bc825bc-5589-4e0b-b380-38fceee3231b	g.chr15:90167424C>A	ENST00000268138.7	+	20	3988	c.3883C>A	c.(3883-3885)Cca>Aca	p.P1295T	TICRR_ENST00000560985.1_Missense_Mutation_p.P1294T|KIF7_ENST00000558928.1_Intron			Q7Z2Z1	TICRR_HUMAN	TOPBP1-interacting checkpoint and replication regulator	1295	Pro-rich.				cell cycle checkpoint (GO:0000075)|DNA repair (GO:0006281)|DNA replication (GO:0006260)|formation of translation preinitiation complex (GO:0001731)|mitotic DNA replication checkpoint (GO:0033314)|regulation of DNA-dependent DNA replication initiation (GO:0030174)|response to ionizing radiation (GO:0010212)	nucleus (GO:0005634)	chromatin binding (GO:0003682)										TCCAAAAAGACCAGGGAATTC	0.453																																																0													130.0	130.0	130.0					15																	90167424		2200	4299	6499	SO:0001583	missense	90381			AK123612	CCDS10352.2	15q26.1	2012-07-11	2012-07-11	2012-07-11	ENSG00000140534	ENSG00000140534			28704	protein-coding gene	gene with protein product	"""TOPBP1-interacting replication-stimulating protein"", ""SLD3 homolog (S. cerevisiae)"""	613298	"""chromosome 15 open reading frame 42"""	C15orf42		20116089, 20080954	Standard	NM_152259		Approved	MGC45866, FLJ41618, Treslin, SLD3	uc002boe.3	Q7Z2Z1	OTTHUMG00000149648	ENST00000268138.7:c.3883C>A	15.37:g.90167424C>A	ENSP00000268138:p.Pro1295Thr		B2RE07|B3KVV9|D3IUT4|Q8N4X8|Q8NCH6|Q9BU55	Missense_Mutation	SNP	ENST00000268138.7	37	CCDS10352.2	.	.	.	.	.	.	.	.	.	.	C	7.260	0.605084	0.14002	.	.	ENSG00000140534	ENST00000268138	T	0.08807	3.05	4.86	0.564	0.17302	.	1.025460	0.07794	N	0.955425	T	0.06554	0.0168	L	0.29908	0.895	0.09310	N	1	B	0.29646	0.253	B	0.30572	0.117	T	0.42565	-0.9444	10	0.41790	T	0.15	0.056	4.5613	0.12161	0.1235:0.6083:0.1205:0.1477	.	1295	Q7Z2Z1	TICRR_HUMAN	T	1295	ENSP00000268138:P1295T	ENSP00000268138:P1295T	P	+	1	0	C15orf42	87968428	0.000000	0.05858	0.000000	0.03702	0.251000	0.25915	0.024000	0.13555	0.554000	0.29061	0.655000	0.94253	CCA		0.453	TICRR-001	KNOWN	NAGNAG_splice_site|basic|appris_candidate_longest|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000312856.1	NM_152259		43	94	43	94
MYO15A	51168	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	17	18053797	18053797	+	Missense_Mutation	SNP	G	G	A	rs530783345		TCGA-DU-6402-01A-11D-1705-08	TCGA-DU-6402-10A-01D-1705-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	896ec7d7-5443-49bb-969b-7b483e9b518c	3bc825bc-5589-4e0b-b380-38fceee3231b	g.chr17:18053797G>A	ENST00000205890.5	+	36	7605	c.7267G>A	c.(7267-7269)Ggt>Agt	p.G2423S	MYO15A_ENST00000418233.3_5'Flank	NM_016239.3	NP_057323.3	Q9UKN7	MYO15_HUMAN	myosin XVA	2423	Tail.				inner ear morphogenesis (GO:0042472)|locomotory behavior (GO:0007626)|sensory perception of sound (GO:0007605)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|myosin complex (GO:0016459)|stereocilium (GO:0032420)	ATP binding (GO:0005524)|motor activity (GO:0003774)			breast(5)|central_nervous_system(2)|endometrium(17)|kidney(3)|large_intestine(16)|lung(27)|ovary(3)|pancreas(1)|prostate(6)|skin(13)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(2)	99	all_neural(463;0.228)					AGGCCAGCCCGGTGGAGGCAG	0.617													G|||	1	0.000199681	0.0	0.0	5008	,	,		17268	0.001		0.0	False		,,,				2504	0.0															0													63.0	79.0	74.0					17																	18053797		2126	4246	6372	SO:0001583	missense	51168			AF144094	CCDS42271.1	17p11.2	2011-09-27			ENSG00000091536	ENSG00000091536		"""Myosins / Myosin superfamily : Class XV"""	7594	protein-coding gene	gene with protein product		602666		DFNB3, MYO15		9603736	Standard	NM_016239		Approved		uc021trl.1	Q9UKN7	OTTHUMG00000059390	ENST00000205890.5:c.7267G>A	17.37:g.18053797G>A	ENSP00000205890:p.Gly2423Ser		B4DFC7	Missense_Mutation	SNP	ENST00000205890.5	37	CCDS42271.1	.	.	.	.	.	.	.	.	.	.	G	9.784	1.175990	0.21704	.	.	ENSG00000091536	ENST00000205890	D	0.90324	-2.65	4.67	-0.308	0.12773	.	.	.	.	.	D	0.86393	0.5922	L	0.53249	1.67	0.09310	N	1	B	0.19445	0.036	B	0.12837	0.008	T	0.73569	-0.3941	9	0.33940	T	0.23	.	10.9018	0.47056	0.2928:0.0:0.7072:0.0	.	2423	Q9UKN7	MYO15_HUMAN	S	2423	ENSP00000205890:G2423S	ENSP00000205890:G2423S	G	+	1	0	MYO15A	17994522	0.084000	0.21492	0.185000	0.23176	0.113000	0.19764	1.122000	0.31295	0.078000	0.16900	-1.810000	0.00614	GGT		0.617	MYO15A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000132048.1	NM_016239		10	44	10	44
NF1	4763	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	17	29663747	29663747	+	Nonsense_Mutation	SNP	T	T	G			TCGA-DU-6402-01A-11D-1705-08	TCGA-DU-6402-10A-01D-1705-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	896ec7d7-5443-49bb-969b-7b483e9b518c	3bc825bc-5589-4e0b-b380-38fceee3231b	g.chr17:29663747T>G	ENST00000358273.4	+	42	6625	c.6242T>G	c.(6241-6243)tTa>tGa	p.L2081*	NF1_ENST00000417592.2_5'Flank|NF1_ENST00000356175.3_Nonsense_Mutation_p.L2060*|NF1_ENST00000444181.2_5'Flank	NM_001042492.2	NP_001035957.1	P21359	NF1_HUMAN	neurofibromin 1	2081					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.?(3)	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)		ATTGCTATTTTAGCACGCTAC	0.408			"""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	11	Whole gene deletion(8)|Unknown(3)	soft_tissue(7)|autonomic_ganglia(2)|lung(1)|central_nervous_system(1)											184.0	156.0	166.0					17																	29663747		2203	4300	6503	SO:0001587	stop_gained	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.6242T>G	17.37:g.29663747T>G	ENSP00000351015:p.Leu2081*		O00662|Q14284|Q14930|Q14931|Q9UMK3	Nonsense_Mutation	SNP	ENST00000358273.4	37	CCDS42292.1	.	.	.	.	.	.	.	.	.	.	T	48	14.269026	0.99787	.	.	ENSG00000196712	ENST00000358273;ENST00000356175;ENST00000456735	.	.	.	5.48	5.48	0.80851	.	0.000000	0.64402	D	0.000001	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	15.865	0.79057	0.0:0.0:0.0:1.0	.	.	.	.	X	2081;2060;1726	.	ENSP00000348498:L2060X	L	+	2	0	NF1	26687873	1.000000	0.71417	0.988000	0.46212	0.988000	0.76386	7.537000	0.82033	2.185000	0.69588	0.533000	0.62120	TTA		0.408	NF1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000256351.2	NM_000267		23	61	23	61
ANKRD30B	374860	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	18	14763803	14763803	+	Silent	SNP	G	G	A	rs186852668		TCGA-DU-6402-01A-11D-1705-08	TCGA-DU-6402-10A-01D-1705-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	896ec7d7-5443-49bb-969b-7b483e9b518c	3bc825bc-5589-4e0b-b380-38fceee3231b	g.chr18:14763803G>A	ENST00000358984.4	+	7	1119	c.939G>A	c.(937-939)acG>acA	p.T313T	ANKRD30B_ENST00000579292.1_Intron|ANKRD30B_ENST00000447268.2_Silent_p.T313T	NM_001145029.1	NP_001138501.1	Q9BXX2	AN30B_HUMAN	ankyrin repeat domain 30B	313										breast(3)|endometrium(4)|kidney(3)|lung(8)|ovary(1)|prostate(2)|skin(1)	22						TGGAGGGAACGTCTGCCAAAA	0.478													a|||	1	0.000199681	0.0008	0.0	5008	,	,		16791	0.0		0.0	False		,,,				2504	0.0															0													66.0	65.0	65.0					18																	14763803		692	1591	2283	SO:0001819	synonymous_variant	374860			BC028407	CCDS54182.1	18p11.21	2013-01-10			ENSG00000180777	ENSG00000180777		"""Ankyrin repeat domain containing"""	24165	protein-coding gene	gene with protein product						11280766	Standard	NM_001145029		Approved	NY-BR-1.1	uc010dlo.2	Q9BXX2		ENST00000358984.4:c.939G>A	18.37:g.14763803G>A			B4DGP1|F8WAG3|Q4G175	Silent	SNP	ENST00000358984.4	37	CCDS54182.1																																																																																				0.478	ANKRD30B-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000443557.1	NM_001145029		8	14	8	14
NEDD4L	23327	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	18	56008358	56008358	+	Missense_Mutation	SNP	A	A	G			TCGA-DU-6402-01A-11D-1705-08	TCGA-DU-6402-10A-01D-1705-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	896ec7d7-5443-49bb-969b-7b483e9b518c	3bc825bc-5589-4e0b-b380-38fceee3231b	g.chr18:56008358A>G	ENST00000400345.3	+	14	1497	c.1214A>G	c.(1213-1215)aAt>aGt	p.N405S	NEDD4L_ENST00000456173.2_Missense_Mutation_p.N264S|NEDD4L_ENST00000382850.4_Missense_Mutation_p.N385S|NEDD4L_ENST00000356462.6_Intron|NEDD4L_ENST00000589054.1_Intron|NEDD4L_ENST00000431212.2_Missense_Mutation_p.N284S|NEDD4L_ENST00000435432.2_Missense_Mutation_p.N264S|NEDD4L_ENST00000586263.1_Missense_Mutation_p.N377S|NEDD4L_ENST00000357895.5_Missense_Mutation_p.N397S|NEDD4L_ENST00000256830.9_Intron|NEDD4L_ENST00000456986.1_Missense_Mutation_p.N284S|NEDD4L_ENST00000256832.7_Missense_Mutation_p.N264S	NM_001144967.2	NP_001138439.1	Q96PU5	NED4L_HUMAN	neural precursor cell expressed, developmentally down-regulated 4-like, E3 ubiquitin protein ligase	405	WW 2. {ECO:0000255|PROSITE- ProRule:PRU00224}.				cellular sodium ion homeostasis (GO:0006883)|excretion (GO:0007588)|gene expression (GO:0010467)|ion transmembrane transport (GO:0034220)|negative regulation of potassium ion transmembrane transport (GO:1901380)|negative regulation of potassium ion transmembrane transporter activity (GO:1901017)|negative regulation of protein localization to cell surface (GO:2000009)|negative regulation of sodium ion transmembrane transport (GO:1902306)|negative regulation of sodium ion transmembrane transporter activity (GO:2000650)|negative regulation of systemic arterial blood pressure (GO:0003085)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transforming growth factor beta receptor signaling pathway (GO:0030512)|positive regulation of cation channel activity (GO:2001259)|positive regulation of caveolin-mediated endocytosis (GO:2001288)|positive regulation of endocytosis (GO:0045807)|positive regulation of protein catabolic process (GO:0045732)|positive regulation of sodium ion transport (GO:0010765)|proteasome-mediated ubiquitin-dependent protein catabolic process (GO:0043161)|protein K48-linked ubiquitination (GO:0070936)|protein monoubiquitination (GO:0006513)|protein ubiquitination (GO:0016567)|protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:0042787)|regulation of ion transmembrane transport (GO:0034765)|regulation of membrane depolarization (GO:0003254)|regulation of membrane potential (GO:0042391)|regulation of membrane repolarization (GO:0060306)|regulation of potassium ion transmembrane transporter activity (GO:1901016)|regulation of protein catabolic process (GO:0042176)|regulation of tight junction assembly (GO:2000810)|response to metal ion (GO:0010038)|response to salt stress (GO:0009651)|sodium ion transport (GO:0006814)|transcription initiation from RNA polymerase II promoter (GO:0006367)|transcription, DNA-templated (GO:0006351)|transforming growth factor beta receptor signaling pathway (GO:0007179)|transmembrane transport (GO:0055085)|ubiquitin-dependent protein catabolic process via the multivesicular body sorting pathway (GO:0043162)|ventricular cardiac muscle cell action potential (GO:0086005)|viral life cycle (GO:0019058)|viral process (GO:0016032)|water homeostasis (GO:0030104)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|intracellular (GO:0005622)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	ion channel binding (GO:0044325)|ligase activity (GO:0016874)|potassium channel inhibitor activity (GO:0019870)|potassium channel regulator activity (GO:0015459)|sodium channel inhibitor activity (GO:0019871)|sodium channel regulator activity (GO:0017080)|ubiquitin-protein transferase activity (GO:0004842)			breast(1)|endometrium(7)|kidney(3)|large_intestine(10)|lung(11)|ovary(1)|prostate(4)	37						TACTATGTCAATCATAACAAT	0.478																																																0													68.0	64.0	66.0					18																	56008358		2016	4167	6183	SO:0001583	missense	23327			AF210730	CCDS45872.1, CCDS45873.1, CCDS45874.1, CCDS45875.1, CCDS45876.1, CCDS58632.1, CCDS59323.1	18q21.31	2014-08-12	2012-02-23		ENSG00000049759				7728	protein-coding gene	gene with protein product		606384	"""neural precursor cell expressed, developmentally down-regulated 4-like"""			10594025, 11244092, 18322022	Standard	NM_001144965		Approved	KIAA0439, RSP5, NEDD4-2	uc002lgy.3	Q96PU5	OTTHUMG00000179875	ENST00000400345.3:c.1214A>G	18.37:g.56008358A>G	ENSP00000383199:p.Asn405Ser		O43165|Q3LSM7|Q7Z5F1|Q7Z5F2|Q7Z5N3|Q8N5A7|Q8WUU9|Q9BW58|Q9H2W4|Q9NT88	Missense_Mutation	SNP	ENST00000400345.3	37	CCDS45872.1	.	.	.	.	.	.	.	.	.	.	A	32	5.174768	0.94807	.	.	ENSG00000049759	ENST00000400345;ENST00000382850;ENST00000256832;ENST00000456986;ENST00000357895;ENST00000435432;ENST00000456173;ENST00000431212	D;D;D;D;D;D;D;D	0.92149	-2.98;-2.98;-2.98;-2.98;-2.98;-2.98;-2.98;-2.98	6.0	6.0	0.97389	WW/Rsp5/WWP (6);	0.039861	0.85682	D	0.000000	D	0.96386	0.8821	M	0.86268	2.805	0.80722	D	1	P;P;D;P;P	0.69078	0.866;0.859;0.997;0.942;0.928	P;P;D;P;P	0.77004	0.591;0.511;0.989;0.714;0.591	D	0.96813	0.9598	10	0.72032	D	0.01	.	16.5047	0.84268	1.0:0.0:0.0:0.0	.	377;397;264;405;385	Q96PU5-6;Q96PU5-7;Q3LSM7;Q96PU5;Q96PU5-5	.;.;.;NED4L_HUMAN;.	S	405;385;264;284;397;264;264;284	ENSP00000383199:N405S;ENSP00000372301:N385S;ENSP00000256832:N264S;ENSP00000411947:N284S;ENSP00000350569:N397S;ENSP00000393395:N264S;ENSP00000405440:N264S;ENSP00000389406:N284S	ENSP00000256832:N264S	N	+	2	0	NEDD4L	54159338	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	9.314000	0.96306	2.297000	0.77311	0.533000	0.62120	AAT		0.478	NEDD4L-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000448749.1			4	7	4	7
CD70	970	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	19	6590911	6590911	+	Missense_Mutation	SNP	C	C	T	rs148772362		TCGA-DU-6402-01A-11D-1705-08	TCGA-DU-6402-10A-01D-1705-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	896ec7d7-5443-49bb-969b-7b483e9b518c	3bc825bc-5589-4e0b-b380-38fceee3231b	g.chr19:6590911C>T	ENST00000245903.3	-	1	252	c.103G>A	c.(103-105)Gtg>Atg	p.V35M	CD70_ENST00000423145.3_Missense_Mutation_p.V35M	NM_001252.3	NP_001243.1	P32970	CD70_HUMAN	CD70 molecule	35					cell proliferation (GO:0008283)|cell-cell signaling (GO:0007267)|extrinsic apoptotic signaling pathway (GO:0097191)|immune response (GO:0006955)|signal transduction (GO:0007165)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	protease binding (GO:0002020)|receptor binding (GO:0005102)			endometrium(1)|haematopoietic_and_lymphoid_tissue(3)|large_intestine(6)|skin(1)	11						ATGCACACCACGAGGCAGATC	0.627																																					Pancreas(183;2617 2876 10173 34193)											0								C	MET/VAL	1,4405	2.1+/-5.4	0,1,2202	67.0	68.0	68.0		103	-4.6	0.0	19	dbSNP_134	68	0,8600		0,0,4300	no	missense	CD70	NM_001252.3	21	0,1,6502	TT,TC,CC		0.0,0.0227,0.0077	benign	35/194	6590911	1,13005	2203	4300	6503	SO:0001583	missense	970			L08096	CCDS12170.1	19p13	2013-05-22	2006-10-27	2006-10-27		ENSG00000125726		"""Tumor necrosis factor (ligand) superfamily"", ""CD molecules"""	11937	protein-coding gene	gene with protein product		602840	"""tumor necrosis factor (ligand) superfamily, member 7"""	CD27LG, TNFSF7		8387892, 8120384	Standard	NM_001252		Approved	CD27L	uc002mfi.3	P32970		ENST00000245903.3:c.103G>A	19.37:g.6590911C>T	ENSP00000245903:p.Val35Met		B4DPR8|Q53XX4|Q96J57	Missense_Mutation	SNP	ENST00000245903.3	37	CCDS12170.1	.	.	.	.	.	.	.	.	.	.	C	7.743	0.701715	0.15172	2.27E-4	0.0	ENSG00000125726	ENST00000423145;ENST00000245903	.	.	.	2.28	-4.56	0.03431	.	2.073560	0.02924	N	0.138341	T	0.11410	0.0278	N	0.08118	0	0.09310	N	1	D;P	0.53745	0.962;0.865	B;B	0.42495	0.389;0.086	T	0.10222	-1.0639	9	0.39692	T	0.17	-1.9962	0.9184	0.01309	0.1984:0.3197:0.2838:0.1981	.	35;35	B4DPR8;P32970	.;CD70_HUMAN	M	35	.	ENSP00000245903:V35M	V	-	1	0	CD70	6541911	0.000000	0.05858	0.000000	0.03702	0.003000	0.03518	-0.648000	0.05391	-2.299000	0.00659	-0.694000	0.03704	GTG		0.627	CD70-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000457860.1			32	62	32	62
UBE2M	9040	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	19	59068093	59068093	+	Missense_Mutation	SNP	T	T	C			TCGA-DU-6402-01A-11D-1705-08	TCGA-DU-6402-10A-01D-1705-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	896ec7d7-5443-49bb-969b-7b483e9b518c	3bc825bc-5589-4e0b-b380-38fceee3231b	g.chr19:59068093T>C	ENST00000253023.3	-	4	886	c.308A>G	c.(307-309)aAc>aGc	p.N103S	CHMP2A_ENST00000601220.1_5'Flank|CHMP2A_ENST00000600118.1_5'Flank|CHMP2A_ENST00000312547.2_5'Flank|AC016629.8_ENST00000600534.1_RNA|AC016629.8_ENST00000593642.1_RNA|AC016629.8_ENST00000600726.1_RNA	NM_003969.3	NP_003960.1	P61081	UBC12_HUMAN	ubiquitin-conjugating enzyme E2M	103					cellular protein modification process (GO:0006464)|positive regulation of neuron apoptotic process (GO:0043525)|protein neddylation (GO:0045116)|protein ubiquitination (GO:0016567)|transforming growth factor beta receptor signaling pathway (GO:0007179)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)	ATP binding (GO:0005524)|NEDD8 ligase activity (GO:0019788)|ribosomal S6-glutamic acid ligase activity (GO:0018169)|ubiquitin-protein transferase activity (GO:0004842)			large_intestine(1)|lung(2)|ovary(1)|pancreas(1)	5		all_cancers(17;4.4e-22)|all_epithelial(17;2.15e-16)|Lung NSC(17;1.24e-06)|all_lung(17;5.41e-06)|Colorectal(82;3.46e-05)|Renal(17;0.00179)|all_neural(62;0.00607)|Ovarian(87;0.0443)|Breast(46;0.0928)|Medulloblastoma(540;0.184)		UCEC - Uterine corpus endometrioid carcinoma (67;0.0434)|all cancers(4;1.39e-13)|Epithelial(4;1.01e-10)|OV - Ovarian serous cystadenocarcinoma(4;2.34e-09)|GBM - Glioblastoma multiforme(193;0.0102)|Lung(386;0.179)		GAGGTCAATGTTGGGGTGATA	0.582																																																0													95.0	85.0	88.0					19																	59068093		2203	4300	6503	SO:0001583	missense	9040			AB012191	CCDS12987.1	19q13.43	2011-05-19	2011-05-19		ENSG00000130725	ENSG00000130725		"""Ubiquitin-conjugating enzymes E2"""	12491	protein-coding gene	gene with protein product		603173	"""ubiquitin-conjugating enzyme E2M (homologous to yeast UBC12)"", ""ubiquitin-conjugating enzyme E2M (UBC12 homolog, yeast)"""			9694792	Standard	NM_003969		Approved	hUbc12, UBC12	uc002qtl.4	P61081		ENST00000253023.3:c.308A>G	19.37:g.59068093T>C	ENSP00000253023:p.Asn103Ser		O76069|Q8VC50	Missense_Mutation	SNP	ENST00000253023.3	37	CCDS12987.1	.	.	.	.	.	.	.	.	.	.	T	21.6	4.171960	0.78452	.	.	ENSG00000130725	ENST00000253023	T	0.56103	0.48	4.77	4.77	0.60923	Ubiquitin-conjugating enzyme, E2 (2);Ubiquitin-conjugating enzyme/RWD-like (2);	0.000000	0.64402	D	0.000001	T	0.81616	0.4860	H	0.98594	4.275	0.51767	D	0.999931	D	0.89917	1.0	D	0.97110	1.0	D	0.87008	0.2121	10	0.87932	D	0	-36.8635	10.8931	0.47006	0.0:0.0:0.0:1.0	.	103	P61081	UBC12_HUMAN	S	103	ENSP00000253023:N103S	ENSP00000253023:N103S	N	-	2	0	UBE2M	63759905	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	6.699000	0.74613	2.157000	0.67596	0.533000	0.62120	AAC		0.582	UBE2M-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000467097.1	NM_003969		18	35	18	35
PRAMEF4	400735	hgsc.bcm.edu;broad.mit.edu	37	1	12941802	12941802	+	Missense_Mutation	SNP	C	C	T			TCGA-DU-6402-01A-11D-1705-08	TCGA-DU-6402-10A-01D-1705-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	896ec7d7-5443-49bb-969b-7b483e9b518c	3bc825bc-5589-4e0b-b380-38fceee3231b	g.chr1:12941802C>T	ENST00000235349.5	-	3	818	c.748G>A	c.(748-750)Gtt>Att	p.V250I		NM_001009611.2	NP_001009611.1	O60810	PRAM4_HUMAN	PRAME family member 4	250					negative regulation of apoptotic process (GO:0043066)|negative regulation of cell differentiation (GO:0045596)|negative regulation of retinoic acid receptor signaling pathway (GO:0048387)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of cell proliferation (GO:0008284)					breast(1)|endometrium(2)|kidney(1)|large_intestine(4)|lung(10)|ovary(2)|prostate(3)|skin(1)	24	Ovarian(185;0.249)	Lung NSC(185;3.67e-05)|all_lung(284;4.03e-05)|Renal(390;0.000147)|Breast(348;0.000278)|Colorectal(325;0.00058)|Ovarian(437;0.00965)|Hepatocellular(190;0.0245)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.00812)|Colorectal(212;4.88e-06)|Kidney(185;4.89e-05)|KIRC - Kidney renal clear cell carcinoma(229;0.000194)|COAD - Colon adenocarcinoma(227;0.000241)|BRCA - Breast invasive adenocarcinoma(304;0.000293)|STAD - Stomach adenocarcinoma(313;0.0072)|READ - Rectum adenocarcinoma(331;0.0649)		TCTGGGGAAACGTAGCGAGAG	0.488																																																0													231.0	278.0	261.0					1																	12941802		1434	2488	3922	SO:0001583	missense	400735				CCDS30592.1	1p36.21	2013-01-17			ENSG00000243073	ENSG00000243073		"""-"""	31971	protein-coding gene	gene with protein product							Standard	NM_001009611		Approved	RP5-845O24.6	uc001aun.2	O60810	OTTHUMG00000001987	ENST00000235349.5:c.748G>A	1.37:g.12941802C>T	ENSP00000235349:p.Val250Ile		Q5LJB5	Missense_Mutation	SNP	ENST00000235349.5	37	CCDS30592.1	.	.	.	.	.	.	.	.	.	.	c	0.003	-2.430291	0.00184	.	.	ENSG00000243073	ENST00000235349	T	0.47177	0.85	1.48	-2.96	0.05547	.	1.767480	0.03339	N	0.194469	T	0.16727	0.0402	N	0.02181	-0.65	0.09310	N	1	B	0.13145	0.007	B	0.09377	0.004	T	0.08432	-1.0722	10	0.09590	T	0.72	.	2.3053	0.04173	0.234:0.315:0.0:0.451	.	250	O60810	PRAM4_HUMAN	I	250	ENSP00000235349:V250I	ENSP00000235349:V250I	V	-	1	0	PRAMEF4	12864389	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-2.393000	0.01055	-1.053000	0.03218	-0.755000	0.03482	GTT		0.488	PRAMEF4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000005518.1	NM_001009611		83	239	83	239
TCHH	7062	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	1	152082385	152082385	+	Missense_Mutation	SNP	C	C	T			TCGA-DU-6402-01A-11D-1705-08	TCGA-DU-6402-10A-01D-1705-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	896ec7d7-5443-49bb-969b-7b483e9b518c	3bc825bc-5589-4e0b-b380-38fceee3231b	g.chr1:152082385C>T	ENST00000368804.1	-	2	3307	c.3308G>A	c.(3307-3309)cGc>cAc	p.R1103H		NM_007113.2	NP_009044.2	Q07283	TRHY_HUMAN	trichohyalin	1103	10 X 30 AA tandem repeats.				keratinization (GO:0031424)	cytoskeleton (GO:0005856)	calcium ion binding (GO:0005509)			NS(2)|breast(4)|central_nervous_system(1)|cervix(1)|endometrium(20)|kidney(9)|large_intestine(16)|lung(33)|ovary(3)|pancreas(1)|prostate(4)|skin(5)|upper_aerodigestive_tract(2)|urinary_tract(4)	105	Hepatocellular(266;0.0877)|Melanoma(130;0.116)|all_hematologic(923;0.127)		LUSC - Lung squamous cell carcinoma(543;0.206)			CCGCTCCTGGCGCCTTCTCTT	0.612																																																0													89.0	92.0	91.0					1																	152082385		1971	4138	6109	SO:0001583	missense	7062			L09190	CCDS41396.1	1q21-q23	2013-01-10		2006-01-27	ENSG00000159450	ENSG00000159450		"""EF-hand domain containing"""	11791	protein-coding gene	gene with protein product		190370		THH		1431214	Standard	NM_007113		Approved		uc001ezp.3	Q07283	OTTHUMG00000013066	ENST00000368804.1:c.3308G>A	1.37:g.152082385C>T	ENSP00000357794:p.Arg1103His		Q5VUI3	Missense_Mutation	SNP	ENST00000368804.1	37	CCDS41396.1	.	.	.	.	.	.	.	.	.	.	C	7.652	0.683101	0.14907	.	.	ENSG00000159450	ENST00000368804	T	0.05925	3.37	3.07	1.04	0.20106	.	.	.	.	.	T	0.02230	0.0069	L	0.29908	0.895	0.09310	N	1	D	0.76494	0.999	P	0.50082	0.63	T	0.40496	-0.9560	9	0.42905	T	0.14	.	3.7653	0.08620	0.4368:0.4379:0.0:0.1253	.	1103	Q07283	TRHY_HUMAN	H	1103	ENSP00000357794:R1103H	ENSP00000357794:R1103H	R	-	2	0	TCHH	150349009	0.001000	0.12720	0.043000	0.18650	0.033000	0.12548	-0.022000	0.12480	0.041000	0.15688	-0.361000	0.07541	CGC		0.612	TCHH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000036671.2	NM_007113		22	48	22	48
CD1E	913	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	1	158324220	158324220	+	Missense_Mutation	SNP	C	C	T	rs368204233		TCGA-DU-6402-01A-11D-1705-08	TCGA-DU-6402-10A-01D-1705-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	896ec7d7-5443-49bb-969b-7b483e9b518c	3bc825bc-5589-4e0b-b380-38fceee3231b	g.chr1:158324220C>T	ENST00000368167.3	+	2	351	c.112C>T	c.(112-114)Cgc>Tgc	p.R38C	CD1E_ENST00000368166.3_Intron|CD1E_ENST00000368157.1_Intron|CD1E_ENST00000368161.3_Missense_Mutation_p.R38C|CD1E_ENST00000464822.1_Intron|CD1E_ENST00000452291.2_Intron|CD1E_ENST00000368155.3_Missense_Mutation_p.R38C|CD1E_ENST00000368160.3_Missense_Mutation_p.R38C|CD1E_ENST00000444681.2_Intron|CD1E_ENST00000368163.3_Missense_Mutation_p.R38C|CD1E_ENST00000434258.1_Missense_Mutation_p.R36C|CD1E_ENST00000368164.3_Intron|CD1E_ENST00000368154.1_Intron|CD1E_ENST00000368156.1_Missense_Mutation_p.R38C|CD1E_ENST00000368165.3_Missense_Mutation_p.R38C	NM_030893.3	NP_112155.2	P15812	CD1E_HUMAN	CD1e molecule	38					antigen processing and presentation (GO:0019882)|immune response (GO:0006955)	endosome (GO:0005768)|Golgi apparatus (GO:0005794)|integral component of plasma membrane (GO:0005887)|lysosome (GO:0005764)	lipid binding (GO:0008289)	p.R38C(1)		breast(2)|endometrium(2)|kidney(1)|large_intestine(6)|lung(27)|pancreas(1)|prostate(4)|skin(4)|stomach(1)|urinary_tract(1)	49	all_hematologic(112;0.0378)					GCTGTCCTTCCGCATGCTCCA	0.542																																																1	Substitution - Missense(1)	endometrium(1)						C	CYS/ARG,CYS/ARG,CYS/ARG,CYS/ARG,CYS/ARG,CYS/ARG,CYS/ARG,,,,,,	1,4341		0,1,2170	123.0	126.0	125.0		112,112,112,112,112,112,112,,,,,,	0.6	0.0	1		125	0,8564		0,0,4282	no	missense,missense,missense,missense,missense,missense,missense,intron,intron,intron,intron,intron,intron	CD1E	NM_001042583.2,NM_001042584.2,NM_001042585.2,NM_001185107.1,NM_001185108.1,NM_001185115.1,NM_030893.3,NM_001042586.2,NM_001042587.2,NM_001185110.1,NM_001185112.1,NM_001185113.1,NM_001185114.1	180,180,180,180,180,180,180,,,,,,	0,1,6452	TT,TC,CC		0.0,0.023,0.0077	probably-damaging,probably-damaging,probably-damaging,probably-damaging,probably-damaging,probably-damaging,probably-damaging,,,,,,	38/377,38/291,38/322,38/299,38/232,38/287,38/389,,,,,,	158324220	1,12905	2171	4282	6453	SO:0001583	missense	913			AJ289111	CCDS41417.1, CCDS41418.1, CCDS41419.1, CCDS41420.1, CCDS41421.1, CCDS41422.1, CCDS53387.1, CCDS53388.1, CCDS53389.1, CCDS53390.1, CCDS53384.1, CCDS53385.1, CCDS53386.1	1q23.1	2014-01-14	2006-03-28		ENSG00000158488	ENSG00000158488		"""CD molecules"", ""Immunoglobulin superfamily / C1-set domain containing"""	1638	protein-coding gene	gene with protein product		188411	"""CD1E antigen, e polypeptide"", ""CD1e antigen"""			10948205	Standard	NM_001042585		Approved		uc001fse.3	P15812	OTTHUMG00000017515	ENST00000368167.3:c.112C>T	1.37:g.158324220C>T	ENSP00000357149:p.Arg38Cys		B4DZV3|E7EP01|Q5TDJ9|Q5TDK3|Q5TDK4|Q5TDK5|Q5TDK6|Q5TDK8|Q5TDL1|Q712E4|Q712E5|Q712E6|Q712E7|Q712E8|Q712E9|Q712F0|Q712F1|Q712F2|Q712F3|Q712F4|Q712F5|Q96TD0|Q96TD1|Q9UMM1|Q9Y5M3	Missense_Mutation	SNP	ENST00000368167.3	37	CCDS41417.1	.	.	.	.	.	.	.	.	.	.	C	16.89	3.247039	0.59103	2.3E-4	0.0	ENSG00000158488	ENST00000434258;ENST00000368167;ENST00000368165;ENST00000368163;ENST00000368160;ENST00000368161;ENST00000368156;ENST00000368155	T;T;T;T;T;T;T;T	0.08984	3.03;3.03;3.19;3.03;3.03;3.03;3.39;3.35	3.57	0.586	0.17434	MHC classes I/II-like antigen recognition protein (1);MHC class I-like antigen recognition (1);	0.890661	0.09357	N	0.813286	T	0.12987	0.0315	M	0.84082	2.675	0.09310	N	1	D;B;B;D;D;D;B;D	0.89917	1.0;0.049;0.049;1.0;0.999;1.0;0.049;1.0	D;B;B;D;D;D;B;D	0.79784	0.958;0.008;0.008;0.952;0.929;0.993;0.008;0.985	T	0.08806	-1.0704	10	0.87932	D	0	-2.786	3.1139	0.06367	0.2099:0.5556:0.0:0.2345	.	36;38;38;38;38;38;38;38	E7ET31;P15812-5;P15812-7;P15812-2;P15812;P15812-3;P15812-6;P15812-4	.;.;.;.;CD1E_HUMAN;.;.;.	C	36;38;38;38;38;38;38;38	ENSP00000401957:R36C;ENSP00000357149:R38C;ENSP00000357147:R38C;ENSP00000357145:R38C;ENSP00000357142:R38C;ENSP00000357143:R38C;ENSP00000357138:R38C;ENSP00000357137:R38C	ENSP00000357137:R38C	R	+	1	0	CD1E	156590844	0.001000	0.12720	0.001000	0.08648	0.579000	0.36224	0.009000	0.13219	0.136000	0.18733	0.563000	0.77884	CGC		0.542	CD1E-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000046353.3	NM_030893		29	90	29	90
RYR2	6262	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	1	237777663	237777663	+	Missense_Mutation	SNP	A	A	T			TCGA-DU-6402-01A-11D-1705-08	TCGA-DU-6402-10A-01D-1705-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	896ec7d7-5443-49bb-969b-7b483e9b518c	3bc825bc-5589-4e0b-b380-38fceee3231b	g.chr1:237777663A>T	ENST00000366574.2	+	37	5552	c.5235A>T	c.(5233-5235)aaA>aaT	p.K1745N	RYR2_ENST00000542537.1_Missense_Mutation_p.K1729N|RYR2_ENST00000360064.6_Missense_Mutation_p.K1743N	NM_001035.2	NP_001026.2	Q92736	RYR2_HUMAN	ryanodine receptor 2 (cardiac)	1745	4 X approximate repeats.				BMP signaling pathway (GO:0030509)|calcium ion transport (GO:0006816)|calcium ion transport into cytosol (GO:0060402)|calcium-mediated signaling (GO:0019722)|calcium-mediated signaling using intracellular calcium source (GO:0035584)|canonical Wnt signaling pathway (GO:0060070)|cardiac muscle contraction (GO:0060048)|cardiac muscle hypertrophy (GO:0003300)|cell communication by electrical coupling involved in cardiac conduction (GO:0086064)|cellular calcium ion homeostasis (GO:0006874)|cellular response to caffeine (GO:0071313)|cellular response to epinephrine stimulus (GO:0071872)|cytosolic calcium ion homeostasis (GO:0051480)|detection of calcium ion (GO:0005513)|embryonic heart tube morphogenesis (GO:0003143)|establishment of protein localization to endoplasmic reticulum (GO:0072599)|ion transmembrane transport (GO:0034220)|left ventricular cardiac muscle tissue morphogenesis (GO:0003220)|positive regulation of calcium-transporting ATPase activity (GO:1901896)|positive regulation of heart rate (GO:0010460)|positive regulation of ryanodine-sensitive calcium-release channel activity by adrenergic receptor signaling pathway involved in positive regulation of cardiac muscle contraction (GO:0086094)|positive regulation of sequestering of calcium ion (GO:0051284)|Purkinje myocyte to ventricular cardiac muscle cell signaling (GO:0086029)|regulation of cardiac muscle contraction (GO:0055117)|regulation of cardiac muscle contraction by regulation of the release of sequestered calcium ion (GO:0010881)|regulation of heart rate (GO:0002027)|release of sequestered calcium ion into cytosol (GO:0051209)|release of sequestered calcium ion into cytosol by sarcoplasmic reticulum (GO:0014808)|response to caffeine (GO:0031000)|response to hypoxia (GO:0001666)|response to redox state (GO:0051775)|sarcoplasmic reticulum calcium ion transport (GO:0070296)|transmembrane transport (GO:0055085)|type B pancreatic cell apoptotic process (GO:0097050)|ventricular cardiac muscle cell action potential (GO:0086005)	calcium channel complex (GO:0034704)|extracellular vesicular exosome (GO:0070062)|junctional sarcoplasmic reticulum membrane (GO:0014701)|membrane (GO:0016020)|plasma membrane (GO:0005886)|protein complex (GO:0043234)|sarcoplasmic reticulum (GO:0016529)|sarcoplasmic reticulum membrane (GO:0033017)|smooth endoplasmic reticulum (GO:0005790)|Z disc (GO:0030018)	calcium channel activity (GO:0005262)|calcium ion binding (GO:0005509)|calcium-induced calcium release activity (GO:0048763)|calcium-release channel activity (GO:0015278)|calmodulin binding (GO:0005516)|enzyme binding (GO:0019899)|identical protein binding (GO:0042802)|intracellular ligand-gated calcium channel activity (GO:0005218)|ion channel binding (GO:0044325)|protein kinase A catalytic subunit binding (GO:0034236)|protein kinase A regulatory subunit binding (GO:0034237)|ryanodine-sensitive calcium-release channel activity (GO:0005219)|suramin binding (GO:0043924)			NS(4)|breast(8)|central_nervous_system(11)|cervix(2)|endometrium(39)|haematopoietic_and_lymphoid_tissue(5)|kidney(17)|large_intestine(83)|liver(4)|lung(353)|ovary(18)|pancreas(5)|prostate(12)|skin(8)|stomach(1)|upper_aerodigestive_tract(12)|urinary_tract(4)	586	Ovarian(103;0.103)	all_cancers(173;0.000368)|Melanoma(53;0.0179)|all_epithelial(177;0.0225)	OV - Ovarian serous cystadenocarcinoma(106;0.00606)			AGAACAAAAAACACGGCCTTC	0.517																																																0													65.0	65.0	65.0					1																	237777663		2047	4198	6245	SO:0001583	missense	6262			X91869	CCDS55691.1	1q43	2014-09-17			ENSG00000198626	ENSG00000198626		"""Ion channels / Ryanodine receptors"", ""EF-hand domain containing"""	10484	protein-coding gene	gene with protein product		180902	"""arrhythmogenic right ventricular dysplasia 2"""	ARVD2		2380170, 8406504, 11159936	Standard	NM_001035		Approved	ARVC2, VTSIP	uc001hyl.1	Q92736	OTTHUMG00000039543	ENST00000366574.2:c.5235A>T	1.37:g.237777663A>T	ENSP00000355533:p.Lys1745Asn		Q15411|Q546N8|Q5T3P2	Missense_Mutation	SNP	ENST00000366574.2	37	CCDS55691.1	.	.	.	.	.	.	.	.	.	.	G	12.24	1.879479	0.33162	.	.	ENSG00000198626	ENST00000366574;ENST00000360064;ENST00000542537	T;T;T	0.73897	-0.79;-0.79;-0.79	5.43	2.53	0.30540	.	0.000000	0.64402	D	0.000006	T	0.66509	0.2796	L	0.50333	1.59	0.80722	D	1	B	0.27498	0.18	B	0.30179	0.112	T	0.56025	-0.8047	10	0.31617	T	0.26	.	10.2109	0.43141	0.4104:0.0:0.5896:0.0	.	1745	Q92736	RYR2_HUMAN	N	1745;1743;1729	ENSP00000355533:K1745N;ENSP00000353174:K1743N;ENSP00000443798:K1729N	ENSP00000353174:K1743N	K	+	3	2	RYR2	235844286	0.989000	0.36119	0.967000	0.41034	0.819000	0.46315	0.315000	0.19451	0.028000	0.15324	-0.128000	0.14901	AAA		0.517	RYR2-001	KNOWN	non_canonical_conserved|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000095402.2	NM_001035		12	22	12	22
PHACTR3	116154	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	20	58349322	58349322	+	Silent	SNP	G	G	A			TCGA-DU-6402-01A-11D-1705-08	TCGA-DU-6402-10A-01D-1705-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	896ec7d7-5443-49bb-969b-7b483e9b518c	3bc825bc-5589-4e0b-b380-38fceee3231b	g.chr20:58349322G>A	ENST00000371015.1	+	7	1418	c.951G>A	c.(949-951)ggG>ggA	p.G317G	PHACTR3_ENST00000395639.4_Silent_p.G206G|PHACTR3_ENST00000361300.4_Silent_p.G206G|PHACTR3_ENST00000359926.3_Silent_p.G314G|PHACTR3_ENST00000355648.4_Silent_p.G276G|PHACTR3_ENST00000395636.2_Silent_p.G276G|PHACTR3_ENST00000541461.1_Silent_p.G276G	NM_001281507.1|NM_080672.3	NP_001268436.1|NP_542403.1	Q96KR7	PHAR3_HUMAN	phosphatase and actin regulator 3	317						nucleus (GO:0005634)	protein phosphatase inhibitor activity (GO:0004864)			endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(13)|liver(2)|lung(32)|ovary(3)|pancreas(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(2)	59	all_lung(29;0.00344)		BRCA - Breast invasive adenocarcinoma(7;2.76e-09)			AAAGTAAAGGGTCTCCAAAGA	0.527																																																0													46.0	50.0	49.0					20																	58349322		2203	4300	6503	SO:0001819	synonymous_variant	116154			AJ311122	CCDS13480.1, CCDS13481.1, CCDS42895.1, CCDS56202.1	20q13.32-q13.33	2014-06-13	2004-05-20	2004-05-20	ENSG00000087495	ENSG00000087495		"""Phosphatase and actin regulators"""	15833	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 123"""	608725	"""chromosome 20 open reading frame 101"""	C20orf101		15107502	Standard	NM_001199505		Approved	PPP1R123	uc002yau.3	Q96KR7	OTTHUMG00000032869	ENST00000371015.1:c.951G>A	20.37:g.58349322G>A			B1AKX0|B1AN68|B1AN69|B2RB46|Q32P33|Q707P6|Q9H4T4	Silent	SNP	ENST00000371015.1	37	CCDS13480.1																																																																																				0.527	PHACTR3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079923.3	NM_080672		14	34	14	34
LRRC3	81543	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	21	45877263	45877263	+	Missense_Mutation	SNP	G	G	A			TCGA-DU-6402-01A-11D-1705-08	TCGA-DU-6402-10A-01D-1705-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	896ec7d7-5443-49bb-969b-7b483e9b518c	3bc825bc-5589-4e0b-b380-38fceee3231b	g.chr21:45877263G>A	ENST00000291592.4	+	2	1053	c.736G>A	c.(736-738)Gcc>Acc	p.A246T	LRRC3-AS1_ENST00000426578.1_RNA|LRRC3DN_ENST00000596691.1_5'Flank	NM_030891.3	NP_112153.1	Q9BY71	LRRC3_HUMAN	leucine rich repeat containing 3	246						integral component of membrane (GO:0016021)				endometrium(2)|kidney(1)|lung(1)|urinary_tract(1)	5		Breast(209;0.00908)		COAD - Colon adenocarcinoma(84;0.148)|Lung(125;0.195)		TCTGCCCAGCGCCCCCGCCTC	0.652																																																0													35.0	41.0	39.0					21																	45877263		2201	4298	6499	SO:0001583	missense	81543			AB058646	CCDS13711.1	21q22.3	2011-12-07	2002-06-20		ENSG00000160233	ENSG00000160233			14965	protein-coding gene	gene with protein product			"""chromosome 21 open reading frame 102"""	C21orf102		12036297	Standard	NM_030891		Approved		uc002zfa.3	Q9BY71	OTTHUMG00000040847	ENST00000291592.4:c.736G>A	21.37:g.45877263G>A	ENSP00000291592:p.Ala246Thr		Q0VDJ2	Missense_Mutation	SNP	ENST00000291592.4	37	CCDS13711.1	.	.	.	.	.	.	.	.	.	.	G	1.300	-0.605111	0.03717	.	.	ENSG00000160233	ENST00000291592	T	0.56941	0.43	4.87	2.35	0.29111	.	0.370050	0.26058	N	0.026590	T	0.24084	0.0583	N	0.03115	-0.41	0.31541	N	0.659897	B	0.19935	0.04	B	0.08055	0.003	T	0.15150	-1.0447	10	0.23891	T	0.37	-23.1118	7.5686	0.27894	0.5423:0.0:0.4577:0.0	.	246	Q9BY71	LRRC3_HUMAN	T	246	ENSP00000291592:A246T	ENSP00000291592:A246T	A	+	1	0	LRRC3	44701691	0.954000	0.32549	0.812000	0.32479	0.263000	0.26337	2.927000	0.48900	0.229000	0.21039	0.491000	0.48974	GCC		0.652	LRRC3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000098095.3			13	33	13	33
SFI1	9814	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	22	32013006	32013006	+	Missense_Mutation	SNP	G	G	C	rs143349198		TCGA-DU-6402-01A-11D-1705-08	TCGA-DU-6402-10A-01D-1705-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	896ec7d7-5443-49bb-969b-7b483e9b518c	3bc825bc-5589-4e0b-b380-38fceee3231b	g.chr22:32013006G>C	ENST00000400288.2	+	31	3559	c.3454G>C	c.(3454-3456)Gaa>Caa	p.E1152Q	SFI1_ENST00000443326.1_Missense_Mutation_p.E1070Q|SFI1_ENST00000474741.1_Intron|SFI1_ENST00000540643.1_Missense_Mutation_p.E1097Q|SFI1_ENST00000400289.1_Missense_Mutation_p.E1070Q|SFI1_ENST00000443011.1_Missense_Mutation_p.E999Q|SFI1_ENST00000414585.1_Silent_p.L997L|SFI1_ENST00000432498.1_Missense_Mutation_p.E1121Q	NM_001007467.2	NP_001007468.1	A8K8P3	SFI1_HUMAN	Sfi1 homolog, spindle assembly associated (yeast)	1152					G2/M transition of mitotic cell cycle (GO:0000086)|mitotic cell cycle (GO:0000278)|negative regulation of phosphatase activity (GO:0010923)	cytoskeleton (GO:0005856)|cytosol (GO:0005829)	phosphatase binding (GO:0019902)			NS(2)|breast(3)|central_nervous_system(1)|cervix(1)|endometrium(5)|large_intestine(7)|liver(1)|lung(11)|ovary(1)|prostate(3)|upper_aerodigestive_tract(3)	38						CCTTGAGGCTGAACTTGAGGA	0.567																																																0													85.0	91.0	89.0					22																	32013006		2111	4224	6335	SO:0001583	missense	9814			AB011114	CCDS43004.1, CCDS43005.1, CCDS58803.1, CCDS58804.1	22q12.2	2014-06-13			ENSG00000198089	ENSG00000198089			29064	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 139"""	612765				14504268	Standard	NM_001007467		Approved	KIAA0542, PISD, PPP1R139	uc003ale.4	A8K8P3	OTTHUMG00000030249	ENST00000400288.2:c.3454G>C	22.37:g.32013006G>C	ENSP00000383145:p.Glu1152Gln		A1L373|A1L387|A2A2L2|B1AKL9|B5MDB7|B7Z1V6|B7Z8G3|B7ZBE2|B7ZBE3|O60289|Q2TAN8|Q5W1B5|Q86TK0|Q8N4U8|Q8N8C1|Q8WU14	Missense_Mutation	SNP	ENST00000400288.2	37	CCDS43004.1	.	.	.	.	.	.	.	.	.	.	G	17.02	3.282723	0.59867	.	.	ENSG00000198089	ENST00000432498;ENST00000540643;ENST00000443326;ENST00000421060;ENST00000443011;ENST00000400289;ENST00000400288	T;T;T;T;T;T	0.19394	2.38;2.38;2.23;2.15;2.23;2.4	5.45	5.45	0.79879	.	0.000000	0.85682	D	0.000000	T	0.28167	0.0695	N	0.08118	0	0.80722	D	1	D;D;D;D;D;D;D	0.89917	1.0;1.0;1.0;1.0;1.0;1.0;0.998	D;D;D;D;D;D;D	0.91635	0.999;0.997;0.999;0.999;0.998;0.999;0.994	T	0.34551	-0.9824	10	0.87932	D	0	.	16.0229	0.80512	0.0:0.0:1.0:0.0	.	1097;1058;999;735;1070;1121;1152	A8K8P3-9;A8K8P3-10;D3YTJ2;B7ZBE1;A8K8P3-3;A8K8P3-2;A8K8P3	.;.;.;.;.;.;SFI1_HUMAN	Q	1121;1097;1070;901;999;1070;1152	ENSP00000402679:E1121Q;ENSP00000443025:E1097Q;ENSP00000416469:E1070Q;ENSP00000401199:E999Q;ENSP00000383146:E1070Q;ENSP00000383145:E1152Q	ENSP00000383145:E1152Q	E	+	1	0	SFI1	30343006	0.999000	0.42202	0.967000	0.41034	0.239000	0.25481	3.619000	0.54196	2.569000	0.86673	0.563000	0.77884	GAA		0.567	SFI1-023	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000337180.3	NM_014775		19	31	19	31
DEPDC5	9681	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	22	32302244	32302244	+	Missense_Mutation	SNP	C	C	T			TCGA-DU-6402-01A-11D-1705-08	TCGA-DU-6402-10A-01D-1705-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	896ec7d7-5443-49bb-969b-7b483e9b518c	3bc825bc-5589-4e0b-b380-38fceee3231b	g.chr22:32302244C>T	ENST00000382112.3	+	42	4616	c.4546C>T	c.(4546-4548)Cgg>Tgg	p.R1516W	DEPDC5_ENST00000400246.1_Silent_p.S1504S|DEPDC5_ENST00000535622.1_Missense_Mutation_p.R1425W|DEPDC5_ENST00000266091.3_Missense_Mutation_p.R1503W|DEPDC5_ENST00000400249.2_Missense_Mutation_p.R1494W|DEPDC5_ENST00000382111.2_Silent_p.S1504S|DEPDC5_ENST00000539165.1_Missense_Mutation_p.R342W|DEPDC5_ENST00000400248.2_Missense_Mutation_p.R1494W|DEPDC5_ENST00000382105.2_3'UTR	NM_001136029.2|NM_001242896.1	NP_001129501.1|NP_001229825.1	O75140	DEPD5_HUMAN	DEP domain containing 5	1525					intracellular signal transduction (GO:0035556)	cytosol (GO:0005829)|lysosomal membrane (GO:0005765)|perinuclear region of cytoplasm (GO:0048471)	GTPase activator activity (GO:0005096)			breast(1)|central_nervous_system(5)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(8)|lung(24)|ovary(5)|pancreas(2)|prostate(3)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	63						AGGGCAGCAGCGGCGGCGGCG	0.607																																																0													29.0	34.0	33.0					22																	32302244		1941	4130	6071	SO:0001583	missense	9681			AB014545	CCDS43006.1, CCDS43007.1, CCDS46692.1, CCDS56229.1, CCDS74849.1	22q12.3	2013-04-29			ENSG00000100150	ENSG00000100150			18423	protein-coding gene	gene with protein product		614191				23542697, 23542701	Standard	NM_001242896		Approved	KIAA0645, DEP.5	uc011alu.2	O75140	OTTHUMG00000030926	ENST00000382112.3:c.4546C>T	22.37:g.32302244C>T	ENSP00000371546:p.Arg1516Trp		A6H8V6|A8MPX9|B4DH93|B9EGN9|Q5K3V5|Q5THY9|Q5THZ0|Q5THZ1|Q5THZ3|Q68DR1|Q6MZX3|Q6PEZ1|Q9UGV8|Q9UH13	Missense_Mutation	SNP	ENST00000382112.3	37	CCDS46692.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	22.9|22.9	4.349882|4.349882	0.82132|0.82132	.|.	.|.	ENSG00000100150|ENSG00000100150	ENST00000433147|ENST00000535622;ENST00000266091;ENST00000400249;ENST00000382109;ENST00000382112;ENST00000400248;ENST00000539165	.|T;T;T;T;T	.|0.34072	.|1.38;1.81;1.81;1.82;1.81	4.99|4.99	3.95|3.95	0.45737|0.45737	.|.	.|0.091579	.|0.44483	.|D	.|0.000449	T|T	0.50973|0.50973	0.1647|0.1647	L|L	0.46157|0.46157	1.445|1.445	0.58432|0.58432	D|D	0.999999|0.999999	.|D;D;D;D;D	.|0.89917	.|1.0;1.0;1.0;1.0;1.0	.|D;D;D;D;D	.|0.83275	.|0.993;0.988;0.996;0.993;0.99	T|T	0.51593|0.51593	-0.8686|-0.8686	5|10	.|0.62326	.|D	.|0.03	.|.	11.9504|11.9504	0.52952|0.52952	0.3159:0.6841:0.0:0.0|0.3159:0.6841:0.0:0.0	.|.	.|1525;1425;1503;1516;1494	.|B9EGN9;B4DH93;O75140-4;A8MPX9;O75140	.|.;.;.;.;DEPD5_HUMAN	V|W	900|1425;1503;1494;1425;1516;1494;342	.|ENSP00000440210:R1425W;ENSP00000266091:R1503W;ENSP00000383108:R1494W;ENSP00000371546:R1516W;ENSP00000383107:R1494W	.|ENSP00000266091:R1503W	A|R	+|+	2|1	0|2	DEPDC5|DEPDC5	30632244|30632244	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.990000|0.990000	0.78478|0.78478	2.237000|2.237000	0.43061|0.43061	1.214000|1.214000	0.43395|0.43395	0.462000|0.462000	0.41574|0.41574	GCG|CGG		0.607	DEPDC5-006	NOVEL	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000129087.1	NM_014662		14	33	14	33
PDIA6	10130	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	2	10929977	10929977	+	Silent	SNP	G	G	A			TCGA-DU-6402-01A-11D-1705-08	TCGA-DU-6402-10A-01D-1705-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	896ec7d7-5443-49bb-969b-7b483e9b518c	3bc825bc-5589-4e0b-b380-38fceee3231b	g.chr2:10929977G>A	ENST00000272227.3	-	8	885	c.738C>T	c.(736-738)ggC>ggT	p.G246G	PDIA6_ENST00000404824.2_Silent_p.G294G|PDIA6_ENST00000381611.4_Silent_p.G251G|PDIA6_ENST00000404371.2_Silent_p.G298G|PDIA6_ENST00000540494.1_Silent_p.G243G	NM_001282707.1|NM_005742.2	NP_001269636.1|NP_005733.1	Q15084	PDIA6_HUMAN	protein disulfide isomerase family A, member 6	246	Thioredoxin 2. {ECO:0000255|PROSITE- ProRule:PRU00691}.				activation of signaling protein activity involved in unfolded protein response (GO:0006987)|apoptotic cell clearance (GO:0043277)|cell redox homeostasis (GO:0045454)|cellular protein metabolic process (GO:0044267)|endoplasmic reticulum unfolded protein response (GO:0030968)|protein folding (GO:0006457)|response to endoplasmic reticulum stress (GO:0034976)	endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|endoplasmic reticulum-Golgi intermediate compartment (GO:0005793)|extracellular vesicular exosome (GO:0070062)|plasma membrane (GO:0005886)	protein disulfide isomerase activity (GO:0003756)			central_nervous_system(1)|endometrium(3)|kidney(2)|large_intestine(2)|lung(8)|prostate(2)	18	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.191)			Epithelial(75;0.149)|OV - Ovarian serous cystadenocarcinoma(76;0.15)		CAGGAGACTCGCCTTTCTGAA	0.423																																					GBM(73;509 1219 34219 41343 41551)											0													73.0	74.0	74.0					2																	10929977		2203	4300	6503	SO:0001819	synonymous_variant	10130			BC001312	CCDS1675.1, CCDS62852.1, CCDS62853.1, CCDS62854.1, CCDS62855.1	2p25.1	2009-11-20	2005-06-29	2005-03-03	ENSG00000143870	ENSG00000143870	5.3.4.1	"""Protein disulfide isomerases"""	30168	protein-coding gene	gene with protein product	"""protein disulfide isomerase-related protein"""	611099	"""thioredoxin domain containing 7 (protein disulfide isomerase)"", ""protein disulfide isomerase-associated 6"""	TXNDC7		7590364, 12204115	Standard	XM_005246145		Approved	P5, ERp5	uc002rau.3	Q15084	OTTHUMG00000090479	ENST00000272227.3:c.738C>T	2.37:g.10929977G>A			B3KY95|B5MCQ5|B7Z254|B7Z4M8|F8WA83|Q53RC7|Q6ZSH5|Q99778	Silent	SNP	ENST00000272227.3	37	CCDS1675.1																																																																																				0.423	PDIA6-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000206933.1	NM_005742		24	65	24	65
KCNS3	3790	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	2	18113581	18113581	+	Missense_Mutation	SNP	C	C	A			TCGA-DU-6402-01A-11D-1705-08	TCGA-DU-6402-10A-01D-1705-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	896ec7d7-5443-49bb-969b-7b483e9b518c	3bc825bc-5589-4e0b-b380-38fceee3231b	g.chr2:18113581C>A	ENST00000403915.1	+	3	1757	c.1306C>A	c.(1306-1308)Cct>Act	p.P436T	KCNS3_ENST00000465292.1_Intron|KCNS3_ENST00000304101.4_Missense_Mutation_p.P436T	NM_001282428.1	NP_001269357.1	Q9BQ31	KCNS3_HUMAN	potassium voltage-gated channel, delayed-rectifier, subfamily S, member 3	436					energy reserve metabolic process (GO:0006112)|potassium ion transport (GO:0006813)|protein homooligomerization (GO:0051260)|regulation of insulin secretion (GO:0050796)|small molecule metabolic process (GO:0044281)|synaptic transmission (GO:0007268)	cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|plasma membrane (GO:0005886)|voltage-gated potassium channel complex (GO:0008076)	delayed rectifier potassium channel activity (GO:0005251)|potassium channel regulator activity (GO:0015459)			endometrium(5)|kidney(1)|large_intestine(7)|lung(11)|ovary(4)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	32	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.158)					TCATGAGCTACCTTACTTTAA	0.453																																																0													201.0	182.0	189.0					2																	18113581		2203	4300	6503	SO:0001583	missense	3790			AF043472	CCDS1692.1	2p24	2011-07-05			ENSG00000170745	ENSG00000170745		"""Potassium channels"", ""Voltage-gated ion channels / Potassium channels"""	6302	protein-coding gene	gene with protein product		603888				10484328, 16382104	Standard	NM_002252		Approved	Kv9.3	uc002rcw.3	Q9BQ31	OTTHUMG00000044150	ENST00000403915.1:c.1306C>A	2.37:g.18113581C>A	ENSP00000385968:p.Pro436Thr		D6W520|O43651|Q4ZFY1|Q96B56	Missense_Mutation	SNP	ENST00000403915.1	37	CCDS1692.1	.	.	.	.	.	.	.	.	.	.	C	11.85	1.760546	0.31137	.	.	ENSG00000170745	ENST00000403915;ENST00000304101	D;D	0.96967	-4.19;-4.19	6.07	6.07	0.98685	.	.	.	.	.	D	0.97860	0.9297	M	0.71581	2.175	0.80722	D	1	D	0.89917	1.0	D	0.83275	0.996	D	0.96316	0.9232	9	0.25106	T	0.35	.	20.6439	0.99570	0.0:1.0:0.0:0.0	.	436	Q9BQ31	KCNS3_HUMAN	T	436	ENSP00000385968:P436T;ENSP00000305824:P436T	ENSP00000305824:P436T	P	+	1	0	KCNS3	17977062	1.000000	0.71417	1.000000	0.80357	0.990000	0.78478	7.487000	0.81328	2.884000	0.98904	0.655000	0.94253	CCT		0.453	KCNS3-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000323808.1	NM_002252		34	69	34	69
CLHC1	130162	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	2	55404777	55404777	+	Missense_Mutation	SNP	C	C	G			TCGA-DU-6402-01A-11D-1705-08	TCGA-DU-6402-10A-01D-1705-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	896ec7d7-5443-49bb-969b-7b483e9b518c	3bc825bc-5589-4e0b-b380-38fceee3231b	g.chr2:55404777C>G	ENST00000401408.1	-	12	1870	c.1525G>C	c.(1525-1527)Ggc>Cgc	p.G509R	CLHC1_ENST00000494539.1_5'UTR|CLHC1_ENST00000407122.1_Missense_Mutation_p.G509R|CLHC1_ENST00000406437.2_Missense_Mutation_p.G60R|CLHC1_ENST00000406076.1_Missense_Mutation_p.G387R	NM_152385.2	NP_689598.2	Q8NHS4	CLHC1_HUMAN	clathrin heavy chain linker domain containing 1	509																	AGCTTAATGCCAACTTTTTTC	0.353																																																0													149.0	142.0	144.0					2																	55404777		2202	4300	6502	SO:0001583	missense	130162				CCDS33201.1, CCDS46287.1	2p16.1	2012-08-03	2012-08-03	2012-08-03	ENSG00000162994	ENSG00000162994			26453	protein-coding gene	gene with protein product			"""chromosome 2 open reading frame 63"""	C2orf63			Standard	NM_152385		Approved	FLJ31438	uc002ryi.2	Q8NHS4	OTTHUMG00000151918	ENST00000401408.1:c.1525G>C	2.37:g.55404777C>G	ENSP00000384869:p.Gly509Arg		B2RDV1|Q53R93|Q8N403	Missense_Mutation	SNP	ENST00000401408.1	37	CCDS33201.1	.	.	.	.	.	.	.	.	.	.	C	13.95	2.390663	0.42410	.	.	ENSG00000162994	ENST00000406437;ENST00000407122;ENST00000401408;ENST00000406076	T;T;T;T	0.40756	1.02;2.14;2.14;2.14	5.64	5.64	0.86602	.	0.227923	0.36778	N	0.002414	T	0.64692	0.2621	M	0.74881	2.28	0.21325	N	0.999724	D	0.89917	1.0	D	0.76575	0.988	T	0.60429	-0.7265	10	0.72032	D	0.01	-1.0685	15.1923	0.73053	0.0:1.0:0.0:0.0	.	509	Q8NHS4	CB063_HUMAN	R	60;509;509;387	ENSP00000384810:G60R;ENSP00000385778:G509R;ENSP00000384869:G509R;ENSP00000385512:G387R	ENSP00000384869:G509R	G	-	1	0	C2orf63	55258281	0.731000	0.28111	0.231000	0.23993	0.105000	0.19272	4.232000	0.58645	2.658000	0.90341	0.555000	0.69702	GGC		0.353	CLHC1-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000324412.4	NM_152385		17	48	17	48
B3GNT7	93010	hgsc.bcm.edu;broad.mit.edu	37	2	232263412	232263412	+	Missense_Mutation	SNP	G	G	A			TCGA-DU-6402-01A-11D-1705-08	TCGA-DU-6402-10A-01D-1705-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	896ec7d7-5443-49bb-969b-7b483e9b518c	3bc825bc-5589-4e0b-b380-38fceee3231b	g.chr2:232263412G>A	ENST00000287590.5	+	2	1243	c.982G>A	c.(982-984)Gtc>Atc	p.V328I		NM_145236.2	NP_660279.1	Q8NFL0	B3GN7_HUMAN	UDP-GlcNAc:betaGal beta-1,3-N-acetylglucosaminyltransferase 7	328					carbohydrate metabolic process (GO:0005975)|cellular protein metabolic process (GO:0044267)|glycosaminoglycan metabolic process (GO:0030203)|keratan sulfate biosynthetic process (GO:0018146)|keratan sulfate metabolic process (GO:0042339)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)|small molecule metabolic process (GO:0044281)	Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)	galactosyltransferase activity (GO:0008378)			endometrium(2)|kidney(1)|large_intestine(7)|lung(4)|ovary(1)|prostate(1)|skin(1)	17		Renal(207;0.025)|all_hematologic(139;0.094)|Acute lymphoblastic leukemia(138;0.164)|Medulloblastoma(418;0.232)		Epithelial(121;3.22e-11)|LUSC - Lung squamous cell carcinoma(224;0.0115)|Lung(119;0.0139)		GATCGACGACGTCTTTCTGGG	0.672																																																0													38.0	45.0	43.0					2																	232263412		2020	4175	6195	SO:0001583	missense	93010			AK000770	CCDS46540.1	2q36.1	2013-02-21			ENSG00000156966	ENSG00000156966		"""Beta 3-glycosyltransferases"""	18811	protein-coding gene	gene with protein product		615313				12061784	Standard	NM_145236		Approved	beta3GnT7	uc002vrs.3	Q8NFL0	OTTHUMG00000153880	ENST00000287590.5:c.982G>A	2.37:g.232263412G>A	ENSP00000287590:p.Val328Ile		B3KWY4|B7WNP0	Missense_Mutation	SNP	ENST00000287590.5	37	CCDS46540.1	.	.	.	.	.	.	.	.	.	.	G	20.9	4.073903	0.76415	.	.	ENSG00000156966	ENST00000287590	T	0.52295	0.67	5.05	5.05	0.67936	.	0.000000	0.85682	D	0.000000	T	0.70404	0.3220	M	0.77486	2.375	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	T	0.74878	-0.3514	10	0.72032	D	0.01	.	17.4035	0.87467	0.0:0.0:1.0:0.0	.	328	Q8NFL0	B3GN7_HUMAN	I	328	ENSP00000287590:V328I	ENSP00000287590:V328I	V	+	1	0	B3GNT7	231971656	1.000000	0.71417	0.997000	0.53966	0.409000	0.31022	9.823000	0.99369	2.355000	0.79922	0.561000	0.74099	GTC		0.672	B3GNT7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000332827.1	NM_145236		18	39	18	39
GIGYF2	26058	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	2	233681681	233681681	+	Missense_Mutation	SNP	G	G	A	rs149585458		TCGA-DU-6402-01A-11D-1705-08	TCGA-DU-6402-10A-01D-1705-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	896ec7d7-5443-49bb-969b-7b483e9b518c	3bc825bc-5589-4e0b-b380-38fceee3231b	g.chr2:233681681G>A	ENST00000409547.1	+	22	2620	c.2309G>A	c.(2308-2310)cGg>cAg	p.R770Q	GIGYF2_ENST00000452341.2_Missense_Mutation_p.R601Q|GIGYF2_ENST00000373566.3_Missense_Mutation_p.R792Q|GIGYF2_ENST00000409196.3_Missense_Mutation_p.R764Q|GIGYF2_ENST00000409480.1_Missense_Mutation_p.R792Q|GIGYF2_ENST00000373563.4_Missense_Mutation_p.R770Q|GIGYF2_ENST00000409451.3_Missense_Mutation_p.R791Q	NM_015575.3	NP_056390.2	Q6Y7W6	PERQ2_HUMAN	GRB10 interacting GYF protein 2	770	Gln-rich.|Glu-rich.				adult locomotory behavior (GO:0008344)|cell death (GO:0008219)|cellular protein metabolic process (GO:0044267)|feeding behavior (GO:0007631)|homeostasis of number of cells within a tissue (GO:0048873)|insulin-like growth factor receptor signaling pathway (GO:0048009)|mitotic G1 DNA damage checkpoint (GO:0031571)|multicellular organism growth (GO:0035264)|musculoskeletal movement (GO:0050881)|negative regulation of translation (GO:0017148)|neuromuscular process controlling balance (GO:0050885)|post-embryonic development (GO:0009791)|spinal cord motor neuron differentiation (GO:0021522)	membrane (GO:0016020)	poly(A) RNA binding (GO:0044822)			NS(1)|biliary_tract(1)|breast(3)|central_nervous_system(4)|cervix(1)|endometrium(11)|kidney(2)|large_intestine(17)|lung(11)|ovary(5)|prostate(2)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)	63		Breast(86;0.00279)|all_hematologic(139;0.00793)|Renal(207;0.0112)|Acute lymphoblastic leukemia(138;0.0182)|all_lung(227;0.0271)|Lung NSC(271;0.0839)		Epithelial(121;7.37e-16)|BRCA - Breast invasive adenocarcinoma(100;0.000472)|LUSC - Lung squamous cell carcinoma(224;0.00902)|Lung(119;0.0118)|GBM - Glioblastoma multiforme(43;0.0145)		GAAATTCTTCGGCGACAGCAG	0.488																																																0								G	GLN/ARG,GLN/ARG,GLN/ARG,GLN/ARG	0,4406		0,0,2203	180.0	167.0	171.0		2309,2372,2291,2309	3.8	1.0	2	dbSNP_134	171	1,8599	1.2+/-3.3	0,1,4299	no	missense,missense,missense,missense	GIGYF2	NM_001103146.1,NM_001103147.1,NM_001103148.1,NM_015575.3	43,43,43,43	0,1,6502	AA,AG,GG		0.0116,0.0,0.0077	probably-damaging,probably-damaging,probably-damaging,probably-damaging	770/1300,791/1321,764/1294,770/1300	233681681	1,13005	2203	4300	6503	SO:0001583	missense	26058			U80751	CCDS33401.1, CCDS46542.1, CCDS46543.1	2q37.1	2011-07-06	2008-02-11	2008-02-11	ENSG00000204120	ENSG00000204120		"""Trinucleotide (CAG) repeat containing"""	11960	protein-coding gene	gene with protein product	"""GYF domain containing 2"""	612003	"""PERQ amino acid rich, with GYF domain 2"", ""PERQ amino acid rich, with GYF domain 3"", ""trinucleotide repeat containing 15"", ""Parkinson disease (autosomal recessive, early onset) 11"""	PERQ2, PERQ3, TNRC15, PARK11		9225980, 9734811, 12771153, 18358451, 19279319	Standard	NM_015575		Approved	KIAA0642, GYF2	uc002vtk.4	Q6Y7W6	OTTHUMG00000153237	ENST00000409547.1:c.2309G>A	2.37:g.233681681G>A	ENSP00000386537:p.Arg770Gln		A6H8W4|B9EG55|E9PBB0|O75137|Q7Z2Z8|Q7Z3I2|Q96HU4|Q9NV82	Missense_Mutation	SNP	ENST00000409547.1	37	CCDS33401.1	.	.	.	.	.	.	.	.	.	.	G	13.69	2.311904	0.40895	0.0	1.16E-4	ENSG00000204120	ENST00000373566;ENST00000414511;ENST00000373563;ENST00000409480;ENST00000409547;ENST00000535418;ENST00000423659;ENST00000409196;ENST00000409451;ENST00000440945;ENST00000452341	T;T;T;T;T;T;T;T;T	0.80214	-1.02;-1.02;-1.02;-1.02;-1.35;-1.02;-1.02;-1.02;-1.02	3.76	3.76	0.43208	.	0.060442	0.64402	D	0.000009	D	0.85261	0.5656	L	0.58669	1.825	0.58432	D	0.999991	D;D;D;D	0.71674	0.998;0.997;0.997;0.997	D;D;D;D	0.72982	0.979;0.953;0.953;0.953	T	0.82004	-0.0672	10	0.19147	T	0.46	-21.767	13.2555	0.60076	0.0:0.0:1.0:0.0	.	601;791;770;764	E9PC50;A6H8W4;Q6Y7W6;E9PBB0	.;.;PERQ2_HUMAN;.	Q	792;713;770;792;770;770;713;764;791;764;601	ENSP00000362667:R792Q;ENSP00000362664:R770Q;ENSP00000386765:R792Q;ENSP00000386537:R770Q;ENSP00000404195:R713Q;ENSP00000387070:R764Q;ENSP00000387170:R791Q;ENSP00000410297:R764Q;ENSP00000411505:R601Q	ENSP00000362664:R770Q	R	+	2	0	GIGYF2	233389925	1.000000	0.71417	1.000000	0.80357	0.338000	0.28826	7.000000	0.76290	2.104000	0.64026	0.462000	0.41574	CGG		0.488	GIGYF2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000330316.2	NM_001103146		67	108	67	108
PROM1	8842	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	4	15991422	15991422	+	Missense_Mutation	SNP	A	A	G			TCGA-DU-6402-01A-11D-1705-08	TCGA-DU-6402-10A-01D-1705-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	896ec7d7-5443-49bb-969b-7b483e9b518c	3bc825bc-5589-4e0b-b380-38fceee3231b	g.chr4:15991422A>G	ENST00000510224.1	-	19	2257	c.2009T>C	c.(2008-2010)cTg>cCg	p.L670P	PROM1_ENST00000505450.1_Missense_Mutation_p.L661P|PROM1_ENST00000543373.1_Missense_Mutation_p.L661P|PROM1_ENST00000540805.1_Missense_Mutation_p.L670P|PROM1_ENST00000508167.1_Missense_Mutation_p.L661P|PROM1_ENST00000447510.2_Missense_Mutation_p.L670P|PROM1_ENST00000539194.1_Missense_Mutation_p.L670P			O43490	PROM1_HUMAN	prominin 1	670					camera-type eye photoreceptor cell differentiation (GO:0060219)|glomerular parietal epithelial cell differentiation (GO:0072139)|glomerular visceral epithelial cell differentiation (GO:0072112)|photoreceptor cell maintenance (GO:0045494)|positive regulation of nephron tubule epithelial cell differentiation (GO:2000768)|retina layer formation (GO:0010842)|retina morphogenesis in camera-type eye (GO:0060042)	apical plasma membrane (GO:0016324)|brush border (GO:0005903)|cell surface (GO:0009986)|endoplasmic reticulum (GO:0005783)|endoplasmic reticulum-Golgi intermediate compartment (GO:0005793)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|photoreceptor outer segment (GO:0001750)|photoreceptor outer segment membrane (GO:0042622)|plasma membrane (GO:0005886)|stereocilium (GO:0032420)|vesicle (GO:0031982)	actinin binding (GO:0042805)|cadherin binding (GO:0045296)			breast(2)|central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(2)|kidney(4)|large_intestine(4)|liver(1)|lung(11)|ovary(3)|pancreas(1)|upper_aerodigestive_tract(2)	35						ATCTCTTTTCAGGGAGTTCCT	0.413																																																0													106.0	100.0	102.0					4																	15991422		1839	4094	5933	SO:0001583	missense	8842			AF027208	CCDS47029.1, CCDS54746.1, CCDS54747.1, CCDS54748.1	4p15	2013-06-06	2001-11-28	2003-03-28	ENSG00000007062	ENSG00000007062		"""CD molecules"""	9454	protein-coding gene	gene with protein product		604365	"""prominin (mouse)-like 1"", ""macular dystrophy, retinal 2"", ""Stargardt disease 4 (autosomal dominant)"""	PROML1, MCDR2, STGD4		11467842	Standard	NM_006017		Approved	AC133, CD133, RP41, CORD12	uc003goo.2	O43490	OTTHUMG00000160180	ENST00000510224.1:c.2009T>C	4.37:g.15991422A>G	ENSP00000426809:p.Leu670Pro		Q6SV49|Q6SV50|Q6SV51|Q6SV52|Q6SV53|Q96EN6	Missense_Mutation	SNP	ENST00000510224.1	37	CCDS47029.1	.	.	.	.	.	.	.	.	.	.	A	18.07	3.542537	0.65198	.	.	ENSG00000007062	ENST00000447510;ENST00000540805;ENST00000539194;ENST00000505450;ENST00000508167;ENST00000510224;ENST00000543373	T;T;T;T;T;T;T	0.58797	0.31;0.31;0.31;0.31;0.31;0.31;0.31	5.03	5.03	0.67393	.	0.135739	0.50627	D	0.000109	T	0.74382	0.3709	M	0.79123	2.44	0.58432	D	0.999996	D;D;D;D;D;D	0.89917	1.0;1.0;1.0;1.0;1.0;1.0	D;D;D;D;D;D	0.85130	0.997;0.997;0.994;0.997;0.977;0.997	T	0.77736	-0.2476	10	0.87932	D	0	-3.5936	11.0659	0.47974	1.0:0.0:0.0:0.0	.	661;670;661;670;661;670	O43490-5;O43490-6;O43490-4;O43490-7;O43490-2;O43490	.;.;.;.;.;PROM1_HUMAN	P	670;670;670;661;661;670;661	ENSP00000415481:L670P;ENSP00000438045:L670P;ENSP00000443620:L670P;ENSP00000426090:L661P;ENSP00000427346:L661P;ENSP00000426809:L670P;ENSP00000445526:L661P	ENSP00000415481:L670P	L	-	2	0	PROM1	15600520	0.089000	0.21612	0.006000	0.13384	0.123000	0.20343	3.675000	0.54605	2.111000	0.64477	0.533000	0.62120	CTG		0.413	PROM1-004	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000359595.2	NM_006017		6	7	6	7
CCKAR	886	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	4	26483467	26483467	+	Silent	SNP	G	G	A	rs150897748		TCGA-DU-6402-01A-11D-1705-08	TCGA-DU-6402-10A-01D-1705-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	896ec7d7-5443-49bb-969b-7b483e9b518c	3bc825bc-5589-4e0b-b380-38fceee3231b	g.chr4:26483467G>A	ENST00000295589.3	-	5	1274	c.1080C>T	c.(1078-1080)taC>taT	p.Y360Y		NM_000730.2	NP_000721.1	P32238	CCKAR_HUMAN	cholecystokinin A receptor	360					axonogenesis (GO:0007409)|cholecystokinin signaling pathway (GO:0038188)|digestion (GO:0007586)|feeding behavior (GO:0007631)|forebrain development (GO:0030900)|neuron migration (GO:0001764)|phospholipase C-activating G-protein coupled receptor signaling pathway (GO:0007200)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|response to nutrient (GO:0007584)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	cholecystokinin receptor activity (GO:0004951)			NS(2)|central_nervous_system(2)|endometrium(2)|kidney(2)|large_intestine(4)|liver(1)|lung(14)|pancreas(1)|skin(1)	29		Breast(46;0.0503)			Ceruletide(DB00403)	AGGAGGAGGTGTAGGACAGGA	0.627																																																0								G		1,4405	2.1+/-5.4	0,1,2202	128.0	120.0	123.0		1080	3.2	1.0	4	dbSNP_134	123	0,8600		0,0,4300	no	coding-synonymous	CCKAR	NM_000730.2		0,1,6502	AA,AG,GG		0.0,0.0227,0.0077		360/429	26483467	1,13005	2203	4300	6503	SO:0001819	synonymous_variant	886			L19315	CCDS3438.1	4p15.2	2013-09-20			ENSG00000163394	ENSG00000163394		"""GPCR / Class A : Cholecystokinin receptors"""	1570	protein-coding gene	gene with protein product		118444					Standard	NM_000730		Approved		uc003gse.1	P32238	OTTHUMG00000128567	ENST00000295589.3:c.1080C>T	4.37:g.26483467G>A			B2R9Z5	Silent	SNP	ENST00000295589.3	37	CCDS3438.1																																																																																				0.627	CCKAR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250418.2			20	93	20	93
MUC7	4589	hgsc.bcm.edu;ucsc.edu	37	4	71347577	71347577	+	Silent	SNP	C	C	T	rs41424846	byFrequency	TCGA-DU-6402-01A-11D-1705-08	TCGA-DU-6402-10A-01D-1705-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	896ec7d7-5443-49bb-969b-7b483e9b518c	3bc825bc-5589-4e0b-b380-38fceee3231b	g.chr4:71347577C>T	ENST00000304887.5	+	3	1306	c.1116C>T	c.(1114-1116)gaC>gaT	p.D372D	MUC7_ENST00000456088.1_Silent_p.D372D|MUC7_ENST00000413702.1_Silent_p.D372D	NM_152291.2	NP_689504.2	Q8TAX7	MUC7_HUMAN	mucin 7, secreted	372					cellular protein metabolic process (GO:0044267)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	extracellular vesicular exosome (GO:0070062)|Golgi lumen (GO:0005796)				central_nervous_system(1)|endometrium(3)|kidney(5)|large_intestine(2)|lung(23)|ovary(3)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	42			Lung(101;0.211)			GAATTATTGACGACATGGTGG	0.338																																																0													49.0	54.0	52.0					4																	71347577		2203	4300	6503	SO:0001819	synonymous_variant	4589			BC025688	CCDS3541.1	4q13.3	2008-02-05	2006-03-14		ENSG00000171195	ENSG00000171195		"""Mucins"""	7518	protein-coding gene	gene with protein product		158375	"""mucin 7, salivary"""			8838308	Standard	NM_152291		Approved	FLJ27047, MG2	uc003hfj.3	Q8TAX7	OTTHUMG00000129916	ENST00000304887.5:c.1116C>T	4.37:g.71347577C>T			Q9UCD7|Q9UCD8	Silent	SNP	ENST00000304887.5	37	CCDS3541.1																																																																																				0.338	MUC7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252168.2	NM_152291		19	52	19	52
PPEF2	5470	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	4	76812812	76812812	+	Missense_Mutation	SNP	C	C	T			TCGA-DU-6402-01A-11D-1705-08	TCGA-DU-6402-10A-01D-1705-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	896ec7d7-5443-49bb-969b-7b483e9b518c	3bc825bc-5589-4e0b-b380-38fceee3231b	g.chr4:76812812C>T	ENST00000286719.7	-	4	586	c.230G>A	c.(229-231)aGc>aAc	p.S77N	PPEF2_ENST00000510607.1_5'Flank	NM_006239.2	NP_006230.2	O14830	PPE2_HUMAN	protein phosphatase, EF-hand calcium binding domain 2	77					detection of stimulus involved in sensory perception (GO:0050906)|negative regulation of MAPK cascade (GO:0043409)|negative regulation of peptidyl-threonine phosphorylation (GO:0010801)|protein dephosphorylation (GO:0006470)|regulation of JUN kinase activity (GO:0043506)|regulation of MAP kinase activity (GO:0043405)|visual perception (GO:0007601)	cilium (GO:0005929)|cytoplasm (GO:0005737)	calcium ion binding (GO:0005509)|Hsp70 protein binding (GO:0030544)|Hsp90 protein binding (GO:0051879)|iron ion binding (GO:0005506)|manganese ion binding (GO:0030145)|mitogen-activated protein kinase kinase kinase binding (GO:0031435)|protein serine/threonine phosphatase activity (GO:0004722)			breast(1)|central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(7)|lung(25)|ovary(2)|pancreas(1)|prostate(4)|skin(1)|upper_aerodigestive_tract(3)|urinary_tract(2)	50			Lung(101;0.0809)|LUSC - Lung squamous cell carcinoma(112;0.0934)			GTCGTTGTGGCTGCTGGGGAT	0.522																																					NSCLC(105;1359 1603 15961 44567 47947)											0													269.0	239.0	249.0					4																	76812812		2203	4300	6503	SO:0001583	missense	5470			AF023456	CCDS34013.1	4q21.1	2013-01-10			ENSG00000156194	ENSG00000156194		"""Serine/threonine phosphatases / Protein phosphatase, catalytic subunits"", ""EF-hand domain containing"""	9244	protein-coding gene	gene with protein product	"""protein phosphatase 7, catalytic subunit, beta isozyme"""	602256				9326663, 12051765	Standard	NM_006239		Approved	PPP7CB	uc003hix.3	O14830	OTTHUMG00000160915	ENST00000286719.7:c.230G>A	4.37:g.76812812C>T	ENSP00000286719:p.Ser77Asn		O14831	Missense_Mutation	SNP	ENST00000286719.7	37	CCDS34013.1	.	.	.	.	.	.	.	.	.	.	C	11.60	1.686443	0.29962	.	.	ENSG00000156194	ENST00000286719;ENST00000337500	T	0.54479	0.57	5.13	3.39	0.38822	.	0.971136	0.08605	N	0.920917	T	0.41465	0.1160	N	0.25957	0.775	0.36945	D	0.892573	B;B	0.33494	0.414;0.034	B;B	0.38985	0.287;0.035	T	0.18241	-1.0343	10	0.17832	T	0.49	-1.3289	7.2597	0.26197	0.0:0.7264:0.0:0.2736	.	77;77	O14830-2;O14830	.;PPE2_HUMAN	N	77	ENSP00000286719:S77N	ENSP00000286719:S77N	S	-	2	0	PPEF2	77031836	1.000000	0.71417	0.542000	0.28115	0.904000	0.53231	1.464000	0.35288	0.551000	0.29008	0.591000	0.81541	AGC		0.522	PPEF2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000362929.1	NM_006239		99	224	99	224
FAT4	79633	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	4	126239159	126239159	+	Silent	SNP	C	C	T			TCGA-DU-6402-01A-11D-1705-08	TCGA-DU-6402-10A-01D-1705-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	896ec7d7-5443-49bb-969b-7b483e9b518c	3bc825bc-5589-4e0b-b380-38fceee3231b	g.chr4:126239159C>T	ENST00000394329.3	+	1	1606	c.1593C>T	c.(1591-1593)ctC>ctT	p.L531L		NM_024582.4	NP_078858.4	Q6V0I7	FAT4_HUMAN	FAT atypical cadherin 4	531	Cadherin 5. {ECO:0000255|PROSITE- ProRule:PRU00043}.				branching involved in ureteric bud morphogenesis (GO:0001658)|cerebral cortex development (GO:0021987)|digestive tract development (GO:0048565)|heart morphogenesis (GO:0003007)|heterophilic cell-cell adhesion (GO:0007157)|hippo signaling (GO:0035329)|homophilic cell adhesion (GO:0007156)|inner ear receptor stereocilium organization (GO:0060122)|neurogenesis (GO:0022008)|ossification involved in bone maturation (GO:0043931)|plasma membrane organization (GO:0007009)|regulation of metanephric nephron tubule epithelial cell differentiation (GO:0072307)	apical part of cell (GO:0045177)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			NS(6)|autonomic_ganglia(1)|breast(4)|central_nervous_system(3)|cervix(3)|endometrium(27)|haematopoietic_and_lymphoid_tissue(3)|kidney(10)|large_intestine(93)|liver(3)|lung(120)|ovary(9)|pancreas(2)|prostate(21)|skin(31)|stomach(1)|upper_aerodigestive_tract(12)|urinary_tract(6)	355						ATAGCGGCCTCGTGACCACTG	0.547											OREG0016317	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																																				0													56.0	60.0	59.0					4																	126239159		2190	4285	6475	SO:0001819	synonymous_variant	79633			AY356402	CCDS3732.3	4q28.1	2013-05-31	2013-05-31		ENSG00000196159	ENSG00000196159		"""Cadherins / Cadherin-related"""	23109	protein-coding gene	gene with protein product	"""cadherin-related family member 11"""	612411	"""FAT tumor suppressor homolog 4 (Drosophila)"""			15003449	Standard	NM_024582		Approved	CDHF14, FAT-J, CDHR11	uc003ifj.4	Q6V0I7	OTTHUMG00000133100	ENST00000394329.3:c.1593C>T	4.37:g.126239159C>T		1548	A8K5Z6|B5MDG4|Q3LIA6|Q8TCK7|Q9H5T6	Silent	SNP	ENST00000394329.3	37	CCDS3732.3																																																																																				0.547	FAT4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256765.2	NM_024582		16	34	16	34
MARCH11	441061	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	5	16067657	16067657	+	Missense_Mutation	SNP	T	T	C			TCGA-DU-6402-01A-11D-1705-08	TCGA-DU-6402-10A-01D-1705-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	896ec7d7-5443-49bb-969b-7b483e9b518c	3bc825bc-5589-4e0b-b380-38fceee3231b	g.chr5:16067657T>C	ENST00000332432.8	-	4	1331	c.1132A>G	c.(1132-1134)Aat>Gat	p.N378D		NM_001102562.1	NP_001096032.1	A6NNE9	MARHB_HUMAN	membrane-associated ring finger (C3HC4) 11	378					protein ubiquitination (GO:0016567)	cytoplasmic vesicle (GO:0031410)|integral component of membrane (GO:0016021)	ligase activity (GO:0016874)|zinc ion binding (GO:0008270)			NS(1)|central_nervous_system(1)|endometrium(2)|large_intestine(1)|lung(14)|urinary_tract(1)	20						CTCATCCGATTGAACAGGTGC	0.478																																																0													190.0	182.0	185.0					5																	16067657		1935	4134	6069	SO:0001583	missense	441061			BC150513	CCDS47192.1	5p15.1	2013-01-09			ENSG00000183654	ENSG00000183654		"""RING-type (C3HC4) zinc fingers"", ""MARCH membrane-associated ring fingers"""	33609	protein-coding gene	gene with protein product		613338				17604280	Standard	NM_001102562		Approved	MARCH-XI	uc003jfo.2	A6NNE9	OTTHUMG00000161789	ENST00000332432.8:c.1132A>G	5.37:g.16067657T>C	ENSP00000333181:p.Asn378Asp		A7E2S6	Missense_Mutation	SNP	ENST00000332432.8	37	CCDS47192.1	.	.	.	.	.	.	.	.	.	.	T	12.15	1.850836	0.32699	.	.	ENSG00000183654	ENST00000332432	T	0.18174	2.23	5.44	5.44	0.79542	.	0.467852	0.23834	N	0.044114	T	0.10465	0.0256	N	0.08118	0	0.35469	D	0.797169	B	0.34290	0.447	B	0.33521	0.165	T	0.33059	-0.9883	10	0.31617	T	0.26	-9.2497	15.7894	0.78343	0.0:0.0:0.0:1.0	.	378	A6NNE9	MARHB_HUMAN	D	378	ENSP00000333181:N378D	ENSP00000333181:N378D	N	-	1	0	MARCH11	16120657	1.000000	0.71417	0.992000	0.48379	0.184000	0.23303	3.628000	0.54259	2.178000	0.69098	0.533000	0.62120	AAT		0.478	MARCH11-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000366096.2	NM_001102562		45	124	45	124
PCDHA2	56146	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	5	140176070	140176070	+	Silent	SNP	C	C	T			TCGA-DU-6402-01A-11D-1705-08	TCGA-DU-6402-10A-01D-1705-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	896ec7d7-5443-49bb-969b-7b483e9b518c	3bc825bc-5589-4e0b-b380-38fceee3231b	g.chr5:140176070C>T	ENST00000526136.1	+	1	1521	c.1521C>T	c.(1519-1521)taC>taT	p.Y507Y	PCDHA2_ENST00000520672.2_Silent_p.Y507Y|PCDHA1_ENST00000504120.2_Intron|PCDHA2_ENST00000378132.1_Silent_p.Y507Y|PCDHA1_ENST00000394633.3_Intron	NM_018905.2	NP_061728.1	Q9Y5H9	PCDA2_HUMAN	protocadherin alpha 2	507	Cadherin 5. {ECO:0000255|PROSITE- ProRule:PRU00043}.				cell adhesion (GO:0007155)|homophilic cell adhesion (GO:0007156)|nervous system development (GO:0007399)	integral component of plasma membrane (GO:0005887)	calcium ion binding (GO:0005509)			NS(1)|breast(1)|endometrium(10)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(16)|lung(26)|ovary(4)|prostate(6)|skin(2)|upper_aerodigestive_tract(1)	71			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			TGTCGAGCTACGTTTCGGTGC	0.682																																																0													64.0	66.0	65.0					5																	140176070		2203	4299	6502	SO:0001819	synonymous_variant	56146			AF152480	CCDS54914.1, CCDS64269.1	5q31	2010-11-26				ENSG00000204969		"""Cadherins / Protocadherins : Clustered"""	8668	other	complex locus constituent	"""KIAA0345-like 12"""	606308				10380929	Standard	NM_018905		Approved			Q9Y5H9		ENST00000526136.1:c.1521C>T	5.37:g.140176070C>T			O75287|Q9BTV3	Silent	SNP	ENST00000526136.1	37	CCDS54914.1																																																																																				0.682	PCDHA2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000372877.3	NM_018905		13	43	13	43
PCDHB2	56133	hgsc.bcm.edu;broad.mit.edu	37	5	140475880	140475880	+	Silent	SNP	C	C	T			TCGA-DU-6402-01A-11D-1705-08	TCGA-DU-6402-10A-01D-1705-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	896ec7d7-5443-49bb-969b-7b483e9b518c	3bc825bc-5589-4e0b-b380-38fceee3231b	g.chr5:140475880C>T	ENST00000194155.4	+	1	1654	c.1506C>T	c.(1504-1506)ctC>ctT	p.L502L		NM_018936.2	NP_061759.1	Q9Y5E7	PCDB2_HUMAN	protocadherin beta 2	502	Cadherin 5. {ECO:0000255|PROSITE- ProRule:PRU00043}.				calcium-dependent cell-cell adhesion (GO:0016339)|cell adhesion (GO:0007155)|homophilic cell adhesion (GO:0007156)|nervous system development (GO:0007399)|synapse assembly (GO:0007416)|synaptic transmission (GO:0007268)	integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)	calcium ion binding (GO:0005509)			NS(1)|breast(1)|endometrium(3)|kidney(1)|large_intestine(22)|lung(24)|ovary(3)|pancreas(1)|prostate(3)|skin(7)|upper_aerodigestive_tract(3)|urinary_tract(2)	71			KIRC - Kidney renal clear cell carcinoma(527;0.00185)|Kidney(363;0.00339)			ACCTGCCCCTCGCCTCCCTGG	0.692																																																0													65.0	69.0	68.0					5																	140475880		2203	4297	6500	SO:0001819	synonymous_variant	56133			AF152495	CCDS4244.1	5q31	2010-01-26			ENSG00000112852	ENSG00000112852		"""Cadherins / Protocadherins : Clustered"""	8687	other	protocadherin		606328				10380929	Standard	NM_018936		Approved	PCDH-BETA2	uc003lil.3	Q9Y5E7	OTTHUMG00000129606	ENST00000194155.4:c.1506C>T	5.37:g.140475880C>T			Q4KMU1	Silent	SNP	ENST00000194155.4	37	CCDS4244.1																																																																																				0.692	PCDHB2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251801.2	NM_018936		15	116	15	116
PKHD1	5314	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	6	51882309	51882309	+	Silent	SNP	C	C	T	rs557919334		TCGA-DU-6402-01A-11D-1705-08	TCGA-DU-6402-10A-01D-1705-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	896ec7d7-5443-49bb-969b-7b483e9b518c	3bc825bc-5589-4e0b-b380-38fceee3231b	g.chr6:51882309C>T	ENST00000371117.3	-	34	5774	c.5499G>A	c.(5497-5499)tcG>tcA	p.S1833S	PKHD1_ENST00000340994.4_Silent_p.S1833S	NM_138694.3	NP_619639.3	P08F94	PKHD1_HUMAN	polycystic kidney and hepatic disease 1 (autosomal recessive)	1833			S -> L (in ARPKD). {ECO:0000269|PubMed:12846734}.		cellular calcium ion homeostasis (GO:0006874)|cilium assembly (GO:0042384)|homeostatic process (GO:0042592)|kidney development (GO:0001822)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cellular component movement (GO:0051271)|negative regulation of NF-kappaB transcription factor activity (GO:0032088)|negative regulation of protein kinase B signaling (GO:0051898)|positive regulation of cell proliferation (GO:0008284)|regulation of centrosome duplication (GO:0010824)|regulation of ERK1 and ERK2 cascade (GO:0070372)|regulation of TOR signaling (GO:0032006)|single organismal cell-cell adhesion (GO:0016337)	anchored component of external side of plasma membrane (GO:0031362)|apical plasma membrane (GO:0016324)|centrosome (GO:0005813)|ciliary basal body (GO:0036064)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|mitotic spindle (GO:0072686)|perinuclear region of cytoplasm (GO:0048471)|primary cilium (GO:0072372)	receptor activity (GO:0004872)			NS(1)|autonomic_ganglia(1)|breast(8)|central_nervous_system(5)|cervix(1)|endometrium(16)|haematopoietic_and_lymphoid_tissue(4)|kidney(11)|large_intestine(59)|lung(139)|ovary(16)|prostate(8)|skin(20)|soft_tissue(1)|stomach(2)|upper_aerodigestive_tract(7)|urinary_tract(5)	304	Lung NSC(77;0.0605)					GGTAAGGCCACGATTCAAGCA	0.512													C|||	0	0.0	0.0	0.0	5008	,	,		21659	0.0		0.0	False		,,,				2504	0.0															0													196.0	169.0	178.0					6																	51882309		2203	4300	6503	SO:0001819	synonymous_variant	5314			AF480064	CCDS4935.1, CCDS4936.1	6p21.2-p12	2012-11-26	2003-04-16		ENSG00000170927	ENSG00000170927			9016	protein-coding gene	gene with protein product	"""tigmin"", ""polyductin"", ""fibrocystin"""	606702	"""TIG multiple domains 1"""	TIGM1		9503014	Standard	NM_138694		Approved	ARPKD, FCYT	uc003pah.1	P08F94	OTTHUMG00000014841	ENST00000371117.3:c.5499G>A	6.37:g.51882309C>T			Q5VUA2|Q5VUA3|Q5VWV1|Q86Z26|Q8TCZ9	Silent	SNP	ENST00000371117.3	37	CCDS4935.1																																																																																				0.512	PKHD1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000040893.1	NM_138694		26	110	26	110
DDC	1644	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	7	50611629	50611629	+	Missense_Mutation	SNP	G	G	A	rs371272735		TCGA-DU-6402-01A-11D-1705-08	TCGA-DU-6402-10A-01D-1705-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	896ec7d7-5443-49bb-969b-7b483e9b518c	3bc825bc-5589-4e0b-b380-38fceee3231b	g.chr7:50611629G>A	ENST00000444124.2	-	2	355	c.155C>T	c.(154-156)aCg>aTg	p.T52M	DDC_ENST00000380984.4_Missense_Mutation_p.T52M|DDC_ENST00000431062.1_Missense_Mutation_p.T52M|DDC_ENST00000357936.5_Missense_Mutation_p.T52M|AC018705.5_ENST00000454521.1_RNA|DDC_ENST00000426377.1_Missense_Mutation_p.T52M	NM_001082971.1	NP_001076440	P20711	DDC_HUMAN	dopa decarboxylase (aromatic L-amino acid decarboxylase)	52					catecholamine biosynthetic process (GO:0042423)|cellular amino acid metabolic process (GO:0006520)|cellular nitrogen compound metabolic process (GO:0034641)|cellular response to alkaloid (GO:0071312)|cellular response to drug (GO:0035690)|cellular response to growth factor stimulus (GO:0071363)|circadian rhythm (GO:0007623)|dopamine biosynthetic process (GO:0042416)|indolalkylamine biosynthetic process (GO:0046219)|isoquinoline alkaloid metabolic process (GO:0033076)|multicellular organismal aging (GO:0010259)|phytoalexin metabolic process (GO:0052314)|response to pyrethroid (GO:0046684)|serotonin biosynthetic process (GO:0042427)|small molecule metabolic process (GO:0044281)|synaptic vesicle amine transport (GO:0015842)	axon (GO:0030424)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|neuronal cell body (GO:0043025)|synaptic vesicle (GO:0008021)	amino acid binding (GO:0016597)|aromatic-L-amino-acid decarboxylase activity (GO:0004058)|enzyme binding (GO:0019899)|L-dopa decarboxylase activity (GO:0036468)|pyridoxal phosphate binding (GO:0030170)			breast(1)|endometrium(4)|kidney(3)|large_intestine(2)|lung(23)|ovary(4)|skin(2)|stomach(1)	40	Glioma(55;0.08)|all_neural(89;0.245)				Amantadine(DB00915)|Carbidopa(DB00190)|Cycloserine(DB00260)|Droxidopa(DB06262)|Flupentixol(DB00875)|L-DOPA(DB01235)|L-Tryptophan(DB00150)|Methyldopa(DB00968)	GTCCTCAAACGTGTCTGGCTC	0.557																																																0								G	MET/THR,MET/THR,MET/THR,MET/THR,MET/THR,MET/THR,MET/THR	1,4405	2.1+/-5.4	0,1,2202	151.0	137.0	142.0		155,155,155,155,155,155,155	5.1	0.0	7		142	0,8600		0,0,4300	no	missense,missense,missense,missense,missense,missense,missense	DDC	NM_000790.3,NM_001082971.1,NM_001242886.1,NM_001242887.1,NM_001242888.1,NM_001242889.1,NM_001242890.1	81,81,81,81,81,81,81	0,1,6502	AA,AG,GG		0.0,0.0227,0.0077	benign,benign,benign,benign,benign,benign,benign	52/481,52/481,52/443,52/433,52/403,52/388,52/339	50611629	1,13005	2203	4300	6503	SO:0001583	missense	1644				CCDS5511.1, CCDS56485.1, CCDS56486.1, CCDS56487.1, CCDS75598.1, CCDS75599.1	7p12.1	2012-08-30			ENSG00000132437	ENSG00000132437	4.1.1.28		2719	protein-coding gene	gene with protein product		107930				1612608	Standard	NM_001082971		Approved	AADC	uc003tpf.4	P20711	OTTHUMG00000023353	ENST00000444124.2:c.155C>T	7.37:g.50611629G>A	ENSP00000403644:p.Thr52Met		C9IYA0|E7ER62|E7EU95|Q16723|Q5W5T9|Q75MJ6	Missense_Mutation	SNP	ENST00000444124.2	37	CCDS5511.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	13.32|13.32	2.201142|2.201142	0.38905|0.38905	2.27E-4|2.27E-4	0.0|0.0	ENSG00000132437|ENSG00000132437	ENST00000430300|ENST00000357936;ENST00000431062;ENST00000426377;ENST00000444124;ENST00000380984	.|T;T;T;T;T	.|0.38240	.|1.15;1.15;1.15;1.15;1.15	5.92|5.92	5.05|5.05	0.67936|0.67936	.|Pyridoxal phosphate-dependent transferase, major domain (1);	.|0.460942	.|0.26677	.|N	.|0.023067	T|T	0.40094|0.40094	0.1103|0.1103	M|M	0.76574|0.76574	2.34|2.34	0.09310|0.09310	N|N	1|1	.|B;B	.|0.24533	.|0.105;0.105	.|B;B	.|0.24701	.|0.055;0.055	T|T	0.36016|0.36016	-0.9765|-0.9765	5|10	.|0.46703	.|T	.|0.11	-15.5943|-15.5943	11.7667|11.7667	0.51935|0.51935	0.0689:0.1313:0.7998:0.0|0.0689:0.1313:0.7998:0.0	.|.	.|52;52	.|Q53Y41;P20711	.|.;DDC_HUMAN	C|M	18|52	.|ENSP00000350616:T52M;ENSP00000399184:T52M;ENSP00000395069:T52M;ENSP00000403644:T52M;ENSP00000370371:T52M	.|ENSP00000350616:T52M	R|T	-|-	1|2	0|0	DDC|DDC	50579123|50579123	0.043000|0.043000	0.20138|0.20138	0.006000|0.006000	0.13384|0.13384	0.609000|0.609000	0.37215|0.37215	2.125000|2.125000	0.42016|0.42016	1.521000|1.521000	0.48983|0.48983	0.655000|0.655000	0.94253|0.94253	CGT|ACG		0.557	DDC-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000342593.1			38	166	38	166
GRM3	2913	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	7	86415593	86415593	+	Missense_Mutation	SNP	G	G	A			TCGA-DU-6402-01A-11D-1705-08	TCGA-DU-6402-10A-01D-1705-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	896ec7d7-5443-49bb-969b-7b483e9b518c	3bc825bc-5589-4e0b-b380-38fceee3231b	g.chr7:86415593G>A	ENST00000361669.2	+	3	1584	c.485G>A	c.(484-486)cGg>cAg	p.R162Q	GRM3_ENST00000439827.1_Missense_Mutation_p.R162Q|AC005009.2_ENST00000418031.1_RNA|GRM3_ENST00000546348.1_Intron|AC005009.2_ENST00000452471.1_RNA|GRM3_ENST00000394720.2_Missense_Mutation_p.R160Q|GRM3_ENST00000536043.1_Missense_Mutation_p.R34Q	NM_000840.2	NP_000831.2	Q14832	GRM3_HUMAN	glutamate receptor, metabotropic 3	162					adenylate cyclase-inhibiting G-protein coupled glutamate receptor signaling pathway (GO:0007196)|negative regulation of adenylate cyclase activity (GO:0007194)|regulation of synaptic transmission, glutamatergic (GO:0051966)|synaptic transmission (GO:0007268)	astrocyte projection (GO:0097449)|axon (GO:0030424)|dendritic spine (GO:0043197)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|postsynaptic density (GO:0014069)|postsynaptic membrane (GO:0045211)|presynaptic membrane (GO:0042734)	calcium channel regulator activity (GO:0005246)|G-protein coupled receptor activity (GO:0004930)|glutamate receptor activity (GO:0008066)|group II metabotropic glutamate receptor activity (GO:0001641)			NS(2)|breast(6)|central_nervous_system(2)|endometrium(4)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(9)|lung(43)|ovary(3)|pancreas(2)|prostate(4)|skin(25)|upper_aerodigestive_tract(5)	109	Esophageal squamous(14;0.0058)|all_lung(186;0.132)|Lung NSC(181;0.142)					AACCTGCTGCGGCTCTTCCAG	0.522																																					GBM(52;969 1098 3139 52280)											0													151.0	163.0	159.0					7																	86415593		2203	4300	6503	SO:0001583	missense	2913				CCDS5600.1	7q21.1-q21.2	2012-08-29			ENSG00000198822	ENSG00000198822		"""GPCR / Class C : Glutamate receptors, metabotropic"", ""Glutamate receptors"""	4595	protein-coding gene	gene with protein product		601115				8824806	Standard	NM_000840		Approved	GPRC1C, mGlu3, MGLUR3	uc003uid.3	Q14832	OTTHUMG00000022884	ENST00000361669.2:c.485G>A	7.37:g.86415593G>A	ENSP00000355316:p.Arg162Gln		Q2PNZ6|Q75MV4|Q75N17|Q86YG6|Q8TBH9	Missense_Mutation	SNP	ENST00000361669.2	37	CCDS5600.1	.	.	.	.	.	.	.	.	.	.	G	24.3	4.510994	0.85389	.	.	ENSG00000198822	ENST00000361669;ENST00000454217;ENST00000536043;ENST00000439827;ENST00000394720	D;D;D;D;D	0.82619	-1.63;-1.63;-1.63;-1.63;-1.63	5.68	5.68	0.88126	GPCR, family 3, conserved site (1);Extracellular ligand-binding receptor (1);	0.000000	0.85682	D	0.000000	D	0.89438	0.6715	L	0.55103	1.725	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.85130	0.997;0.996;0.997	D	0.88183	0.2872	10	0.42905	T	0.14	.	18.7805	0.91930	0.0:0.0:1.0:0.0	.	34;162;162	F5GYZ2;G5E9K2;Q14832	.;.;GRM3_HUMAN	Q	162;34;34;162;160	ENSP00000355316:R162Q;ENSP00000405427:R34Q;ENSP00000441407:R34Q;ENSP00000398767:R162Q;ENSP00000378209:R160Q	ENSP00000355316:R162Q	R	+	2	0	GRM3	86253529	1.000000	0.71417	0.493000	0.27502	0.959000	0.62525	9.725000	0.98778	2.693000	0.91896	0.655000	0.94253	CGG		0.522	GRM3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253362.2			69	257	69	257
SLC26A3	1811	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	7	107423751	107423751	+	Missense_Mutation	SNP	C	C	T			TCGA-DU-6402-01A-11D-1705-08	TCGA-DU-6402-10A-01D-1705-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	896ec7d7-5443-49bb-969b-7b483e9b518c	3bc825bc-5589-4e0b-b380-38fceee3231b	g.chr7:107423751C>T	ENST00000340010.5	-	9	1202	c.1018G>A	c.(1018-1020)Gta>Ata	p.V340I	SLC26A3_ENST00000422236.2_Missense_Mutation_p.V305I	NM_000111.2	NP_000102.1	P40879	S26A3_HUMAN	solute carrier family 26 (anion exchanger), member 3	340					anion transport (GO:0006820)|cellular response to cAMP (GO:0071320)|excretion (GO:0007588)|intracellular pH elevation (GO:0051454)|ion transport (GO:0006811)|membrane hyperpolarization (GO:0060081)|regulation of RNA biosynthetic process (GO:2001141)|regulation of transcription, DNA-templated (GO:0006355)|sperm capacitation (GO:0048240)|transmembrane transport (GO:0055085)	apical plasma membrane (GO:0016324)|brush border membrane (GO:0031526)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)|sperm midpiece (GO:0097225)	anion:anion antiporter activity (GO:0015301)|bicarbonate transmembrane transporter activity (GO:0015106)|chloride transmembrane transporter activity (GO:0015108)|secondary active sulfate transmembrane transporter activity (GO:0008271)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription cofactor activity (GO:0003712)|transporter activity (GO:0005215)			breast(1)|central_nervous_system(3)|cervix(1)|endometrium(3)|kidney(1)|large_intestine(4)|lung(18)|ovary(4)|prostate(1)|skin(6)|upper_aerodigestive_tract(3)|urinary_tract(1)	46						CAATCTCCTACGGTGTTTTGG	0.418																																																0													87.0	85.0	86.0					7																	107423751		2203	4300	6503	SO:0001583	missense	1811			L02785	CCDS5748.1	7q31	2014-09-17	2013-07-18		ENSG00000091138	ENSG00000091138		"""Solute carriers"""	3018	protein-coding gene	gene with protein product		126650	"""congenital chloride diarrhea"", ""solute carrier family 26, member 3"""	DRA, CLD		8020951, 11087667	Standard	NM_000111		Approved		uc003ver.2	P40879	OTTHUMG00000154812	ENST00000340010.5:c.1018G>A	7.37:g.107423751C>T	ENSP00000345873:p.Val340Ile			Missense_Mutation	SNP	ENST00000340010.5	37	CCDS5748.1	.	.	.	.	.	.	.	.	.	.	T	2.337	-0.352052	0.05173	.	.	ENSG00000091138	ENST00000422236;ENST00000340010	D;D	0.92699	-3.09;-3.09	5.28	5.28	0.74379	Sulphate transporter (1);	0.146062	0.64402	N	0.000011	T	0.74589	0.3736	N	0.02685	-0.53	0.09310	N	1	B;B	0.09022	0.002;0.002	B;B	0.08055	0.003;0.002	T	0.62909	-0.6754	10	0.02654	T	1	.	4.587	0.12287	0.1336:0.2153:0.0:0.6511	.	305;340	G5E9U3;P40879	.;S26A3_HUMAN	I	305;340	ENSP00000415817:V305I;ENSP00000345873:V340I	ENSP00000345873:V340I	V	-	1	0	SLC26A3	107210987	0.016000	0.18221	0.905000	0.35620	0.099000	0.18886	0.293000	0.19029	0.947000	0.37659	-0.254000	0.11334	GTA		0.418	SLC26A3-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000337190.1	NM_000111		21	79	21	79
BRAF	673	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	7	140453154	140453154	+	Missense_Mutation	SNP	T	T	C	rs121913338		TCGA-DU-6402-01A-11D-1705-08	TCGA-DU-6402-10A-01D-1705-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	896ec7d7-5443-49bb-969b-7b483e9b518c	3bc825bc-5589-4e0b-b380-38fceee3231b	g.chr7:140453154T>C	ENST00000288602.6	-	15	1841	c.1781A>G	c.(1780-1782)gAt>gGt	p.D594G		NM_004333.4	NP_004324.2	P15056	BRAF_HUMAN	B-Raf proto-oncogene, serine/threonine kinase	594	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.		D -> G (in NHL). {ECO:0000269|PubMed:14612909}.		activation of MAPKK activity (GO:0000186)|CD4-positive, alpha-beta T cell differentiation (GO:0043367)|cellular response to calcium ion (GO:0071277)|cellular response to drug (GO:0035690)|fibroblast growth factor receptor signaling pathway (GO:0008543)|long-term synaptic potentiation (GO:0060291)|myeloid progenitor cell differentiation (GO:0002318)|negative regulation of apoptotic process (GO:0043066)|negative regulation of endothelial cell apoptotic process (GO:2000352)|negative regulation of fibroblast migration (GO:0010764)|negative regulation of neuron apoptotic process (GO:0043524)|negative regulation of synaptic vesicle exocytosis (GO:2000301)|neurotrophin TRK receptor signaling pathway (GO:0048011)|organ morphogenesis (GO:0009887)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of gene expression (GO:0010628)|positive regulation of peptidyl-serine phosphorylation (GO:0033138)|positive regulation of stress fiber assembly (GO:0051496)|positive regulation of substrate adhesion-dependent cell spreading (GO:1900026)|positive T cell selection (GO:0043368)|protein heterooligomerization (GO:0051291)|protein phosphorylation (GO:0006468)|regulation of cell proliferation (GO:0042127)|response to cAMP (GO:0051591)|response to epidermal growth factor (GO:0070849)|response to peptide hormone (GO:0043434)|small GTPase mediated signal transduction (GO:0007264)|somatic stem cell maintenance (GO:0035019)|synaptic transmission (GO:0007268)|visual learning (GO:0008542)	cell body (GO:0044297)|cytosol (GO:0005829)|mitochondrion (GO:0005739)|neuron projection (GO:0043005)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|identical protein binding (GO:0042802)|MAP kinase kinase kinase activity (GO:0004709)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)	p.D594G(35)|p.D594V(3)	SLC45A3/BRAF(2)|AGTRAP/BRAF(2)|FAM131B_ENST00000443739/BRAF(7)|AKAP9_ENST00000356239/BRAF(10)|KIAA1549/BRAF(703)|FCHSD1/BRAF(2)	NS(588)|adrenal_gland(3)|autonomic_ganglia(3)|biliary_tract(29)|bone(7)|breast(21)|central_nervous_system(99)|cervix(6)|endometrium(33)|eye(72)|gastrointestinal_tract_(site_indeterminate)(2)|genital_tract(4)|haematopoietic_and_lymphoid_tissue(436)|kidney(3)|large_intestine(6953)|liver(17)|lung(192)|oesophagus(4)|ovary(275)|pancreas(15)|pituitary(1)|prostate(25)|salivary_gland(1)|skin(6285)|small_intestine(12)|soft_tissue(40)|stomach(11)|testis(7)|thyroid(12220)|upper_aerodigestive_tract(13)|urinary_tract(3)	27380	Melanoma(164;0.00956)				Dabrafenib(DB08912)|Regorafenib(DB08896)|Sorafenib(DB00398)|Vemurafenib(DB08881)	TAGACCAAAATCACCTATTTT	0.373		61	"""Mis, T, O"""	"""AKAP9, KIAA1549"""	"""melanoma, colorectal, papillary thyroid, borderline ov, Non small-cell lung cancer (NSCLC), cholangiocarcinoma, pilocytic astrocytoma"""		Cardio-facio-cutaneous syndrome		Cardiofaciocutaneous syndrome																												Colon(40;35 892 2973 5743 27438)		Dom	yes		7	7q34	673	v-raf murine sarcoma viral oncogene homolog B1	yes	E	38	Substitution - Missense(38)	large_intestine(16)|skin(8)|haematopoietic_and_lymphoid_tissue(5)|lung(4)|stomach(2)|endometrium(2)|ovary(1)											107.0	100.0	103.0					7																	140453154		2203	4300	6503	SO:0001583	missense	673	Familial Cancer Database	CFC, CFCS	M95712	CCDS5863.1	7q34	2014-09-17	2014-06-26		ENSG00000157764	ENSG00000157764			1097	protein-coding gene	gene with protein product		164757	"""v-raf murine sarcoma viral oncogene homolog B"""			2284096, 1565476	Standard	NM_004333		Approved	BRAF1	uc003vwc.4	P15056	OTTHUMG00000157457	ENST00000288602.6:c.1781A>G	7.37:g.140453154T>C	ENSP00000288602:p.Asp594Gly		A4D1T4|B6HY61|B6HY62|B6HY63|B6HY64|B6HY65|B6HY66|Q13878|Q3MIN6|Q9UDP8|Q9Y6T3	Missense_Mutation	SNP	ENST00000288602.6	37	CCDS5863.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	27.9|27.9	4.868575|4.868575	0.91587|0.91587	.|.	.|.	ENSG00000157764|ENSG00000157764	ENST00000288602|ENST00000496384	D|.	0.99853|.	-7.18|.	5.65|5.65	5.65|5.65	0.86999|0.86999	Serine-threonine/tyrosine-protein kinase (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);|.	0.000000|.	0.85682|.	D|.	0.000000|.	D|D	0.86830|0.86830	0.6027|0.6027	H|H	0.94658|0.94658	3.565|3.565	0.80722|0.80722	D|D	1|1	D|.	0.64830|.	0.994|.	D|.	0.74348|.	0.983|.	D|D	0.90563|0.90563	0.4517|0.4517	10|5	0.87932|.	D|.	0|.	.|.	15.9326|15.9326	0.79675|0.79675	0.0:0.0:0.0:1.0|0.0:0.0:0.0:1.0	.|.	594|.	P15056|.	BRAF_HUMAN|.	G|V	594|202	ENSP00000288602:D594G|.	ENSP00000288602:D594G|.	D|I	-|-	2|1	0|0	BRAF|BRAF	140099623|140099623	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.999000|0.999000	0.98932|0.98932	7.921000|7.921000	0.87530|0.87530	2.169000|2.169000	0.68431|0.68431	0.529000|0.529000	0.55759|0.55759	GAT|ATT		0.373	BRAF-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000348886.1	NM_004333		22	90	22	90
DAPK1	1612	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	9	90301560	90301560	+	Missense_Mutation	SNP	G	G	A			TCGA-DU-6402-01A-11D-1705-08	TCGA-DU-6402-10A-01D-1705-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	896ec7d7-5443-49bb-969b-7b483e9b518c	3bc825bc-5589-4e0b-b380-38fceee3231b	g.chr9:90301560G>A	ENST00000408954.3	+	21	2654	c.2319G>A	c.(2317-2319)atG>atA	p.M773I	DAPK1_ENST00000472284.1_Missense_Mutation_p.M773I|DAPK1_ENST00000469640.2_Missense_Mutation_p.M773I|DAPK1_ENST00000358077.5_Missense_Mutation_p.M773I|DAPK1_ENST00000491893.1_Missense_Mutation_p.M773I	NM_004938.2	NP_004929.2	P53355	DAPK1_HUMAN	death-associated protein kinase 1	773					apoptotic process (GO:0006915)|apoptotic signaling pathway (GO:0097190)|cellular response to interferon-gamma (GO:0071346)|extrinsic apoptotic signaling pathway via death domain receptors (GO:0008625)|intracellular signal transduction (GO:0035556)|negative regulation of apoptotic process (GO:0043066)|negative regulation of extrinsic apoptotic signaling pathway via death domain receptors (GO:1902042)|negative regulation of translation (GO:0017148)|positive regulation of apoptotic process (GO:0043065)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|regulation of apoptotic process (GO:0042981)|regulation of autophagy (GO:0010506)|regulation of N-methyl-D-aspartate selective glutamate receptor activity (GO:2000310)	actin cytoskeleton (GO:0015629)|cytoplasm (GO:0005737)	ATP binding (GO:0005524)|calmodulin binding (GO:0005516)|calmodulin-dependent protein kinase activity (GO:0004683)|identical protein binding (GO:0042802)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)			breast(5)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(27)|liver(2)|lung(17)|ovary(1)|prostate(2)|skin(3)|stomach(1)	72						CCAAAGGGATGCTGGAGGTGT	0.577									Chronic Lymphocytic Leukemia, Familial Clustering of																																							0													85.0	99.0	94.0					9																	90301560		2129	4229	6358	SO:0001583	missense	1612	Familial Cancer Database	Familial CLL	X76104	CCDS43842.1	9q34.1	2013-01-10			ENSG00000196730	ENSG00000196730		"""Ankyrin repeat domain containing"""	2674	protein-coding gene	gene with protein product		600831				8530096	Standard	XM_005251757		Approved	DAPK	uc004apd.3	P53355	OTTHUMG00000020150	ENST00000408954.3:c.2319G>A	9.37:g.90301560G>A	ENSP00000386135:p.Met773Ile		B7ZLD2|B7ZLE7|Q14CQ7|Q1W5W0|Q68CP8|Q6ZRZ3|Q9BTL8	Missense_Mutation	SNP	ENST00000408954.3	37	CCDS43842.1	.	.	.	.	.	.	.	.	.	.	G	12.96	2.095524	0.36952	.	.	ENSG00000196730	ENST00000358077;ENST00000472284;ENST00000469640;ENST00000408954;ENST00000491893	T;T;T;T;T	0.66638	-0.08;-0.08;-0.08;-0.08;-0.22	5.29	4.39	0.52855	.	0.384716	0.22242	N	0.062669	T	0.40398	0.1115	N	0.08118	0	0.31532	N	0.660995	B;B	0.06786	0.001;0.001	B;B	0.06405	0.002;0.002	T	0.35076	-0.9803	10	0.23891	T	0.37	.	5.3922	0.16249	0.0777:0.1532:0.6249:0.1442	.	773;773	B7ZLE7;P53355	.;DAPK1_HUMAN	I	773	ENSP00000350785:M773I;ENSP00000417076:M773I;ENSP00000418885:M773I;ENSP00000386135:M773I;ENSP00000419026:M773I	ENSP00000350785:M773I	M	+	3	0	DAPK1	89491380	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	1.165000	0.31822	1.456000	0.47831	0.655000	0.94253	ATG		0.577	DAPK1-010	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000356843.1	NM_004938		10	11	10	11
MUM1L1	139221	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	X	105449891	105449891	+	Missense_Mutation	SNP	G	G	A	rs182594028		TCGA-DU-6402-01A-11D-1705-08	TCGA-DU-6402-10A-01D-1705-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	896ec7d7-5443-49bb-969b-7b483e9b518c	3bc825bc-5589-4e0b-b380-38fceee3231b	g.chrX:105449891G>A	ENST00000357175.2	+	4	1115	c.466G>A	c.(466-468)Gca>Aca	p.A156T	MUM1L1_ENST00000372552.1_Missense_Mutation_p.A156T|MUM1L1_ENST00000337685.2_Missense_Mutation_p.A156T	NM_001171020.1	NP_001164491.1	Q5H9M0	MUML1_HUMAN	melanoma associated antigen (mutated) 1-like 1	156						extracellular vesicular exosome (GO:0070062)				autonomic_ganglia(1)|breast(3)|central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(6)|lung(11)|ovary(2)|pancreas(1)|skin(2)|upper_aerodigestive_tract(1)	31						ATGCTTGTTAGCATCTTCAGA	0.413													G|||	4	0.0010596	0.0	0.0058	3775	,	,		15304	0.0		0.0	False		,,,				2504	0.0															0													69.0	57.0	61.0					X																	105449891		1926	4111	6037	SO:0001583	missense	139221			AK090835	CCDS55469.1	Xq22.3	2008-02-05			ENSG00000157502	ENSG00000157502			26583	protein-coding gene	gene with protein product							Standard	NM_152423		Approved	FLJ33516	uc004emf.2	Q5H9M0	OTTHUMG00000022146	ENST00000357175.2:c.466G>A	X.37:g.105449891G>A	ENSP00000349699:p.Ala156Thr		D3DUX2|Q49AS5|Q8N2C0|Q96MT6	Missense_Mutation	SNP	ENST00000357175.2	37	CCDS55469.1	4	0.0024110910186859553	0	0.0	4	0.011049723756906077	0	0.0	0	0.0	G	7.390	0.630595	0.14322	.	.	ENSG00000157502	ENST00000357175;ENST00000337685;ENST00000372552	T;T;T	0.22336	1.96;1.96;1.96	4.8	0.573	0.17363	.	0.990854	0.08184	N	0.984969	T	0.08492	0.0211	L	0.27053	0.805	0.09310	N	1	B	0.27732	0.187	B	0.22601	0.04	T	0.37103	-0.9720	10	0.17832	T	0.49	-14.5525	5.5584	0.17129	0.1745:0.2753:0.5503:0.0	.	156	Q5H9M0	MUML1_HUMAN	T	156	ENSP00000349699:A156T;ENSP00000338641:A156T;ENSP00000361632:A156T	ENSP00000338641:A156T	A	+	1	0	MUM1L1	105336547	0.000000	0.05858	0.000000	0.03702	0.007000	0.05969	0.155000	0.16362	-0.137000	0.11455	-0.340000	0.08031	GCA		0.413	MUM1L1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057795.1	NM_152423		14	6	14	6
HTR3C	170572	broad.mit.edu;ucsc.edu	37	3	183774718	183774718	+	Nonsense_Mutation	SNP	C	C	T	rs576349792		TCGA-DU-6402-01A-11D-1705-08	TCGA-DU-6402-10A-01D-1705-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	896ec7d7-5443-49bb-969b-7b483e9b518c	3bc825bc-5589-4e0b-b380-38fceee3231b	g.chr3:183774718C>T	ENST00000318351.1	+	5	479	c.445C>T	c.(445-447)Cga>Tga	p.R149*		NM_130770.2	NP_570126.2	Q8WXA8	5HT3C_HUMAN	5-hydroxytryptamine (serotonin) receptor 3C, ionotropic	149					ion transmembrane transport (GO:0034220)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	extracellular ligand-gated ion channel activity (GO:0005230)	p.R149*(1)		central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(6)|lung(14)|ovary(1)|prostate(1)|skin(2)|stomach(2)	32	all_cancers(143;2.33e-10)|Ovarian(172;0.0303)		Epithelial(37;1.74e-35)|OV - Ovarian serous cystadenocarcinoma(80;3.11e-22)		Ergoloid mesylate(DB01049)	CAGTGAAGGTCGAATTAAGTA	0.478													C|||	1	0.000199681	0.0	0.0	5008	,	,		18842	0.0		0.0	False		,,,				2504	0.001															1	Substitution - Nonsense(1)	large_intestine(1)											210.0	181.0	191.0					3																	183774718		2203	4300	6503	SO:0001587	stop_gained	170572			AF459285	CCDS3250.1	3q27	2012-05-22	2012-02-03		ENSG00000178084	ENSG00000178084		"""5-HT (serotonin) receptors"", ""Ligand-gated ion channels / 5-HT (serotonin) receptors, ionotropic"""	24003	protein-coding gene	gene with protein product		610121	"""5-hydroxytryptamine (serotonin) receptor 3, family member C"""			12801637, 15157181	Standard	NM_130770		Approved		uc003fmk.3	Q8WXA8	OTTHUMG00000156862	ENST00000318351.1:c.445C>T	3.37:g.183774718C>T	ENSP00000322617:p.Arg149*		A2RRR5	Nonsense_Mutation	SNP	ENST00000318351.1	37	CCDS3250.1	.	.	.	.	.	.	.	.	.	.	.	25.6	4.652301	0.88056	.	.	ENSG00000178084	ENST00000318351	.	.	.	4.92	3.13	0.36017	.	1.917420	0.02636	N	0.104856	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	0.066	7.8166	0.29263	0.1611:0.7531:0.0:0.0857	.	.	.	.	X	149	.	ENSP00000322617:R149X	R	+	1	2	HTR3C	185257412	0.000000	0.05858	0.001000	0.08648	0.507000	0.33981	0.131000	0.15870	0.677000	0.31305	0.655000	0.94253	CGA		0.478	HTR3C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000346296.1	NM_130770		39	104	39	104
CLEC12A	160364	broad.mit.edu;ucsc.edu	37	12	10124176	10124176	+	5'UTR	SNP	A	A	G			TCGA-DU-6402-01A-11D-1705-08	TCGA-DU-6402-10A-01D-1705-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	896ec7d7-5443-49bb-969b-7b483e9b518c	3bc825bc-5589-4e0b-b380-38fceee3231b	g.chr12:10124176A>G	ENST00000304361.4	+	0	163				CLEC12A_ENST00000355690.4_Splice_Site_p.D4G|CLEC12A_ENST00000434319.2_5'UTR|CLEC12A_ENST00000350667.4_5'Flank	NM_138337.5|NM_201623.3	NP_612210.4|NP_963917.2	Q5QGZ9	CL12A_HUMAN	C-type lectin domain family 12, member A							integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	carbohydrate binding (GO:0030246)			breast(1)|endometrium(1)|kidney(3)|large_intestine(2)|lung(6)|skin(2)|upper_aerodigestive_tract(1)	16						CTTTGTCAAGATTTCTTTACA	0.318																																					Melanoma(197;1487 2125 16611 22221 34855)											0													74.0	79.0	77.0					12																	10124176		2203	4295	6498	SO:0001623	5_prime_UTR_variant	160364			AY498550	CCDS8608.1, CCDS8609.1, CCDS55803.1, CCDS73442.1	12p13.31	2010-08-17			ENSG00000172322	ENSG00000172322		"""C-type lectin domain containing"""	31713	protein-coding gene	gene with protein product		612088					Standard	NM_201623		Approved	CLL-1, MICL	uc001qwq.3	Q5QGZ9		ENST00000304361.4:c.-20A>G	12.37:g.10124176A>G			B2RA16|Q6P4H1|Q6RH77|Q6RH78|Q8TDQ6	Splice_Site	SNP	ENST00000304361.4	37	CCDS8608.1	.	.	.	.	.	.	.	.	.	.	A	2.738	-0.262858	0.05754	.	.	ENSG00000172322	ENST00000355690	T	0.02121	4.44	4.0	-8.0	0.01126	.	.	.	.	.	T	0.01061	0.0035	.	.	.	0.09310	N	1	P	0.41597	0.756	B	0.27170	0.077	T	0.24476	-1.0159	8	0.27785	T	0.31	.	6.09	0.19989	0.4238:0.1366:0.0:0.4396	.	4	Q5QGZ9-1	.	G	4	ENSP00000347916:D4G	ENSP00000347916:D4G	D	+	2	0	CLEC12A	10015443	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-0.977000	0.03782	-3.064000	0.00255	-1.001000	0.02504	GAT		0.318	CLEC12A-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000399545.1	NM_138337		19	32	19	32
UGT2B17	7367	broad.mit.edu;ucsc.edu	37	4	69434170	69434170	+	Silent	SNP	C	C	T			TCGA-DU-6402-01A-11D-1705-08	TCGA-DU-6402-10A-01D-1705-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	896ec7d7-5443-49bb-969b-7b483e9b518c	3bc825bc-5589-4e0b-b380-38fceee3231b	g.chr4:69434170C>T	ENST00000317746.2	-	1	75	c.33G>A	c.(31-33)ctG>ctA	p.L11L		NM_001077.3	NP_001068.1	O75795	UDB17_HUMAN	UDP glucuronosyltransferase 2 family, polypeptide B17	11					cellular glucuronidation (GO:0052695)|steroid metabolic process (GO:0008202)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|membrane (GO:0016020)	glucuronosyltransferase activity (GO:0015020)			central_nervous_system(1)|endometrium(4)|kidney(1)|large_intestine(7)|lung(14)|ovary(2)|prostate(1)	30					Losartan(DB00678)	TGAGCTGCATCAGCAGAAAGA	0.423																																					Melanoma(18;649 833 28984 37818 38500)											0													179.0	179.0	179.0					4																	69434170		2091	3969	6060	SO:0001819	synonymous_variant	7367			U59209	CCDS3523.1	4q13	2008-02-05	2005-07-20		ENSG00000197888	ENSG00000197888		"""UDP glucuronosyltransferases"""	12547	protein-coding gene	gene with protein product		601903	"""UDP glycosyltransferase 2 family, polypeptide B17"""			8798464	Standard	NM_001077		Approved		uc021xov.1	O75795	OTTHUMG00000129305	ENST00000317746.2:c.33G>A	4.37:g.69434170C>T				Silent	SNP	ENST00000317746.2	37	CCDS3523.1																																																																																				0.423	UGT2B17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251436.1	NM_001077		47	307	47	307
COBLL1	22837	broad.mit.edu;ucsc.edu	37	2	165578649	165578649	+	Missense_Mutation	SNP	G	G	T			TCGA-DU-6402-01A-11D-1705-08	TCGA-DU-6402-10A-01D-1705-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	896ec7d7-5443-49bb-969b-7b483e9b518c	3bc825bc-5589-4e0b-b380-38fceee3231b	g.chr2:165578649G>T	ENST00000392717.2	-	7	1050	c.1046C>A	c.(1045-1047)gCa>gAa	p.A349E	COBLL1_ENST00000194871.6_Missense_Mutation_p.A377E|COBLL1_ENST00000342193.4_Missense_Mutation_p.A311E|COBLL1_ENST00000375458.2_Missense_Mutation_p.A311E|COBLL1_ENST00000409184.3_Missense_Mutation_p.A349E|COBLL1_ENST00000491126.2_Intron			Q53SF7	COBL1_HUMAN	cordon-bleu WH2 repeat protein-like 1	349						extracellular vesicular exosome (GO:0070062)				central_nervous_system(2)|cervix(1)|endometrium(3)|kidney(4)|large_intestine(12)|liver(1)|lung(12)|ovary(3)|pancreas(1)|prostate(1)|skin(4)|stomach(1)|upper_aerodigestive_tract(2)	47						CTGGATGTGTGCAAGGTCTTG	0.488																																																0													74.0	77.0	76.0					2																	165578649		2203	4300	6503	SO:0001583	missense	22837			AB023194	CCDS2223.2, CCDS63045.1	2q24.3	2012-12-07	2012-12-07		ENSG00000082438	ENSG00000082438			23571	protein-coding gene	gene with protein product		610318	"""COBL-like 1"""				Standard	NM_001278458		Approved	KIAA0977	uc002ucp.3	Q53SF7	OTTHUMG00000074019	ENST00000392717.2:c.1046C>A	2.37:g.165578649G>T	ENSP00000376478:p.Ala349Glu		A6NMZ3|Q6IQ33|Q7Z3I6|Q9BRH4|Q9UG88|Q9Y2I3	Missense_Mutation	SNP	ENST00000392717.2	37		.	.	.	.	.	.	.	.	.	.	G	9.621	1.133835	0.21123	.	.	ENSG00000082438	ENST00000375458;ENST00000342193;ENST00000409184;ENST00000392717;ENST00000194871	D	0.92805	-3.11	6.17	-1.53	0.08611	Cordon-bleu domain (1);	0.609642	0.16107	N	0.229293	D	0.86748	0.6007	L	0.58101	1.795	0.09310	N	1	B;B;B	0.21688	0.059;0.059;0.047	B;B;B	0.27076	0.045;0.076;0.021	T	0.71839	-0.4471	10	0.17369	T	0.5	-0.2379	6.5223	0.22283	0.0599:0.2762:0.4433:0.2205	.	349;377;349	Q53SF7;B7Z2P5;Q53SF7-2	COBL1_HUMAN;.;.	E	311;311;349;349;377	ENSP00000194871:A377E	ENSP00000194871:A377E	A	-	2	0	COBLL1	165286895	0.000000	0.05858	0.000000	0.03702	0.011000	0.07611	0.425000	0.21346	-0.157000	0.11059	-0.175000	0.13238	GCA		0.488	COBLL1-202	KNOWN	basic|appris_candidate	protein_coding	protein_coding		NM_014900		21	58	21	58
RPSAP52	204010	broad.mit.edu;ucsc.edu	37	12	66152273	66152273	+	RNA	SNP	T	T	G			TCGA-DU-6402-01A-11D-1705-08	TCGA-DU-6402-10A-01D-1705-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	896ec7d7-5443-49bb-969b-7b483e9b518c	3bc825bc-5589-4e0b-b380-38fceee3231b	g.chr12:66152273T>G	ENST00000489520.2	-	0	670					NR_026825.2				ribosomal protein SA pseudogene 52																		TCTGACCCACTGAGGGAGCTC	0.498																																																0																																												204010					12q14.3	2010-09-24			ENSG00000241749	ENSG00000241749			35752	pseudogene	pseudogene						19123937	Standard	NR_026825		Approved		uc001sso.4		OTTHUMG00000157608		12.37:g.66152273T>G				RNA	SNP	ENST00000489520.2	37																																																																																					0.498	RPSAP52-002	KNOWN	basic	processed_transcript	pseudogene	OTTHUMT00000349256.2	NG_006174		5	11	5	11
RPL10L	140801	broad.mit.edu;ucsc.edu	37	14	47120403	47120403	+	Silent	SNP	G	G	A			TCGA-DU-6402-01A-11D-1705-08	TCGA-DU-6402-10A-01D-1705-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	896ec7d7-5443-49bb-969b-7b483e9b518c	3bc825bc-5589-4e0b-b380-38fceee3231b	g.chr14:47120403G>A	ENST00000298283.3	-	1	625	c.537C>T	c.(535-537)gaC>gaT	p.D179D		NM_080746.2	NP_542784.1	Q96L21	RL10L_HUMAN	ribosomal protein L10-like	179					spermatogenesis (GO:0007283)|translation (GO:0006412)	cytosolic large ribosomal subunit (GO:0022625)|membrane (GO:0016020)|nucleus (GO:0005634)|polysome (GO:0005844)	structural constituent of ribosome (GO:0003735)			endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(3)|lung(20)|ovary(1)	27						CTTCAAATTCGTCAGCATTAA	0.517																																																0													101.0	98.0	99.0					14																	47120403		2203	4300	6503	SO:0001819	synonymous_variant	140801			AB063608	CCDS32071.1	14q21.2	2011-09-15			ENSG00000165496	ENSG00000165496		"""L ribosomal proteins"""	17976	protein-coding gene	gene with protein product						19123937	Standard	NM_080746		Approved		uc001wwg.3	Q96L21	OTTHUMG00000157869	ENST00000298283.3:c.537C>T	14.37:g.47120403G>A			Q8IUD1	Silent	SNP	ENST00000298283.3	37	CCDS32071.1																																																																																				0.517	RPL10L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000349819.1			27	78	27	78
ACSM2A	123876	broad.mit.edu;ucsc.edu	37	16	20476848	20476848	+	Nonsense_Mutation	SNP	C	C	T	rs146541514		TCGA-DU-6402-01A-11D-1705-08	TCGA-DU-6402-10A-01D-1705-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	896ec7d7-5443-49bb-969b-7b483e9b518c	3bc825bc-5589-4e0b-b380-38fceee3231b	g.chr16:20476848C>T	ENST00000573854.1	+	3	301	c.187C>T	c.(187-189)Cga>Tga	p.R63*	ACSM2A_ENST00000575558.1_3'UTR|ACSM2A_ENST00000219054.6_Nonsense_Mutation_p.R63*|ACSM2A_ENST00000417235.2_5'UTR|ACSM2A_ENST00000536134.1_5'UTR|ACSM2A_ENST00000396104.2_Nonsense_Mutation_p.R63*|ACSM2A_ENST00000575690.1_Nonsense_Mutation_p.R63*|ACSM2A_ENST00000424070.1_Nonsense_Mutation_p.R63*	NM_001010845.2	NP_001010845	Q08AH3	ACS2A_HUMAN	acyl-CoA synthetase medium-chain family member 2A	63					fatty acid metabolic process (GO:0006631)|glucose homeostasis (GO:0042593)|medium-chain fatty-acyl-CoA metabolic process (GO:0036112)|triglyceride homeostasis (GO:0070328)	mitochondrion (GO:0005739)	ATP binding (GO:0005524)|butyrate-CoA ligase activity (GO:0047760)|metal ion binding (GO:0046872)			breast(2)|central_nervous_system(2)|endometrium(1)|kidney(1)|large_intestine(3)|lung(34)|ovary(1)|skin(6)|stomach(1)	51						GGCTGGCAAGCGACTCCCAAG	0.517																																																0													40.0	40.0	40.0					16																	20476848		2203	4300	6503	SO:0001587	stop_gained	123876			AK091878, AK096039	CCDS32401.1	16p12.3	2014-08-08	2007-06-20	2007-06-20	ENSG00000183747	ENSG00000183747		"""Acyl-CoA synthetase family"""	32017	protein-coding gene	gene with protein product		614358	"""acyl-CoA synthetase medium-chain family member 2"""	ACSM2			Standard	NM_001010845		Approved	A-923A4.1, MGC150530	uc010bwe.3	Q08AH3	OTTHUMG00000177401	ENST00000573854.1:c.187C>T	16.37:g.20476848C>T	ENSP00000459451:p.Arg63*		B3KTT9|O75202	Nonsense_Mutation	SNP	ENST00000573854.1	37	CCDS32401.1	.	.	.	.	.	.	.	.	.	.	C	13.30	2.196045	0.38806	.	.	ENSG00000183747	ENST00000219054;ENST00000424070;ENST00000396104	.	.	.	3.76	-4.19	0.03835	.	0.237045	0.21779	N	0.069224	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-11.848	6.8132	0.23817	0.6822:0.2071:0.0:0.1107	.	.	.	.	X	63	.	ENSP00000219054:R63X	R	+	1	2	ACSM2A	20384349	0.028000	0.19301	0.478000	0.27316	0.108000	0.19459	0.013000	0.13310	-0.254000	0.09500	0.298000	0.19748	CGA		0.517	ACSM2A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000436764.1	NM_001010845		6	23	6	23
NF1	4763	broad.mit.edu;hgsc.bcm.edu	37	17	29548901	29548901	+	Frame_Shift_Del	DEL	G	G	-			TCGA-DU-6402-01A-11D-1705-08	TCGA-DU-6402-10A-01D-1705-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	896ec7d7-5443-49bb-969b-7b483e9b518c	3bc825bc-5589-4e0b-b380-38fceee3231b	g.chr17:29548901delG	ENST00000358273.4	+	15	2058	c.1675delG	c.(1675-1677)gatfs	p.D559fs	NF1_ENST00000431387.4_Frame_Shift_Del_p.D559fs|NF1_ENST00000356175.3_Frame_Shift_Del_p.D559fs	NM_001042492.2	NP_001035957.1	P21359	NF1_HUMAN	neurofibromin 1	559					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)		AGATAGCATTGATTTGTGGAA	0.289			"""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)											63.0	61.0	62.0					17																	29548901		2202	4298	6500	SO:0001589	frameshift_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.1675delG	17.37:g.29548901delG	ENSP00000351015:p.Asp559fs		O00662|Q14284|Q14930|Q14931|Q9UMK3	Frame_Shift_Del	DEL	ENST00000358273.4	37	CCDS42292.1																																																																																				0.289	NF1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000256351.2	NM_000267		23	44	23	44
SDK2	54549	broad.mit.edu;ucsc.edu	37	17	71410870	71410870	+	Silent	SNP	G	G	A			TCGA-DU-6402-01A-11D-1705-08	TCGA-DU-6402-10A-01D-1705-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	896ec7d7-5443-49bb-969b-7b483e9b518c	3bc825bc-5589-4e0b-b380-38fceee3231b	g.chr17:71410870G>A	ENST00000392650.3	-	18	2397	c.2397C>T	c.(2395-2397)caC>caT	p.H799H	SDK2_ENST00000388726.3_Silent_p.H799H	NM_001144952.1	NP_001138424.1	Q58EX2	SDK2_HUMAN	sidekick cell adhesion molecule 2	799	Fibronectin type-III 3. {ECO:0000255|PROSITE-ProRule:PRU00316}.				cell adhesion (GO:0007155)	integral component of membrane (GO:0016021)		p.H799H(1)		breast(4)|central_nervous_system(2)|cervix(1)|endometrium(10)|haematopoietic_and_lymphoid_tissue(3)|kidney(8)|large_intestine(15)|lung(31)|ovary(3)|prostate(2)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(3)	86						TGGCTTCCGCGTGCACATTGC	0.597																																																1	Substitution - coding silent(1)	breast(1)											90.0	75.0	80.0					17																	71410870		2203	4300	6503	SO:0001819	synonymous_variant	54549			AB040947	CCDS45769.1	17q21.31	2013-02-11	2011-12-09		ENSG00000069188	ENSG00000069188		"""Immunoglobulin superfamily / I-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"", ""Fibronectin type III domain containing"""	19308	protein-coding gene	gene with protein product		607217	"""sidekick homolog 2 (chicken)"""			12230981, 15213259	Standard	NM_001144952		Approved	FLJ10832, KIAA1514	uc010dfm.3	Q58EX2	OTTHUMG00000152726	ENST00000392650.3:c.2397C>T	17.37:g.71410870G>A			A6NMR8|C9JA57|Q86VY3|Q9NTD2|Q9NVB3|Q9P214	Silent	SNP	ENST00000392650.3	37	CCDS45769.1																																																																																				0.597	SDK2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000327598.2	NM_019064		16	26	16	26
