#version 2.4
## 
## Oncotator v1.8.0.0 | Flat File Reference hg19 | GENCODE v19 EFFECT | UniProt_AAxform 2014_12 | ClinVar 12.03.20 | ESP 6500SI-V2 | ORegAnno UCSC Track | dbSNP build 142 | CCLE_By_GP 09292010 | COSMIC v62_291112 | 1000gp3 20130502 | UniProt_AA 2014_12 | dbNSFP v2.4 | ESP 6500SI-V2 | COSMIC_FusionGenes v62_291112 | gencode_xref_refseq metadata_v19 | CCLE_By_Gene 09292010 | ACHILLES_Lineage_Results 110303 | CGC full_2012-03-15 | UniProt 2014_12 | HumanDNARepairGenes 20110905 | HGNC Sept172014 | COSMIC_Tissue 291112 | Familial_Cancer_Genes 20110905 | TUMORScape 20100104 | Ensembl ICGC MUCOPA | TCGAScape 110405 | MutSig Published Results 20110905 
Hugo_Symbol	Entrez_Gene_Id	Center	NCBI_Build	Chromosome	Start_position	End_position	Strand	Variant_Classification	Variant_Type	Reference_Allele	Tumor_Seq_Allele1	Tumor_Seq_Allele2	dbSNP_RS	dbSNP_Val_Status	Tumor_Sample_Barcode	Matched_Norm_Sample_Barcode	Match_Norm_Seq_Allele1	Match_Norm_Seq_Allele2	Tumor_Validation_Allele1	Tumor_Validation_Allele2	Match_Norm_Validation_Allele1	Match_Norm_Validation_Allele2	Verification_Status	Validation_Status	Mutation_Status	Sequencing_Phase	Sequence_Source	Validation_Method	Score	BAM_file	Sequencer	Tumor_Sample_UUID	Matched_Norm_Sample_UUID	Genome_Change	Annotation_Transcript	Transcript_Strand	Transcript_Exon	Transcript_Position	cDNA_Change	Codon_Change	Protein_Change	Other_Transcripts	Refseq_mRNA_Id	Refseq_prot_Id	SwissProt_acc_Id	SwissProt_entry_Id	Description	UniProt_AApos	UniProt_Region	UniProt_Site	UniProt_Natural_Variations	UniProt_Experimental_Info	GO_Biological_Process	GO_Cellular_Component	GO_Molecular_Function	COSMIC_overlapping_mutations	COSMIC_fusion_genes	COSMIC_tissue_types_affected	COSMIC_total_alterations_in_gene	Tumorscape_Amplification_Peaks	Tumorscape_Deletion_Peaks	TCGAscape_Amplification_Peaks	TCGAscape_Deletion_Peaks	DrugBank	ref_context	gc_content	CCLE_ONCOMAP_overlapping_mutations	CCLE_ONCOMAP_total_mutations_in_gene	CGC_Mutation_Type	CGC_Translocation_Partner	CGC_Tumor_Types_Somatic	CGC_Tumor_Types_Germline	CGC_Other_Diseases	DNARepairGenes_Role	FamilialCancerDatabase_Syndromes	MUTSIG_Published_Results	OREGANNO_ID	OREGANNO_Values	i_1000gp3_AA	i_1000gp3_AC	i_1000gp3_AF	i_1000gp3_AFR_AF	i_1000gp3_AMR_AF	i_1000gp3_AN	i_1000gp3_CIEND	i_1000gp3_CIPOS	i_1000gp3_CS	i_1000gp3_DP	i_1000gp3_EAS_AF	i_1000gp3_END	i_1000gp3_EUR_AF	i_1000gp3_IMPRECISE	i_1000gp3_MC	i_1000gp3_MEINFO	i_1000gp3_MEND	i_1000gp3_MLEN	i_1000gp3_MSTART	i_1000gp3_NS	i_1000gp3_SAS_AF	i_1000gp3_SVLEN	i_1000gp3_SVTYPE	i_1000gp3_TSD	i_AAChange	i_ACHILLES_Lineage_Results_Top_Genes	i_CGC_Cancer Germline Mut	i_CGC_Cancer Molecular Genetics	i_CGC_Cancer Somatic Mut	i_CGC_Cancer Syndrome	i_CGC_Chr	i_CGC_Chr Band	i_CGC_GeneID	i_CGC_Name	i_CGC_Other Germline Mut	i_CGC_Tissue Type	i_COSMIC_Codon	i_COSMIC_Gene	i_COSMIC_n_overlapping_mutations	i_COSMIC_overlapping_mutation_descriptions	i_COSMIC_overlapping_primary_sites	i_ChromChange	i_Chromosome_hg18	i_ClinVar_ASSEMBLY	i_ClinVar_HGMD_ID	i_ClinVar_SYM	i_ClinVar_TYPE	i_ClinVar_rs	i_Drug_Target	i_ESP_AA	i_ESP_AAC	i_ESP_AA_AC	i_ESP_AA_AGE	i_ESP_AA_GTC	i_ESP_AvgAAsampleReadDepth	i_ESP_AvgEAsampleReadDepth	i_ESP_AvgSampleReadDepth	i_ESP_CA	i_ESP_CDP	i_ESP_CG	i_ESP_CP	i_ESP_Chromosome	i_ESP_DBSNP	i_ESP_DP	i_ESP_EA_AC	i_ESP_EA_AGE	i_ESP_EA_GTC	i_ESP_EXOME_CHIP	i_ESP_FG	i_ESP_GL	i_ESP_GM	i_ESP_GS	i_ESP_GTC	i_ESP_GTS	i_ESP_GWAS_PUBMED	i_ESP_MAF	i_ESP_PH	i_ESP_PP	i_ESP_Position	i_ESP_TAC	i_ESP_TotalAAsamplesCovered	i_ESP_TotalEAsamplesCovered	i_ESP_TotalSamplesCovered	i_End_position_hg18	i_Ensembl_so_accession	i_Ensembl_so_term	i_Entrez_Gene_Id	i_Exon	i_Familial_Cancer_Genes_Reference	i_Familial_Cancer_Genes_Synonym	i_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_Start_position_hg18	i_TranscriptID	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
GAL3ST4	79690	hgsc.bcm.edu	37	7	99758239	99758239	+	Missense_Mutation	SNP	G	G	A			TCGA-AG-3580-01A-01W-0831-10	TCGA-AG-3580-10A-01W-0831-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454			SOLID	TCGA-AG-3580-01A-01W-0831-10	TCGA-AG-3580-10A-01W-0831-10	g.chr7:99758239G>A	ENST00000360039.4	-	4	1165	c.773C>T	c.(772-774)gCc>gTc	p.A258V	C7orf43_ENST00000457641.1_5'Flank|GAL3ST4_ENST00000413800.1_Missense_Mutation_p.A258V|GAL3ST4_ENST00000426974.2_Missense_Mutation_p.A196V|GAL3ST4_ENST00000411994.1_Missense_Mutation_p.P157S|GAL3ST4_ENST00000423751.1_Missense_Mutation_p.P157S|C7orf43_ENST00000316937.3_5'Flank|C7orf43_ENST00000419841.1_5'Flank	NM_024637.4	NP_078913.3	Q96RP7	G3ST4_HUMAN	galactose-3-O-sulfotransferase 4	258					cell-cell signaling (GO:0007267)|glycoprotein metabolic process (GO:0009100)|oligosaccharide metabolic process (GO:0009311)|proteoglycan biosynthetic process (GO:0030166)|sulfur compound metabolic process (GO:0006790)	extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|membrane (GO:0016020)	3'-phosphoadenosine 5'-phosphosulfate binding (GO:0050656)|galactose 3-O-sulfotransferase activity (GO:0050694)|galactosylceramide sulfotransferase activity (GO:0001733)|proteoglycan sulfotransferase activity (GO:0050698)	p.A258V(1)		cervix(1)|endometrium(3)|kidney(1)|large_intestine(6)|lung(8)|ovary(5)|prostate(1)|upper_aerodigestive_tract(1)	26	Lung NSC(181;0.0181)|all_lung(186;0.0284)|Esophageal squamous(72;0.0439)					ATGGATGAGGGCATTGGGATT	0.552																																					p.A258V												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C773T	7						.						116.0	122.0	120.0					7																	99758239		2203	4294	6497	99596175	SO:0001583	missense	79690	exon4			AF316113	CCDS5688.1	7q22.1	2007-04-02			ENSG00000197093	ENSG00000197093		"""Sulfotransferases, membrane-bound"""	24145	protein-coding gene	gene with protein product		608235				11333265	Standard	NM_024637		Approved	FLJ12116	uc003utu.3	Q96RP7	OTTHUMG00000154885	ENST00000360039.4:c.773C>T	7.37:g.99758239G>A	ENSP00000353142:p.Ala258Val		99596175	NM_024637	A4D2A8|B4DWL8|D6W5U5|Q8N3P7|Q8WZ17|Q96E33|Q9HA78	Missense_Mutation	SNP	ENST00000360039.4	37	CCDS5688.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	10.34|10.34	1.324023|1.324023	0.24080|0.24080	.|.	.|.	ENSG00000197093|ENSG00000197093	ENST00000413800;ENST00000360039;ENST00000426974|ENST00000423751;ENST00000411994	T;T;T|.	0.36157|.	1.39;1.39;1.27|.	4.45|4.45	2.58|2.58	0.30949|0.30949	.|.	3.209450|.	0.01787|.	U|.	0.032105|.	T|T	0.32585|0.32585	0.0834|0.0834	N|N	0.14661|0.14661	0.345|0.345	0.25610|0.25610	N|N	0.986505|0.986505	B;B|.	0.30763|.	0.294;0.22|.	B;B|.	0.24974|.	0.057;0.036|.	T|T	0.30736|0.30736	-0.9968|-0.9968	10|6	0.25106|0.87932	T|D	0.35|0	-0.0676|-0.0676	12.3731|12.3731	0.55265|0.55265	0.0:0.3248:0.6752:0.0|0.0:0.3248:0.6752:0.0	.|.	196;258|.	B4DWL8;Q96RP7|.	.;G3ST4_HUMAN|.	V|S	258;258;196|157	ENSP00000400451:A258V;ENSP00000353142:A258V;ENSP00000398304:A196V|.	ENSP00000353142:A258V|ENSP00000414733:P157S	A|P	-|-	2|1	0|0	GAL3ST4|GAL3ST4	99596175|99596175	0.875000|0.875000	0.30112|0.30112	0.892000|0.892000	0.35008|0.35008	0.266000|0.266000	0.26442|0.26442	1.173000|1.173000	0.31920|0.31920	0.474000|0.474000	0.27392|0.27392	0.511000|0.511000	0.50034|0.50034	GCC|CCC		0.552	GAL3ST4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000337495.2	NM_024637	
EPHA1	2041	hgsc.bcm.edu	37	7	143095154	143095154	+	Missense_Mutation	SNP	G	G	A			TCGA-AG-3580-01A-01W-0831-10	TCGA-AG-3580-10A-01W-0831-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454			SOLID	TCGA-AG-3580-01A-01W-0831-10	TCGA-AG-3580-10A-01W-0831-10	g.chr7:143095154G>A	ENST00000275815.3	-	8	1560	c.1474C>T	c.(1474-1476)Cgg>Tgg	p.R492W		NM_005232.4	NP_005223.4	P21709	EPHA1_HUMAN	EPH receptor A1	492	Fibronectin type-III 2. {ECO:0000255|PROSITE-ProRule:PRU00316}.		R -> Q (in dbSNP:rs11768549). {ECO:0000269|PubMed:17344846}.		activation of Rho GTPase activity (GO:0032862)|angiogenesis (GO:0001525)|cell surface receptor signaling pathway (GO:0007166)|negative regulation of cell migration (GO:0030336)|negative regulation of protein kinase activity (GO:0006469)|peptidyl-tyrosine phosphorylation (GO:0018108)|positive regulation of angiogenesis (GO:0045766)|positive regulation of cell migration (GO:0030335)|positive regulation of cell proliferation (GO:0008284)|positive regulation of cell-matrix adhesion (GO:0001954)|positive regulation of stress fiber assembly (GO:0051496)|protein autophosphorylation (GO:0046777)|regulation of Rac GTPase activity (GO:0032314)|substrate adhesion-dependent cell spreading (GO:0034446)	integral component of plasma membrane (GO:0005887)	ATP binding (GO:0005524)|protein kinase activity (GO:0004672)|protein kinase binding (GO:0019901)|transmembrane-ephrin receptor activity (GO:0005005)	p.R492W(1)		NS(1)|breast(1)|central_nervous_system(1)|endometrium(4)|kidney(3)|large_intestine(11)|lung(21)|ovary(4)|skin(1)|stomach(1)|urinary_tract(3)	51	Melanoma(164;0.205)	Myeloproliferative disorder(862;0.0255)				ATCTGGTACCGTTCTTCATCC	0.572																																					p.R492W												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C1474T	7						.						118.0	102.0	108.0					7																	143095154		2203	4300	6503	142805276	SO:0001583	missense	2041	exon8			M18391	CCDS5884.1	7q32-q36	2013-02-11	2004-10-28		ENSG00000146904	ENSG00000146904	2.7.10.1	"""EPH receptors"", ""Sterile alpha motif (SAM) domain containing"", ""Fibronectin type III domain containing"""	3385	protein-coding gene	gene with protein product		179610	"""EphA1"""	EPHT, EPHT1		9267020	Standard	NM_005232		Approved	EPH	uc003wcz.3	P21709	OTTHUMG00000155894	ENST00000275815.3:c.1474C>T	7.37:g.143095154G>A	ENSP00000275815:p.Arg492Trp		142805276	NM_005232	A1L3V3|B5A966|B5A967|Q15405	Missense_Mutation	SNP	ENST00000275815.3	37	CCDS5884.1	.	.	.	.	.	.	.	.	.	.	G	4.133	0.022909	0.08006	.	.	ENSG00000146904	ENST00000275815	T	0.58210	0.35	4.52	-5.3	0.02738	Fibronectin, type III (4);Immunoglobulin-like fold (1);	0.240490	0.28332	N	0.015722	T	0.17619	0.0423	N	0.02011	-0.69	0.22156	N	0.999323	B	0.09022	0.002	B	0.01281	0.0	T	0.08310	-1.0728	10	0.54805	T	0.06	.	4.7865	0.13227	0.354:0.0:0.2565:0.3895	.	492	P21709	EPHA1_HUMAN	W	492	ENSP00000275815:R492W	ENSP00000275815:R492W	R	-	1	2	EPHA1	142805276	0.212000	0.23540	0.725000	0.30721	0.011000	0.07611	0.100000	0.15231	-0.742000	0.04790	-1.827000	0.00596	CGG		0.572	EPHA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000342154.1		
NINL	22981	hgsc.bcm.edu	37	20	25456725	25456725	+	Missense_Mutation	SNP	C	C	T	rs199894600		TCGA-AG-3580-01A-01W-0831-10	TCGA-AG-3580-10A-01W-0831-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454			SOLID	TCGA-AG-3580-01A-01W-0831-10	TCGA-AG-3580-10A-01W-0831-10	g.chr20:25456725C>T	ENST00000278886.6	-	17	3275	c.3202G>A	c.(3202-3204)Gtc>Atc	p.V1068I	NINL_ENST00000422516.1_Intron	NM_025176.4	NP_079452.3	Q9Y2I6	NINL_HUMAN	ninein-like	1068					G2/M transition of mitotic cell cycle (GO:0000086)|mitotic cell cycle (GO:0000278)	cytosol (GO:0005829)|microtubule (GO:0005874)	calcium ion binding (GO:0005509)	p.V1068I(1)		breast(2)|central_nervous_system(1)|cervix(1)|endometrium(6)|kidney(1)|large_intestine(13)|lung(25)|ovary(2)|pancreas(1)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	57						GCCCGGACGACGTCTTCCAGA	0.468																																					p.V1068I												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G3202A	20						.	C	ILE/VAL	0,4406		0,0,2203	122.0	105.0	111.0		3202	-1.7	0.0	20		111	1,8599	1.2+/-3.3	0,1,4299	no	missense	NINL	NM_025176.4	29	0,1,6502	TT,TC,CC		0.0116,0.0,0.0077	possibly-damaging	1068/1383	25456725	1,13005	2203	4300	6503	25404725	SO:0001583	missense	22981	exon17				CCDS33452.1	20p11.22-p11.1	2013-01-10			ENSG00000101004	ENSG00000101004		"""EF-hand domain containing"""	29163	protein-coding gene	gene with protein product	"""ninein-like protein"""	609580				10231032	Standard	XM_005260678		Approved	KIAA0980, NLP	uc002wux.1	Q9Y2I6	OTTHUMG00000032127	ENST00000278886.6:c.3202G>A	20.37:g.25456725C>T	ENSP00000278886:p.Val1068Ile		25404725	NM_025176	A6NJN0|B3V9H6|B7Z1V8|Q5JYP0|Q8NE38|Q9NQE3	Missense_Mutation	SNP	ENST00000278886.6	37	CCDS33452.1	.	.	.	.	.	.	.	.	.	.	C	5.566	0.289211	0.10513	0.0	1.16E-4	ENSG00000101004	ENST00000278886	T	0.05649	3.41	4.85	-1.74	0.08056	.	0.693416	0.13792	N	0.362420	T	0.04272	0.0118	L	0.50333	1.59	0.20975	N	0.999811	P	0.36282	0.546	B	0.26864	0.074	T	0.39840	-0.9594	10	0.23891	T	0.37	-4.8659	5.271	0.15624	0.1429:0.3365:0.0:0.5207	.	1068	Q9Y2I6	NINL_HUMAN	I	1068	ENSP00000278886:V1068I	ENSP00000278886:V1068I	V	-	1	0	NINL	25404725	0.001000	0.12720	0.009000	0.14445	0.008000	0.06430	-0.221000	0.09202	-0.288000	0.09051	-0.258000	0.10820	GTC		0.468	NINL-007	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000078445.3	NM_025176	
CECR1	51816	hgsc.bcm.edu	37	22	17690464	17690464	+	Missense_Mutation	SNP	G	G	A	rs151283756	byFrequency	TCGA-AG-3580-01A-01W-0831-10	TCGA-AG-3580-10A-01W-0831-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454			SOLID	TCGA-AG-3580-01A-01W-0831-10	TCGA-AG-3580-10A-01W-0831-10	g.chr22:17690464G>A	ENST00000399839.1	-	2	374	c.104C>T	c.(103-105)gCg>gTg	p.A35V	CECR1_ENST00000262607.3_Missense_Mutation_p.A35V|CECR1_ENST00000449907.2_5'UTR|CECR1_ENST00000399837.2_Missense_Mutation_p.A35V	NM_001282227.1|NM_001282228.1	NP_001269156.1|NP_001269157.1	Q9NZK5	CECR1_HUMAN	cat eye syndrome chromosome region, candidate 1	35	Dimerization.				adenosine catabolic process (GO:0006154)|hypoxanthine salvage (GO:0043103)|inosine biosynthetic process (GO:0046103)|multicellular organismal development (GO:0007275)	extracellular space (GO:0005615)	adenosine deaminase activity (GO:0004000)|adenosine receptor binding (GO:0031685)|growth factor activity (GO:0008083)|heparin binding (GO:0008201)|protein homodimerization activity (GO:0042803)|proteoglycan binding (GO:0043394)|zinc ion binding (GO:0008270)	p.A35V(2)		endometrium(1)|kidney(2)|large_intestine(6)|liver(1)|lung(10)|ovary(2)|prostate(2)|stomach(1)	25		all_epithelial(15;0.0152)|Lung NSC(13;0.0875)|all_lung(157;0.106)				CAACAGATGCGCCCGTGTTTC	0.552																																					p.A35V												.	.	2	Substitution - Missense(2)	large_intestine(1)|lung(1)	c.C104T	22						.	G	VAL/ALA	0,4406		0,0,2203	49.0	49.0	49.0		104	-1.8	0.0	22	dbSNP_134	49	4,8596	3.7+/-12.6	0,4,4296	yes	missense	CECR1	NM_017424.2	64	0,4,6499	AA,AG,GG		0.0465,0.0,0.0308	benign	35/512	17690464	4,13002	2203	4300	6503	16070464	SO:0001583	missense	51816	exon1			AF190746	CCDS13742.1, CCDS13743.1, CCDS63395.1, CCDS74809.1	22q11.2	2008-02-22			ENSG00000093072	ENSG00000093072			1839	protein-coding gene	gene with protein product		607575		IDGFL		10756095	Standard	NM_001282225		Approved	ADGF	uc002zmk.1	Q9NZK5	OTTHUMG00000030726	ENST00000399839.1:c.104C>T	22.37:g.17690464G>A	ENSP00000382733:p.Ala35Val		16070464	NM_017424	A8K9H4|Q6ICF1|Q86UB6|Q8NCJ2|Q96K41	Missense_Mutation	SNP	ENST00000399839.1	37	CCDS13742.1	.	.	.	.	.	.	.	.	.	.	G	10.58	1.390416	0.25118	0.0	4.65E-4	ENSG00000093072	ENST00000399839;ENST00000262607;ENST00000399837;ENST00000543038;ENST00000441548	T;T;T	0.47177	0.85;0.85;0.85	4.76	-1.79	0.07932	Adenosine/AMP deaminase N-terminal (1);	0.780754	0.12113	N	0.498308	T	0.26122	0.0637	N	0.19112	0.55	0.09310	N	0.999999	B	0.26445	0.149	B	0.12156	0.007	T	0.07271	-1.0781	10	0.44086	T	0.13	.	6.2898	0.21053	0.0:0.2281:0.2995:0.4724	.	35	Q9NZK5	CECR1_HUMAN	V	35	ENSP00000382733:A35V;ENSP00000262607:A35V;ENSP00000382731:A35V	ENSP00000262607:A35V	A	-	2	0	CECR1	16070464	0.000000	0.05858	0.000000	0.03702	0.005000	0.04900	0.105000	0.15333	-0.861000	0.04094	-0.268000	0.10319	GCG		0.552	CECR1-002	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000316079.1		
APOC2	344	hgsc.bcm.edu	37	19	45452096	45452096	+	Missense_Mutation	SNP	C	C	T			TCGA-AG-3580-01A-01W-0831-10	TCGA-AG-3580-10A-01W-0831-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454			SOLID	TCGA-AG-3580-01A-01W-0831-10	TCGA-AG-3580-10A-01W-0831-10	g.chr19:45452096C>T	ENST00000590360.1	+	3	316	c.194C>T	c.(193-195)cCc>cTc	p.P65L	APOC4-APOC2_ENST00000589057.1_Missense_Mutation_p.P142L|APOC2_ENST00000592257.1_Silent_p.A44A|APOC4_ENST00000419266.2_3'UTR|APOC2_ENST00000252490.4_Missense_Mutation_p.P65L|APOC2_ENST00000591597.1_Intron|APOC2_ENST00000585786.1_Missense_Mutation_p.P65L			P02655	APOC2_HUMAN	apolipoprotein C-II	65	Lipoprotein lipase cofactor.				cholesterol efflux (GO:0033344)|cholesterol homeostasis (GO:0042632)|chylomicron remnant clearance (GO:0034382)|chylomicron remodeling (GO:0034371)|high-density lipoprotein particle clearance (GO:0034384)|lipid catabolic process (GO:0016042)|lipoprotein metabolic process (GO:0042157)|negative regulation of catalytic activity (GO:0043086)|negative regulation of cholesterol transport (GO:0032375)|negative regulation of lipid metabolic process (GO:0045833)|negative regulation of receptor-mediated endocytosis (GO:0048261)|negative regulation of very-low-density lipoprotein particle clearance (GO:0010916)|phospholipid efflux (GO:0033700)|phototransduction, visible light (GO:0007603)|positive regulation of fatty acid biosynthetic process (GO:0045723)|positive regulation of lipoprotein lipase activity (GO:0051006)|positive regulation of phospholipase activity (GO:0010518)|positive regulation of phospholipid catabolic process (GO:0060697)|positive regulation of triglyceride catabolic process (GO:0010898)|positive regulation of very-low-density lipoprotein particle remodeling (GO:0010902)|retinoid metabolic process (GO:0001523)|reverse cholesterol transport (GO:0043691)|small molecule metabolic process (GO:0044281)|triglyceride homeostasis (GO:0070328)|triglyceride-rich lipoprotein particle remodeling (GO:0034370)|very-low-density lipoprotein particle remodeling (GO:0034372)	chylomicron (GO:0042627)|early endosome (GO:0005769)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|intermediate-density lipoprotein particle (GO:0034363)|low-density lipoprotein particle (GO:0034362)|spherical high-density lipoprotein particle (GO:0034366)|very-low-density lipoprotein particle (GO:0034361)	lipase inhibitor activity (GO:0055102)|lipid binding (GO:0008289)|lipoprotein lipase activator activity (GO:0060230)|phospholipase activator activity (GO:0016004)|phospholipase binding (GO:0043274)|protein homodimerization activity (GO:0042803)	p.P65L(1)		kidney(1)|large_intestine(1)|liver(1)|lung(3)	6	Lung NSC(12;0.00858)|all_lung(12;0.0197)	Ovarian(192;0.0728)|all_neural(266;0.112)		OV - Ovarian serous cystadenocarcinoma(262;0.00327)|Epithelial(262;0.174)		ACATACCTGCCCGCTGTAGAT	0.582																																					p.P65L												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C194T	19						.						88.0	95.0	93.0					19																	45452096		2203	4300	6503	50143936	SO:0001583	missense	344	exon3			X00568	CCDS12650.1	19q13.2	2013-01-24			ENSG00000234906	ENSG00000234906		"""Apolipoproteins"""	609	protein-coding gene	gene with protein product		608083					Standard	NM_000483		Approved			P02655	OTTHUMG00000180847	ENST00000590360.1:c.194C>T	19.37:g.45452096C>T	ENSP00000466775:p.Pro65Leu		50143936	NM_000483	C0JYY4|Q9BS39|Q9UDE3|Q9UNK3	Missense_Mutation	SNP	ENST00000590360.1	37	CCDS12650.1	.	.	.	.	.	.	.	.	.	.	C	10.15	1.272478	0.23221	.	.	ENSG00000234906	ENST00000252490	T	0.80909	-1.43	4.29	-2.65	0.06095	ApoC-II domain (1);	1.128180	0.06943	U	0.813166	T	0.68265	0.2982	L	0.60455	1.87	0.09310	N	1	B	0.25441	0.126	B	0.22601	0.04	T	0.48163	-0.9059	10	0.11485	T	0.65	-3.2707	1.2448	0.01970	0.2772:0.3998:0.143:0.1801	.	65	P02655	APOC2_HUMAN	L	65	ENSP00000252490:P65L	ENSP00000252490:P65L	P	+	2	0	APOC2	50143936	0.000000	0.05858	0.000000	0.03702	0.015000	0.08874	0.134000	0.15932	-0.557000	0.06126	-0.781000	0.03364	CCC		0.582	APOC2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000453261.1	NM_000483	
CACNG8	59283	hgsc.bcm.edu	37	19	54485410	54485410	+	Silent	SNP	G	G	A			TCGA-AG-3580-01A-01W-0831-10	TCGA-AG-3580-10A-01W-0831-10	G	G	.	.	.	.	Unknown	Unknown	Somatic	Phase_I	Capture	.			SOLID	TCGA-AG-3580-01A-01W-0831-10	TCGA-AG-3580-10A-01W-0831-10	g.chr19:54485410G>A	ENST00000270458.2	+	4	688	c.585G>A	c.(583-585)gaG>gaA	p.E195E	MIR935_ENST00000401179.1_RNA	NM_031895.5	NP_114101	Q8WXS5	CCG8_HUMAN	calcium channel, voltage-dependent, gamma subunit 8	195					calcium ion transport (GO:0006816)|regulation of alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity (GO:2000311)|synaptic transmission (GO:0007268)	alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex (GO:0032281)|cell junction (GO:0030054)|endocytic vesicle membrane (GO:0030666)|plasma membrane (GO:0005886)|postsynaptic density (GO:0014069)|postsynaptic membrane (GO:0045211)|voltage-gated calcium channel complex (GO:0005891)	voltage-gated calcium channel activity (GO:0005245)	p.E195E(1)		kidney(1)|large_intestine(3)|lung(8)|urinary_tract(1)	13	all_cancers(19;0.0385)|all_epithelial(19;0.0207)|all_lung(19;0.145)|Lung NSC(19;0.168)|Ovarian(34;0.19)			GBM - Glioblastoma multiforme(134;0.162)		GGGACGAGGAGAAGAAAAACC	0.627																																					p.E195E												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.G585A	19						.						52.0	42.0	46.0					19																	54485410		2202	4299	6501	59177222	SO:0001819	synonymous_variant	59283	exon4			AF288388	CCDS33104.1	19q13.4	2008-05-02			ENSG00000142408	ENSG00000142408		"""Calcium channel subunits"""	13628	protein-coding gene	gene with protein product		606900				11170751	Standard	NM_031895		Approved		uc002qcs.2	Q8WXS5	OTTHUMG00000064908	ENST00000270458.2:c.585G>A	19.37:g.54485410G>A			59177222	NM_031895	Q9BXT0|Q9BY23	Silent	SNP	ENST00000270458.2	37	CCDS33104.1																																																																																				0.627	CACNG8-001	KNOWN	non_ATG_start|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000139361.3		
DLC1	10395	hgsc.bcm.edu	37	8	12957275	12957275	+	Silent	SNP	G	G	A			TCGA-AG-3580-01A-01W-0831-10	TCGA-AG-3580-10A-01W-0831-10	G	G	.	.	.	.	Unknown	Unknown	Somatic	Phase_I	Capture	.			SOLID	TCGA-AG-3580-01A-01W-0831-10	TCGA-AG-3580-10A-01W-0831-10	g.chr8:12957275G>A	ENST00000276297.4	-	9	2980	c.2571C>T	c.(2569-2571)agC>agT	p.S857S	DLC1_ENST00000520226.1_Silent_p.S346S|DLC1_ENST00000358919.2_Silent_p.S420S|DLC1_ENST00000512044.2_Silent_p.S454S	NM_182643.2	NP_872584.2	Q96QB1	RHG07_HUMAN	DLC1 Rho GTPase activating protein	857	Focal adhesion-targeting (FAT).				actin cytoskeleton organization (GO:0030036)|activation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0006919)|apoptotic process (GO:0006915)|focal adhesion assembly (GO:0048041)|forebrain development (GO:0030900)|heart morphogenesis (GO:0003007)|hindbrain morphogenesis (GO:0021575)|negative regulation of cell migration (GO:0030336)|negative regulation of cell proliferation (GO:0008285)|negative regulation of Rho protein signal transduction (GO:0035024)|negative regulation of stress fiber assembly (GO:0051497)|neural tube closure (GO:0001843)|positive regulation of execution phase of apoptosis (GO:1900119)|positive regulation of protein dephosphorylation (GO:0035307)|positive regulation of Rho GTPase activity (GO:0032321)|regulation of actin cytoskeleton organization (GO:0032956)|regulation of cell shape (GO:0008360)|regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)	caveola (GO:0005901)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|focal adhesion (GO:0005925)|nucleus (GO:0005634)	lipid binding (GO:0008289)|Rho GTPase activator activity (GO:0005100)|SH2 domain binding (GO:0042169)	p.S857S(1)		NS(2)|breast(2)|cervix(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(39)|lung(32)|ovary(4)|pancreas(2)|prostate(4)|skin(2)|stomach(2)|upper_aerodigestive_tract(5)|urinary_tract(1)	110						TGGGGCTGTCGCTACTGTTTT	0.582																																					p.S857S												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C2571T	8						.						68.0	61.0	63.0					8																	12957275		2203	4300	6503	13001646	SO:0001819	synonymous_variant	10395	exon9			AF035119	CCDS5989.1, CCDS5990.1, CCDS5991.1, CCDS5991.2, CCDS55201.1	8p22	2014-06-20	2014-06-20		ENSG00000164741	ENSG00000164741		"""Rho GTPase activating proteins"", ""StAR-related lipid transfer (START) domain containing"""	2897	protein-coding gene	gene with protein product	"""StAR-related lipid transfer (START) domain containing 12"""	604258	"""deleted in liver cancer 1"""			9605766, 11214970	Standard	NM_182643		Approved	HP, ARHGAP7, STARD12, DLC-1, p122-RhoGAP	uc003wwm.2	Q96QB1	OTTHUMG00000090825	ENST00000276297.4:c.2571C>T	8.37:g.12957275G>A			13001646	NM_182643	B4DR10|B8PTI0|E9PDZ8|E9PF76|E9PGY9|O14868|O43199|Q7Z5R8|Q86UC6|Q9C0E0|Q9H7A2	Silent	SNP	ENST00000276297.4	37	CCDS5989.1																																																																																				0.582	DLC1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000207632.2	NM_182643, NM_006094	
VPS13B	157680	hgsc.bcm.edu	37	8	100050684	100050684	+	Missense_Mutation	SNP	C	C	T			TCGA-AG-3580-01A-01W-0831-10	TCGA-AG-3580-10A-01W-0831-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454			SOLID	TCGA-AG-3580-01A-01W-0831-10	TCGA-AG-3580-10A-01W-0831-10	g.chr8:100050684C>T	ENST00000358544.2	+	3	292	c.181C>T	c.(181-183)Cat>Tat	p.H61Y	VPS13B_ENST00000395996.1_Missense_Mutation_p.H61Y|VPS13B_ENST00000441350.2_Missense_Mutation_p.H61Y|VPS13B_ENST00000355155.1_Missense_Mutation_p.H61Y|VPS13B_ENST00000357162.2_Missense_Mutation_p.H61Y	NM_017890.4	NP_060360.3	Q7Z7G8	VP13B_HUMAN	vacuolar protein sorting 13 homolog B (yeast)	61					protein transport (GO:0015031)			p.H61Y(1)		NS(1)|autonomic_ganglia(1)|breast(6)|central_nervous_system(4)|cervix(3)|endometrium(11)|haematopoietic_and_lymphoid_tissue(4)|kidney(10)|large_intestine(37)|lung(78)|ovary(8)|pancreas(3)|prostate(5)|skin(9)|upper_aerodigestive_tract(4)|urinary_tract(9)	193	Breast(36;3.73e-07)		OV - Ovarian serous cystadenocarcinoma(57;0.00636)			TTTAAGTGGACATATTCATGA	0.284																																					p.H61Y	Colon(161;2205 2542 7338 31318)											.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C181T	8						.						59.0	58.0	58.0					8																	100050684		2203	4296	6499	100119860	SO:0001583	missense	157680	exon3			AJ608772	CCDS6280.1, CCDS6281.1, CCDS6283.1, CCDS47903.1	8q22-q23	2014-09-17	2006-12-19	2005-04-08	ENSG00000132549	ENSG00000132549			2183	protein-coding gene	gene with protein product		607817	"""Cohen syndrome 1"""	CHS1, COH1		7920642, 15498460	Standard	NM_181661		Approved		uc003yiv.4	Q7Z7G8	OTTHUMG00000140383	ENST00000358544.2:c.181C>T	8.37:g.100050684C>T	ENSP00000351346:p.His61Tyr		100119860	NM_152564	C9JD30|Q709C6|Q709C7|Q7Z7G4|Q7Z7G5|Q7Z7G6|Q7Z7G7|Q8NB77|Q9NWV1|Q9Y4E7	Missense_Mutation	SNP	ENST00000358544.2	37	CCDS6280.1	.	.	.	.	.	.	.	.	.	.	C	19.18	3.777790	0.70107	.	.	ENSG00000132549	ENST00000355155;ENST00000357162;ENST00000358544;ENST00000395996;ENST00000441350	D;D;D;D;D	0.82619	-1.63;-1.63;-1.63;-1.63;-1.63	5.65	5.65	0.86999	.	0.060483	0.64402	D	0.000005	T	0.82245	0.4995	N	0.20845	0.615	0.80722	D	1	P;P;P;P;B	0.48640	0.808;0.84;0.913;0.839;0.125	P;P;P;P;B	0.52758	0.584;0.708;0.648;0.502;0.064	T	0.82981	-0.0187	10	0.46703	T	0.11	.	19.7238	0.96153	0.0:1.0:0.0:0.0	.	61;61;61;61;61	Q7Z7G8-2;Q7Z7G8;Q7Z7G8-3;Q7Z7G8-4;Q7Z7G8-5	.;VP13B_HUMAN;.;.;.	Y	61	ENSP00000347281:H61Y;ENSP00000349685:H61Y;ENSP00000351346:H61Y;ENSP00000379318:H61Y;ENSP00000398472:H61Y	ENSP00000347281:H61Y	H	+	1	0	VPS13B	100119860	1.000000	0.71417	1.000000	0.80357	0.934000	0.57294	7.729000	0.84864	2.649000	0.89929	0.561000	0.74099	CAT		0.284	VPS13B-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000277138.1	NM_184042	
CASZ1	54897	hgsc.bcm.edu	37	1	10720133	10720133	+	Silent	SNP	G	G	A	rs72858531	byFrequency	TCGA-AG-3580-01A-01W-0831-10	TCGA-AG-3580-10A-01W-0831-10	G	G	.	.	.	.	Unknown	Unknown	Somatic	Phase_I	Capture	.			SOLID	TCGA-AG-3580-01A-01W-0831-10	TCGA-AG-3580-10A-01W-0831-10	g.chr1:10720133G>A	ENST00000377022.3	-	6	1283	c.966C>T	c.(964-966)ggC>ggT	p.G322G	CASZ1_ENST00000344008.5_Silent_p.G322G|CASZ1_ENST00000478728.2_5'Flank	NM_001079843.2	NP_001073312.1	Q86V15	CASZ1_HUMAN	castor zinc finger 1	322					multicellular organismal development (GO:0007275)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|intracellular membrane-bounded organelle (GO:0043231)|nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)	p.G322G(1)		breast(1)|central_nervous_system(2)|cervix(1)|endometrium(9)|large_intestine(13)|lung(18)|ovary(2)|prostate(5)|skin(2)|urinary_tract(1)	54	Ovarian(185;0.203)|all_lung(157;0.204)	Lung NSC(185;4.96e-06)|all_lung(284;1.22e-05)|Renal(390;0.000147)|Breast(348;0.00093)|Colorectal(325;0.00212)|Hepatocellular(190;0.00913)|Ovarian(437;0.0229)|Myeloproliferative disorder(586;0.0255)	STAD - Stomach adenocarcinoma(5;0.0224)	UCEC - Uterine corpus endometrioid carcinoma (279;0.0265)|Colorectal(212;3.54e-08)|COAD - Colon adenocarcinoma(227;9.56e-06)|BRCA - Breast invasive adenocarcinoma(304;0.000219)|Kidney(185;0.00142)|KIRC - Kidney renal clear cell carcinoma(229;0.00381)|READ - Rectum adenocarcinoma(331;0.0419)|STAD - Stomach adenocarcinoma(132;0.0623)		GCAGATTCTCGCCGGTCTTCA	0.582																																					p.G322G												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C966T	1						.						86.0	94.0	92.0					1																	10720133		2203	4300	6503	10642720	SO:0001819	synonymous_variant	54897	exon6			AK000328	CCDS120.2, CCDS41246.1	1p36.22	2013-01-07	2007-02-02		ENSG00000130940	ENSG00000130940		"""Zinc fingers, C2H2-type"""	26002	protein-coding gene	gene with protein product	"""zinc finger protein 693"", ""survival related gene"""	609895	"""castor homolog 1, zinc finger (Drosophila)"""			16631614, 21252912	Standard	NM_001079843		Approved	FLJ20321, ZNF693, castor, cst, SRG	uc001aro.4	Q86V15	OTTHUMG00000002035	ENST00000377022.3:c.966C>T	1.37:g.10720133G>A			10642720	NM_001079843	Q078S9|Q2EN02|Q5T9S1|Q6ZNM8|Q8WX49|Q8WX50|Q9BT16|Q9NXC6	Silent	SNP	ENST00000377022.3	37	CCDS41246.1																																																																																				0.582	CASZ1-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000005673.2	NM_017766	
FLG	2312	hgsc.bcm.edu	37	1	152276799	152276799	+	Silent	SNP	G	G	A	rs138567818	byFrequency	TCGA-AG-3580-01A-01W-0831-10	TCGA-AG-3580-10A-01W-0831-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454			SOLID	TCGA-AG-3580-01A-01W-0831-10	TCGA-AG-3580-10A-01W-0831-10	g.chr1:152276799G>A	ENST00000368799.1	-	3	10598	c.10563C>T	c.(10561-10563)tcC>tcT	p.S3521S	FLG-AS1_ENST00000593011.1_RNA|FLG-AS1_ENST00000420707.1_RNA	NM_002016.1	NP_002007.1	P20930	FILA_HUMAN	filaggrin	3521	Ser-rich.				establishment of skin barrier (GO:0061436)|keratinocyte differentiation (GO:0030216)|multicellular organismal development (GO:0007275)	cytoplasmic membrane-bounded vesicle (GO:0016023)|intermediate filament (GO:0005882)|nucleus (GO:0005634)	calcium ion binding (GO:0005509)|structural molecule activity (GO:0005198)	p.S3521S(1)		autonomic_ganglia(1)|breast(13)|central_nervous_system(5)|cervix(2)|endometrium(38)|haematopoietic_and_lymphoid_tissue(1)|kidney(16)|large_intestine(57)|lung(211)|ovary(13)|pancreas(1)|prostate(15)|skin(24)|stomach(5)|upper_aerodigestive_tract(10)|urinary_tract(12)	424	Hepatocellular(266;0.0877)|Melanoma(130;0.116)|all_hematologic(923;0.127)		LUSC - Lung squamous cell carcinoma(543;0.206)			GTCCCTGGCCGGACTGTGAGT	0.557									Ichthyosis																												p.S3521S												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C10563T	1						.	T		4,4402		0,4,2199	206.0	207.0	206.0		10563	-5.4	0.0	1	dbSNP_134	206	0,8596		0,0,4298	no	coding-synonymous	FLG	NM_002016.1		0,4,6497	AA,AG,GG		0.0,0.0908,0.0308		3521/4062	152276799	4,12998	2203	4298	6501	150543423	SO:0001819	synonymous_variant	2312	exon3	Familial Cancer Database	X-linked Ichthyosis, Steroid Sulfatase Deficiency, Ichthyosis Vulgaris	XM_048104	CCDS30860.1	1q21.3	2013-01-10			ENSG00000143631	ENSG00000143631		"""EF-hand domain containing"""	3748	protein-coding gene	gene with protein product		135940				2740331, 2248957, 16444271	Standard	NM_002016		Approved		uc001ezu.1	P20930	OTTHUMG00000012202	ENST00000368799.1:c.10563C>T	1.37:g.152276799G>A			150543423	NM_002016	Q01720|Q5T583|Q9UC71	Silent	SNP	ENST00000368799.1	37	CCDS30860.1																																																																																				0.557	FLG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000033742.1	NM_002016	
FCRL2	79368	hgsc.bcm.edu	37	1	157738276	157738276	+	Missense_Mutation	SNP	C	C	T			TCGA-AG-3580-01A-01W-0831-10	TCGA-AG-3580-10A-01W-0831-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454			SOLID	TCGA-AG-3580-01A-01W-0831-10	TCGA-AG-3580-10A-01W-0831-10	g.chr1:157738276C>T	ENST00000361516.3	-	5	859	c.811G>A	c.(811-813)Ggc>Agc	p.G271S	FCRL2_ENST00000392274.3_Missense_Mutation_p.G271S|FCRL2_ENST00000368181.4_Intron|FCRL2_ENST00000469986.1_5'Flank	NM_030764.3	NP_110391.2	Q96LA5	FCRL2_HUMAN	Fc receptor-like 2	271	Ig-like C2-type 3.				cell-cell signaling (GO:0007267)|positive regulation of signal transduction (GO:0009967)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	SH3/SH2 adaptor activity (GO:0005070)	p.G271S(1)		central_nervous_system(2)|cervix(1)|endometrium(3)|kidney(2)|large_intestine(7)|lung(29)|ovary(1)|pancreas(1)|prostate(3)|skin(2)	51	all_hematologic(112;0.0378)		LUSC - Lung squamous cell carcinoma(543;0.24)			TAATATTTGCCGGCATCACTC	0.507																																					p.G271S												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G811A	1						.						181.0	180.0	180.0					1																	157738276		2203	4300	6503	156004900	SO:0001583	missense	79368	exon5			AF319438	CCDS1168.1	1q23.1	2013-01-14	2002-01-14	2005-03-23	ENSG00000132704	ENSG00000132704		"""CD molecules"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	14875	protein-coding gene	gene with protein product		606509	"""SH2 domain-containing phosphatase anchor protein 1"""	SPAP1		11162587	Standard	NM_030764		Approved	FCRH2, IRTA4, CD307b	uc001fre.2	Q96LA5	OTTHUMG00000019399	ENST00000361516.3:c.811G>A	1.37:g.157738276C>T	ENSP00000355157:p.Gly271Ser		156004900	NM_030764	A0N0M5|A1L307|A6NMS0|Q6NTA1|Q9BZI4|Q9BZI5|Q9BZI6	Missense_Mutation	SNP	ENST00000361516.3	37	CCDS1168.1	.	.	.	.	.	.	.	.	.	.	C	15.87	2.959991	0.53400	.	.	ENSG00000132704	ENST00000361516;ENST00000392274	T;T	0.25912	1.77;1.77	3.89	2.97	0.34412	Immunoglobulin I-set (1);Immunoglobulin subtype 2 (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	0.000000	0.45606	D	0.000346	T	0.51449	0.1675	H	0.98664	4.295	0.09310	N	1	D;D	0.89917	1.0;1.0	D;D	0.91635	0.998;0.999	T	0.53027	-0.8496	10	0.72032	D	0.01	.	7.6821	0.28520	0.0:0.8815:0.0:0.1185	.	271;271	B4DVJ9;Q96LA5	.;FCRL2_HUMAN	S	271	ENSP00000355157:G271S;ENSP00000376100:G271S	ENSP00000355157:G271S	G	-	1	0	FCRL2	156004900	0.000000	0.05858	0.010000	0.14722	0.005000	0.04900	0.798000	0.27014	0.956000	0.37904	0.655000	0.94253	GGC		0.507	FCRL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051408.2	NM_030764	
MAN1C1	57134	hgsc.bcm.edu	37	1	26107553	26107553	+	Nonsense_Mutation	SNP	C	C	T			TCGA-AG-3580-01A-01W-0831-10	TCGA-AG-3580-10A-01W-0831-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454			SOLID	TCGA-AG-3580-01A-01W-0831-10	TCGA-AG-3580-10A-01W-0831-10	g.chr1:26107553C>T	ENST00000374332.4	+	10	1930	c.1600C>T	c.(1600-1602)Cga>Tga	p.R534*	MAN1C1_ENST00000374329.1_Nonsense_Mutation_p.R305*|MAN1C1_ENST00000263979.3_Nonsense_Mutation_p.R354*	NM_020379.2	NP_065112.1	Q9NR34	MA1C1_HUMAN	mannosidase, alpha, class 1C, member 1	534					cellular protein metabolic process (GO:0044267)|post-translational protein modification (GO:0043687)|protein N-linked glycosylation (GO:0006487)|protein N-linked glycosylation via asparagine (GO:0018279)	extracellular vesicular exosome (GO:0070062)|Golgi membrane (GO:0000139)|integral component of Golgi membrane (GO:0030173)	calcium ion binding (GO:0005509)|mannosyl-oligosaccharide 1,2-alpha-mannosidase activity (GO:0004571)	p.R534*(1)		NS(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(8)|lung(7)|pancreas(1)|prostate(1)|skin(2)	25		Colorectal(325;3.78e-05)|Lung NSC(340;0.000181)|all_lung(284;0.000245)|Renal(390;0.000714)|Ovarian(437;0.00159)|Breast(348;0.0156)|Myeloproliferative disorder(586;0.0257)|all_neural(195;0.0515)|Esophageal squamous(538;0.232)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0574)|OV - Ovarian serous cystadenocarcinoma(117;2.46e-25)|Colorectal(126;1.15e-07)|COAD - Colon adenocarcinoma(152;4.31e-06)|STAD - Stomach adenocarcinoma(196;0.00125)|BRCA - Breast invasive adenocarcinoma(304;0.00141)|KIRC - Kidney renal clear cell carcinoma(1967;0.00146)|GBM - Glioblastoma multiforme(114;0.0149)|READ - Rectum adenocarcinoma(331;0.0803)		GTACCTGTGGCGACAGACCCA	0.617																																					p.R534X												.	.	1	Substitution - Nonsense(1)	large_intestine(1)	c.C1600T	1						.						76.0	78.0	78.0					1																	26107553		2203	4300	6503	25980140	SO:0001587	stop_gained	57134	exon10			AF261655	CCDS265.1	1p35	2008-02-05			ENSG00000117643	ENSG00000117643			19080	protein-coding gene	gene with protein product						10915796	Standard	XM_005245945		Approved	HMIC	uc001bkm.2	Q9NR34	OTTHUMG00000004417	ENST00000374332.4:c.1600C>T	1.37:g.26107553C>T	ENSP00000363452:p.Arg534*		25980140	NM_020379	A6NNE2|B2RNP2|Q9Y545	Nonsense_Mutation	SNP	ENST00000374332.4	37	CCDS265.1	.	.	.	.	.	.	.	.	.	.	C	43	10.494022	0.99415	.	.	ENSG00000117643	ENST00000374332;ENST00000374331;ENST00000263979;ENST00000374329	.	.	.	5.25	5.25	0.73442	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	12.0824	0.53677	0.2928:0.7072:0.0:0.0	.	.	.	.	X	534;354;354;305	.	ENSP00000263979:R354X	R	+	1	2	MAN1C1	25980140	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	1.541000	0.36126	2.459000	0.83118	0.561000	0.74099	CGA		0.617	MAN1C1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000012828.3	NM_020379	
WDTC1	23038	hgsc.bcm.edu	37	1	27622879	27622879	+	Nonsense_Mutation	SNP	C	C	A			TCGA-AG-3580-01A-01W-0831-10	TCGA-AG-3580-10A-01W-0831-10	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454			SOLID	TCGA-AG-3580-01A-01W-0831-10	TCGA-AG-3580-10A-01W-0831-10	g.chr1:27622879C>A	ENST00000319394.3	+	10	1471	c.936C>A	c.(934-936)tgC>tgA	p.C312*	WDTC1_ENST00000361771.3_Nonsense_Mutation_p.C312*	NM_001276252.1|NM_015023.3	NP_001263181.1|NP_055838.2	Q8N5D0	WDTC1_HUMAN	WD and tetratricopeptide repeats 1	312					cellular chemical homeostasis (GO:0055082)|cellular response to insulin stimulus (GO:0032869)|glucose metabolic process (GO:0006006)|in utero embryonic development (GO:0001701)|multicellular organism growth (GO:0035264)|negative regulation of fatty acid biosynthetic process (GO:0045717)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|protein ubiquitination (GO:0016567)|regulation of cell size (GO:0008361)	cytosol (GO:0005829)|nucleus (GO:0005634)	enzyme inhibitor activity (GO:0004857)	p.C312*(1)		central_nervous_system(1)|endometrium(5)|kidney(1)|large_intestine(7)|lung(5)|ovary(1)|skin(1)	21		all_cancers(24;3.12e-19)|all_epithelial(13;4.18e-18)|Colorectal(325;0.000147)|all_lung(284;0.000366)|Lung NSC(340;0.000548)|Renal(390;0.00211)|Breast(348;0.00257)|Myeloproliferative disorder(586;0.0393)|Ovarian(437;0.0707)|all_neural(195;0.0966)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0443)|OV - Ovarian serous cystadenocarcinoma(117;1.09e-27)|Colorectal(126;8.83e-09)|COAD - Colon adenocarcinoma(152;1.02e-06)|BRCA - Breast invasive adenocarcinoma(304;0.000544)|KIRC - Kidney renal clear cell carcinoma(1967;0.00201)|STAD - Stomach adenocarcinoma(196;0.00321)|READ - Rectum adenocarcinoma(331;0.0476)		CTAGAAAATGCCACTCCTCGG	0.512																																					p.C312X												.	.	1	Substitution - Nonsense(1)	large_intestine(1)	c.C936A	1						.						172.0	168.0	169.0					1																	27622879		2203	4300	6503	27495466	SO:0001587	stop_gained	23038	exon10			AK023778	CCDS296.1, CCDS60044.1	1p35.3	2013-01-11			ENSG00000142784	ENSG00000142784		"""DDB1 and CUL4 associated factors"", ""WD repeat domain containing"", ""Tetratricopeptide (TTC) repeat domain containing"""	29175	protein-coding gene	gene with protein product	"""adipose homolog (Drosophila)"", ""DDB1 and CUL4 associated factor 9"""					12717455, 19238144	Standard	NM_015023		Approved	KIAA1037, ADP, DCAF9	uc009vst.3	Q8N5D0	OTTHUMG00000004273	ENST00000319394.3:c.936C>A	1.37:g.27622879C>A	ENSP00000317971:p.Cys312*		27495466	NM_015023	D3DPL5|Q5SSC5|Q9NV87|Q9UPW4	Nonsense_Mutation	SNP	ENST00000319394.3	37		.	.	.	.	.	.	.	.	.	.	C	40	8.245321	0.98724	.	.	ENSG00000142784	ENST00000319394;ENST00000361771	.	.	.	5.67	1.03	0.20045	.	0.192591	0.56097	D	0.000023	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.38643	T	0.18	.	7.0046	0.24830	0.0:0.5885:0.1246:0.2869	.	.	.	.	X	312	.	ENSP00000317971:C312X	C	+	3	2	WDTC1	27495466	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	2.356000	0.44116	0.309000	0.22966	0.655000	0.94253	TGC		0.512	WDTC1-201	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding		NM_015023	
EXO5	64789	hgsc.bcm.edu	37	1	40981147	40981148	+	Frame_Shift_Del	DEL	AA	AA	-			TCGA-AG-3580-01A-01W-0831-10	TCGA-AG-3580-10A-01W-0831-10	AA	AA	AA	-	AA	AA	Unknown	Valid	Somatic	Phase_I	Capture	454			SOLID	TCGA-AG-3580-01A-01W-0831-10	TCGA-AG-3580-10A-01W-0831-10	g.chr1:40981147_40981148delAA	ENST00000372703.1	+	2	2005_2006	c.931_932delAA	c.(931-933)aaafs	p.K311fs	EXO5_ENST00000296380.4_Frame_Shift_Del_p.K311fs|EXO5_ENST00000358527.2_Frame_Shift_Del_p.K311fs|RP11-656D10.6_ENST00000437060.1_RNA|RP11-656D10.5_ENST00000453437.1_RNA			Q9H790	EXO5_HUMAN	exonuclease 5	311					DNA catabolic process, exonucleolytic (GO:0000738)|interstrand cross-link repair (GO:0036297)	cytosol (GO:0005829)|nucleus (GO:0005634)	4 iron, 4 sulfur cluster binding (GO:0051539)|DNA binding (GO:0003677)|metal ion binding (GO:0046872)|protein homodimerization activity (GO:0042803)|single-stranded DNA 3'-5' exodeoxyribonuclease activity (GO:0008310)|single-stranded DNA 5'-3' exodeoxyribonuclease activity (GO:0045145)	p.K311fs*25(1)									TGTAGCCTTCAAAGAGAAGGAG	0.52																																					p.311_311del												.	.	1	Deletion - Frameshift(1)	large_intestine(1)	c.931_932del	1						.																																			40753735	SO:0001589	frameshift_variant	64789	exon3			AK024797	CCDS453.1	1p34.2	2012-11-02	2012-10-30	2012-10-30	ENSG00000164002	ENSG00000164002			26115	protein-coding gene	gene with protein product			"""chromosome 1 open reading frame 176"", ""defects in morphology 1 homolog (S. cerevisiae)"""	C1orf176, DEM1		23095756	Standard	NM_022774		Approved	FLJ21144	uc001cfp.3	Q9H790	OTTHUMG00000007305	ENST00000372703.1:c.931_932delAA	1.37:g.40981147_40981148delAA	ENSP00000361788:p.Lys311fs		40753734	NM_022774	D3DPV4|Q5SWM7|Q5SWM8|Q5SWM9|Q5SWN0|Q5SWN1|Q8WTW9	Frame_Shift_Del	DEL	ENST00000372703.1	37	CCDS453.1																																																																																				0.520	EXO5-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000019087.1	NM_022774	
CRB1	23418	hgsc.bcm.edu	37	1	197397039	197397039	+	Missense_Mutation	SNP	C	C	A			TCGA-AG-3580-01A-01W-0831-10	TCGA-AG-3580-10A-01W-0831-10	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454			SOLID	TCGA-AG-3580-01A-01W-0831-10	TCGA-AG-3580-10A-01W-0831-10	g.chr1:197397039C>A	ENST00000367400.3	+	7	2719	c.2584C>A	c.(2584-2586)Ctg>Atg	p.L862M	CRB1_ENST00000367399.2_Missense_Mutation_p.L750M|CRB1_ENST00000538660.1_Intron|CRB1_ENST00000544212.1_Missense_Mutation_p.L343M|CRB1_ENST00000535699.1_Missense_Mutation_p.L793M|CRB1_ENST00000367397.1_Missense_Mutation_p.L243M	NM_201253.2	NP_957705.1	P82279	CRUM1_HUMAN	crumbs family member 1, photoreceptor morphogenesis associated	862	Laminin G-like 2. {ECO:0000255|PROSITE- ProRule:PRU00122}.				cell-cell signaling (GO:0007267)|establishment or maintenance of cell polarity (GO:0007163)|eye photoreceptor cell development (GO:0042462)|plasma membrane organization (GO:0007009)	extracellular region (GO:0005576)|integral component of membrane (GO:0016021)|microvillus (GO:0005902)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)	p.L862M(1)		NS(1)|breast(4)|central_nervous_system(2)|cervix(3)|endometrium(13)|kidney(4)|large_intestine(21)|lung(58)|ovary(7)|prostate(3)|skin(10)|upper_aerodigestive_tract(4)|urinary_tract(2)	132						CAACCAAAATCTGGAATTCTT	0.413																																					p.L862M												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C2584A	1						.						91.0	86.0	88.0					1																	197397039		2203	4300	6503	195663662	SO:0001583	missense	23418	exon7				CCDS1390.1, CCDS53454.1, CCDS58052.1, CCDS58053.1	1q31-q32.1	2014-02-06	2014-02-06		ENSG00000134376	ENSG00000134376			2343	protein-coding gene	gene with protein product		604210	"""crumbs (Drosophila) homolog 1"", ""crumbs homolog 1 (Drosophila)"""	RP12		10373321, 10508521	Standard	NM_201253		Approved	LCA8	uc001gtz.3	P82279	OTTHUMG00000035663	ENST00000367400.3:c.2584C>A	1.37:g.197397039C>A	ENSP00000356370:p.Leu862Met		195663662	NM_201253	A2A308|B7Z5T2|B9EG71|Q5K3A6|Q5TC28|Q5VUT1|Q6N027|Q8WWY0|Q8WWY1	Missense_Mutation	SNP	ENST00000367400.3	37	CCDS1390.1	.	.	.	.	.	.	.	.	.	.	C	11.88	1.769368	0.31320	.	.	ENSG00000134376	ENST00000535699;ENST00000367400;ENST00000367399;ENST00000544212;ENST00000367397;ENST00000367401	D;D;D;D;D	0.82081	-1.57;-1.52;-1.52;-1.52;-1.52	4.98	4.04	0.47022	Concanavalin A-like lectin/glucanase (1);Concanavalin A-like lectin/glucanase, subgroup (1);Laminin G domain (1);	.	.	.	.	D	0.88966	0.6581	M	0.69248	2.105	0.58432	D	0.999999	P;P;D;B	0.89917	0.828;0.875;1.0;0.429	B;B;D;B	0.97110	0.328;0.241;1.0;0.133	D	0.87448	0.2399	9	0.34782	T	0.22	.	14.2297	0.65882	0.0:0.9233:0.0:0.0767	.	793;750;511;862	F5H0L2;P82279-3;P82279-4;P82279	.;.;.;CRUM1_HUMAN	M	793;862;750;343;243;511	ENSP00000438786:L793M;ENSP00000356370:L862M;ENSP00000356369:L750M;ENSP00000444556:L343M;ENSP00000356367:L243M	ENSP00000356367:L243M	L	+	1	2	CRB1	195663662	0.961000	0.32948	0.946000	0.38457	0.310000	0.27922	2.220000	0.42908	2.458000	0.83093	0.555000	0.69702	CTG		0.413	CRB1-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000086565.2	NM_201253	
P2RY6	5031	hgsc.bcm.edu	37	11	73007862	73007862	+	Missense_Mutation	SNP	G	G	A	rs201497467	byFrequency	TCGA-AG-3580-01A-01W-0831-10	TCGA-AG-3580-10A-01W-0831-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454			SOLID	TCGA-AG-3580-01A-01W-0831-10	TCGA-AG-3580-10A-01W-0831-10	g.chr11:73007862G>A	ENST00000393590.2	+	2	598	c.299G>A	c.(298-300)cGc>cAc	p.R100H	P2RY6_ENST00000349767.2_Missense_Mutation_p.R100H|P2RY6_ENST00000393592.2_Missense_Mutation_p.R100H|P2RY6_ENST00000542092.1_Missense_Mutation_p.R100H|P2RY6_ENST00000538328.1_Missense_Mutation_p.R100H|P2RY6_ENST00000540342.1_Missense_Mutation_p.R100H|P2RY6_ENST00000393591.1_Missense_Mutation_p.R100H|P2RY6_ENST00000540124.1_Missense_Mutation_p.R100H	NM_001277207.1|NM_001277208.1	NP_001264136.1|NP_001264137.1	Q15077	P2RY6_HUMAN	pyrimidinergic receptor P2Y, G-protein coupled, 6	100					phospholipase C-activating G-protein coupled receptor signaling pathway (GO:0007200)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	G-protein coupled purinergic nucleotide receptor activity (GO:0045028)|G-protein coupled receptor activity (GO:0004930)	p.R100H(2)		endometrium(1)|kidney(1)|large_intestine(1)|lung(6)|ovary(1)|prostate(2)|skin(2)	14						TTCGCCTGCCGCCTGGTCCGC	0.607													G|||	2	0.000399361	0.0	0.0029	5008	,	,		19382	0.0		0.0	False		,,,				2504	0.0				p.R100H												.	.	2	Substitution - Missense(2)	large_intestine(1)|prostate(1)	c.G299A	11						.						137.0	123.0	128.0					11																	73007862		2200	4293	6493	72685510	SO:0001583	missense	5031	exon4				CCDS8220.1	11q13.5	2012-08-08				ENSG00000171631		"""Purinergic receptors"", ""GPCR / Class A : Purinergic receptors, P2Y"""	8543	protein-coding gene	gene with protein product		602451				8670200	Standard	NM_176797		Approved	P2Y6	uc001otr.4	Q15077		ENST00000393590.2:c.299G>A	11.37:g.73007862G>A	ENSP00000377215:p.Arg100His		72685510	NM_176798	Q15754	Missense_Mutation	SNP	ENST00000393590.2	37	CCDS8220.1	1	4.578754578754579E-4	0	0.0	1	0.0027624309392265192	0	0.0	0	0.0	G	17.27	3.347709	0.61183	.	.	ENSG00000171631	ENST00000540342;ENST00000542092;ENST00000349767;ENST00000393592;ENST00000544437;ENST00000393591;ENST00000540124;ENST00000393590;ENST00000535931;ENST00000538328	T;T;T;T;T;T;T;T;T;T	0.72942	-0.7;-0.7;-0.7;-0.7;-0.7;-0.7;-0.7;-0.7;-0.7;-0.7	4.36	3.45	0.39498	GPCR, rhodopsin-like superfamily (1);	0.138244	0.43919	D	0.000510	T	0.80964	0.4725	M	0.77616	2.38	0.34990	D	0.754975	D	0.89917	1.0	D	0.70935	0.971	D	0.85594	0.1248	10	0.87932	D	0	.	8.377	0.32449	0.2025:0.0:0.7975:0.0	.	100	Q15077	P2RY6_HUMAN	H	100	ENSP00000443427:R100H;ENSP00000445652:R100H;ENSP00000309771:R100H;ENSP00000377217:R100H;ENSP00000441079:R100H;ENSP00000377216:R100H;ENSP00000442551:R100H;ENSP00000377215:R100H;ENSP00000440770:R100H;ENSP00000442990:R100H	ENSP00000309771:R100H	R	+	2	0	P2RY6	72685510	1.000000	0.71417	1.000000	0.80357	0.641000	0.38312	2.687000	0.46976	1.181000	0.42912	0.491000	0.48974	CGC		0.607	P2RY6-007	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000397349.1		
SIM1	6492	hgsc.bcm.edu	37	6	100838246	100838246	+	Silent	SNP	G	G	A	rs143803280	byFrequency	TCGA-AG-3580-01A-01W-0831-10	TCGA-AG-3580-10A-01W-0831-10	G	G	.	.	.	.	Unknown	Unknown	Somatic	Phase_I	Capture	.			SOLID	TCGA-AG-3580-01A-01W-0831-10	TCGA-AG-3580-10A-01W-0831-10	g.chr6:100838246G>A	ENST00000369208.3	-	12	3074	c.2292C>T	c.(2290-2292)aaC>aaT	p.N764N	SIM1_ENST00000262901.4_Silent_p.N764N			P81133	SIM1_HUMAN	single-minded family bHLH transcription factor 1	764	Single-minded C-terminal. {ECO:0000255|PROSITE-ProRule:PRU00632}.				cell differentiation (GO:0030154)|nervous system development (GO:0007399)|transcription, DNA-templated (GO:0006351)|ureteric bud development (GO:0001657)	nucleus (GO:0005634)	DNA binding (GO:0003677)|sequence-specific DNA binding transcription factor activity (GO:0003700)|signal transducer activity (GO:0004871)	p.N764N(1)		breast(1)|central_nervous_system(4)|endometrium(5)|kidney(1)|large_intestine(15)|lung(34)|ovary(4)|prostate(1)|skin(5)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(5)	79		all_cancers(76;9.88e-06)|Acute lymphoblastic leukemia(125;4.99e-11)|all_hematologic(75;5.82e-08)|all_epithelial(107;0.0248)|Colorectal(196;0.13)		BRCA - Breast invasive adenocarcinoma(108;0.0774)		ATCAGCTTCCGTTGGTTATTA	0.398													G|||	8	0.00159744	0.003	0.0	5008	,	,		19807	0.003		0.0	False		,,,				2504	0.001				p.N764N												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C2292T	6						.	G		18,4388	26.2+/-53.5	0,18,2185	130.0	130.0	130.0		2292	4.9	1.0	6	dbSNP_134	130	0,8600		0,0,4300	yes	coding-synonymous	SIM1	NM_005068.2		0,18,6485	AA,AG,GG		0.0,0.4085,0.1384		764/767	100838246	18,12988	2203	4300	6503	100944967	SO:0001819	synonymous_variant	6492	exon11			U70212	CCDS5045.1	6q16.3	2013-10-17	2013-10-17		ENSG00000112246	ENSG00000112246		"""Basic helix-loop-helix proteins"""	10882	protein-coding gene	gene with protein product		603128	"""single-minded (Drosophila) homolog 1"", ""single-minded homolog 1 (Drosophila)"""			9199934, 11448938	Standard	NM_005068		Approved	bHLHe14	uc003pqj.4	P81133	OTTHUMG00000015275	ENST00000369208.3:c.2292C>T	6.37:g.100838246G>A			100944967	NM_005068	Q5TDP7	Silent	SNP	ENST00000369208.3	37	CCDS5045.1																																																																																				0.398	SIM1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041628.3	NM_005068	
UFL1	23376	hgsc.bcm.edu	37	6	96997370	96997370	+	Missense_Mutation	SNP	C	C	T			TCGA-AG-3580-01A-01W-0831-10	TCGA-AG-3580-10A-01W-0831-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454			SOLID	TCGA-AG-3580-01A-01W-0831-10	TCGA-AG-3580-10A-01W-0831-10	g.chr6:96997370C>T	ENST00000369278.4	+	14	1669	c.1603C>T	c.(1603-1605)Cgc>Tgc	p.R535C		NM_015323.4	NP_056138.1	O94874	UFL1_HUMAN	UFM1-specific ligase 1	535					negative regulation of NF-kappaB transcription factor activity (GO:0032088)|negative regulation of protein ubiquitination (GO:0031397)|osteoblast differentiation (GO:0001649)|protein ufmylation (GO:0071569)|regulation of proteasomal ubiquitin-dependent protein catabolic process (GO:0032434)|response to endoplasmic reticulum stress (GO:0034976)	cytoplasm (GO:0005737)|endoplasmic reticulum (GO:0005783)|membrane (GO:0016020)|nucleus (GO:0005634)	UFM1 conjugating enzyme activity (GO:0071568)	p.R535C(1)									GGGCAGAAAACGCACAATCAA	0.368																																					p.R535C												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C1603T	6						.						70.0	68.0	69.0					6																	96997370		2203	4298	6501	97104091	SO:0001583	missense	23376	exon14			BC036379	CCDS5034.1	6q16.3	2011-08-18	2011-08-18	2011-08-18	ENSG00000014123	ENSG00000014123			23039	protein-coding gene	gene with protein product	"""novel LZAP-binding protein"", ""Regulator of CDK5RAP3 and DDRGK1"""	613372	"""KIAA0776"""	KIAA0776		20018847, 20164180, 20228063, 20531390	Standard	NM_015323		Approved	NLBP, Maxer, RCAD	uc003por.3	O94874	OTTHUMG00000015238	ENST00000369278.4:c.1603C>T	6.37:g.96997370C>T	ENSP00000358283:p.Arg535Cys		97104091	NM_015323	A0PJ53|B4DJ57|C0H5X5|Q8N765|Q9NTQ0	Missense_Mutation	SNP	ENST00000369278.4	37	CCDS5034.1	.	.	.	.	.	.	.	.	.	.	C	20.4	3.984953	0.74474	.	.	ENSG00000014123	ENST00000369278	T	0.51071	0.72	5.73	5.73	0.89815	.	0.152710	0.64402	D	0.000016	T	0.41880	0.1178	L	0.47716	1.5	0.45837	D	0.998709	D	0.69078	0.997	P	0.47299	0.543	T	0.43426	-0.9392	10	0.72032	D	0.01	-1.9566	18.8905	0.92399	0.0:1.0:0.0:0.0	.	535	O94874	UFL1_HUMAN	C	535	ENSP00000358283:R535C	ENSP00000358283:R535C	R	+	1	0	KIAA0776	97104091	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	2.345000	0.44018	2.693000	0.91896	0.650000	0.86243	CGC		0.368	UFL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041557.1	NM_015323	
MED23	9439	hgsc.bcm.edu	37	6	131908863	131908863	+	Missense_Mutation	SNP	G	G	A			TCGA-AG-3580-01A-01W-0831-10	TCGA-AG-3580-10A-01W-0831-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454			SOLID	TCGA-AG-3580-01A-01W-0831-10	TCGA-AG-3580-10A-01W-0831-10	g.chr6:131908863G>A	ENST00000368068.3	-	29	4242	c.4063C>T	c.(4063-4065)Cct>Tct	p.P1355S	MED23_ENST00000545957.1_Missense_Mutation_p.P996S|MED23_ENST00000368058.1_Missense_Mutation_p.P1361S|MED23_ENST00000354577.4_Missense_Mutation_p.P1361S|MED23_ENST00000479213.1_5'UTR|MED23_ENST00000368060.3_Missense_Mutation_p.P1355S|MED23_ENST00000403834.3_Missense_Mutation_p.P1361S	NM_004830.3	NP_004821.2	Q9ULK4	MED23_HUMAN	mediator complex subunit 23	1355					gene expression (GO:0010467)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|regulation of transcription, DNA-templated (GO:0006355)|transcription initiation from RNA polymerase II promoter (GO:0006367)	mediator complex (GO:0016592)|nucleoplasm (GO:0005654)|transcription factor complex (GO:0005667)	transcription coactivator activity (GO:0003713)	p.P1355S(1)|p.P1361S(1)		NS(1)|breast(3)|central_nervous_system(1)|endometrium(1)|kidney(4)|large_intestine(12)|lung(15)|ovary(1)|pancreas(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(2)	44	Breast(56;0.0753)			GBM - Glioblastoma multiforme(226;0.0115)|OV - Ovarian serous cystadenocarcinoma(155;0.0608)		TTAGACTGAGGTGCTGGAGAC	0.468																																					p.P1361S												.	.	2	Substitution - Missense(2)	large_intestine(2)	c.C4081T	6						.						125.0	107.0	113.0					6																	131908863		2203	4300	6503	131950556	SO:0001583	missense	9439	exon30			AF104255	CCDS5146.1, CCDS5147.1, CCDS59039.1	6q22.33-q24.1	2008-02-05	2007-08-08	2007-07-30	ENSG00000112282	ENSG00000112282			2372	protein-coding gene	gene with protein product		605042	"""cofactor required for Sp1 transcriptional activation, subunit 3, 130kDa"""	CRSP3		9989412	Standard	NM_004830		Approved	CRSP130, DRIP130, Sur2	uc003qcs.2	Q9ULK4	OTTHUMG00000015565	ENST00000368068.3:c.4063C>T	6.37:g.131908863G>A	ENSP00000357047:p.Pro1355Ser		131950556	NM_015979	B9TX55|O95403|Q5JWT3|Q5JWT4|Q6P9H6|Q9H0J2|Q9NTT9|Q9NTU0|Q9Y5P7|Q9Y667	Missense_Mutation	SNP	ENST00000368068.3	37	CCDS5147.1	.	.	.	.	.	.	.	.	.	.	G	12.45	1.942229	0.34283	.	.	ENSG00000112282	ENST00000354577;ENST00000368068;ENST00000403834;ENST00000368060;ENST00000368058;ENST00000545957	.	.	.	5.8	4.94	0.65067	.	0.321864	0.37012	N	0.002298	T	0.19327	0.0464	N	0.08118	0	0.80722	D	1	B;B	0.19331	0.02;0.035	B;B	0.18871	0.01;0.023	T	0.07966	-1.0745	9	0.25106	T	0.35	-12.7633	12.0537	0.53522	0.1386:0.0:0.8614:0.0	.	1355;1361	Q9ULK4;Q9ULK4-3	MED23_HUMAN;.	S	1361;1355;1361;1355;1361;996	.	ENSP00000346588:P1361S	P	-	1	0	MED23	131950556	1.000000	0.71417	0.798000	0.32154	0.635000	0.38103	3.796000	0.55507	1.469000	0.48083	-0.150000	0.13652	CCT		0.468	MED23-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000042215.1		
KCNJ12	3768	hgsc.bcm.edu	37	17	21319682	21319682	+	Missense_Mutation	SNP	C	C	T	rs80203231	byFrequency	TCGA-AG-3580-01A-01W-0831-10	TCGA-AG-3580-10A-01W-0831-10	C	C	C	C	C	T	Unknown	Valid	LOH	Phase_I	Capture	454			SOLID	TCGA-AG-3580-01A-01W-0831-10	TCGA-AG-3580-10A-01W-0831-10	g.chr17:21319682C>T	ENST00000583088.1	+	3	1923	c.1028C>T	c.(1027-1029)tCg>tTg	p.S343L	KCNJ12_ENST00000331718.5_Missense_Mutation_p.S343L	NM_021012.4	NP_066292.2	Q14500	KCJ12_HUMAN	potassium inwardly-rectifying channel, subfamily J, member 12	343				S -> L (in Ref. 2; AAC50615). {ECO:0000305}.	muscle contraction (GO:0006936)|potassium ion transmembrane transport (GO:0071805)|potassium ion transport (GO:0006813)|protein homotetramerization (GO:0051289)|regulation of heart contraction (GO:0008016)|synaptic transmission (GO:0007268)	integral component of membrane (GO:0016021)|intrinsic component of membrane (GO:0031224)|plasma membrane (GO:0005886)	inward rectifier potassium channel activity (GO:0005242)	p.S343L(3)		NS(1)|breast(4)|endometrium(4)|kidney(1)|large_intestine(5)|lung(39)|ovary(5)|skin(8)|stomach(3)	70				Colorectal(15;0.0183)|COAD - Colon adenocarcinoma(3;0.0732)	Dofetilide(DB00204)|Yohimbine(DB01392)	ATTGACTACTCGCACTTCCAC	0.582										Prostate(3;0.18)																											p.S343L												.	.	3	Substitution - Missense(3)	ovary(2)|large_intestine(1)	c.C1028T	17						.						155.0	153.0	154.0					17																	21319682		2203	4300	6503	21260275	SO:0001583	missense	3768	exon3			L36069	CCDS11219.1	17p11.1	2011-07-05	2004-01-13		ENSG00000184185	ENSG00000184185		"""Potassium channels"", ""Voltage-gated ion channels / Potassium channels, Inwardly rectifying"""	6258	protein-coding gene	gene with protein product		602323	"""potassium inwardly-rectifying channel, subfamily J, inhibitor 1"""	KCNJN1		7859381, 12417321, 16382105	Standard	NM_021012		Approved	Kir2.2, Kir2.2v, IRK2, hIRK1	uc021tss.1	Q14500	OTTHUMG00000132039	ENST00000583088.1:c.1028C>T	17.37:g.21319682C>T	ENSP00000463778:p.Ser343Leu		21260275	NM_021012	O43401|Q15756|Q8NG63	Missense_Mutation	SNP	ENST00000583088.1	37	CCDS11219.1	.	.	.	.	.	.	.	.	.	.	C	19.60	3.857121	0.71834	.	.	ENSG00000184185	ENST00000331718	D	0.92858	-3.12	5.76	5.76	0.90799	Immunoglobulin E-set (1);Potassium channel, inwardly rectifying, Kir, conserved region 2 (2);Potassium channel, inwardly rectifying, Kir, cytoplasmic (1);	0.057257	0.64402	D	0.000001	D	0.92551	0.7634	M	0.77486	2.375	0.80722	D	1	B	0.27013	0.166	B	0.25140	0.058	D	0.90235	0.4282	10	0.62326	D	0.03	.	19.9738	0.97296	0.0:1.0:0.0:0.0	.	343	Q14500	IRK12_HUMAN	L	343	ENSP00000328150:S343L	ENSP00000328150:S343L	S	+	2	0	KCNJ12	21260275	1.000000	0.71417	0.994000	0.49952	0.997000	0.91878	7.686000	0.84128	2.732000	0.93576	0.655000	0.94253	TCG		0.582	KCNJ12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255060.2	NM_021012	
EIF5A	1984	hgsc.bcm.edu	37	17	7213108	7213108	+	Missense_Mutation	SNP	G	G	A			TCGA-AG-3580-01A-01W-0831-10	TCGA-AG-3580-10A-01W-0831-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454			SOLID	TCGA-AG-3580-01A-01W-0831-10	TCGA-AG-3580-10A-01W-0831-10	g.chr17:7213108G>A	ENST00000336458.8	+	2	555	c.154G>A	c.(154-156)Ggc>Agc	p.G52S	EIF5A_ENST00000416016.2_Missense_Mutation_p.G52S|EIF5A_ENST00000572815.1_Missense_Mutation_p.G52S|EIF5A_ENST00000576930.1_Missense_Mutation_p.G52S|EIF5A_ENST00000336452.7_Missense_Mutation_p.G82S|EIF5A_ENST00000571955.1_Missense_Mutation_p.G52S|EIF5A_ENST00000419711.2_Missense_Mutation_p.G52S|EIF5A_ENST00000573542.1_Missense_Mutation_p.G52S	NM_001970.4	NP_001961.1	P63241	IF5A1_HUMAN	eukaryotic translation initiation factor 5A	52	DOHH-binding.				apoptotic process (GO:0006915)|cellular protein metabolic process (GO:0044267)|mRNA export from nucleus (GO:0006406)|nucleocytoplasmic transport (GO:0006913)|peptidyl-lysine modification to peptidyl-hypusine (GO:0008612)|positive regulation of cell proliferation (GO:0008284)|positive regulation of translational elongation (GO:0045901)|positive regulation of translational termination (GO:0045905)|post-translational protein modification (GO:0043687)|protein export from nucleus (GO:0006611)|translational frameshifting (GO:0006452)	annulate lamellae (GO:0005642)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|nuclear pore (GO:0005643)|nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)|protein N-terminus binding (GO:0047485)|ribosome binding (GO:0043022)|RNA binding (GO:0003723)|translation elongation factor activity (GO:0003746)|U6 snRNA binding (GO:0017070)	p.G52S(1)		endometrium(2)|kidney(1)|large_intestine(2)|urinary_tract(1)	6						TGGCAAGCACGGCCACGCCAA	0.537																																					p.G52S												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G154A	17						.						139.0	123.0	128.0					17																	7213108		2203	4300	6503	7153832	SO:0001583	missense	1984	exon2				CCDS11099.1, CCDS45601.1	17p13-p12	2009-05-01			ENSG00000132507	ENSG00000132507			3300	protein-coding gene	gene with protein product		600187				7759117	Standard	NM_001143760		Approved	EIF5A1, EIF-5A, MGC99547, MGC104255	uc002gfr.3	P63241	OTTHUMG00000102197	ENST00000336458.8:c.154G>A	17.37:g.7213108G>A	ENSP00000336776:p.Gly52Ser		7153832	NM_001143761	A8K9A0|D3DTP2|P10159|Q16182|Q7L7L3|Q7Z4L1|Q9D0G2	Missense_Mutation	SNP	ENST00000336458.8	37	CCDS11099.1	.	.	.	.	.	.	.	.	.	.	G	33	5.283327	0.95489	.	.	ENSG00000132507	ENST00000336452;ENST00000336458;ENST00000419711;ENST00000416016	T;T;T;T	0.51325	0.71;0.71;0.71;0.71	4.55	4.55	0.56014	KOW (1);Translation protein SH3-like (1);Translation protein SH3-like, subgroup (1);	0.000000	0.64402	D	0.000002	T	0.77631	0.4159	H	0.97587	4.035	0.80722	D	1	D;D	0.76494	0.999;0.999	P;P	0.61592	0.891;0.889	D	0.86645	0.1894	10	0.87932	D	0	-4.1262	16.2348	0.82365	0.0:0.0:1.0:0.0	.	52;82	P63241;P63241-2	IF5A1_HUMAN;.	S	82;52;52;52	ENSP00000336702:G82S;ENSP00000336776:G52S;ENSP00000390677:G52S;ENSP00000396073:G52S	ENSP00000336702:G82S	G	+	1	0	EIF5A	7153832	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	8.972000	0.93424	2.380000	0.81148	0.505000	0.49811	GGC		0.537	EIF5A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000220047.3	NM_001970	
KIAA0195	9772	hgsc.bcm.edu	37	17	73489892	73489892	+	Missense_Mutation	SNP	G	G	A			TCGA-AG-3580-01A-01W-0831-10	TCGA-AG-3580-10A-01W-0831-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454			SOLID	TCGA-AG-3580-01A-01W-0831-10	TCGA-AG-3580-10A-01W-0831-10	g.chr17:73489892G>A	ENST00000314256.7	+	18	2696	c.2302G>A	c.(2302-2304)Gag>Aag	p.E768K	KIAA0195_ENST00000579208.1_Missense_Mutation_p.E419K|AC100787.1_ENST00000579379.1_RNA|KIAA0195_ENST00000375248.5_Missense_Mutation_p.E778K	NM_014738.4	NP_055553.3	Q12767	K0195_HUMAN	KIAA0195	768						integral component of membrane (GO:0016021)|nucleus (GO:0005634)		p.E768K(1)		breast(2)|endometrium(5)|kidney(2)|large_intestine(7)|lung(17)|ovary(5)|skin(2)|stomach(1)|urinary_tract(1)	42	all_cancers(13;3.15e-09)|all_epithelial(9;5.94e-10)|Breast(9;1.85e-09)|all_lung(278;0.246)		all cancers(21;5.01e-07)|Epithelial(20;5e-06)|Lung(188;0.0809)|LUSC - Lung squamous cell carcinoma(166;0.154)			CAAGTGCATCGAGCTGGTACA	0.612																																					p.E768K												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G2302A	17						.						129.0	107.0	114.0					17																	73489892		2203	4300	6503	71001487	SO:0001583	missense	9772	exon18				CCDS32732.1	17q25.1	2012-03-01			ENSG00000177728	ENSG00000177728			28983	protein-coding gene	gene with protein product						8724849	Standard	NM_014738		Approved	TMEM94	uc002jnz.4	Q12767		ENST00000314256.7:c.2302G>A	17.37:g.73489892G>A	ENSP00000313885:p.Glu768Lys		71001487	NM_014738	O75536|Q86XF1	Missense_Mutation	SNP	ENST00000314256.7	37	CCDS32732.1	.	.	.	.	.	.	.	.	.	.	G	19.43	3.826697	0.71143	.	.	ENSG00000177728	ENST00000314256;ENST00000375248	T;T	0.51325	0.72;0.71	5.45	5.45	0.79879	.	0.000000	0.85682	D	0.000000	T	0.69753	0.3146	M	0.73598	2.24	0.80722	D	1	D;D;D	0.76494	0.999;0.999;0.999	D;D;D	0.78314	0.98;0.991;0.98	T	0.68561	-0.5376	10	0.40728	T	0.16	-30.3485	19.2744	0.94026	0.0:0.0:1.0:0.0	.	778;778;768	B4DGC6;C9JL75;Q12767	.;.;K0195_HUMAN	K	768;778	ENSP00000313885:E768K;ENSP00000364397:E778K	ENSP00000313885:E768K	E	+	1	0	KIAA0195	71001487	1.000000	0.71417	0.990000	0.47175	0.992000	0.81027	9.755000	0.98912	2.564000	0.86499	0.561000	0.74099	GAG		0.612	KIAA0195-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000447303.1	NM_014738	
PRMT7	54496	hgsc.bcm.edu	37	16	68373360	68373360	+	Missense_Mutation	SNP	G	G	A			TCGA-AG-3580-01A-01W-0831-10	TCGA-AG-3580-10A-01W-0831-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454			SOLID	TCGA-AG-3580-01A-01W-0831-10	TCGA-AG-3580-10A-01W-0831-10	g.chr16:68373360G>A	ENST00000339507.5	+	8	1470	c.640G>A	c.(640-642)Gtt>Att	p.V214I	PRMT7_ENST00000449359.3_Missense_Mutation_p.V164I|PRMT7_ENST00000348497.4_Missense_Mutation_p.V140I|PRMT7_ENST00000564441.1_3'UTR|PRMT7_ENST00000441236.1_Missense_Mutation_p.V164I			Q9NVM4	ANM7_HUMAN	protein arginine methyltransferase 7	214	SAM-dependent MTase PRMT-type 1. {ECO:0000255|PROSITE-ProRule:PRU01015}.				cell differentiation (GO:0030154)|DNA methylation involved in gamete generation (GO:0043046)|histone arginine methylation (GO:0034969)|histone methylation (GO:0016571)|peptidyl-arginine methylation (GO:0018216)|peptidyl-arginine methylation, to asymmetrical-dimethyl arginine (GO:0019919)|peptidyl-arginine methylation, to symmetrical-dimethyl arginine (GO:0019918)|regulation of gene expression by genetic imprinting (GO:0006349)|regulation of protein binding (GO:0043393)|regulation of transcription, DNA-templated (GO:0006355)|spliceosomal snRNP assembly (GO:0000387)|transcription, DNA-templated (GO:0006351)	cytosol (GO:0005829)|nucleolus (GO:0005730)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	[myelin basic protein]-arginine N-methyltransferase activity (GO:0016277)|histone binding (GO:0042393)|histone methyltransferase activity (H4-R3 specific) (GO:0044020)|histone-arginine N-methyltransferase activity (GO:0008469)|protein-arginine omega-N asymmetric methyltransferase activity (GO:0035242)|protein-arginine omega-N monomethyltransferase activity (GO:0035241)|protein-arginine omega-N symmetric methyltransferase activity (GO:0035243)|ribonucleoprotein complex binding (GO:0043021)|S-adenosylmethionine-dependent methyltransferase activity (GO:0008757)	p.V214I(1)		endometrium(3)|kidney(2)|large_intestine(3)|lung(10)|pancreas(1)|urinary_tract(1)	20		Ovarian(137;0.192)		OV - Ovarian serous cystadenocarcinoma(108;0.0155)|Epithelial(162;0.0629)		CGTCCCTCCCGTTGACGTGGA	0.592																																					p.V214I												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G640A	16						.						121.0	94.0	103.0					16																	68373360		2198	4300	6498	66930861	SO:0001583	missense	54496	exon8			AK001502	CCDS10866.1, CCDS54033.1	16q22.1	2008-02-05			ENSG00000132600	ENSG00000132600		"""Protein arginine methyltransferases"""	25557	protein-coding gene	gene with protein product		610087				15044439	Standard	NM_001184824		Approved	FLJ10640, KIAA1933	uc002evy.2	Q9NVM4	OTTHUMG00000137556	ENST00000339507.5:c.640G>A	16.37:g.68373360G>A	ENSP00000343103:p.Val214Ile		66930861	NM_019023	B3KPR0|B3KUG9|B4E379|Q96PV5|Q9H9L0	Missense_Mutation	SNP	ENST00000339507.5	37	CCDS10866.1	.	.	.	.	.	.	.	.	.	.	g	7.369	0.626379	0.14257	.	.	ENSG00000132600	ENST00000449359;ENST00000441236;ENST00000348497;ENST00000339507	T;T;T;T	0.22539	1.95;1.95;1.95;1.95	5.51	-4.68	0.03309	.	1.330100	0.04538	N	0.387670	T	0.07999	0.0200	N	0.08118	0	0.09310	N	1	B;B;B;B	0.31256	0.09;0.141;0.021;0.316	B;B;B;B	0.23852	0.03;0.012;0.002;0.049	T	0.15378	-1.0439	10	0.34782	T	0.22	1.4427	2.7344	0.05236	0.2074:0.1352:0.4502:0.2072	.	164;140;214;214	Q9NVM4-3;Q9NVM4-2;Q9NVM4;Q9NVM4-4	.;.;ANM7_HUMAN;.	I	164;164;140;214	ENSP00000414716:V164I;ENSP00000409324:V164I;ENSP00000345775:V140I;ENSP00000343103:V214I	ENSP00000343103:V214I	V	+	1	0	PRMT7	66930861	0.000000	0.05858	0.000000	0.03702	0.008000	0.06430	-0.065000	0.11617	-1.176000	0.02747	-1.068000	0.02270	GTT		0.592	PRMT7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000268892.3	NM_019023	
EEFSEC	60678	hgsc.bcm.edu	37	3	127983522	127983522	+	Silent	SNP	G	G	T			TCGA-AG-3580-01A-01W-0831-10	TCGA-AG-3580-10A-01W-0831-10	G	G	.	.	.	.	Unknown	Unknown	Somatic	Phase_I	Capture	.			SOLID	TCGA-AG-3580-01A-01W-0831-10	TCGA-AG-3580-10A-01W-0831-10	g.chr3:127983522G>T	ENST00000254730.6	+	4	738	c.684G>T	c.(682-684)gtG>gtT	p.V228V	EEFSEC_ENST00000483457.1_Intron	NM_021937.3	NP_068756.2	P57772	SELB_HUMAN	eukaryotic elongation factor, selenocysteine-tRNA-specific	228					selenocysteine incorporation (GO:0001514)	mitochondrion (GO:0005739)|nucleus (GO:0005634)|ribonucleoprotein complex (GO:0030529)	GTP binding (GO:0005525)|GTPase activity (GO:0003924)|ribonucleoprotein complex binding (GO:0043021)|selenocysteine insertion sequence binding (GO:0035368)|translation elongation factor activity (GO:0003746)|tRNA binding (GO:0000049)	p.V228V(1)		NS(1)|endometrium(3)|kidney(4)|large_intestine(6)|lung(10)|ovary(1)	25						TCATGTCTGTGGACCACTGTT	0.557																																					p.V228V												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.G684T	3						.						202.0	167.0	179.0					3																	127983522		2203	4300	6503	129466212	SO:0001819	synonymous_variant	60678	exon4				CCDS33849.1	3q21.3	2007-05-25			ENSG00000132394	ENSG00000132394			24614	protein-coding gene	gene with protein product	"""elongation factor for selenoprotein translation"""	607695				10970870, 15229221	Standard	XM_005247696		Approved	SELB, EFSEC	uc003eki.3	P57772	OTTHUMG00000159659	ENST00000254730.6:c.684G>T	3.37:g.127983522G>T			129466212	NM_021937	Q96HZ6	Silent	SNP	ENST00000254730.6	37	CCDS33849.1																																																																																				0.557	EEFSEC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000356738.2	NM_021937	
ACAD9	28976	hgsc.bcm.edu	37	3	128621414	128621414	+	Missense_Mutation	SNP	A	A	G			TCGA-AG-3580-01A-01W-0831-10	TCGA-AG-3580-10A-01W-0831-10	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	Capture	454			SOLID	TCGA-AG-3580-01A-01W-0831-10	TCGA-AG-3580-10A-01W-0831-10	g.chr3:128621414A>G	ENST00000308982.7	+	9	982	c.901A>G	c.(901-903)Aac>Gac	p.N301D	ACAD9_ENST00000511526.1_3'UTR	NM_014049.4	NP_054768.2	Q9H845	ACAD9_HUMAN	acyl-CoA dehydrogenase family, member 9	301						dendrite (GO:0030425)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	acyl-CoA dehydrogenase activity (GO:0003995)|flavin adenine dinucleotide binding (GO:0050660)	p.N301D(1)		central_nervous_system(1)|endometrium(1)|large_intestine(7)|lung(12)|ovary(3)|prostate(1)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)	30						GAACATCCTCAACAGCGGCCG	0.622																																					p.N301D												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.A901G	3						.						104.0	98.0	100.0					3																	128621414		2203	4300	6503	130104104	SO:0001583	missense	28976	exon9			AF078854	CCDS3053.1	3q21.3	2013-05-24	2010-04-30		ENSG00000177646	ENSG00000177646		"""Mitochondrial respiratory chain complex assembly factors"""	21497	protein-coding gene	gene with protein product		611103	"""acyl-Coenzyme A dehydrogenase family, member 9"""			12359260, 21057504, 20816094	Standard	NM_014049		Approved	NPD002, MGC14452	uc003ela.4	Q9H845	OTTHUMG00000159942	ENST00000308982.7:c.901A>G	3.37:g.128621414A>G	ENSP00000312618:p.Asn301Asp		130104104	NM_014049	D3DNB8|Q8WXX3	Missense_Mutation	SNP	ENST00000308982.7	37	CCDS3053.1	.	.	.	.	.	.	.	.	.	.	A	28.1	4.894767	0.91962	.	.	ENSG00000177646	ENST00000308982;ENST00000334167	D	0.96136	-3.92	5.19	5.19	0.71726	Acyl-CoA dehydrogenase/oxidase (1);Acyl-CoA dehydrogenase/oxidase C-terminal (2);Acyl-CoA oxidase/dehydrogenase, type 1 (1);	0.000000	0.85682	D	0.000000	D	0.96100	0.8729	L	0.39633	1.23	0.80722	D	1	D;D;D	0.89917	0.991;1.0;1.0	D;D;D	0.97110	0.975;0.998;1.0	D	0.96427	0.9316	10	0.66056	D	0.02	.	12.991	0.58618	1.0:0.0:0.0:0.0	.	178;251;301	Q9H9W4;Q59FN3;Q9H845	.;.;ACAD9_HUMAN	D	301;168	ENSP00000312618:N301D	ENSP00000312618:N301D	N	+	1	0	ACAD9	130104104	1.000000	0.71417	1.000000	0.80357	0.990000	0.78478	8.533000	0.90617	1.953000	0.56701	0.533000	0.62120	AAC		0.622	ACAD9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000358405.1	NM_014049	
IFT122	55764	hgsc.bcm.edu	37	3	129183577	129183577	+	Silent	SNP	G	G	A			TCGA-AG-3580-01A-01W-0831-10	TCGA-AG-3580-10A-01W-0831-10	G	G	.	.	.	.	Unknown	Unknown	Somatic	Phase_I	Capture	.			SOLID	TCGA-AG-3580-01A-01W-0831-10	TCGA-AG-3580-10A-01W-0831-10	g.chr3:129183577G>A	ENST00000348417.2	+	7	593	c.516G>A	c.(514-516)ccG>ccA	p.P172P	IFT122_ENST00000507564.1_Silent_p.P223P|IFT122_ENST00000349441.2_Silent_p.P120P|IFT122_ENST00000504021.1_Silent_p.P125P|IFT122_ENST00000347300.2_Silent_p.P172P|IFT122_ENST00000440957.2_Silent_p.P22P|IFT122_ENST00000296266.3_Silent_p.P223P|IFT122_ENST00000431818.2_Silent_p.P22P	NM_052989.1	NP_443715.1	Q9HBG6	IF122_HUMAN	intraflagellar transport 122	172					camera-type eye morphogenesis (GO:0048593)|ciliary receptor clustering involved in smoothened signaling pathway (GO:0060830)|cilium morphogenesis (GO:0060271)|embryonic body morphogenesis (GO:0010172)|embryonic digit morphogenesis (GO:0042733)|embryonic forelimb morphogenesis (GO:0035115)|embryonic heart tube development (GO:0035050)|embryonic heart tube left/right pattern formation (GO:0060971)|establishment of protein localization to organelle (GO:0072594)|intraciliary anterograde transport (GO:0035720)|intraciliary retrograde transport (GO:0035721)|limb development (GO:0060173)|negative regulation of epithelial cell proliferation (GO:0050680)|negative regulation of smoothened signaling pathway (GO:0045879)|negative regulation of smoothened signaling pathway involved in ventral spinal cord patterning (GO:0021914)|neural tube closure (GO:0001843)|protein localization to cilium (GO:0061512)|signal transduction downstream of smoothened (GO:0007227)|smoothened signaling pathway involved in dorsal/ventral neural tube patterning (GO:0060831)	ciliary basal body (GO:0036064)|cytoplasm (GO:0005737)|intraciliary transport particle A (GO:0030991)|membrane (GO:0016020)|photoreceptor connecting cilium (GO:0032391)|primary cilium (GO:0072372)		p.P223P(1)		breast(3)|cervix(1)|endometrium(9)|large_intestine(10)|lung(21)|ovary(2)|prostate(1)|skin(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	52						TCGAGCGGCCGGGGGGCTCCC	0.507																																					p.P120P												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.G360A	3						.						99.0	107.0	104.0					3																	129183577		2203	4300	6503	130666267	SO:0001819	synonymous_variant	55764	exon5			AF244930	CCDS3059.1, CCDS3060.1, CCDS3061.1, CCDS3062.1, CCDS63770.1, CCDS63772.1, CCDS63773.1	3q21	2014-07-03	2014-07-03	2005-11-02	ENSG00000163913	ENSG00000163913		"""WD repeat domain containing"", ""Intraflagellar transport homologs"""	13556	protein-coding gene	gene with protein product		606045	"""WD repeat domain 10"", ""intraflagellar transport 122 homolog (Chlamydomonas)"""	WDR10		11242542	Standard	NM_052985		Approved	WDR140, WDR10p, SPG	uc003emm.3	Q9HBG6	OTTHUMG00000159516	ENST00000348417.2:c.516G>A	3.37:g.129183577G>A			130666267	NM_052990	B3KW53|B4DEY9|B4DPW7|E7EQF4|E9PDG2|E9PDX2|G3XAB1|H7C3C0|Q53G36|Q8TC06|Q9BTB9|Q9BTY4|Q9HAT9|Q9HBG5|Q9NV68|Q9UF80	Silent	SNP	ENST00000348417.2	37	CCDS3061.1																																																																																				0.507	IFT122-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000355852.1	NM_018262	
ERP27	121506	hgsc.bcm.edu	37	12	15087827	15087827	+	Missense_Mutation	SNP	T	T	C			TCGA-AG-3580-01A-01W-0831-10	TCGA-AG-3580-10A-01W-0831-10	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	Capture	454			SOLID	TCGA-AG-3580-01A-01W-0831-10	TCGA-AG-3580-10A-01W-0831-10	g.chr12:15087827T>C	ENST00000266397.2	-	3	869	c.296A>G	c.(295-297)tAc>tGc	p.Y99C		NM_152321.2	NP_689534.1	Q96DN0	ERP27_HUMAN	endoplasmic reticulum protein 27	99	Thioredoxin.					endoplasmic reticulum (GO:0005783)		p.Y99C(1)		breast(2)|cervix(2)|endometrium(2)|kidney(3)|large_intestine(4)|lung(3)|prostate(2)|skin(1)	19						AGTGATGTTGTAGTGTGTCAG	0.473																																					p.Y99C												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.A296G	12						.						129.0	110.0	116.0					12																	15087827		2203	4300	6503	14979094	SO:0001583	missense	121506	exon3			AK056677	CCDS8670.1, CCDS73450.1	12p12.3	2011-10-19	2009-02-23	2007-03-26	ENSG00000139055	ENSG00000139055		"""Protein disulfide isomerases"""	26495	protein-coding gene	gene with protein product	"""protein disulfide isomerase family A, member 8"""	610642	"""chromosome 12 open reading frame 46"", ""endoplasmic reticulum protein 27 kDa"""	C12orf46		12975309, 16940051	Standard	XM_005253303		Approved	FLJ32115, ERp27, PDIA8	uc001rco.3	Q96DN0	OTTHUMG00000168741	ENST00000266397.2:c.296A>G	12.37:g.15087827T>C	ENSP00000266397:p.Tyr99Cys		14979094	NM_152321		Missense_Mutation	SNP	ENST00000266397.2	37	CCDS8670.1	.	.	.	.	.	.	.	.	.	.	T	13.00	2.106642	0.37145	.	.	ENSG00000139055	ENST00000266397	T	0.26373	1.74	4.46	3.27	0.37495	Thioredoxin-like fold (2);	0.067697	0.64402	D	0.000009	T	0.44644	0.1303	M	0.71581	2.175	0.80722	D	1	D	0.89917	1.0	D	0.85130	0.997	T	0.31943	-0.9925	10	0.52906	T	0.07	-10.1405	7.2567	0.26181	0.1962:0.0:0.0:0.8038	.	99	Q96DN0	ERP27_HUMAN	C	99	ENSP00000266397:Y99C	ENSP00000266397:Y99C	Y	-	2	0	ERP27	14979094	1.000000	0.71417	0.994000	0.49952	0.308000	0.27856	2.821000	0.48065	0.980000	0.38523	0.533000	0.62120	TAC		0.473	ERP27-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000400868.1	NM_152321	
KRAS	3845	hgsc.bcm.edu	37	12	25398284	25398284	+	Missense_Mutation	SNP	C	C	T	rs121913529		TCGA-AG-3580-01A-01W-0831-10	TCGA-AG-3580-10A-01W-0831-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454			SOLID	TCGA-AG-3580-01A-01W-0831-10	TCGA-AG-3580-10A-01W-0831-10	g.chr12:25398284C>T	ENST00000256078.4	-	2	98	c.35G>A	c.(34-36)gGt>gAt	p.G12D	KRAS_ENST00000556131.1_Missense_Mutation_p.G12D|KRAS_ENST00000311936.3_Missense_Mutation_p.G12D|KRAS_ENST00000557334.1_Missense_Mutation_p.G12D	NM_033360.2	NP_203524.1	P01116	RASK_HUMAN	Kirsten rat sarcoma viral oncogene homolog	12			G -> A (in a colorectal cancer sample; somatic mutation). {ECO:0000269|PubMed:16959974}.|G -> C (in lung carcinoma; somatic mutation). {ECO:0000269|PubMed:16533793, ECO:0000269|PubMed:6320174}.|G -> D (in pancreatic carcinoma, GASC and lung carcinoma; somatic mutation). {ECO:0000269|PubMed:16533793, ECO:0000269|PubMed:16959974, ECO:0000269|PubMed:7773929, ECO:0000269|PubMed:8439212}.|G -> R (in lung cancer and bladder cancer; somatic mutation). {ECO:0000269|PubMed:6695174}.|G -> S (in lung carcinoma and GASC; somatic mutation). {ECO:0000269|PubMed:16533793, ECO:0000269|PubMed:16959974, ECO:0000269|PubMed:7773929}.|G -> V (in lung carcinoma, pancreatic carcinoma, colon cancer and GASC; somatic mutation, constitutively activated). {ECO:0000269|PubMed:14534542, ECO:0000269|PubMed:16533793, ECO:0000269|PubMed:16959974, ECO:0000269|PubMed:22711838, ECO:0000269|PubMed:3034404, ECO:0000269|PubMed:6092920, ECO:0000269|PubMed:8439212}.		actin cytoskeleton organization (GO:0030036)|activation of MAPKK activity (GO:0000186)|axon guidance (GO:0007411)|blood coagulation (GO:0007596)|cytokine-mediated signaling pathway (GO:0019221)|epidermal growth factor receptor signaling pathway (GO:0007173)|epithelial tube branching involved in lung morphogenesis (GO:0060441)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|GTP catabolic process (GO:0006184)|innate immune response (GO:0045087)|insulin receptor signaling pathway (GO:0008286)|leukocyte migration (GO:0050900)|MAPK cascade (GO:0000165)|negative regulation of cell differentiation (GO:0045596)|negative regulation of neuron apoptotic process (GO:0043524)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of cell proliferation (GO:0008284)|positive regulation of gene expression (GO:0010628)|positive regulation of MAP kinase activity (GO:0043406)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of nitric-oxide synthase activity (GO:0051000)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of Rac protein signal transduction (GO:0035022)|Ras protein signal transduction (GO:0007265)|regulation of long-term neuronal synaptic plasticity (GO:0048169)|regulation of synaptic transmission, GABAergic (GO:0032228)|response to glucocorticoid (GO:0051384)|response to mineralocorticoid (GO:0051385)|small GTPase mediated signal transduction (GO:0007264)|social behavior (GO:0035176)|striated muscle cell differentiation (GO:0051146)|visual learning (GO:0008542)	focal adhesion (GO:0005925)|membrane (GO:0016020)|membrane raft (GO:0045121)|mitochondrion (GO:0005739)|plasma membrane (GO:0005886)	GDP binding (GO:0019003)|GMP binding (GO:0019002)|GTP binding (GO:0005525)|protein complex binding (GO:0032403)	p.G12D(8562)|p.G12V(5775)|p.G12A(1407)|p.G12F(46)|p.G12L(8)|p.G12I(4)|p.G12E(3)|p.G12W(3)|p.G12Y(2)|p.G12fs*3(1)|p.G12C(1)|p.G12N(1)	UBE2L3/KRAS(2)	NS(6)|adrenal_gland(1)|autonomic_ganglia(3)|biliary_tract(532)|bone(2)|breast(32)|central_nervous_system(14)|cervix(50)|endometrium(411)|eye(4)|gastrointestinal_tract_(site_indeterminate)(7)|genital_tract(1)|haematopoietic_and_lymphoid_tissue(385)|kidney(8)|large_intestine(15267)|liver(29)|lung(3407)|oesophagus(16)|ovary(612)|pancreas(3739)|penis(1)|peritoneum(6)|prostate(96)|salivary_gland(6)|skin(45)|small_intestine(68)|soft_tissue(88)|stomach(207)|testis(17)|thymus(5)|thyroid(159)|upper_aerodigestive_tract(68)|urinary_tract(57)	25349	all_cancers(2;1e-35)|all_epithelial(2;1.97e-38)|all_lung(3;2.1e-23)|Lung NSC(3;1.16e-22)|Acute lymphoblastic leukemia(6;0.00231)|all_hematologic(7;0.00259)|Melanoma(3;0.0301)|Colorectal(261;0.11)|Ovarian(17;0.12)		OV - Ovarian serous cystadenocarcinoma(3;1.23e-21)|Epithelial(3;1.31e-20)|all cancers(3;5.45e-18)|STAD - Stomach adenocarcinoma(2;2.68e-05)			GCCTACGCCACCAGCTCCAAC	0.348	G12A(KMS28BM_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|G12A(KPNSI9S_AUTONOMIC_GANGLIA)|G12A(MM1S_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|G12A(NCIH1573_LUNG)|G12A(NCIH2009_LUNG)|G12A(RERFLCAD1_LUNG)|G12A(RPMI8226_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|G12A(SW1116_LARGE_INTESTINE)|G12D(AGS_STOMACH)|G12D(ASPC1_PANCREAS)|G12D(COLO678_LARGE_INTESTINE)|G12D(HEC1A_ENDOMETRIUM)|G12D(HEC50B_ENDOMETRIUM)|G12D(HEYA8_OVARY)|G12D(HPAC_PANCREAS)|G12D(HPAFII_PANCREAS)|G12D(KARPAS620_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|G12D(KOPN8_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|G12D(KP4_PANCREAS)|G12D(L33_PANCREAS)|G12D(LS180_LARGE_INTESTINE)|G12D(LS513_LARGE_INTESTINE)|G12D(MCAS_OVARY)|G12D(PANC0203_PANCREAS)|G12D(PANC0403_PANCREAS)|G12D(PANC0504_PANCREAS)|G12D(PANC0813_PANCREAS)|G12D(PANC1_PANCREAS)|G12D(PK1_PANCREAS)|G12D(PK59_PANCREAS)|G12D(SKLU1_LUNG)|G12D(SNUC2A_LARGE_INTESTINE)|G12D(SU8686_PANCREAS)|G12D(SUIT2_PANCREAS)|G12D(SW1990_PANCREAS)|G12V(A498_KIDNEY)|G12V(CAPAN2_PANCREAS)|G12V(CFPAC1_PANCREAS)|G12V(COLO668_LUNG)|G12V(CORL23_LUNG)|G12V(DANG_PANCREAS)|G12V(HCC56_LARGE_INTESTINE)|G12V(HUPT4_PANCREAS)|G12V(KP3_PANCREAS)|G12V(LCLC97TM1_LUNG)|G12V(NCIH2444_LUNG)|G12V(NCIH441_LUNG)|G12V(NCIH727_LUNG)|G12V(PANC0327_PANCREAS)|G12V(PATU8902_PANCREAS)|G12V(PATU8988S_PANCREAS)|G12V(QGP1_PANCREAS)|G12V(RCM1_LARGE_INTESTINE)|G12V(RERFLCAD2_LUNG)|G12V(RKN_OVARY)|G12V(SH10TC_STOMACH)|G12V(SHP77_LUNG)|G12V(SNGM_ENDOMETRIUM)|G12V(SW403_LARGE_INTESTINE)|G12V(SW480_LARGE_INTESTINE)|G12V(SW620_LARGE_INTESTINE)|G12V(SW900_LUNG)|G12V(YAPC_PANCREAS)	119	Mis		"""pancreatic, colorectal, lung, thyroid, AML, others"""				Noonan syndrome;Cardiofaciocutaneous syndrome	TSP Lung(1;<1E-08)|Multiple Myeloma(2;<1E-6)																											p.G12D	Pancreas(8;6 143 191 305 2070 2426 4376 10944 11745 26467 38091 50869)		Dom	yes		12	12p12.1	3845	v-Ki-ras2 Kirsten rat sarcoma 2 viral oncogene homolog		"""L, E, M, O"""	KRAS,haematopoietic_and_lymphoid_tissue,NS,Substitution - Missense,0	.	15813	Substitution - Missense(15812)|Deletion - Frameshift(1)	large_intestine(9453)|pancreas(3002)|lung(1512)|ovary(500)|biliary_tract(369)|endometrium(319)|haematopoietic_and_lymphoid_tissue(163)|stomach(124)|prostate(59)|thyroid(55)|small_intestine(43)|upper_aerodigestive_tract(30)|urinary_tract(30)|soft_tissue(28)|skin(27)|cervix(22)|liver(16)|breast(11)|testis(9)|oesophagus(8)|central_nervous_system(7)|peritoneum(5)|kidney(4)|eye(4)|gastrointestinal_tract_(site_indeterminate)(3)|NS(3)|thymus(3)|autonomic_ganglia(2)|salivary_gland(1)|bone(1)	c.G35A	12						.						91.0	81.0	85.0					12																	25398284		2203	4300	6503	25289551	SO:0001583	missense	3845	exon2	Familial Cancer Database	Male Turner syndrome, Pterygium Colli syndrome, incl. Noonan-like/Multiple Giant Cell Lesion syndrome; Noonan s. with multiple lentigines/LEOPARD syndrome;CFC, CFCS	BC010502	CCDS8702.1, CCDS8703.1	12p12.1	2014-09-17	2013-07-08	2005-01-24	ENSG00000133703	ENSG00000133703			6407	protein-coding gene	gene with protein product		190070	"""v-Ki-ras2 Kirsten rat sarcoma 2 viral oncogene homolog"", ""v-Ki-ras2 Kirsten rat sarcoma viral oncogene homolog"""	KRAS2			Standard	NM_004985		Approved	KRAS1	uc001rgp.1	P01116		ENST00000256078.4:c.35G>A	12.37:g.25398284C>T	ENSP00000256078:p.Gly12Asp		25289551	NM_004985	A8K8Z5|B0LPF9|P01118|Q96D10	Missense_Mutation	SNP	ENST00000256078.4	37	CCDS8703.1	.	.	.	.	.	.	.	.	.	.	C	23.4	4.409094	0.83340	.	.	ENSG00000133703	ENST00000311936;ENST00000557334;ENST00000256078;ENST00000556131	T;T;T;T	0.78595	-1.19;-1.19;-1.19;-1.19	5.68	5.68	0.88126	Small GTP-binding protein domain (1);	0.000000	0.85682	D	0.000000	D	0.85919	0.5809	M	0.91818	3.245	0.80722	D	1	B;P	0.35714	0.385;0.517	B;B	0.41619	0.257;0.361	D	0.87870	0.2670	10	0.87932	D	0	.	18.3719	0.90409	0.0:1.0:0.0:0.0	.	12;12	P01116-2;P01116	.;RASK_HUMAN	D	12	ENSP00000308495:G12D;ENSP00000452512:G12D;ENSP00000256078:G12D;ENSP00000451856:G12D	ENSP00000256078:G12D	G	-	2	0	KRAS	25289551	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.743000	0.85020	2.668000	0.90789	0.563000	0.77884	GGT		0.348	KRAS-004	KNOWN	not_organism_supported|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000412232.1	NM_033360	
ARHGEF25	115557	hgsc.bcm.edu	37	12	58010124	58010124	+	Missense_Mutation	SNP	G	G	A	rs116051216		TCGA-AG-3580-01A-01W-0831-10	TCGA-AG-3580-10A-01W-0831-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454			SOLID	TCGA-AG-3580-01A-01W-0831-10	TCGA-AG-3580-10A-01W-0831-10	g.chr12:58010124G>A	ENST00000286494.4	+	14	1938	c.1478G>A	c.(1477-1479)cGg>cAg	p.R493Q	AC025165.8_ENST00000610219.1_RNA|AC025165.8_ENST00000356672.3_RNA|ARHGEF25_ENST00000333972.7_Missense_Mutation_p.R532Q|AC025165.8_ENST00000593846.1_RNA|AC025165.8_ENST00000444467.1_RNA	NM_182947.3	NP_891992	Q86VW2	ARHGP_HUMAN	Rho guanine nucleotide exchange factor (GEF) 25	493	Sufficient to bind activated GNAQ.					cytosol (GO:0005829)|myofibril (GO:0030016)|plasma membrane (GO:0005886)	Rho guanyl-nucleotide exchange factor activity (GO:0005089)	p.R493Q(1)		breast(2)|central_nervous_system(1)|endometrium(1)|large_intestine(7)|lung(10)|pancreas(1)|prostate(1)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)	28						AGCCTGGGGCGGCCAAGAGGG	0.592													G|||	1	0.000199681	0.0008	0.0	5008	,	,		17880	0.0		0.0	False		,,,				2504	0.0				p.R532Q												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G1595A	12						.	G	GLN/ARG,GLN/ARG	1,4405	2.1+/-5.4	0,1,2202	62.0	66.0	65.0		1595,1478	4.8	1.0	12	dbSNP_132	65	0,8600		0,0,4300	no	missense,missense	ARHGEF25	NM_001111270.1,NM_182947.2	43,43	0,1,6502	AA,AG,GG		0.0,0.0227,0.0077	probably-damaging,probably-damaging	532/620,493/581	58010124	1,13005	2203	4300	6503	56296391	SO:0001583	missense	115557	exon15				CCDS8947.1, CCDS44931.1	12q13.3	2011-11-16			ENSG00000240771	ENSG00000240771		"""Rho guanine nucleotide exchange factors"""	30275	protein-coding gene	gene with protein product	"""RAC/CDC42 exchange factor"""	610215				12547822	Standard	NM_182947		Approved	GEFT, p63RhoGEF	uc009zpy.4	Q86VW2	OTTHUMG00000152516	ENST00000286494.4:c.1478G>A	12.37:g.58010124G>A	ENSP00000286494:p.Arg493Gln		56296391	NM_001111270	A6NJH5|A9CQZ6|F8W7Z4|Q8WV84|Q96E63	Missense_Mutation	SNP	ENST00000286494.4	37	CCDS8947.1	1	4.578754578754579E-4	1	0.0020325203252032522	0	0.0	0	0.0	0	0.0	g	20.3	3.974957	0.74360	2.27E-4	0.0	ENSG00000240771	ENST00000333972;ENST00000286494	T;T	0.21734	1.99;1.99	4.77	4.77	0.60923	Pleckstrin homology-type (1);	0.000000	0.34067	N	0.004298	T	0.39200	0.1069	L	0.50333	1.59	0.47183	D	0.999344	D;D	0.76494	0.999;0.994	D;D	0.77557	0.99;0.921	T	0.05801	-1.0863	10	0.54805	T	0.06	.	13.5047	0.61477	0.0:0.0:1.0:0.0	.	532;493	F8W7Z4;Q86VW2	.;ARHGP_HUMAN	Q	532;493	ENSP00000335560:R532Q;ENSP00000286494:R493Q	ENSP00000286494:R493Q	R	+	2	0	ARHGEF25	56296391	1.000000	0.71417	0.998000	0.56505	0.954000	0.61252	4.786000	0.62425	2.655000	0.90218	0.650000	0.86243	CGG		0.592	ARHGEF25-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000326561.1	NM_133483	
E2F7	144455	hgsc.bcm.edu	37	12	77449722	77449722	+	Silent	SNP	G	G	A			TCGA-AG-3580-01A-01W-0831-10	TCGA-AG-3580-10A-01W-0831-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454			SOLID	TCGA-AG-3580-01A-01W-0831-10	TCGA-AG-3580-10A-01W-0831-10	g.chr12:77449722G>A	ENST00000322886.7	-	3	517	c.282C>T	c.(280-282)gcC>gcT	p.A94A	E2F7_ENST00000416496.2_Silent_p.A94A	NM_203394.2	NP_976328.2	Q96AV8	E2F7_HUMAN	E2F transcription factor 7	94					chorionic trophoblast cell differentiation (GO:0060718)|DNA damage response, signal transduction by p53 class mediator (GO:0030330)|hepatocyte differentiation (GO:0070365)|negative regulation of cell proliferation (GO:0008285)|negative regulation of cytokinesis (GO:0032466)|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 involved in G1/S transition of mitotic cell cycle (GO:0071930)|placenta development (GO:0001890)|positive regulation of DNA endoreduplication (GO:0032877)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|sprouting angiogenesis (GO:0002040)|trophoblast giant cell differentiation (GO:0060707)	nucleus (GO:0005634)|transcription factor complex (GO:0005667)	core promoter binding (GO:0001047)|identical protein binding (GO:0042802)|RNA polymerase II regulatory region sequence-specific DNA binding (GO:0000977)|RNA polymerase II transcription regulatory region sequence-specific DNA binding transcription factor activity involved in negative regulation of transcription (GO:0001227)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription corepressor activity (GO:0003714)	p.A94A(2)		central_nervous_system(1)|endometrium(3)|kidney(4)|large_intestine(15)|lung(14)|ovary(3)|upper_aerodigestive_tract(2)	42						TATCTGGGCTGGCAGCACTAA	0.458																																					p.A94A												.	.	2	Substitution - coding silent(2)	large_intestine(2)	c.C282T	12						.						155.0	149.0	151.0					12																	77449722		2203	4300	6503	75973853	SO:0001819	synonymous_variant	144455	exon3			BC016658	CCDS9016.1	12q21.1	2008-02-05				ENSG00000165891			23820	protein-coding gene	gene with protein product		612046				12893818	Standard	NM_203394		Approved		uc001sym.4	Q96AV8	OTTHUMG00000169969	ENST00000322886.7:c.282C>T	12.37:g.77449722G>A			75973853	NM_203394	A6NC74|B2RMR7|B3KTZ5|B3KUP8|B5MED9	Silent	SNP	ENST00000322886.7	37	CCDS9016.1																																																																																				0.458	E2F7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000406716.1	XM_084871	
E2F7	144455	hgsc.bcm.edu	37	12	77449753	77449753	+	Missense_Mutation	SNP	G	G	T			TCGA-AG-3580-01A-01W-0831-10	TCGA-AG-3580-10A-01W-0831-10	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454			SOLID	TCGA-AG-3580-01A-01W-0831-10	TCGA-AG-3580-10A-01W-0831-10	g.chr12:77449753G>T	ENST00000322886.7	-	3	486	c.251C>A	c.(250-252)aCa>aAa	p.T84K	E2F7_ENST00000416496.2_Missense_Mutation_p.T84K	NM_203394.2	NP_976328.2	Q96AV8	E2F7_HUMAN	E2F transcription factor 7	84					chorionic trophoblast cell differentiation (GO:0060718)|DNA damage response, signal transduction by p53 class mediator (GO:0030330)|hepatocyte differentiation (GO:0070365)|negative regulation of cell proliferation (GO:0008285)|negative regulation of cytokinesis (GO:0032466)|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 involved in G1/S transition of mitotic cell cycle (GO:0071930)|placenta development (GO:0001890)|positive regulation of DNA endoreduplication (GO:0032877)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|sprouting angiogenesis (GO:0002040)|trophoblast giant cell differentiation (GO:0060707)	nucleus (GO:0005634)|transcription factor complex (GO:0005667)	core promoter binding (GO:0001047)|identical protein binding (GO:0042802)|RNA polymerase II regulatory region sequence-specific DNA binding (GO:0000977)|RNA polymerase II transcription regulatory region sequence-specific DNA binding transcription factor activity involved in negative regulation of transcription (GO:0001227)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription corepressor activity (GO:0003714)	p.T84K(2)		central_nervous_system(1)|endometrium(3)|kidney(4)|large_intestine(15)|lung(14)|ovary(3)|upper_aerodigestive_tract(2)	42						CAGGTTAGCTGTGGGTGTCCA	0.438																																					p.T84K												.	.	2	Substitution - Missense(2)	large_intestine(2)	c.C251A	12						.						158.0	153.0	154.0					12																	77449753		2203	4300	6503	75973884	SO:0001583	missense	144455	exon3			BC016658	CCDS9016.1	12q21.1	2008-02-05				ENSG00000165891			23820	protein-coding gene	gene with protein product		612046				12893818	Standard	NM_203394		Approved		uc001sym.4	Q96AV8	OTTHUMG00000169969	ENST00000322886.7:c.251C>A	12.37:g.77449753G>T	ENSP00000323246:p.Thr84Lys		75973884	NM_203394	A6NC74|B2RMR7|B3KTZ5|B3KUP8|B5MED9	Missense_Mutation	SNP	ENST00000322886.7	37	CCDS9016.1	.	.	.	.	.	.	.	.	.	.	G	34	5.354426	0.95830	.	.	ENSG00000165891	ENST00000322886;ENST00000416496;ENST00000550669;ENST00000547316	D;D;D;D	0.84944	-1.92;-1.92;-1.92;-1.92	5.7	5.7	0.88788	.	0.000000	0.85682	D	0.000000	D	0.92922	0.7748	M	0.80183	2.485	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.91635	0.999;0.997	D	0.93350	0.6717	10	0.87932	D	0	-21.1697	18.8265	0.92121	0.0:0.0:1.0:0.0	.	84;84	F8VSE7;Q96AV8	.;E2F7_HUMAN	K	84	ENSP00000323246:T84K;ENSP00000393639:T84K;ENSP00000448245:T84K;ENSP00000449033:T84K	ENSP00000323246:T84K	T	-	2	0	E2F7	75973884	1.000000	0.71417	1.000000	0.80357	0.991000	0.79684	9.869000	0.99810	2.683000	0.91414	0.650000	0.86243	ACA		0.438	E2F7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000406716.1	XM_084871	
FAT4	79633	hgsc.bcm.edu	37	4	126370389	126370389	+	Missense_Mutation	SNP	G	G	T			TCGA-AG-3580-01A-01W-0831-10	TCGA-AG-3580-10A-01W-0831-10	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454			SOLID	TCGA-AG-3580-01A-01W-0831-10	TCGA-AG-3580-10A-01W-0831-10	g.chr4:126370389G>T	ENST00000394329.3	+	9	8231	c.8218G>T	c.(8218-8220)Gtc>Ttc	p.V2740F	FAT4_ENST00000335110.5_Missense_Mutation_p.V1038F	NM_024582.4	NP_078858.4	Q6V0I7	FAT4_HUMAN	FAT atypical cadherin 4	2740	Cadherin 26. {ECO:0000255|PROSITE- ProRule:PRU00043}.				branching involved in ureteric bud morphogenesis (GO:0001658)|cerebral cortex development (GO:0021987)|digestive tract development (GO:0048565)|heart morphogenesis (GO:0003007)|heterophilic cell-cell adhesion (GO:0007157)|hippo signaling (GO:0035329)|homophilic cell adhesion (GO:0007156)|inner ear receptor stereocilium organization (GO:0060122)|neurogenesis (GO:0022008)|ossification involved in bone maturation (GO:0043931)|plasma membrane organization (GO:0007009)|regulation of metanephric nephron tubule epithelial cell differentiation (GO:0072307)	apical part of cell (GO:0045177)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)	p.V2740F(4)		NS(6)|autonomic_ganglia(1)|breast(4)|central_nervous_system(3)|cervix(3)|endometrium(27)|haematopoietic_and_lymphoid_tissue(3)|kidney(10)|large_intestine(93)|liver(3)|lung(120)|ovary(9)|pancreas(2)|prostate(21)|skin(31)|stomach(1)|upper_aerodigestive_tract(12)|urinary_tract(6)	355						ATCTCATTATGTCCTAACCAT	0.358																																					p.V2740F												.	.	4	Substitution - Missense(4)	upper_aerodigestive_tract(2)|large_intestine(2)	c.G8218T	4						.						68.0	69.0	68.0					4																	126370389		2203	4299	6502	126589839	SO:0001583	missense	79633	exon9			AY356402	CCDS3732.3	4q28.1	2013-05-31	2013-05-31		ENSG00000196159	ENSG00000196159		"""Cadherins / Cadherin-related"""	23109	protein-coding gene	gene with protein product	"""cadherin-related family member 11"""	612411	"""FAT tumor suppressor homolog 4 (Drosophila)"""			15003449	Standard	NM_024582		Approved	CDHF14, FAT-J, CDHR11	uc003ifj.4	Q6V0I7	OTTHUMG00000133100	ENST00000394329.3:c.8218G>T	4.37:g.126370389G>T	ENSP00000377862:p.Val2740Phe		126589839	NM_024582	A8K5Z6|B5MDG4|Q3LIA6|Q8TCK7|Q9H5T6	Missense_Mutation	SNP	ENST00000394329.3	37	CCDS3732.3	.	.	.	.	.	.	.	.	.	.	G	3.613	-0.079218	0.07141	.	.	ENSG00000196159	ENST00000394329;ENST00000335110	T;T	0.01821	4.62;4.62	5.6	1.54	0.23209	Cadherin (4);Cadherin-like (1);	0.895446	0.09019	U	0.860422	T	0.01800	0.0057	L	0.28192	0.835	0.09310	N	1	B;B;B	0.27013	0.091;0.166;0.135	B;B;B	0.31337	0.021;0.128;0.06	T	0.49031	-0.8981	10	0.56958	D	0.05	.	4.7413	0.13013	0.5097:0.1648:0.3256:0.0	.	1038;2740;2740	Q6V0I7-2;Q6V0I7;Q6V0I7-3	.;FAT4_HUMAN;.	F	2740;1038	ENSP00000377862:V2740F;ENSP00000335169:V1038F	ENSP00000335169:V1038F	V	+	1	0	FAT4	126589839	0.000000	0.05858	0.059000	0.19551	0.039000	0.13416	0.140000	0.16056	0.353000	0.24079	-0.145000	0.13849	GTC		0.358	FAT4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256765.2	NM_024582	
POU4F2	5458	hgsc.bcm.edu	37	4	147561780	147561780	+	Silent	SNP	G	G	A	rs371952832		TCGA-AG-3580-01A-01W-0831-10	TCGA-AG-3580-10A-01W-0831-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454			SOLID	TCGA-AG-3580-01A-01W-0831-10	TCGA-AG-3580-10A-01W-0831-10	g.chr4:147561780G>A	ENST00000281321.3	+	2	1298	c.1050G>A	c.(1048-1050)acG>acA	p.T350T	AC093887.1_ENST00000584185.1_RNA	NM_004575.2	NP_004566.2	Q12837	PO4F2_HUMAN	POU class 4 homeobox 2	350					axon extension (GO:0048675)|axon guidance (GO:0007411)|intracellular estrogen receptor signaling pathway (GO:0030520)|MAPK cascade (GO:0000165)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|neuromuscular process controlling balance (GO:0050885)|neuron differentiation (GO:0030182)|positive regulation of cell differentiation (GO:0045597)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|retina development in camera-type eye (GO:0060041)|retinal ganglion cell axon guidance (GO:0031290)|sensory perception of sound (GO:0007605)	nucleus (GO:0005634)	chromatin binding (GO:0003682)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in negative regulation of transcription (GO:0001078)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)	p.T350T(1)		NS(1)|breast(1)|endometrium(7)|kidney(3)|large_intestine(11)|lung(8)|skin(1)|upper_aerodigestive_tract(1)	33	all_hematologic(180;0.151)					GCAAGCGCACGTCCATCGCTG	0.622																																					p.T350T												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.G1050A	4						.						83.0	87.0	86.0					4																	147561780		2203	4300	6503	147781230	SO:0001819	synonymous_variant	5458	exon2			U06233	CCDS34074.1	4q31.22	2011-06-20	2007-07-13					"""Homeoboxes / POU class"""	9219	protein-coding gene	gene with protein product		113725	"""POU domain, class 4, transcription factor 2"", ""POU domain class 4, transcription factor 2"""	BRN3B		8332509	Standard	NM_004575		Approved	Brn-3b	uc003ikv.3	Q12837		ENST00000281321.3:c.1050G>A	4.37:g.147561780G>A			147781230	NM_004575	B1PJR6|B2RC84|Q13883|Q14987	Silent	SNP	ENST00000281321.3	37	CCDS34074.1																																																																																				0.622	POU4F2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000367020.1	NM_004575	
FSTL5	56884	hgsc.bcm.edu	37	4	162376191	162376191	+	Missense_Mutation	SNP	G	G	T			TCGA-AG-3580-01A-01W-0831-10	TCGA-AG-3580-10A-01W-0831-10	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454			SOLID	TCGA-AG-3580-01A-01W-0831-10	TCGA-AG-3580-10A-01W-0831-10	g.chr4:162376191G>T	ENST00000306100.5	-	15	2242	c.1806C>A	c.(1804-1806)ttC>ttA	p.F602L	FSTL5_ENST00000427802.2_Missense_Mutation_p.F592L|FSTL5_ENST00000379164.4_Missense_Mutation_p.F601L|FSTL5_ENST00000536695.1_Missense_Mutation_p.F601L	NM_001128427.2|NM_020116.4	NP_001121899.1|NP_064501.2	Q8N475	FSTL5_HUMAN	follistatin-like 5	602						extracellular region (GO:0005576)	calcium ion binding (GO:0005509)	p.F602L(1)		central_nervous_system(1)|cervix(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(4)|kidney(3)|large_intestine(18)|lung(43)|ovary(4)|pancreas(2)|prostate(2)|skin(2)|upper_aerodigestive_tract(2)	91	all_hematologic(180;0.24)			COAD - Colon adenocarcinoma(41;0.179)		TGGTGGGAATGAAAAAATCAT	0.413																																					p.F602L												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C1806A	4						.						168.0	126.0	140.0					4																	162376191		2203	4300	6503	162595641	SO:0001583	missense	56884	exon15			BC036502	CCDS3802.1, CCDS47157.1, CCDS47158.1	4q32.3	2013-01-11			ENSG00000168843	ENSG00000168843		"""EF-hand domain containing"", ""Immunoglobulin superfamily / I-set domain containing"""	21386	protein-coding gene	gene with protein product						10574462, 15527507	Standard	NM_020116		Approved	DKFZp566D234, KIAA1263	uc003iqh.4	Q8N475	OTTHUMG00000161397	ENST00000306100.5:c.1806C>A	4.37:g.162376191G>T	ENSP00000305334:p.Phe602Leu		162595641	NM_020116	E9PCP6|Q9NSW7|Q9ULF7	Missense_Mutation	SNP	ENST00000306100.5	37	CCDS3802.1	.	.	.	.	.	.	.	.	.	.	G	23.6	4.435731	0.83885	.	.	ENSG00000168843	ENST00000306100;ENST00000379164;ENST00000427802;ENST00000536695	T;T;T;T	0.29142	1.58;1.58;1.58;1.58	5.24	3.49	0.39957	WD40/YVTN repeat-like-containing domain (1);	0.096460	0.64402	D	0.000001	T	0.41488	0.1161	M	0.74467	2.265	0.53688	D	0.999978	P;P;P	0.44521	0.518;0.837;0.748	B;P;B	0.47430	0.138;0.547;0.283	T	0.38993	-0.9635	10	0.72032	D	0.01	.	11.3949	0.49836	0.1496:0.0:0.8504:0.0	.	592;601;602	E9PCP6;F8VZ90;Q8N475	.;.;FSTL5_HUMAN	L	602;601;592;601	ENSP00000305334:F602L;ENSP00000368462:F601L;ENSP00000389270:F592L;ENSP00000440409:F601L	ENSP00000305334:F602L	F	-	3	2	FSTL5	162595641	1.000000	0.71417	0.977000	0.42913	0.951000	0.60555	3.624000	0.54231	0.688000	0.31529	0.655000	0.94253	TTC		0.413	FSTL5-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000364773.2	NM_020116	
UGT2B7	7364	hgsc.bcm.edu	37	4	69968606	69968606	+	Missense_Mutation	SNP	G	G	A			TCGA-AG-3580-01A-01W-0831-10	TCGA-AG-3580-10A-01W-0831-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454			SOLID	TCGA-AG-3580-01A-01W-0831-10	TCGA-AG-3580-10A-01W-0831-10	g.chr4:69968606G>A	ENST00000508661.1	+	3	979	c.952G>A	c.(952-954)Gaa>Aaa	p.E318K	UGT2B7_ENST00000305231.7_Missense_Mutation_p.E318K|UGT2B7_ENST00000509763.1_3'UTR			P16662	UD2B7_HUMAN	UDP glucuronosyltransferase 2 family, polypeptide B7	318					androgen metabolic process (GO:0008209)|cellular glucuronidation (GO:0052695)|lipid metabolic process (GO:0006629)	endoplasmic reticulum (GO:0005783)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|membrane (GO:0016020)	glucuronosyltransferase activity (GO:0015020)	p.E318K(1)		autonomic_ganglia(1)|endometrium(3)|kidney(4)|large_intestine(6)|lung(16)|ovary(1)|prostate(1)|skin(4)|upper_aerodigestive_tract(1)|urinary_tract(1)	38					Atorvastatin(DB01076)|Carbamazepine(DB00564)|Chenodeoxycholic acid(DB06777)|Codeine(DB00318)|Dabigatran etexilate(DB06695)|Dapagliflozin(DB06292)|Diclofenac(DB00586)|Epirubicin(DB00445)|Etodolac(DB00749)|Ezetimibe(DB00973)|Flunitrazepam(DB01544)|Flurbiprofen(DB00712)|Fluvastatin(DB01095)|Ibuprofen(DB01050)|Indomethacin(DB00328)|Losartan(DB00678)|Lovastatin(DB00227)|Mitiglinide(DB01252)|Morphine(DB00295)|Mycophenolate mofetil(DB00688)|Mycophenolic acid(DB01024)|Naproxen(DB00788)|Oxazepam(DB00842)|Pitavastatin(DB08860)|Silodosin(DB06207)|Simvastatin(DB00641)|Suprofen(DB00870)|Tapentadol(DB06204)|Valproic Acid(DB00313)|Zidovudine(DB00495)	TAACATGACAGAAGAAAGGGC	0.448																																					p.E318K												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G952A	4						.						183.0	177.0	179.0					4																	69968606		2203	4300	6503	70003195	SO:0001583	missense	7364	exon3			BC030974	CCDS3526.1	4q13	2008-02-05	2005-07-20		ENSG00000171234	ENSG00000171234		"""UDP glucuronosyltransferases"""	12554	protein-coding gene	gene with protein product		600068	"""UDP glycosyltransferase 2 family, polypeptide B7"""			2159463, 7835904	Standard	NM_001074		Approved	UGT2B9	uc003heg.4	P16662	OTTHUMG00000129404	ENST00000508661.1:c.952G>A	4.37:g.69968606G>A	ENSP00000427659:p.Glu318Lys		70003195	NM_001074	B2R810|Q6GTW0	Missense_Mutation	SNP	ENST00000508661.1	37		.	.	.	.	.	.	.	.	.	.	G	6.699	0.497663	0.12762	.	.	ENSG00000171234	ENST00000502942;ENST00000305231;ENST00000508661	T;T;T	0.67345	-0.26;-0.26;-0.26	3.0	2.12	0.27331	.	0.964170	0.08529	U	0.932329	T	0.67496	0.2899	L	0.56396	1.775	0.09310	N	1	B;B	0.21905	0.062;0.019	B;B	0.36922	0.236;0.04	T	0.59188	-0.7501	9	.	.	.	.	9.9502	0.41634	0.0:0.2088:0.7912:0.0	.	318;318	E9PBP8;P16662	.;UD2B7_HUMAN	K	69;318;318	ENSP00000426206:E69K;ENSP00000304811:E318K;ENSP00000427659:E318K	.	E	+	1	0	UGT2B7	70003195	0.000000	0.05858	0.139000	0.22197	0.127000	0.20565	0.911000	0.28584	0.551000	0.29008	0.585000	0.79938	GAA		0.448	UGT2B7-002	PUTATIVE	basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000362103.1	NM_001074	
TLL1	7092	hgsc.bcm.edu	37	4	166976380	166976380	+	Silent	SNP	C	C	T	rs142933283		TCGA-AG-3580-01A-01W-0831-10	TCGA-AG-3580-10A-01W-0831-10	C	C	.	.	.	.	Unknown	Unknown	Somatic	Phase_I	Capture	.			SOLID	TCGA-AG-3580-01A-01W-0831-10	TCGA-AG-3580-10A-01W-0831-10	g.chr4:166976380C>T	ENST00000061240.2	+	13	2324	c.1677C>T	c.(1675-1677)gaC>gaT	p.D559D	RNA5SP170_ENST00000517150.1_RNA|TLL1_ENST00000507499.1_Silent_p.D582D	NM_012464.4	NP_036596.3	O43897	TLL1_HUMAN	tolloid-like 1	559	CUB 2. {ECO:0000255|PROSITE- ProRule:PRU00059}.				cell differentiation (GO:0030154)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|skeletal system development (GO:0001501)	extracellular region (GO:0005576)	calcium ion binding (GO:0005509)|metalloendopeptidase activity (GO:0004222)|zinc ion binding (GO:0008270)	p.D559D(1)		NS(1)|breast(1)|central_nervous_system(1)|endometrium(7)|kidney(4)|large_intestine(21)|lung(26)|ovary(2)|prostate(5)|skin(6)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	77	all_hematologic(180;0.221)	Melanoma(52;0.0315)|Prostate(90;0.0405)		GBM - Glioblastoma multiforme(119;0.103)		TTGTTTCTGACGGAACTGTGA	0.363																																					p.D559D												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C1677T	4						.	T		0,4406		0,0,2203	122.0	118.0	120.0		1677	-4.5	0.8	4	dbSNP_134	120	2,8598	818.9+/-406.8	0,2,4298	no	coding-synonymous	TLL1	NM_012464.4		0,2,6501	TT,TC,CC		0.0233,0.0,0.0154		559/1014	166976380	2,13004	2203	4300	6503	167195830	SO:0001819	synonymous_variant	7092	exon13			AF282732	CCDS3811.1, CCDS56342.1	4q32-q33	2008-07-29			ENSG00000038295	ENSG00000038295			11843	protein-coding gene	gene with protein product		606742				10516436	Standard	NM_012464		Approved		uc003irh.2	O43897	OTTHUMG00000161112	ENST00000061240.2:c.1677C>T	4.37:g.166976380C>T			167195830	NM_012464	B2RMU2|Q96AN3|Q9NQS4	Silent	SNP	ENST00000061240.2	37	CCDS3811.1																																																																																				0.363	TLL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000363821.1		
TFPI	7035	hgsc.bcm.edu	37	2	188348879	188348879	+	Silent	SNP	C	C	T			TCGA-AG-3580-01A-01W-0831-10	TCGA-AG-3580-10A-01W-0831-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454			SOLID	TCGA-AG-3580-01A-01W-0831-10	TCGA-AG-3580-10A-01W-0831-10	g.chr2:188348879C>T	ENST00000233156.3	-	6	894	c.600G>A	c.(598-600)ccG>ccA	p.P200P	TFPI_ENST00000409676.1_Silent_p.P200P|TFPI_ENST00000392365.1_Silent_p.P200P|AC007319.1_ENST00000412276.1_RNA|TFPI_ENST00000339091.4_Silent_p.P200P|AC007319.1_ENST00000453517.1_RNA	NM_006287.4	NP_006278.1	P10646	TFPI1_HUMAN	tissue factor pathway inhibitor (lipoprotein-associated coagulation inhibitor)	200					blood coagulation (GO:0007596)|blood coagulation, extrinsic pathway (GO:0007598)|negative regulation of endopeptidase activity (GO:0010951)	anchored component of membrane (GO:0031225)|cell surface (GO:0009986)|endoplasmic reticulum (GO:0005783)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|plasma membrane (GO:0005886)	endopeptidase inhibitor activity (GO:0004866)|serine-type endopeptidase inhibitor activity (GO:0004867)	p.P200P(2)		breast(1)|endometrium(1)|kidney(1)|large_intestine(3)|lung(2)|skin(1)	9			OV - Ovarian serous cystadenocarcinoma(117;0.0554)		Coagulation factor VIIa(DB00036)|Dalteparin(DB06779)	TGGTTGATTGCGGAGTCAGGG	0.378																																					p.P200P												.	.	2	Substitution - coding silent(2)	large_intestine(2)	c.G600A	2						.						100.0	102.0	102.0					2																	188348879		2203	4299	6502	188057124	SO:0001819	synonymous_variant	7035	exon6				CCDS2294.1, CCDS33349.1	2q32	2008-06-02			ENSG00000003436	ENSG00000003436			11760	protein-coding gene	gene with protein product	"""extrinsic pathway inhibitor"""	152310		LACI		1993173	Standard	XM_005246818		Approved	EPI, TFI, TFPI1	uc002upy.3	P10646	OTTHUMG00000132634	ENST00000233156.3:c.600G>A	2.37:g.188348879C>T			188057124	NM_006287	O95103|Q53TS4	Silent	SNP	ENST00000233156.3	37	CCDS2294.1																																																																																				0.378	TFPI-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255881.1	NM_006287	
NCOA1	8648	hgsc.bcm.edu	37	2	24896255	24896255	+	Missense_Mutation	SNP	G	G	A			TCGA-AG-3580-01A-01W-0831-10	TCGA-AG-3580-10A-01W-0831-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454			SOLID	TCGA-AG-3580-01A-01W-0831-10	TCGA-AG-3580-10A-01W-0831-10	g.chr2:24896255G>A	ENST00000406961.1	+	7	929	c.277G>A	c.(277-279)Gat>Aat	p.D93N	NCOA1_ENST00000288599.5_Missense_Mutation_p.D93N|RNU6-936P_ENST00000384005.1_RNA|NCOA1_ENST00000405141.1_Missense_Mutation_p.D93N|NCOA1_ENST00000348332.3_Missense_Mutation_p.D93N|NCOA1_ENST00000407230.1_De_novo_Start_OutOfFrame|NCOA1_ENST00000395856.3_Missense_Mutation_p.D93N|NCOA1_ENST00000538539.1_Missense_Mutation_p.D93N			Q15788	NCOA1_HUMAN	nuclear receptor coactivator 1	93					androgen receptor signaling pathway (GO:0030521)|cellular lipid metabolic process (GO:0044255)|cellular response to hormone stimulus (GO:0032870)|cerebellum development (GO:0021549)|cerebral cortex development (GO:0021987)|estrous cycle phase (GO:0060206)|hippocampus development (GO:0021766)|histone H4 acetylation (GO:0043967)|hypothalamus development (GO:0021854)|labyrinthine layer morphogenesis (GO:0060713)|lactation (GO:0007595)|male gonad development (GO:0008584)|male mating behavior (GO:0060179)|ovulation cycle (GO:0042698)|positive regulation of apoptotic process (GO:0043065)|positive regulation of female receptivity (GO:0045925)|positive regulation of neuron differentiation (GO:0045666)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription from RNA polymerase II promoter by galactose (GO:0000435)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of cellular response to drug (GO:2001038)|response to estradiol (GO:0032355)|response to progesterone (GO:0032570)|response to retinoic acid (GO:0032526)|small molecule metabolic process (GO:0044281)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|neuron projection (GO:0043005)|nuclear chromatin (GO:0000790)|nucleoplasm (GO:0005654)	androgen receptor binding (GO:0050681)|chromatin binding (GO:0003682)|enzyme binding (GO:0019899)|histone acetyltransferase activity (GO:0004402)|ligand-dependent nuclear receptor binding (GO:0016922)|ligand-dependent nuclear receptor transcription coactivator activity (GO:0030374)|nuclear hormone receptor binding (GO:0035257)|protein N-terminus binding (GO:0047485)|RNA polymerase II regulatory region DNA binding (GO:0001012)|RNA polymerase II transcription coactivator activity (GO:0001105)|signal transducer activity (GO:0004871)|transcription coactivator activity (GO:0003713)	p.D93N(2)	PAX3/NCOA1(8)	breast(3)|cervix(1)|endometrium(3)|kidney(2)|large_intestine(13)|lung(26)|ovary(2)|prostate(1)|skin(1)|urinary_tract(1)	53	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)					AACTGATGACGATGTACAGAA	0.348			T	PAX3	alveolar rhadomyosarcoma																																p.D93N			Dom	yes		2	2p23	8648	nuclear receptor coactivator 1		M	.	.	2	Substitution - Missense(2)	large_intestine(2)	c.G277A	2						.						96.0	99.0	98.0					2																	24896255		2203	4300	6503	24749759	SO:0001583	missense	8648	exon5			U40396	CCDS1712.1, CCDS1713.1, CCDS42660.1	2p23	2011-07-01			ENSG00000084676	ENSG00000084676		"""Chromatin-modifying enzymes / K-acetyltransferases"", ""Basic helix-loop-helix proteins"""	7668	protein-coding gene	gene with protein product		602691				7481822, 9575154	Standard	XM_005264625		Approved	SRC1, F-SRC-1, NCoA-1, KAT13A, RIP160, bHLHe74	uc002rfk.3	Q15788	OTTHUMG00000125523	ENST00000406961.1:c.277G>A	2.37:g.24896255G>A	ENSP00000385216:p.Asp93Asn		24749759	NM_003743	O00150|O43792|O43793|Q13071|Q13420|Q2T9G5|Q53SX3|Q6GVI5|Q7KYV3	Missense_Mutation	SNP	ENST00000406961.1	37	CCDS1712.1	.	.	.	.	.	.	.	.	.	.	G	29.8	5.034222	0.93575	.	.	ENSG00000084676	ENST00000406961;ENST00000405141;ENST00000538539;ENST00000348332;ENST00000288599;ENST00000395856	T;T;T;T;T;T	0.01947	4.54;4.54;4.54;4.54;4.54;4.54	4.84	4.84	0.62591	Helix-loop-helix DNA-binding (2);	0.214512	0.47852	D	0.000218	T	0.06050	0.0157	L	0.42245	1.32	0.80722	D	1	D;P;B	0.59767	0.986;0.782;0.325	P;B;B	0.52627	0.704;0.261;0.115	T	0.28933	-1.0028	10	0.72032	D	0.01	.	17.7266	0.88367	0.0:0.0:1.0:0.0	.	93;93;93	Q15788-3;Q15788;Q15788-2	.;NCOA1_HUMAN;.	N	93	ENSP00000385216:D93N;ENSP00000385097:D93N;ENSP00000444039:D93N;ENSP00000320940:D93N;ENSP00000288599:D93N;ENSP00000379197:D93N	ENSP00000288599:D93N	D	+	1	0	NCOA1	24749759	1.000000	0.71417	1.000000	0.80357	0.914000	0.54420	9.469000	0.97679	2.498000	0.84270	0.561000	0.74099	GAT		0.348	NCOA1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000246852.3	NM_147223	
PIKFYVE	200576	hgsc.bcm.edu	37	2	209207315	209207315	+	Nonsense_Mutation	SNP	C	C	T			TCGA-AG-3580-01A-01W-0831-10	TCGA-AG-3580-10A-01W-0831-10	C	C	.	.	.	.	Unknown	Unknown	Somatic	Phase_I	Capture	.			SOLID	TCGA-AG-3580-01A-01W-0831-10	TCGA-AG-3580-10A-01W-0831-10	g.chr2:209207315C>T	ENST00000264380.4	+	32	5127	c.4969C>T	c.(4969-4971)Cga>Tga	p.R1657*		NM_015040.3	NP_055855.2	Q9Y2I7	FYV1_HUMAN	phosphoinositide kinase, FYVE finger containing	1657					cellular protein metabolic process (GO:0044267)|intracellular signal transduction (GO:0035556)|myelin assembly (GO:0032288)|phosphatidylinositol biosynthetic process (GO:0006661)|phosphatidylinositol phosphorylation (GO:0046854)|phosphatidylinositol-3-phosphate biosynthetic process (GO:0036092)|phospholipid metabolic process (GO:0006644)|protein localization to nucleus (GO:0034504)|retrograde transport, endosome to Golgi (GO:0042147)|small molecule metabolic process (GO:0044281)	cell-cell junction (GO:0005911)|cytoplasmic vesicle (GO:0031410)|cytosol (GO:0005829)|early endosome membrane (GO:0031901)|endosome membrane (GO:0010008)|Golgi membrane (GO:0000139)|late endosome membrane (GO:0031902)|membrane raft (GO:0045121)|perinuclear region of cytoplasm (GO:0048471)|vesicle membrane (GO:0012506)	1-phosphatidylinositol-3-phosphate 5-kinase activity (GO:0000285)|1-phosphatidylinositol-4-phosphate 5-kinase activity (GO:0016308)|ATP binding (GO:0005524)|phosphatidylinositol-3,5-bisphosphate 5-phosphatase activity (GO:0043813)|zinc ion binding (GO:0008270)	p.R1657*(1)		NS(1)|autonomic_ganglia(1)|breast(1)|central_nervous_system(1)|endometrium(14)|kidney(6)|large_intestine(25)|lung(40)|ovary(7)|pancreas(1)|prostate(3)|skin(3)|upper_aerodigestive_tract(2)|urinary_tract(2)	107						TGAACATGAACGAGTGCCCAT	0.338																																					p.R1657X												.	.	1	Substitution - Nonsense(1)	large_intestine(1)	c.C4969T	2						.						174.0	156.0	162.0					2																	209207315		2203	4300	6503	208915560	SO:0001587	stop_gained	200576	exon32			AB023198	CCDS2382.1, CCDS33368.1, CCDS54431.1	2q34	2014-01-15	2009-04-17	2009-04-17	ENSG00000115020	ENSG00000115020		"""Zinc fingers, FYVE domain containing"""	23785	protein-coding gene	gene with protein product	"""zinc finger, FYVE domain containing 29"""	609414	"""phosphatidylinositol-3-phosphate/phosphatidylinositol 5-kinase, type III"""	PIP5K3		9858586, 12270933	Standard	NM_015040		Approved	MGC40423, KIAA0981, PIKfyve, PIP5K, p235, ZFYVE29, FAB1	uc002vcz.3	Q9Y2I7	OTTHUMG00000132945	ENST00000264380.4:c.4969C>T	2.37:g.209207315C>T	ENSP00000264380:p.Arg1657*		208915560	NM_015040	Q08AR7|Q08AR8|Q53ST3|Q53T36|Q8N5H0|Q8NB67	Nonsense_Mutation	SNP	ENST00000264380.4	37	CCDS2382.1	.	.	.	.	.	.	.	.	.	.	C	46	12.107369	0.99636	.	.	ENSG00000115020	ENST00000264380	.	.	.	5.42	5.42	0.78866	.	0.000000	0.64402	D	0.000001	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.14252	T	0.57	-16.3541	19.5723	0.95425	0.0:1.0:0.0:0.0	.	.	.	.	X	1657	.	ENSP00000264380:R1657X	R	+	1	2	PIKFYVE	208915560	1.000000	0.71417	1.000000	0.80357	0.917000	0.54804	4.178000	0.58284	2.695000	0.91970	0.557000	0.71058	CGA		0.338	PIKFYVE-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256477.2	NM_015040	
FAM214B	80256	hgsc.bcm.edu	37	9	35108115	35108115	+	Missense_Mutation	SNP	A	A	G			TCGA-AG-3580-01A-01W-0831-10	TCGA-AG-3580-10A-01W-0831-10	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	Capture	454			SOLID	TCGA-AG-3580-01A-01W-0831-10	TCGA-AG-3580-10A-01W-0831-10	g.chr9:35108115A>G	ENST00000378561.1	-	2	3212	c.157T>C	c.(157-159)Ttt>Ctt	p.F53L	FAM214B_ENST00000378554.2_Missense_Mutation_p.F53L|FAM214B_ENST00000488109.2_Missense_Mutation_p.F53L|FAM214B_ENST00000378557.1_Missense_Mutation_p.F53L|FAM214B_ENST00000322813.5_Missense_Mutation_p.F53L|FAM214B_ENST00000605244.1_Missense_Mutation_p.F53L|FAM214B_ENST00000603301.1_Missense_Mutation_p.F53L|FAM214B_ENST00000605392.1_5'Flank|FAM214B_ENST00000378566.1_Intron			Q7L5A3	F214B_HUMAN	family with sequence similarity 214, member B	53						nucleus (GO:0005634)		p.F53L(1)									GGAGGGGAAAAGATGGATACC	0.667																																					p.F53L												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.T157C	9						.						19.0	20.0	19.0					9																	35108115		2159	4229	6388	35098115	SO:0001583	missense	80256	exon3			AB040972	CCDS6578.1	9p13.2	2011-12-01	2011-12-01	2011-12-01	ENSG00000005238	ENSG00000005238			25666	protein-coding gene	gene with protein product			"""KIAA1539"""	KIAA1539		10819331	Standard	NM_025182		Approved	FLJ11560, bA182N22.6	uc003zwo.3	Q7L5A3	OTTHUMG00000019847	ENST00000378561.1:c.157T>C	9.37:g.35108115A>G	ENSP00000367823:p.Phe53Leu		35098115	NM_025182	B1AML4|B1AML5|D3DRN5|O60377|Q9BQ60|Q9HAI9|Q9P1Y9	Missense_Mutation	SNP	ENST00000378561.1	37	CCDS6578.1	.	.	.	.	.	.	.	.	.	.	A	20.4	3.990536	0.74589	.	.	ENSG00000005238	ENST00000322813;ENST00000378561;ENST00000378557;ENST00000378554	.	.	.	4.72	4.72	0.59763	.	0.087374	0.49305	D	0.000147	T	0.30978	0.0782	L	0.47716	1.5	0.31712	N	0.639336	P	0.38827	0.649	B	0.36186	0.219	T	0.27606	-1.0069	9	0.11485	T	0.65	-2.9156	9.738	0.40399	0.8458:0.0:0.0:0.1542	.	53	Q7L5A3	K1539_HUMAN	L	53	.	ENSP00000319897:F53L	F	-	1	0	KIAA1539	35098115	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	3.035000	0.49759	1.991000	0.58162	0.459000	0.35465	TTT		0.667	FAM214B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052261.1	NM_025182	
DGKH	160851	hgsc.bcm.edu	37	13	42795478	42795478	+	Missense_Mutation	SNP	G	G	A			TCGA-AG-3580-01A-01W-0831-10	TCGA-AG-3580-10A-01W-0831-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454			SOLID	TCGA-AG-3580-01A-01W-0831-10	TCGA-AG-3580-10A-01W-0831-10	g.chr13:42795478G>A	ENST00000337343.4	+	29	3542	c.3521G>A	c.(3520-3522)cGt>cAt	p.R1174H	DGKH_ENST00000379274.2_Missense_Mutation_p.R1038H|DGKH_ENST00000261491.5_Intron|DGKH_ENST00000540693.1_Intron|DGKH_ENST00000536612.1_Missense_Mutation_p.R1038H|DGKH_ENST00000538674.1_Intron|DGKH_ENST00000498255.2_Intron	NM_178009.3	NP_821077.1	Q86XP1	DGKH_HUMAN	diacylglycerol kinase, eta	1174	SAM. {ECO:0000255|PROSITE- ProRule:PRU00184}.				blood coagulation (GO:0007596)|intracellular signal transduction (GO:0035556)|platelet activation (GO:0030168)|protein kinase C-activating G-protein coupled receptor signaling pathway (GO:0007205)|protein oligomerization (GO:0051259)	cytoplasm (GO:0005737)|endosome (GO:0005768)|nuclear membrane (GO:0031965)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|diacylglycerol kinase activity (GO:0004143)|metal ion binding (GO:0046872)|NAD+ kinase activity (GO:0003951)	p.R1174H(1)		breast(2)|endometrium(3)|kidney(5)|large_intestine(11)|lung(9)|ovary(4)|pancreas(1)|prostate(1)|skin(2)|stomach(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	43		Lung NSC(96;1.02e-05)|Prostate(109;0.0168)|Lung SC(185;0.0262)|Breast(139;0.0709)|Hepatocellular(98;0.114)		OV - Ovarian serous cystadenocarcinoma(117;5.88e-05)|GBM - Glioblastoma multiforme(144;0.000935)|BRCA - Breast invasive adenocarcinoma(63;0.109)		ATCTTCATCCGTCATGACATC	0.418																																					p.R1174H												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G3521A	13						.						201.0	182.0	188.0					13																	42795478		2203	4300	6503	41693478	SO:0001583	missense	160851	exon29			AB078967	CCDS9381.1, CCDS9382.1, CCDS55898.1	13q13.3	2013-01-10			ENSG00000102780	ENSG00000102780		"""Sterile alpha motif (SAM) domain containing"", ""Pleckstrin homology (PH) domain containing"""	2854	protein-coding gene	gene with protein product		604071				8702685	Standard	XM_005266271		Approved	DGKeta	uc001uyl.2	Q86XP1	OTTHUMG00000016804	ENST00000337343.4:c.3521G>A	13.37:g.42795478G>A	ENSP00000337572:p.Arg1174His		41693478	NM_178009	A2A2W7|A6NFX7|B4DZ34|Q5VZW0|Q6PI56|Q86XP2|Q8N3N0|Q8N7J9	Missense_Mutation	SNP	ENST00000337343.4	37	CCDS9381.1	.	.	.	.	.	.	.	.	.	.	G	24.7	4.564522	0.86439	.	.	ENSG00000102780	ENST00000337343;ENST00000379274;ENST00000536612	D;D;D	0.85411	-1.98;-1.98;-1.98	5.58	4.74	0.60224	Sterile alpha motif domain (2);Sterile alpha motif/pointed domain (2);Sterile alpha motif, type 2 (1);	0.585977	0.18731	N	0.132735	D	0.89979	0.6872	L	0.57130	1.785	0.80722	D	1	D;D	0.71674	0.991;0.998	P;D	0.65323	0.891;0.934	D	0.90224	0.4274	10	0.66056	D	0.02	.	14.4946	0.67678	0.0707:0.0:0.9293:0.0	.	1038;1174	Q86XP1-3;Q86XP1	.;DGKH_HUMAN	H	1174;1038;1038	ENSP00000337572:R1174H;ENSP00000368576:R1038H;ENSP00000445114:R1038H	ENSP00000337572:R1174H	R	+	2	0	DGKH	41693478	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	7.295000	0.78780	1.371000	0.46172	-0.258000	0.10820	CGT		0.418	DGKH-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044699.2	NM_178009	
ADAMTS14	140766	hgsc.bcm.edu	37	10	72511261	72511261	+	Missense_Mutation	SNP	C	C	T			TCGA-AG-3580-01A-01W-0831-10	TCGA-AG-3580-10A-01W-0831-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454			SOLID	TCGA-AG-3580-01A-01W-0831-10	TCGA-AG-3580-10A-01W-0831-10	g.chr10:72511261C>T	ENST00000373207.1	+	17	2455	c.2455C>T	c.(2455-2457)Cgc>Tgc	p.R819C	ADAMTS14_ENST00000373208.1_Missense_Mutation_p.R822C	NM_080722.3	NP_542453.2	Q8WXS8	ATS14_HUMAN	ADAM metallopeptidase with thrombospondin type 1 motif, 14	819	Spacer.				collagen catabolic process (GO:0030574)|collagen fibril organization (GO:0030199)|extracellular matrix organization (GO:0030198)	extracellular region (GO:0005576)|proteinaceous extracellular matrix (GO:0005578)	metalloendopeptidase activity (GO:0004222)|zinc ion binding (GO:0008270)	p.R822C(1)		NS(1)|autonomic_ganglia(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(11)|lung(15)|ovary(7)|prostate(3)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	50						GGGTGGCCCCCGCAGCAGCCT	0.632																																					p.R819C												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C2455T	10						.						54.0	56.0	55.0					10																	72511261		2203	4300	6503	72181267	SO:0001583	missense	140766	exon17			AF358666	CCDS7306.1, CCDS7307.1	10q21	2008-08-01	2005-08-19		ENSG00000138316	ENSG00000138316		"""ADAM metallopeptidases with thrombospondin type 1 motif"""	14899	protein-coding gene	gene with protein product		607506	"""a disintegrin-like and metalloprotease (reprolysin type) with thrombospondin type 1 motif, 14"""			11779638	Standard	NM_139155		Approved		uc001jrg.3	Q8WXS8	OTTHUMG00000018414	ENST00000373207.1:c.2455C>T	10.37:g.72511261C>T	ENSP00000362303:p.Arg819Cys		72181267	NM_080722	Q5T4G0|Q5T4G1|Q8TE55|Q8TEY8	Missense_Mutation	SNP	ENST00000373207.1	37	CCDS7306.1	.	.	.	.	.	.	.	.	.	.	C	17.56	3.420019	0.62622	.	.	ENSG00000138316	ENST00000373208;ENST00000373207	T;T	0.53857	0.6;0.6	4.38	3.4	0.38934	ADAM-TS Spacer 1 (1);	0.074410	0.52532	D	0.000073	T	0.65626	0.2709	M	0.65498	2.005	0.44603	D	0.99757	D;D	0.89917	1.0;1.0	D;D	0.71414	0.959;0.973	T	0.67887	-0.5554	10	0.72032	D	0.01	.	9.1718	0.37086	0.3256:0.6744:0.0:0.0	.	819;822	Q8WXS8;Q5T4G1	ATS14_HUMAN;.	C	822;819	ENSP00000362304:R822C;ENSP00000362303:R819C	ENSP00000362303:R819C	R	+	1	0	ADAMTS14	72181267	1.000000	0.71417	1.000000	0.80357	0.968000	0.65278	3.559000	0.53756	2.280000	0.76307	0.563000	0.77884	CGC		0.632	ADAMTS14-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000048522.1	NM_080722	
HAPLN1	1404	hgsc.bcm.edu	37	5	82937441	82937441	+	Silent	SNP	G	G	A			TCGA-AG-3580-01A-01W-0831-10	TCGA-AG-3580-10A-01W-0831-10	G	G	.	.	.	.	Unknown	Unknown	Somatic	Phase_I	Capture	.			SOLID	TCGA-AG-3580-01A-01W-0831-10	TCGA-AG-3580-10A-01W-0831-10	g.chr5:82937441G>A	ENST00000274341.4	-	5	1789	c.939C>T	c.(937-939)agC>agT	p.S313S		NM_001884.3	NP_001875.1	P10915	HPLN1_HUMAN	hyaluronan and proteoglycan link protein 1	313	Link 2. {ECO:0000255|PROSITE- ProRule:PRU00323}.				cell adhesion (GO:0007155)|extracellular matrix organization (GO:0030198)	extracellular region (GO:0005576)|proteinaceous extracellular matrix (GO:0005578)	hyaluronic acid binding (GO:0005540)	p.S313S(2)		breast(1)|endometrium(1)|kidney(1)|large_intestine(12)|liver(1)|lung(15)|ovary(1)|prostate(1)|skin(1)	34		Lung NSC(167;0.0484)|all_lung(232;0.0522)|Ovarian(174;0.142)		OV - Ovarian serous cystadenocarcinoma(54;7.82e-42)|Epithelial(54;5.88e-35)|all cancers(79;1.14e-29)	Hyaluronan(DB08818)	GGTAGCGGACGCTGCCATCCG	0.537																																					p.S313S												.	.	2	Substitution - coding silent(2)	large_intestine(2)	c.C939T	5						.						108.0	113.0	111.0					5																	82937441		2203	4300	6503	82973197	SO:0001819	synonymous_variant	1404	exon5				CCDS4061.1	5q14.3	2013-01-11	2004-03-16	2004-03-17	ENSG00000145681	ENSG00000145681		"""Immunoglobulin superfamily / V-set domain containing"""	2380	protein-coding gene	gene with protein product	"""Cartilage link protein"", ""hyaluronan and proteoglycan link protein 1"""	115435	"""cartilage linking protein 1"""	CRTL1		2286376, 2320422	Standard	NM_001884		Approved		uc003kin.3	P10915	OTTHUMG00000119045	ENST00000274341.4:c.939C>T	5.37:g.82937441G>A			82973197	NM_001884	B2R9A9	Silent	SNP	ENST00000274341.4	37	CCDS4061.1																																																																																				0.537	HAPLN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000239256.2	NM_001884	
APC	324	hgsc.bcm.edu	37	5	112175060	112175060	+	Nonsense_Mutation	SNP	G	G	T			TCGA-AG-3580-01A-01W-0831-10	TCGA-AG-3580-10A-01W-0831-10	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454			SOLID	TCGA-AG-3580-01A-01W-0831-10	TCGA-AG-3580-10A-01W-0831-10	g.chr5:112175060G>T	ENST00000457016.1	+	16	4149	c.3769G>T	c.(3769-3771)Gaa>Taa	p.E1257*	CTC-554D6.1_ENST00000520401.1_Intron|APC_ENST00000508376.2_Nonsense_Mutation_p.E1257*|APC_ENST00000257430.4_Nonsense_Mutation_p.E1257*			P25054	APC_HUMAN	adenomatous polyposis coli	1257	Responsible for down-regulation through a process mediated by direct ubiquitination.|Ser-rich.				anterior/posterior pattern specification (GO:0009952)|apoptotic process (GO:0006915)|axis specification (GO:0009798)|axonogenesis (GO:0007409)|canonical Wnt signaling pathway (GO:0060070)|canonical Wnt signaling pathway involved in negative regulation of apoptotic process (GO:0044336)|canonical Wnt signaling pathway involved in positive regulation of apoptotic process (GO:0044337)|cell adhesion (GO:0007155)|cell cycle arrest (GO:0007050)|cell migration (GO:0016477)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|cellular response to DNA damage stimulus (GO:0006974)|chromosome organization (GO:0051276)|cytoplasmic microtubule organization (GO:0031122)|dorsal/ventral pattern formation (GO:0009953)|hair follicle development (GO:0001942)|kidney development (GO:0001822)|metaphase/anaphase transition of mitotic cell cycle (GO:0007091)|mitotic cytokinesis (GO:0000281)|mitotic spindle assembly checkpoint (GO:0007094)|muscle cell cellular homeostasis (GO:0046716)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of cell proliferation (GO:0008285)|negative regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0045736)|negative regulation of epithelial cell proliferation involved in prostate gland development (GO:0060770)|negative regulation of MAPK cascade (GO:0043409)|negative regulation of microtubule depolymerization (GO:0007026)|negative regulation of odontogenesis (GO:0042483)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cell adhesion (GO:0045785)|positive regulation of cell division (GO:0051781)|positive regulation of cell migration (GO:0030335)|positive regulation of epithelial cell differentiation (GO:0030858)|positive regulation of microtubule polymerization (GO:0031116)|positive regulation of protein catabolic process (GO:0045732)|positive regulation of pseudopodium assembly (GO:0031274)|protein complex assembly (GO:0006461)|proximal/distal pattern formation (GO:0009954)|regulation of attachment of spindle microtubules to kinetochore (GO:0051988)|regulation of microtubule-based process (GO:0032886)|regulation of nitrogen compound metabolic process (GO:0051171)|regulation of osteoblast differentiation (GO:0045667)|regulation of osteoclast differentiation (GO:0045670)|retina development in camera-type eye (GO:0060041)|somatic stem cell maintenance (GO:0035019)|T cell differentiation in thymus (GO:0033077)|thymus development (GO:0048538)|tight junction assembly (GO:0070830)	axonal growth cone (GO:0044295)|beta-catenin destruction complex (GO:0030877)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytoplasmic microtubule (GO:0005881)|cytosol (GO:0005829)|kinetochore (GO:0000776)|lamellipodium (GO:0030027)|lateral plasma membrane (GO:0016328)|microtubule plus-end (GO:0035371)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|ruffle membrane (GO:0032587)|tight junction (GO:0005923)	beta-catenin binding (GO:0008013)|gamma-catenin binding (GO:0045295)|microtubule binding (GO:0008017)|microtubule plus-end binding (GO:0051010)|protein kinase binding (GO:0019901)|protein kinase regulator activity (GO:0019887)	p.E1257*(1)|p.K1192fs*3(1)|p.?(1)		NS(7)|adrenal_gland(6)|biliary_tract(5)|bone(6)|breast(29)|central_nervous_system(12)|cervix(2)|endometrium(12)|haematopoietic_and_lymphoid_tissue(6)|kidney(8)|large_intestine(2768)|liver(15)|lung(39)|oesophagus(1)|ovary(12)|pancreas(27)|prostate(15)|salivary_gland(2)|skin(14)|small_intestine(34)|soft_tissue(55)|stomach(136)|thyroid(22)|upper_aerodigestive_tract(8)|urinary_tract(20)	3261		all_cancers(142;3.01e-27)|all_epithelial(76;2.3e-18)|all_hematologic(541;4.32e-09)|Ovarian(225;1.78e-06)|Lung NSC(167;0.000195)|Breast(839;0.000231)|all_lung(232;0.000247)|Colorectal(10;0.000355)|Prostate(80;0.00133)		OV - Ovarian serous cystadenocarcinoma(64;1.09e-113)|Epithelial(69;3.79e-112)|all cancers(49;1.67e-104)|BRCA - Breast invasive adenocarcinoma(61;0.00136)|COAD - Colon adenocarcinoma(37;0.00155)|Colorectal(14;0.00191)		TATTAACCAAGAAACAATACA	0.378		12	"""D, Mis, N, F, S"""		"""colorectal, pancreatic, desmoid, hepatoblastoma, glioma, other CNS"""	"""colorectal, pancreatic, desmoid, hepatoblastoma, glioma, other CNS"""			Turcot syndrome;Hereditary Desmoid Disease;Familial Adenomatous Polyposis	TSP Lung(16;0.13)																											p.E1239X	NSCLC(107;854 1218 9699 17025 28335 47076 52975)|Esophageal Squamous(32;282 584 32991 36563 39392 49665 50115)	yes	Rec	yes	Adenomatous polyposis coli; Turcot syndrome	5	5q21	324	adenomatous polyposis of the colon gene		"""E, M, O"""	.	.	3	Substitution - Nonsense(1)|Unknown(1)|Deletion - Frameshift(1)	large_intestine(1)|soft_tissue(1)|skin(1)	c.G3715T	5						.						49.0	51.0	50.0					5																	112175060		2202	4300	6502	112202959	SO:0001587	stop_gained	324	exon14	Familial Cancer Database	Brain tumor-colorectal polyp(osis) syndrome;Familial Infiltrative Mesenteric Fibromatosis;FAP, incl.: Gardner s., Attenuated FAP, Flat Adenoma s., Oldfield s,	M74088	CCDS4107.1	5q21-q22	2014-09-17	2008-01-08		ENSG00000134982	ENSG00000134982		"""Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"", ""Armadillo repeat containing"""	583	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 46"""	611731	"""adenomatosis polyposis coli"""			1651563	Standard	NM_001127511		Approved	DP2, DP3, DP2.5, PPP1R46	uc003kpy.4	P25054	OTTHUMG00000128806	ENST00000457016.1:c.3769G>T	5.37:g.112175060G>T	ENSP00000413133:p.Glu1257*		112202959	NM_001127511	D3DT03|Q15162|Q15163|Q93042	Nonsense_Mutation	SNP	ENST00000457016.1	37	CCDS4107.1	.	.	.	.	.	.	.	.	.	.	G	40	8.200291	0.98701	.	.	ENSG00000134982	ENST00000457016;ENST00000257430;ENST00000508376;ENST00000512211	.	.	.	6.03	6.03	0.97812	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	-23.9656	20.5568	0.99304	0.0:0.0:1.0:0.0	.	.	.	.	X	1257	.	.	E	+	1	0	APC	112202959	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	9.476000	0.97823	2.861000	0.98227	0.655000	0.94253	GAA		0.378	APC-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250738.2	NM_000038	
