#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
ANK3	288	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	10	61958113	61958113	+	Silent	SNP	T	T	C			TCGA-HT-7606-01A-11D-2086-08	TCGA-HT-7606-10A-01D-2086-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	9734311d-3183-459b-8200-7104fba3bf64	7c7214f7-036a-4ac9-9883-1a93d9eb6f10	g.chr10:61958113T>C	ENST00000280772.2	-	14	1865	c.1674A>G	c.(1672-1674)ttA>ttG	p.L558L	ANK3_ENST00000373827.2_Silent_p.L552L|ANK3_ENST00000503366.1_Silent_p.L541L	NM_020987.3	NP_066267.2	Q12955	ANK3_HUMAN	ankyrin 3, node of Ranvier (ankyrin G)	558					axon guidance (GO:0007411)|axonogenesis (GO:0007409)|cytoskeletal anchoring at plasma membrane (GO:0007016)|establishment of protein localization (GO:0045184)|Golgi to plasma membrane protein transport (GO:0043001)|maintenance of protein location in plasma membrane (GO:0072660)|membrane assembly (GO:0071709)|mitotic cytokinesis (GO:0000281)|neuromuscular junction development (GO:0007528)|neuronal action potential (GO:0019228)|plasma membrane organization (GO:0007009)|positive regulation of cell communication by electrical coupling (GO:0010650)|positive regulation of gene expression (GO:0010628)|positive regulation of homotypic cell-cell adhesion (GO:0034112)|positive regulation of membrane depolarization during cardiac muscle cell action potential (GO:1900827)|positive regulation of membrane potential (GO:0045838)|positive regulation of protein targeting to membrane (GO:0090314)|positive regulation of sodium ion transmembrane transporter activity (GO:2000651)|positive regulation of sodium ion transport (GO:0010765)|protein localization to plasma membrane (GO:0072659)|protein targeting to plasma membrane (GO:0072661)|regulation of potassium ion transport (GO:0043266)|signal transduction (GO:0007165)	axon initial segment (GO:0043194)|basolateral plasma membrane (GO:0016323)|cell surface (GO:0009986)|costamere (GO:0043034)|dendrite (GO:0030425)|endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|intercalated disc (GO:0014704)|lateral plasma membrane (GO:0016328)|lysosome (GO:0005764)|neuromuscular junction (GO:0031594)|node of Ranvier (GO:0033268)|paranode region of axon (GO:0033270)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)|sarcolemma (GO:0042383)|sarcoplasmic reticulum (GO:0016529)|spectrin-associated cytoskeleton (GO:0014731)|T-tubule (GO:0030315)|Z disc (GO:0030018)	cadherin binding (GO:0045296)|cytoskeletal protein binding (GO:0008092)|ion channel binding (GO:0044325)|protein binding, bridging (GO:0030674)|spectrin binding (GO:0030507)|structural constituent of cytoskeleton (GO:0005200)			NS(4)|breast(7)|central_nervous_system(5)|endometrium(19)|haematopoietic_and_lymphoid_tissue(5)|kidney(14)|large_intestine(30)|liver(2)|lung(59)|ovary(8)|pancreas(2)|prostate(5)|skin(26)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(7)	196						TTGTTATAGATAAAGACGCTC	0.498																																																0													77.0	79.0	78.0					10																	61958113		2203	4300	6503	SO:0001819	synonymous_variant	288			U13616	CCDS7258.1, CCDS7259.1, CCDS55711.1, CCDS55712.1	10q21	2013-01-10			ENSG00000151150	ENSG00000151150		"""Ankyrin repeat domain containing"""	494	protein-coding gene	gene with protein product	"""ankyrin-3, node of Ranvier"", ""ankyrin-G"""	600465				7665168	Standard	NM_020987		Approved		uc001jky.3	Q12955	OTTHUMG00000018288	ENST00000280772.2:c.1674A>G	10.37:g.61958113T>C			B1AQT2|B4DIL1|E9PE32|Q13484|Q5CZH9|Q5VXD5|Q7Z3G4|Q9H0P5	Silent	SNP	ENST00000280772.2	37	CCDS7258.1																																																																																				0.498	ANK3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000048201.4	NM_020987		14	19	14	19
OR2AG2	338755	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	11	6789589	6789589	+	Silent	SNP	G	G	A			TCGA-HT-7606-01A-11D-2086-08	TCGA-HT-7606-10A-01D-2086-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	9734311d-3183-459b-8200-7104fba3bf64	7c7214f7-036a-4ac9-9883-1a93d9eb6f10	g.chr11:6789589G>A	ENST00000338569.2	-	1	697	c.600C>T	c.(598-600)taC>taT	p.Y200Y		NM_001004490.1	NP_001004490.1	A6NM03	O2AG2_HUMAN	olfactory receptor, family 2, subfamily AG, member 2	200						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			breast(1)|central_nervous_system(1)|endometrium(3)|large_intestine(2)|lung(13)|ovary(1)|skin(5)|stomach(1)|urinary_tract(1)	28		Medulloblastoma(188;0.00776)|all_neural(188;0.0652)		Epithelial(150;2.15e-08)|BRCA - Breast invasive adenocarcinoma(625;0.129)		CACCTGTCACGTATATTATAA	0.493																																																0													95.0	86.0	89.0					11																	6789589		2201	4296	6497	SO:0001819	synonymous_variant	338755			AB065539	CCDS31413.1	11p15.4	2012-08-09		2004-03-10	ENSG00000188124	ENSG00000188124		"""GPCR / Class A : Olfactory receptors"""	15143	protein-coding gene	gene with protein product				OR2AG2P			Standard	NM_001004490		Approved		uc001meq.1	A6NM03	OTTHUMG00000165868	ENST00000338569.2:c.600C>T	11.37:g.6789589G>A				Silent	SNP	ENST00000338569.2	37	CCDS31413.1																																																																																				0.493	OR2AG2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000386775.1	NM_001004490		10	18	10	18
SIPA1	6494	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	11	65408733	65408733	+	Missense_Mutation	SNP	G	G	A			TCGA-HT-7606-01A-11D-2086-08	TCGA-HT-7606-10A-01D-2086-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	9734311d-3183-459b-8200-7104fba3bf64	7c7214f7-036a-4ac9-9883-1a93d9eb6f10	g.chr11:65408733G>A	ENST00000394224.3	+	2	637	c.341G>A	c.(340-342)cGa>cAa	p.R114Q	SIPA1_ENST00000534313.1_Missense_Mutation_p.R114Q|SIPA1_ENST00000527525.1_Missense_Mutation_p.R114Q|SIPA1_ENST00000394227.3_Missense_Mutation_p.R114Q	NM_153253.29	NP_694985.29	Q96FS4	SIPA1_HUMAN	signal-induced proliferation-associated 1	114					cell proliferation (GO:0008283)|cellular response to water deprivation (GO:0042631)|cytoskeleton organization (GO:0007010)|intracellular signal transduction (GO:0035556)|negative regulation of cell adhesion (GO:0007162)|negative regulation of cell cycle (GO:0045786)|negative regulation of cell growth (GO:0030308)|positive regulation of GTPase activity (GO:0043547)|positive regulation of Rap GTPase activity (GO:0032854)|signal transduction (GO:0007165)	cytosol (GO:0005829)|membrane (GO:0016020)|nucleus (GO:0005634)|protein complex (GO:0043234)|transport vesicle (GO:0030133)	GTPase activator activity (GO:0005096)|Rap GTPase activator activity (GO:0046582)			cervix(1)|endometrium(2)|large_intestine(2)|lung(3)|prostate(1)|urinary_tract(1)	10						CTTGAGCCTCGATGGTTTGCC	0.632																																																0													81.0	82.0	81.0					11																	65408733		2201	4297	6498	SO:0001583	missense	6494			AH006363, BC010492, BM677738	CCDS8108.1	11q13.3	2008-09-12	2008-09-12		ENSG00000213445	ENSG00000213445			10885	protein-coding gene	gene with protein product		602180				9027487	Standard	NM_006747		Approved	SPA1	uc001ofb.2	Q96FS4	OTTHUMG00000166541	ENST00000394224.3:c.341G>A	11.37:g.65408733G>A	ENSP00000377771:p.Arg114Gln		O14518|O60484|O60618|Q2YD83	Missense_Mutation	SNP	ENST00000394224.3	37	CCDS8108.1	.	.	.	.	.	.	.	.	.	.	G	17.81	3.480582	0.63849	.	.	ENSG00000213445	ENST00000534313;ENST00000527525;ENST00000394224;ENST00000394227	D;D;D;D	0.83335	-1.69;-1.71;-1.69;-1.71	5.05	4.14	0.48551	.	0.116963	0.28977	U	0.013540	T	0.77377	0.4121	L	0.57536	1.79	0.38847	D	0.956192	P;P	0.39696	0.683;0.555	B;B	0.32864	0.154;0.073	T	0.80190	-0.1485	10	0.72032	D	0.01	-8.3935	11.535	0.50633	0.0888:0.0:0.9112:0.0	.	114;114	F6RY50;Q96FS4	.;SIPA1_HUMAN	Q	114	ENSP00000436269:R114Q;ENSP00000433686:R114Q;ENSP00000377771:R114Q;ENSP00000377774:R114Q	ENSP00000377771:R114Q	R	+	2	0	SIPA1	65165309	1.000000	0.71417	1.000000	0.80357	0.972000	0.66771	4.214000	0.58527	1.274000	0.44362	0.561000	0.74099	CGA		0.632	SIPA1-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000390356.1	NM_006747		67	105	67	105
PLEKHA5	54477	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	12	19489486	19489486	+	Missense_Mutation	SNP	A	A	C			TCGA-HT-7606-01A-11D-2086-08	TCGA-HT-7606-10A-01D-2086-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	9734311d-3183-459b-8200-7104fba3bf64	7c7214f7-036a-4ac9-9883-1a93d9eb6f10	g.chr12:19489486A>C	ENST00000299275.6	+	16	2183	c.2177A>C	c.(2176-2178)gAa>gCa	p.E726A	PLEKHA5_ENST00000538714.1_Missense_Mutation_p.E784A|PLEKHA5_ENST00000359180.3_Missense_Mutation_p.E726A|PLEKHA5_ENST00000539256.1_Missense_Mutation_p.E484A|PLEKHA5_ENST00000543806.1_Missense_Mutation_p.E645A|PLEKHA5_ENST00000424268.1_Missense_Mutation_p.E657A|PLEKHA5_ENST00000317589.4_Missense_Mutation_p.E726A|PLEKHA5_ENST00000429027.2_Missense_Mutation_p.E829A|PLEKHA5_ENST00000355397.3_Missense_Mutation_p.E784A	NM_019012.5	NP_061885.2	Q9HAU0	PKHA5_HUMAN	pleckstrin homology domain containing, family A member 5	726					reproductive system development (GO:0061458)	cytosol (GO:0005829)|membrane (GO:0016020)	1-phosphatidylinositol binding (GO:0005545)|phosphatidylinositol-3,5-bisphosphate binding (GO:0080025)|phosphatidylinositol-3-phosphate binding (GO:0032266)|phosphatidylinositol-4-phosphate binding (GO:0070273)|phosphatidylinositol-5-phosphate binding (GO:0010314)			autonomic_ganglia(1)|central_nervous_system(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(6)|lung(14)|ovary(2)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	35	Acute lymphoblastic leukemia(4;0.000455)|all_hematologic(4;0.00804)					GATAAGTTAGAATACGATGTA	0.348																																					Pancreas(196;329 2193 11246 14234 19524)											0													104.0	107.0	106.0					12																	19489486		2203	4300	6503	SO:0001583	missense	54477			AF302150	CCDS8682.1, CCDS44840.1, CCDS44840.2, CCDS55809.1, CCDS58213.1, CCDS58214.1	12p12	2013-01-10			ENSG00000052126	ENSG00000052126		"""Pleckstrin homology (PH) domain containing"""	30036	protein-coding gene	gene with protein product		607770				11214970, 11001876	Standard	NM_001143821		Approved	PEPP2, KIAA1686, FLJ10667	uc031qgo.1	Q9HAU0	OTTHUMG00000167921	ENST00000299275.6:c.2177A>C	12.37:g.19489486A>C	ENSP00000299275:p.Glu726Ala		A0JP03|B4DGS1|E9PHQ3|F5H0I0|Q6NSF8|Q86ST7|Q8N3K6|Q96DY9|Q9BVR4|Q9C0H7|Q9H924|Q9NVK8	Missense_Mutation	SNP	ENST00000299275.6	37	CCDS8682.1	.	.	.	.	.	.	.	.	.	.	A	21.2	4.116830	0.77323	.	.	ENSG00000052126	ENST00000317589;ENST00000355397;ENST00000359180;ENST00000542828;ENST00000429027;ENST00000299275;ENST00000539256;ENST00000538714;ENST00000424268;ENST00000543806;ENST00000536974;ENST00000538972	T;T;T;T;T;T;T;T;T;T;T	0.14391	2.51;2.51;2.51;2.51;2.51;2.51;2.51;2.51;2.51;2.51;2.51	4.78	4.78	0.61160	.	0.102292	0.64402	D	0.000004	T	0.42675	0.1213	M	0.86651	2.83	0.42385	D	0.9925	D;D;D;D;D;D;D;D	0.89917	1.0;0.984;0.985;0.999;0.998;0.995;0.991;0.991	D;P;P;D;D;P;P;P	0.91635	0.999;0.784;0.831;0.995;0.946;0.809;0.783;0.892	T	0.52320	-0.8591	10	0.87932	D	0	-14.7473	13.9686	0.64225	1.0:0.0:0.0:0.0	.	726;645;657;829;726;829;726;784	Q9HAU0-4;F5H0I0;E7EME8;B4DHK5;Q9HAU0-5;E9PHQ3;Q9HAU0;Q9HAU0-2	.;.;.;.;.;.;PKHA5_HUMAN;.	A	726;784;726;830;829;726;484;784;657;645;618;63	ENSP00000325155:E726A;ENSP00000347560:E784A;ENSP00000352104:E726A;ENSP00000404296:E829A;ENSP00000299275:E726A;ENSP00000440611:E484A;ENSP00000439673:E784A;ENSP00000400411:E657A;ENSP00000439837:E645A;ENSP00000440371:E618A;ENSP00000443553:E63A	ENSP00000299275:E726A	E	+	2	0	PLEKHA5	19380753	1.000000	0.71417	1.000000	0.80357	0.990000	0.78478	6.316000	0.72857	1.789000	0.52484	0.383000	0.25322	GAA		0.348	PLEKHA5-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000397013.1	NM_019012		26	40	26	40
LRRK1	79705	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	15	101588788	101588788	+	Silent	SNP	A	A	G			TCGA-HT-7606-01A-11D-2086-08	TCGA-HT-7606-10A-01D-2086-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	9734311d-3183-459b-8200-7104fba3bf64	7c7214f7-036a-4ac9-9883-1a93d9eb6f10	g.chr15:101588788A>G	ENST00000388948.3	+	22	3584	c.3225A>G	c.(3223-3225)acA>acG	p.T1075T	RP11-505E24.2_ENST00000559857.1_RNA|RP11-505E24.3_ENST00000558979.1_RNA|LRRK1_ENST00000284395.5_Silent_p.T1072T	NM_024652.3	NP_078928.3			leucine-rich repeat kinase 1											breast(2)|central_nervous_system(6)|endometrium(12)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(14)|lung(25)|ovary(4)|prostate(1)|skin(1)	72	Melanoma(26;0.00505)|Lung NSC(78;0.00793)|all_lung(78;0.0094)		OV - Ovarian serous cystadenocarcinoma(32;0.000932)|LUSC - Lung squamous cell carcinoma(107;0.187)|Lung(145;0.23)			GCTGTAGCACATTCAGAGTGA	0.448																																																0													127.0	127.0	127.0					15																	101588788		1892	4128	6020	SO:0001819	synonymous_variant	79705			AB058693	CCDS42086.1	15q26.3	2007-01-29			ENSG00000154237	ENSG00000154237			18608	protein-coding gene	gene with protein product		610986				11347906, 14654223	Standard	XM_005254979		Approved	FLJ23119, KIAA1790, Roco1, RIPK6	uc002bwr.3	Q38SD2	OTTHUMG00000165514	ENST00000388948.3:c.3225A>G	15.37:g.101588788A>G				Silent	SNP	ENST00000388948.3	37	CCDS42086.1																																																																																				0.448	LRRK1-003	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000384567.2	NM_024652		58	35	58	35
TP53	7157	hgsc.bcm.edu;broad.mit.edu	37	17	7577121	7577121	+	Missense_Mutation	SNP	G	G	A	rs121913343		TCGA-HT-7606-01A-11D-2086-08	TCGA-HT-7606-10A-01D-2086-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	9734311d-3183-459b-8200-7104fba3bf64	7c7214f7-036a-4ac9-9883-1a93d9eb6f10	g.chr17:7577121G>A	ENST00000269305.4	-	8	1006	c.817C>T	c.(817-819)Cgt>Tgt	p.R273C	TP53_ENST00000359597.4_Missense_Mutation_p.R273C|TP53_ENST00000455263.2_Missense_Mutation_p.R273C|TP53_ENST00000574684.1_5'Flank|TP53_ENST00000413465.2_Intron|TP53_ENST00000420246.2_Missense_Mutation_p.R273C|TP53_ENST00000445888.2_Missense_Mutation_p.R273C	NM_000546.5|NM_001126112.2|NM_001126118.1|NM_001276760.1|NM_001276761.1	NP_000537.3|NP_001119584.1|NP_001119590.1|NP_001263689.1|NP_001263690.1	P04637	P53_HUMAN	tumor protein p53	273	Interaction with AXIN1. {ECO:0000250}.|Interaction with DNA.|Interaction with E4F1.|Interaction with HIPK1. {ECO:0000250}.|Required for interaction with ZNF385A.		R -> C (in LFS; germline mutation and in sporadic cancers; somatic mutation). {ECO:0000269|PubMed:16959974, ECO:0000269|PubMed:17224074, ECO:0000269|PubMed:7887414, ECO:0000269|PubMed:9450901}.|R -> G (in LFS; germline mutation and in sporadic cancers; somatic mutation).|R -> H (in LFS; germline mutation and in sporadic cancers; somatic mutation; abolishes sequence-specific DNA binding; does not induce SNAI1 degradation; dbSNP:rs28934576). {ECO:0000269|PubMed:1394225, ECO:0000269|PubMed:1565144, ECO:0000269|PubMed:16959974, ECO:0000269|PubMed:1699228, ECO:0000269|PubMed:1868473, ECO:0000269|PubMed:7682763, ECO:0000269|Ref.14}.|R -> L (in LFS; germline mutation and in sporadic cancers; somatic mutation). {ECO:0000269|PubMed:16959974}.|R -> N (in a sporadic cancer; somatic mutation; requires 2 nucleotide substitutions).|R -> P (in sporadic cancers; somatic mutation).|R -> Q (in sporadic cancers; somatic mutation).|R -> S (in a familial cancer not matching LFS; germline mutation and in sporadic cancers; somatic mutation).|R -> Y (in a sporadic cancer; somatic mutation; requires 2 nucleotide substitutions).		apoptotic process (GO:0006915)|B cell lineage commitment (GO:0002326)|base-excision repair (GO:0006284)|blood coagulation (GO:0007596)|cell aging (GO:0007569)|cell cycle arrest (GO:0007050)|cell differentiation (GO:0030154)|cell proliferation (GO:0008283)|cellular protein localization (GO:0034613)|cellular response to DNA damage stimulus (GO:0006974)|cellular response to drug (GO:0035690)|cellular response to glucose starvation (GO:0042149)|cellular response to hypoxia (GO:0071456)|cellular response to ionizing radiation (GO:0071479)|cellular response to UV (GO:0034644)|cerebellum development (GO:0021549)|chromatin assembly (GO:0031497)|determination of adult lifespan (GO:0008340)|DNA damage response, signal transduction by p53 class mediator (GO:0030330)|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest (GO:0006977)|DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator (GO:0006978)|DNA strand renaturation (GO:0000733)|double-strand break repair (GO:0006302)|embryonic organ development (GO:0048568)|ER overload response (GO:0006983)|gastrulation (GO:0007369)|in utero embryonic development (GO:0001701)|intrinsic apoptotic signaling pathway (GO:0097193)|intrinsic apoptotic signaling pathway by p53 class mediator (GO:0072332)|intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator (GO:0042771)|mitotic cell cycle arrest (GO:0071850)|mitotic G1 DNA damage checkpoint (GO:0031571)|multicellular organism growth (GO:0035264)|multicellular organismal development (GO:0007275)|necroptotic process (GO:0070266)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cell growth (GO:0030308)|negative regulation of cell proliferation (GO:0008285)|negative regulation of DNA replication (GO:0008156)|negative regulation of fibroblast proliferation (GO:0048147)|negative regulation of helicase activity (GO:0051097)|negative regulation of macromitophagy (GO:1901525)|negative regulation of neuroblast proliferation (GO:0007406)|negative regulation of reactive oxygen species metabolic process (GO:2000378)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|negative regulation of transforming growth factor beta receptor signaling pathway (GO:0030512)|neuron apoptotic process (GO:0051402)|Notch signaling pathway (GO:0007219)|nucleotide-excision repair (GO:0006289)|oligodendrocyte apoptotic process (GO:0097252)|oxidative stress-induced premature senescence (GO:0090403)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cardiac muscle cell apoptotic process (GO:0010666)|positive regulation of cell aging (GO:0090343)|positive regulation of cell cycle arrest (GO:0071158)|positive regulation of histone deacetylation (GO:0031065)|positive regulation of intrinsic apoptotic signaling pathway (GO:2001244)|positive regulation of mitochondrial membrane permeability (GO:0035794)|positive regulation of neuron apoptotic process (GO:0043525)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|positive regulation of protein insertion into mitochondrial membrane involved in apoptotic signaling pathway (GO:1900740)|positive regulation of protein oligomerization (GO:0032461)|positive regulation of reactive oxygen species metabolic process (GO:2000379)|positive regulation of release of cytochrome c from mitochondria (GO:0090200)|positive regulation of thymocyte apoptotic process (GO:0070245)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|protein complex assembly (GO:0006461)|protein import into nucleus, translocation (GO:0000060)|protein localization (GO:0008104)|protein tetramerization (GO:0051262)|Ras protein signal transduction (GO:0007265)|regulation of apoptotic process (GO:0042981)|regulation of mitochondrial membrane permeability (GO:0046902)|regulation of mitochondrial membrane permeability involved in apoptotic process (GO:1902108)|regulation of tissue remodeling (GO:0034103)|regulation of transcription, DNA-templated (GO:0006355)|release of cytochrome c from mitochondria (GO:0001836)|replicative senescence (GO:0090399)|response to antibiotic (GO:0046677)|response to gamma radiation (GO:0010332)|response to ischemia (GO:0002931)|response to salt stress (GO:0009651)|response to X-ray (GO:0010165)|rRNA transcription (GO:0009303)|somitogenesis (GO:0001756)|T cell differentiation in thymus (GO:0033077)|T cell lineage commitment (GO:0002360)|T cell proliferation involved in immune response (GO:0002309)|transforming growth factor beta receptor signaling pathway (GO:0007179)|viral process (GO:0016032)	chromatin (GO:0000785)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)|nuclear chromatin (GO:0000790)|nuclear matrix (GO:0016363)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|PML body (GO:0016605)|protein complex (GO:0043234)|replication fork (GO:0005657)	ATP binding (GO:0005524)|chaperone binding (GO:0051087)|chromatin binding (GO:0003682)|copper ion binding (GO:0005507)|damaged DNA binding (GO:0003684)|DNA binding (GO:0003677)|enzyme binding (GO:0019899)|histone acetyltransferase binding (GO:0035035)|histone deacetylase regulator activity (GO:0035033)|identical protein binding (GO:0042802)|p53 binding (GO:0002039)|protease binding (GO:0002020)|protein heterodimerization activity (GO:0046982)|protein kinase binding (GO:0019901)|protein N-terminus binding (GO:0047485)|protein phosphatase 2A binding (GO:0051721)|protein phosphatase binding (GO:0019903)|receptor tyrosine kinase binding (GO:0030971)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|RNA polymerase II core promoter sequence-specific DNA binding (GO:0000979)|RNA polymerase II transcription factor binding (GO:0001085)|RNA polymerase II transcription regulatory region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001228)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription factor binding (GO:0008134)|transcription regulatory region DNA binding (GO:0044212)|ubiquitin protein ligase binding (GO:0031625)|zinc ion binding (GO:0008270)	p.R273C(481)|p.R273S(16)|p.R273G(9)|p.0?(8)|p.?(2)|p.R273fs*72(2)|p.R273fs*33(2)|p.R273fs*32(2)|p.V272>?(2)|p.F270fs*72(1)|p.R273_C275delRVC(1)|p.L265_K305del41(1)|p.S269fs*21(1)|p.E258fs*71(1)|p.R273fs*71(1)|p.F270_D281del12(1)|p.E271_R273delEVR(1)|p.V272_K292del21(1)		NS(16)|adrenal_gland(37)|autonomic_ganglia(16)|biliary_tract(273)|bone(108)|breast(2530)|central_nervous_system(1264)|cervix(68)|endometrium(223)|eye(24)|fallopian_tube(1)|gastrointestinal_tract_(site_indeterminate)(1)|genital_tract(16)|haematopoietic_and_lymphoid_tissue(1301)|kidney(96)|large_intestine(5124)|liver(897)|lung(2388)|meninges(5)|oesophagus(1473)|ovary(1659)|pancreas(452)|penis(10)|peritoneum(33)|pituitary(4)|placenta(1)|pleura(3)|prostate(235)|salivary_gland(43)|skin(791)|small_intestine(14)|soft_tissue(220)|stomach(1158)|testis(11)|thymus(21)|thyroid(54)|upper_aerodigestive_tract(2271)|urinary_tract(1259)|vagina(6)|vulva(79)	24185		all_cancers(10;1.01e-06)|Myeloproliferative disorder(207;0.0122)|Prostate(122;0.081)		GBM - Glioblastoma multiforme(2;1.59e-06)|READ - Rectum adenocarcinoma(115;0.174)	Acetylsalicylic acid(DB00945)	GCACAAACACGCACCTCAAAG	0.542	R273C(8MGBA_CENTRAL_NERVOUS_SYSTEM)|R273C(BL70_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|R273C(EFO27_OVARY)|R273C(KARPAS299_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|R273C(MFE319_ENDOMETRIUM)|R273C(NCIH1048_LUNG)|R273C(PANC0213_PANCREAS)|R273C(PF382_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|R273C(RDES_BONE)|R273C(RH30_SOFT_TISSUE)|R273C(RPMI8402_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|R273C(SH10TC_STOMACH)|R273C(SJRH30_SOFT_TISSUE)|R273C(SUDHL4_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|R273C(SW1710_URINARY_TRACT)|R273C(SW1783_CENTRAL_NERVOUS_SYSTEM)|R273C(TT2609C02_THYROID)	111	"""Mis, N, F"""		"""breast, colorectal, lung, sarcoma, adrenocortical, glioma, multiple other tumour types"""	"""breast, sarcoma, adrenocortical carcinoma, glioma, multiple other tumour types"""		Other conserved DNA damage response genes	Osteosarcoma, Familial Clustering of;Li-Fraumeni syndrome;Hereditary Breast-Ovarian Cancer, non-BRCA1/2;Hereditary Adrenocortical Cancer;Endometrial Cancer, Familial Clustering of	HNSCC(1;<9.43e-08)|TCGA GBM(1;<1E-08)|TSP Lung(2;<1E-08)|TCGA Ovarian(1;<1.89e-07)|Multiple Myeloma(5;0.019)																											Pancreas(47;798 1329 9957 10801)	yes	Rec	yes	Li-Fraumeni syndrome	17	17p13	7157	tumor protein p53		"""L, E, M, O"""	533	Substitution - Missense(506)|Whole gene deletion(8)|Deletion - Frameshift(8)|Deletion - In frame(5)|Insertion - Frameshift(2)|Unknown(2)|Complex(2)	central_nervous_system(117)|large_intestine(108)|ovary(32)|haematopoietic_and_lymphoid_tissue(31)|upper_aerodigestive_tract(30)|stomach(25)|urinary_tract(23)|lung(21)|breast(21)|liver(20)|endometrium(17)|oesophagus(17)|bone(16)|pancreas(15)|prostate(8)|skin(7)|cervix(6)|biliary_tract(6)|kidney(3)|thyroid(3)|vulva(2)|genital_tract(1)|penis(1)|adrenal_gland(1)|salivary_gland(1)|small_intestine(1)	GRCh37	CM010471|CM010473|CM951233	TP53	M	rs121913343						65.0	56.0	59.0					17																	7577121		2203	4300	6503	SO:0001583	missense	7157	Familial Cancer Database	Familial Osteogenic Sarcoma;LFS, SBLA syndrome (Sarcoma Breast Leukemia Adrenal cancer), incl.: Cancer with In Vitro Radioresistence, Familial, Li-Fraumeni-like s.;BRCAX;Familial Adrenocortical Carcinoma;	AF307851	CCDS11118.1, CCDS45605.1, CCDS45606.1, CCDS73963.1, CCDS73964.1, CCDS73965.1, CCDS73966.1, CCDS73967.1, CCDS73968.1, CCDS73969.1, CCDS73970.1, CCDS73971.1	17p13.1	2014-09-17	2008-01-16		ENSG00000141510	ENSG00000141510			11998	protein-coding gene	gene with protein product	"""Li-Fraumeni syndrome"""	191170				6396087, 3456488, 2047879	Standard	NM_001126115		Approved	p53, LFS1	uc002gij.3	P04637	OTTHUMG00000162125	ENST00000269305.4:c.817C>T	17.37:g.7577121G>A	ENSP00000269305:p.Arg273Cys		Q15086|Q15087|Q15088|Q16535|Q16807|Q16808|Q16809|Q16810|Q16811|Q16848|Q2XN98|Q3LRW1|Q3LRW2|Q3LRW3|Q3LRW4|Q3LRW5|Q86UG1|Q8J016|Q99659|Q9BTM4|Q9HAQ8|Q9NP68|Q9NPJ2|Q9NZD0|Q9UBI2|Q9UQ61	Missense_Mutation	SNP	ENST00000269305.4	37	CCDS11118.1	.	.	.	.	.	.	.	.	.	.	G	17.48	3.400216	0.62177	.	.	ENSG00000141510	ENST00000359597;ENST00000269305;ENST00000455263;ENST00000420246;ENST00000445888;ENST00000396473;ENST00000509690	D;D;D;D;D;D	0.99869	-7.34;-7.34;-7.34;-7.34;-7.34;-7.34	4.92	3.95	0.45737	p53, DNA-binding domain (1);p53-like transcription factor, DNA-binding (1);p53/RUNT-type transcription factor, DNA-binding domain (1);	0.000000	0.85682	D	0.000000	D	0.99851	0.9931	M	0.90759	3.145	0.80722	D	1	D;D;D;D	0.89917	1.0;1.0;1.0;1.0	D;D;D;D	0.91635	0.998;0.998;0.999;0.996	D	0.96877	0.9643	10	0.87932	D	0	-11.9995	11.2235	0.48869	0.0895:0.0:0.9105:0.0	.	273;273;273;273	P04637-2;P04637-3;P04637;Q1MSW8	.;.;P53_HUMAN;.	C	273;273;273;273;273;262;141	ENSP00000352610:R273C;ENSP00000269305:R273C;ENSP00000398846:R273C;ENSP00000391127:R273C;ENSP00000391478:R273C;ENSP00000425104:R141C	ENSP00000269305:R273C	R	-	1	0	TP53	7517846	1.000000	0.71417	0.066000	0.19879	0.723000	0.41478	4.540000	0.60664	1.299000	0.44798	0.462000	0.41574	CGT		0.542	TP53-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000367397.1	NM_000546		9	0	9	0
GAS2L2	246176	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	17	34079638	34079638	+	Missense_Mutation	SNP	C	C	T			TCGA-HT-7606-01A-11D-2086-08	TCGA-HT-7606-10A-01D-2086-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	9734311d-3183-459b-8200-7104fba3bf64	7c7214f7-036a-4ac9-9883-1a93d9eb6f10	g.chr17:34079638C>T	ENST00000254466.6	-	1	259	c.232G>A	c.(232-234)Gcc>Acc	p.A78T	GAS2L2_ENST00000587565.1_Missense_Mutation_p.A78T	NM_139285.3	NP_644814.1	Q8NHY3	GA2L2_HUMAN	growth arrest-specific 2 like 2	78	CH. {ECO:0000255|PROSITE- ProRule:PRU00044}.				cell cycle arrest (GO:0007050)|microtubule bundle formation (GO:0001578)|negative regulation of microtubule depolymerization (GO:0007026)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)	actin filament binding (GO:0051015)|cytoskeletal adaptor activity (GO:0008093)|microtubule binding (GO:0008017)			central_nervous_system(1)|endometrium(1)|large_intestine(7)|lung(14)|ovary(2)|pancreas(1)|prostate(2)|skin(3)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	35		Ovarian(249;0.17)		UCEC - Uterine corpus endometrioid carcinoma (308;0.0182)		GCCAGGAAGGCCAGGGCAGCG	0.652																																																0													74.0	65.0	68.0					17																	34079638		2203	4300	6503	SO:0001583	missense	246176			AF508784	CCDS11298.1	17q21	2014-05-06			ENSG00000132139	ENSG00000270765			24846	protein-coding gene	gene with protein product		611398				12584248	Standard	NM_139285		Approved	GAR17	uc002hjv.2	Q8NHY3	OTTHUMG00000188386	ENST00000254466.6:c.232G>A	17.37:g.34079638C>T	ENSP00000254466:p.Ala78Thr		Q8NHY4	Missense_Mutation	SNP	ENST00000254466.6	37	CCDS11298.1	.	.	.	.	.	.	.	.	.	.	C	21.4	4.139724	0.77775	.	.	ENSG00000132139	ENST00000254466;ENST00000359507	T	0.41758	0.99	5.46	5.46	0.80206	Calponin homology domain (5);	0.199649	0.41500	D	0.000866	T	0.51991	0.1707	L	0.34521	1.04	0.50632	D	0.999887	D	0.71674	0.998	D	0.69824	0.966	T	0.26780	-1.0093	10	0.15066	T	0.55	-27.4173	18.4678	0.90762	0.0:1.0:0.0:0.0	.	78	Q8NHY3	GA2L2_HUMAN	T	78	ENSP00000254466:A78T	ENSP00000254466:A78T	A	-	1	0	GAS2L2	31103751	1.000000	0.71417	1.000000	0.80357	0.922000	0.55478	4.592000	0.61027	2.847000	0.97988	0.591000	0.81541	GCC		0.652	GAS2L2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256497.1	NM_139285		23	38	23	38
HELZ	9931	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	17	65174991	65174991	+	Missense_Mutation	SNP	C	C	T	rs374896136		TCGA-HT-7606-01A-11D-2086-08	TCGA-HT-7606-10A-01D-2086-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	9734311d-3183-459b-8200-7104fba3bf64	7c7214f7-036a-4ac9-9883-1a93d9eb6f10	g.chr17:65174991C>T	ENST00000358691.5	-	13	1380	c.1214G>A	c.(1213-1215)cGt>cAt	p.R405H	HELZ_ENST00000580168.1_Missense_Mutation_p.R405H	NM_014877.3	NP_055692	P42694	HELZ_HUMAN	helicase with zinc finger	405						membrane (GO:0016020)|nucleus (GO:0005634)	ATP binding (GO:0005524)|helicase activity (GO:0004386)|metal ion binding (GO:0046872)|poly(A) RNA binding (GO:0044822)			NS(1)|breast(5)|endometrium(9)|kidney(3)|large_intestine(11)|liver(1)|lung(24)|ovary(1)|pancreas(1)|prostate(1)|skin(8)|upper_aerodigestive_tract(2)|urinary_tract(2)	69	all_cancers(12;1.24e-11)|Breast(2;1.05e-17)|all_epithelial(3;3.87e-13)					AGAATCCCAACGTTTAGCTGT	0.348																																																0								C	HIS/ARG	0,3662		0,0,1831	107.0	104.0	105.0		1214	6.1	1.0	17		105	1,8173		0,1,4086	no	missense	HELZ	NM_014877.3	29	0,1,5917	TT,TC,CC		0.0122,0.0,0.0084	probably-damaging	405/1943	65174991	1,11835	1831	4087	5918	SO:0001583	missense	9931			D29677	CCDS42374.1	17q24.2	2013-01-18			ENSG00000198265	ENSG00000198265		"""Zinc fingers, CCCH-type domain containing"""	16878	protein-coding gene	gene with protein product	"""down-regulated in human cancers"""	606699				10471385, 12691822	Standard	NM_014877		Approved	KIAA0054, HUMORF5, DHRC	uc002jfx.4	P42694	OTTHUMG00000179555	ENST00000358691.5:c.1214G>A	17.37:g.65174991C>T	ENSP00000351524:p.Arg405His		I6L9H4	Missense_Mutation	SNP	ENST00000358691.5	37	CCDS42374.1	.	.	.	.	.	.	.	.	.	.	C	17.70	3.454312	0.63290	0.0	1.22E-4	ENSG00000198265	ENST00000358691;ENST00000417253	D;T	0.85702	-2.02;1.15	6.07	6.07	0.98685	.	0.000000	0.85682	D	0.000000	D	0.90310	0.6969	L	0.44542	1.39	0.80722	D	1	D;P	0.89917	1.0;0.953	D;P	0.73380	0.98;0.475	D	0.89573	0.3815	10	0.56958	D	0.05	-16.4745	20.6525	0.99598	0.0:1.0:0.0:0.0	.	405;405	B7ZLW2;P42694	.;HELZ_HUMAN	H	405	ENSP00000351524:R405H;ENSP00000411144:R405H	ENSP00000351524:R405H	R	-	2	0	HELZ	62605453	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	7.385000	0.79763	2.890000	0.99128	0.585000	0.79938	CGT		0.348	HELZ-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000447068.1	NM_014877		17	37	17	37
EPS15L1	58513	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	19	16487940	16487940	+	Silent	SNP	C	C	T			TCGA-HT-7606-01A-11D-2086-08	TCGA-HT-7606-10A-01D-2086-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	9734311d-3183-459b-8200-7104fba3bf64	7c7214f7-036a-4ac9-9883-1a93d9eb6f10	g.chr19:16487940C>T	ENST00000248070.6	-	22	2512	c.2373G>A	c.(2371-2373)ccG>ccA	p.P791P	EPS15L1_ENST00000535753.2_Intron|EPS15L1_ENST00000594975.1_Intron|EPS15L1_ENST00000455140.2_Silent_p.P791P	NM_021235.2	NP_067058.1	Q9UBC2	EP15R_HUMAN	epidermal growth factor receptor pathway substrate 15-like 1	791	15 X 3 AA repeats of D-P-F.|Pro-rich.				endocytosis (GO:0006897)|epidermal growth factor receptor signaling pathway (GO:0007173)|negative regulation of epidermal growth factor receptor signaling pathway (GO:0042059)	clathrin coat of coated pit (GO:0030132)|membrane (GO:0016020)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			breast(2)|central_nervous_system(1)|cervix(1)|endometrium(2)|kidney(3)|large_intestine(3)|lung(12)|ovary(4)|skin(2)	30						GACCGCTGGGCGGTTTAGGCC	0.612											OREG0025332	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																																				0													99.0	101.0	100.0					19																	16487940		2203	4300	6503	SO:0001819	synonymous_variant	58513			AF110265	CCDS32944.1, CCDS58653.1, CCDS58654.1, CCDS59363.1	19p13.12	2013-01-10				ENSG00000127527		"""EF-hand domain containing"""	24634	protein-coding gene	gene with protein product							Standard	NM_001258374		Approved	eps15R	uc002ndx.4	Q9UBC2		ENST00000248070.6:c.2373G>A	19.37:g.16487940C>T		710	A2RRF3|A5PL29|B4DKA3	Silent	SNP	ENST00000248070.6	37	CCDS32944.1																																																																																				0.612	EPS15L1-006	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000461040.1	NM_021235		15	23	15	23
FGR	2268	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	1	27943402	27943402	+	Silent	SNP	G	G	A			TCGA-HT-7606-01A-11D-2086-08	TCGA-HT-7606-10A-01D-2086-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	9734311d-3183-459b-8200-7104fba3bf64	7c7214f7-036a-4ac9-9883-1a93d9eb6f10	g.chr1:27943402G>A	ENST00000374005.3	-	7	936	c.648C>T	c.(646-648)ttC>ttT	p.F216F	FGR_ENST00000545953.1_Silent_p.F150F|FGR_ENST00000399173.1_Silent_p.F216F|FGR_ENST00000374004.1_Silent_p.F216F	NM_005248.2	NP_005239.1	P09769	FGR_HUMAN	FGR proto-oncogene, Src family tyrosine kinase	216	SH2. {ECO:0000255|PROSITE- ProRule:PRU00191}.				blood coagulation (GO:0007596)|defense response to Gram-positive bacterium (GO:0050830)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|immune response-regulating cell surface receptor signaling pathway (GO:0002768)|innate immune response (GO:0045087)|integrin-mediated signaling pathway (GO:0007229)|peptidyl-tyrosine phosphorylation (GO:0018108)|positive regulation of cell migration (GO:0030335)|positive regulation of cytokine secretion (GO:0050715)|positive regulation of mast cell degranulation (GO:0043306)|positive regulation of phosphatidylinositol 3-kinase activity (GO:0043552)|positive regulation of phosphatidylinositol 3-kinase signaling (GO:0014068)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|regulation of cell shape (GO:0008360)|regulation of innate immune response (GO:0045088)|regulation of phagocytosis (GO:0050764)|regulation of protein kinase activity (GO:0045859)|response to virus (GO:0009615)	actin cytoskeleton (GO:0015629)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|mitochondrial inner membrane (GO:0005743)|plasma membrane (GO:0005886)|ruffle membrane (GO:0032587)	ATP binding (GO:0005524)|Fc-gamma receptor I complex binding (GO:0034988)|immunoglobulin receptor binding (GO:0034987)|non-membrane spanning protein tyrosine kinase activity (GO:0004715)|phosphotyrosine binding (GO:0001784)|protein kinase binding (GO:0019901)|protein tyrosine kinase activity (GO:0004713)			breast(1)|endometrium(2)|kidney(1)|large_intestine(3)|lung(4)|prostate(1)|skin(4)	16		all_lung(284;2.05e-05)|Colorectal(325;3.46e-05)|Lung NSC(340;3.67e-05)|Renal(390;0.00121)|Breast(348;0.0021)|Ovarian(437;0.00503)|Myeloproliferative disorder(586;0.0255)|all_neural(195;0.0381)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0416)|OV - Ovarian serous cystadenocarcinoma(117;1.25e-24)|Colorectal(126;1.24e-08)|COAD - Colon adenocarcinoma(152;1.7e-06)|BRCA - Breast invasive adenocarcinoma(304;0.00244)|KIRC - Kidney renal clear cell carcinoma(1967;0.0027)|STAD - Stomach adenocarcinoma(196;0.00303)|READ - Rectum adenocarcinoma(331;0.0419)		GCACCGAGTTGAACTGAACCC	0.562																																																0													170.0	149.0	156.0					1																	27943402		2203	4300	6503	SO:0001819	synonymous_variant	2268			BC064382	CCDS305.1	1p36.2-p36.1	2014-06-25	2014-06-25		ENSG00000000938	ENSG00000000938		"""SH2 domain containing"""	3697	protein-coding gene	gene with protein product		164940	"""Gardner-Rasheed feline sarcoma viral (v-fgr) oncogene homolog"", ""v-fgr feline Gardner-Rasheed sarcoma viral oncogene homolog"", ""feline Gardner-Rasheed sarcoma viral oncogene homolog"""	SRC2		3922831	Standard	NM_001042729		Approved	c-fgr, p55c-fgr	uc001bom.3	P09769	OTTHUMG00000003516	ENST00000374005.3:c.648C>T	1.37:g.27943402G>A			D3DPL7|Q9UIQ3	Silent	SNP	ENST00000374005.3	37	CCDS305.1																																																																																				0.562	FGR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000009772.1	NM_005248		70	141	70	141
ZSCAN20	7579	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	1	33960425	33960425	+	Silent	SNP	T	T	G			TCGA-HT-7606-01A-11D-2086-08	TCGA-HT-7606-10A-01D-2086-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	9734311d-3183-459b-8200-7104fba3bf64	7c7214f7-036a-4ac9-9883-1a93d9eb6f10	g.chr1:33960425T>G	ENST00000361328.3	+	8	2634	c.2481T>G	c.(2479-2481)ccT>ccG	p.P827P		NM_145238.3	NP_660281	P17040	ZSC20_HUMAN	zinc finger and SCAN domain containing 20	827					transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(2)|central_nervous_system(1)|endometrium(3)|kidney(2)|large_intestine(8)|lung(11)|ovary(2)|pancreas(1)|stomach(1)	31		Myeloproliferative disorder(586;0.0255)|all_neural(195;0.211)				GTAGTGAGCCTGGGGGAAACT	0.448																																																0													156.0	153.0	154.0					1																	33960425		1912	4137	6049	SO:0001819	synonymous_variant	7579			X52360	CCDS41300.1	1p34.3	2013-01-08	2007-02-20	2007-02-20	ENSG00000121903	ENSG00000121903		"""-"", ""Zinc fingers, C2H2-type"""	13093	protein-coding gene	gene with protein product		611315	"""zinc finger protein 31 (KOX 29)"", ""zinc finger protein 31"""	ZNF360, ZNF31		2288909	Standard	NM_145238		Approved	KOX29	uc001bxj.4	P17040	OTTHUMG00000004173	ENST00000361328.3:c.2481T>G	1.37:g.33960425T>G			A8K2D0|B1ALI4|B1ALI5|B1ALI6|Q6ZN23|Q96FA9|Q96H84	Silent	SNP	ENST00000361328.3	37	CCDS41300.1																																																																																				0.448	ZSCAN20-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000277003.2	NM_145238		93	154	93	154
LRRC8D	55144	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	1	90400076	90400076	+	Silent	SNP	C	C	T	rs370858889		TCGA-HT-7606-01A-11D-2086-08	TCGA-HT-7606-10A-01D-2086-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	9734311d-3183-459b-8200-7104fba3bf64	7c7214f7-036a-4ac9-9883-1a93d9eb6f10	g.chr1:90400076C>T	ENST00000337338.5	+	3	1856	c.1449C>T	c.(1447-1449)ccC>ccT	p.P483P	LRRC8D_ENST00000394593.3_Silent_p.P483P	NM_001134479.1	NP_001127951.1	Q7L1W4	LRC8D_HUMAN	leucine rich repeat containing 8 family, member D	483					ion transport (GO:0006811)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)				breast(2)|central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(10)|lung(10)|ovary(2)|skin(1)	29		all_lung(203;0.0894)|Lung NSC(277;0.227)		all cancers(265;0.0109)|Epithelial(280;0.0427)		CGGGGGTGCCCGATGCTGTCT	0.468																																																0								C	,	1,4405	2.1+/-5.4	0,1,2202	47.0	47.0	47.0		1449,1449	-1.8	1.0	1		47	0,8600		0,0,4300	no	coding-synonymous,coding-synonymous	LRRC8D	NM_001134479.1,NM_018103.4	,	0,1,6502	TT,TC,CC		0.0,0.0227,0.0077	,	483/859,483/859	90400076	1,13005	2203	4300	6503	SO:0001819	synonymous_variant	55144			AK001332	CCDS726.1	1p22.2	2008-02-05	2005-06-29	2005-06-29	ENSG00000171492	ENSG00000171492			16992	protein-coding gene	gene with protein product		612890	"""leucine rich repeat containing 5"""	LRRC5			Standard	NM_018103		Approved	FLJ10470	uc001dnn.3	Q7L1W4	OTTHUMG00000010583	ENST00000337338.5:c.1449C>T	1.37:g.90400076C>T			D3DT29|Q6UWB2|Q9NVW3	Silent	SNP	ENST00000337338.5	37	CCDS726.1																																																																																				0.468	LRRC8D-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000029203.2	NM_018103		13	34	13	34
CFHR5	81494	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	1	196953247	196953247	+	Missense_Mutation	SNP	C	C	T			TCGA-HT-7606-01A-11D-2086-08	TCGA-HT-7606-10A-01D-2086-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	9734311d-3183-459b-8200-7104fba3bf64	7c7214f7-036a-4ac9-9883-1a93d9eb6f10	g.chr1:196953247C>T	ENST00000256785.4	+	3	519	c.410C>T	c.(409-411)cCt>cTt	p.P137L	CFHR5_ENST00000367414.5_Missense_Mutation_p.P161L			Q9BXR6	FHR5_HUMAN	complement factor H-related 5	137	Sushi 2. {ECO:0000255|PROSITE- ProRule:PRU00302}.				complement activation, alternative pathway (GO:0006957)	extracellular region (GO:0005576)				NS(2)|breast(2)|endometrium(2)|kidney(1)|large_intestine(7)|liver(2)|lung(23)|pancreas(1)|prostate(3)|skin(4)|upper_aerodigestive_tract(2)	49						TGGTCCACTCCTCCCATATGC	0.348																																																0													80.0	72.0	75.0					1																	196953247		2203	4300	6503	SO:0001583	missense	81494			AF295327	CCDS1387.1	1q31.3	2014-09-17		2006-02-28	ENSG00000134389	ENSG00000134389		"""Complement system"""	24668	protein-coding gene	gene with protein product	"""factor H related protein 5"""	608593		CFHL5		11058592, 12041828	Standard	NM_030787		Approved	FHR5, FHR-5	uc001gts.4	Q9BXR6	OTTHUMG00000036517	ENST00000256785.4:c.410C>T	1.37:g.196953247C>T	ENSP00000256785:p.Pro137Leu		Q2NKK2	Missense_Mutation	SNP	ENST00000256785.4	37	CCDS1387.1	.	.	.	.	.	.	.	.	.	.	C	10.22	1.291466	0.23564	.	.	ENSG00000134389	ENST00000367414;ENST00000256785	T;T	0.65732	-0.17;-0.17	3.53	0.136	0.14780	Complement control module (2);Sushi/SCR/CCP (3);	.	.	.	.	T	0.50137	0.1598	L	0.54323	1.7	0.09310	N	1	B	0.24576	0.106	B	0.31016	0.123	T	0.39099	-0.9630	9	0.20519	T	0.43	.	2.3428	0.04264	0.1931:0.4952:0.1894:0.1223	.	137	Q9BXR6	FHR5_HUMAN	L	161;137	ENSP00000356384:P161L;ENSP00000256785:P137L	ENSP00000256785:P137L	P	+	2	0	CFHR5	195219870	0.001000	0.12720	0.004000	0.12327	0.034000	0.12701	-0.020000	0.12525	0.094000	0.17404	0.313000	0.20887	CCT		0.348	CFHR5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000088814.2	NM_030787		21	49	21	49
ASPM	259266	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	1	197091601	197091601	+	Missense_Mutation	SNP	G	G	A	rs201067420		TCGA-HT-7606-01A-11D-2086-08	TCGA-HT-7606-10A-01D-2086-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	9734311d-3183-459b-8200-7104fba3bf64	7c7214f7-036a-4ac9-9883-1a93d9eb6f10	g.chr1:197091601G>A	ENST00000367409.4	-	14	3771	c.3515C>T	c.(3514-3516)aCg>aTg	p.T1172M	ASPM_ENST00000367408.1_Missense_Mutation_p.T422M|ASPM_ENST00000294732.7_Missense_Mutation_p.T1172M	NM_018136.4	NP_060606.3	Q8IZT6	ASPM_HUMAN	asp (abnormal spindle) homolog, microcephaly associated (Drosophila)	1172	CH 2. {ECO:0000255|PROSITE- ProRule:PRU00044}.				developmental growth (GO:0048589)|forebrain neuroblast division (GO:0021873)|maintenance of centrosome location (GO:0051661)|mitotic nuclear division (GO:0007067)|negative regulation of asymmetric cell division (GO:0045769)|negative regulation of neuron differentiation (GO:0045665)|neuron migration (GO:0001764)|oogenesis (GO:0048477)|positive regulation of canonical Wnt signaling pathway (GO:0090263)|positive regulation of neuroblast proliferation (GO:0002052)|spermatogenesis (GO:0007283)	cytoplasm (GO:0005737)|midbody (GO:0030496)|nucleus (GO:0005634)|spindle pole (GO:0000922)		p.T1172M(1)		breast(6)|central_nervous_system(2)|cervix(2)|endometrium(10)|kidney(9)|large_intestine(28)|liver(1)|lung(87)|ovary(5)|pancreas(2)|prostate(6)|skin(4)|urinary_tract(3)	165						ACCAGTTTGCGTACATTCCAC	0.413													G|||	1	0.000199681	0.0	0.0	5008	,	,		19208	0.001		0.0	False		,,,				2504	0.0															1	Substitution - Missense(1)	endometrium(1)											108.0	94.0	99.0					1																	197091601		2203	4300	6503	SO:0001583	missense	259266			AY367065	CCDS1389.1, CCDS55672.1	1q31	2008-02-05	2006-09-12		ENSG00000066279	ENSG00000066279			19048	protein-coding gene	gene with protein product		605481	"""microcephaly, primary autosomal recessive 5"", ""asp (abnormal spindle)-like, microcephaly associated (Drosophila)"""	MCPH5		11078481	Standard	NM_018136		Approved	Calmbp1, ASP, FLJ10517, FLJ10549	uc001gtu.3	Q8IZT6	OTTHUMG00000036277	ENST00000367409.4:c.3515C>T	1.37:g.197091601G>A	ENSP00000356379:p.Thr1172Met		Q4G1H1|Q5VYL3|Q86UX4|Q8IUL2|Q8IZJ7|Q8IZJ8|Q8IZJ9|Q8N4D1|Q9NVS1|Q9NVT6	Missense_Mutation	SNP	ENST00000367409.4	37	CCDS1389.1	1	4.578754578754579E-4	0	0.0	0	0.0	1	0.0017482517482517483	0	0.0	G	10.69	1.420472	0.25639	.	.	ENSG00000066279	ENST00000367409;ENST00000294732;ENST00000367408	T;T;T	0.58652	0.32;1.59;1.31	5.96	4.11	0.48088	Calmodulin-regulated spectrin-associated protein, CH domain (1);Calponin homology domain (3);	0.648225	0.15474	N	0.260459	T	0.39410	0.1077	L	0.29908	0.895	0.09310	N	1	B;P	0.40660	0.161;0.726	B;B	0.31495	0.058;0.131	T	0.21348	-1.0248	10	0.52906	T	0.07	.	8.5021	0.33163	0.1337:0.1258:0.7405:0.0	.	1172;1172	Q4G1H1;Q8IZT6	.;ASPM_HUMAN	M	1172;1172;422	ENSP00000356379:T1172M;ENSP00000294732:T1172M;ENSP00000356378:T422M	ENSP00000294732:T1172M	T	-	2	0	ASPM	195358224	0.697000	0.27767	0.003000	0.11579	0.874000	0.50279	3.915000	0.56409	0.877000	0.35895	-0.224000	0.12420	ACG		0.413	ASPM-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000088256.1	NM_018136		11	25	11	25
SLC25A1	6576	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	22	19164192	19164192	+	Missense_Mutation	SNP	T	T	G			TCGA-HT-7606-01A-11D-2086-08	TCGA-HT-7606-10A-01D-2086-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	9734311d-3183-459b-8200-7104fba3bf64	7c7214f7-036a-4ac9-9883-1a93d9eb6f10	g.chr22:19164192T>G	ENST00000215882.5	-	7	802	c.646A>C	c.(646-648)Aag>Cag	p.K216Q	SLC25A1_ENST00000461267.1_5'UTR|CLTCL1_ENST00000442042.2_5'Flank|SLC25A1_ENST00000451283.1_Missense_Mutation_p.K113Q	NM_005984.3	NP_005975.1	P53007	TXTP_HUMAN	solute carrier family 25 (mitochondrial carrier; citrate transporter), member 1	216					carbohydrate metabolic process (GO:0005975)|cellular lipid metabolic process (GO:0044255)|citrate transport (GO:0015746)|gluconeogenesis (GO:0006094)|glucose metabolic process (GO:0006006)|long-chain fatty-acyl-CoA biosynthetic process (GO:0035338)|small molecule metabolic process (GO:0044281)|triglyceride biosynthetic process (GO:0019432)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|mitochondrial inner membrane (GO:0005743)|nucleus (GO:0005634)	citrate transmembrane transporter activity (GO:0015137)			cervix(1)|lung(1)	2	Colorectal(54;0.0993)	all_lung(157;9.94e-09)		Lung(27;0.124)		TTCATGGGCTTGTTGGGGTTG	0.592																																																0													40.0	45.0	43.0					22																	19164192		2203	4300	6503	SO:0001583	missense	6576			U25147	CCDS13758.1, CCDS74817.1	22q11	2013-05-22			ENSG00000100075	ENSG00000100075		"""Solute carriers"""	10979	protein-coding gene	gene with protein product		190315	"""solute carrier family 20 (mitochondrial citrate transporter), member 3"""	SLC20A3		8666394, 9254007	Standard	NM_001256534		Approved	CTP	uc002zoz.4	P53007	OTTHUMG00000150123	ENST00000215882.5:c.646A>C	22.37:g.19164192T>G	ENSP00000215882:p.Lys216Gln		A8K8E8|Q9BSK6	Missense_Mutation	SNP	ENST00000215882.5	37	CCDS13758.1	.	.	.	.	.	.	.	.	.	.	T	16.93	3.258388	0.59321	.	.	ENSG00000100075	ENST00000215882;ENST00000451283	T;T	0.78924	-1.22;-1.22	5.48	5.48	0.80851	Mitochondrial carrier domain (2);	0.183953	0.48286	D	0.000199	T	0.74627	0.3741	L	0.38531	1.155	0.80722	D	1	P;B	0.41159	0.74;0.287	P;B	0.44673	0.457;0.292	T	0.75502	-0.3295	10	0.44086	T	0.13	-5.8507	15.5644	0.76277	0.0:0.0:0.0:1.0	.	223;216	D9HTE9;P53007	.;TXTP_HUMAN	Q	216;113	ENSP00000215882:K216Q;ENSP00000401480:K113Q	ENSP00000215882:K216Q	K	-	1	0	SLC25A1	17544192	1.000000	0.71417	1.000000	0.80357	0.373000	0.29922	6.152000	0.71812	2.068000	0.61886	0.379000	0.24179	AAG		0.592	SLC25A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000316441.1	NM_005984		12	26	12	26
IDH1	3417	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	2	209113112	209113112	+	Missense_Mutation	SNP	C	C	T	rs121913500		TCGA-HT-7606-01A-11D-2086-08	TCGA-HT-7606-10A-01D-2086-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	9734311d-3183-459b-8200-7104fba3bf64	7c7214f7-036a-4ac9-9883-1a93d9eb6f10	g.chr2:209113112C>T	ENST00000415913.1	-	4	776	c.395G>A	c.(394-396)cGt>cAt	p.R132H	IDH1_ENST00000345146.2_Missense_Mutation_p.R132H|IDH1_ENST00000446179.1_Missense_Mutation_p.R132H	NM_001282387.1	NP_001269316.1	O75874	IDHC_HUMAN	isocitrate dehydrogenase 1 (NADP+), soluble	132			R -> C (in colorectal cancer and glioma samples; glioblastoma multiforme; somatic mutation; abolishes magnesium binding and alters enzyme activity so that isocitrate is no longer converted to alpha- ketoglutarate but instead alpha- ketoglutarate is converted to R(-)-2- hydroxyglutarate). {ECO:0000269|PubMed:16959974, ECO:0000269|PubMed:19117336}.|R -> G (in a glioma sample; glioblastoma multiforme; somatic mutation). {ECO:0000269|PubMed:19117336}.|R -> H (in a glioma sample; glioblastoma multiforme; somatic mutation; abolishes magnesium binding and alters enzyme activity so that isocitrate is no longer converted to alpha-ketoglutarate but instead alpha-ketoglutarate is converted to R(-)-2-hydroxyglutarate). {ECO:0000269|PubMed:18772396}.|R -> L (in a glioma sample; glioblastoma multiforme; somatic mutation; abolishes magnesium binding and alters enzyme activity so that isocitrate is no longer converted to alpha-ketoglutarate but instead alpha-ketoglutarate is converted to R(-)-2-hydroxyglutarate). {ECO:0000269|PubMed:19117336}.|R -> S (in a glioma sample; glioblastoma multiforme; somatic mutation; abolishes magnesium binding and alters enzyme activity so that isocitrate is no longer converted to alpha-ketoglutarate but instead alpha-ketoglutarate is converted to R(-)-2-hydroxyglutarate). {ECO:0000269|PubMed:18772396}.		2-oxoglutarate metabolic process (GO:0006103)|cellular lipid metabolic process (GO:0044255)|female gonad development (GO:0008585)|glutathione metabolic process (GO:0006749)|glyoxylate cycle (GO:0006097)|isocitrate metabolic process (GO:0006102)|NADPH regeneration (GO:0006740)|response to oxidative stress (GO:0006979)|response to steroid hormone (GO:0048545)|small molecule metabolic process (GO:0044281)|tricarboxylic acid cycle (GO:0006099)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|mitochondrion (GO:0005739)|peroxisomal matrix (GO:0005782)|peroxisome (GO:0005777)	isocitrate dehydrogenase (NADP+) activity (GO:0004450)|magnesium ion binding (GO:0000287)|NAD binding (GO:0051287)|NADP binding (GO:0050661)|protein homodimerization activity (GO:0042803)|receptor binding (GO:0005102)	p.R132H(2774)|p.R132L(59)|p.R132V(1)|p.G131_R132>VL(1)		NS(1)|autonomic_ganglia(2)|biliary_tract(24)|bone(237)|central_nervous_system(3764)|endometrium(3)|haematopoietic_and_lymphoid_tissue(794)|kidney(2)|large_intestine(7)|lung(7)|prostate(6)|skin(5)|soft_tissue(12)|thyroid(22)|urinary_tract(1)	4887				Epithelial(149;0.0322)|LUSC - Lung squamous cell carcinoma(261;0.0711)|Lung(261;0.136)		ATAAGCATGACGACCTATGAT	0.393			Mis		gliobastoma																																Pancreas(158;264 1958 3300 35450 36047)		Dom	yes		2	2q33.3	3417	"""isocitrate dehydrogenase 1 (NADP+), soluble"""		O	2835	Substitution - Missense(2834)|Complex - compound substitution(1)	central_nervous_system(2579)|haematopoietic_and_lymphoid_tissue(205)|bone(43)|prostate(4)|biliary_tract(2)|urinary_tract(1)|skin(1)											79.0	73.0	75.0					2																	209113112		2203	4300	6503	SO:0001583	missense	3417				CCDS2381.1	2q34	2014-09-17			ENSG00000138413	ENSG00000138413	1.1.1.42		5382	protein-coding gene	gene with protein product		147700					Standard	NM_005896		Approved		uc002vcu.3	O75874	OTTHUMG00000132943	ENST00000415913.1:c.395G>A	2.37:g.209113112C>T	ENSP00000390265:p.Arg132His		Q567U4|Q6FHQ6|Q7Z3V0|Q93090|Q9NTJ9|Q9UKW8	Missense_Mutation	SNP	ENST00000415913.1	37	CCDS2381.1	.	.	.	.	.	.	.	.	.	.	C	25.6	4.657324	0.88154	.	.	ENSG00000138413	ENST00000345146;ENST00000446179;ENST00000415913;ENST00000415282	D;D;D;D	0.86956	-2.19;-2.19;-2.19;-2.19	5.57	4.69	0.59074	Isopropylmalate dehydrogenase-like domain (2);	0.000000	0.85682	D	0.000000	D	0.93145	0.7817	H	0.99379	4.54	0.80722	D	1	B	0.25486	0.127	B	0.25405	0.06	D	0.92324	0.5868	10	0.87932	D	0	-20.0399	14.3783	0.66895	0.0:0.9288:0.0:0.0712	.	132	O75874	IDHC_HUMAN	H	132	ENSP00000260985:R132H;ENSP00000410513:R132H;ENSP00000390265:R132H;ENSP00000391075:R132H	ENSP00000260985:R132H	R	-	2	0	IDH1	208821357	1.000000	0.71417	0.997000	0.53966	0.992000	0.81027	6.088000	0.71371	1.356000	0.45884	0.555000	0.69702	CGT		0.393	IDH1-006	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000336672.1			35	56	35	56
VIL1	7429	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	2	219295519	219295519	+	Silent	SNP	C	C	T			TCGA-HT-7606-01A-11D-2086-08	TCGA-HT-7606-10A-01D-2086-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	9734311d-3183-459b-8200-7104fba3bf64	7c7214f7-036a-4ac9-9883-1a93d9eb6f10	g.chr2:219295519C>T	ENST00000248444.5	+	10	1108	c.1020C>T	c.(1018-1020)gcC>gcT	p.A340A	VIL1_ENST00000392114.2_Silent_p.A29A|VIL1_ENST00000440053.1_Silent_p.A340A	NM_007127.2	NP_009058.2	P09327	VILI_HUMAN	villin 1	340	Core.				actin filament capping (GO:0051693)|actin filament depolymerization (GO:0030042)|actin filament polymerization (GO:0030041)|actin filament severing (GO:0051014)|cellular response to epidermal growth factor stimulus (GO:0071364)|cellular response to hepatocyte growth factor stimulus (GO:0035729)|cytoplasmic actin-based contraction involved in cell motility (GO:0060327)|epidermal growth factor receptor signaling pathway (GO:0007173)|epithelial cell differentiation (GO:0030855)|positive regulation of actin filament bundle assembly (GO:0032233)|positive regulation of cell migration (GO:0030335)|positive regulation of epithelial cell migration (GO:0010634)|protein complex assembly (GO:0006461)|regulation of actin nucleation (GO:0051125)|regulation of cell shape (GO:0008360)|regulation of lamellipodium morphogenesis (GO:2000392)|regulation of wound healing (GO:0061041)|response to bacterium (GO:0009617)	actin filament bundle (GO:0032432)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|filopodium (GO:0030175)|filopodium tip (GO:0032433)|lamellipodium (GO:0030027)|microvillus (GO:0005902)|ruffle (GO:0001726)	actin filament binding (GO:0051015)|calcium ion binding (GO:0005509)|cysteine-type endopeptidase inhibitor activity involved in apoptotic process (GO:0043027)|identical protein binding (GO:0042802)|lysophosphatidic acid binding (GO:0035727)|phosphatidylinositol-4,5-bisphosphate binding (GO:0005546)|protein homodimerization activity (GO:0042803)			NS(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(4)|lung(20)|ovary(2)|prostate(3)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(1)	41		Renal(207;0.0474)		Epithelial(149;6.88e-07)|all cancers(144;0.00013)|LUSC - Lung squamous cell carcinoma(224;0.008)|Lung(261;0.00942)		CTGAGTCGGCCGTCTTTCAGC	0.597																																																0													78.0	70.0	73.0					2																	219295519		2203	4300	6503	SO:0001819	synonymous_variant	7429			X12901	CCDS2417.1	2q35	2012-10-02			ENSG00000127831	ENSG00000127831			12690	protein-coding gene	gene with protein product		193040		VIL		2846586	Standard	NM_007127		Approved	D2S1471	uc002via.3	P09327	OTTHUMG00000133112	ENST00000248444.5:c.1020C>T	2.37:g.219295519C>T			B2R9A7|Q53S11|Q96AC8	Silent	SNP	ENST00000248444.5	37	CCDS2417.1																																																																																				0.597	VIL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256778.3	NM_007127		19	47	19	47
PCDHA11	56138	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	5	140249016	140249016	+	Missense_Mutation	SNP	G	G	A			TCGA-HT-7606-01A-11D-2086-08	TCGA-HT-7606-10A-01D-2086-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	9734311d-3183-459b-8200-7104fba3bf64	7c7214f7-036a-4ac9-9883-1a93d9eb6f10	g.chr5:140249016G>A	ENST00000398640.2	+	1	328	c.328G>A	c.(328-330)Gtg>Atg	p.V110M	PCDHA10_ENST00000506939.2_Intron|PCDHA1_ENST00000394633.3_Intron|PCDHA4_ENST00000530339.1_Intron|PCDHA10_ENST00000307360.5_Intron|PCDHA3_ENST00000522353.2_Intron|PCDHA4_ENST00000512229.2_Intron|PCDHA6_ENST00000527624.1_Intron|PCDHA5_ENST00000529859.1_Intron|PCDHA5_ENST00000529619.1_Intron|PCDHA9_ENST00000532602.1_Intron|PCDHA8_ENST00000531613.1_Intron|PCDHA7_ENST00000525929.1_Intron|PCDHA1_ENST00000504120.2_Intron|PCDHA2_ENST00000526136.1_Intron|PCDHA6_ENST00000529310.1_Intron	NM_018902.3	NP_061725.1	Q9Y5I1	PCDAB_HUMAN	protocadherin alpha 11	110	Cadherin 1. {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)			breast(1)|lung(1)	2			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			GGAGGTGATCGTGGACAGGCC	0.552																																																0													132.0	148.0	143.0					5																	140249016		2203	4298	6501	SO:0001583	missense	56138			AF152476	CCDS47284.1, CCDS75326.1	5q31	2010-11-26			ENSG00000249158	ENSG00000249158		"""Cadherins / Protocadherins : Clustered"""	8665	other	complex locus constituent	"""KIAA0345-like 3"", ""ortholog of mouse CNR7"""	606317		CNRS7		10380929, 10662547	Standard	NM_018902		Approved	CNR7, CRNR7, CNRN7, PCDH-ALPHA11		Q9Y5I1	OTTHUMG00000163369	ENST00000398640.2:c.328G>A	5.37:g.140249016G>A	ENSP00000381636:p.Val110Met		B2RN58|O75279	Missense_Mutation	SNP	ENST00000398640.2	37	CCDS47284.1	.	.	.	.	.	.	.	.	.	.	G	16.06	3.014629	0.54468	.	.	ENSG00000249158	ENST00000398640	T	0.37915	1.17	5.59	5.59	0.84812	Cadherin, N-terminal (1);Cadherin (3);Cadherin-like (1);	.	.	.	.	T	0.53674	0.1811	M	0.76433	2.335	0.29584	N	0.848945	D;D	0.76494	0.999;0.986	P;P	0.53146	0.61;0.719	T	0.56721	-0.7932	9	0.56958	D	0.05	.	16.6165	0.84917	0.0:0.1297:0.8703:0.0	.	110;110	Q9Y5I1-2;Q9Y5I1	.;PCDAB_HUMAN	M	110	ENSP00000381636:V110M	ENSP00000381636:V110M	V	+	1	0	PCDHA11	140229200	0.000000	0.05858	0.999000	0.59377	0.864000	0.49448	-0.153000	0.10144	2.628000	0.89032	0.655000	0.94253	GTG		0.552	PCDHA11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000372885.2	NM_018902		147	171	147	171
DUSP22	56940	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	6	348774	348774	+	Silent	SNP	G	G	T			TCGA-HT-7606-01A-11D-2086-08	TCGA-HT-7606-10A-01D-2086-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	9734311d-3183-459b-8200-7104fba3bf64	7c7214f7-036a-4ac9-9883-1a93d9eb6f10	g.chr6:348774G>T	ENST00000344450.5	+	7	884	c.441G>T	c.(439-441)cgG>cgT	p.R147R	DUSP22_ENST00000604971.1_Silent_p.R44R|DUSP22_ENST00000605035.1_3'UTR|DUSP22_ENST00000605315.1_Silent_p.R44R|DUSP22_ENST00000419235.2_Silent_p.R147R|DUSP22_ENST00000603453.1_Silent_p.R44R	NM_020185.3	NP_064570.1	Q9NRW4	DUS22_HUMAN	dual specificity phosphatase 22	147					apoptotic process (GO:0006915)|cell proliferation (GO:0008283)|inactivation of MAPK activity (GO:0000188)|multicellular organismal development (GO:0007275)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of JNK cascade (GO:0046330)|protein dephosphorylation (GO:0006470)|regulation of cell proliferation (GO:0042127)|transforming growth factor beta receptor signaling pathway (GO:0007179)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	protein tyrosine phosphatase activity (GO:0004725)|protein tyrosine/serine/threonine phosphatase activity (GO:0008138)			central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(4)|lung(16)|ovary(1)|skin(2)	26	all_hematologic(77;0.228)	Breast(5;0.0249)|all_hematologic(90;0.0489)		OV - Ovarian serous cystadenocarcinoma(45;0.0277)|BRCA - Breast invasive adenocarcinoma(62;0.0669)		TCCAGTATCGGCAGTGGCTGA	0.522																																																0													162.0	146.0	151.0					6																	348774		2203	4300	6503	SO:0001819	synonymous_variant	56940			AF165519	CCDS4468.1, CCDS69035.1	6p25.3	2013-09-19			ENSG00000112679	ENSG00000112679		"""Protein tyrosine phosphatases / Class I Cys-based PTPs : Atypical dual specificity phosphatases"""	16077	protein-coding gene	gene with protein product						9205128, 11717427	Standard	NM_001286555		Approved	MKPX, JSP1, JKAP, VHX	uc003msx.3	Q9NRW4	OTTHUMG00000014113	ENST00000344450.5:c.441G>T	6.37:g.348774G>T			B4DK56|Q59GW2|Q5VWR2|Q96AR1	Silent	SNP	ENST00000344450.5	37	CCDS4468.1	.	.	.	.	.	.	.	.	.	.	G	8.957	0.969510	0.18659	.	.	ENSG00000112679	ENST00000419235	.	.	.	5.07	2.19	0.27852	.	.	.	.	.	T	0.43567	0.1253	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.33979	-0.9847	4	.	.	.	.	8.5656	0.33538	0.1315:0.2758:0.5927:0.0	.	.	.	.	S	85	.	.	A	+	1	0	DUSP22	293774	0.995000	0.38212	1.000000	0.80357	0.759000	0.43091	0.213000	0.17521	0.606000	0.29965	0.655000	0.94253	GCA		0.522	DUSP22-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000039621.1	NM_020185		24	103	24	103
FIGNL1	63979	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	7	50513534	50513534	+	Silent	SNP	T	T	C			TCGA-HT-7606-01A-11D-2086-08	TCGA-HT-7606-10A-01D-2086-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	9734311d-3183-459b-8200-7104fba3bf64	7c7214f7-036a-4ac9-9883-1a93d9eb6f10	g.chr7:50513534T>C	ENST00000419119.1	-	2	3005	c.1452A>G	c.(1450-1452)gcA>gcG	p.A484A	FIGNL1_ENST00000433017.1_Silent_p.A484A|FIGNL1_ENST00000395556.2_Silent_p.A484A|FIGNL1_ENST00000356889.4_Silent_p.A484A			Q6PIW4	FIGL1_HUMAN	fidgetin-like 1	484					ATP metabolic process (GO:0046034)|cellular response to ionizing radiation (GO:0071479)|negative regulation of apoptotic process (GO:0043066)|negative regulation of intrinsic apoptotic signaling pathway (GO:2001243)|osteoblast differentiation (GO:0001649)|osteoblast proliferation (GO:0033687)|regulation of cell cycle (GO:0051726)|regulation of double-strand break repair via homologous recombination (GO:0010569)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|nuclear chromosome (GO:0000228)|nucleus (GO:0005634)	ATP binding (GO:0005524)|hydrolase activity (GO:0016787)|magnesium ion binding (GO:0000287)			endometrium(3)|kidney(1)|large_intestine(5)|lung(13)|ovary(3)|prostate(3)|upper_aerodigestive_tract(1)	29	Glioma(55;0.08)|all_neural(89;0.245)	Acute lymphoblastic leukemia(4;3.73e-08)|all_hematologic(4;7.51e-06)				CAGCAAACAATGCACGGACCA	0.443																																																0													98.0	94.0	95.0					7																	50513534		2203	4300	6503	SO:0001819	synonymous_variant	63979			AK023142	CCDS5510.1	7p12.2	2010-04-21			ENSG00000132436	ENSG00000132436		"""ATPases / AAA-type"""	13286	protein-coding gene	gene with protein product		615383					Standard	XM_005271783		Approved		uc003tpc.3	Q6PIW4	OTTHUMG00000022866	ENST00000419119.1:c.1452A>G	7.37:g.50513534T>C			D3DVM6|Q86V18|Q8ND59|Q9H8P1|Q9H917	Silent	SNP	ENST00000419119.1	37	CCDS5510.1																																																																																				0.443	FIGNL1-004	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000342579.1	NM_001042762		50	84	50	84
ZNF138	7697	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	7	64292367	64292367	+	Missense_Mutation	SNP	A	A	C			TCGA-HT-7606-01A-11D-2086-08	TCGA-HT-7606-10A-01D-2086-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	9734311d-3183-459b-8200-7104fba3bf64	7c7214f7-036a-4ac9-9883-1a93d9eb6f10	g.chr7:64292367A>C	ENST00000359735.3	+	4	923	c.576A>C	c.(574-576)aaA>aaC	p.K192N	ZNF138_ENST00000397136.2_Missense_Mutation_p.K192N|ZNF138_ENST00000440155.2_Missense_Mutation_p.K223N|ZNF138_ENST00000440598.1_3'UTR|ZNF138_ENST00000437743.1_Missense_Mutation_p.K217N|ZNF138_ENST00000430838.2_3'UTR|ZNF138_ENST00000307355.7_Missense_Mutation_p.K249N	NM_001271637.1|NM_001271639.1	NP_001258566.1|NP_001258568.1	P52744	ZN138_HUMAN	zinc finger protein 138	192					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.K192K(1)		kidney(1)|large_intestine(3)|lung(2)|stomach(1)	7		Lung NSC(55;0.0795)|all_lung(88;0.18)				CTGGAGAAAAACCCTATAAAT	0.368																																																1	Substitution - coding silent(1)	large_intestine(1)											45.0	49.0	48.0					7																	64292367		2203	4299	6502	SO:0001583	missense	7697			U09847	CCDS34645.1, CCDS34645.2, CCDS55115.1, CCDS64659.1, CCDS64660.1, CCDS64661.1, CCDS75607.1	7q11.21	2013-01-08	2005-07-11		ENSG00000197008	ENSG00000197008		"""Zinc fingers, C2H2-type"", ""-"""	12922	protein-coding gene	gene with protein product		604080	"""zinc finger protein 138 (clone pHZ-32)"""				Standard	NM_006524		Approved	pHZ-32	uc031sxl.1	P52744	OTTHUMG00000156603	ENST00000359735.3:c.576A>C	7.37:g.64292367A>C	ENSP00000352770:p.Lys192Asn		B4DFX2|B4DP87|E9PHI7|E9PHK7	Missense_Mutation	SNP	ENST00000359735.3	37		.	.	.	.	.	.	.	.	.	.	.	12.39	1.925007	0.34002	.	.	ENSG00000197008	ENST00000307355;ENST00000359735;ENST00000440155;ENST00000437743;ENST00000397136	T;T;T;T;T	0.26067	1.76;1.76;1.76;1.76;1.76	0.85	-0.454	0.12197	Zinc finger, C2H2 (1);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.42245	0.1194	M	0.72353	2.195	0.26014	N	0.981951	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.97110	1.0;0.995;1.0	T	0.21895	-1.0232	9	0.72032	D	0.01	.	3.786	0.08700	0.6826:0.0:0.3174:0.0	.	223;217;192	E9PHI7;E7EWC5;P52744	.;.;ZN138_HUMAN	N	249;192;223;217;192	ENSP00000303533:K249N;ENSP00000352770:K192N;ENSP00000407262:K223N;ENSP00000399528:K217N;ENSP00000380325:K192N	ENSP00000303533:K249N	K	+	3	2	ZNF138	63929802	0.110000	0.22057	0.013000	0.15412	0.013000	0.08279	0.118000	0.15605	0.166000	0.19597	0.164000	0.16699	AAA		0.368	ZNF138-201	KNOWN	basic	protein_coding	protein_coding		NM_006524		16	19	16	19
SEMA3C	10512	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	7	80374454	80374454	+	Missense_Mutation	SNP	G	G	A			TCGA-HT-7606-01A-11D-2086-08	TCGA-HT-7606-10A-01D-2086-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	9734311d-3183-459b-8200-7104fba3bf64	7c7214f7-036a-4ac9-9883-1a93d9eb6f10	g.chr7:80374454G>A	ENST00000265361.3	-	18	2573	c.2012C>T	c.(2011-2013)aCg>aTg	p.T671M	SEMA3C_ENST00000419255.2_Missense_Mutation_p.T671M|SEMA3C_ENST00000544525.1_Missense_Mutation_p.T689M	NM_006379.3	NP_006370.1	Q99985	SEM3C_HUMAN	sema domain, immunoglobulin domain (Ig), short basic domain, secreted, (semaphorin) 3C	671					axon guidance (GO:0007411)|blood vessel remodeling (GO:0001974)|cardiac right ventricle morphogenesis (GO:0003215)|dichotomous subdivision of terminal units involved in salivary gland branching (GO:0060666)|immune response (GO:0006955)|limb bud formation (GO:0060174)|neural crest cell migration (GO:0001755)|neural tube development (GO:0021915)|outflow tract morphogenesis (GO:0003151)|post-embryonic development (GO:0009791)|pulmonary myocardium development (GO:0003350)|response to drug (GO:0042493)|somitogenesis (GO:0001756)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)	receptor activity (GO:0004872)			NS(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(4)|lung(17)|ovary(1)|skin(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	34						CCATTTGTCCGTCACAACAGC	0.478																																																0													85.0	78.0	80.0					7																	80374454		2203	4300	6503	SO:0001583	missense	10512			AB000220	CCDS5596.1	7q21-q31	2013-01-11			ENSG00000075223	ENSG00000075223		"""Semaphorins"", ""Immunoglobulin superfamily / I-set domain containing"""	10725	protein-coding gene	gene with protein product		602645		SEMAE		7748561, 9168980	Standard	NM_006379		Approved	SemE	uc003uhj.3	Q99985	OTTHUMG00000023447	ENST00000265361.3:c.2012C>T	7.37:g.80374454G>A	ENSP00000265361:p.Thr671Met		B4DRL8	Missense_Mutation	SNP	ENST00000265361.3	37	CCDS5596.1	.	.	.	.	.	.	.	.	.	.	G	13.34	2.207937	0.39003	.	.	ENSG00000075223	ENST00000265361;ENST00000419255;ENST00000544525	T;T;T	0.26660	1.73;1.73;1.72	5.56	4.67	0.58626	.	0.195272	0.53938	D	0.000054	T	0.19604	0.0471	N	0.24115	0.695	0.80722	D	1	B;B	0.18610	0.029;0.017	B;B	0.24974	0.057;0.026	T	0.03673	-1.1014	10	0.41790	T	0.15	.	13.8331	0.63393	0.0732:0.0:0.9268:0.0	.	689;671	F5H1Z7;Q99985	.;SEM3C_HUMAN	M	671;671;689	ENSP00000265361:T671M;ENSP00000411193:T671M;ENSP00000445649:T689M	ENSP00000265361:T671M	T	-	2	0	SEMA3C	80212390	1.000000	0.71417	0.999000	0.59377	0.752000	0.42762	6.044000	0.71012	2.636000	0.89361	0.650000	0.86243	ACG		0.478	SEMA3C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253279.1	NM_006379		24	39	24	39
JPH1	56704	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	8	75171665	75171665	+	Missense_Mutation	SNP	C	C	T			TCGA-HT-7606-01A-11D-2086-08	TCGA-HT-7606-10A-01D-2086-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	9734311d-3183-459b-8200-7104fba3bf64	7c7214f7-036a-4ac9-9883-1a93d9eb6f10	g.chr8:75171665C>T	ENST00000342232.4	-	3	1253	c.1213G>A	c.(1213-1215)Gcg>Acg	p.A405T		NM_020647.2	NP_065698.1	Q9HDC5	JPH1_HUMAN	junctophilin 1	405	Ala-rich.				calcium ion transport into cytosol (GO:0060402)|muscle organ development (GO:0007517)|regulation of ryanodine-sensitive calcium-release channel activity (GO:0060314)	integral component of membrane (GO:0016021)|junctional membrane complex (GO:0030314)|junctional sarcoplasmic reticulum membrane (GO:0014701)|plasma membrane (GO:0005886)|Z disc (GO:0030018)	structural constituent of muscle (GO:0008307)			endometrium(4)|kidney(1)|large_intestine(4)|lung(10)|ovary(2)|skin(1)|upper_aerodigestive_tract(2)	24	Breast(64;0.00576)		BRCA - Breast invasive adenocarcinoma(89;0.0499)|Epithelial(68;0.0728)|all cancers(69;0.176)			ACAGCTCTCGCGATGTCGCAC	0.607																																																0													47.0	50.0	49.0					8																	75171665		2203	4300	6503	SO:0001583	missense	56704			AB042634	CCDS6217.1	8q21	2008-07-03			ENSG00000104369	ENSG00000104369			14201	protein-coding gene	gene with protein product		605266				10891348, 10949023	Standard	XM_005251273		Approved	JP-1	uc003yae.3	Q9HDC5	OTTHUMG00000164524	ENST00000342232.4:c.1213G>A	8.37:g.75171665C>T	ENSP00000344488:p.Ala405Thr		B2RTZ0	Missense_Mutation	SNP	ENST00000342232.4	37	CCDS6217.1	.	.	.	.	.	.	.	.	.	.	C	34	5.360880	0.95877	.	.	ENSG00000104369	ENST00000342232	T	0.76839	-1.05	5.1	5.1	0.69264	.	0.000000	0.85682	D	0.000000	D	0.89273	0.6668	M	0.86097	2.795	0.58432	D	0.999994	D	0.89917	1.0	D	0.81914	0.995	D	0.90515	0.4484	10	0.87932	D	0	.	17.7907	0.88551	0.0:1.0:0.0:0.0	.	405	Q9HDC5	JPH1_HUMAN	T	405	ENSP00000344488:A405T	ENSP00000344488:A405T	A	-	1	0	JPH1	75334219	1.000000	0.71417	0.982000	0.44146	0.966000	0.64601	6.390000	0.73204	2.809000	0.96659	0.655000	0.94253	GCG		0.607	JPH1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000379102.1			18	26	18	26
NUDCD1	84955	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	8	110287672	110287672	+	Missense_Mutation	SNP	A	A	C			TCGA-HT-7606-01A-11D-2086-08	TCGA-HT-7606-10A-01D-2086-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	9734311d-3183-459b-8200-7104fba3bf64	7c7214f7-036a-4ac9-9883-1a93d9eb6f10	g.chr8:110287672A>C	ENST00000239690.4	-	7	1456	c.1082T>G	c.(1081-1083)gTa>gGa	p.V361G	NUDCD1_ENST00000427660.2_Missense_Mutation_p.V332G	NM_032869.3	NP_116258.2			NudC domain containing 1											breast(1)|kidney(1)|large_intestine(4)|lung(15)|ovary(1)|prostate(2)|skin(1)	25	all_neural(195;0.219)		OV - Ovarian serous cystadenocarcinoma(57;1.56e-12)			ATCTCCAATTACTAGCTCTGG	0.383																																																0													121.0	117.0	118.0					8																	110287672		2203	4300	6503	SO:0001583	missense	84955			AF283302	CCDS6312.1, CCDS47910.1	8q23	2005-02-07			ENSG00000120526	ENSG00000120526			24306	protein-coding gene	gene with protein product		606109				11416219	Standard	NM_032869		Approved	CML66, FLJ14991	uc003ynb.4	Q96RS6	OTTHUMG00000164931	ENST00000239690.4:c.1082T>G	8.37:g.110287672A>C	ENSP00000239690:p.Val361Gly			Missense_Mutation	SNP	ENST00000239690.4	37	CCDS6312.1	.	.	.	.	.	.	.	.	.	.	A	23.0	4.357869	0.82243	.	.	ENSG00000120526	ENST00000239690;ENST00000427660	T;T	0.78003	-1.14;-1.14	6.07	6.07	0.98685	CS-like domain (1);HSP20-like chaperone (1);	0.319686	0.33534	N	0.004802	D	0.87350	0.6155	M	0.79123	2.44	0.40632	D	0.98186	D;P;D	0.60575	0.988;0.884;0.973	D;P;P	0.63703	0.917;0.678;0.886	D	0.89214	0.3566	10	0.87932	D	0	-5.2419	15.8218	0.78654	1.0:0.0:0.0:0.0	.	274;361;332	Q96RS6-3;Q96RS6;Q96RS6-2	.;NUDC1_HUMAN;.	G	361;332	ENSP00000239690:V361G;ENSP00000410707:V332G	ENSP00000239690:V361G	V	-	2	0	NUDCD1	110356848	0.880000	0.30214	0.130000	0.21974	0.984000	0.73092	7.529000	0.81952	2.326000	0.78906	0.533000	0.62120	GTA		0.383	NUDCD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000380996.1	NM_032869		11	31	11	31
EPPK1	83481	hgsc.bcm.edu;broad.mit.edu	37	8	144940576	144940576	+	Silent	SNP	C	C	T			TCGA-HT-7606-01A-11D-2086-08	TCGA-HT-7606-10A-01D-2086-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	9734311d-3183-459b-8200-7104fba3bf64	7c7214f7-036a-4ac9-9883-1a93d9eb6f10	g.chr8:144940576C>T	ENST00000525985.1	-	2	6917	c.6846G>A	c.(6844-6846)tcG>tcA	p.S2282S				P58107	EPIPL_HUMAN	epiplakin 1	2282						cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)	poly(A) RNA binding (GO:0044822)			NS(1)|autonomic_ganglia(1)|breast(1)|central_nervous_system(5)|cervix(1)|endometrium(8)|kidney(4)|large_intestine(2)|lung(30)|ovary(2)|pancreas(1)|prostate(10)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	71	all_cancers(97;1.42e-10)|all_epithelial(106;1.99e-09)|Lung NSC(106;0.000126)|all_lung(105;0.000354)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155)		OV - Ovarian serous cystadenocarcinoma(54;2.46e-41)|Epithelial(56;2.88e-40)|all cancers(56;1.82e-35)|Colorectal(110;0.055)|BRCA - Breast invasive adenocarcinoma(115;0.105)			CCTCCTCCACCGACAGCCTCA	0.736																																																0													58.0	55.0	56.0					8																	144940576		2162	4237	6399	SO:0001819	synonymous_variant	83481			AB051895	CCDS75800.1	8q24.3	2014-09-17				ENSG00000261150			15577	protein-coding gene	gene with protein product	"""epidermal autoantigen 450K"""	607553				11278896, 15671067	Standard	NM_031308		Approved	EPIPL1	uc003zaa.1	P58107		ENST00000525985.1:c.6846G>A	8.37:g.144940576C>T			Q76E58|Q9NSU9	Silent	SNP	ENST00000525985.1	37																																																																																					0.736	EPPK1-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000382675.1	NM_031308		4	73	4	73
ZFP37	7539	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	9	115811700	115811700	+	Silent	SNP	T	T	C			TCGA-HT-7606-01A-11D-2086-08	TCGA-HT-7606-10A-01D-2086-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	9734311d-3183-459b-8200-7104fba3bf64	7c7214f7-036a-4ac9-9883-1a93d9eb6f10	g.chr9:115811700T>C	ENST00000374227.3	-	3	318	c.291A>G	c.(289-291)agA>agG	p.R97R	ZFP37_ENST00000553380.1_Silent_p.R112R|ZFP37_ENST00000555206.1_Silent_p.R98R	NM_001282515.1|NM_001282518.1	NP_001269444.1|NP_001269447.1	Q9Y6Q3	ZFP37_HUMAN	ZFP37 zinc finger protein	97	KRAB. {ECO:0000255|PROSITE- ProRule:PRU00119}.				regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|sequence-specific DNA binding transcription factor activity (GO:0003700)|zinc ion binding (GO:0008270)			NS(1)|breast(3)|cervix(1)|endometrium(1)|kidney(3)|large_intestine(6)|lung(14)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(3)|urinary_tract(3)	38						CTTGACTGGGTCTTTTCCCCT	0.403																																																0													125.0	122.0	123.0					9																	115811700		2203	4300	6503	SO:0001819	synonymous_variant	7539			AF022158	CCDS6787.1, CCDS65109.1, CCDS65110.1	9q32	2013-01-08	2012-11-27		ENSG00000136866	ENSG00000136866		"""Zinc fingers, C2H2-type"", ""-"""	12863	protein-coding gene	gene with protein product		602951	"""zinc finger protein homologous to Zfp37 in mouse"", ""zinc finger protein 37 homolog (mouse)"""				Standard	NM_001282515		Approved	ZNF906	uc004bgm.1	Q9Y6Q3	OTTHUMG00000021019	ENST00000374227.3:c.291A>G	9.37:g.115811700T>C			A0AVJ9|B4DVX4|G3V3L7|Q5T7Q4	Silent	SNP	ENST00000374227.3	37	CCDS6787.1																																																																																				0.403	ZFP37-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000055439.1	NM_003408		27	7	27	7
DDX31	64794	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	9	135522404	135522404	+	Missense_Mutation	SNP	T	T	C	rs562635248		TCGA-HT-7606-01A-11D-2086-08	TCGA-HT-7606-10A-01D-2086-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	9734311d-3183-459b-8200-7104fba3bf64	7c7214f7-036a-4ac9-9883-1a93d9eb6f10	g.chr9:135522404T>C	ENST00000372159.3	-	12	1475	c.1324A>G	c.(1324-1326)Agt>Ggt	p.S442G	DDX31_ENST00000372153.1_Missense_Mutation_p.S442G|DDX31_ENST00000438527.3_Missense_Mutation_p.S313G|DDX31_ENST00000310532.2_Missense_Mutation_p.S442G	NM_022779.7	NP_073616.6	Q9H8H2	DDX31_HUMAN	DEAD (Asp-Glu-Ala-Asp) box polypeptide 31	442	Helicase ATP-binding. {ECO:0000255|PROSITE-ProRule:PRU00541}.					nucleus (GO:0005634)	ATP binding (GO:0005524)|ATP-dependent helicase activity (GO:0008026)|poly(A) RNA binding (GO:0044822)			breast(1)|central_nervous_system(2)|endometrium(4)|kidney(3)|large_intestine(4)|lung(10)|prostate(1)|skin(1)|urinary_tract(1)	27				OV - Ovarian serous cystadenocarcinoma(145;2.67e-06)|Epithelial(140;7.61e-05)		ACAGAAATACTGACTGGATCA	0.493																																																0													98.0	88.0	92.0					9																	135522404		2203	4300	6503	SO:0001583	missense	64794			AF427339	CCDS6951.1, CCDS6952.1	9q34.2	2012-04-17	2003-06-13		ENSG00000125485	ENSG00000125485		"""DEAD-boxes"", ""Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"""	16715	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 25"""		"""DEAD/H (Asp-Glu-Ala-Asp/His) box polypeptide 31"""				Standard	NM_022779		Approved	FLJ13633, FLJ23349, FLJ14578, PPP1R25	uc004cbq.1	Q9H8H2	OTTHUMG00000020843	ENST00000372159.3:c.1324A>G	9.37:g.135522404T>C	ENSP00000361232:p.Ser442Gly		Q5K6N2|Q5K6N3|Q5K6N4|Q5VZJ4|Q5VZJ9|Q96E91|Q96NY2|Q96SX5|Q9H5K6	Missense_Mutation	SNP	ENST00000372159.3	37	CCDS6951.1	.	.	.	.	.	.	.	.	.	.	T	13.56	2.273670	0.40194	.	.	ENSG00000125485	ENST00000372159;ENST00000372155;ENST00000372153;ENST00000438527;ENST00000310532	T;T;T;T	0.42131	4.38;0.98;4.32;0.98	5.46	4.3	0.51218	DEAD-like helicase (2);	0.190725	0.64402	D	0.000004	T	0.43986	0.1272	L	0.32530	0.975	0.80722	D	1	P;P	0.52170	0.951;0.839	P;B	0.53224	0.721;0.2	T	0.34625	-0.9821	10	0.56958	D	0.05	-1.8117	11.9434	0.52913	0.0:0.0:0.1454:0.8546	.	442;442	Q9H8H2-2;Q9H8H2	.;DDX31_HUMAN	G	442;442;442;313;442	ENSP00000361232:S442G;ENSP00000361226:S442G;ENSP00000387730:S313G;ENSP00000310539:S442G	ENSP00000310539:S442G	S	-	1	0	DDX31	134512225	1.000000	0.71417	0.988000	0.46212	0.789000	0.44602	2.720000	0.47252	0.879000	0.35944	0.533000	0.62120	AGT		0.493	DDX31-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000054794.1	NM_138620		40	60	40	60
GSPT2	23708	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	X	51488448	51488448	+	Missense_Mutation	SNP	G	G	A			TCGA-HT-7606-01A-11D-2086-08	TCGA-HT-7606-10A-01D-2086-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	9734311d-3183-459b-8200-7104fba3bf64	7c7214f7-036a-4ac9-9883-1a93d9eb6f10	g.chrX:51488448G>A	ENST00000340438.4	+	1	1968	c.1726G>A	c.(1726-1728)Gtg>Atg	p.V576M		NM_018094.4	NP_060564.2	Q8IYD1	ERF3B_HUMAN	G1 to S phase transition 2	576					cell cycle (GO:0007049)|cellular protein metabolic process (GO:0044267)|gene expression (GO:0010467)|mRNA metabolic process (GO:0016071)|nuclear-transcribed mRNA catabolic process, nonsense-mediated decay (GO:0000184)|RNA metabolic process (GO:0016070)|translation (GO:0006412)|translational termination (GO:0006415)	cytosol (GO:0005829)	GTP binding (GO:0005525)|GTPase activity (GO:0003924)|poly(A) RNA binding (GO:0044822)			breast(2)|cervix(1)|endometrium(3)|kidney(2)|large_intestine(1)|lung(8)|ovary(2)|upper_aerodigestive_tract(1)	20	Ovarian(276;0.236)					ACCCCGCTTCGTGAAACAAGA	0.418																																																0													102.0	89.0	94.0					X																	51488448		2203	4300	6503	SO:0001583	missense	23708			AI285711	CCDS14336.1	Xp11.22	2008-05-14			ENSG00000189369	ENSG00000189369			4622	protein-coding gene	gene with protein product		300418				10575220	Standard	NM_018094		Approved	eRF3b, FLJ10441	uc004dpl.3	Q8IYD1	OTTHUMG00000021538	ENST00000340438.4:c.1726G>A	X.37:g.51488448G>A	ENSP00000341247:p.Val576Met		Q9H909|Q9NVY0|Q9NY44	Missense_Mutation	SNP	ENST00000340438.4	37	CCDS14336.1	.	.	.	.	.	.	.	.	.	.	G	17.01	3.278888	0.59758	.	.	ENSG00000189369	ENST00000340438;ENST00000502175	T	0.35421	1.31	4.75	4.75	0.60458	Translation elongation factor EF1A/initiation factor IF2gamma, C-terminal (1);Translation elongation factor EFTu/EF1A, C-terminal (1);	0.000000	0.85682	D	0.000000	T	0.61825	0.2378	M	0.82132	2.575	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	T	0.66666	-0.5866	10	0.87932	D	0	-9.2185	14.5557	0.68100	0.0:0.0:1.0:0.0	.	576	Q8IYD1	ERF3B_HUMAN	M	576;493	ENSP00000341247:V576M	ENSP00000341247:V576M	V	+	1	0	GSPT2	51505188	1.000000	0.71417	0.963000	0.40424	0.994000	0.84299	7.141000	0.77330	2.615000	0.88500	0.596000	0.82720	GTG		0.418	GSPT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056587.1			24	24	24	24
ZCCHC5	203430	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	X	77912924	77912924	+	Missense_Mutation	SNP	G	G	T			TCGA-HT-7606-01A-11D-2086-08	TCGA-HT-7606-10A-01D-2086-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	9734311d-3183-459b-8200-7104fba3bf64	7c7214f7-036a-4ac9-9883-1a93d9eb6f10	g.chrX:77912924G>T	ENST00000321110.1	-	2	1289	c.994C>A	c.(994-996)Ctc>Atc	p.L332I		NM_152694.2	NP_689907.1	Q8N8U3	ZCHC5_HUMAN	zinc finger, CCHC domain containing 5	332							nucleic acid binding (GO:0003676)|zinc ion binding (GO:0008270)			breast(3)|central_nervous_system(1)|cervix(1)|endometrium(2)|kidney(3)|large_intestine(6)|lung(18)|ovary(1)|prostate(1)|skin(1)	37						CCTTGGCAGAGTTGATGGATG	0.463																																																0													73.0	61.0	65.0					X																	77912924		2203	4300	6503	SO:0001583	missense	203430			AK096184	CCDS14440.1	Xq13.3	2008-02-05			ENSG00000179300	ENSG00000179300		"""Zinc fingers, CCHC domain containing"""	22997	protein-coding gene	gene with protein product						15716091, 16093683	Standard	NM_152694		Approved	FLJ38865, Mar3, Mart3, ZHC5	uc004edc.1	Q8N8U3	OTTHUMG00000021892	ENST00000321110.1:c.994C>A	X.37:g.77912924G>T	ENSP00000316794:p.Leu332Ile		B2RMZ0|Q5JQE9	Missense_Mutation	SNP	ENST00000321110.1	37	CCDS14440.1	.	.	.	.	.	.	.	.	.	.	G	6.550	0.469828	0.12461	.	.	ENSG00000179300	ENST00000321110	T	0.40476	1.03	3.2	1.42	0.22433	.	0.214672	0.20878	U	0.084053	T	0.45074	0.1324	L	0.54323	1.7	0.09310	N	1	D	0.65815	0.995	P	0.56474	0.799	T	0.24012	-1.0172	10	0.41790	T	0.15	.	4.7244	0.12935	0.3088:0.0:0.6912:0.0	.	332	Q8N8U3	ZCHC5_HUMAN	I	332	ENSP00000316794:L332I	ENSP00000316794:L332I	L	-	1	0	ZCCHC5	77799580	0.879000	0.30193	0.074000	0.20217	0.017000	0.09413	1.625000	0.37029	0.240000	0.21263	-0.322000	0.08575	CTC		0.463	ZCCHC5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057319.1	NM_152694		9	23	9	23
TENM1	10178	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	X	123525932	123525932	+	Silent	SNP	C	C	T			TCGA-HT-7606-01A-11D-2086-08	TCGA-HT-7606-10A-01D-2086-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	9734311d-3183-459b-8200-7104fba3bf64	7c7214f7-036a-4ac9-9883-1a93d9eb6f10	g.chrX:123525932C>T	ENST00000371130.3	-	27	5700	c.5637G>A	c.(5635-5637)ggG>ggA	p.G1879G	STAG2_ENST00000469481.1_Intron|TENM1_ENST00000422452.2_Silent_p.G1886G	NM_014253.3	NP_055068.2	Q9UKZ4	TEN1_HUMAN	teneurin transmembrane protein 1	1879					immune response (GO:0006955)|negative regulation of cell proliferation (GO:0008285)|nervous system development (GO:0007399)|neuropeptide signaling pathway (GO:0007218)|positive regulation of actin filament polymerization (GO:0030838)|positive regulation of filopodium assembly (GO:0051491)|positive regulation of intracellular protein transport (GO:0090316)|positive regulation of MAP kinase activity (GO:0043406)|positive regulation of peptidyl-serine phosphorylation (GO:0033138)|regulation of transcription from RNA polymerase III promoter (GO:0006359)|response to stress (GO:0006950)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|endoplasmic reticulum (GO:0005783)|extracellular region (GO:0005576)|Golgi apparatus (GO:0005794)|integral component of plasma membrane (GO:0005887)|nuclear matrix (GO:0016363)|nuclear speck (GO:0016607)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)	heparin binding (GO:0008201)|protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)										TCCAAATTTTCCCATCAGCCC	0.378																																																0													78.0	65.0	69.0					X																	123525932		2203	4300	6503	SO:0001819	synonymous_variant	10178			AF100772	CCDS14609.1, CCDS55488.1	Xq25	2012-10-02	2012-10-02	2012-10-02	ENSG00000009694	ENSG00000009694			8117	protein-coding gene	gene with protein product		300588	"""tenascin M"", ""odz, odd Oz/ten-m homolog 1 (Drosophila)"""	ODZ3, TNM, ODZ1		10331952, 10341219	Standard	NM_001163278		Approved	TEN-M1	uc010nqy.3	Q9UKZ4	OTTHUMG00000022721	ENST00000371130.3:c.5637G>A	X.37:g.123525932C>T			B2RTR5|Q5JZ17	Silent	SNP	ENST00000371130.3	37	CCDS14609.1																																																																																				0.378	TENM1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000058985.1	NM_014253		15	8	15	8
KCNJ8	3764	broad.mit.edu;ucsc.edu	37	12	21926252	21926252	+	Missense_Mutation	SNP	T	T	C			TCGA-HT-7606-01A-11D-2086-08	TCGA-HT-7606-10A-01D-2086-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	9734311d-3183-459b-8200-7104fba3bf64	7c7214f7-036a-4ac9-9883-1a93d9eb6f10	g.chr12:21926252T>C	ENST00000240662.2	-	2	644	c.299A>G	c.(298-300)gAc>gGc	p.D100G		NM_004982.3	NP_004973.1	Q15842	KCNJ8_HUMAN	potassium inwardly-rectifying channel, subfamily J, member 8	100					defense response to virus (GO:0051607)|heart development (GO:0007507)|kidney development (GO:0001822)|potassium ion import (GO:0010107)|potassium ion transport (GO:0006813)|response to exogenous dsRNA (GO:0043330)|response to lipopolysaccharide (GO:0032496)|response to pH (GO:0009268)|synaptic transmission (GO:0007268)|vasodilation (GO:0042311)	ATP-sensitive potassium channel complex (GO:0008282)|mitochondrion (GO:0005739)|myofibril (GO:0030016)|plasma membrane (GO:0005886)|sarcolemma (GO:0042383)|voltage-gated potassium channel complex (GO:0008076)	ATP binding (GO:0005524)|ATP-activated inward rectifier potassium channel activity (GO:0015272)|inward rectifier potassium channel activity (GO:0005242)			cervix(1)|endometrium(1)|kidney(2)|large_intestine(6)|lung(10)|ovary(1)|prostate(3)|skin(3)|upper_aerodigestive_tract(1)	28					Gliquidone(DB01251)|Glisoxepide(DB01289)|Glyburide(DB01016)|Levosimendan(DB00922)|Phenformin(DB00914)|Thiamylal(DB01154)|Yohimbine(DB01392)	AGCATAGATGTCCCCATGGGC	0.507											OREG0021704	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																																				0													116.0	105.0	109.0					12																	21926252		2203	4300	6503	SO:0001583	missense	3764			BC000544	CCDS8692.1	12p12.1	2011-07-05			ENSG00000121361	ENSG00000121361		"""Potassium channels"", ""Voltage-gated ion channels / Potassium channels, Inwardly rectifying"""	6269	protein-coding gene	gene with protein product		600935				8595887, 16382105	Standard	NM_004982		Approved	Kir6.1	uc001rff.4	Q15842	OTTHUMG00000169093	ENST00000240662.2:c.299A>G	12.37:g.21926252T>C	ENSP00000240662:p.Asp100Gly	752	O00657	Missense_Mutation	SNP	ENST00000240662.2	37	CCDS8692.1	.	.	.	.	.	.	.	.	.	.	T	17.46	3.395959	0.62177	.	.	ENSG00000121361	ENST00000240662;ENST00000539350;ENST00000537950	D;D	0.97114	-4.25;-4.25	4.44	4.44	0.53790	Potassium channel, inwardly rectifying, Kir, conserved region 2 (1);	0.237081	0.41500	D	0.000878	D	0.96636	0.8902	M	0.85299	2.745	0.58432	D	0.999999	B	0.31655	0.334	B	0.32805	0.153	D	0.96937	0.9685	10	0.72032	D	0.01	.	13.8791	0.63672	0.0:0.0:0.0:1.0	.	100	Q15842	IRK8_HUMAN	G	100	ENSP00000240662:D100G;ENSP00000440012:D100G	ENSP00000240662:D100G	D	-	2	0	KCNJ8	21817519	1.000000	0.71417	1.000000	0.80357	0.949000	0.60115	7.854000	0.86942	1.868000	0.54150	0.383000	0.25322	GAC		0.507	KCNJ8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402226.1	NM_004982		34	37	34	37
SMARCA4	6597	broad.mit.edu;ucsc.edu	37	19	11132434	11132434	+	Missense_Mutation	SNP	C	C	A			TCGA-HT-7606-01A-11D-2086-08	TCGA-HT-7606-10A-01D-2086-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	9734311d-3183-459b-8200-7104fba3bf64	7c7214f7-036a-4ac9-9883-1a93d9eb6f10	g.chr19:11132434C>A	ENST00000429416.3	+	20	2931	c.2650C>A	c.(2650-2652)Cac>Aac	p.H884N	SMARCA4_ENST00000344626.4_Missense_Mutation_p.H884N|SMARCA4_ENST00000444061.3_Missense_Mutation_p.H884N|SMARCA4_ENST00000541122.2_Missense_Mutation_p.H884N|SMARCA4_ENST00000450717.3_Missense_Mutation_p.H884N|SMARCA4_ENST00000413806.3_Missense_Mutation_p.H884N|SMARCA4_ENST00000589677.1_Missense_Mutation_p.H884N|SMARCA4_ENST00000358026.2_Missense_Mutation_p.H884N|SMARCA4_ENST00000590574.1_Missense_Mutation_p.H884N	NM_001128844.1	NP_001122316.1	P51532	SMCA4_HUMAN	SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily a, member 4	884	Helicase ATP-binding. {ECO:0000255|PROSITE-ProRule:PRU00541}.				aortic smooth muscle cell differentiation (GO:0035887)|ATP catabolic process (GO:0006200)|ATP-dependent chromatin remodeling (GO:0043044)|blastocyst growth (GO:0001832)|blastocyst hatching (GO:0001835)|cell morphogenesis (GO:0000902)|chromatin remodeling (GO:0006338)|definitive erythrocyte differentiation (GO:0060318)|DNA methylation on cytosine within a CG sequence (GO:0010424)|embryonic hindlimb morphogenesis (GO:0035116)|embryonic organ morphogenesis (GO:0048562)|epidermis morphogenesis (GO:0048730)|extracellular matrix organization (GO:0030198)|forebrain development (GO:0030900)|glial cell fate determination (GO:0007403)|heart trabecula formation (GO:0060347)|hindbrain development (GO:0030902)|histone H3 acetylation (GO:0043966)|keratinocyte differentiation (GO:0030216)|lens fiber cell development (GO:0070307)|liver development (GO:0001889)|methylation-dependent chromatin silencing (GO:0006346)|negative regulation of androgen receptor signaling pathway (GO:0060766)|negative regulation of cell growth (GO:0030308)|negative regulation of G1/S transition of mitotic cell cycle (GO:2000134)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription from RNA polymerase II promoter during mitosis (GO:0007070)|negative regulation of transcription, DNA-templated (GO:0045892)|neural retina development (GO:0003407)|nucleosome disassembly (GO:0006337)|positive regulation by host of viral transcription (GO:0043923)|positive regulation of DNA binding (GO:0043388)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|stem cell maintenance (GO:0019827)|vasculogenesis (GO:0001570)	extracellular space (GO:0005615)|heterochromatin (GO:0000792)|membrane (GO:0016020)|nBAF complex (GO:0071565)|npBAF complex (GO:0071564)|nuclear chromatin (GO:0000790)|nuclear euchromatin (GO:0005719)|nucleolus (GO:0005730)|nucleus (GO:0005634)|perichromatin fibrils (GO:0005726)|protein complex (GO:0043234)|SWI/SNF complex (GO:0016514)	androgen receptor binding (GO:0050681)|ATP binding (GO:0005524)|chromatin binding (GO:0003682)|DNA-dependent ATPase activity (GO:0008094)|helicase activity (GO:0004386)|lysine-acetylated histone binding (GO:0070577)|p53 binding (GO:0002039)|protein N-terminus binding (GO:0047485)|RNA polymerase II regulatory region sequence-specific DNA binding (GO:0000977)|RNA polymerase II transcription coactivator activity (GO:0001105)|Tat protein binding (GO:0030957)|transcription coactivator activity (GO:0003713)|transcription corepressor activity (GO:0003714)	p.?(1)		adrenal_gland(1)|autonomic_ganglia(1)|breast(6)|central_nervous_system(23)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(8)|large_intestine(16)|liver(4)|lung(60)|ovary(10)|pancreas(7)|prostate(3)|skin(8)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(2)	163		all_lung(6;0.0512)|Lung NSC(9;0.0568)				GGACGAAGGTCACCGCATGAA	0.622			"""F, N, Mis"""		NSCLC																																		Rec	yes		19	19p13.2	6597	"""SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily a, member 4"""		E	1	Unknown(1)	lung(1)											81.0	64.0	70.0					19																	11132434		2202	4300	6502	SO:0001583	missense	6597			D26156	CCDS12253.1, CCDS45972.1, CCDS45973.1, CCDS54217.1, CCDS54218.1	19p13.3	2014-09-17	2006-11-09		ENSG00000127616	ENSG00000127616			11100	protein-coding gene	gene with protein product	"""SNF2-like 4"", ""global transcription activator homologous sequence"", ""sucrose nonfermenting-like 4"", ""mitotic growth and transcription activator"", ""BRM/SWI2-related gene 1"", ""homeotic gene regulator"", ""nuclear protein GRB1"", ""brahma protein-like 1"", ""ATP-dependent helicase SMARCA4"""	603254		SNF2L4		8208605	Standard	NM_003072		Approved	hSNF2b, BRG1, BAF190, SNF2, SWI2, SNF2-BETA, SNF2LB, FLJ39786	uc010dxo.3	P51532	OTTHUMG00000169272	ENST00000429416.3:c.2650C>A	19.37:g.11132434C>A	ENSP00000395654:p.His884Asn		B1A8Z4|B1A8Z5|B1A8Z6|B1A8Z7|E9PBR8|O95052|Q9HBD3	Missense_Mutation	SNP	ENST00000429416.3	37	CCDS12253.1	.	.	.	.	.	.	.	.	.	.	C	25.0	4.597075	0.87055	.	.	ENSG00000127616	ENST00000429416;ENST00000358026;ENST00000421844;ENST00000344626;ENST00000541122;ENST00000444061;ENST00000450717;ENST00000413806	D;D;D;D;D;D;D	0.98280	-4.84;-4.84;-4.84;-4.84;-4.84;-4.84;-4.84	4.66	4.66	0.58398	DEAD-like helicase (2);SNF2-related (1);	0.000000	0.85682	D	0.000000	D	0.99354	0.9773	H	0.97516	4.02	0.80722	D	1	D;D;D;D;D;D;D;D	0.89917	1.0;1.0;1.0;0.999;0.996;1.0;1.0;1.0	D;D;D;D;D;D;D;D	0.91635	0.992;0.992;0.992;0.992;0.953;0.999;0.992;0.992	D	0.98427	1.0580	10	0.87932	D	0	-53.571	16.4906	0.84200	0.0:1.0:0.0:0.0	.	884;884;884;884;884;104;884;884	B1A8Z6;B1A8Z4;B1A8Z7;Q9HBD4;B1A8Z5;B4E0F1;A7E2E1;P51532	.;.;.;.;.;.;.;SMCA4_HUMAN	N	884;884;948;884;884;884;884;884	ENSP00000395654:H884N;ENSP00000350720:H884N;ENSP00000343896:H884N;ENSP00000445036:H884N;ENSP00000392837:H884N;ENSP00000397783:H884N;ENSP00000414727:H884N	ENSP00000343896:H884N	H	+	1	0	SMARCA4	10993434	1.000000	0.71417	1.000000	0.80357	0.875000	0.50365	7.651000	0.83577	2.425000	0.82216	0.655000	0.94253	CAC		0.622	SMARCA4-007	KNOWN	alternative_5_UTR|basic|CCDS	protein_coding	protein_coding	OTTHUMT00000452638.2	NM_003072		14	19	14	19
PCDH18	54510	broad.mit.edu;ucsc.edu	37	4	138452008	138452008	+	Missense_Mutation	SNP	T	T	C			TCGA-HT-7606-01A-11D-2086-08	TCGA-HT-7606-10A-01D-2086-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	9734311d-3183-459b-8200-7104fba3bf64	7c7214f7-036a-4ac9-9883-1a93d9eb6f10	g.chr4:138452008T>C	ENST00000344876.4	-	1	1621	c.1235A>G	c.(1234-1236)gAa>gGa	p.E412G	PCDH18_ENST00000507846.1_Missense_Mutation_p.E192G|PCDH18_ENST00000510305.1_Intron|PCDH18_ENST00000511115.1_Intron|PCDH18_ENST00000412923.2_Missense_Mutation_p.E412G	NM_019035.3	NP_061908.1	Q9HCL0	PCD18_HUMAN	protocadherin 18	412	Cadherin 4. {ECO:0000255|PROSITE- ProRule:PRU00043}.				brain development (GO:0007420)|homophilic cell adhesion (GO:0007156)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			NS(1)|breast(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(27)|lung(21)|ovary(2)|pancreas(4)|prostate(3)|skin(12)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	86	all_hematologic(180;0.24)					ATAATTGTTTTCATATGTCTT	0.403																																																0													108.0	117.0	114.0					4																	138452008		2203	4300	6503	SO:0001583	missense	54510			AL137471	CCDS34064.1, CCDS75193.1	4q28.3	2010-01-26			ENSG00000189184	ENSG00000189184		"""Cadherins / Protocadherins : Non-clustered"""	14268	protein-coding gene	gene with protein product		608287				10835267, 11549318	Standard	XM_005263070		Approved	KIAA1562, PCDH68L	uc003ihe.4	Q9HCL0	OTTHUMG00000161348	ENST00000344876.4:c.1235A>G	4.37:g.138452008T>C	ENSP00000355082:p.Glu412Gly		A8K7K3|B7ZKT1|Q52LS2	Missense_Mutation	SNP	ENST00000344876.4	37	CCDS34064.1	.	.	.	.	.	.	.	.	.	.	T	13.81	2.349489	0.41599	.	.	ENSG00000189184	ENST00000344876;ENST00000412923;ENST00000507846	T;T;T	0.35605	1.3;1.3;1.3	6.03	6.03	0.97812	Cadherin (4);Cadherin-like (1);	0.000000	0.44483	D	0.000449	T	0.45756	0.1358	N	0.17674	0.51	0.80722	D	1	D;B;D	0.89917	1.0;0.144;1.0	D;B;D	0.97110	1.0;0.062;1.0	T	0.37526	-0.9702	10	0.30854	T	0.27	.	16.5724	0.84622	0.0:0.0:0.0:1.0	.	192;412;412	D6RIG4;Q9HCL0-2;Q9HCL0	.;.;PCD18_HUMAN	G	412;412;192	ENSP00000355082:E412G;ENSP00000390688:E412G;ENSP00000425903:E192G	ENSP00000355082:E412G	E	-	2	0	PCDH18	138671458	1.000000	0.71417	1.000000	0.80357	0.757000	0.42996	6.243000	0.72384	2.313000	0.78055	0.455000	0.32223	GAA		0.403	PCDH18-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000364614.1	NM_019035		3	26	3	26
RBM41	55285	broad.mit.edu;hgsc.bcm.edu	37	X	106331986	106331986	+	Frame_Shift_Del	DEL	C	C	-			TCGA-HT-7606-01A-11D-2086-08	TCGA-HT-7606-10A-01D-2086-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	9734311d-3183-459b-8200-7104fba3bf64	7c7214f7-036a-4ac9-9883-1a93d9eb6f10	g.chrX:106331986delC	ENST00000372479.3	-	5	637	c.607delG	c.(607-609)gaafs	p.E204fs	RBM41_ENST00000372487.1_Frame_Shift_Del_p.E204fs|RBM41_ENST00000203616.8_Frame_Shift_Del_p.E228fs	NM_018301.3	NP_060771.3	Q96IZ5	RBM41_HUMAN	RNA binding motif protein 41	204							nucleotide binding (GO:0000166)|RNA binding (GO:0003723)			breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(2)|lung(5)|ovary(1)|upper_aerodigestive_tract(1)	13						TGAAACTCTTCAAGACGTTTT	0.428																																																0													108.0	94.0	99.0					X																	106331986		2203	4300	6503	SO:0001589	frameshift_variant	55285			BC006986	CCDS14526.1, CCDS55472.1	Xq22.3	2013-02-12			ENSG00000089682	ENSG00000089682		"""RNA binding motif (RRM) containing"""	25617	protein-coding gene	gene with protein product						12477932	Standard	NM_001171080		Approved	FLJ11016	uc004emz.3	Q96IZ5	OTTHUMG00000022156	ENST00000372479.3:c.607delG	X.37:g.106331986delC	ENSP00000361557:p.Glu204fs		Q5JSN7|Q5JSN8|Q9H8F7|Q9NV04	Frame_Shift_Del	DEL	ENST00000372479.3	37	CCDS14526.1																																																																																				0.428	RBM41-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000057819.1	NM_018301		15	26	15	26
